pax_global_header00006660000000000000000000000064130402271050014504gustar00rootroot0000000000000052 comment=d75e86de325527b28a1a3b7e79d4572319dc2bc4 trunk-2017.01a/000077500000000000000000000000001304022710500131625ustar00rootroot00000000000000trunk-2017.01a/.gitattributes000066400000000000000000000000621304022710500160530ustar00rootroot00000000000000# Ignore all diffs in line endings * -crlf trunk-2017.01a/.gitignore000066400000000000000000000012371304022710500151550ustar00rootroot00000000000000tags .project VERSION yade.1 debian/changelog debian/control doc/epydoc doc/sphinx/WallStresses doc/sphinx/_build/ doc/sphinx/_publications.bib doc/sphinx/abc.xml doc/sphinx/modules.rst doc/sphinx/publications.rst doc/sphinx/references.rst doc/sphinx/yade.eudoxos.rst doc/sphinx/yade.export.rst doc/sphinx/yade.linterpolation.rst doc/sphinx/yade.log.rst doc/sphinx/yade.pack.rst doc/sphinx/yade.plot.rst doc/sphinx/yade.post2d.rst doc/sphinx/yade.qt.rst doc/sphinx/yade.timing.rst doc/sphinx/yade.utils.rst doc/sphinx/yade.wrapper.rst doc/sphinx/yade.ymport.rst doc/sphinx/yade.polyhedra_utils.rst doc/sphinx/yade.gridpfacet.rst .kdev4/ *.kdev4 *.pyc *~ .idea trunk.iml trunk-2017.01a/.mailmap000066400000000000000000000043011304022710500146010ustar00rootroot00000000000000Anton Gladky Anton Gladky Francois Kneib Francois Kneib Francois Kneib François Kneib Francois Kneib Francois Francois Kneib françois # Christian Jakob christian # Jan Stránský Jan Stransky Jan Stránský Jan Stránský <_honzik@centrum.cz> Jan Stránský Jan Stránský # Chao Yuan cyuan Chao Yuan cyuanLaptop Chao Yuan Thinkpad # Jerome Duriez Jerome Duriez Jerome Duriez jduriez Jerome Duriez jduriez # Luc Scholtes Luc Scholtes lucScholtes Luc Scholtes scholtes # Bruno Chareyre Bruno Chareyre # Donia Marzougui Donia Donia Marzougui Donia Donia Marzougui Donia Marzougui Donia Marzougui dmarzougui # Alexander Eulitz Kubeu # Raphael Maurin Raphaël Maurin # Luc Sibille Luc Sibille Luc Sibille lsibille trunk-2017.01a/.travis.yml000066400000000000000000000023751304022710500153020ustar00rootroot00000000000000language: cpp dist: trusty compiler: - gcc virtualenv: system_site_packages: true notifications: email: recipients: - yade-dev@lists.launchpad.net - gladk@debian.org on_success: change on_failure: always before_script: - sudo bash -c 'echo "deb http://www.yade-dem.org/packages/ trusty/" >> /etc/apt/sources.list' - wget -O - http://www.yade-dem.org/packages/yadedev_pub.gpg | sudo apt-key add - - sudo apt-get update -qq - sudo apt-get install -y cmake debhelper freeglut3-dev help2man ipython libboost-all-dev libbz2-dev libcgal-dev libeigen3-dev libgl1-mesa-dev libgts-dev libloki-dev libmetis-dev libopenblas-dev libqglviewer-dev libsuitesparse-dev libvtk5-dev libxi-dev libxmu-dev pyqt4-dev-tools python-all-dev python-argparse python-gts python-imaging python-matplotlib python-minieigen python-numpy python-qt4 python-support python-tk python-xlib zlib1g-dev dvipng graphviz libjs-jquery lmodern python-bibtex python-sphinx texlive-fonts-recommended texlive-latex-extra texlive-latex-recommended texlive-pictures texlive-xetex tipa - mkdir build - cd build - cmake -DCMAKE_INSTALL_PREFIX=./../inst -DSUFFIX=-trunk .. script: - make - make install - ./../inst/bin/yade-trunk --test - ./../inst/bin/yade-trunk --check trunk-2017.01a/CMakeLists.txt000066400000000000000000000712311304022710500157260ustar00rootroot00000000000000# The YADE has the following parameters to configure: # CMAKE_INSTALL_PREFIX: path, where Yade will be installed (/usr/local by default) # LIBRARY_OUTPUT_PATH: path to install libraries (lib by default) # DEBUG: compile in debug-mode (OFF by default) # CMAKE_VERBOSE_MAKEFILE: output additional information during compiling (OFF by default) # SUFFIX: suffix, added after binary-names (version number by default) # NOSUFFIX: do not add a suffix after binary-name (OFF by default) # YADE_VERSION: explicitely set version number (is defined from git-directory by default) # ENABLE_GUI: enable GUI option (ON by default) # ENABLE_CGAL: enable CGAL option (ON by default) # ENABLE_VTK: enable VTK-export option (ON by default) # ENABLE_OPENMP: enable OpenMP-parallelizing option (ON by default) # ENABLE_GTS: enable GTS-option (ON by default) # ENABLE_GL2PS: enable GL2PS-option (ON by default) # ENABLE_LINSOLV: enable LINSOLV-option (ON by default) # ENABLE_PFVFLOW: enable PFVFLOW-option, FlowEngine (ON by default) # ENABLE_LBMFLOW: enable LBMFLOW-option, LBM_ENGINE (ON by default) # ENABLE_SPH: enable SPH-option, Smoothed Particle Hydrodynamics (OFF by default) # ENABLE_LIQMIGRATION: enable LIQMIGRATION-option, see [Mani2013] for details (OFF by default) # ENABLE_MASK_ARBITRARY: enable MASK_ARBITRARY option (OFF by default) # ENABLE_PROFILING: enable profiling, e.g. shows some more metrics, which can define bottlenecks of the code (OFF by default) # ENABLE_POTENTIAL_PARTICLES: enable potential particles option (OFF by default) # runtimePREFIX: used for packaging, when install directory is not the same is runtime directory (/usr/local by default) # CHUNKSIZE: set >1, if you want several sources to be compiled at once. Increases compilation speed and RAM-consumption during it (1 by default) # VECTORIZE: enables vectorization and alignment in Eigen3 library, experimental (OFF by default) # USE_QT5: use QT5 for GUI (ON by default) project(Yade C CXX) cmake_minimum_required(VERSION 2.8.11) set(CMAKE_MODULE_PATH "${CMAKE_CURRENT_SOURCE_DIR}/cMake") INCLUDE(FindPythonInterp) INCLUDE(FindOpenMP) INCLUDE(FindQt4) INCLUDE(FindPkgConfig) INCLUDE(GetVersion) INCLUDE(FindOpenGL) INCLUDE(FindGTS) INCLUDE(FindGL2PS) INCLUDE(FindCGAL) INCLUDE(FindNumPy) INCLUDE(FindLoki) INCLUDE(FindPythonModule) INCLUDE(GNUInstallDirs) INCLUDE_DIRECTORIES (${CMAKE_SOURCE_DIR}) #=========================================================== # HACK!!! If the version of gcc is 4.8 or greater, we add -ftrack-macro-expansion=0 # and -save-temps into compiler to reduce the memory consumption during compilation. # See http://bugs.debian.org/726009 for more information # Can be removed later, if gcc fixes its regression # Taken from http://stackoverflow.com/questions/4058565/check-gcc-minor-in-cmake EXECUTE_PROCESS(COMMAND ${CMAKE_C_COMPILER} -dumpversion OUTPUT_VARIABLE GCC_VERSION) IF (GCC_VERSION VERSION_GREATER 4.8 OR GCC_VERSION VERSION_EQUAL 4.8) MESSAGE(STATUS "GCC Version >= 4.8. Adding -ftrack-macro-expansion=0 and -save-temps") ADD_DEFINITIONS("-ftrack-macro-expansion=0 -save-temps") ENDIF() #=========================================================== IF ("${CMAKE_CXX_COMPILER} ${CMAKE_CXX_COMPILER_ARG1}" MATCHES ".*clang") ADD_DEFINITIONS("-ftemplate-depth-512 -fstack-protector ") ELSE() IF (GCC_VERSION VERSION_GREATER 4.9 OR GCC_VERSION VERSION_EQUAL 4.9) MESSAGE(STATUS "GCC Version >= 4.9. Adding -fstack-protector-strong") ADD_DEFINITIONS("-fstack-protector-strong") ELSE() ADD_DEFINITIONS("-fstack-protector") ENDIF() ENDIF() SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -fPIC -O2 --param=ssp-buffer-size=4 -Wformat -Wformat-security -Werror=format-security -Wall -std=c++11 -fext-numeric-literals") IF (DEBUG) SET(CMAKE_VERBOSE_MAKEFILE 1) SET(CMAKE_BUILD_TYPE Debug) ADD_DEFINITIONS("-DYADE_DEBUG -g") ELSE (DEBUG) ADD_DEFINITIONS("-DNDEBUG") ENDIF (DEBUG) #=========================================================== # Add possibility to use local boost installation (e.g. -DLocalBoost=1.46.1) IF ( NOT LocalBoost ) SET(LocalBoost "1.47.0") # Minimal required Boost version ENDIF ( NOT LocalBoost ) FIND_PACKAGE(Boost ${LocalBoost} COMPONENTS python thread filesystem iostreams regex serialization system date_time REQUIRED) INCLUDE_DIRECTORIES (${Boost_INCLUDE_DIRS}) # for checking purpose MESSAGE("-- Boost_VERSION: " ${Boost_VERSION}) MESSAGE("-- Boost_LIB_VERSION: " ${Boost_LIB_VERSION}) MESSAGE("-- Boost_INCLUDE_DIRS: " ${Boost_INCLUDE_DIRS}) MESSAGE("-- Boost_LIBRARIES: " ${Boost_LIBRARIES}) #=========================================================== FIND_PACKAGE(NumPy REQUIRED) INCLUDE_DIRECTORIES(${NUMPY_INCLUDE_DIRS}) FIND_PACKAGE(Loki REQUIRED) INCLUDE_DIRECTORIES(${LOKI_INCLUDE_DIR}) FIND_PACKAGE(Eigen3 REQUIRED) FIND_PACKAGE(BZip2 REQUIRED) FIND_PACKAGE(ZLIB REQUIRED) SET(Python_ADDITIONAL_VERSIONS 2.7) FIND_PACKAGE(PythonLibs REQUIRED) INCLUDE_DIRECTORIES(${PYTHON_INCLUDE_PATH}) #=========================================================== SET(DEFAULT ON CACHE INTERNAL "Default value for enabled by default options") SET(LINKLIBS "") SET(CONFIGURED_FEATS "") SET(DISABLED_FEATS "") OPTION(ENABLE_VTK "Enable VTK" ${DEFAULT}) OPTION(ENABLE_OPENMP "Enable OpenMP" ${DEFAULT}) OPTION(ENABLE_GTS "Enable GTS" ${DEFAULT}) OPTION(ENABLE_GUI "Enable GUI" ${DEFAULT}) OPTION(ENABLE_CGAL "Enable CGAL" ${DEFAULT}) OPTION(ENABLE_GL2PS "Enable GL2PS" ${DEFAULT}) OPTION(ENABLE_LINSOLV "Enable direct solver for the flow engines (experimental)" ${DEFAULT}) OPTION(ENABLE_PFVFLOW "Enable flow engine (experimental)" ${DEFAULT}) OPTION(ENABLE_SPH "Enable SPH" OFF) OPTION(ENABLE_LBMFLOW "Enable LBM engine (very experimental)" ON) OPTION(ENABLE_LIQMIGRATION "Enable liquid control (very experimental), see [Mani2013] for details" OFF) OPTION(ENABLE_MASK_ARBITRARY "Enable arbitrary precision of bitmask variables (only Body::groupMask yet implemented) (experimental). Use -DMASK_ARBITRARY_SIZE=int to set number of used bits (256 by default)" OFF) OPTION(ENABLE_PROFILING "Enable profiling, e.g. shows some more metrics, which can define bottlenecks of the code (OFF by default)" OFF) OPTION(ENABLE_POTENTIAL_PARTICLES "Enable potential particles" OFF) OPTION(USE_QT5 "USE Qt5 for GUI" ON) OPTION(ENABLE_POTENTIAL_BLOCKS "Enable PotentialBlocks" OFF) #=========================================================== # Use Eigen3 by default IF (EIGEN3_FOUND) INCLUDE_DIRECTORIES(${EIGEN3_INCLUDE_DIR}) MESSAGE(STATUS "Found Eigen3, version: ${EIGEN3_VERSION}") # Minimal required version 3.2.1 IF ((${EIGEN3_MAJOR_VERSION} LESS 2) OR ((${EIGEN3_MAJOR_VERSION} EQUAL 2) AND (${EIGEN3_MINOR_VERSION} LESS 1))) MESSAGE(FATAL_ERROR "Minimal required Eigen3 version is 3.2.1, please update Eigen3!") ENDIF ((${EIGEN3_MAJOR_VERSION} LESS 2) OR ((${EIGEN3_MAJOR_VERSION} EQUAL 2) AND (${EIGEN3_MINOR_VERSION} LESS 1))) IF (NOT VECTORIZE) MESSAGE(STATUS "Disable vectorization") ADD_DEFINITIONS("-DEIGEN_DONT_VECTORIZE -DEIGEN_DONT_ALIGN -DEIGEN_DISABLE_UNALIGNED_ARRAY_ASSERT") ELSE (NOT VECTORIZE) MESSAGE(STATUS "Enable vectorization") ENDIF (NOT VECTORIZE) ENDIF(EIGEN3_FOUND) #=========================================================== INCLUDE_DIRECTORIES(${BZIP2_INCLUDE_DIR}) INCLUDE_DIRECTORIES(${ZLIB_INCLUDE_DIRS}) SET(LINKLIBS "${LINKLIBS};${BZIP2_LIBRARIES};${ZLIB_LIBRARIES};") #=========================================================== IF((Boost_MAJOR_VERSION EQUAL 1) OR (Boost_MAJOR_VERSION GREATER 1) AND ((Boost_MINOR_VERSION EQUAL 53) OR (Boost_MINOR_VERSION GREATER 53))) SET(CONFIGURED_FEATS "${CONFIGURED_FEATS} Odeint") ADD_DEFINITIONS("-DYADE_ODEINT") ELSE((Boost_MAJOR_VERSION EQUAL 1) OR (Boost_MAJOR_VERSION GREATER 1) AND ((Boost_MINOR_VERSION EQUAL 53) OR (Boost_MINOR_VERSION GREATER 53))) SET(DISABLED_FEATS "${DISABLED_FEATS} Odeint") MESSAGE(STATUS "Boost Odeint can be enabled, only if Boost>=1.53 is used") ENDIF((Boost_MAJOR_VERSION EQUAL 1) OR (Boost_MAJOR_VERSION GREATER 1) AND ((Boost_MINOR_VERSION EQUAL 53) OR (Boost_MINOR_VERSION GREATER 53))) #=========================================================== IF(ENABLE_VTK) FIND_PACKAGE(VTK COMPONENTS vtkCommonCore vtkIOImage vtkIOXML vtkFiltersCore vtkImagingCore vtkRenderingCore vtkImagingGeneral vtkImagingHybrid) IF(VTK_FOUND) INCLUDE_DIRECTORIES(${VTK_INCLUDE_DIRS}) LINK_DIRECTORIES( ${VTK_LIBRARY_DIRS} ) SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DYADE_VTK") MESSAGE(STATUS "Found VTK") SET(CONFIGURED_FEATS "${CONFIGURED_FEATS} VTK") ELSE(VTK_FOUND) MESSAGE(STATUS "VTK NOT found") SET(ENABLE_VTK OFF) SET(DISABLED_FEATS "${DISABLED_FEATS} VTK") ENDIF(VTK_FOUND) ELSE(ENABLE_VTK) SET(DISABLED_FEATS "${DISABLED_FEATS} VTK") ENDIF(ENABLE_VTK) #=========================================================== IF(ENABLE_OPENMP) FIND_PACKAGE(OpenMP) IF(OPENMP_FOUND) SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DYADE_OPENMP ${OpenMP_CXX_FLAGS}") MESSAGE(STATUS "Found OpenMP") SET(CONFIGURED_FEATS "${CONFIGURED_FEATS} OpenMP") ELSE(OPENMP_FOUND) MESSAGE(STATUS "OpenMP NOT found") SET(ENABLE_OPENMP OFF) SET(DISABLED_FEATS "${DISABLED_FEATS} OPENMP") ENDIF(OPENMP_FOUND) ELSE(ENABLE_OPENMP) SET(DISABLED_FEATS "${DISABLED_FEATS} OPENMP") ENDIF(ENABLE_OPENMP) #=========================================================== IF(ENABLE_GTS) FIND_PACKAGE(GTS) FIND_PACKAGE(glib2) IF(GTS_FOUND AND GLIB2_FOUND) SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DYADE_GTS ${CMAKE_GTS_CXX_FLAGS}") SET(CMAKE_LD_FLAGS "${CMAKE_LD_FLAGS} ${GTS_LIBRARIES}") INCLUDE_DIRECTORIES(${GTS_INCLUDE_DIR}) INCLUDE_DIRECTORIES(${GLIB2_INCLUDE_DIRS}) MESSAGE(STATUS "Found GTS") SET(CONFIGURED_FEATS "${CONFIGURED_FEATS} GTS") ELSE(GTS_FOUND AND GLIB2_FOUND) MESSAGE(STATUS "GTS NOT found") SET(DISABLED_FEATS "${DISABLED_FEATS} GTS") SET(ENABLE_GTS OFF) ENDIF(GTS_FOUND AND GLIB2_FOUND) ELSE(ENABLE_GTS) SET(DISABLED_FEATS "${DISABLED_FEATS} GTS") ENDIF(ENABLE_GTS) #=========================================================== IF(ENABLE_GUI) FIND_PACKAGE(OpenGL) FIND_PACKAGE(GLUT) FIND_PACKAGE(glib2) IF(USE_QT5) FIND_PACKAGE(QGLVIEWER-qt5 REQUIRED) FIND_PACKAGE(Qt5 CONFIG REQUIRED Widgets Xml OpenGL) SET(CMAKE_AUTOMOC ON) FIND_PACKAGE(Qt5Widgets) IF(Qt5Widgets_FOUND AND OPENGL_FOUND AND GLUT_FOUND AND GLIB2_FOUND AND QGLVIEWER_FOUND) SET(GUI_LIBS ${GLUT_LIBRARY} ${QGLVIEWER_LIBRARIES}) SET(GUI_SRC_LIB "lib/opengl/GLUtils.cpp") SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DYADE_OPENGL -DYADE_QT5") MESSAGE(STATUS "Found GUI-Qt5-LIBS") SET(CONFIGURED_FEATS "${CONFIGURED_FEATS} GUI-Qt5") ELSE(Qt5Widgets_FOUND AND OPENGL_FOUND AND GLUT_FOUND AND GLIB2_FOUND AND QGLVIEWER_FOUND) MESSAGE(STATUS "GUI-Qt5-LIBS NOT found") SET(DISABLED_FEATS "${DISABLED_FEATS} GUI-Qt5") SET(ENABLE_GUI OFF) ENDIF(Qt5Widgets_FOUND AND OPENGL_FOUND AND GLUT_FOUND AND GLIB2_FOUND AND QGLVIEWER_FOUND) ELSE(USE_QT5) # Use Qt4 FIND_PACKAGE(QGLVIEWER-qt4 REQUIRED) FIND_PACKAGE(Qt4 COMPONENTS QtCore QtGui QtOpenGL) IF(QT4_FOUND AND OPENGL_FOUND AND GLUT_FOUND AND GLIB2_FOUND AND QGLVIEWER_FOUND) SET(GUI_LIBS ${GLUT_LIBRARY} ${OPENGL_LIBRARY} ${QGLVIEWER_LIBRARIES}) SET(GUI_SRC_LIB "lib/opengl/GLUtils.cpp") SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DYADE_OPENGL -DYADE_QT4") INCLUDE_DIRECTORIES(${GLIB2_INCLUDE_DIRS}) INCLUDE_DIRECTORIES(${QT_INCLUDES}) MESSAGE(STATUS "Found GUI-LIBS") SET(CONFIGURED_FEATS "${CONFIGURED_FEATS} GUI") ELSE(QT4_FOUND AND OPENGL_FOUND AND GLUT_FOUND AND GLIB2_FOUND AND QGLVIEWER_FOUND) MESSAGE(STATUS "GUI-LIBS NOT found") SET(DISABLED_FEATS "${DISABLED_FEATS} GUI") SET(ENABLE_GUI OFF) ENDIF(QT4_FOUND AND OPENGL_FOUND AND GLUT_FOUND AND GLIB2_FOUND AND QGLVIEWER_FOUND) ENDIF(USE_QT5) ELSE(ENABLE_GUI) SET(DISABLED_FEATS "${DISABLED_FEATS} GUI") ENDIF(ENABLE_GUI) #=========================================================== # This one will automatically enable CGAL IF(ENABLE_PFVFLOW) IF (NOT ENABLE_CGAL) MESSAGE(STATUS "PFVFLOW depends on CGAL, attempting to turn ENABLE_CGAL ON") SET(ENABLE_CGAL ON) ENDIF (NOT ENABLE_CGAL) ENDIF(ENABLE_PFVFLOW) #=========================================================== IF(ENABLE_CGAL) INCLUDE(FindGMP) FIND_PACKAGE(CGAL) FIND_PACKAGE(GMP) IF(CGAL_FOUND AND GMP_FOUND AND (NOT("${CMAKE_CXX_COMPILER} ${CMAKE_CXX_COMPILER_ARG1}" MATCHES ".*clang"))) #Check for clang should be removed, when CGAL will be compilable by clang #INCLUDE_DIRECTORIES(${CGAL_INCLUDE_DIR}) #INCLUDE_DIRECTORIES(${GMP_INCLUDE_DIR}) #INCLUDE_DIRECTORIES(${GMPXX_INCLUDE_DIR}) FILE(GLOB CGAL_SRC_LIB "lib/triangulation/*.cpp") SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CGAL_DEFINITIONS} -DYADE_CGAL") SET(LINKLIBS "${LINKLIBS};${CGAL_LIBRARIES};${GMP_LIBRARIES};${GMPXX_LIBRARIES};") MESSAGE(STATUS "Found CGAL") SET(CONFIGURED_FEATS "${CONFIGURED_FEATS} CGAL") ADD_DEFINITIONS("-DCGAL_DISABLE_ROUNDING_MATH_CHECK -frounding-math") IF(ENABLE_PFVFLOW) SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DFLOW_ENGINE") SET(CONFIGURED_FEATS "${CONFIGURED_FEATS} PFVFLOW") ELSE(ENABLE_PFVFLOW) SET(DISABLED_FEATS "${DISABLED_FEATS} PFVFLOW") ENDIF(ENABLE_PFVFLOW) ELSE(CGAL_FOUND AND GMP_FOUND AND (NOT("${CMAKE_CXX_COMPILER} ${CMAKE_CXX_COMPILER_ARG1}" MATCHES ".*clang"))) MESSAGE(STATUS "CGAL NOT found") SET(DISABLED_FEATS "${DISABLED_FEATS} CGAL") SET(ENABLE_CGAL OFF) IF(ENABLE_PFVFLOW) SET(DISABLED_FEATS "${DISABLED_FEATS} PFVFLOW") MESSAGE(STATUS "CGAL NOT found: PFVFLOW disabled") ENDIF(ENABLE_PFVFLOW) ENDIF(CGAL_FOUND AND GMP_FOUND AND (NOT("${CMAKE_CXX_COMPILER} ${CMAKE_CXX_COMPILER_ARG1}" MATCHES ".*clang"))) ELSE(ENABLE_CGAL) SET(DISABLED_FEATS "${DISABLED_FEATS} CGAL") ENDIF(ENABLE_CGAL) #=========================================================== IF(ENABLE_LINSOLV) FIND_PACKAGE(Cholmod) FIND_PACKAGE(OpenBlas) FIND_PACKAGE(Metis) IF(CHOLMOD_FOUND AND OPENBLAS_FOUND AND METIS_FOUND) SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} ${CGAL_DEFINITIONS} -DLINSOLV -DFLOW_ENGINE") SET(LINKLIBS "${LINKLIBS};${CHOLMOD_LIBRARIES};${AMD_LIBRARY};${CAMD_LIBRARY};${COLAMD_LIBRARY};${CCOLAMD_LIBRARY};${OPENBLAS_LIBRARY};${METIS_LIBRARY}") INCLUDE_DIRECTORIES(${METIS_INCLUDE_DIR} ${CHOLMOD_INCLUDE_DIR}) MESSAGE(STATUS "Found Cholmod") MESSAGE(STATUS "Found OpenBlas") MESSAGE(STATUS "Found Metis") SET(CONFIGURED_FEATS "${CONFIGURED_FEATS} LINSOLV") ELSE(CHOLMOD_FOUND AND OPENBLAS_FOUND AND METIS_FOUND) MESSAGE(STATUS "Missing dependency for LINSOLV, disabled") SET(DISABLED_FEATS "${DISABLED_FEATS} LINSOLV") SET(ENABLE_LINSOLV OFF) ENDIF(CHOLMOD_FOUND AND OPENBLAS_FOUND AND METIS_FOUND) ELSE(ENABLE_LINSOLV) SET(DISABLED_FEATS "${DISABLED_FEATS} LINSOLV") ENDIF(ENABLE_LINSOLV) #=============================================== IF(ENABLE_SPH) ADD_DEFINITIONS("-DYADE_SPH") SET(CONFIGURED_FEATS "${CONFIGURED_FEATS} SPH") ELSE(ENABLE_SPH) SET(DISABLED_FEATS "${DISABLED_FEATS} SPH") ENDIF(ENABLE_SPH) #=============================================== IF(ENABLE_LIQMIGRATION) ADD_DEFINITIONS("-DYADE_LIQMIGRATION") SET(CONFIGURED_FEATS "${CONFIGURED_FEATS} LIQMIGRATION") ELSE(ENABLE_LIQMIGRATION) SET(DISABLED_FEATS "${DISABLED_FEATS} LIQMIGRATION") ENDIF(ENABLE_LIQMIGRATION) #=============================================== IF(ENABLE_GL2PS) FIND_PACKAGE(GL2PS) IF(GL2PS_FOUND) INCLUDE_DIRECTORIES(${GL2PS_INCLUDE_DIR}) SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DYADE_GL2PS") SET(LINKLIBS "${LINKLIBS};${GL2PS_LIBRARIES};") MESSAGE(STATUS "Found GL2PS") SET(CONFIGURED_FEATS "${CONFIGURED_FEATS} GL2PS") ELSE(GL2PS_FOUND) MESSAGE(STATUS "GL2PS NOT found") SET(DISABLED_FEATS "${DISABLED_FEATS} GL2PS") SET(ENABLE_GL2PS OFF) ENDIF(GL2PS_FOUND) ELSE(ENABLE_GL2PS) SET(DISABLED_FEATS "${DISABLED_FEATS} GL2PS") ENDIF(ENABLE_GL2PS) INCLUDE_DIRECTORIES(${PYTHON_INCLUDE_DIRS}) INCLUDE_DIRECTORIES(${CMAKE_BINARY_DIR}) #=========================================================== IF(ENABLE_LBMFLOW) SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DLBM_ENGINE") SET(CONFIGURED_FEATS "${CONFIGURED_FEATS} LBMFLOW") MESSAGE("LBMFLOW is still experimental, building and running LBM engine are at your own risk!") ELSE(ENABLE_LBMFLOW) SET(DISABLED_FEATS "${DISABLED_FEATS} LBMFLOW") ENDIF(ENABLE_LBMFLOW) #=============================================== IF(ENABLE_MASK_ARBITRARY) ADD_DEFINITIONS("-DYADE_MASK_ARBITRARY") SET(CONFIGURED_FEATS "${CONFIGURED_FEATS} MASK_ARBITRARY") IF(NOT MASK_ARBITRARY_SIZE) SET(MASK_ARBITRARY_SIZE "256") ENDIF(NOT MASK_ARBITRARY_SIZE) ADD_DEFINITIONS(-DYADE_MASK_ARBITRARY_SIZE=${MASK_ARBITRARY_SIZE}) MESSAGE("MASK_ARBITRARY_SIZE = ${MASK_ARBITRARY_SIZE}") ELSE(ENABLE_MASK_ARBITRARY) SET(DISABLED_FEATS "${DISABLED_FEATS} MASK_ARBITRARY") ENDIF(ENABLE_MASK_ARBITRARY) #=========================================================== IF(ENABLE_PROFILING) SET(CONFIGURED_FEATS "${CONFIGURED_FEATS} PROFILING") ADD_DEFINITIONS("-DUSE_TIMING_DELTAS -DISC_TIMING") ELSE(ENABLE_PROFILING) SET(DISABLED_FEATS "${DISABLED_FEATS} PROFILING") ENDIF(ENABLE_PROFILING) #=========================================================== IF(ENABLE_POTENTIAL_PARTICLES) FIND_PACKAGE(OpenBlas REQUIRED) FIND_PACKAGE(LAPACK REQUIRED) IF(OPENBLAS_FOUND AND LAPACK_FOUND) ADD_DEFINITIONS("-DYADE_POTENTIAL_PARTICLES") SET(LINKLIBS "${LINKLIBS};${OPENBLAS_LIBRARY};${LAPACK_LIBRARY}") MESSAGE(STATUS "Found OpenBlas") MESSAGE(STATUS "Found Lapack") SET(CONFIGURED_FEATS "${CONFIGURED_FEATS} PotentialParticles") ELSE(OPENBLAS_FOUND AND LAPACK_FOUND) MESSAGE(STATUS "Missing dependency for PotentialParticles, disabled") SET(DISABLED_FEATS "${DISABLED_FEATS} PotentialParticles") SET(ENABLE_POTENTIAL_PARTICLES OFF) ENDIF(OPENBLAS_FOUND AND LAPACK_FOUND) ELSE(ENABLE_POTENTIAL_PARTICLES) SET(DISABLED_FEATS "${DISABLED_FEATS} PotentialParticles") ENDIF(ENABLE_POTENTIAL_PARTICLES) #=========================================================== #=========================================================== IF(ENABLE_POTENTIAL_BLOCKS) INCLUDE(FindCLP) FIND_PACKAGE(OpenBlas REQUIRED) FIND_PACKAGE(LAPACK REQUIRED) IF(CLP_FOUND AND OPENBLAS_FOUND AND LAPACK_FOUND) ADD_DEFINITIONS("-DYADE_POTENTIAL_BLOCKS") INCLUDE_DIRECTORIES(${CLP_INCLUDE_DIR} ${CLP2_INCLUDE_DIR} ) SET(LINKLIBS "${LINKLIBS};${CLP_LIBRARY};${CLP2_LIBRARY};${CLP3_LIBRARY};${OPENBLAS_LIBRARY};${LAPACK_LIBRARY}") MESSAGE(STATUS "Found CLP") SET(CONFIGURED_FEATS "${CONFIGURED_FEATS} PotentialBlocks") ELSE(CLP_FOUND AND OPENBLAS_FOUND AND LAPACK_FOUND) MESSAGE(STATUS "CLP NOT found") SET(DISABLED_FEATS "${DISABLED_FEATS} PotentialBlocks") SET(ENABLE_POTENTIAL_BLOCKS OFF) ENDIF(CLP_FOUND AND OPENBLAS_FOUND AND LAPACK_FOUND) ELSE(ENABLE_POTENTIAL_BLOCKS) SET(DISABLED_FEATS "${DISABLED_FEATS} PotentialBlocks") ENDIF(ENABLE_POTENTIAL_BLOCKS) #=========================================================== IF (INSTALL_PREFIX) SET(CMAKE_INSTALL_PREFIX ${INSTALL_PREFIX}) MESSAGE(WARNING "Use CMAKE_INSTALL_PREFIX option instead of INSTALL_PREFIX! It will be removed soon.") ENDIF (INSTALL_PREFIX) IF (CMAKE_INSTALL_PREFIX) MESSAGE("Yade will be installed to ${CMAKE_INSTALL_PREFIX}") ELSE (CMAKE_INSTALL_PREFIX) MESSAGE("Yade will be installed to default path ${CMAKE_INSTALL_PREFIX}, if you want to override it use -DCMAKE_INSTALL_PREFIX option.") ENDIF (CMAKE_INSTALL_PREFIX) IF (NOT SUFFIX) SET (SUFFIX "-${YADE_VERSION}") ENDIF (NOT SUFFIX) IF(NOSUFFIX) #For packaging SET (SUFFIX "") ENDIF(NOSUFFIX) #For packaging IF(NOT LIBRARY_OUTPUT_PATH) #For packaging SET (LIBRARY_OUTPUT_PATH ${CMAKE_INSTALL_LIBDIR}) ENDIF(NOT LIBRARY_OUTPUT_PATH) #For packaging IF (NOT runtimePREFIX) SET (runtimePREFIX ${CMAKE_INSTALL_PREFIX}) ENDIF (NOT runtimePREFIX) MESSAGE (STATUS "Suffix is set to " ${SUFFIX}) MESSAGE (STATUS "LIBRARY_OUTPUT_PATH is set to " ${LIBRARY_OUTPUT_PATH}) MESSAGE (STATUS "runtimePREFIX is set to " ${runtimePREFIX}) #=========================================================== SET(YADE_LIB_PATH ${CMAKE_INSTALL_PREFIX}/${LIBRARY_OUTPUT_PATH}/yade${SUFFIX}) SET(YADE_EXEC_PATH ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_BINDIR}) SET(YADE_PY_PATH ${YADE_LIB_PATH}/py) SET(YADE_DOC_PATH ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_DATAROOTDIR}/doc/yade${SUFFIX}) SET(YADE_MAN_PATH ${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_MANDIR}) SET(CMAKE_SKIP_BUILD_RPATH FALSE) SET(CMAKE_BUILD_WITH_INSTALL_RPATH FALSE) SET(CMAKE_INSTALL_RPATH "${YADE_LIB_PATH};${YADE_PY_PATH};${YADE_PY_PATH}/yade/;${YADE_PY_PATH}/yade/qt;${YADE_PY_PATH}/gts") SET(CMAKE_INSTALL_RPATH_USE_LINK_PATH TRUE) #=========================================================== IF(ENABLE_GUI) ADD_SUBDIRECTORY("${CMAKE_SOURCE_DIR}/gui") ENDIF(ENABLE_GUI) ADD_SUBDIRECTORY("${CMAKE_SOURCE_DIR}/py") #=========================================================== FILE(GLOB SRC_CORE "core/*.cpp") FILE(GLOB_RECURSE SRC_PKG "pkg/*.cpp") FILE(GLOB SRC_LIB "lib/*.cpp") SET(SRC_LIB "${SRC_LIB};lib/base/Math.cpp;lib/factory/ClassFactory.cpp;lib/factory/DynLibManager.cpp") SET(SRC_LIB "${SRC_LIB};lib/serialization/Serializable.cpp;lib/pyutil/gil.cpp;core/main/pyboot.cpp;${GUI_SRC_LIB};${CGAL_SRC_LIB}") IF(ENABLE_POTENTIAL_PARTICLES) SET(SRC_LIB "${SRC_LIB};lib/computational-geometry/MarchingCube.cpp") ENDIF(ENABLE_POTENTIAL_PARTICLES) #=========================================================== IF (CHUNKSIZE) INCLUDE(CombineSources) COMBINE_SOURCES(${CMAKE_BINARY_DIR}/core "${SRC_CORE}" ${CHUNKSIZE}) FILE(GLOB SRC_CORE_COMBINED "${CMAKE_BINARY_DIR}/core.*.cpp") COMBINE_SOURCES(${CMAKE_BINARY_DIR}/pkg "${SRC_PKG}" ${CHUNKSIZE}) FILE(GLOB SRC_PKG_COMBINED "${CMAKE_BINARY_DIR}/pkg.*.cpp") COMBINE_SOURCES(${CMAKE_BINARY_DIR}/lib "${SRC_LIB}" ${CHUNKSIZE}) FILE(GLOB SRC_LIB_COMBINED "${CMAKE_BINARY_DIR}/lib.*.cpp") ADD_LIBRARY(yade SHARED ${SRC_LIB_COMBINED} ${SRC_CORE_COMBINED} ${SRC_PKG_COMBINED}) ELSE (CHUNKSIZE) ADD_LIBRARY(yade SHARED ${SRC_CORE} ${SRC_PKG} ${SRC_LIB}) ENDIF (CHUNKSIZE) #=========================================================== find_python_module(minieigen REQUIRED) find_python_module(Tkinter REQUIRED) #=========================================================== ADD_LIBRARY(boot SHARED ${CMAKE_CURRENT_SOURCE_DIR}/core/main/pyboot.cpp) SET_TARGET_PROPERTIES(boot PROPERTIES PREFIX "" LINK_FLAGS "-Wl,--as-needed" ) TARGET_LINK_LIBRARIES(yade ${Boost_LIBRARIES} ${PYTHON_LIBRARIES} ${LINKLIBS} -lrt) SET_TARGET_PROPERTIES(yade PROPERTIES LINK_FLAGS "-Wl,--as-needed" ) TARGET_LINK_LIBRARIES(boot yade) IF(ENABLE_VTK) IF(${VTK_MAJOR_VERSION} GREATER 5) TARGET_LINK_LIBRARIES(yade ${VTK_LIBRARIES}) ADD_DEFINITIONS("-DYADE_VTK6") MESSAGE(STATUS "VTK version >5 is found") ELSE(${VTK_MAJOR_VERSION} GREATER 5) TARGET_LINK_LIBRARIES(yade vtkHybrid) ENDIF(${VTK_MAJOR_VERSION} GREATER 5) ENDIF(ENABLE_VTK) IF(ENABLE_GUI) TARGET_LINK_LIBRARIES(yade _GLViewer ${GUI_LIBS}) ENDIF(ENABLE_GUI) #==================================== #Back compatibility with scons SET (realVersion ${YADE_VERSION}) SET (version ${YADE_VERSION}) SET (pyExecutable ${PYTHON_EXECUTABLE}) SET (profile "default") SET (sourceRoot "${CMAKE_CURRENT_SOURCE_DIR}") #==================================== CONFIGURE_FILE(core/main/yade-batch.in "${CMAKE_BINARY_DIR}/bins/yade${SUFFIX}-batch") CONFIGURE_FILE(core/main/main.py.in "${CMAKE_BINARY_DIR}/bins/yade${SUFFIX}") CONFIGURE_FILE(py/config.py.in "${CMAKE_BINARY_DIR}/config.py") CONFIGURE_FILE(py/__init__.py.in "${CMAKE_BINARY_DIR}/__init__.py") #=========================================================== # Create header files for PFV from FlowEngine.hpp.in-template. # All @TEMPLATE_FLOW_NAME@ are replacing by a given names SET (TEMPLATE_FLOW_NAMES DFNFlowEngineT DummyFlowEngineT FlowEngineT FlowEngine_PeriodicInfo SoluteFlowEngineT UnsaturatedEngineT TwoPhaseFlowEngineT) FOREACH(TF ${TEMPLATE_FLOW_NAMES}) SET (TEMPLATE_FLOW_NAME ${TF}) CONFIGURE_FILE(pkg/pfv/FlowEngine.hpp.in "${CMAKE_BINARY_DIR}/pkg/pfv/FlowEngine_${TF}.hpp" @ONLY) CONFIGURE_FILE(pkg/pfv/FlowEngine.ipp.in "${CMAKE_BINARY_DIR}/pkg/pfv/FlowEngine_${TF}.ipp" @ONLY) ENDFOREACH(TF) INCLUDE_DIRECTORIES("${CMAKE_BINARY_DIR}/pkg/pfv/") #=========================================================== INSTALL(PROGRAMS "${CMAKE_BINARY_DIR}/bins/yade${SUFFIX}-batch" DESTINATION ${YADE_EXEC_PATH}/) INSTALL(PROGRAMS "${CMAKE_BINARY_DIR}/bins/yade${SUFFIX}" DESTINATION ${YADE_EXEC_PATH}/) INSTALL(FILES "${CMAKE_BINARY_DIR}/config.py" DESTINATION ${YADE_PY_PATH}/yade/) INSTALL(FILES "${CMAKE_BINARY_DIR}/__init__.py" DESTINATION ${YADE_PY_PATH}/yade/) FILE(GLOB filesPYChecks "${CMAKE_CURRENT_SOURCE_DIR}/scripts/checks-and-tests/checks/*.py") INSTALL(FILES ${filesPYChecks} DESTINATION ${YADE_PY_PATH}/yade/tests/checks) FILE(GLOB filesPYChecksData "${CMAKE_CURRENT_SOURCE_DIR}/scripts/checks-and-tests/checks/data/*") INSTALL(FILES ${filesPYChecksData} DESTINATION ${YADE_PY_PATH}/yade/tests/checks/data) INSTALL(FILES "${CMAKE_CURRENT_SOURCE_DIR}/doc/yade-logo-note.png" DESTINATION "${YADE_DOC_PATH}/img") INSTALL(TARGETS boot DESTINATION "${YADE_PY_PATH}/yade/") INSTALL(TARGETS yade DESTINATION ${YADE_LIB_PATH}) #=========================================================== MESSAGE(STATUS "===========================================================") MESSAGE(STATUS "Yade configured with following features:${CONFIGURED_FEATS}") MESSAGE(STATUS "Disabled features:${DISABLED_FEATS}") IF (DEBUG) MESSAGE(STATUS "Debug build") SET (debugbuild " (debug build)") ELSE (DEBUG) MESSAGE(STATUS "Optimized build") ENDIF (DEBUG) IF (CHUNKSIZE) MESSAGE(STATUS "CHUNKSIZE is set to " ${CHUNKSIZE}) ENDIF (CHUNKSIZE) MESSAGE(STATUS "===========================================================") #=========================================================== #Building doc ADD_CUSTOM_TARGET(doc) FILE(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/doc) FILE(MAKE_DIRECTORY ${CMAKE_BINARY_DIR}/doc/sphinx) ADD_CUSTOM_COMMAND( TARGET doc PRE_BUILD COMMAND rm -rf ${CMAKE_BINARY_DIR}/doc/sphinx/_build COMMAND cp -r ${CMAKE_CURRENT_SOURCE_DIR}/doc/* ${CMAKE_BINARY_DIR}/doc COMMAND PYTHONPATH=${CMAKE_BINARY_DIR}/doc/sphinx ${YADE_EXEC_PATH}/yade${SUFFIX} yadeSphinx.py WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/doc/sphinx DEPENDS ${YADE_EXEC_PATH}/yade${SUFFIX} ) ADD_CUSTOM_COMMAND( TARGET doc POST_BUILD COMMAND xelatex Yade.tex COMMAND xelatex Yade.tex WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/doc/sphinx/_build/latex DEPENDS ${YADE_EXEC_PATH}/yade${SUFFIX} ${CMAKE_BINARY_DIR}/doc/sphinx/_build/latex/Yade.tex ) ADD_CUSTOM_COMMAND( TARGET doc POST_BUILD COMMAND rm -rf ${YADE_DOC_PATH}/html COMMAND mv ${CMAKE_BINARY_DIR}/doc/sphinx/_build/html ${YADE_DOC_PATH}/html COMMAND mv ${CMAKE_BINARY_DIR}/doc/sphinx/_build/latex/Yade.pdf ${YADE_DOC_PATH}/ WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/doc/sphinx/_build/latex DEPENDS ${YADE_EXEC_PATH}/yade${SUFFIX} ${CMAKE_BINARY_DIR}/doc/sphinx/_build/latex/Yade.tex ) ADD_CUSTOM_COMMAND( TARGET doc POST_BUILD COMMAND mv ${CMAKE_BINARY_DIR}/doc/sphinx/_build/epub/Yade.epub ${YADE_DOC_PATH}/ || true WORKING_DIRECTORY ${CMAKE_BINARY_DIR}/doc/sphinx/_build/latex DEPENDS ${YADE_EXEC_PATH}/yade${SUFFIX} ${CMAKE_BINARY_DIR}/doc/sphinx/_build/latex/Yade.tex ) #=========================================================== #Building manpage ADD_CUSTOM_TARGET(manpage) ADD_CUSTOM_COMMAND( TARGET manpage POST_BUILD COMMAND help2man ${YADE_EXEC_PATH}/yade${SUFFIX} > yade${SUFFIX}.1 COMMAND help2man ${YADE_EXEC_PATH}/yade${SUFFIX}-batch > yade${SUFFIX}-batch.1 COMMAND mkdir -p ${YADE_MAN_PATH} COMMAND mv *.1 ${YADE_MAN_PATH} WORKING_DIRECTORY ${CMAKE_BINARY_DIR} DEPENDS ${YADE_EXEC_PATH}/yade${SUFFIX} /usr/bin/help2man ) #=========================================================== #Execute standard checks ADD_CUSTOM_TARGET(check) ADD_CUSTOM_COMMAND( TARGET check POST_BUILD COMMAND ${YADE_EXEC_PATH}/yade${SUFFIX} --test COMMAND ${YADE_EXEC_PATH}/yade${SUFFIX} --check WORKING_DIRECTORY ${CMAKE_BINARY_DIR} DEPENDS ${YADE_EXEC_PATH}/yade${SUFFIX} ) #=========================================================== trunk-2017.01a/ChangeLog000066400000000000000000024270271304022710500147520ustar00rootroot00000000000000================================================== yade-2017.01a Thu, Jan 19 22:07:25 2017 +0100 Anton Gladky (20): Remove RELEASE file. Add some notes about how to make releases. Make Yade compatible with VTK7. Use C++11 constructions for InteractionLoop. Optimize using of ndarray. Partly fix webpage help show. LP:1598174 Final fix for LP:1598174 Add missing dependency on python-pyqt5.qtwebkit. Fix load/save in GUI-QT5. Drop unused typedef. Disable LAW2_SCGEOM_CAPILLARYPHYS_Capillarity1 by default. Remove some deprecated scripts. Increase the size of force container. +1 paper. Provide a proper functioning with IPython5. Add -fext-numeric-literals to fix FTBFS against boost_1.62 Fix yade with IPython5. Update distro names in documentation Add missing header include Add RELEASE file. Bruno Chareyre (12): +2 articles (thanks to Bettina Suhr) + 1 proceedings (thanks to Bettina Suhr) Update citing_yade.bib revert the revert ca0e29ac57 list authors of the doc as in doi:10.5281/zenodo.34073 a note on using distcc and ccache minor editing of installation page Master thesis Morales2012a Introduce Network::surfaceSolidThroatInPore() for partial solid surfaces per half-throat make the recursion conditional for invasion in multiphase flow push a file missing in commit e91ff135b7 Yade bibtex: "and others" invalid for less than 9 authors Chao Yuan (4): Add cell label for phase cluster. NW-res label 0, W-res label 1, disconnected w-clusters start from 2. label can be saved in savePhaseVtk. fix comment on label. clean UnsaturatedEngine, move all functions to TwoPhaseFlowEngine. Revert DryingEngine. Francois Kneib (1): Fix O.engines in examples/cylinders/cylinderconnection-roots.py Jan Stránský (11): fixed a small bug in shear force computation in CPM model Added PolyhedraSplitter example Changed L3Geom to ScGeom in tutorial example scripts fixed a minor compilation issue in ConcretePM Fixed call of _utils.interactionAnglesHistogram with default arduments making all Law2::go virtual Matrix_computeUnitaryPositive, changed computeThinX to computeFullX flags User's manual, added how to visualize force chain in Paraview UnstructuredGrid: fiexd little bug in manual setting of facet position from vertices added pack.inHalfSpace and pack.inConvexPolygon + example script fixed another little bug in utils.UnstructuredGrid Jerome Duriez (11): Doc clarification for TriaxialStressController.externalWork (http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg12083.html) Doc of utils.readParamsFromTable() hopefully improved Friendlier BibTex entries for 2015 doc. To avoid Smilauer and et al in manuscripts Doc Getting help section updated to reflect current practice Including interface orientation data in CapillaryPhys code Capillary scripts commit (http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg12103.html). Located in a new examples/capillaryLaplaceYoung folder intended to illustrates capillary Law2. With one new simulation script example and another old one, moved here Typo and minor corrections of previous capillary commit Capillary law2: erasing when necessary sphere-non sphere interactions (bug LP: #1628273) + minor changes Capillary law2: restricting test shape. Plus minor change in capillaryLaplaceYoung/README text file Doc: small updates in PartialEngine and KinematicEngines References .bib files: including new entries Raphael Maurin (4): HydroForceEngine: add a condition to ignore particles fixed on the sideWalls. Add an example for the use of HydroForceEngine HydroForceEngine: new fluctuation model for the example script + small correction Add new simple discrete random walk fluctuation model, to be used with the new example script fluidizedBed.py Change the condition for applying the fluid force from p>0 to p>=0, which is more appropriate Add two example scripts for the use of HydroForceEngine One simple example to get familiar with the application of buoyancy (buoyantParticles.py). One example simulating a fluidized bed configuration to get familiar with both the application of a fluid velocity profile and of turbulent fluctuation with the DRW models (fluidizedBed.py) bchareyre (19): fix invalid pointer, thanks Jerome (https://lists.launchpad.net/yade-dev/msg12791.html) (doc) clarify the meaning of TriaxialStressController::externalWork fix 1 compile warning reordering bib references remove latex/multicolumn from sphinx conf.py (compile error on some systems) Law2_ScGeom_CapillaryPhys_Capillarity: cache getClassIndex() for use in a loop fix wrong access to a Network::boundary by index FlowEngine: enable the definition of continuum scale permeability independent of particle sizes Introduce DryingEngine (two phase flow with convection in one phase) Implement Darcy scale permeability in FlowEngine, introduce alphaShapes (commented), some code cleaning and smallfixes (FlowEngine) optionaly include/skip bounding cells when calculating the average pore pressure fix negative volumes issue in triangulation cells, consistentlyy remove the includeBoundary option (a workaround) in averageVelocity TwoPhaseFlowEngine: better integration of fluid clusters merging PhaseCluster code with r3975 fix compile warnings small optimization in Clump::updateProperties update phaseCluster attributes: volume, interfacial area, etc. + various smallfixes in the cluster labelling further improvement of the cluster labeling in multiphase model 2PFLOW engine: remove useless int from getInterfaces()'s parameters booncw (2): Pushing Potential Blocks based on CWBoonEtAl2012 Computers&Geotechnics/CWBoon 2013 PhD thesis, but using CLP as linear programming Solver. CLP can be downloaded from Synaptic Package Manager: coinor-clp, coinor-libclp-dev, coinor-libclp1, coinor-libosi1v5. To enable this, set ENABLE_POTENTIAL_BLOCKS to ON in CMakeLists.txt" revising Potential Blocks to the latest version to run slope analysis raphm1 (1): ViscoelasticPM : fix resolution problem in find_cn_from_en function Change the value of the initial perturbation for the resolution of the equation to obtain the damping from the restitution coefficient. Allows for a much wider range of resolution in terms of mass, stiffness and restitution coefficient. Put a limiter to avoid division by zero and force the loop to print the warning message if "error" goes to nan (no warning in these cases previously) ================================================== yade-2016.06a Tue, Jun 14 20:30:53 2016 +0200 Anton Gladky (88): Remove release. Clean some unused macroses (old wm3-stuff) Remove some global headers Raise minimal boost version to 1.47 Add -DNDEBUG if compiling in release mode Tiny code refactoring Clean some warnings and old stuff. Return removed header back. Fix warning in newer matplotlib. Drop old commented stuff in python-scrips. Remove flags and preSteps from scene Remove deprecated findBoundDispatcherInEnginesIfNoFunctorsAndWarn Remove PISC_DEBUG. Fix typo in installation sections of doce. Thanks to Jan. Export normal and viscous part of the visco-elastic contact Remove confusing part in installation part of documentation regarding Qt5. Fix typo in CMakeLists Tiny updates of examples of LudingPM. Fix compilation warnings. Update formatting in SpherePack Fix an order of calculation of c in SpherePack Fix some compilation warnings. Fix cappitalization typo in Lapack (case-sensitive in this case). Respect VTK6 in PotentialParticles. Add .travis.yml for CI. Remove version restriction on sphinx. Use trusty as build-env. Add -y parameter to apt-get install. Fix numpy import on travis. Fix segfault during save/load of CapViscModels Add one more check-script (capillary models) Fix typo in check-script. Fix crash in Ig2_Facet_Polyhedra_PolyhedraGeom vtkExporter: increase number of leading zeros to 8 Move implementation of methods of ForceContainer in cpp. Split implementation of ForceContainer in parallel and serial. Add zero-forces to the youngest body after simulation load. Closes LP:1560171 Drop parallel execution in replaceByClumps. Closes LP:1559098 Add import of polyhedras from the file. Add an opportunity to shift, scale and rotate imported polyhedrons Minor fixes in Polyhedra_splitter. Fix division by zero crash in Polyhedra Add CGAL_DISABLE_ROUNDING_MATH_CHECK, -frounding-math when CGAL is enabled. Fix some formatting issues. Non-invasive fixes in polyhedra_splitter. Get max-min coefs in polyhedra_splitter simpler. Use tuple as a parameter for SplitPolyhedraDouble Add check script for polyhedra crash. Use explicitly -DNDEBUG instead of CMAKE_CXX_FLAGS_RELEASE Check isnan in some coordinates before calling CGAL. Minor formatting fixes in Polyhedra. Add check-script for save/load of clumps. Disable checkPolyhedraCrush. It is unstable now. Fix checkPolyhedraCrush Remove polyhedra_utils import from "ymport" Add prefix std:: to isnan and isinf. Update checkPolyhedraCrush Update files for ppa-infrastructure. Undef NDEBUG in all polyhedra files. Add pause for checkSaveLoadClumps to escape race condition. Use variadic arguments in DynLibDispatcher. Fix crash in polyhedra, if maxFs=0. Fix checkPolyhedraCrush (remove qt) Remove unused functionality in Dispatcher. Set Qt5 by default. Add mathcmaker for normalCohesion and shearCohesion. Split QGLViewer.cmake on qt4 and qt5 versions. Add .gitattributes to ignore line endings. Migrate buildppa to python3. Replace some "#define"(s) by functions. Remove some machine-specific items in documentation. Add unit test for matchmaker. Replace vector by unordered_map data structure in Matchmaker. Minor fix in documentation. Replace some "defines" by functions. Remove numpy.hpp. Fix bug in polyhedra_splitter. Some cosmetic fixes in core-files. Enable C++14. Revert 2dc99 and ed8dcb. Use unordered_map instead of map for MapId2IntrT Use unordered_map only for Boost >= 1.56 Back to C++11. Revert using unordered_map in Body. Scale mass and inertia in spheresModify. Reduce size of flags in Bounds of InsertionSortCollider Fix bug in MatchMaker. Add RELEASE file. Bruno Chareyre (16): add labels to default engines for easier showcases fix ambiguous syntax, fixing https://bugs.launchpad.net/bugs/1514477 introduce 2nd edition of the documentation and contact for consuting (in homepage) update the webpage about citation with 2nd edition, add 1st edition as an external reference, update pdf metadata fix one DOI of the 2nd ed. documentation Add missing toctree's for the citable book versions fix typo in installation page fixed DOI fix some hyperlinks pointing to the old geo.hmg.inpg.fr declare mask attribute for FlowEngine, fixes a compile error use FlowEngine's mask consistently implement standalone plastic-shear energy counter in CohesiveFrictional Law2 define constrictions with consistent cell's ids (see https://answers.launchpad.net/yade/+question/288118) fix a compile error update boost version in prerequisites (installation page) Documentation: include unp in the equations of Law2_ScGeom6D_CohFrictPhys_CohesionMoment Burak Er (1): Implement deformable elements ChiaWeng Boon (1): Commit Potential Particles: non-spherical particles for DEM Francois Kneib (8): TesselationWrapper : add a security that prevents user to access the strain tensor of a particle (aka deformation) outside its boundaries. Fix a tensor access in local displacement calculation. Fix a bug in Tesselationwrapper: one of the bounding planes was not rightly positionned. Fix in TesselationWrapper: allow the tesselation to compute right triangulation in the boundaries of a periodic boundaries conditions simulation. Add 5 setters for bodies pos,vel,ori,angVel,color to workaround the memory leak bug when assigning attributes from python (see https://bugs.launchpad.net/yade/+bug/1041084). They are not supposed to stay in the code for a long period (remove them when the bug is solved), but are useful in sims that massively change values of python/c++ binded attributes. Simplify one line in TesselationWrapper. Fix the debug build that failed to compile due to a mistake in pkg/dem/Polyhedra.cpp Fix the inspector GUI for Qt5, thanks to Mark S. Bentley. Jan Stránský (30): Merge pull request #47 from booncw/master Potential particles modification Merge branch 'master' of github.com:yade/trunk Potential particles modifications added forgotten file from previous commit Modified python interface for O.forces.addF(...,permanent=True) and addT(...,permanent=True) fixed some warnings during docs build Added frictAngle MatchMaker for Ip2_FrictMat_CpmMat_FrictPhys set b.aspherical=True in utils.polyhedron and utils.tetraPoly Polyhedra modification Added a material model for mortar layer Polyhedra.setVertices improvement, preventing memory leaks (question #290947 and bug #1570679) Interaction::reset explicitly resets also its functorCache Fixed a strange bug in Law2_PolyhedraGeom_PolyhedraPhys_Volumetric and shearForce Added useRef parameters to VTKExporter.exportPolyhedra and VTKExporter.exportInteractions Modified MortarMat Merge branch 'master' of github.com:yade/trunk fixed computation of shearForce in Law2_PolyhedraGeom_PolyhedraPhys_Volumetric added and modified examples for MortarMat Merge branch 'master' of github.com:yade/trunk added MatchMaker for E in Ip2_CmpMat_CpmMat_CpmPhys Fixed a bug in pack.inSphere, related to question #292846 Merge branch 'master' of github.com:yade/trunk VTKRecorder, added orientation for box export (question #293635) Modification of CPM Fixed ymport.textPolyhedra function (bug #1582775) added x_y_z_r_attrs format to ymport.textExt Added an example for generation of 'agglomerate' packing Fixed Law2_Cpm default parameter to keep backward compatibility (question #294657) Better default value from previous commit Jerome Duriez (12): +1 journal paper Incorporating previous +1 paper in JCFpm doc + another journal paper makeCloud doc changes with the hope to make it clearer for all users Doc of TriaxStressController.porosity precised Doc improvements of previous commit improved Last doc improvement of previous commit normalForce and shearForce convention (sustained by #2) precised in docs fabricTensor() now ok for non-periodic simulations. revertSign attribute removed as well getSpheres*() functions: getting rid of dynamic test, see http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg11956.html fabricTensor(): unify the behavior regarding boundary interactions whether split=0 or 1: they are now disregarded in both cases fabricTensor(): re introducing all kind of interactions in the loop, with the new possibility defining a cutoff. See http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg11982.html Klaus Thoeni (23): fix some typos and add some more details fix Anton's previous commit (make doc was not working) fix documentation for Note some polishing gts shift and scale apparently only take three float values, hence changed Merge branch 'master' of github.com:yade/trunk move grid specific functions in separate module and add some more doc add some more examples, show same functionality as with chained cylinders update doc add Grid and pFacet references Initial version of the PFacet implementation (contributed by Anna Effeindzourou) Examples for creating pfacets update tests according to new gridpfacet module remove postLoad function as not used, this fixes as well serialization problem in --test better handling of double contacts, get gid of function ScGem goOneWay improved documentation add definition for cylinder and cylinderConnection basen on gridConnection, add warning for chainedCylinder usage examples for cylinder and cylinderConnection example with many cylinders and 2 pFacets QT5 is default now correct some typos similar to example in chained-cylinder-roots.py add reference Raphael Maurin (6): HydroForceEngine: modify the turbulent fluctuations formulation and add a new DRW model The turbulent fluctuations model takes now the form of a function of HydroForceEngine and is not anymore called from a flag. In addition, an alternative DRW model has been added. HydroForceEngine: adapt the averageProfile function for bi-disperse mixtures. Evaluate the streamwise, spanwise and wall-normal average particle velocity for the two defined types of particles. HydroForceEngine: modify turbulent fluctuation model. Add a fluctuation along the spanwise (y) direction. Reset the fluctuation to zero when the particle is out of the flow (fix a bug) Comment a bit more the turbulentFluctuation function HydroForceEngine, hpp file completing the last commit Add references add a link in the publications bchareyre (1): compute external work correctly in TriaxialStressController ================================================== yade-1.20.0 Fri, Oct 9 21:20:00 2015 +0200 Anton Gladky (57): Remove RELEASE file. Simplify definition of build flags Fix some warnings during compilation. For clang use -fstack-protector instead of -fstack-protector-strong Ignore project files of idea IDE Refactoring of Math.hpp Make minieigen external package mandatory. Add -fstack-protector-strong only for gcc >=4.9 Some warning fixes. Add ENABLE_PROFILING option Set some metric-measures in ViscElCap. Revert adding frounding-math flag Replace INSTALL_PREFIX by CMAKE_INSTALL_PREFIX Remove deprecated in Yade BOOST_PYTHON_FUNCTION_OVERLOADS macros. Fix some more compilation warnings. Fix some more compilation warnings. Minor fix in CMakeLists.txt Fix hexagonal packing, should not be undesired overlap any more. Make Serializable.hpp more readable. Remove deprecated parameters. Move STLReader into STLImporter +1 master thesis at TU Freiberg. Fix crash by export-VTK of interactions after body removal. Split description of ViscoelasticPM to make it more readable. Let exist interactions between clumpMembers of the same clump. Skip force calculation in SPH-clump Add warning about CGAL in Ubuntu 14.04 Trusty Add ISC_TIMING pre preprocessor directive. Drop support of Ubuntu 12.04 Precise Merge pull request #46 from timpovall/master Non invasive refactoring of InsertionSortCollider Revert previous commit. Add a second option to fix the compilation with CGAL on 14.04 Remove deprecated code with very old boost. Implement viscous damping for capillary phase. Fix SPH force calculation between clump members. Fix compilation with QGLViewer>=2.6.3 Prepare Qt5-build. Fix compilation against gqlviewer-qt4. Fix check-script +1 conference First steps in Qt5. Prepare Qt5 build. Update python files due to Qt5. Some more updates toward Qt5. Qt5-migration is alsmot finished. Fix Qt5 compilation. Fix crash in Qt5. Fix QThread issue. Add information about compilation against Qt5. Add missing function in TesselationWrapper Remove some unused headers and defs. Fix compilation if openmp is disabled Fix compilation introduced in last commit. Add talk, hold in Particles 2015 Add hourglass example Add RELEASE file. Bruno Chareyre (15): Save relative rotations in ScGeom6D (unmark "nosave") since it is required for reloading correctly. CohesiveFrictionalInteractions: removed "nosave" flags for contact moments +1 journal paper +1 journal paper add a virtual function returning rotational stiffness of the interactions - returning zero if not overloaded account for the rotational stiffness of interactions in GlobalStiffnessTimeStepper apply the spin of the velocity gradient on particles in periodic BCs small typo Added book chapter Installation: http://www.yade-dem.org/packages is required for an external library (eigen or cgal? not sure now) more accurate defintion of fluctuational velocity/spin for kinetic energy in periodic BCs correct value of volume for id<6 in TesselationWrapper when O.bodies does not have bounding objects fix segfault when InteractionContainer::found() access out of bounds add function has() to O.interactions to check if (id1,id2) exists + fix doc of O.interactions remove useless int parameter of O.interactions.all(), instead filter non-real interactions optionaly based on bool Chao Yuan (3): -add getPotentialPendularSpheresPair() function. -set pore throat radius between two fictious cells negative in invadeBoundary=true mode. add a new version of capillary law. (pushed by Caroline) Francois Kneib (2): New viewer feature : display tori instead of spheres for 2D simulations. So if the viewer looks toward the right axis, on can see circles instead of disks. Modifications in pkg/common/Gl1_Primitives.*pp 3 new parameters in Gl1_Sphere : circleView, circleRelThickness, circleAllowedRotationAxis. A new condition to enable circleView. The code is based on initGlutGlList() method for spheres. Add an example script for the tori DISPLAY feature. Jan Stránský (4): fixed compilation warning added Polyhedra.setVertices function, which also updates internal variables (shape.v=... does not) Added Facet.setVertices function to prevent memory leaks (see bug 1041084, #8) corrected bug in utils.UnstructuredGrid.updateElements (question #267761) Janek Kozicki (2): Fix bug in InteractionContainer::eraseNonReal Fix: CGAL ERROR: assertion violation! Jerome Duriez (5): Add missing space in error message Doc of sphSph attribute of plotDirections precized Introduction of surface tension as an attribute, and comments about code objects related to capillary files Addition in doc of Omega.engines to state it is = to O.engines in python Removal of python O.engines reference Raphael Maurin (9): getStressProfile: output format modification + add calculation of granular temperature and kinetic stress tensor Law2_ScGeom_ViscElPhys_Basic: add a new formulation + check Add a new formulation of the law when imposing in the material young, poisson, and normal restitution coefficient. The effective spring constants ks and kn are evaluated "classically" with the young modulus and the poisson's ratio. The specificity of the formulation stands in the fact that it is the restitution coefficient of the contact (en = 2*en1*en2/(en1+en2)) that is imposed, and not the damping constant. To achieve this, the damping constant of the contact is evaluated resolving numerically the analytical expression 21 of [Schwager2007] (with a minus sign, there is a mistake in the article) with a Newton-Raphson algorithm (This was made by Francois Kneib). This does not seem to affect the calculation time. With this formulation, there is no tangential viscous damping, and it is usually not possible to access value of normal restitution coefficient lower than 0.1 (in that case the numerical resolution does not converged in the maximum 15 iteration allowed in the code) Together with the new formulation, add a short check script to verify that the imposed restitution coefficient is the one obtained. Law2_ScGeom_ViscElPhys_Basic: complete the documentation Add a more precise documentation of the law integrating the last commit. I didn't complete the formulation associated with Pournin2001 (precising en,es,tc) as I am not using it and I do not know it much. Fix compilation error in the documentation of Law2_ScGeom_ViscElPhys_Basic Error inserted in commit d47b8574e8fcc2dc09b926404f08081f2194cfde Add a function in shop to evaluate average depth profiles of particle velocity (x,y,z components), and solid volume fraction. HydroForceEngine: switch averageProfile function into a method + modify documentation Tutorial examples: remove all deprecated 'utils.' and GravityEngine in the example scripts Modify getDepthProfile to possibly average on spheres of selected radius only HydroForceEngine: modify averageProfile function to handle bi-disperse sample Add evaluation of the average solid volume fraction and drag force depth profiles considering the two particle size (taken as input) as independent. Timothy Povall (1): Removed line calling FindVTK.cmake, as this file no longer exists thomassweijen (1): Updates towards merging of both capillarity codes ================================================== yade-1.14.0 Tue, 21 Apr 2015 22:36:55 +0200 Anton Gladky (36): Remove RELEASE file. Fix typo in SPH. Move SPH-body parameters into body->state. Add one more kernel function in SPH. Change sign in calculation of viscosity in SPH Simplify Lucy kernel function Remove Cs parameter from VTK-export (sph only). Implement second variant of BSpline kernel function. Fix typo in Bspline kernel functio (sph). Fix date typo in Changelog Move Vf and Vmin from Body`s parameter to Body->state. Replace struct intReal by standard std::pair Prevent returning of a real value from void-function. Fix probably a wrong using of if-condition. Minor fix of using of std::abs function. Drop some if-conditions, which have always constant value. Drop default inclusion of DFNFLOW. Add some missing #ifdef YADE_CGAL. Fix check-script for LIQMIGRATION. Drop -frounding-math compiler flag from FindCGAL. Drop embedded floating_point_utilities_v3. Reintroduce floating_point_utilities_v3. Add missing files from last commit. Add LiqMigrEnabled parameter. Fix compilation with GCC-5. (Closes: #778190) +2 Project works Add an opportunity to list works, other than master thesis. Fix body unselecting. (Closes: LP:1423130) Fix MatplotlibDeprecationWarning: The use of 0 Remove DirSearchYade, MicroMacroAnalysis and someFile.pdf Clean current directory after --check Check file existance before its moving and removing. Add information, how to be notidied after each commit. Add an opportunity to set frictAngl through MatchMaker in ViscEl Add an option coordNumber to be exported in VTK. Add one more master thesis. Bruno Chareyre (28): FlowEngine: set cell's id in periodic triangulations + couple smallfix fix bad bugs in DFNFlowEngine following uninitialized 'isClump' use the dedicated solver in DFNFlowEngine some code documentation FlowEngine: discard blocked cells completely when assembling the permeability matrix #undef DFNFLOW FlowEngine: enhanced setter macro, detect changes in imposed pressure and update the linear system accordingly explicit error message when trying to interpolate capillary forces out-of-range of the data files fix save/load QGL camera state via text files Documentation. Define sign convention globaly in TriaxialStressController docstring, not repeated in attributes documentation bib reference of 1st workshop fix mistakes in conferences.bib +13 journal papers using yade +14 conference papers small update in the publication page fix and sort some bib references + change the title of the conference section +1 journal paper +1 conference paper +1 journal paper and fix alphabetic ordering of a few items FlowEngine safely impose flux at every iteration without remeshing + documentation implement blockHook for PeriodicFlowEngine as well Add .mailmap file defining git alias for multiple adress emails sphinx '..only::' directive removing some parts that break in latex integrate Ning's FEMxDEM doc in yade's doc add references in relation with FEMxDEM + couple fixes in *.bib remove FEMxDEM readme, replace by FEMxDEM.rst for inclusion in doc remove '..only:' from sphinx files - not yet supported on older sphinx then breaking the html build | update bib's Update introduction.rst Chao Yuan (7): move computePoreThroatRadius() to 2PFlow -move initialization() to 2PF -fix inconsistency in invasionSingleCell and getMaxImbibitionPC; clean code; remove savePhaseVTK in Unsat -remove cleanInterfaceWithinPore() in Unsat. fix inconsistency of side boundary cell pressure of closeBC drainage. Add some comments on FlowEngine(by bruno). Fix error in computing cell->info.solidLine Christian Jakob (10): fix force and torque vtk output for boxes temporary fix for pfv vtk output when vertex ids were not zero-based fix fusion detection for hertz model in capillary law reduce error message spam for capillary law remove unused testing function in capillary law fix previous commit for case (fusionDetection && hertz model) in capillary law (re-initiate bodiesMenisciiList at first real contact) and add some comments improve/fix documentation about clumps insert link to user manual in documentation of NewtonIntegrator update DEM background doc for clumps some code cleaning in clump methods Francois Kneib (1): Add the Yubuntu (live-usb with Xubuntu and Yade) alternative for installation. Jan Stránský (10): PolyhedraMat and PolyhedraPhys are now inherited from FrictMat and FrictPhys, modified related examples Added Ig2_Sphere_Polyhedra_ScGeom Added examples for Ig2_Sphere_Polyhedra_ScGeom, added ymport.ele function Added documentation of Ig2_Sphere_Polyhedra_ScGeom Allowed Polyhedra-Wall interaction if Wall.sense==0 fixed Cpm for Sphere-Box interactions added export.textPolyhedra function added Elias2014 article to yade-articles.bib add attrs parameter to export.textPolyhedra modified Clump::updateProprties to handel non-spherical bodies, added associated example box inertia computation correction Jerome Duriez (19): Sign convention change for fCap, to be consistent with global framework. Plus other minor changes. As discussed in http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg10868.html and http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg10877.html Doc hyperlinks, and erase of commented lines Many changes towards a more consistent sign convention throughout the code for stresses and strains. Should fix e.g. https://bugs.launchpad.net/yade/+bug/1381282. The goal is to know directly the meaning of a strain or stress value each time one is encountered. Relying on the classical Continuum Mechanics convention (editorial choice...). A global announcement is planned in a couple of days, in case some errors appear in the meantime. Other changes regarding sign convention. Add of deprecation warnings (existing in the code and at execution) in the doc. Fix of script-session2.py previously broken See https://bugs.launchpad.net/yade/+bug/1394942 answer # 3 Minor doc fixes Anecdotic doc change, see http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg10972.html Add of O.thisScene() function to know in which scene we are Add of sphSph parameter in plotDirections() to take into account only sph-sph interactions in polar histograms. Seems it does not modify really the plots, but it is easier to figure out with the parameter TSC engine: internal compaction now may consider isotropic tensile cases. See http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg11047.html Removal of parallel loops in capillary Law2: needs maybe more verification, and improvements for fusion detection Typo in the doc (missing space) Correction of minor inconsistency between comment and command Extra parenthesis removed in doc Doc of capillary law2, concerning fusionDetection, precised (see https://lists.launchpad.net/yade-dev/msg11792.html) Doc typos Parallelization of one loop of Law2_ScGeom_CapillaryPhys_Capillarity (see http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg11238.html) and some comments Typo in ScGeom, precision about twist doc (axis) in ScGeom6D Minor fix of previous commit (hyperlink) Klaus Thoeni (2): update references update some links and typos Luc Scholtes (3): changes for DFNFlow + corrections in JCFpm associated with the use of the never erase flag minor changes in DFN Flow add references Luc Sibille (5): Add 2 article references in yade-articles.bib correct a proceeding reference correct reference key in 1 proceeding fix missing comas after key references add fragile parameter to CohFrictMat and redefine unpMax CohFrictPhys Ning GUO (2): Ning Guo's FEMxDEM package added to trunk Example REV generation for FEMxDEM Raphael Maurin (6): add some references in yade-conference.bib Switch a private argument to public in HydroforceEngine. HydroForceEngine: minor fix + add an averaging function Minor fix : modify some default value of the parameters, remove unecessary parameters. Add a 1D averaging function which evaluate the average depth profiles of the solid volume fraction, the solid velocity, and the drag force. The averaging is weighted by the volume occupied by the particles in the layer considered. Add new function to compute stress tensor depth profile. Compute and return the stress tensor for each cell of height dz, between two limit points given by the user. The stress tensor computed include contributions from both particles inertia and Love-Weber stress tensor. This last take into account only the part of the branch vector contained in the cell. Minor fix in getStressProfile. The order of the argument in _utils.cpp was not the right one. HydroForceEngine: small modifications in the averaging function. Perform the averaging also on the y and z component of the particle velocity, instead of only x before. T Sweijen (7): update for dynamic two-phase flow small correction add initSolver() delta t for dynamic two-phase flow add function to get the pore body radius add one get functions for pore volume and rename that of inscribed sphere add one get functions for pore volume and rename that of inscribed sphere ================================================== yade-1.12.0 Mon, 20 Oct 2014 21:22:00 +0200 Anton Gladky (27): Remove RELEASE file. Use toleranceWarning and toleranceCritical for DEM-PFV check. Fix crash after clumps removing. Closes LP:1354433 Add checkClumpHopper autotest. Fix crash after removal of the whole clump. Fix calculation of massR in ViscoelasticPM Fix cs calculation in ViscoelasticPM Fix ViscElPM one more time. Create an array of clump`s memberIds to remove. Return fictional value from deprecated functions. Respect returnin value in computeForceTorqueViscEl Update Schwager2007 URL Add one more paper Merge pull request #44 from fifthguy/master Add firstIterRun parameter to PyRunner. Use system call "sphinx-build" instead of python module. Fix compilation error in PeriodicFlow.hpp Set python versions explicitly. Move function declarations of _utils.cpp into .hpp Fix runtime error in debug mode and without openmp. Drop including "yade/" folder in cpp and hpp files. Fix docs-generation. SPH-code refactoring. Use only vtkCommonCore vtkIOImage vtkIOXML components for VTK. Use Python 2.7 only Reintroduce viscosity in SPH-modell. Add RELEASE file. Bruno Chareyre (33): -include UnsaturatedEngine to start Chao's work fix a few mistakes and make a real (not empty) test function - replace hand-defined positions by scene's positions Merge branch 'master' of https://github.com/yade/trunk into chaoUnsat remove pack.particleSD and variants, unmaintained and deprecated by makeCloud (functions kept temporarily but returning error) fix https://bugs.launchpad.net/yade/+bug/1362090 fix https://bugs.launchpad.net/yade/+bug/1308074 fix https://bugs.launchpad.net/yade/+bug/1368591 + remove a useless test remove a temporary fix for https://bugs.launchpad.net/yade/+bug/923929, after better fix in https://github.com/yade/trunk/commit/4ea76ad6e47ac5074a389ad61712a0840e8560a5, thanks Anton parallel removal of old interactions replace LOG_ERROR by LOG_WARN for notifying deprecation of GravityEngine improve falling back to 1-thread in parrallel collider (fix https://bugs.launchpad.net/yade/+bug/1368591) fix missing brackets resulting in wrong permeability in periodic PFV point to Bourrier2013 for a partial explanation of the CohesiveFrictional contact law fix doc regarding requestErase() - https://bugs.launchpad.net/yade/+bug/1370736, thanks Jan selective blocking of cells of the mesh in FlowEngines (preliminary steps) remove empty file PFV: don't skip perm calculation for blocked cells, yet fix filename remove cpp with wrong filename reset id of erased bodies; enabling this: b=Body(); O.bodies.erase(O.bodies.append(b)); O.bodies.append(b) turn DeprecationWarning (not displayed) into UserWarning (displayed) since the error messages where cryptic no indexing of blocked cells in PFV decrease verbosity of blocking PFV cells DFNFlow unblock cells as fractures reach them + additional attributes in JCFPM split resetNetwork and resetLinearSystem + add more getter/setter split TwoPhaseFlowEngine in hpp/cpp for inclusion in child engines #ifdef guard for openmp function don't overwrite imposed fluid pressure when initializing the values (more flexible) + a function returning barycenter + improved "locate" for interpolation increased flexibility of imposing fluid pressure in FlowEngine's specialized getter/setter's for TwoPhaseFlowEngine + no re-indexing of cells in UnsatEngine better #def/#ifdef logic for TwoPhaseFlowEngine rename cellCenter->cellBarycenter (missing in prev. commit) Chao Yuan (86): - my first work on drainage simulation Commit the first working code for drainage - make the FAR constant more flexible (a parameter in addBoundaries) -add poreRadius -a test commit to escape big mess... Merge github.com:yade/trunk into chaoUnsat -add saveLatticeNode functions for generating axial-normal slice with "0" and "1" -add isWaterReservoir, isAirReservoir. -add another version for drainage. -delete unnecessary recursion for invadeSingleCell2() Merge github.com:yade/trunk into chaoUnsat Merge github.com:yade/trunk into chaoUnsat -add UnsatCellInfo, UnsatVertexInfo clean code -add temp function for pore connection Merge github.com:yade/trunk into chaoUnsat -update boundary attributes -a backup for laptop -add UnsatVertexInfo(void) for future use -test commit -test commit Merge remote-tracking branch 'origin/chaoUnsat' into chaoUnsat Merge github.com:yade/trunk into chaoUnsat -clean code add capillaryCellVolume in cellinfo, optimize getSaturation() -replace cell->info().p with isAir/WaterReservoir -add solidLine in cell info. partly code for force. clean code, fix mistake on Facet_Force. a test version of computing fluid force. fix solidLine[i][j] when facetNFictious case(1). -fix noCache. -fix solidLine[i][j] when facetNFictious case(2). -clean code. fix reservoir attr. change boundcells.isWaterReservoir=true when finish drainage. clean code. add temp test func. add cell->info().trapCapP; fix pressure calculation for trapped phase. clean code. Merge github.com:yade/trunk into chaoUnsat clean code.add action() add getSaturation2() for mode 2. Merge github.com:yade/trunk into chaoUnsat borrow saveVTK from FlowEngine normalize two invade modes. make computeForce optional;a bakcup a temporary save, change waterReservoir=bound[2], add invadeBounday option -make invade from boundary optional.(default false) -fix Line_Solid_Pore() in Network. Merge github.com:yade/trunk into chaoUnsat -big change, inherit from FlowEngine. remove old files clean code fix force calculation. add compute specific interficial area, lots of bugs... fix computeCellInterfacialArea with fictious vertex -test. no big change. Merge github.com:yade/trunk into chaoUnsat Merge github.com:yade/trunk into chaoUnsat Merge github.com:yade/trunk into chaoUnsat -fix ‘python’ declared bug -clean some info in debug -fix core dump in computerForcePoreForceWithCache, currentTes shoule be solver->T[solver->currentTes],NOT solver->T[currentTes] Merge github.com:yade/trunk into chaoUnsat Merge github.com:yade/trunk into chaoUnsat -update with PFV -use bndCondValue to mark reservoir. -fix reservoirs determination; fix invade(), Pw can be negative (mode1) -change invade rule, use bndCondValue to determine invasion. reservoirInfo depends on bndCondValue; merge isInvadeBoundary.(mode1) -change invade rule for mode2. merge some functions -fix getWindowsSaturations. -add pore radius checking funcs(tmp) -rename variables for computePoreRadius(); clean code. -clean code Merge github.com:yade/trunk into chaoUnsat Merge github.com:yade/trunk into chaoUnsat -add debugOut to test isInvadeBoundary=True isPhaseTrapped=True -insert debugOut. (core dump fixed by ulimit -s 16000) Merge github.com:yade/trunk into chaoUnsat This is TwoPhaseFlowEngine (alpha version) yeah! Merge github.com:yade/trunk into chaoUnsat -merge TwoPhaseFlowEngine, add more cell infos. Merge branch 'master' of github.com:yade/trunk -add savePhaseVtk. rename function. -remove check cell.index Merge branch 'master' of github.com:yade/trunk comment #define TWOPHASEFLOW Christian Jakob (6): insert updatePorosity option in TriaxialStressController fix long line in github doc small fix of a warning in NewtonIntegrator minor fix in doc introduction.rst include fluid stiffness for TSC for undrained flow condition fix fluidStiffness for TSC when FlowEngine is deactivated Dominik Boemer (1): Add check-script for ViscoElasticPM. Francois (1): Correct contact tracking bugs for grids. They essencially came from the new logic of laws that have to return booleans. Jan Stransky (7): Added force and torque export to VTKRecorder (question #252413) fixed typo in utils.polyhedron function enable periodic simulations with Polhedron and Tetra rename PolyhedraVolumetricLaw -> Law2_PolyhedraGeom_PolyhedraPhys_Veolumetric deleted vtk output of force for boxes (bug #1376734) added Polyhedra::GetSurfaces function Added volumePower attribute to Law2_PolyhedraGeom_PolyhedraPhys_Volumetric, Polyhedra code small cleanup Janek Kozicki (2): Fix bug in 'inspect' that made editing values annoying. Merge doc/sphinx/references.bib into doc/references.bib Jerome Duriez (3): Re-write of "Yade on GitHub" wiki page in sphinx doc. Anecdotic commit to keep a track (in code comment) of a useful link for JCFpm paraview analysis Removal of very last wiki-link github-related in rst files Raphael Maurin (1): New force engine to couple Yade with a 1D RANS code. Add a new force engine applying the main hydrodynamical forces in function of a 1D average fluid velocity vector which depends only on the depth. The engine is calculating at each time step the drag, lift and buoyant forces for each particle. Complete the references for the documentation associated to the engine. T Sweijen (1): Merge two-phase flow engine Thinkpad (1): -a test commit from laptop cyuan (7): a small change for check reservoir boundingCells. -add temp function for generating sample windows, calculating responding saturation... -add savePhaseVtk Merge github.com:yade/trunk into chaoUnsat Merge github.com:yade/trunk into chaoUnsat -replace abs, max, min by std::abs, std::max, std::min Merge github.com:yade/trunk into chaoUnsat cyuanLaptop (1): -change debugOut fifthguy (1): Fixed a bug that appeared when running the uniaxial-post.py script from examples. Edited py/post2d.py to capture exception while importing Vector3 from minieigen. jduriez (12): Correction of an error using psd() with monodisperse packings (false = False in python). Add of an explanatory message Few changes in capillary doc: assumption of null wetting angle, hyperlinks, and some comments in source code One forgotten change during previous commit about TriaxialStressController <-> 3DTriaxialEngine ? https://github.com/yade/trunk/commit/77bc6d75b780bcbad5bdadc5bb3645badb009cd9 Adding mention of different save files kinds. Tried to comment differences, please correct if I was wrong Typos and precisions in capillary doc porosity() function infers now a volume value for non-periodic cases, rather than throwing an error. Positiv volume values eventually passed as argument override this inferred value porosity doc changed according to previous commit getStress() considers now an adequate volume value for non-periodic case (values passed as parameters may still also be taken into account) Re-introducing change from https://github.com/yade/trunk/commit/ab91b3cf8654f6d563dede10184e784a8ce84219, reverted since, without reason Improvement of https://github.com/yade/trunk/commit/05599b23808991dbfef6b85400c7ddd32be594e0 regarding volume computation in getStress for non periodic cases Typo in CapillaryPhys doc Parallelization of interaction loops in Law2_..._Capillarity (which is in fact not a LawFunctor handled by InteractionLoop). Moreover adopting the FOREACH iterator for the non-parallel flavour. ================================================== yade-1.11.0 Mon, 4 Aug 2014 18:54:00 +0200 Alexander Eulitz (9): small corrections of messed up indentations another indentation fixed rearranged compilation and installing procedure so that hints for multicore compilation are placed directly after the make command typo fix fixed --cores implementation and improved arg-parse argument documentation. improved doc of betan and betas replacing damping coefficient betan and betas by damping ratio betan and betas rearranged indentation of examplarily folder structure for yade complation Added hint about make errors during compilation when user does not posses root priviledges. Anton Gladky (58): Delete RELEASE file. Add YADE_PTR_DYN_CAST to define dynamic_cast. Remove all "using namespace std;" Fix compilation with disabled openmp. Roll back last 2 commits. Remove most of "using namespace std;" Replace math.h by cmath in includes. Remove some more "using namespace std;" Remove "using namespace std;" everywhere. Tests are failing. Replace abs by std::abs. Clean up in header inclusions. First stage of C++11 implementing. Add missing header. Remove isIndexable and isFactorable. Use boost::shared_ptr for C++11 as well. Drop Qt3 workaround Enable LBM by default. Enable C++11 by default. Do not consider Eigen3 like a feature. Capitalize feature list. Use double precision for VTKREcorder. Do not use -DTYPEOF, use explicit decltype Move definitions of YADE_PTR_CAST YADE_CAST YADE_PTR_DYN_CAST into Math.hpp Remove -std=c++0x definition for pygts. Join [CohFrict]Mat, Phys and Ip2_. Move Ip2_*_MindlinCapillaryPhys into HertzMindlin Move Ip2_*_CapillaryPhys. into CapillaryPhys. Move Ip2_FrictMat_* into FrictPhys Move all NormalInelastic files into NormalInelasticPM Join all InelastCohFrict files into InelastCohFrictPM. Join all KinemC*Engine.* into KinemC__Engine.* Set C++11 only for CXX-files, not C Update LICENSE file, does not need exception any more Cut off some header inclusions. Disable reusing of removed body ids. Fix compilation. Replace nullptr by reset(). Join all Bo1_* into Bo1_Aabb Remove some more .cpp-files. Move many Gl1_* into Gl1_Primitives. Remove some more small cpp-files. Remove some warnings. Remove LBMbody.cpp and LBMlink.cpp. Remove Indexable.cpp Exclude Indexable.cpp from CMakeLists.txt Redirect --test output into stdout Modify slightly description of save-loadVars Change stderr to stdout in greeting message. Update Vaclav`s occupation in sphinx-doc Cut long line in HertzMindlin.hpp Move some YADE_PLUGINS into common.cpp Fix most of compilation warnings. Return false in BubbleMat, if no penetration. Fix and enable DEM-PFV-check.py. Replace L3eom by SCgeom in stl and gts examples. Use global interpreter lock (GIL) in OpenGLRenderer. Update mtTkinter version. Remove NEWS file (outdated). Bruno Chareyre (9): Revert "Revert "Set minimal required Eigen3 version 3.2.1"" / Thanks Anton for uploading the backport replace abs by std::abs (complement of https://github.com/yade/trunk/commit/1997c194c0aa759cae101a3dd0a559fcf049b29f) +2 conf papers Law2 return bool - fix https://bugs.launchpad.net/yade/+bug/1324190 add missing 'return bool' in some Law2's Revert "implement more accurate porosity calculation..." (temporary required in order to revert 915fd94606af6 without conflict)" Revert "fix typos and indents; cut long lines.. - please no formatting commits (+there is nothing wrong in long lines). Please reapply the documentation part." make growParticles fatser for clumps use Shop::growParticles in TriaxialStressController (fix https://bugs.launchpad.net/yade/+bug/1351275) Christian Jakob (5): fix typos and indents; cut long lines in TriaxialStressController; bit more documentation of stressMask implement more accurate porosity calculation for clumps in TriaxialStressController; inserted updateClumpProperties command in Triax tutorial Merge branch 'master' of github.com:yade/trunk make PFV compatible with clumps (clumps are treated as spheres with equivalent radius - valid for nearly spherical clumps) reapply 9e512fd50083 Francois (1): Simplify the contact detection in Ig2_GridConnection_GridConnection_GridCoGridCoGeom. Jan Stransky (3): fixed bug in export.VTKExporter.exportInteractions (question #250922) modification of utils.UnstructuredMesh, added utils.polyhedron fixed bug in MASK_ARBITRARY feature Jerome Duriez (7): Correction of some broken sphinx links: yade._utils => yade.utils Removal of a double : Improvement of previous commit: there was no extra : but a missing blank line Export principal stresses and directions in VTKRecorder Some shortening in VTKRecorder, mainly according to http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg10370.html Revert sign convention in bstresses in VTKRecorder (tension=positiv now) Slight modif in JCFpm doc. To better describe the logic of the code. Kubeu (1): replaced "root" from last commit Nolan Dyck (2): Update BubbleMat.hpp and BubbleMat.cpp Update bubble example script. ================================================== yade-1.10.0 Wed, 25 Jun 2014 19:35:00 +0200 Anton Gladky (47): Delete Release file. Add orientation parameter to ymport.textClumps Resize ForceContainer after each body insert Added assert to get*Unsynced function Better fix for ForceContainer-size-change Remove extra/floating_point_utilities_v3 Remove some 'using namespace boost' Remove some more `using namespace boost`. Remove all remaining `using namespace boost` Fix compilation in DEBIG-mode. Link against libboost_date. Fix LP:1322274 Set the mask to a clump the same as the first member of it. Revert removal of embedded floating_point_utilities_v3. Add particleconserve parameter to LiqControl. Replace features by CONFIGURED_FEATS. Prevent first empty item in features. Add checkLiquidMigration autotest. Better check for DEM-PFV-check.py Add missing header. Add --as-needed flag to yade-lib. Comment some lines, where defined unused variables. Minor fix in documentation of viscoelastic. At every sync check, whether ForceContainer is large enough. Disable parallel code in conditionalyEraseNonReal Skip interactions, where one of body isClump Fix doc-compilation for IPython >=2 Enable vectorization in eigen3-lib Do not use Eigen3 in parallel mode. Recommend minimal Eigen3 version 3.2.1. Set minimal required Eigen3 version 3.2.1 Add NOVECTORIZE option Prevent adding liqVol-parameters into VTK-files Prevent crash in liqVolIterBody Disable vectorization by default. Replace Quaternion.Identity by Quaternion((1,0,0),0) In state pos_set and ori_set use passing by value. Add addLiqInter function to set liquid "properly" Liquid migration model, code refactoring. Add script to changes commit`s author`s names. Fix typo in installation. PFV code refactoring. Fix typo in previous commit. Fix templates names. Clean in ymport.stl Remove service-messages in CMakeLists Add missed #pragma once Add RELEASE file. Bruno Chareyre (11): CohFritMat documentation document Ip2_CohFrictMat more make the parallel collider warning more explicit regarding turning collider.ompThreads=1 CohesiveFrictional contacts: make them elastic only if strength<0 (previous condition was <=0) + Lingran's elastic energy of contact moments fix fluidForce=0 after remeshing + allow constant positions for DFNFlowEngine make FlowEngine::setPositionsBuffer virtual missing declaration of function fix default attribute in DFNFlow CohesiveFrictionalContactLaw does not warn about incremental formulation of rolling/twisting moments when the moments are elastic fix bug in FlowEngine::updateBCs() (reported by Luc Scholtes, thanks) Revert "Set minimal required Eigen3 version 3.2.1" Christian Jakob (2): remove relicts of Dem3Dof and code cleaning increase maximum length of char filename in saveVtk method for FlowEngine Francois (1): Update the documentation for Law2_ScGridCoGeom_NormalInelasticityPhys. At this moment it's not done, but it will be fixed and come with a reference article during 2014. Jan Stransky (4): Body::groupMask may be optionally boost::python::long_, subsequently modified code where necessary fixed bug in yade.export.exportFacetsAsMesh (thanks Jan Havelka for reporting) added mask_t type for bitmask variables to be int or optionally std::bitset of fixed (yet arbitrary) size. Added bitset to/from python long conversion. Added MASK_ARBITRARY cmake option. Subsequent changes in other files corrected git warning in CMakeLists.txt Jerome Duriez (6): Correction of mispelling in example script name of one Law2 Minor changes in JCFpm Important change in Kinem.. engines. Both changes in position and velocities of boundary bodies were still existing, while now changes in position should be handled by NewtonIntegrator JCFpm : doc of JCFpmPhys.FnMax precised (minor change). And formulation of kn for onJoint interactions according to JCFpmPhys.crossSection (rather than mean of surfaces) to be consistent with the whole formulation ("major" change : this may impact the results of previous scripts depending on psd and how much the mechanical behaviour of joint is important) Doc of VTKRecorder.skipFacetIntr precised so that it better corresponds to code Extra s in previous commit removed.. Klaus Thoeni (4): remove old code improve output and remove first iteration in calculation velocity estimation add definition for functor order set number of iterations to be run correctly (thanks Alex) ================================================== yade-1.09.0 Sun, 18 May 2014 17:32:07 +0200 Alexander Eulitz (1): corrected a little bug in description of yadedaily-installation and added example and folder structure for compilation Anton Gladky (97): Remove RELEASE-file. Fix setting of wall's color. +1 reference. Replace some bazaar-links by github. Update installation instructions. Update INSTALL file. Fix version definition for IPython>1.0.0 Fix warning for IPython > 1.0.0 Add radiusTopInner, radiusBottomInner to facetCone and facetCylinder. Increase number of steps in checkWeight.py Prevent returning a reference to local temp object. Prevent binding a reference member to a temp. value. Remove notice on the main page about daily packages on Launchpad. Some more changes on the main page. Add Lambert formulation into capillary models. Use enum instead of string to keep capyllar type. Update config of mini-dinstall. Do not ignore k* and c* parameters if mass==0 Add billiard example script. Introduce YADE_ODEINT feature Implement binary-arch only builds for yadedaily. Fix split delimiter Fix library name for new openblas. Output some additional messages, when DEBUG mode is enabled. Fix compilation with libqglviewer>=2.5.1 Fix compilation with libqglviewer>=2.5.1 Add informational message, if VTK6 is found. Disable some debug-messages, because they break compilation. Check, whether manipulatedFrame exist, if not - create it. Set mouse parameters, only if frame is created. Better fix for QGLviewer next version. Fix compilation. Move all force and torque calculation into separate function Move capillary functions out of ViscEl-classes. Implement Soulie capillary model. Add an example to test different capillary models. Deprecate getViscoelasticFromSpheresInteraction. Update examples and test-scripts due to deprecating of getViscoelasticFromSpheresInteraction. Update Warning about last changes. Use MatchMaker to set tc, et and en in ViscEl model Update URL in getViscoelastic Fix compilation in ViscElCap. Minor description update. Replace isnan by isfinite to let the numbers be 0. Remove last capillar-parameters from ViscEl. Remove massMultiply paramter Fix compilation. Implement experimental SPH-model Add gradients and laplacian of the kernel functions. Implement some more kernel functions. Remove duplicated code. Normalize parameters of kernel functions. Produce meaningful error message. Add Cs parameters to particles, visualize them in VTK. Export in VTK some more SPH-parameters. Get a coordination number from body. Use bool return type for force calculation. Add watercolumn example for SPH. Add example script to test different kernel functions. Add README to examples SPH. Fix conflict. Fix eigen3 inclusions. Add one more example for sph. Split all capillary function into smaller one. Add YADE_SPH macroses to fix FTBFS, when SPH disabled Minor fix (replace #ifdef by #endif) Add an opportunity to change liquid volume during simulation. Disable temporarly Cs calculation in SPH. Fix interaction removal in VeiscoElPM Store an information about active liquid contacts. Add -= operator to OpenMPAccumulator. Fix compilation with clang, when openmp is switched off. Add OpenMPVector for thread-safe vector work. Minor fix in installation section of documentation. Export current value from PIDController. Add a note in installation section of docs. Do not link libloki and boost_date_time. Fix scrolling direction for libQGLviewer > 2.5.0 One more minor fix in zooming. Implement Liquid Migration model (experimental). Replace LIQCONTROL by LIQMIGRATION. Fix compilation with clang. Set capillary parameters to 0. instead of -1. Fix Id export in ymport.textClumps Remove YADE_DEPREC_DOF_LIST prepocessor. Add blockedMovement parameter to state of body Add conveyor example. Minor fix in documentation/installation. Add mask parameter to NewtonIntegrator Replace png-pictures by xpm. Fix the beginning camera position in GUI. Remove integrateInertia=False from packs.py. Add discretization parameter to appendClumped. Do not use getTorqueUnsynced and forces.getForceUnsynced in clumps Make addForceTorqueFromMembers more readable. Revert last change in Newtonintegrator. One more revert in NewtonIntegrator. Bruno Chareyre (60): avoid crash when Vh==NULL in FlowEngine. The sphere is ignored in the flow problem, otherwise FlowEngine runs as usual. Merge branch 'master' of github.com:yade/trunk remove redundant "from yade import *" in example scripts, as it mess-up scopes small change in PFV checkTest fix a bug in ISCollider that would create interactions with unbounded bodies remove deprecated code linked to queuing requestErase'd interactions in an older version of the collider Merge pull request #39 from lsibille/master Merge pull request #38 from Kubeu/patch-4 Merge pull request #37 from Kubeu/patch-3 Merge pull request #36 from Kubeu/patch-2 Better behavior of QGLViewer for shift+select and moving bodies (fixes LP bug 806469) let libparmetis be used as an alternative of libmetis Add hideBody/showBody to selectively display bodies in the 3D view Merge pull request #40 from burak-er/master Parallel InsertionSortCollider fix compilation issues for ENABLE_OPENMP=OFF some renaming and code cleaning in PFV code some renaming and code cleaning in PFV code (part2) PFV: First step in refactoring templates dummy engine for showing how to derive from FlowEngine + a preliminary version of DFNFlow make FlowEngine a template yade class Periodic version of flow engine in separate source files PFV: simplify (c++ wise) value assignement to Info types. More refactoring. Final step of code cleaning. fix a bug in PFV code (fictious vetices not defined correctly) minor changes in FlowEngine remove a useless data member fix compile error due to dirty hack (cpp's included by another cpp) Added documentation for changing the velocity gradient of periodic cell TriaxialStressController: reference sample sizes can be modified by users (was previously read-only) ignore *~ files in git status update biblio references Hack YADE_CLASS macro to make it work with c++ templates (introduces a macro for pyClass name different from c++ class name) new YADE_CLASS_PYCLASS_... macro, missing in previous commit update bibliographic reference in a script introduce CellInfo::getInfo() for more generic interpolation between triangulations better detection of changes in Cell::velGrad fix the example script periodic-simple-shear.py - introduce SoluteFlowEngine (from Thomas Sweijen) - move Flow classes to a separate folder fix include paths after moving files to pkg/pfv fix include path pkg/pfv Bugfixes in PeriodicFlowEngine, as discussed with Donia remove useless FlowBoundingSphere.cpp fix https://bugs.launchpad.net/yade/+bug/1301443 undef flag, so SoluteFlow doesn't break compilation on buildbot. update about openblas+openmp on 12.04 initialize CellInfo members (avoids hardly detectable bugs) + remove artifact facets from loop when cell1==cell2 remove an inacurate reference, introduce another one fix bad link to capillary files clean of commented blocks Merge pull request #43 from bchareyre/pc fix gravity checkScript (es -> 'et') enable run/pause from QGLViewer (retun key) + fix compile warning remove empty file add FlowEngine::doInterpolate to force interpolation during mesh swap Add user defined boundary condition to FlowEngine add authors in files headers -fix bibliographic link add missing #ifdef, breaking compilation without LINSOLV + better volume computation fix compile error in 298f0b6 switch to 1-thread colliding when problem detected in parallel run (fix https://bugs.launchpad.net/yade/+bug/1314736) Burak Er (1): added an adaptive Runge Kutta integrator scheme. Also, added an example using this integrator. Christian Jakob (15): allow user to set an output folder for PFV-based saveVtk() method Merge branch 'master' of github.com:yade/trunk fix compilation bug in InsertionSortCollider.hpp fix a bug in inertia tensor calculation for clumps if integrateInertia=True extend/fix replaceByClumps() method for multiple overlapping clump templates absorb bool integrateInertia from Clump::updateProperties by int discretization Merge branch 'master' of github.com:yade/trunk Parallelize replaceByClumps(): drastically reduce generation time of clump replacement if discretization>0 fix bugs in Clump::updateProperties, fixes https://bugs.launchpad.net/yade/+bug/1273172 introduce updateClumpProperties() method in yadeWrapper - can be used e.g. when clumps are imported in yade update of O.bodies.erase(): it can erase clump members too when erasing a clump Merge branch 'master' of github.com:yade/trunk remove typenames from Polyhedra.cpp (fixes compiler error) let ymport.textClumps() return all ids from members and clumps fix some indents Francois (2): Undo modifications about ViscElMat into Ip2_FrictMat_FrictMat_FrictPhys. The young modulus and poisson ratio have to be set for both materials to perform a contact between a frictMat body and a viscElMat body. Add a comment for that. Fix 2 bugs linked to the Grids : - in utils.py : remove a factor 2 in the calculation of the bending stiffness kr. - in Grid.cpp : fix a bug that occured in the Sphere-GridConnection contact. The contact was not detected in a very specific case : if the sphere was next to a node and the node goes from a convex (angle>180°) form to a concav (angle<180°) form. Jan Stransky (13): added vtk export of polyhedral particles improvement of previous commit (vtk polyhedra export) added example of paraview sphere "solid sections" improvement of export.textExt function to support arbitrary quantity export added O.stopAtTime (question246284) chenged return type of O.stopAtTime from previous commit fixed some errors and warnings for documentation build one more little info inside code export.VTKExporter: improved comments, fixed bug (thanks Jan Havelka for reporting), updated corresponding example script code cleanup in ConcretePM, fixed one more bug in export.VTKExporter added exportContactPoints function to exporter.VTKExporter, updated example script fixed export.VTKExporter.exportContactPoints for nonexisting interactions Polyhedra implementation improvement (Contributed by Jan Elias) modification of utils.calm function (bug 1318513) Jerome Duriez (15): Change in the doc of ymport.text/textExt to better reflect the behaviour A doc sentence for pericell recorder in VTKRecorder Typo in doc of CohFric Law2 : the shear adhesion is a_s, not a_n Typos and link syntax in doc of CohFrictPhys Typo correction in porosity() doc : porosity instead of poro sity (in 2 words) Use of correct version of requestErase() in JCFpm (https://bugs.launchpad.net/yade/+bug/1273775) Small changes in JCFpm IP logic : it is now possible to have new contacts that are always cohesive, and "poisson"=0 is possible (=> ks = 0 rather than infinity...) Small improvement in JCFPM doc about the cracks file, and typo in user.rst Mistake in hyperlink previous commit Copy paste mistake in State and typo UniaxialStrainer doc Proposal of correction of UniaxialStrainer, in relation with https://bugs.launchpad.net/yade/+bug/1300167 Add of an external reference, about the "derivation" of bodyStressTensor Correction of copy-paste mistake in doc of Bound Hyperlink about sortAxis in InsertionSortCollider doc Minor changes (not affecting results) in these scripts towards an easier understanding Klaus Thoeni (2): Correct shear stiffness averaging for Ip2_FrictMat_FrictMat_ViscoFrictPhys new simple contact law with normal viscose damping which allows to specify kn and ks/kn in Ip2 Kubeu (3): Added Antons hint to first install external depencies of Yade before following installation instructions small typo fix typofix Luc Sibille (10): add test on alphaKtw to allow nil value of twisting stiffness engine to compute a fluid flow with the lattice Boltzmann method LBM Definition of the basic elements used by the LBM engine definition of the compilation option ENABLE_LBMFLOW to make the compilation of the LBM engine optional, this option is disable by default remove all LBM file Merge remote-tracking branch 'upstream/master' definition of the LBM engine inside a lbm directory, with license GPLv2 definition of the compilation option ENABLE_LBMFLOW to make the compilation of the LBM engine optional, this option is disable by default A buoyancy example for the DEM-LBM coupling Merge branch 'master' of github.com:yade/trunk ================================================== yade-1.07.0 Fri, 10 Jan 2014 21:23:33 +0100 Anton Gladky (37): Remove RELEASE file. Add -ftrack-macro-expansion=0, if gcc>=4.8 Provide VTK6-support. Use ADD_DEFINITIONS instead of adding those directly in CXX_FLAGS. Remove information about yade-stable from Readme. Add BicyclePedalEngine as a new kinematic motion. Add -save-temps if GCC-4.8 is used. Split Grid into Grid and Grid_GUI. Add information about missing packages in documentation and external PPA. Closes: LP:1250928 Add notice about using libqglviewer-qt4-dev instead of libqglviewer-dev on older Ubuntu versions. Add script to create PPA-packages. (Not finished) Use othermirror for some ubuntu versions. Add stl-gts example. Add qt.View() to clumps-example. Add one more check-script to check the functionality of ViscoElastic PM. Consider massMultiply-parameter, calculating parameters in ViscoElasticPM. Add functions to save and load clumps. Set the higher pripority in sys.path to self-compiled modules. Closes LP:1254708 Fix volume calculation. Closes LP:1261415 Set the higher pripority in sys.path to self-compiled modules in yade-batch. Update scripts for PPA. Add configuration files, needed for PPA. Minor update of PPA scripts. Update information about yadedaily prebuilt packages. Add support for qglviewer>=2.5.0. Open GUI in packs/packs.py after 1 step to show all elements. Raise warning, if no spheres are produced by regular* commands. Update information about daily-packages. Set one more paramter -ftemplate-depth-512 for clang Prevent attraction forces in ViscPM due to viscosity Add some more steps to checkWeight-script. Minor formatting in references. Remove cout accidentally added in a prev. commit. Minor change of setFromTwoVectors in utils.py. Rename createtar.py to buildppa.py. Minor fix in docs. Add RELEASE-file. Bruno Chareyre (17): a function to increase the size of a single sphere (~>Thomas swelling) easier manipulation of state files in TesselationWrapper restore the python wrapping of utils.growParticles() as it was before fb02a74 (changed by mistake, sorry Christian) give unique identifiers to trangulation's cells FlowEngine::nCells retruns the number of finite cells; FlowEngine::getVertices returns the vertices of a cell defined by its id make cmake output more consistent when missing dependency for LinSolv Fix the behavior of FlowEngine.updateTriangulation=True FlowEngine: increment a counter correctly small changes in the installation section regarding suitesparse and related libs installation.rst: smallfix in indentation remove a not necessary sorting in FlowEngine, as it triggers a critical bug in the STL (http://gcc.gnu.org/bugzilla/show_bug.cgi?id=58800) correct target values of the DEM-PFV checktest Fix paths to online and packaged documentation (fix url error with GUI's hyperlinks) DEM Background chapter: a note on the semantic strain vs. displacement for contact kinematics Merge branch 'master' of github.com:yade/trunk fix undefined "key" in triax-tutorial/script-session1.py +1 published paper Christian Jakob (1): small fix in an example script tetra/oneTetra.py Francois (3): Fix missing REGISTER_CLASS_INDEX(...) into ViscElPhys. This macro is essential for a right law dispatch ! Corrected a minor mistake in code comments : k=2*r*E Allow the contact between (coh)frictMat and viscElMat as frictPhys. Almost everything was done by inheritance, just had to convert stiffnesses to modulus and modulus to stiffnesses to ensure material compatibility. Note that for the moment the timeStepper cannot handle this kind of simulations -> will be fixed soon. Jan Stransky (4): Modified error message if not yade.runtime.hasDisplay (bug #1241817) fixed SyntaxError from previous commit uncomment and modify utils.forcesOnCoordPlane function corrected mistake in examples/test/triax.py Jerome Duriez (15): - Introducing (uncommenting in fact) tens/shearBreakRel variables in JCFpmState : relative part of broken interactions per body (instead of absolute number). - Few changes in some doc of JCFpm variables. Quite important changes in JCFpm code Modifying JCFpm example scripts so that they still work after previous commit Re-put some commented lines, after discussion of this thread (https://lists.launchpad.net/yade-dev/msg10185.html), thanks Anton. The comments solution is (at the moment ?) finally still used to avoid putting a new variable in VTKRecorder.. A script example for JCFpm : two rock parts with one joint in the middle, like in laboratory experiments Some forgotten corrections in some example scripts, so that they still work after changes of today in JCFpm Some corrections in the JCFpm doc (hyperlinks...) (Hopefully) Fixing some rst links in DEM Background doc Some changes in the doc of getStress() function, to be consistent with the source code (https://answers.launchpad.net/yade/+question/239919) Merge branch 'master' of github.com:yade/trunk Idem as previous commit Restoring the 2d version of growParticle previously erased by mistake.. Some hyperlinks in JCFpm doc corrected Typos and hyperlinks corrected in Peri3dController doc Correction of a link in TesselationWrapper() doc Klaus Thoeni (1): add CGAL link and delete libgmp3 from install list Raphael Maurin (1): Change in the calculation of the normal and tangential stiffness and damping. The change affects only the behavior when one of the two parameters is zero, e.g. for two particles with different stiffness k1 and k2, the contact stiffness will always be k = k1*k2/(k1+k2). Before it gave the same except when k2 = 0 (respectively k1 = 0), where it gave k = k1 (resp. k=k2). This is done to ensure continuity in the behavior when one of the two parameter tend to zero. Add a function contactParameterCalculation in Ip2_ViscElMat_ViscElMat_ViscElPhys to avoid code duplication. ================================================== yade-1.05.0 Mon, Oct 28 19:49:48 2013 +0200 Anton Gladky (19): Add system-component of boost to be linked. Fix typo in equations in getViscoelasticFromSpheresInteraction (documentation). Thanks to Medack (TU Freiberg). Explicitly link BZip2-library Explicitly link ZLIB-library Update installation docs, add libbz2-dev zlib1g-dev. Fix LudingPM. Rename variables in LudingPM (Theta->Delta). Fix k2-calculation in LudingPM. Update script for LudingPM. Split gui/qt4/GLViewer.cpp. Remove pkg/dem/DomainLimiter.* Recover DomainLimiter (LawTester should be moved somewhere). Remove some warnings. Update numpy_boost.hpp from svn. Remove executes bit on py, cpp and h-files. Split Shop.cpp on Shop_01.cpp and Shop_02.cpp Fix compilation. Remove stable-PPA reference from documentation. Replace all libboost-*-dev by libboost-all-dev. Christian Jakob (19): complete description of clump methods in users manual fix a bug in inertia tensor approximation scheme fix some links in users manual and Scene doc fix description of default material in users manual fixing/updating refs and links in users manual - part 1 removed SpherePadder description from users manual fixing/updating refs and links in users manual - part 2 (finished) adapt buoyancy example with new O.forces.addF() method and make it look nicer update in Clump::updateProperties: included new bool integrateInertia and int discretization and adapt clump(), appendClumpend(), addToClump(), releaseFromClump(), replaceByClumps() and growParticles() create links to some example scripts in wrapper increase initialization speed of examples/packs/packs.py (fix https://bugs.launchpad.net/yade/+bug/1229783) try to fix (still broken) refs in users manual Merge branch 'master' of github.com:yade/trunk make getRoundness() more flexible: empty excludeList is no more needed as input argument; adapt replaceByClumps-example.py and associated part in users manual small fix in users manual fix a link in TesselationWrapper fix a link in TesselationWrapper (second try) fix buoyancy example for clumps removed typenames from Polyhedra.cpp, make gcc < version 4.7 happy Donia (4): Save the relative velocities of particles. Compute edgesSurfaces if viscousShear is true. Save the interactions only between spheres into a vector. get the shear and normal viscous stress in each interaction. Jan Stransky (10): marginal modifications Merge branch 'master' of github.com:yade/trunk Added periodic cell VTK export (to VTKRecorder and export.VTKExporter) Merge branch 'master' of github.com:yade/trunk added forgotten example file fixed bug in export.VTKExporter from one previous commits Merge branch 'master' of github.com:yade/trunk Polyhedra implementation + examples (Contributed by Jan Elias). adding examples with tetrehadron modeled by new Polyhedron class CombinedKinematicEngine will not call its 'dead' subengines (question #237437) Jerome Duriez (6): Correction of typo in comment Proposal of new (similar but more compact) examples using JCFpm classes. A choice can be made one day after some feedback ? Some changes in JCFpm documentation (add of external references, and removal of cross reference towards the CFpm model which does not exist anymore). In cpp, some commented lines to add (in the future ?) some post-pro features that could maybe break current saves of (existing ??) current users Commiting changes discussed briefly in https://lists.launchpad.net/yade-dev/msg09979.html. Mainly written by L. Scholtes, they allow to vizualize with paraview some features of JCFpm classes. It adds then 2 recorders, "jcfpm" and "cracks", that are separated mainly for historical reasons.. They are anyway now documented Add of pylab.ion() in plotNumInteractionsHistogram() and plotDirections() so that yade does not hang anymore after launch of these functions (even after closing the plot window, here). Still thanks to Vaclav ! (http://stackoverflow.com/questions/9753885/pylab-matplotlib-show-waits-until-window-closes) Anecdotic changes in an example script Klaus Thoeni (2): resolve problem with mask in GridConnection ignore local kdevelope specific files on git ================================================== yade-1.00.0 Sun, Sep 29 23:10:48 2013 +0200 Anton Gladky (64): Remove release file. Add documentation, how to render particle with ParaView`s PointSprite plugin. Fix spelling errors. Add Changelog. Add different capillar models into ViscoElasticPM. Add links to equations, consider not only monodisperse particles. Fix s parameter for Willet-formulation of capillar. Add one more critical-calculation to capillar model. Cleanings in viscoelastic capillar modell. Move capillar calculation into another function not to overload VPM. Modify Weigart`s model. Update equations for Weigart`s capillar model. Update capillar equations and names of schemas. Move references to a references.bib. Add comment on liquid bridges. Fix some warnings (clang). Fix compilation. Implement rotational resistance in ViscoElasticPM. Add massMultiply-parameter to ViscoElasticPM to have an opportunity to set kn, kt, cn and ct without multiplication on mass. Implement Rabinovich`s capillar model. Fix wrong calculation of the average rotational resistance. Split ViscoelasticPM on capillar and dry parts. Prevent devision by 0 in capillar Rabinovich model. Prepare for flowengine compilation. Merge libplugins, libsupport and libcore in libyade. Fix FindCholmod.cmake. Fix compilation of FlowBoundingSphere.ipp Replace Cholmod-Feature by LinSolv. Minor fix in CMakeList (FlowEnginge). Implement PID controller to have a servo-engine. Fix tests due to failing clumps-autotests. Use combinedengine for ServoPIDController. Fix hopefully clumps-autotests. Add LudingPM. Merge branch 'ndyck' Add an example for LudingPM. Use libyade again. Revert Bruno`s revert. Fix configuration issue with CHUNKSIZE>0. Drop RockPM. Remove ParticleSizeDistrbutionRPMRecorder. Remove CohesiveStateRPMRecorder. Show PFVflow and LinSolv in disabled features, if they are disabled. Include loki-library dirs and link against them. Fixes compilation on HPC TU Freiberg. Set LinSolv and PFVFLOW ON by default. Add recommended build-dependency for LinSolv and PFVFlow into documentation. Replace ifndef/define-constructions by "#pragma once" in lib/triangulation, where it is possible. Minor fix in capillary models in ViscoelasticPM. Add [Pournin2001] into the description of ViscoelasticPM. Minor fix in calculation s_crit in ViscoelasticPM. Add information about github-hosting into the main page. Add a notification to the screen, whether the current build is debugbuild. Remove explicit linking of libstdcxx. Use skipScripts variable to skip some scripts on check-tests. Skip temporarly DEM-PFV-check.py to let daily-builds packages be built. Remove kde-files from the trunk. Minor fix in installation section of documentation. Remove Fedora list package from documentation. The list is unsupported. Add Antypov2011 reference and some links in Hertz-Mindlin model. Fix some compilation warnings (GCC). Replace libqglviewer-qt4-dev on libqglviewer-dev in installation section. Fix errors in ForceContainer, detected by clang. Fix compilation error. Add export into LIGGGHTS-format. 1.00.0 Bruno Chareyre (68): +1 journal article Add the color of the periodic cell a registered attribute. - fix a bug that would let the capillary tables empty when postLoad was not triggered Add function getCapillaryStress(), equivalent of getStress() but for capillary forces -code cleaning fix a latex equation FlowEngine: exclude corner cases when listing constrictions sizes along the void path +1 article -fix url of an article +4 journal papers +1 journal article - add "LINSOLV" source code for DEM-PFV coupling with direct sparse solvers add strainRate attribute to TriaxialStressController + fix bug in example script Revert "Merge libplugins, libsupport and libcore in libyade." Cause: the new cmake system breaks buildbot and does not work for chunkSize>0 - add getSceneAsString() to pass scenes between instances without going through the hard drive fix CMakeList for chunkSize>=1 - enable load/save from/to python strings with O.sceneToString and O.stringToScene (for communication between parallel instances of yade) -fix the return type of stringToScene() clean the flow code (part 1) cleaning the flow code (smallfix of part 1) cleaning the flow code (part2) cleaning the flow code (part3 and last) -first example script for the fluid coupling with the DEM-PFV method - new conference and journal papers fixed reference +1 PhD thesis - more documentation of TesselationWrapper, with a section in user manual and pointer to published equations. git ignore changes to .gitignore undo previous change in gitignore, not the right way to fix Turn a LOG_DEBUG into LOG_ERROR/return, to escape segfault. (ref: https://bugs.launchpad.net/bugs/1208878) Add an optional argument to O.forces.f() and O.forces.t() to get correct forces on clumps. doc improvement and more cross-links for TesselationWrapper and FlowEngine -enable user defined forces on bodies applying permanently (with updated user manual) +1 conference paper -workaround https://bugs.launchpad.net/yade/+bug/1183402#3, allowing startup imports with optional argument example: $yade -lscipy.interpolate -fix '-l' command line option (no import lib was crashing) fix uninitialized member of ForceContainer fix compile warnings (unused variables) - smallfixes in documentation fix FlowEngine docstring fix duplicate bib reference small fix in bib entries remove duplicate bib reference commit small fix and update in bib files make default FlowEngine::permeabilityFactor less absurd (crashing by default sucks) regression (check-)test for FlowEngine remove Dem3Dof form Yade (also eudoxos module, mostly based on Dem3Dof) - remove Dem3Dof from documentation remove eudoxos from build system (+ remove from VTKRecorder, that was left behind) remove Dem3Dof from a docstring remove Dem3Dof from alias various fixes and improvements in checkTests - increase verbosity of DEM-PFV checkTest remove some debugging code left in chekList.py make sure FlowEngine has been compiled before trying the checkTest DEM-PFV, as suggested by Klaus make the DEM-PFV checktest fully determinist with a data file for initial positions new attributes in FlowEngine to access low level cholmod/metis data \#include in FlowEngine.cpp (why is it not needed on lucid?!) add #ifdef LINSOLV guards in appropriate places in case someone (e.g. buildbot) compiles without cholmod one more #ifdef LINSOLV guard add a cmake path for metis.h on wheezy Return a warning at startup if X rendering is unavailable despite gui is required. User manual: correct the meaning of body.dynamic + remove utils. prefixes Typo fix in prog.rst Fix sphinx warning (no :gui: role) yadeSphinx.py: remove eudoxos module from the build list -remove empty section of doc: External modules revert 3d7ca8577 (doc/current hyperlink), see also https://lists.launchpad.net/yade-dev/msg10035.html. Chiara Modenese (1): Prevent the normal force become negative when viscous damping is applied. Christian Jakob (23): added new example showing implementation of buoyancy small fix in new example from previous commit small fix of description in new buoyancy example include integration scheme for inertia tensors of clumps; inertia/masses/volumes of clumps are updated automatically by call of updateProperties method; removed adaptClumpMasses method and example script Merge branch 'master' of github.com:yade/trunk make getRoundness() faster shorten the code of Clump.cpp: switched getClumpVolumeAndAdaptInertia() method into updateProperties() small fix of a comment small fix in an example script Merge branch 'master' of github.com:yade/trunk remove unused #include in Clump.cpp limit number of cubes for clump inertia integration scheme to 1000000; avoids worst case scenario with R_clump_member(s)< iterator 2. Clean an horrible block of code (not only ugly, it was also slow) - introduce a position buffer for faster updates of volumes Use retriangulation conditions more consistently. The solvers are not swapped before a given fraction of the permutation interval now, to reduce overheads. small change in the initialization logic, now defining the two position buffers if "first" make ompThread an attribute of Engine, as it likely to be used more and more in the future. It is then inherited by InteractionLoop and ParallelEngine Parallelize volume updates and the computation of fluid forces fix a typo introduced in previous commit, giving compile error in FlowEngine remove traces of the SpherePadder module, which is broken and unmaintained (with author's agreement) make grids periodic use EpsVolPercent_RTRG consistently in periodic flow: negative value is ignored, just like the non-periodic case Adapt setContactProperties to pass argument in radians to Shop::setContactFriction -fix conversion mistake (radian/degree) update variable names to denote the unit of friction angle (rad), and make this explicit in the documentation - include elasticity in the normal lubrication force - fix ompThreads assignment in flow engine, resulting in numThreads=-1 by default, then "libgomp: Out of memory" Fix the F9-F12 keys binding for IPython>=0.12 -add the correct prefactor in normal lubrication relation -overlap the two triangulations during one iteration in order to have the "previous" forces defined in the normal lubrication equation Update the documentation of the ompThreads attribute. - fix again the offset of ids in SpherePack.toSimulation (previous fix was assuming two bodies per clump) - fix https://bugs.launchpad.net/yade/+bug/923929 again, as shown by François it could still happen in some cases (see example in the bug report) - remove the check/throw when generating aperiodic 2D packings, since the algorithm actually support that. Define O.engine with a default list at startup, with example script and notes in the documentation. remove utils prefix - Updates and improvements in the triax-tutorial material - smallfix in a note in introduction.rst fixed version of the triax script for clumps Remove first iteration form "--performance" option measurements -transfer the normal lubrication force correctly when retriangulating -doc fix -fix the sign of the normal lubrication force in the periodic case fix compile warning (actually fix the functions as well, as they were not returning results at all!) - doc fix -remove remaining debug lines periodic update of publications fix a typo in bibtex file, +1 ref - one fix in articles, yet more references in conferences fix/add Tran's reference - use "orientation" parameter in utils.box (fix bug/1111514) - improved version of TriaxialStressController, controling not onlt stress but also strain rate - making the interface more similar (but still not exactly like) PeriTriaxController. - TriaxialCompressionEngine and ThreeDTriaxialEngine become almost useless - reflected in the example script which now uses only TriaxialStressController -micro-fix (no need to define an initial timestep) -code cleaning - fix the default value of orientation in utils.box. [1,0,0,0] is NOT a quaternion. -add a few python bindings to the periodic engine for manipulations of the internal tesselation -fix the detection of (not) already computed tesselation -make volume() functional also when PeriodicFlow is actually in use uncouple the compilation of flow code and linsolv, so that it is possible to effectively compile the flow engines without cholmod remove useless "sigma_iso" and "isAxisymetric" members from TTController - make an old engine deprecated, not compiled now, to be removed later more #ifdef guards, to allow flow engine without linsolv remove sigma_iso from the triax example script fix syntax error in a doc string (blocking the buildbot https://yade-dem.org/buildbot/builders/yade-full/builds/1741/steps/shell_3/logs/stdio) -deprecation warnings in ThreeD and TriaxialCompression engines -change the default value of FlowEngine::pressureForce, a flow engine is supposed to compute a flow by default... smallfix in example script - 3 new references - add "Open Source Discrete Element Method" explicitely in the home page, google has to find us nicer documentation of equations for stiffness definition remove useless #define - ship a copy of ipython_directive.py from ipython/HEAD for ipython 0.13 ipython version was checked in two different places, forgot the second one. Still no confirmation of the fix. - some lines comited by mistake, sorry for that. - escape crash on non-iterable __doc__ (some qt class) - define new attributes needed for ipython_directives.py >= 0.13 - fix existing *.rst to use strictly 3 blank spaces in multiline directives (i.e. " ...:") - reference name Tran2012a appearing twice -> renaming Tran2012b - re-introduce the @supress of Christian (removed during experiments) Christian Jakob (21): add addToClump() method in yadeWrapper improvements in clump logic - part 1 Improvements in clump logic - part 2 Added new example script, that show usage of addToClump() and releaseFromClump() Improvements in clump logic - part 3 + 4. shorten the code of replaceByClumps() add a check of python input for replaceByClumps() method further improvements in clump logic some fixes in documentation of wrapper and state fix documentation of clumpTemplate in utils.py Merge remote branch 'upstream/master' let replaceByClumps return a list of tuples with new clump ids and associated sphere ids Merge remote branch 'upstream/master' avgNumInteractions now takes care of clumps some improvements for previous commit doc fix in utils.py and exclude unused Clump.hpp in _utils.cpp updated documentation of clumps in user manual and small fixes in doc in yadeWrapper Merge branch 'master' of github.com:yade/trunk bug fix in replaceByClumps, that could lead to set negative masses on bodies and shorten the code yet another doc improvement in wrapper and user manual concerning replaceByClumps method replaced errors by warnings in addToClump and releaseFromClump in wrapper Donia Marzougui (5): Fix the computation of viscous forces by using the correct positions of bodies (updated in buildTriangulation), and fix some variable names. Remove fictious spheres from the computation of edge surfaces (employed in the computation of viscous forces) Correct the computation of the viscous and normal stress per particle. Correct the sign of some parameters in the computation of the viscous forces. Correct the normal lubrication force. Francois Kneib (24): Continue the implementation of grids : - add GridConnexion Aabb - add GridNode-GridNode Ig2 functor : Ig2_GridNode_GridNode_GridNodeGeom6D - add GridNode-GridNode contact geometry : GridNodeGeom6D - add an example script : examples/grids/Simple_Grid_Falling.py - update utils.py (minor change) Add the possibility of avoiding the contact detection between a group of particle. -> the vector "avoidSelfInteractionMasks" contains a list of masks : all particles having the same mask will not collide if this mask is inside this list. -> the "mayCollide" method now check this too. -> avoidSelfInteractionMasks can be set in python with a list of int. Add the Sphere-GridConnection frictionnal contact : -> new contact geometry : ScGridCoGeom -> new Ig2 : Ig2_Sphere_GridConnection_ScGridCoGeom -> new Law2 : Law2_ScGridCoGeom_FrictPhys_CundallStrack -> update utils.py to handle the new contact type (using avoidSelfInteractionMasks) Merge branch 'master' of github.com:yade/trunk Add the contact following and avoid multiple contact when a sphere is sliding on a grid. -Grids : Fix some minor bugs in Ig2_Sphere_GridConnection_ScGridCoGeom::go(...). -Collider : Change the vector of masks "avoidSelfInteractionMasks" to a single mask "avoidSelfInteractionMask". Create and correct documentation. Grids : - modify the rendering. - Apply correct DEM laws in utils.py to set right kn, ks, kr, and ktw. Now the grid behavior no longer depends on the spacial discretization you make. Modified setContactFriction method. Now it has to be used with an angle in radian unit, no longer in degrees. Try to fix documentation in this files, everywere "yref" appears in the online documentation. Fix Grid periodicity, and allow periodic sphere-grid contacts. Disable a boring warning into the grid construction. Fix a bug in SpherePack.toSimulation. There was a big problem when you tried to add clumped SpherePack (with makeClumpCloud() for example). Corrected toSimulation() (for the last time I hope :-) ). Fix a bug in growParticles(...) method. Growing a clump is now really homothetic. Before that, growing clumps seemed to be homothetic but at the next timestep the original position of members was reseted. Add Inelastic ChainedCylinder behavior law (by Ignacio Olmedo). Create inelastic material and related physics, Ip2 and Law2. Example script and complete documentation will come soon. Add the ability to save to a file a SpherePack containing some Clumps. Into SpherePack : now the toFile method writes a fifth column containing the clump number (-1 if the sphere isn't clumped). The fromFile method uses the new information to append clumped Spheres. Into Shop : loadSpheresFromFile method is modified to read and return the fifth column. Old files with 4 columns are still compatible. Into CapillaryTriaxialTest and CohesiveTriaxialTest : Shop::loadSpheresFromFile is sometimes used here, so remove the clumpId information to match the "BasicSphere" typedef. getStress(...) method : exclude gridNode-gridNode contacts for the stress computing. growParticles(...) method : avoid growing gridNode and gridConnection. Fix some Grids bugs. A minor spelling correction. Add a little class summary and explanations into Grid.hpp. Fix a bug into utils.py when creating a Grid in a non-periodic scene. In the sphinx documentation, add the https GitHub read-only method : git clone https://github.com/yade/trunk.git Avoid GridNode-GridNode contact stiffnesses (kn and ks) to be changed when the growParticles(...) method is used. (GridNodes are not concerned by this method). Add a missing space in the dependencies code lines. François Kneib (1): Correct a remaining bug into the toSimulation() python function. Jan Stransky (9): little modifications added example script for CombinedKinematicEngine little modifications of ConcretePM modification of ConcretePM, improved utils.intrsOfEachBody function improved yade executable: optparse->argparse, yade executable is now loadable as python module modified yade executable, fixing bug 1134422 complete optparse->argparse, --generate-manpage should work improvement of ConcretePM, remover warnings in pack module (randomDensePack and randomPeriPack functions) modified ConcretePM, corrected Peri3dController related examples Jan Stránský (1): minor changes françois (1): makeClumpCloud(...) now takes a "seed" parameter to generate always the same pack. ================================================== yade-0.90.0 Sat, Oct 13 15:16:55 2012 +0200 Anton Gladky (142): Remove RELEASE file. Fix cmake-file to compile. Fix paths in core-files. Update CMakeLists.txt. Fix pygts module. Fix standalone compilation of InteractionLoop.hpp. Enable pymodules on cmake-build. Add version definition to cmake-build. Fix suffix and runtimeprefix in cmake-build. Fix compilation error with gcc-4.7 Fix facetBox generation with height=0. Fix permissions on main.py.in file. Fix installation of binaries in cmake-build. Remove log4cxx from scons-file. Fix binary installation at cmake-build. Remove an explicit defining and importing of listdcxx. Install some py-files for cmake-build. Install glviewer in cmake-build. Fix path install in cmake-build. Update CmakeLists. Return explicite defining of libstdcxx. Causes error. Use rpath for lib-installation. Fix linking of core-libraries. Fix some more linkings in cmake-build. Reinitilize interactions after adding a body. Closes LP:1001194 Move gui-cmake to gui-folder Move cmake for python modules to py-folder. Separate python modules in cmake-build Fix some liking in cmake-build Some fixes in cmake-build. Add autotest to check bug LP:1001194 Give the newly created body an id, which is the size of bodyContainer. Remove lowestFree. Nicer fix for LP:1001194 Add scene->doSort variable. One more fix for LP:1001194. Thanks to Bruno. Fix linking of opengl in cmake-build Fix vtk-linking in cmake-build Install pack.py for cmake-build Add notice about python-demgengeo Add URLs on python-demgengeo package. Fix links. Fix some more linking problems in cmake-build Fix plugin search path in cmake-build Cosmetic changes in cmake-build Fix performance tests. Fix overlinking in cmale-build Make vtk mandatory. Fix -batch binary in cmake-build Partly fix QT in cmake-build. Still not functional yet. Return vtk-feature, but not use it Fix gui in cmake-build. Minor fix in cmake-build Add 2 dependencies to install-section for cmake-build. Enable "options" for cmake-build. Remove technical output during cmake-build. Fix compilation error during non-gui cmake-build Revert vtk-feature. Not mandatory again. Add debug-build to cmake. Use Predicate functions, only when gts is enabled. Place -lrt flag into the right place. Fix rpath issue Remove combine_sources function. Fix header definitions in openmp-accu Fix check-test during no_gts build Fix import libstdcxx on old systems Display information about disabled features Add NOSUFFIX option for packaging. Add lrt to linking on cmake-build Fix linking problem of cgal libraries in cmake-build Fix "typo" in VTKRecorder. Thanks to Vaclav. Remove path to python in some scripts. Move all main libs to usr/lib/yade folder Move minieigen to py-folder Add doSort-option to InsertionSortCollider for forced resorting of interactions. Minor fix in cmake-build Link miniEigen with boost-python libs. Thanks to Klaus Thoeni. Fix version definition for git and bzr. Enable use of custom Boost-libraries. Thanks to Klaus Thoeni. Try to fix cgal compilation. Add possibility to set the lib-path. Fix libpath, if it is non-standard. Fix CGAL-feature for cmake-build. Fix libpath with scons. Replace LIBPATHINST by LIBRARY_OUTPUT_PATH. Fix version definition and generation of pdf. Change Version option to YADE_VERSION. Add option description into CMakeList file. Start to update installation documentation. Start to update documentation on installation. Describe compilation and installation processes with cmake. Minor fix in instalaltion section. Remove scons from documentation. Remove compilation instruction for Gentoo. Check, whether newly added bodies to a clump are already members of the existing clump. Closes LP:1017367 Fix handling ipython 0.13 version. Return CHUNKSIZE option. Update documentation on installation. Better fix for ipython-versions. Hopefully the ipython-interface will not be broken in a future. Remove some bzr-notes from documentation. Remove scons. Minor fix in documentation. Add chainId parameter to body. Implement stopAtTime parameter. Add iterBorn and timeBorn parameters to interactions. Rename chainId to chain. Add python-wrapper to utils.facet Remove timeBorn option in interactions. Remove debug and rebuild options from docs and starting scripts (not functional with cmake) Fix execution error. Use vtkQuad for exporting boxes in vtk-format. (Closes: LP:1026474) Let to use relative paths in INSTALL_PREFIX variable. Remove clumps, if no bodies are present there. Fixes LP:1031644. Remove clump members from clumps during body erase. Move Clump.* files to core/ Add "make doc" command for easier documentation build. Fix some warnings. Add bodiesHandling.facetsDimensions function to get parameters of group of facets. Replace the variables "max" and "min" on "minVal" and "maxVal" in spheresPackDimensions to escape coincidence withi function names Add README.rst file for github Add getBodyIdsContacts to get the list of bodies, contacting with the checked one. Keep pointers of interactions for all bodies, not only where otherId>Id. Add ENABLE_FIXBUGINTRS option. Fix an error in interaction container. Add checkIntrs flag into body to escape useless checks of interaction. Fix segfault with FIXBUGINTRS enbled. Add regression test to check the erasing of bodies, which are in contact. One more step to fix bug of facet-sphere mass interaction. Add function to disable some interactions, if the sphere contacts with several facaets of the same chain. Prevent errors in facetCylinder, if height=0.0 Move fixbugintrs stuff from Newtonintegrator to shop.cpp and constitutive law. Move fixbugintrs stuff into viscoelasticpm, for a quicker compilation. Integrate some ideas into RockPM Some minor fixes in eigen-macroses. Remove testcode for fixing LP:850864 Fix serialize-template for matrix6r. Fix version read from RELEASE file. Fix version number output at Yade start. Fix some compilation warnings. Fix warning due to mix class/struct definition. Honor the flags, which are set in environment. Fix compilation warning »_POSIX_C_SOURCE« redefiniert." Disable CGAL, if compilator is clang. Add information, how to compile Yade with Clang-compiler. Fix batch-mode on platforms, where cpuinfo is not available. Remove rebuild-option from batch-mode. Remove old testing macros in VTKRecorder. Remove accidentally added file in examples. Add normalVel parameter for SpheresFactory to set explicitely direction of velocity for newly generated particles. Backward compatibility is saved. Add RELEASE file for 0.90.0 version. Bruno Chareyre (61): - Direct solver used for periodic BCs and/or compressible fluid - saveVTK for periodic BCs - fix rare but possible junk permeability values (define max/min) -FlowEngine uses boost::thread to precompute triangulation and Cholesky factor while yade is running - interplate using barycenters of old trangulation, instead of voro-center of new triangulation, avoids inconsistencies - make sure voidVolume is positive (FIXME: hardcoded number a.t.m.) - normalize the definition of minimum void volume -add a simple getStress function (periodic or not) move an insert in a more logical place A new contact law adding creep (Standard Material Model) to CundallStrack -missing in previous commit restore the option to NOT homomDeform in periodic BCs (may be rarely used, e.g. when veru big bodies are part of the simulation) restore the option to NOT homoDeform (see previous commit too) - let PeriTriaxController accept very large bodies in the simulation. This change makes it possible to simulate bi-periodic BCs with 2 large planes bounding one coordinate. Example script comming soon. - remove junk output left after debugging work - compatibility of the 6D cohesive-moment law with periodic BCs. - add a simpler way to turn contacts cohesive one by one via an Ip::flag -fix force application in cohesive law (was breaking chained cylinder and sent buildbot error) replace Dem3Dof by ScGeom where CundallStrack is used -remove a series of contact laws as discussed in https://blueprints.launchpad.net/yade/+spec/cleancontactlaws remove contact laws (again), as discussed in https://blueprints.launchpad.net/yade/+spec/cleancontactlaws - Implement multithread solving for the periodic flow - Start implementing CHOLMOD solver using Eigen3 support - Fix flow engine compilation with cmake (some variable with multiple definitions breaking per-file compilation) - CHOLMOD handling in cmake - be quiet when cholmod is disabled remove some "cerr" -reset initCohesion flag for each contact after initializing (else it's rested at each step...) -add functions to export network constrictions and normal and track a point in the triangulation using secondary flow engine (Bruno+Wenrui) - better parameter (vector > 3 doubles) - use cell handles vector instead of CGAL's cell iterators for faster loops - make mirror permeabilities i->j vs. j->i exactly equal in the periodic cases to avoid non-positive definite matrices - fix a few mistakes in permeabillity min/max bounding (permeabilityFactor was not included, and the min was way too high, changing 50% of the values) - make multithread run possible also in the periodic case smallfix in documentation Fix compile warnings. - add export functions for writing system matrix to files reverts commit afa59f17d59a90d3049b9c51c41d28e29fc9081e, which messed up flow code. -fix conflict Document Tesselation wrapper a bit more. Add a complete example script. small optimizations in PeriodicFlow, start implementing matrix-based froce computation (commented blocks) documentation here and there Documentation documentaion fix - a unique function for fluid velocity in cells for both periodic and non-periodic - make fluid velocity computed correctly even on boundary cells with imposed pressure - the boundary are now included in computation average velocity in the simulation - A new function to get total flux through a boundary - Simplify the usage of GSTiemeStepper: no need to set dt at all as soon as GST is present, and setting dt manualy will not disable the timestepper. - Introduce density scaling example script for timestepper and density scaling Small change in the logic of cylinder-cylinder interactions sort exemple scripts documentation fix adapt the interface to the new timestepper logic doc hyperlink for density scaling fix compile error (sorry, it was working with chunksize>1) - remove a loop in Newton as suggested by Anton (Thanks) - update example script - adjustents of strain rate in ex. script Still smallfixes in density scaling Revert "Fix the computation of the shear lubrication force and add the torque of the viscous shear force applied on particles." This commit erased some of the previous changes. Please Donia double-check what you commit everytime. fix two compile warnings The \` are displayed correctly by sphinx. Get them back (at the price of many warnings?...) - remove some "invertSign" in stress functions - add a utils::function to change friction without the need to instantiate a TTCompression engine - make use of Shop::setContactFriction() make warning conditional or it will flood my terminal... example script for cohesive and/or rotational law some updates in this example script make autostop possible again (but still disabled by default) -enable 0-thickness bounding boxes example script for triax+clumps -A new function to grow particles and clumps cleaning script clean sources Chiara Modenese (3): Check the body existence before creating an interaction. (Closes: LP:803774) Add a new entry to yade-conference.bib. Add some entries into yade-conferences.bib Christian Jakob (9): improvements in Law2_ScGeom_CapillaryPhys_Capillarity Fix memory leak in capillary law and make isBroken flag compatible with fusionDetection include calm function fix mask bug in calm function export boxes with vtkrecorder (not tested, boxesCells missing) export boxes with vtkrecorder (visualization works, but is not ok) fix uniax.py and periodic.py example scripts fix and improvements of some example scripts delete unneeded file Donia (2): Fix the computation of the shear torque. Fix the computation of the torque and rename some variables. Donia Marzougui (12): Add spheres' rotation to the computation of the viscous shear force. Compute the viscous shear bulk stress. small fix in min Y Merge branch 'master' of github.com:yade/trunk Add the normal and tangential lubrication force Compute the viscous shear stress for each body Add rotation of spheres in the computation of velocity, Compute the viscous and normal stresses applied on each body, add the normal and shear lubrication forces Fix the names and tests of forces and stresses applied on particles Merge branch 'master' of github.com:yade/trunk Fix the computation of the shear lubrication force and add the torque of the viscous shear force applied on particles. Fix the computation of the shear lubrication force and add the torque of the shear viscous force applied on particles. Fix the computation of the shear lubrication force. Fix the computation of the normal lubrication force remove the computation of some characteristics lengths for two fictious spheres. Francois Kneib (5): Add the contact between two different ChainedCylinders. -> add new contact geometry : "ChCylGeom6D" -> modified "Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D()" to instantiate the new contact geometry when it is necessary -> add new law : "Law2_ChCylGeom6D_CohFrictPhys_CohesionMoment()" -> add new CohFrictMat parameters : "CohFrictMat.cylCylNormalCoh" and "CohFrictMat.cylCylShearCoh". They are used to set the cohesion between two different ChainedCylinders ("CohFrictMat.normalCohesion" and "CohFrictMat.shearCohesion" was already used inside a ChainedCylinder). Fix bugs into "Ig2_Sphere_ChainedCylinder_CylScGeom6D" and "Ig2_Sphere_ChainedCylinder_CylScGeom" Fix an ScGeom6D bug : declare the cylCyl boolean variable as hidden in the YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY instead of in the ScGeom6D class core. Merge branch 'master' of github.com:yade/trunk -python function for handling grid objetcs Create new classes to add grid simulations. Grid are made of GridNodes and GridConnection (two new shapes inheriting from Sphere) Jan Stránský (15): added periodic cell's deformation and strain measures improvement of Cell documentation Cell class improvement made stressTensorOfPeriodicCell deprecated Fixed bug in export.VTKExporter, corrected some docstrings little more fixes in export module docstrings Added Law2_ScGeom_CpmPhys_Cpm class other modifications of CpmMat related classes Added Ip2_FrictMat_CpmMat_FrictPhys functor corrected mistake from previous commit Fixed compilation issues in ConcretePM.cpp reported by Anton Added utils.setNewVerticesOfFacet function improved documentation (corrected some warnings and errors during building docs, added inherited-members directive) improvement of ymport.unv and export.VTKExporter add example file for previous commit fixed small bug in export.VTKExporter.exportFacetsAsMesh add geom.facetSphere another bug fix of export.VTKExporter.exportFacetsAsMesh Klaus Thoeni (1): - add possibility to use local boost installation (e.g. -DLocalBoost=1.46.1) ================================================== yade-0.80.0 Wed, May 2 21:05:12 2012 +0200 Anton Gladky (81): Add forgotten format to ymport.textExt Replace python-numeric on python-numpy in installation section of documentation Fix --test Add check on body existance in GlobalStiffnessTimeStepper. Fixes LP:891540 Fix closeGap for side walls of cylinders and cones Return back fix from r2961. Bruno, please, make a check before commit. Add VTK-5.8 to header search path Fix compilation with VTK-5.8. Remove vtksqlite. Make the code workable with ipython 0.11 Hopefully fix compilation error on clean environment. Do not let PWaveTimeStep return "infinity" Add maxMass parameter to Spheresfactory Update description of maxMass Fix compilation with boost >=1.47 DomainLimiter: * Delete spheres only * Add mass calculation * Add volume calculation * Add mask-parameter Add mass-parameter to VTKRecorder. Add eigen2-option into scons to force compiling with eigen2. Fix eigen2 compiling, when "eigen2=False" by default. Check newly created spheres on intersection with spheres, which were created in one iteration in SpheresFactory. Hopefully fixes "jumping sphere" problem, discussed here [1] Minor changes for ipython 0.11 and 0.12 Add speed-parameter to Scene and Omega Fix calculation speed show in batch-system Fix prediction of finish time in batch-mode. Fix compilation warnings on Ubuntu Precise. Use gravity inside of NewtonIntegrator in examples and in tests. Return the average speed of calculation from the last 10 iterations instead of current speed for the last step. Hopefully makes prediction of finish-time in batch-mode more accurate. 1. Fix a compilation error with eigen2 2. Add a variable to define number of steps, which are taken into account by speed calculation. Rename .bzrignore to .gitignore. Merge pull request #1 from gladk/master Start to update main sphinx page. Merge pull request #2 from gladk/master Fix --check and --performance tests after moving testing scripts. Add deleted by mistake update of main sphinx page. Update of the main sphinx page. Fix version defininition with git. Ignore *.pyc files. Merge pull request #4 from jakob-ifgt/master Fix version number for gits. Caused error during doc-build. ResetRandomPosition should be a child of PeriodicEngine, not GlobalEngine. Fix some examples. Reenable gts-scripts. Let facetBunker.hBunker be zero. Add parameters body::iterBorn and body::timeBorn to track the moment, when the particle was added to simulation. Fix link to a wiki-page. Add libboost-program-options-dev to installation section. Add gtk2-engines-pixbuf to installation section. Escapes "Gtk-WARNING **: Im Modulpfad »pixmap« konnte keine Themen-Engine gefunden werden". Escape warning due to ipython 0.12. Do not output a false backtrace with ipython >= 0.10 due to log4cxx crash. Add python-bibtex to installation section of documentation. Remove useless check of ipython version. Now all systems must have >=10. Do not redeclare cundallInteractionPhysics and mindlinInteractionPhysics in local scopes, as they should be global. Fixes crash LP:966186. Add gmp for linking, when cgal-feature is activated. Fixes LP:968188 Fix unicode characters. Parse Yade.tex and remove empty verbatim-blocks. Happens on Precise. Add ipython_directive for ipython 0.12. Some adjustments to build docs on Precise-systems. Prevent cross-importing of yade modules. Closes LP:980000 Make nice output in ipython 0.12 like it was in 0.11. Make main.py.in more readable. Remove accidentally added ipython_directive012 extensions for all ipython versions. Remove log4cxx support and yade.log module. Fix compilation error on Debian Sid due to changed API of python-git module. Minor update of examples. Add isActive parameter to Interactions. Merge branch 'master' of github.com:yade/trunk Let isActive flag be changeble. Remove "never_use_this_one" option from scons. Remove "sphere-padder" option from scons. Fix autotest "rotation matrix from quaternion". Remove subdomains feature. Fix compilation warnings. Initialize angle* variables. Add geom.facetParallelepiped function. Remove executable-flag from scripts. Remove executable line in some examples (it cannot be in /usr/local folder on all machines). Fix some typos. Change default value in Real-variables from NULL to -1.0. Fox compilation warnings. Fix compilation warnings. Fix some typos. Add RELEASE file for 0.80.0 version. Bruno Chareyre (72): - (failed) attempt to fix the documentation of export.py - fix doc generation for the export module. Still some fixes needed concerning doc convention (wrong parameter declaration for some functions) - makeCloud can now generate spheres on a plane (see https://answers.launchpad.net/yade/+question/175606) remove unused bool "is2D". - makeCloud handles periodic 2D clouds with uniform distribution and psd - yet more fixes. The auto-setting of cell.size was not correct (typo in components) - code cleaning - Documentation of the capillary law (warn users on distanceFactor and neverErase flags, as in http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg07391.html. - 2 additional references - make body iterators jump empty slots, as suggested and discussed here: http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg07406.html - revert the (now useless) fix of r2961, similar tests can be removed in many places after the change in pointer logic is well tested. - remove a script, as agreed by Christian (https://answers.launchpad.net/yade/+question/178830) - add/use the "neverErase" flag in Hertz laws. - back to ordinary vector<>:iterator for bodyContainer - smart body pointers again, also fixing the erase(0) case inside begin(). - remove the if(body) test in GSTS loop. - attempt to fix https://bugs.launchpad.net/yade/+bug/897237 - small fix in the theoretical background Should finally fix https://bugs.launchpad.net/yade/+bug/897237 - capillary model: nullify Fcap and volume when P changes from something to zero - remove the if(!b) test in a few important places (proof of concept + don't waste time doing the same test twice) - fix wrong shape type testing that was giving wronf solid volume. - update publications - fix one bug mentionned in https://bugs.launchpad.net/yade/+bug/901146 (makeCloud with undefined num and psd) - more articles - normalize psdCumm2 after the scaling, not before (since the scaling is determined from absolute psdCumm2). - make it possible to include bodies larger than period conditionally, using allowLargerThanPeriod flag (as discussed in https://answers.launchpad.net/yade/+question/181411, thanks Giulia for the scipt) - document undocumented parameters of bodies creation (in utils.sphere) - enable interaction of two larger-than period bodies (e.g. cylinder vs. box) in addition to previous commit. - point to the "allowBiggerThanPeriod" flag in the LOG_FATAL message. - improvements in TW interface so that one can save and load "state" files to be used for defining deformations (this will actually be used by E. Ando for analyzing experimental data!) - code cleaning - make deformation analysis possible for arbitrary simulations (no longer depends on TriaxialEngine for defining the bounds) - fixed undefined variable when Triaxial engine is not present - erase bodies before adding spheres from file - Fix typo (thanks for pointing out Klaus, actually the "i" was correct: elastic-plastic means that the law is incrementaly elastic OR plastic, while elasto-plastic laws can be both at the same time) - big reorganization of the triangulation lib, which becomes a template library. Usage of different "info" classes for different engines is now possible, so that TWrapper doesn't have to instantiate useless variables inherited from the flow problem, and vice-versa. Will also worj for periodic flow model coming soon. - general code cleaning and removal of old files - a few hyperlinks fixed in *.bib's - remove custom dependencies breaking compilation Merge the "collide" branch to trunk (branch history at https://code.launchpad.net/~bruno-chareyre/yade/collide2) - missing reference update - remove the velocityBins lines in tests since velocityBins are removed from trunk - Draft version of the periodic fluid model from Donia Marzougui smallfix in flow model - fix a bracket mistake triggering ghosts definition after each insertion in periodic::triangulate() - add tests on boundary ids (<0?) before doing anything on them. - account for sweepLength in bounds comparisons of Collider::probeVolume() - removed unused file - Collider: fix the probe function (account for current body's position + typo in one comparison) - Newton: remove the useless "force" from damping2nd parameters, don't apply meanfield vel when not periodic (only diff is it avoids a multiplication of null matrix and vector), make gravity attribute work correctly - GravityEngine: add LOG_ERROR on deprecation (LOG_WARNING are not displayed in prebuilt package right?), better use Newton::gravity to save cpu time. - Clump.hpp: fix the template function that was using the old saveMaximaVelocity, use the new saveMaximaDisplacement instead - PeriIsoCompressor: never pause() in some c++ code, since it resuults in stuck GUI without a chance to run more timesteps - dispatching: don't make bboxes larger for static bodies - gravity : deprec. warning - collider: try and fix Anton's crash (https://lists.launchpad.net/yade-dev/msg08256.html and next in the thread) - Newton: workaround the resetForce bug in OMP build (https://bugs.launchpad.net/yade/+bug/923929) - small changes left behind in a previous commit (fix the "undefined IPCells") problem - include periodic PeriodicFlow in the triangulation lib - Compute the critical timestep correctly when clumps are present. - make the "smoothing" of strain rate evolution configurable via a registered attribute (default=unchanged behavior) - tell more explicitely that Young/Poisson is interpreted differently in different functors in their respective doc - make the LWStress function return pyList instead of tuple - documentation in makeCloud - default stiffness are zero, not NaN - TWrapper: python binding for local deformations - Flow: fixes in the periodic BCs - Flow: improvements in BCs handling and imposed fluxes, toward per-step update of the RHS + code cleaning - Periodic flow: support for optimized solvers (not in trunk) by introducing cells indexes - Periodic flow: optimization of periodicity by precomputed Hsize[k]*gradP products - SpherePack: more code documentation in makeCloud - missing in previous commit (sorry) - fix periodicity of interactions when large bodies are present. Demo script comming soon. - implement the compatibility between periodic fluid model and large bodies in PBCs using the "boundary" objects - Make unbalancedForce() account for Newton::gravity (and my first git commit!) - mirroring bzr3038 + bzr3039 - example script for large bodies in periodic BCs compile error; remove warnings; add last diffs from Donia Smallfix in index.html - fix doc string in the SpherePack.toSimulation function (crashing my terminal...) - update one reference Merge branch 'master' of github.com:yade/trunk - fix bug https://answers.launchpad.net/yade/+question/192152 in SpherePack.toSimulation() - fix a documentation bug (https://bugs.launchpad.net/yade/+bug/978234) fix a warning in DomainLimiter make periodic triax engine ScGeom friendly (a few scripts to be fixed in next commits) - remove reversedForces flag and/or use ScGeom in the example scripts for periodicity Merge branch 'master' of github.com:yade/trunk - add the possibility of updating only the RHS in the fluid problem, without rebuilding the triangulation+matrix Fix bugs introduced by incomplete addition of Real dt in some functions signature (messing virtual inheritance) Merge branch 'master' of github.com:yade/trunk Fix the problem of null pressure measured after retriangulation. Bind a measurePressure() method for the periodic flow engine allow BCs update without retriangulation via Flow::updateBCs() Fix a bug in PeriodicVertexInfo::ghostShift Merge branch 'master' of github.com:yade/trunk Fix a few bugs discovered with Luc: Fluid forces splitted between particles and their images in PBC, and others. Implement the updateBCs feature for PBCs. Enable pressure interpolation in periodic coupling The documentation now reflects the recent changes in collider's logic. Christian Jakob (11): Law2_ScGeom_CapillaryPhys_Capillarity can now be used with Ip2_FrictMat_FrictMat_MindlinCapillaryPhys for hertz model Add forgotten files Added new example script (examples/generate-psd-with-poro-example.py) Fixed examples in example folder, new folder called not-working move all model examples to example folder, fixed all examples, that are not in test folder moving checks and tests to scripts/checks-and-tests and fixing some examples in examples/test moving checks and tests to scripts/checks-and-tests and fixing some examples in examples/test moving checks and tests to scripts/checks-and-tests and fixing some examples in examples/test fixed all examples Improvements in Law2_ScGeom_CapillaryPhys_Capillarity.cpp (included isBroken flag and updated checkFusion) make fusionDetection and isBroken flag compatible Francois Kneib (4): Added the interaction between cohesive sphere and cohesive chained cylinder. Created Ig2_Sphere_ChainedCylinder_CylScGeom6D and Law2_CylScGeom6D_CohFrictPhys_CohesionMoment in Cylinder.cpp. Created CylScGeom6D in CylScGeom6D.cpp. Moved CylScGeom from Cylinder.cpp to CylScGeom6D.cpp Interaction test between a cohesive sphere and a cylinder. Fixed some bugs in Ig2_Sphere_ChainedCylinder_CylScGeom6D() and Ig2_Sphere_ChainedCylinder_CylScGeom(). Now the contact is rightly followed when a sphere move along a chained cylinder. It works with frictional cohesive or frictional contacts. Fixed some bugs in Ig2_Sphere_ChainedCylinder_CylScGeom6D() and Ig2_Sphere_ChainedCylinder_CylScGeom(). Now the contact is rightly followed when a sphere move along a chained cylinder. It works with frictional cohesive and frictional contacts. Jan Stránský (6): 1) modification of CpmState class 2) some changes in py/pack/pack.py Added Matrix6 Added damageTensor to CpmState Fixed bug 922744 (export module) Fixed SpherePack and _getMemoizeDb incompatibility with periodic boundary conditions Corrected assert(Matrix3) in Math.hpp O and wrapper.Omega made part of __builtin__ (equivalent to global variables). Should solve problem of question 182459 Omaga can contain more Scene instances Fix of previous commit Klaus Thoeni (3): 1. delete line which was commented out by Anton 2. derive WirePhys from NormShearPhys in order to use implemented functions which just support NormShearPhys (NormPhys is not supported, however, in the future if more contact laws with normal force only are implemented it might be better to introduce a boolean or so) 1. fix some typos 2. derive WirePhys from FrictPhys 3. compute limitFactor for WirePM 4. add limitFactor and normal force of wires to wpm in VTKRecorder - add capability to deactivate the damping in NewtonIntegrator for individual particle via O.bodies[id].state.isDamped=False - use this new property in examples/WireMatPM/wirecontacttest.py Luc Scholtes (7): add compressibility to fluid flow scheme delete obsolete line in flowEngine.hpp resolve bug 983888 add compressibility to periodic flow engine cleaning pack.py clean FlowBoundingSphere.ipp file Apply changes from Luc Sholtes. Luc Sibille (1): Update some publication references Rémi Cailletaud (4): Added google analytics script to sphinx doc Build infrastructure - removed r0calcul8 from builbot nodes (hardware issues) buildbot now builds two times, with eigen2 and eigen3 now uses xvfb for doc generation (for qt part) buildbot home on slaves changed reenabling r0calcul8 ================================================== yade-0.70.0 Sun, Oct 23 16:49:34 2011 +0200 Anton Gladky (129): 1. Prediction of simulation finish time is added to HTTP-batch server. 1. Fix of a previous commmit. Wrong prediction time. 1. HarmonicMotionEngine is added with example. 1. HarmonicMotionEngine update. 1. HarmonicRotationEngine is added including example in regular-sphere-pack.py 2. TranslationEngine is parallelized with OpenMP. 3. Translation and Rotation engines are working with Dynamic-bodies properly (temporal solution). 1. Regression tests for translation and rotation engines are added (not fully tested yet, but "all tests passed") 1. Changes from 0.60 (debian packaging). 1. scripts/debian-prep creates orig.tar.gz and removes .bzr directory 1. debian-prep creates version number with "1" at the end 1. Backporting changed from 0.60 branch 1. qt4 is "on" by default 2. Syntax fix in documentation. 3. export.text is disabled in regular-sphere-pack example 1. Initial yade.spec is added for RPM packaging 1. Fix bug in VTKRecorder (Thanks, Vaclav) 2. Cohesive-chain test disabled (please, fix it, who can...), https://yade-dem.org/buildbot/builders/yade-full/builds/127 1. Changes in .spec file 1. Some preparation to dpkg ver3. 1. Deleted isDynamic from Translation Engine 1. Commented SubdomainBalancer packs.py to make it workable with default compilation. 1. Partly fixes 692759 1. debian/copyright is changed according to debian requirements. 2. control-template is changed to make the package "lintian clean" 1. Fixed warnings in packs.py->utils.py 2. Created geom.py module for generating geometrical forms from facets. 3. utils.facetBox and utils.facetCylinder have been moved to geom.facetBox and geom.facetCylinder respectively. Backward compatibility is saved. Examples are fixed. 4. closeGap in utils.facetCylinder and utils.facetCone works now only when |anglRange|>math.pi 5. geom.facetBunker is added with corresponding example in pack.py 1. python-imaging is added to installation section of sphinx-docs as well as to debian-dependency 2. geom.facetHelix and facetPolygon are added with examples 1. Closes #702296, if somebody uses rotationengines, please, update! 1. regression tests of kinematic engines are updated and activated. 1. Updated regression tests. Rotation engines. 1. HelixEngine updated, dublicated code deleted. 2. HelixEngine is added to regression tests. 1. Extra Quaternionr q() definition is deleted from RotationEngine (thanks, Bruno) 1. Shop::getStressForEachBody() is now returning stresses for FrictPhys+ScGeom combination; not only NormShearPhys+Dem3DofGeom 1. Added debian/watch to track new yade versions. 2. Some small modifications in debian/control-template to escape lintian warnings. 1. vtk-5.6 path is added to SConstruct to make it compilable with Debain experimental 2. Fixing spelling mistakes in documentation. 3. debian/ -directory changes. 1. Fix lintian warnings in manpages. 1. jquery.js in documentation is now symlink to a packaged jquery, if it is available. 1. Debian-directory cleaning and modifying (checked with lintian -IE --pedantic, no warnings at all). 1. openmp-feature is added into the debian-build options. 1. Hopefully fixes previous error on building PDF (not checked yet). 1. One more try to fix tex-failure. 1. Missing files and licenses are added to debian/copyright 1. yade-support plugin is added to lib/SConscript as described here https://bugs.launchpad.net/yade/+bug/707966/comments/2 1. Hopefully fixes bug 707966, additional libraries are added for linking in shared libraries (vtk*) 1. Small fixes in debian/copyright to escape lintian-warnings. 1. debian/ is moved to scripts directory 2. scripts/debian-prep scripts copies ./scripts/debian/ to ./debian/ 1. Regression test of yade.plot.addAutoData() is partly disabled is due to https://bugs.launchpad.net/yade/+bug/715739 1. Build-script and buildbot-config are moved to scripts/build-infrastructure 1. Updated installation instructions 2. Updated spec-file for RPM-packaging 1. Added a patch to escape -rpath (an ugly and "very" experimental) 1. Fixed Tutorial link in documentation (taken from https://www.yade-dem.org/sphinx/tutorial.html) 2. Some small fixes in documentation 3. Changes in spec-file for RPM-packaging 1. LOG_INFO and LOG_WARN are disabled when log4cxx feature is disabled. 1. Added shop.py. Like shop.cpp but in python not to make yade.utils too crowd 2. Added yade.geom and yade.shop to sphinx 3. Some fixes in docs 4. yade.shop.spheresPackDimensions is added with corresponding example in packs.py 1. scripts/debian-prep does not insert now distribution name into the version number. Update of spec-file for RPM packaging 1. vtkNetCDF was deleted from vtk-libs due to absence in libvtk5.6-dev. Seems functionality is not corrupted. 1. python-sphinx dependency for Debian is changed to >=1.069 1. Added python-imaging to Debian packaging rules. 2. Fix spelling in documentation. 3. Debian-Template yade-doc file is fixed (0.60 version was hard-coded) 1. Update installation information in documentation. Fix in installation documentation 1. RPM-spec file update 2. Old yade.spec was moved from the root directory to scripts/RPM_packaging 1. Fixed some docs 2. shop.spheresPackDimensions can accept now a list of bodies, not only the list of their id's 1. yade.shop module is renamed to yade.bodiesHandling to get more adequate name 2. added bodiesHandling.spheresModify to modify a pack of spheres. Corresponding example is in examples/packs/packs.py 3. added bodiesHandling.sphereDuplicate to make a copy of sphere 1. Renaming shop.py to bodiesHandling.py 1. ForceRecorder renamed to ForceTorqueRecorder 2. TorqueRecorder is added 1. Changed yade.spec file. Seems, working now. INSTALL_PREFIX option is added to CMakeLists.txt CHUNKSIZE option is added to CMakeLists LIB_EIGEN_PATH is added to CMakeLists.txt Typo fix in previous commit Fix formula displaying in utils.getViscoelasticFromSpheresInteraction "mask" parameter is added to GravitiEngines to make it more flexible. 1. ForceRecorder.totalForce and TorqueRecorder.totalTorque are now accessible from python interface 2. Fix in TorqueRecorder: getTorque is added 1. Fix TorqueRecorder calculation utils.shiftBodies function is added to move bodies without velocity update. 1. in utils.sumTorques and utils.sumForces py::tuple has been changed to py::list. I think it is more convinient. 2. added RuntimeError() to checkTestTriax.py. Bruno, are you agree? 1. Added new checkWeight test to --check scripts 2. It is not neccessary now to add the script name into the checkList.py, just drop a new script into the scripts/test/checks directory 1. Updated build-farm script (building Debian and Ubuntu packages for different distributions). 2. Updated installation section of documentation (Gentoo installation). 1. Some changes in installation section (Gentoo) 2. Check tests are now running like --test, returning error code if something went wrong. 1. Performance test is added. Initial script. 1. Small changes in installation section. 2. voxelPorosityTriaxial doctests are transformed to a simple source code demonstration due to results instability (candidate to --checks section http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg06635.html ) 3. Added initial sqlite database of performances on different machines. 1. Fixes bug #724396. Thanks Sergei and Vaclav. 1. Make trunk compilable with Eigen3 (coming soon). No performance test results yet. 1. Color output for --performance tests is added. 1. Fix doc generation of the previous commit. 2. Added a link to revision archive on yade-dem.org Color output in --performance tests is deleted. Add Eigen3 transparent support: if eigen3 persists in the system, it will be used by default, otherwise - eigen2 Fix Eigen3-Eigen2 detection variables. Fixes 748943. Thanks Bruno for pointing out Add "stop" button at the batch-panel Fix spelling errors: allows to... 1. Replace "subscribedBodies" to "ids" almost everywhere in the code. 2. Fix a couple of examples. 1. Move Dragengine from SphereFactory to ForceEngine. 2. Fixes in ForceEngine (crashed, when force applied to non existing body) Add LinearDragEngine 1. Fix a crash, which appears, when force is read from non-existing body. 2. Fix warning in CohesiveFrictionalContactLaw 1. --check tests are now copying into the libDir/py/yade/tests/checks folder to make it available in packaged yade version. 2. Rename "dataTriax" folder to "data" to make this folder and for other tests suitable. Added syncSizesOfContainers to forceContainer::reset() for the case of not using NewtonIntegrator in scripts Remove PressTestEngine, because python-variant works much better Fix an error, when spheresPackDimensions tried to get states of non-existent bodies Skip empty ids in KinematicEngine Fixes nans in ViscoelasticPM, when kn=0 or ks=0. Fixes 804650 Fixes crash, causing by saving-loading simulation with erased bodies. Fixes #803774 Add one more --check scripts to check GravityEngine and NewtonIntegrator Change the number of steps for checkGravity.py Add O.wait() at the end of checkGravity-test. Hopefully will fix the buildbot-error. Add utils.getSpheresMass Add mask-option to SpheresFactory Add ids-parameter to SphereFactory to get the ids of newly created bodies Add utils.psd(). First try Add mask-parameter to utils.getSpheresVolume and utils.getSpheresMass Fix (hopefully) simulation abort, when an interaction::erase is trying to delete an interaction, where one of bodies is already removed from simulation (id2) 1. Add PSD-support to SpheresFactory (not finished, but already working) 2. Add exception in utils.psd(), if all particles have the same diameter Simplify utils.psd() Add forgotten PSDuse-variable initialization in SpheresFactory Add comment on doubtful check of b2 in InteractionContainer::erase Simplify PSD-input data for SpheresFactory Fix file-creation error in yade-batch, when name of log-file is longer, than 255 symbols. The name cuts off now. Add exactDiam flag to SpheresFactory 1. Add example of SpheresFactory into packs.py 2. Add stopIfFailed flag to SpheresFactory. -Remove dublicating item in references Fix some errors during doc-generation Fix crash in capillary law (removed bodies were not checked) Add mask-parameter for spheresPackDimensions Fix mask-check in several places Fix in spheresPackDimensions. The bug appeared, when only mask was inputted Add mask-parameter to spheresModify. Fix a default parameter for ids in spheresPackDimensions Add some more parameters to spheresPackDimensions 1. Remove "consider" parameter from textExp function 2. Add "mask" parameter into textExp function 3. Add one more format for output. Delete all corresponding iterations explicitely, when the body is erased Fix compilation error during debug-mode Move not-working examples into the corresponding folder. Update news Fix link to installation page 0.70.0 Bruno Chareyre (130): - Rename Cohesive law functor with "6D" as in "ScGeom6D" - Same for chanedCylinder's Ig2 functor. - update scripts. - Fix compile crashers due to bad include paths. - Keep robust kernel the default. - re-enable cohesive chain test - declare deprecated names (part of r2543) - revert experimental parameters previously commited by mistake in cylinder script - Make TriaxialTest behave correctly by default - as it used to, i.e. generate the correct number of particles in a cube of size 1. - disable the last comparison on velocities (see https://lists.launchpad.net/yade-dev/msg06178.html) - add the mandatory "bool periodic" parameter for makeCloud. - Prepare linear solver usage in FlowEngine. - Some cleaning. - Add inexes to triangulation cells fro vectorization. - remove a warning in Tesselation.cpp - fix FlowBonding sphere for first iteration and a few other things - make GaussSeidel virtual in FBS - handle different solvers. - small optimization on dt divisions. - FlowEngine : rewrite updateVolume so that cell volumes are not computed twice. - Remove irrelevant remark in SCPE - Some missing "6D" here and ther in decorations (could affect only devirtualized build) - Implement tensile plasticity and add the corresponding parameters in CohFrictPhys. - recent commits broke or modified something in cohesive law. The reg. test points it out. - restore default CohFrict behaviour - PeriTriax : remove the constant-distance approximation in stress definition, using wrapped coordinates instead of radii. - Get back standalone energy tracing in ECL. - Cylinders : handle cylinder-sphere contacts with a fictious state representing interpolated motion between nodes and passed to ScGeom - Cylinders : implement CundallStrack for interaction between 3 bodies (1 body + 2 nodes) - Cylinders : a number of fixes - no more bugs it seems - Cylinders : handle zero-sized element for terminating chains - Cylinders : update scripts; add example script chained-cylinder-roots.py, with cylinders, spheres, and boxes - Ig2_Box_Sphere_ScGeom : small class name fixes ("6D") - utils.py : adapt cylinders linking - ElasticContactLaw : don't use Body::byId when possible - ScGeom6D : put quaternion normalization between #ifdef guards (debug only) - clean the script. - recommit 2608 with fixed reg test (making ratcheting correction negligeable with dist=.999999999999999999*size) - also fix the compile errors - r2608 again, sorry. Local tests are invalidated by last changes in setDynamic, but the commit is correct. - finish implementation of contacts tracking on chained cylinders. - some cleaning and doc update Fix : mistake in prev. commit while cleaning cylinder code. - recommit 2617 without the autoformating from kbibtex. - Doc : give precise references for triaxial algorithms. - Deeper integration of isDynamic semantic : skip velocity integration, damping, DOFs blocking, and exact spherical rotations, when !isDynamic. 0-density bodies should be safe. - Partial DOFs blocking is not implemented yet. - ratcheting documentation : improve and unify source and inline versions. - As in r2615 : skip velocity update, damping, DOFs blocking, and exact spherical rotations, when !isDynamic. 0-density bodies should be safe. This is a merging r2615 with the per-DOF blocking and clump handling from r2621. - updated FIXME, it seems we do the same thing twice -Fix kinetic energy definition. - Fix stripes display - Add secondary light and register light parameters - define specular exponent for smoother display - define and use GL display lists - review and update of documentation in a series of class - adapt TSC and TCE to new non-dynamic behaviour (more changes and cleaning planned) - remove prevNormal and frictionAngle from FrictPhys - Add temporary FrictPhysTransitory for compatibility of old laws - Rename Ip2_2xCohFrictMat_CohFrictPhys for names consistency, as suggested by Janek -As in r2615 and r2622 (both reverted), and partialy in r2626 : skip acceleration, per-dof blocking, damping, and velocity update for bodies and clumps in case of DOF_ALL blocking (per DOF operations are useless in such case). Please don't revert unless there is a reason to compute DOF_ALL's acceleration and it is guaranteed bug-free (see list). Discussion more than welcome, of course. - Fix one mistake in previous commit (incrementing angVel even for asphericals), sorry. - Move clump damping after the foreach(member) loop, so that it will damp the total acceleration at clump's level. - Don't damp clump members. Instead, compute undamped acceleration and damp it at the clump's level. - Similar mechanism implemented for DOF's blocking : compute unblocked accelerations and block at the end (remember blocking one DOF triggers tests and divisions). - Still possible optimizations (especially for spherical rotations and translations), see https://blueprints.launchpad.net/yade/+spec/clump-forces. - One FIXME : aspherical damping is not correct a.t.m. since it uses torque where angAccel should be provided (suggested fix in sources). - Probably fixes a few inconsistencies in previous commits. - Missing in last commit (fix builbot failure) -Fix sphere rendering for closing/opening qtview (closing was deleting existing display lists, new view was empty) -Make quality apply for striped spheres as well -Make it possible to turn duplicated spheres on/off in periodic BC -Separate GLUT and striped spheres functions for clarity -Optimize stripes rendering with GL_TRIANGLE_STRIP - A checkTest for triaxial simulations. - Add a function (and python wrapper) computing the exact mean stress in each sphere. -fix compile error in prev commit. - Integrate check tests in yade options (see README). - Handle PBCs in Shop::getStressLWForEachBody (not tested) - uncouple Hsize and trsf, add setters for attributes Cell::trsf and Cell::refSize, update all scripts. (see http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg06101.html and next in thread). - Fix some temporary stuff left behind (safe but useless) + get back one line of comment removed by mistake. - update periodicity documentation - rename Hsize->hSize to be consistent with names convention. - remove a duplicated ref and add a CGAL ref - one file left behind in last commit, sorry. - Add resetTrsf() to set trsf without side effects. - minor updates of attributes doc to be consistent with recent changes. -Don't maintain refSize in setHsize, in hope that we will not drag it forever, as suggested in https://lists.launchpad.net/yade-dev/msg06836.html. - Fic classname and give working example. - update bodyStressTensor doc. makecloud update (recommit after fix) - Fix psd transformation from mass distrib to number distrib. - Make sure the function will always return the number of particles required by the user as soon as it is psecified. - If num is specified, generate sizes the deterministic way by descending order. - make porosity parameter optional and give it a default value. - update doc and script. - make Cell.size read/write for faster hSize setting. - improve and simplify documentation (the older method is no longer documented) small typo in property name ("sizes" instead of "size") - Move older or redundant interface between #ifdef CELL_BACKW_COMPAT guards. - Replace refSize by current size in PeriTriax - forget adding the "s" in "cell.sizes", since existing scripts are already using "cell.size" -> fix sphinx doc about this. - some more Cell doc. After typing the paragraph on display, I realize w'd better not update refHSize when trsf=s-------------- This line and the following will be ignored -------------- - some more cell doc. As discussed on the list: - Don't update refHSize when trsf is defined - Update it when hSize (like before) or size are assigned - use current size in PeriEngine - remove unneccesary cell attributes - replace setBox by size - update doc (atributes and header) consistently - Forgot to save Cell.h before committing : updated header doc. Yet more cleaning in cell (sorry). - remove FrictPhysTransitory - A few changes in Cell as discussed in the list. - Updated doc. - Attempt to fix buildbot output in triaxCheckTest (LOG_INFO are disabled by default on my machine but the buildbot has a different behavior it seems, which gives lots of junk lines) in the log. - Add a script demonstrating use of inclined initial cell and reseting trsf - Small doc or formatting fixes here and there - add hSize parameter to makeCloud so that it can generate arbitrary parallelepipeds (previously working only by luck on a few special geometries) - documentation - usage in script, which uses now more funny shape (try it!) - Preparation for citation (wiki won't accept text file uploads => commiting to trunk) - Include Yade citation page in doc, and add links in different places. - Add 'InCollection' keyword in bib2rst - One missing file + updated links to individual pdf's in pub.rst.in Missing in previous commits (the most important file...) - Fixing a few links. - more fixes... - A typo left in index.html. Changes in this file are not reflected in documentation built localy, and erasing the _built dir breaks sphinx builds. It makes changes in sphinx main difficult. -link to discussion of citation model - run "xelatex Yade.tex" twice, so that the content table is generated correctly. - Small fix in makeCloud (hSize not passed correctly in recursive calls) Format check tests output better. Small fix in unbalancedForce doc. - per-point imposed pressure mechanism. - per-point imposed pressure mechanism - one fix in permeabilites along boundaries - remove save_vtk flag and add python wrapping - Add functions for constrictions sizes statistics. - Remove a few compile warnings. -fix accents and reference name in Catalano's entries -Update clumps forces and torques in Newton, as in https://blueprints.launchpad.net/yade/+spec/clump-forces. -Update Shop::unbalancedForce accordingly -Remove the old unbalancedForce code from TSController and make it point to the Shop version. - re-fix fluid area definition - some cleaning here and there (Donia+Bruno) - fix fluidArea correction (S0) - Optimal computations by storing fluid/total ratio in cells info - handle changes in cell's volumes sign - add converters from Eigen vectors to CGAL vectors - small fixes in references - cell volume update was disabled -> enable again - Fix the behavior of bodies moved with the mouse with respect to the new isDynamic behaviour. - The velocity is now defined correctly so that contacts on the moved object are computed correctly - use same ordering convention for boundaries in triax and in aabbBoxes. - removed useless variable - correct initialisation of compression axis - Set default values of walls ids - Fix cells volume functions - Add a vertex accessor Tesselation.vertex(body_id) - Various improvements - fix the action condition (was it never tested?) - invert x and y axis for getting stress (the convention changed in r2830) A section on devpt tools and check tests in programmer manual. - doc smallfix - improved section on regression test - fix (in fact workaround...) bad display of double minus (--) in sphinx. - typos End a sentence... (thanks Jerome) - more explicit notes on citing (I realized it was not clear while reviewing a paper citing yade ;-)) - again small fixes in the "development tools" section - remove many warnings - handle viscous shear force gracefully - don't exit the checkList when one checkTest fails, we want all of them tested in all cases - move unstable test out of checks - add Ohloh widget to main page - small fixes in the example script (so that it actually works). - add setImposedPressure that let the p value be modified -shift returned p index - import pack and utils at startup Make accents more bibtex-user-friendly in bibtex entries. typos fixing - fix problems again, sorry - standardize the first page of yade doc and add metadata to the pdf, so that online scanners will identify it correctly (not title:"Smilauer", author: "Catalano"...) - fix a few references - Feng Chen PhD + paper (thanks Feng!) - some small updates - fix typo (thanks Remi) - change sections ordering - an attempt to fix builbot-side compile error in the html version of "formulation" chapter (compile ok locally) - A few fixes on deprecated attributes. Small fix in shear stiffness averaging (thanks Emanuele) code cleaning only (including example usage of stringstream for Ema) - One more entry in PhDs (Jerier) - fix documentation (missing factor in an equation) - fix bug 2) found by chiara (https://answers.launchpad.net/yade/+question/169689) - link to libgmpcxx explicitey if cgal in features. Solves runtime undefined symbol on natty. - Include the material from the school in Grenoble in a subfolder of /scripts Remove files added by mistake. - Add material from the "discrete mechanics" school in Grenoble 2011. - fix the "homoDeform" bug https://bugs.launchpad.net/yade/+bug/836867, and adapt regression tests so they don't test homoDeform=1 - add gravity to Newton - tune front page of the documentation to be more google-scholar-friendly - include gravity a bit differently in Newton, so that it's reflected in scene->forces and accounted in the unbalanced force definition. - one more PhD done with Yade - remove Ohloh widget since it's never clicked and suggest an underestimated number of users - small addition in TSC documentation - fix Newton::gravity usage. Weight is g*mass, not just g... master thesis on yade-fluid coupling uploaded on wiki and added to references. - fix typo - remove the bibtex entry "Yade DEM" without authorship. It could only be misleading and make people use inadequate reference. - fix https://bugs.launchpad.net/yade/+bug/693505 - don't crash the TSRecorder when bodies are removed Chiara Modenese (19): 1. Move alphas parameters to FrictMat as discussed with Bruno (harmonic-average of them is introduced in Ip2 functor). 2. Forgot one inequality when plasticity is applied (maybe I do not like tests so much :-) Sorry, anyway). - Adjust definition of maximum strength for rolling resistance (thanks to Bruno for suggestion). - Get rid of prevNormal (MindlinPhys inherits again from FrictPhys) - Small changes to HM (I added the code for the moment rotation but using quaternions, work in progress to use the incremental formulation instead of that) - Add incremental formulation for the moment rotation (bending only) to HM law (it is very similar to the code for the shear part as written in ScGeom - it has been tested but feedbacks are welcome). PS Let me know if you are interested to have it also in "Law2_ScGeom6D_CohFrictPhys_CohesionMoment" where actually the total formulation is already present. @Bruno: maybe in ScGeom we could add this incremental formulation too? - Add relAngVel function to ScGeom (a similar version can be called from python as done for incidentVel) @Bruno: I would like to add the incremental formulation to CFLaw, how do you suggest to do that? Maybe I can use a bool something like (useIncrementalForm)? - Add the possibility to calculate bending and twisting moments using the incremental formulation in both CFLaw and HMLaw; - Add maximum elastic torsional moment in CFLaw (it should be computed using normal force, I will see how to compute it somehow); - Fix mistake in mindlin.py example script. - Add a seed parameter to makeCloud, particleSD and particleSD2 functions. The parameter is used to initialize the random number generator. - Add calculation of fabric tensor for periodic cell as according to Satake (bib is updated too). The tensor can also be spit into two different parts each of them related to strong and weak contact forces respectively. - Small changes in HM. - Calculation of fabric tensor takes care of the sign of normal force (I think this is the way to do it if we have cohesive forces but I will check again in the existing literature). Also the tensor can be split into two parts according to the mean contact force or a threshold value if this is going to be specified (thanks Vincent for suggestion). - Add a function to HMLaw which computes the ratio of sliding contacts. - Adjust the sign convention in the computation of the fabric tensor. Now the tensor can also be split into tensile and compressive part (simply setting the threshold value equal to 0 - added documentation about that). - Rename (for the fabric tensor function only) compressionPositive to revertSign (that is the meaning indeed - work in progress to use the scene flag and make automatic distinction whichever law is used). - Average stress tensor of periodic cell can also be spit into two contributions, given a threshold value (mean force by default). - Forgot the reference (sorry). Fix doc. - Add formulation for determination of time step for elastic spheres according to Rayleigh wave speed. Fix small bug in HM (only in case of viscous damping). - Wrap Eigen function to get eigenvalues and eigenvectors of a Matrix3r in py - Small fix in HM - For now, add 2d version of particleSD (discrete distribution) - for other type of distributions (like the one generated by makeCloud), something similar can be done. - Fix color map in shop (thanks Vaclav). - Fix bug in Periodic Boundary. scene->cell->prevVelGrad was never updated. It was equivalent to apply homoDeform=2 in place of homoDeform=3. (Thanks, Vaclav) - fix bug 1) as discussed in (https://answers.launchpad.net/yade/+question/169689) Donia Marzougui (1): - Add viscous shear force definition (disabled by default) (Donia+Bruno) Emanuele Catalano (19): - Retriangulation controlled by a volumetric deformation threshold - Substituted pkg-dem in pkg/dem (and similar) to included files - Removed #define flow_engine line from def_type, definition is moved to the scons profile - Reorganized debuggin' - Found and corrected a error in boundary creator - Changed names of .h files - new function for adding bounding planes - Update flow code. - Fixed compilation errors - Fluid velocity calculation takes into account of facets velocities - Update flow code - Update flow code - Correction on facet fluid/solid surfaces calculation - Fixed calculation of fluid velocity in cells - re-fix fluidArea correction (S0) by Donia - Fix error in Volume_cell function. - Fix retriangulation issue - Fixed two warnings in FlowEngine - Changed link to deprecated utils.encodeVideoFromFrames with utils.makeVideo (hope i did it properly, first time I modify docs) - Reordering new function for viscous force calculation - Added computation of average cell permeability for visualization - Removed correction on smallest permeabilities - Porosity computation neglects boundaries - New functions ImposeFlux() and GetFlux() for one-point fluid injection - FlowEngine does not depend on TriaxialCompressionEngine anymore - Clean of useless variables - Consolidation files writers move to python scripts (Flow functions MeasurePorePressure and MeasurePressureProfile do what is needed) - Removed superfluous variables - Fix segfault due to uninitialised normal to walls - Add function to measure slice-averaged pressure values Jan Stránský (5): Little changes in CpmStateUpdater 1. Changes in ConcretePM.cpp 2. added yade.ymport.unv function 3. added yade.export.VTKExporter class 4. added method outer to Vector3 in Python Small changes in yade.ymport.unv and corresponding example Change of CpmMat.relDuctility to CpmMat.crackOpening (making Cpm model more particle size independent) rotation of facets taken into account in yade.export.VTKExporter Janek Kozicki (10): plot.py: added `legendPosition` and `legendPositionSecondary` so we can decide where the legend should be placed, by default it is 'upper left' and 'upper right' Added yade.utils.voxelPorosity and yade.utils.voxelPorosityTriaxial. It allows calculating porosity at any arbitrary sub-volume of a whole sample. See included documentation. small documentation fix standalone example almost works. I still have some problem with sample randomness, and exact answers. Added another variation of simple scene - this one is for energy tracking added nice legend to the plots more flexibility, few more parameters on the top of the script. better default parameters, use dict(...) to read O.energy.items() last correction for simple scene energy tracking example - I forgot to commit changes in CohesiveFrictionalContactLaw but in fact maybe better if those methods for calculating elastic normal & shear energy would be moved somewhere else, maybe to shop? I'm not sure. fix warning, add plastic dissipation tracking Jerome Duriez (17): Details Fixes https://bugs.launchpad.net/yade/+bug/672473 (an error in the script finally...) Details changes in comments of Vector3r forcesOnPlane(..), after http://www.mail-archive.com/yade-users@lists.launchpad.net/msg02610.html. Hoping you agree, Vaclav (if not, do not hesitate to revert !) Few typos corrected in doc, and pack.py. Changes in "normalInelasticity" files suggested by http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg06011.html Fixes https://bugs.launchpad.net/yade/+bug/706937 Minor changes - typos in programmer doc - removal of useless backward compability in system.py - removal or english translations of comments in the three c++ files - some changes in normalInelasticity-test - add of a check version of this script - add of a sentence about these check tests in prog.rst - changes of deprecated function in tutorial scripts - typo in some other rst - add of a note about plot.plot in plot.py - beginning changes in SimpleShear preprocessor - initialization of many variables in Law2_Normal.... - relative difference considered in check test, instead of absolute one - add of some hyperlinks in doc - changes in scripts. At the moment I can run ~20 times the proposed checkTest without fails (did not make more than ~20). Fails occured when interaction disappeared. Wait however a bit... - still small changes in doc mainly - add of a "by" in doc - re let work the .py, modifiying definition of state.blockedDOFS - maintaining of SimpleShear FileGenerator - checkTestNormalInelasticity.py again among check tests. I launched it more than 20 times without crash here Let spheres of SimpleShear be wiser (reducing GSTS->defaultDt) - changes in simpleShear.py - correction of small error in doc (I think) Few changes in doc (sphinx and Sconstruct's one) after https://answers.launchpad.net/yade/+question/169042 - In Law2... add of a requestErase of the interactions with un<0, which was missing. Could help https://bugs.launchpad.net/yade/+bug/810056 ? Klaus Thoeni (11): New implementation of a particle model for wires and rockfall meshes (initial state) 1. Fixed problem in postLoad (regression tests should work now) 2. Add some examples for testing the new WirePM with 2 particles update scripts for the WireMatPM 1. implement packing for the WireMatPM 2. add some examples for the WireMatPM 1. correct affiliation in doc/sphinx/conf.py 2. derive WirePM from FrictMat 3. add value which indicates how far interactions are from normal failing (currently just used in WirePM) 1. move value which indicates how far interactions are from normal failing to WirePhys since only WirePM is using it 1. update WirePM scripts in scripts/test/WireMatPM 2. add a simple example for interaction of FrictMat and WireMat: examples/WireMatPM/wirecontacttest.py 1. add some more comments 1. add some more comments 2. correct some typos 1. fix problem (segmentation fault) for save/load simulations with WireMat 2. correct some typos 1. update scripts 2. add unbalancedForce to diagram in wirecontacttest.py Rémi Cailletaud (5): Added buildbot master.cfg file in scripts dir - removed log4cxx from build options beacause of wrong exit status (https://bugs.launchpad.net/yade/+bug/410250) buildbot now creates a source targz Build infrastructure : buildot script modified after an update of nagios probes modifiied buildbot configuration to fix tarball build Sergei Dorofeenko (15): fix Bug 672623; fix some examples merge with trunk 1.Add silent switcher to NozzleFactory; 2.Fix examples merge with trunk 1.Fix RotationEngine for new meaning non-dynamic bodies 2.Fix STLImporter 3.!!! Set aspherical=False for a facets. Need more consideration. 4.!!! blockedDOFs for leapfrogAsphericalRotate need more consideration. fix bug [Bug 692452] 1. ViscoelasticPM: release from prevNormal; 2.Small fixes merge with trunk 1. Rename NozzleFactory to SpheresFactory; add derived CircularFactory and QuadroFactory. Example is scripts/test/spheresFactory.py 2. small fixes fix examples 1. Rename QuadroFactory to BoxFactory; some fixing SpheresFactory 2. Rename facet->nf to facet->normal; access to the facet's normal from python 3. Fix examples typo fix and more typo fix fix bug #721107 1.Add utils.trackPerfomance; 2.Small fix Unknown (2): Modify CohFrict* classes as discussed with Bruno on the list. 1. Move alphas parameters to FrictMat as discussed with Bruno (harmonic-average of them is introduced in Ip2 functor). 2. Forgot one inequality when plasticity is applied (maybe I do not like tests so much :-) Sorry, anyway). Václav Šmilauer (75): 1. Fix Clump compilation in debug mode small fixes in scons 1. Replace includes {lib,pkg}-* with {lib,pkg}/*; compiles (no full compilation tested) 1. Implement an initial version of generating loose clump packings of predefined configuration with SpherePack (TODO: do not recompute clump properties when adding them using toSimulation for each of them separately, but use those precomputed on given configurations). See scripts/test/clumpPack.py 2. Make selection of clump member highlight the whole clump in OpenGL 2. Add Dong2010 article to articles done with yade (authors contacted for fulltext) 1. Fix particle highlighting bug introduced lastly 2. Enhance the SpherePack.makeClumpCloud routine to be much more efficient (uses bounding spheres) 3. Add Ig2_Wall_Sphere_ScGeom 4. Enhance scripts/test/clumpPack.py Some experiments with cmake 1. Add optional MatchMaker to Ip2_FrictMat_FrictMat_FrictPhys to decide how to compute contact friction angle. 1. Fix include paths pkg-common to pkg/common etc, merge other changes. 1. Allow O.engines to be modified inside the loop from python 2. Fix include dir creation (thanks, buildbot) 3. Fix Ip2_FrictMat_FrictMat_FrictPhys failure (inversed conditional) 4. Add tests for substepping, modification of O.engines and Engine.dead 5. Remove O.initializers 1. Add energy tracking to GravityEngine, NewtonIntegrator, PeriIsoCompressor (the last one not tested yet) 2. Update scripts/test/energy.py 3. DISABLE cohesive-chain test, since it was already broken by previous Bruno's commits 1. Add detailed docs for plot.saveDataTxt 2. Do not add dissipated energy if zero in Law2_ScGeom_FrictPhys_CundallStrack 3. Set friction to zero in scripts/test/energy.py 1. Do not enable draggable legent if not supported by matplotlib (thansk, buildbot) 1. Fix erroneous assert in the integrator (energy & clumps) 2. Fix bug in distance computation in SpherePack.makeClumpCloud 3. Make scripts/test/energy.py use clumps (and no friction) to have rotations, as Bruno suggested. 1. Fix chunkSize=1 builds (bug introduced by changing include paths) 2. Add octree visualization engine (for debugging clump computation) 3. Make editor of sequence of serializables resize more intelligently 1. Simplify InteractionContainer, move interactions inside bodies (NOT useful for getting all interactions of a body) 2. Advance with cmake a little bit (nothing functional yet) 3. Remove YADE_REQUIRE_FEATURE, use plain #ifdefs instead (empty files will be compiled, oh well) 4. Remove a few files that were apparently not compiled for a very long time. 1. Fix compilation pb with cgal (sorry, cgal does not compile with clang, so does not get much coverage from me). Thanks to Ema for reporting. 1. Initial subdomain support, which includes NewtonIntegrator, GravityEngine, InteractionLoop; new SubdomainOptimizer to put bodies to subdomains. 1. SubdomainOptimizer now splits domain and adjusts later so that there is similar number of particles in all domains 2. Add --cores option, defining CPU affinity; based on some tests, it actually hurts performance... :-| 3. #define likely/unlikely (like in Linux kernel) and use it in a few conditions in loops to help the compiler 4. Fix a strainge numerical "bug" in InsertionSortCollider where the same id has inversion with itself (min>max?) 5. Add pack.inParallelepiped predicate (not yet tested) 6. pack.filterSpherePack now returns SpherePack (the other routines are still to be made consistent...) -- see https://lists.launchpad.net/yade-users/msg03887.html 1. Backport doc generation crash (picked from subdomains) Remove extra asserts to make Anton happier (sorry, forgotten stuff) 1. Add timing statistics to yade-batch 2. Make cmake closer to functional build 3. Fix xmlrpc error in the window between job start and xmlrpc-readiness 4. Add a few options to batch, make cpu affinity optional 5. Add subdomain mask to OpenGLRenderer 6. add unlikely to some conditionals in loops 1. Fix requestErase of erased interaction (thanks to Anton for reporting) Fix INteractionContainer bug, enhance the timing table for batch. 1. Assume cache line size 64 bytes in OpenMPAccumulator, if sysconf reports zero (should fix startup FPU exception reported by Giulia) 1. Merge the subdomain branch, enable subdomains feature to enable 2. Delete some obsolete code in scons 1. Add access to clump member from python 2. Fix Clump i/o (clumpId was not saved) 3. Rename regular-sphere-pack to packs 4. Fix a few bugs (thanks, Anton) 5. Fix SubdomainOptimizer behavior in some corner cases 6. Add some checks to qt4 1. Fix L3Geom, add Sphere+Wall interactions, plus some benchmark scripts 2. Add NewtonIntegrator.kinSplit, to track translational and rotational energy separately 3. Add --randomize option to batch, for running jobs in arbitrary order 4. Make Body::setDynamic() (un)block State.blockedDOFs (for future compat) 5. Add Serializable::cast static casting method 6. Several fixes in utils, plot etc 1. Add MatchMaker(Real) ctor 2. Adjust timing report format for batch (precision) 1. Fixes in L3Geom, L6Geom & friends 2. Add scripts/test/beam-l6geom.py to demonstrate L6Geom 3. Fix LawTester so that ti works with all 6 dofs reliably now 1. Add Gl1_L6Geom, and a few params to Gl1_L3Geom as well 2. Add movie to scripts/test/beam-l6geom.py 1. Remove some obsolete files, update INSTALL and NEWS 2. Make qt._GLViewer properly documented with sphinx Fix compilation error introduced lastly, sorry. 1. yade-batch can run a single job (without parameter table) 2. Avoid some exceptions in plot 1. Make the i/o regression test quiet by adding quiet flag to saveTmp/loadTmp 2. Facet has NaN vertices by default, and Facet.postLoad returns without warning in such case 3. LawTester now has most data as Vector6r instead of 2xVector3r. The syntax changed (backwards-compat with warnings, sorry), path should be disPath, ptOurs, ptGeom, rotOurs, rotGeom is now in uGeom and uTest 4. Add Vector6.head() and Vector6.tail() to return first/second triplet as Vector3 in python (corresponds to start<3>() and end<3>() in eigen2 and head<3>()/tail<3>() in eigen3) 5. Make the qt4 interface display Vector6 properly 1. Fix batch script (thanks, Anton) 2. Fix MatchMaker docscring format 1. Add support for ScGeom6D to LawTester (not tested...) 1. Fix orientation of rotations for ScGeom6D in LawTester 1. Remove Body::flags/FLAG_DYNAMIC, setDynamic now merely sets state->blockedDOFs=State::DOF_ALL etc. 2. Remove some deprecated code chunks 1. Add documentation for Ig2_Sphere_Sphere_L3Geom_Inc 2. Add regression tests for PBC & L3Geom 3. Fix syntax in other docs as necessary 1. Add docs for LawTester, and fix docs elsewhere as well. 1. remove devirt-functors (unused) 2. rename SubdomainOptimizer to SubdomainBalancer 3. remove Dem3DofGeom::scaleDisplacementT (unused) 4. remove Law2_ScGeom_CpmPhys_Cpm (malfunctioning, unused) 5. remove SConscript-mono (unused) 1. Fix NewtonIntegrator (not skipping particles with all DOFs blocked) 2. Disable Translation/RotationEngine tests, non-dynamic bodies changed their meaning and the tests fail. 1. Make batch accept multiple scripts on the command line (see --help) 2. Change syntax for blockedDOFs to be 'xyZ' rather than ['x','y','rz'] (assigning is backwards-compatible with warning) 3. Remove rests of devirt-functors; I thought I've done it already... 1. Create abstract KinematicEngine, allow kinematic engine composition with + (thanks to Jan for suggesting that) 2. Move all KinematicEngine's to pkg/common/KinematicEngines.{hpp,cpp} 3. Change accels in GLViewer so that x,X,y,Y,z,Z make rhe respective axis point upwards etc 4. Change g/G to enable/disable grid (or selectively enable if pressed multiple times) 5. Remove button images in the qt4 ui, use unicode symbols instead 6. Make batch referesh once in 30s by default instead of 5s to avoid congestion on slow uplinks 1. Add forgotten KinematicEngines.{c,h}pp files 2. Remove GroupRelationData & mgpost (is now at https://code.launchpad.net/~yade-dev/yade/mgpost) 1. Fix accidental typo, sorry... 1. Make middle-click paste path to variable in the ui 2. Clean up newton integrator; aspherical integration not called for things with 0 in inertia to avoid nans; this also fixed the problem of inverted normal with Wall 1. Fix NewtonIntegrator for clumps, blockedDOFs &c; msg will be sent to yade-dev 2. Make static attributes properly hyperlinked and documented in the ui 3. Fix yref in L3Geom 1. Clean up NewtonIntegrator following the discussion on the list; adds 1st order damping for aspherical particles; comments welcome. 2. Add Body.intrs() in python 1. Fix an error in Law2_L3Geom_FrictPhys_ElPerfPl (forces were applied at the step the interaction broke); results are now identical to ScGeom/CundallStrack (in the normal sense at least) 2. Add the possibility to specify y-data as functions returning y-data names themselves (see scripts/tests/energy.py) 3. Merge 2 consecutive loops in NewtonIntegrator for clumps 4. Rename plot.legendPosition, plot.legendPositionSecondary to plot.legendLoc (tuple of 2 values), to make it consistent with matplotlib terminology (pylab.legend(...,loc=...)) 1. utils.{sphere,facet,wall} funcs take fixed=True|False now (instead of dynamic=False|True, which gives warning now and will be removed) 2. Make space in the 3d recenter scene 3. x,y,z (X,Y,Z) now set up axis (see help of the 3d), grid is toggled with g only 4. Remove Shop::defaults and few other obsolete funcs 5. Fix bug in torsionweighting in LawTester 6. Rename Ig2_*_L3Geom_Inc to Ig2_*_L3Geom, update .py scripts 7. Rationalize Ig2_*_L3Geom functors, add Sphere+Facet 1. Add some data so that Hertz-Mindlin will work with L3Geom 2. Automatically compute "mass" of cell in PeriTriaxController, if not setFocus 3. Fix auto-plotting of energies in case the simulation is reloaded 4. Fix middle-click on attributes in inspector 1. set color_cycle in matplotlib only when it is supported (fixes test failure) 1. Fix i386 (?) live plot issue 1. Add function checking argument types inside FUNCTOR1D and FUNCTOR2D (requires to include full dispatched type definition in headers) 2. Reorganize the integrator so that its logic is understandable. Functionality not changed. 3. Move most clump code from integrator to clump methods 4. Automtically used InsertionSortCollider::verletDist if possible (used to be sweepLength) 5. Add --refresh param to batch, controlling refresh rate of web summary, logs etc (30s by default) 6. Fix gnuplot export with callable data specifiers 7. Put BodyCallback in #ifdef, since buggy; will be removed shortly, unless gets fixed. 8. Fix unbalanced force computation for clumps. 9. Remove accel and angAccel from state, since it is only used locally in the integrator. Add missing includes, thanks to Klaus for reporting. 1. Better integration of NewtonIntegrator into Clump, avoiding linking cycle with chunkSize=1 1. Fix State.rot() mistake (was returning displacement instead) 2. Add qt.SnapshoeEngine.plot for adding snapshot name to plot.imgData automatically 3. Add plot.savePlotSequence for making movies with plots 4. Rename utils.makeVideo bps to kbps (is really kb/s, not b/s) 5. Rename OpenGLRenderer.displayGhosts to ghosts (shorter, sufficient -- sorry, Bruno) Fix cache line size in OpenMPArrayAccumulator 1. Unbreak the periodic cell. Add the dresden course to sphinx docs. 1. Add a more straightforward SpherePack.ParticleSD2 method, adjust the tutorial 1. Add scene flags about local coordinate systems and force sign convention (not yet used) 2. Fix many things around L3Geom (most importantly, re-normalization was never done, resulting in instabilities), merge code for different particle shapes in a general function handleSpheresLikeContact 3. Fix incorrect import of gts surface due to LC_NUMERIC 4. Add OpenGL-related stuff to yade-support, which might fix linking issues with natty 5. Move Cell::invTrsf and Cell::refSize to private part, so that it 1. Make yade and yade-batch run single-threaded simulations 2. Add warning when specifying -j/--threads/--cores when lacking OpenMP support 1. Change Cell behavior as explained on the list -- trsf can be changed freely, without side-effects; assigning refSize is deprecated (use new O.cell.setBox(...) function for that) 2. SpherePack.toSimulation sets identity transformation, but rotated hSize (if requested) 3. PeriTriaxController uses norms of hSize columns (with inverse transformaiton) as reference lengths ;; TODO (?): it should check that hSize is diagonal, otherwise it will probably behave erroneously 1. Revert some "cleanups" in Cell (LOL, Bruno, we are overwriting each other's work again :-)) 2. Add some regression tests of PBC 3. Make plot.addData aceept vectors and matrices, creating columns for individual components 4. Make compilation of SpherePadder only optional (feature sphere-padder) 1. Add plot.autoAddData with docs. A limitation is that "=" should not be in names of data columns anymore. 2. Add Strong/weak fabric distinction to Gl1_NormPhys (not tested) 3. Degrade VelocityBin's initialization message to debug 4. Add .items() method to EnergyTracker, for fast conversion to list of tuples. 1. Fix plots with line specifiers 2. Fix peri-triax example (sweepDist->verletDist) 1. An attempt to fix OpenMPArrayAccumulator initialization (not tested) 1. Update affiliation 1. Fix OpenMPArrayAccumulator initial zeroing, re-enable plot test 2. Add Matrix3 ctor from Quaternion and vice versa in Python 3. Fix some bugs in L3Geom initial axes orientation 4. Plots now display pointed triangles instead of circles to mark current position (and orientation); plot part after the current point is transparent Nicer fix for 721107 (should work) oops, sorry 1. Invalidate persistent collider data when interactions are cleared (not tested yet) 2. Add renderer pointer to scene, so that functors can find display attributes 3. Gl1_NormPhys honors displacement scaling now 4. Fix scalarOnColorScale bug 5. Add RadialForceEngine, fix AxialGravityEngine fix error in last commit ================================================== yade-0.60.0 Sun, Nov 7 09:55:43 2010 +0100 Anton Gladky (54): 1. utils.facetCylinder and utils.facetBox orientations are changed according to https://lists.launchpad.net/yade-dev/msg04886.html 1. Orientation in ymport module is changed according to https://lists.launchpad.net/yade-dev/msg04886.html 1. Some small fixes 1. Docs small modifications 1. Some bibtex references added from WIKI 1. Some references into bibtex-format migration 1. Moving references to bibtex format is finished. 1. Engine for particle size distribution analyzes is added. (not finished) 1. Engine for PSD-analyze is finished, need testing. 1. Added forgotten include, caused a compilation errorin 2331 1. Changed warning message in case, when installer cant find libraries. http://www.mail-archive.com/yade-users@lists.launchpad.net/msg02202.html 2. Installation instructions were moved from Wiki to Sphinx Documentation. regular-sphere-pack.py fix. It works again. 1. Comments to ParticleSizeDistrbutionRPMRecorder are added. 1. RockPM update. RockPM fix 1. Recorder has new feature "addIterNum" which adds Iteration number to the end of file name. Off by default. 2. Clean ParticleSizeDistrbutionRPMRecorder Fix compillation error Packages names needed for qt4 are added to 'installation' section of documentation. 1. Analyze of specimen diametr is added to PSD engine. VTK and Rock were updated relatively. 1. Added materialId analyze to PSD-engine 2. Changed chmod of CohesiveFrictionalPM 1. Some modifications in PSD-recorder for material analyze 1. Added updating volume specimen variable in rpmState 1. Small but necessary fix One more field added to PSD engine 1. 626409 fix. Thanks to Sergei for spotting that. 1. Fix export.textExt function according to http://www.mail-archive.com/yade-users@lists.launchpad.net/msg02413.html Fix compilation warning in SpherePack::particleSD 1. Fixes issue, described in http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg05009.html 1. Some changes for compilation in Fedora 1. One more fix for compiling in Fedora 1. Some small fixes in debian/ 2. Warning fixes in shop.cpp 1. debian-prep now can accept RELEASE file without version number to create yade-bzr version 1. Changed required version of python-sphinx in debian/control-template to make the trunk builded in Maverick. 1. Fixed wrong MaxDiam determinition, when specimen consists on 1 particle. 2. Added maxX, maxY and maxZ parameter into outputed psd-file for geometry analyze. 1. chunkSize is changed in debian/rules from 2 to 1 1. Fixes an issue, indicated here http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg05162.html ; combined-files in SConstruct during Debian build. 1. Changes in debian/rules due to new conception of debug-build http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg05182.html 1. Changes in debian/rules http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg05185.html 1. scripts/debian now takes the name of person from DEBFULLNAME and DEBEMAIL environment varaibles. 1. Added initial scripts/build-fabric 2. scripts/debian-prep now smoothly handles absenting DEBEMAIL and DBFULLNAME variables 1. build-fabric now builds packages for maverick and lucid for 2 platforms "automatically" Fixed an error in debian-prep 1. build-bot with the main functionality is reasy for testing. 1. Yade menu should appear in respective sections in main menu in Debian-based systems (not tested yet) 2. build-farm should build packages without root priveleges 1. Returning "sudo " to build-farm 1. Command-line parameters are added to build-farm script 1. Fixed pixmap copying in debian/rules 1. Warning blocked in DomainLimiter.cpp:63 1. Some notes on Eigen3 migration 1. Eigen3 compiles now (seems). Vaclav, sorry, I needed to change your template, because it gave an error on Eigen3. 1. Again some changes for Eigen3 compilation 1. Yade now compiles with Eigen3 and with OpenGL feature enabled 1. In PSD-engine wrong maxX, ..Y and ..Z calculation fixed 0.60.0 Bruno Chareyre (45): Local sphinx build : I made it! :) Fixing the command in readme. - give path more clearly, the previous commit was assuming same relative path as mine. revert yade path - Add files for kdev4. - Fix ambiguities in contact geometry and time-step parts. - Add stress getter and python wrapper (replacing reverted r2314). - Add definition of work input from boundaries (resp. macro strain) in TriaxialStressController (resp. PeriTriaxController). - Remove useless spheresVolume (redundant with TriaxialStressController::spheresVolume) - Some cleaning in ScGeom. - Implement precomputed quantities (#define IGCACHE for compiling them). - Experiment precomputation with ElasticContactLaw (#ifdef IGCACHE), other laws should not be impacted yet whatever IGCACHE. - Make authors consistent (Galizzi never touched ElasticContactLaw). - Remove some debugging/commented code left in 2336, sorry. - Update authors again (forgot to "save" before commit...) - More changes in stability section. (we need PFC manual in bibtex references...) - More small fixes. - miniEigen : memory leak source suspected (FIXME added) - ScGeom : #define IGCACHE by default, and keep behaviour unchanged for older functions (still some cleaning to do in this class, after all Law2's have been adapted). - CohFrictLaw : Eigen is returning nan quaternions after trivial operations, it is workarounded in the law. - cylinder : a new shape, first step in experiments for tracking interactions jumping over chained elements. - utils.py : a demo script for chained cylinders - make the example more fun. - Revert last doc change and fix the original. (please don't modify documentation if you are not sure. I can't double-check all commits.) - Implement the distinction between node orientation (integrated in Newton) and beam orientation (always oriented as line between adjacent node). It fixes the starcases appearing in display for large stretch. - Fix path to fulltext. - restore Gl1_ChainedCylinder - kdev4 : I failoed to commit this file apparently. - Cylinder, update contact point consistently with current segment definition. - Fix the poisson=0 case (was returning undefined Ks for division by 0...) - This commit enables wire-like behaviour without moment when ks=0 - Last change in contact plane makes script unstable. Restore stable (but wrong?...) equations. - Cylinder : fix segment orientation, use correct contact point, and clean code. - ScGeom : last step before removing old code, some functors adapted (others are using even older duplicated code apparently) - Small sphinx fixes. - Use precomputed geometry everywhere in functors and remove older code. - Make Dem3DofGeom inherit from ScGeom rather than GenericSphereContact and remove (comment) the latest. - Missing in last commit sorry. - Revert r2365 as a whole (and r2367). - All changes in ScGeom and related functors will be commited again when I have time. - restore virgin yade.kdev4 and add kdev files to bzrignore. - publications update. Restore the part of r2367 concerning ScGeom (+ some more improvments). - restore project file for kdevelop3. -Update functor->momentLaw in the global engine. - More documention in the 2 constitutive laws. - Some code cleaning and test redundancy fix in CohFrictPhys.cpp+CohesiveFrictionalContactLaw.cpp. - adds references cited in the previous commit. - Include a comment on "welltestedness" of ElasticContactLaw. - rename classes : Law2_ScGeom_CohFrictPhys_ElasticPlastic -> Law2_ScGeom_CohFrictPhys_CohesionMoment Law2_Dem3DofGeom_FrictPhys_Basic -> Law2_Dem3DofGeom_FrictPhys_CundallStrack Law2_ScGeom_FrictPhys_Basic -> Law2_ScGeom_FrictPhys_CundallStrack - remove useless attributes, - fix class name in TTest. - Add new IG class ScGeom6D precomputing relative rotations, and associated Ig functors. - Update related classes (CFLaw) - add kdev4 configuration for starting debug from kdevelop -Includes a regression test on dynamic beam flexion. -Move cohesion and moment parameters from functors to bodies and interactions, and define them in Ip2_2xCohFrictMat_... - Fix cylinder reg. test with respect to r2509(2510). - Add output for nan quaternion products #ifdef Q_DEBUG. - Document some flags in Ip2_2xCohFrictMat_CohFrictPhys.hpp. - more debug info for quaternions with nan angle. - Convert ScGeom to ScGeom6D in Ig2_Sphere_Sphere_ScGeom6D::go(), using ScGeom::operator= - Optimize distance check for existing interactions in Ig2_Sphere_Sphere_ScGeom::go() - Implement Ig2_Box_Sphere_ScGeom6D (same conversion to ScGeom6D) - Adapt CohesiveTriaxialTest. - Fix a typo (and test some launchpad+bazar logging feature...) - Add python wrapping for python use of TesselationWrapper (+ a few fixes and formating) - add example commands in docstring. - Remove scene pointer from TW function parameters - sphere-cylinder Ig2 functor (some old uncommited code - still bugged) - TW : really check if body geometry is sphere in the insertion loop (instead of isDynamic). - FE : use the faster insert(begin,end) from TW for triangulation, and move area/volume definition to addBoundary(). Chiara Modenese (22): 1) Add contact damping into HM law. 2) Add functions getIncidentVel (both for periodic and non-periodic case) and rotateShear to ScGeom. 3) Add py script to demonstrate and test the effect of contact damping. Rename rotateShear() to rotate() in ScGeom. 1. Add Engine::dead attribute; if set, the engine will not be run at all (unless explicitly called via () from python or ::action from c++). Useful for temporarily (de)activating engines without having to modify O.engines 2. PeriodicPythonRunner renamed to PyRunner as it is used so often. 3. Add Cell.getVolume() and utils.porosity 4. Check for force&torque NaNs in NewtonIntegrator in debug builds 5. Add --rebuild option which will launch scons before running the simulation itself 6. Some fixes in the HertzMindlin law 7. The qt4 interface will try to open packaged docs, then docs in the source dir and online docs as the last resort. 8. Some fixes in PeriTriaxController (the servo-mechanism) and probably a bug fix in TriaxialStressController (will ask Bruno on the list to confirm the correctness) 1. Add an alternative implementation of PSD-based particle generation; likely to be merged to makeCloud in the future (micro-fix for a spurious startup message) 1. Improved summary http page for yade-multi, includes (clickable) plots and hyperlink to the log (with auth cookie removed) 2. Deprecate PartialEngine::subsribedBodies in favor of ids 3. Remove triangulation lib from ctags dirs (so that tag Facet goes to yade::Facet) 4. The qt controller computes simulation speed locally now 5. Fixes in Hertz-Mindlin 6. Add an alternative SpherePack::particleSD function 7. Make axis labels, highlighted axes etc settable in yade.plot 8. Add yade.plot.saveDataTxt 9. Fix plot names with spaces (so that multiple plots with the same x-axis can be specified) 1. The mindlin law now prevents granular ratcheting by default. 2. Ig2_Sphere_Sphere_ScGeom has now avoidGranularRatcheting bool (true by default, which was the hardcoded value till now as well); add documentation from the source to the real doc, add a few references on that. 3. SpherePack no longer saves vectors as tuples; this also fixes memoization issues with pack.random{Dense,Peri}Pack 4. Add Law2_ScGeom_MindlinPhys_HertzWithLinearShear used for testing differences between linear and non-linear law. (Antons changes) 1. angleRange parameter is added to facetCylinder to create "semi-cylinders", "quarter-cylinders" etc. 2. Prepare Sconstruct for compiling in Fedora (partly) 1. Rename yade-multi to yade-batch; documentation updated 2. Make batch save plots when all jobs are done 3. Add tags d.id and id.d (description and id put together) 1. Re-apply removal of Mathr, sorry Anton, the fault was local. 1. Avoid adding useless lines of nans in plot for unknown variables, add only their column instead 2. Save job figure as soon as the job finishes in the batch 3. Fi O.tags['id.d'] and O.tags['d.id'] tag order 1. Make batch commands clickable; fix encoding issues when the batch page sends job script/table 2. add utils.maxOverlapRatio for sphere-sphere contacts 3. add reinitialization counter to InsertionSortCollider 4. Add VTKRecorder.ascii so that saved XML data might be human-readable (false by default) 1. Resurrect SnapshotEngine 2. Add Gl1_NormPhys for displaying interaction network (http://beta.arcig.cz/~eudoxos/temp/Gl1_NormPhys.avi) 3. Make VTKRecroder work nicely with periodic boundary conditions (repeating interaction on both sides if it crosses the cell boundary using a few hacks) 4. Add Shop::normalShearStressTensors for computing (once more) stress tensor, but normal and shear contributions separately 5. Allow specify particle counts for SpherePack.particleSD 6. utils.makeVideo now uses mencoder (and works, unlike the older gstreamer-based thing, which would not work anymore) 7. Add Matrix3.diagonal() 8. Integrate regression tests suite in the main program (yade --test) 9. Set plot.scientific==True only if the version of pylab installed supports it (thanks to Anton for reporting) 1. Add scripts/test/force-network-video.py 2. Rename attribute flags (Attr::readonly, Attr::triggerPostLoad etc) 3. Detect whether display is available and store it in yade.runtime.hasDisplay (false by default); that restores the behavior of yade.qt, which raises ImportError at no display, and makes yade.plot consistent with tha variable as well 4. Fix total running time for batches 5. Do not send 0 refresh for finished job files (refreshes as frequently as possible, whereas no refresh was desired) 6. Debian package depends on mencoder now 7. qt.SnapshotEngine open the view automatically if needed (not very reliable, though) 8. Add scripts/test/force-network-video.py 9. Fixes in the OpenGLRenderer that avoid crashes; drawWithNames should draw shapes in the same place as draw witout names, making the selection consistent with what is seen (periodic boundaries etc) 10. Move {ScGeom,Dem3DofGeom}::contactPoint to GenericSpheresContact 11. Initial (not yet functional) implementation of the partial slip solution for Hertz-Mindlin (Mindlin-Deresiewitz) 1. Introduce a class for returning or computing scalar values based on combination of 2 ids. [experimental, don't use or ask questions about it now] 1. Rename InteractionDispatchers to InteractionLoop; backwards-compat for python as usual, typedef with deprecated warning in c++; update all scripts and docs to reflect that. 2. Add NozzleFactory, which might be in the future generalized to a generic factory object and a numebr of derived classes with different parameters (such as factory area shape, specification of sphere parameters etc); see scripts/test/shots.py 3. Fix many crashers in the OpenGL code; unbreak particle selection 4. Finalize the MatchMaker class, with convertor from python floats to specify fixed value. 5. MatchMaker is used to specify different coefficients of restitution for different material couples in Ip2_FrictMat_FrictMat_MindlinPhys; viscous constants moved away from Law2_ScGeom_MindlinPhys_Mindlin into MindlinPhys instead. 6. Fix compilation errors caused by unintelligedn 3rd-party Combine builder to scons -- save sombined files to an external file, force refresh of all combined files if the md5 changes. Does not increase compilation time. 7. Add DomainLimiter engine for deleting particles that go ouside some domain (see scripts/test/shots.py) 8. Add DragForceApplier (not yet tested); thans to Stefano for the suggestion. 1. Add #pragma once to MatchMaker (thanks, Remi) 2. Remove a few useless scripts. 1. Make the debug build installed in the same directory as the release build; it is compiled with debug=1 (or True); there is only a single yade executable for both, and the debug plugins are loaded with --debug. I tried to adjust packaging rules a bit, I hope it will not introduce additional errors. --debug and --rebuild work fine together. 2. Add --debug option to yade-batch, which runs yade with --debug. 1. Add LawTester class for prescribing displacements on interactions precisely, see scripts/test/law-test.py 2. plot now displays the last point as a bullet 3. Rename Interaction{Geometry,Physics} to I{Geom,Phys}; rename related classes as well (functors etc) 4. Rename Interaction::interaction{Geometry,Physics} to Interaction::{geom,phys} 5. Add Vector3.normalized() to the eigen wrapper 6. Add framework for arbitrary rendering hooks (GLDrawExtra) run from OpenGLRenderer at the end of the rendering routine (not yet fully tested) 1. Do not return Attr::hidden attributes in dict(); that makes them invisible in the UI as well. 1. Fix batch script with debug builds, thanks to Anton for reporting. 1. Fix a few malformed formulas (my bad) so that LaTeX does not choke on them. Emanuele Catalano (12): - Wide code maintainance - Removed isSuperior/Inferior/Lateral attribute, inside/fictious remain, Localize function removed - FlowEngine is able to receive as input boundary conditions (flow/pressure) to be applied to walls - Oedometer test can be performed via python scripting - A new force calculation scheme (facet scheme) had been implemented - Forgot def_types.h in previous commit (sorry Tieng!) - Added function to compute average cell velocity - Added function to apply sinusoidal external fluid pressures - Solved retriangulation problems in seabed simulations - Code maintenance - Solved compilation errors - Added average_cell and average_grain velocity computation - Updated vtk_file creator function - Moved functions and variables related to geometry in Network.cpp/.h - Update other files to these changes - Code maintenance - Commented flow_engine definition, sorry Sergei - Really solved compilation problem with 'cgal' feature, sorry again - Update flowEngine files - Added missing #ifdef FlowEngine condition - Fixed compilation error Jan Stránský (3): 1. add function yade.utils.stressTensorOfPeriodicCell 2. removed BoundDispatcher from pack.randomDensePack 1. correct some misprints and do some actualization in user's manual. 2. correct mistakes in Shop::stressTensorOfPeriodicCell() 1. modification of Vector6 2. change of Peri3dController (+docs and examples) Janek Kozicki (11): making TriaxialStressController more python friendly. revert last commit fix two typos, replace Real strain[3] with Vector3r strain fix two small typos in docs, add spheresVolume python wrapper for TriaxialStressController. (I need it to calculate void_ratio=voids/sphresVolume) Sphinx documentation for plotting + color plotting. Added missing comment in TriaxialCompressionEngine Let TriaxialStressController calculate sphereVolume for clumps correctly. A trivial fix for exceptions when drawing data that is being modified right now refer to matplotlib manual remove duplicated part about pyplot Added pdf figs (not .svg, they are 5MB big!). added info about TeX usage of plot.labels. small fixes Added a throw condition if two spheres have zero distance. Works in #ifdef YADE_DEBUG only. Jerome Duriez (7): - Re-write of SimpleShear PreProcessor with YADE_CLASS_... macro - Creation of KinemSimpleShearBox, new class containing the features common to the various Kinem...Engines, and from which these Engines inherit now. - Replace of .isDynamic (deprecated) by .dynamic in some python scripts - the script simpleShear.py (renamed from SimpleShear.py) allows now to illustrate/test the various Kinem...Engines - Documentation typos/formatting in few files Few modifications in the doc of NormalInelasticityLaw (class Law2_ScGeom_NormalInelasticityPhys_NormalInelasticity), following the request done http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg05207.html. Not sure it is perfect, but hope it is at least better... Re-write of "NormalInelasticityLaw" with use of ScGeom6D for what concerns rotations. => Rename of the corresponding Law2... Luc Scholtes (1): publication list update Sergei Dorofeenko (6): Viscoelastic basic particle model: move mass of particles from material to interaction Fix bug666246. See https://bugs.launchpad.net/yade/+bug/666246 merge with trunk Fix STLImporter; fix some examples 1. Fix ViscElBasic law to handle periodicity; 2. Add some regression tests Fix bug in Ip2_ViscElMat_ViscElMat_ViscElPhys Václav Šmilauer (88): 1. Docs update 2. Remove Dispatcher::add(string) (only accept functor objects instead) 1. Update documentation (backported to 0.50) 2. Remove the long deprecated object['attribute'] syntax. 1. Update docs 2. add some yade publications in bibtex 1. Port packaging changes from the 0.50 branch 1. Remove dem6dof related classes 2. add a few more publications to the bibtex db 1. Remove old io code in Omega 2. Update yade.eudoxos 3. Fix bug in pack.randomDensePack loading memoized scaled periodic packing from (backported to 0.50 as well) 1. Fix some spiral projection functions 2. Add manpage generation to yade and yade-multi 3. Add manpages to debian packaging, including alternatives (man yade -> man yade-bzr2284 etc) 1. Bugs in Cell (!!! no yet fixed: see scripts/test/peri8.py !!!) 2. Add optional devirtualized functors (experimental) 3. Adjust Peri3dController for large strains and test (modulo the cell bug) 4. doc fixes 1. Fix multiple authors syntax in bibtex (multiple authors MUST be separated by "and", not by comma!!!) 2. Add doctests of all modules, fix where failing 3. Add SpherePack.toSimulation Minor documentation fixes. 1. Split publications in articles, conferences, theses 2. Fix problem with scons 2.0, now it works out of the box 3. Add a better error message for VelocityBins with NaN velocity 1. Add show Paraview documentation to the postprocessing section 2. Fix at least partially the rotated cell bug in shift2 (https://bugs.launchpad.net/yade/+bug/601866), still some issues elsewhere, though. 1. Fix stale potential interactions -- we've been dragging this bug since april, I will backport it to 0.50. You are strongly recommended to update!!! The bug was, in the end, not in the collider, but in the container; it had <= instead of >= in one condition. Sorry. Fix Facet AABB computation in periodic scenes (another important update!) 1. LIVE PLOTTING (thanks to Janek for the idea and the suggestion of mtTkinter). Report bugs. 1. Fix InteractionGeometryDispatcher (in case someone still uses it). 1. Move triaxial documentation from the wiki to sphinx 1. Make utils.saveVars, utils.loadVars and utils.readParamsFromTable synthesize modules in yade.params.* to avoid name clashes in builtins (see docs and user's manual, you have to adapt your code if you use those) 2. Rewrite the installation page in sphinx (sorry, Anton, I hope it is a little more readable now) 3. Fix several undefined xrefs in the docs. 4. Disable wm3-compatibility in eigen wrapper (Vector3.UNIT_X etc) 5. Rename utils.chCylinder to utils.chainedCylinder, update docs there (sorry, Bruno, but chCylinder is really not a self-explanatory name) 1. Fix dispatch-torture scripts/test/dispatcher-torture.py 2. Remove wm3-compat code 3. Escape \d in the doc (must be \\d in c literals) 1. Make GL dispatchers proper classes exposed to python 2. Make State and derived classes indexable 3. Update scripts/test/dispatcher-torture.py 1. Fix compilation error due to free-standing function out (remember: NO FREE FUNCTIONS, everything must be inside classes, otherwise there is the risk of name clashes.) 1. Fix the GL dispatch (was enumerating child classes non-recursively, and your Gl1_ChainedCylinder did not inherit directly from GlShapeFunctor) 2. Do not use '|||' to separate plot axes, use None instead (||| is deprecated) 3. Move the Gl1_ChainedCylinder functor inside #ifdef YADE_OPENGL (please pay attention to that) 1. Add noqt3 feature (still keeps OpenGL available), run qt4 app at the beginning (emits warning) 2. Make GLUtils independent of QGLViewer 3. Add some metadata to attribute docstrings 4. Add scripts to render scene to pyQGLViewer and to show basic serialization interface in PyQt4. 5. Make static attributes non-static in python (enables docstrings) 1. Make static attributes documented (xrefs still not working, though) 2. Add section on the Material-State association to the Programmer's manual 3. Fix syntax error in qt4-attributes.py Fix docs 1. Do not uselessly pass Scene* pointer to Law2 functors (already in LawFunctor) 2. Attempt at Law2_ScGeom_CpmPhys_Cpm (not tested) 1. Add the possibility of custom constructors to python (not a hack as it used to be) 2. Add cached functors to explicitly created interactions (not saved, though) 3. Improve the ScGeom-based Cpm law 4. Change interface of StepDisplacer to specify mov and rot separately (old interface with deltaSe3 works, but warns) 5. Add scripts/test/cpm-dem3dof-scgeom.py to show some differences between the 2 geometry formulations. 1. Turn many fatal warnings in UniaxialStrainer to exceptions, remove some guess-logic 2. Automatically disable live plots in batches. 3. the concrete uniaxial test now has the scGeom switch 1. Some VTK recorder fixes. 2. cpm fixes (untested) 1. Save interaction as vtkPolyData rather than vtkUnstructuredGrid (to allow the Tube filter to operate on it). 1. add noShow to uytils.plotDirections 2. Some fixes for ScGeom+Cpm (still problematic) 1. Preliminary version of PyQt4 interface (3d viewer flickers, reason unknown). Config checks largely absent. 1. Remove linkStrategy option. Specifying chunkSize=1 provides the per-plugin linkage. 2. Add qt4 feature, which conflicts qt3. Qt3 must be now explicitly defined. QT4DIR must be defined (defaults to /usr/share/qt4, which works for debian) 3. Add checks for python modules and prettify boost checks. 4. Remove a lot of legacy code, so that the qt4 build avoids yade::serialization completely 5. Add live inspection and modification of arbitrary sequences, for a showcase see the Inspect button on the simulation tab (Body/Interaction inspection will be rather easy as well) 6. Add common handling of number arrays (Vector3, Matrix3, Quaternion) 7. Add to-python converters for vector> and list (only needed in Dispatchers, avoids tome exceptions) 8. Rename OpenGLRenderingEngine to OpenGLRenderer Path hotfix. 1. Dispatchers cleanup (will continue) 1. Remake inheritance tree for Dispatchers, so that functors are really of the right type. Involves some macro ugliness. 2. Add rudimentary (but working) inspection interface for engines, bodies, interactions 3. Fix compilation without qt3 (will be removed soon, completely) (forgotten file) 1. Make types and attributes in all editors clickable 2. Add editor for Se3, Vector3i, Vector2, Vector2i 3. Fix bugs in eigen's wrapper for Vector2i and Vector3i 1. Fix static properties of Eigen objects (return values, not references - see http://www.mail-archive.com/yade-users@lists.launchpad.net/msg02339.html) 1. SpherePack.makeCloud can distribute grains based on their mass (rather than count) along arbitrary PSD or uniformly if rMean is given (the default behavior is unchanged) 2. SpherePack.psd() function for generating particle size distribution, either based on particle count or their volume (mass) 3. A few fixes in the UI 4. Fix facet "coincident vertices" warning 1. Add script demonstrating mass-based and size-based particle size distributions (PSD) and how to specify and arbitrary function for PSD when generating random loose packing with SpherePack.makeCloud 1. Disable (experimental and malfunctioning) multiblock files with vtk<5.2 (did not exist) 1. Remove qt3 interface 2. Remove yade::serialization and related otherwise useless files 3. Remove lib/loki, use the official Loki library (in /usr/include/loki, package libloki-dev) instead, except for (highly incompatible) Singleton, which was moved to lib/base. merge noqt3 branch 1. Body flags instead of bools + isBounded/setBounded flag. 2. Move body_id_t to Body.hpp 1. Change body_id_t to Body::id_t 2. Assign Body.bounded in py/utils.py funcs (in prep for making BoundDispatcher 1d) 1. Make Bo1 functors really 1D 2. add Body::isBounded/setBounded so that there is a way to ask for a body to not have bound created by BoundDispatcher 3. Change bool Body::dynamic into a bit inside Body::flags 4. Change body_id_t to Body::id_t since boost::serialization can handle class-defined types gracefully 1. Integrate BoundDispatcher into Collider, its python ctor takes list of BoundFunctors now 2. Warning and help if BoundDispatcher is used directly (more precisely: if Collider has no BoundFunctors defined and there is BoundDispatcher in O.engines) 3. Remove Body(id,mask) ctor as it bypasses default value initializers 4. Adjust preprocessors to the previous item 1. Remove BoundDispatcher from O.engines in examples, scripts and sphinx (accidental typos possible, sorry) 1. Remove outputFilename from FileGenerator, pass that as argument directly; remove message as FileGenerator's member; FileGenerator is no longer ThreadWorker (was not used) 2. Remove all variables named 'rootBody' in generators (detail: make SeqSerializable number nicer) 1. Rename some stuff in Omega and Scene to make it consistent with python: Scene::currentIteration->Scene::iter Scene::getSimulationTime()->Scene::time Scene::getComputation...Time()->Scene::getComputationTime() Scene::stopAtIteration->Scene::stopAtIter etc. 2. Fix bug with per-class compilation (thanks to Sega for reporting) 1. Adjust docs for changes in the last commit 2. Add version requirement for python-sphinx to debian/control-template (Anton: that's the reason why the build fails in maverick; I uploaded 1.0~hg... into yade-users/external so it should build fine in a few hours; there is no use uploading 0.6 which is in maverick already) 1. replace {pre,post}ProcessAttributes by {pre,post}{Save,Load} (not virtual) 2. change attribute specification adding and additional attribute flags (read-only from python, not saved, should call postLoad after changing value from python) 3. Macros cleanup in Serializable 4. Support clang for compilation (more than 2x faster) https://yade-dem.org/wiki/Compilation_with_LLVM/clang (documentation not yet update to reflect those changes fully, sorry) 1. Add sub-stepping functionality (step by engines rather than by whole iterations) 2. Expose Scene in python properly (not very well tested yet...) 3. Update documentation about attribute flags 4. Remove some 3rd party files no longer needed 1. Add foce, torque etc display in the body tab of the inspector 2. Make force, torque etc access from python not require thread synchronization (sums up threads on demand) 1. When disabling sub-stepping when the last step is done only partially, all remaining substeps are run at the next step. 1. Fix bugs related to 3d views (centering, secondary views, closing views). Thanks to Sega for reporting. 1. Consistently use SUFFIX for what is the same for debug and non-debug version, and libDir for plugin installation directory. Hopefully that cleans the mess we've had. That should also fix startup problems with --debug that Anton reported 2. Do not #define PREFIX and SUFFIX as macros, since they are not used in the c++ code anymore (and should not be) 1. Link to the standard libstdc++.so.6 (which is instaleld everywhere) instead of libstdc++.so, which is only in the devel package of gcc 2. Full support for compilation with clang (packaged for lucid and maverick now), as explained at https://www.yade-dem.org/wiki/Compilation_with_LLVM/clang#Building_yade (openmp and optimizations do not work) 3. Add function to ScGeom to compute incident velocity from python. 1. Fix QT4CXX key error, thanks to Anton for reporting. 1. Fix startup error with debug-only builds. Sorry, Anton. 1. Enhance the gl-drawer for LawTester. 1. Fix both rotation and shear in LawTester. Signs are now consistent are correspond to displacements as defined on classical beam (x is the axis, y and z are in the shear plane) 1. Clear erro message when running debug-only build without --debug 1. Make number in qt4 show the left-most part if the text field is narrower, rather than the left part 2. Run the debug version if optimized is not available, even without --debug 3. Add the possibility of running the monolithig compilation (mono=True); not fully functional yet. 4. Add warning when using march with clang, which leads to crashes (optimizations are not the cause, in the end) 1. Flattening the file hierarchy, as mentioned previously. No changes to #include paths so far. 2. Change the directory where to install headers to not include yade version 1. Add OpenGLRenderer to DomainLimiter, that should fix the linking issue reported by Janek. 1. Fix debian linkage with MatchMaker (hopefully) 2. Add preliminary and experimental L3Geom class (do not use, do not ask etc -- yet). 1. Make forgotten class members public (sorry, Anton) 1. Enhance LawTester to work with L3Geom, fix some bugs 2. Add uN and uT references inside L3Geom, for respective components of the deformation vector 1. Add Vector6r wrapper (both c++ and python) 2. Fix prefix bug in initialization braking debian packages 3. Fix renames in py/test which made regression tests fail 4. Update LawTester and L3Geom for 6 dofs (not yet tested, please do not use now) 1. Add menu entry for the dbg package (yes, it really does not show up, dunno why either) 2. Add plasticity to Law2_L3Geom_FrictPhys_ElPerfPl, add convenience function to apply local forces 1. Clean up Vector6 and friends 2. Create Matrix_computeUnitaryPositive template to be compat between eigen2 and eigen3 (in the future) 1. undefine pi in MindlinPhys 2. Add isAspherical() flag to Body 3. Adjust kineticEnergy with PBC (not yet fully tested) 4. Make createInteraction work with PBC 5. Fix getIncidentVelocity with PBC and !avoidGranularRatcheting 6. Add some regression tests related to Cell (not yet fully done) 1. syntax hotfix for batch -- thanks, Ema. 1. Fix kinetic energy in PBC 2. Add tests to check PBC: Ek, incident velocity with ScGeom (with and without ratcheting), homothetic resize 3. Make it possible to set O.dt=0, for reasons of testing. 1. Deprecate NewtonIntegrator::homotheticCellResize in favor of Cell::homoDeform (compatibility interface with warning) 2. Add the possibility of homothetically changing positions rather than velocities; avoid the meanfield/fluctuation velocity jazz at the expense of vel not being time derivative of pos 3. Add PBC tests for the previous variant 4. Add defThreads arg to scons, which, if specified, gives default number of threads for simulations, if not overridden with -j 5. Fix a few example scripts, more work ahead come (please help!) 6. Add regression tests for saving/loading yade objects; on maverick, this makes the unregistered class to re-surface (!!) 1. Update the dispatch-torture script. 1. Fix laoding of unitialized LawTester 1. Disable debug messages from ScGeom in both debug and non-debug (!!) builds 1. Fix boost::sertialization class export (changed slightly in boost 1.42, which broke our case); that also solves the issues at maverick 2. Add framework for tracking energies (will be documented at some point), added to Law2_ScGeom_FrictPhys_CundallStrack, see scripts/test/energy.py 3. Convert energy trackers in Hertz-Mindlin to OpenMPAccumulator 4. Make OpenMPAccumulator align storage so that each thread uses one cache line (should be faster) 5. Make OpenMPAccumulator not require zero value pointer (is handled via ZeroInitializer template in lib/base/Math.hpp 6. Make OpenMPAccumulator work transparently with python (it can be used as a regular attribute now), make it boost::serializable as well; it appears transparently as a number in python. 7. Add OpenMPArrayAccumulator, for linear array of values (used in EnergyTracker) 8. Make deprecated attributes with non-g++ compilers (clang); previously, only g++>=4.3 was supported 9. Fix a few example script (not completed) 1. (hopefully) fix build with boost::serialization<1.42 broken by previous commit. 1. Add warning for missing ForceResetter in NewtonIntegrator (based step forces were last reset) 2. Rename *Spiral* to *Helix* (suggested by Jan, thanks!) 3. Generalize the post2d module to handle interactions (not just particles) 1. Fix intiialization problem in Shop::kineticEnergy (thanks, Anton) 2. Several enhancements of the post2d module 3. Fix a few crashers with deleted particles. 4. Improve utils.facetCylinder 1. Add HdapsGravityEngine which reads acceleration from real accelerometer in thinkpads (toy engine) 2. Fix bug in qt4 interface where multi-number entries (Vector3r etc) might have some values zeroed due to wrong order of initial update and signal connects. 1. Make clumps subclass of Shape (instead of Body) 2. Favicon in the batch web interface 3. Fix for clang compilation 1. Fix examples, delete a few other ones 2. Fix a bug in post2d ================================================== yade-0.50.0 Wed, Jun 9 08:30:02 2010 +0200 Anton Gladky (77): Added an example of VTK-recorder using. Thanks Sergei Doroffenko aka Sega Changes in facetBox function to get other facet normals Added import_mesh_geometry function to import mesh files into facets Function import_LSMGenGeo_geometry is added to import into the simulation .geo files, generated by LSMGenGeo libraries. Example is added in ./scripts/test/regular-sphere-pack.py and ./scripts/test/genCylLSM.py Fixes import_LSMGenGeo_geometry and its example Adaptation RockPM and PressTestEngine for material and state classes PressTestEngine is temporarily disabled as it causes YADE crash on start 1. TranslationEngine and PressTestEngines are activated 2. regular-sphere-pack.py is updated according to new material class 1.VTKRecorder is activated, except REC_CPM 1. scale factor is added to ymport.gengeo 1. Trivial change scale factor in regular-sphere-pack.py CohesiveStateRPMRecorder base templates are added. This Engine is for calculating cohesive contacts in the RPM model. 1. Created yade.ymport.gengeo() function for importing LSMGenGeo geometry directly to the YADE simulation without intermediate files. See ./scripts/test/genCylLSM.py 2. yade.ymport.gengeo() (import .geo-files function) was renamed to yade.ymport.gengeoFile() 3. CohesiveStateRPMRecorder is now working. (thanks Vaclav) 1. "Patch" to fix 490223 1. CohesiveStateRPMRecorder now derives from the Recorder 1. REC_INTR in VTK changed to save interaction data not only for CPM model. Very trivial fix in utils.py 1. In utils.facetBox added 'Defence from zero dimensions' 2. regular-sphere-pack.py is updated due to new names 1. Added moveTo und scale parameters for ymport.gmsh function Some syntax fixes: moveTo has been renamed to shift in utils.py and ymport.py ymport.gmsh function was renamed to ymport.mesh one ymport.mesh was renamed back to ymport.gmsh Trivial bug fix 318439 1. gmsh.ymport function is fixes to be more universal 2. "Bad" bug #505783 fix Fix bug 505783 1. Added utils.facetCylinder function to create arbitrarily-aligned cylinder composed of facets 2. utils.facetCylinder example is added to ./scripts/tests/regular-sphere-pack.py 3. RotationEngine example is added to ./scripts/tests/regular-sphere-pack.py 1. utils.facetBox() and utils.facetCylinder() function description where changed according to Epytext format. utils.facetBox() and utils.facetCylinder() description has been formatted to reStructuredText-format. 1. vtk-feature is on by default now 2. Added eigen library like a feature 1. Eigen check library fix. Thanks Bruno 1. Added some more Eigen headers to check in SConstruct 2. Commented the string in py/SConscript which made an error during compiling 3. Added yadeEigen.hpp to make a wrapper for Eigen 1. yadeEigen.hpp is added 1. Some changes for Eigen migration 2. TranslationEngineEigen to test Eigen library 1. Some changes in utils.facetCylinder function 1. Convert a RockPM class to YADE_CLASS_BASE_DOC_ATTRS 1. Convert Recorder class to YADE_CLASS_BASE_DOC_ATTRS 1. Removed TranslationEngineEigen 2. TranslationEngine and PressTestEngine were updated according to a new register standard 2. In SConstruct were added some more Eigen headers to check. 1. YADE_CLASS_BASE_DOC_ATTRDECL_CTOR_PY for CohesiveStateRPMRecorder is added, but not activated. 1. ForceRecorder added. 2. Some minor changes. initRun=true added to ForceRecorder 1. spheresToFile() has been fixed and moved to export file. Do we need "consider=lambda id: True" there? 2. ymport.ascii() was renamed to spheresFromFile; wenjieFormat was deleted there. The function is rewritten, comments are available now. 3. Added export.spheresToFile() and ymport.ascii() examples to regular-sphere-pack.py. 4. In timing.py InteractionDispatcher->InteractionDispatchers 5. Some default values in scons were changed to make YADE compilable with "standard" Ubuntu machine with 4GB RAM: chunkSize=7, jobs=2 Rotate function is added to manualWrap RotationEngine parallelized GravityEngine parallelized Some scons changes. Vaclav`s patch 1. penetrationDepth() is added to DemXDofGeom 1. penetrationDepth() declaration fixed. Thanks to Vaclav. 1. NewtonIntegrator - fixes of normalizing null-vectors 2. penetrationDepth() has been deleted from DemXDofGeom Adaptation to Eigen Library Previous commit correction. Thanks to Vaclav. Fix compilation error Orientation parameter is added for ymport.gmsh() function Small changes in ymport.gmsh() Some changes in utils.ymport module due to new Sphinx requirements. Some examples clean Examples cleaning Trivial genCylLSM.py fix Ubuntu 10.04LTS has GMSH version, where medit-mesh format is changed. It fixes wrong import of newly formatted files. Back compatibility is saved. 1. Quaterion.Rotate() wrapper is added 2. mill.py fixed 1. Examples cleaning 2. Code adopting to Eigen library `materialID` property is added to VTKRecorder VTKRecorder changes: 1. clumpIds recorder changed to clumpId 2. materialID recorder changed to materialId 3. ids recorder changed to id 4. Syntax cleaning 5. Default parameter 'all' is added subscribedBodies parameter is added to VTKRecorder Some fixes in VTKRecorder 1. Parameter groupMask is added to utils.sphere and utils.facet 2. VTKRecorder. subscribedBodies mechanism was changed to VtkRecorder changes: 1. Velocities of particles are now exported as Vector3 and Length component separately. 2. Added 'force' parameter for facets and spheres (sorry, not good tested yet) Force calculation mechanism is changed in VTKRecorder (Thanks to Vaclav). Experimental. VTKRecorder. force->stress. But only for Dem3DofGeom now 1. Some warnings were commented (please, don't leave unused variables!) 2. In Shop created getStressForEachBody method to clean up VTKRecorder a little bit (not tested yet, but compiles) 1. VTKRecorder is static now. 2. function ymport.testExt and export.testExt are added Comment parameter is added to export.textExt groupMask parameter of bodies is now exported to VTK-output as `mask` Blocking the crashing string in ElasticContactLaw in ./examples/rotatingCylinder.py encoding is fixed Some changes in examples 1. Fixes crash in VTKRecorder, when some bodies are erased 0.50.0 Boon Chiaweng (17): BasicPM.cpp hpp BasicPMTest.py in pkg/dem/meta BasicPM @ pkg/dem/meta BasicPM @ pkg/dem BasicPM @ pkg/dem meta local commit local commit Removed BasicPM.cpp and added CundallStrack.cpp. It is a duplication of Law2_Dem3Dof_Elastic_Elastic but written in meta style like RockPM. It is therefore cleaner and more friendly to a beginner. Comment local commit local local committing files which were not uploaded in last commit committing files which were not uploaded in last commit local Cohesionless Moment Rotation LLaw as implemented by Plassiard et al (2009). Verified changed Cohesionless Rotation Law to be cleaner added instructions on how to use ContactLaw with TriaxialTest Bruno Chareyre (102): A flag "neverErase" is added to the contact law to define if it can erase interactions. This flag can be turned on when another constitutive law (e.g. capillaryCohesiveLaw) is in charge of erasing interactions. - fix wrong usage of "neverErase" in TTWater - synchronise versions of ECLaw Fix the path in the warning. Please, never make me do that again!! A (little) bit of cleaning. Fix warnings. And one more back. - fix segfault in test.cpp (testing the triangulation functions) - adapt the collider to state/material State/Mat fix. Fixed : 2 "unused variable" warnings. - fix the bug on bodies type in CFTriaxialTest - rename CohesiveFrictionalBodyParameters => CohesiveFrictionalMat - fix the bias in cloud generation (try and position a sphere of constant radius) - some more cleanup of the code - update of the documentation Add the missing #include AABB Code using the velocity gradient to define periodic deformations (experimental) + script to test it. Needs compilation with #defined VELGRAD (currently needs uncommenting "#define VELGRAD" in 4 files in total). Fix some warnings. -Restore default behaviour even with #define VELGRAD, restore default homotheticCellResize=0 and register it. All py scripts should work whatever VELGRAD, except periodic-triax-velgrad.py (throw without VELGRAD for homotheticCellResize=1). -Clean code -Fix mail adress E.C. Make non-proportional scripts really work with VELGRAD : -Update Hsize when refsize is modified once (this is ugly! needs a cleaner way) -Adapt size control by periodic engines. Sorry for this new change in Cell.h. It will not change for a while now, next commits will be in engines. Add a new periodic compressor engine (candidate for replacing/merging with PeriTriaxController). Most important changes : - stress control using mass - defines the full stress tensor (not only normal stress for each axis) - defines strain with logarithm for comparison with goals and postprocessings - merge stiffness/inertia control in PeriTriaxEngine and remove periEngine - show usage of inertia (commented out) in py script A funny script, and no crash! -Fix the loading path, this example shows how shear create rotations. -A commented suggestion for dispatchers -Get back r1932 in PIC -Fix a wrong assignment of max vels in StressController that was causing non-isotropic compression (introduced a while ago when Luc Si. implemented 3D independant controls probably) Optional porosity in makeCloud, giving a value discards rMean (avoid guessing rMean when you know size and number). -Fix messed comment (save before commit!). Comments. - Rename Poison -> KsOnKn in some preprocessors. Not project-wide : I don't know what laws are used in PHYSPAR'ed files. - some cleaning in TT code - Add CGAL excpetion in GNU GPL license. rename KsOnKn -> KsDivKn. Revert weird changes from JFJ in TWrapper interface (min/max should not be mandatory in any functions!). I managed to remove the variable while adding the comment. Glad nobody noticed yet... - Remove old files - add insert(Scene& scene) to tesselation wrapper (faster) - move TWrapper out of namespace CGT and make it a YADE plugin - move TWrapper sources to pkd-dem/globalEngine, keep different (uncompiled) versions in lib for possible out of tree builds - some more documentation in TWrapper.hpp - missing files in previous commit - fix a member's name in TW - Fix : old names used in #includes and code - Add a function KLA::DefToFile() writing the triangulation and deformations to a file - Use it in MMAnalyser. - Fix read/write details in TriaxialState and few other small fixes - MMA is now fully operational for strain maps - switch some spaces/endlines Fix compile errors in VTKWritter and KLA. - Fix size range in makeCloud. It was generating an interval twice smaller than expected. Update the documentation. Used with uniform distribution, makeCloud now generates radii between mean-rRelFuzz and mean+rRelFuzz. 1. Remove lib/triangulation/TesselationWrapper. No need to keep in Yade files used only for out-of-tree builds + it was confusing to have the same file names twice. 2. Reformat vtk output. 3. Implement more methods to control the input/output of TesselationWrapper, access MicroMacroAnalyser methods via TWrapper interface, return all data in a python array (still commented). 1- move subdivideTriangle in the glNewList section. No reason to do that elsewhere. 2- Suggest using glList even when stripes=false (commented code) for better performance. Both changes affected by this bug for now : https://bugs.launchpad.net/yade/+bug/509084. - Remove the part of the code that was only a hack to display bodies with broken contacts, and remove some spaces. - Uncomment the line assigning deformation values in python::dict get(). - Add MATRIX3R_TO_NUMPY macro in numpy.hpp -Add missing members declarations (forgot to commit the header with a previous commit) Fix a compile error when openMP is not in features. - Global update of the triangulation lib. - Fix some compile errors. - Re-implement arbitrary boudaries ids. - Generalize boundary conditions. - Clean the code. -disable the independant GL display. - Fix compile errors with cgal in features. - Fix compile error (forgot this one in lastr commit) Flow: - Implement bz2 read/write for TriaxialStates - 3rd method for hydraulic force and some optimizations in FlowBS (Ema, I'll let you remove unused code) - new data in cell_info - Mostly some formatting. - Compute the new tesselation in Interpolate(). - remove files not used in yade. - Comment the includes pointing to out of tree files to prevent compile errors with implicit link. - Fix the bug (r2025 probably) in GSTimeStepper (test of line 28). - Register timeSteppers. - numpy : comment and new line at EOF - TW : fix a warning. - PTCollider : remove a "using namespace std" in the header. Some changes in the TCE behaviour. Save the state before stopping simulation, and start compression for reloaded files with autoCompression=true. Please keep intact the behaviour even when the code looks strange, there are reasons behind. I ran 1 week simulations, expecting saved xml at the end, but got nothing... I've included a fews comments about this. - A few more comments and code cleaning. - Fix an error in max_vel's definition. - Register attributes of the stress controller and of derived classes. - Make them "global" engines instead of "partial" (and replace "applyCondition" by "action") - Add a function computing the solid volume of a sphere packing in Shop. - py wrapping for getSpheresVolume (usage : O.getSpheresVolume) - Missing in previous commit and creating compile error, sorry for that. - Some documentation and code cleaning. - Fix syntax error + small changes in the documentation. Fix compile error ifndef YADE_OPENPM. -Register and code cleaning. -Link to the wiki page for general instructions and files download. -One more initialisation in ctor (strain). - Fix : wrong assignnment of friction for boxes. compactFrictionDeg was used in place of boxFrictionDegree. No idea when it was introduced. - Register TriaxialTest (yes!!). - Remove useless transition returning a LOG_ERROR. - More registering! - Remove unused unregistered engine. - Register, rename, clean code, doccument some attributes. - New names in Attic files (follow-up of r2156, more to come). - Add a "cohesiveFrictional" functor for usage in interaction dispatching (functionally replace the global engine CohesiveFrictionalContactLaw, which is still here and used in cohesive preprocessor). - Register "cohesiveFrictional" classes and rename them. - Some cleaning and a fix in the law for brittle failure. -Use new names. - Some fixes in triangulation. Python array still crashing in TW. - Use new names. - Remove SCG_SCHEAR, clean code and documentation a little bit more. - Take "fuzz" into account for the definition of rMean in the generated distribution. - Update the link to capillary files. - Make the radius of fictious sphere equal to the one of real sphere in box-sphere geometry. - Implement energy tracing in ElasticContactLaw - Remove some "#ifdef SCG_SHEAR" - Remove equilibriumDistance and initialEquilibriumDistance from FrictPhys and inheriting code. - Remove rotationBlocked from TriaxialTest. - Fix documentation (backticks in pkg/dem/PreProcessor/TriaxialTest.hpp, pkg/dem/Engine/PartialEngine/TriaxialStressController.hpp, pkg/dem/Engine/PartialEngine/TriaxialCompressionEngine.hpp). - Fix cohesiveFrictional crasher - Initialise saveSImulation correctly in TCE - Remove initialKn/Ks assignment Ip2_2xCohFrictMat_CohFrictPhys - Put back Vector3r::Zero() py wrapping for shop::getSpheresVolume(). Used e.g. for computing porosity in a periodic cell. - Use Shop::kineticEnergy in the recorder (adds the rotational term). - Fix strainRate comparisons for the case dynCell=true. - Simplify the code, removing cellGrow totaly and using gradVel everywhere instead (its time derivative). - Rmk : I suspect some of those changes have been commited before, then reverted, but I couldn't really spot when/why. Actually, the revert attempt broke the "dynCell" behavior. This commit should not change anything for dynCell=false. Let me now if you see a difference. - Fix the distance correction in plastic slip. - Compile error (sorry) : matrix(i,k) instead of matrix[i][k]... (couldn't we overload simply define [][] operator for Eigen matrices?) - Simplify equations inside plastic condition of Dem3Dof (1 sqrt instead of 3, less norm()), add a new function that uses a multiplier instead of maxDisp to take advantage of this new formulation (Vaclav, could you review and tell if we should merge maxDisp/multiplier in one single function with a bool? I didn't want to break any other part so I didn't touch the previous function). - Fix a wrong equation in shop::unbalanced force (max is for body force, not contact force). - hardcode tensor product in PeriIso, as this is instanciating a matrix and it is done for each contact at each step. - Remove one more norm(), return 0 for compatibility. - Fix the plastic dissipation equation in ElasticContactLaw and make plasticDissipation a OpenMPaccumulator. - Fix the name scaleDisplacementT(Real multiplier), handle the case force=0 correctly (thanks Vaclav). - Fix mail adress. - Implement scaleDisplacementT(multiplier) for all functors derived from Dem3DOF. This function is only used in Law2_Dem3DOFGeom_FrictPhys_basic at the moment. - Fix the undefined scene pointer in ElasticContactLaw. - Register TTWater correctly. - Update documentation of some classes, reformat a little, and fix (again) some email adresses. 1 - stress definition in PeriIsoCompressor was wrong for ScGeom (sign mistake due to double-reverse); Missing files in r2249. This commit complete the implementation of periodicity for incremental formulation, with updated relative velocity across periods. It has been tested carefully in periodic triaxial tests. 1. updateShearForce is renamed rotateAndGetShear and DOES NOT update shear force any more : this is Law2's job. Two versions are available, for resp. periodic and non-periodic case so that people don't have to worry about the additional "shift" in function parameters. 2. put the line fs+=ks*dus in laws using the former ScGeom::updateShearForce. 3. Put back Hsize in Cell (I need that each time I write a line in periodicity, really, please don't remove it). 4. The rest is details (fix wm3 incompatibilies, formating, documentation, etc.). - Fix compile error, sorry. - Fix Wm3 build in Dem3DofGeom_FacetSphere.cpp, the Real*Vector had not been reverted in that file. - Workaround https://bugs.launchpad.net/bugs/585898. - Implement Cundall-style positions scaling when (homotheticCellResize=2). - Rename Water=>Capillary (more accurate) - Register CFTTest. Chiara Modenese (5): Added constitutive law with Hertz formulation for contact stiffnesses Make penetrationDepth directly accessible through python Removing variable timeStepOutputInterval from the TT, it was useless. Add tangential values for the stiffnesses in HM law so that GSTS can be used (anyway contact forces are computed from the secant stiffness values to avoid numerical approximations). Avoid to store trialFs to the physics functor as it is already referenced. Correct a banal mistake in failure criterion. - Small changes in HM to handle PBC if scene is periodic (same logic as in ElasticContactLaw.cpp) Emanuele Catalano (16): Add code for flow problem resolution. Updated flow engine files. Made some correction in flowengine files. - Made corrections on flow code - Class registration via new macros introduced Few corrections in flow files. Forgot to delete some line. - Modified the type of some function in FlowBoundingSphere - Adapted FlowEngine to that modifications - Adjusted the use of "currentTes" in FlowEngine - Introduced timing information from engines and functors - Reorganized the code and cleaned from useless stuff - Verified properly re-triangulation - Made corrections on Gauss-Seidel break criterion - Assigned more severe tolerance to permeability computation - Fixed some error due to pointer scene* deletion - Added functions to write Mplotlib files - Adjustments to the code - Fixed retriangulation problems - Flow Code Maintenance - Introduced local permeabilities' correction agent - Fixed retriangulation problems - Walls proper identification is no more ID dependent - New output files for fluid pressure and settlement evolution - Fixed some warning came out with new compiler version - Fixed errors in walls' identification Janek Kozicki (4): fixes #571674 don't segfault when TriaxialStressController is facing clumps Scene.hpp -> remove obsolete comment QtGUIGenerator -> wider view on vector fields TriaxialStateRecorder and TriaxialCompressionEngine -> it was segfaulting with clumps: fix it. was not compiling with wm3 Jerome Duriez (26): Beginning of adapting code about simple shear (to train with bzr almost) - There are still indeed the YADE_REQUIRE_FEATURE(PHYS_PAR) lines which prevent these files to be compiled. - There is only one change that will be detected by your news compilings : change of a line in ElasticContactLaw. I corrected a link towards an URL corresponding to "old wiki" Renaming of all (normally) linked with this famous "ContactLaw1". Thanks to Vaclav for his scripts ! Dplt de SimpleShear hors de attic Re-activation (suppression de YADE_REQ...(PHYS_PAR) ) de RockJointPhys, et RockJointLawRelationships - "SimpleShear" was re-introduced in pkg/, instead of attic/ (Last ?) renaming of classes linked with "my" contact law. The normal inelasticity is now emphasized in the name, because it is what is specific to these classes. NB : this contact law takes also into account a moment transfer. Re-writing of classes CinemCNCEngine, NormalInelastictiyLaw (and those linked : NormalInelasticityPhys and Ip2_2xCohFrictMat_NormalInelasticityPhys) according to the macros replacing former REGISTER_ATTRIBUTES... Move of the line YADE_PLUGIN((...)) of CinemCNCEngine : it was before the "include...", and for Emmanuele it did not compile thus. Moved after the "include". Re-write of CinemKNCEngine according to new macros. Anecdotic changes in CinemCNCEngine Suppressing of commented lines Renaming of Cinem...Engine in an english way : - CNC = Constant Normal Load => CNL - KNC = Constant Normal Stifness => CNS - DNC = Constant Normal Displacement => CND - DTC = Constant Tangential Displacement => CTD - Correct writing of Disp2DPropLoadEngine : in order to perform tests on a shear box, piloted by dispNormal + k*dispTangential = 0 Compilation enabled by the way. - Minor syntax changes of doc of KinemCNSEngine - Suppression of CinemCisEngine, which even me almost never used. - Add of KinemCTDEngine: performs constant tangential displacement (=oedometrical) compressions on the simple shear box - move of KinemCND from pkg/common to pkg/dem. This Engine does not use really any DEM-specific concept, but I guess it will always be used in DEM simulations, so I thought it will be more adequate in dem/ - modify of corresponding "include"... - rewrite of KinemCNDEngine.hpp, with "good" macros - Use of YADE_CLASS_BASE_DOC_* macro family in KinemCNDENgine (it was not in r2082, contrary to what was previously said) - Rename of NormalInelasticityLaw into Law2_ScGeom_NormalInelasticityPhys_NormalInelasticity (I accept sincerely any proposal of shorter file names...) In fact it is not yet a functor, but I want to try to write it in a more proper way... - Corresponding changes in affected files - Details in other files - Rename of NormalInelasticityLaw into Law2_ScGeom_NormalInelasticityPhys_NormalInelasticity (I accept sincerely any proposal of shorter file names...) In fact it is not yet a functor, but I want to try to write it in a more proper way... - Corresponding changes in affected files - Details in other files ANECDOTIC COMMIT - fix typo in Engine.hpp : "fron" corrected by "from" I commit this alone, with no other changes, to make clear to everyone that this change to a central part of Yade is really anecdotic... - the code concerning the inelastic normal law is now in files named NormalInelasticityLaw.* instead of Law2_ScGeom_NormalInelasticityPhys_NormalInelasticity.* The class itself has still the same name (Law2...), but I changed the name of the files for practical reasons, as it seem other people do (files HertzMindlin, CohesiveFrictionalPM for ex). Tell me if this is problematic Re-write of CohesiveFrictionalMat with YADE_BASE... macro. It is not one of "my" files but I wanted to use it with Python, so I did it. I hope noone will be offensed. - Add of a script NormalInelasticityTest to test ... the NormalInelasticityLaw (Law2_ScGeom_NormalInelasticityPhys_NormalInelasticity) Moreover my python problems I had difficulties to obtain "perfect results". I think it is linked to the way un is computed in Ig2_Sphere_Sphere_ScGeom (see for example this "shift2"). Why not making penetrationDepth directly accessible through python ?? - Change of Law2_ScGeom_NormalInelasticityPhys_NormalInelasticity into a real functor instead of an Engine (compilation checked, and that's all) - Run of NormalInelasticityTest, now Law2...NormalInelasticity is a functor => same results as before it seems - Change of .Length() in .norm() in other scripts, as .Length() seems to be deprecated - One more change of .Length() in .norm() - check in NormalInelasticityTest.py that the curves are perfect ! **** "My" files ***** - Law2_ScGeom_NormalInelasticityPhys_NormalInelasticity is now a functor as it should. - Related changes in few files - The script NormalInelasticityTest tests now the tangential component also, and it will normaly soon check the MomentLaw. It illustrates also the various ways of controlling disp$ Fix of https://bugs.launchpad.net/yade/+bug/589516 (sorry, the compilation did not crash on my computer when I tried) - Cleaning changes in NormalInelasticityFiles... =>Add of a new Material storing the info for differences between loading and unloading (related changes) Luc Scholtes (13): - correction of thickness computation in TriaxialStressController - submission of an updated version of cohesiveFrictionalContactLaw called cohesiveFrictionalPM (more details in CohesiveFrictionalPM.hpp). Tried to follow the new rules for variables declaration with documentation... NEW TRY to add the updated version of cohesiveFrictionalContactLaw called cohesiveFrictionalPM (see revision 2068) SORRY FOR THE REDUNDANCY... updated comments in cohesiveFrictionalPM.hpp to be consistent with the computation correction of few bugs in CohesiveFrictionalPM fix almost all of the classes related to CapillaryCohesiveLaw (except TriaxialtestWater) to suit YADE_CLASS_BASE_DOC_* macros. Everything compiles but the efficiency of the code needs to be tested. This version fixes a bug which produced FATAL ERROR when 2100 version was launched. SORRY. Removed CapillaryRecorder and ContactStressRecorder. Renamed SimpleElasticRelationshipsWater to Ip2_FrictMat_FrictMat_CapillaryLawPhys (can probably be removed as it is identical to Ip2_Frictmat_FrictMat_FrictPhys...) and CapillaryCohesiveLaw to CapillaryLaw. Modified all Capillary related files. some updates of capillary files. Rk: all must be tested! -updates for capillary files (doc in Law2_..._Capillarity and changes in CapillaryStressRecorder)\n\n -add a feature to CohesiveFrictionalPM (creation of CFpmState to stock number of broken bonds) fix compiling error in previous rev (but some warnings linked to TriaxialStressController.hpp) new line added at the end of CohesiveFrictionalPM to avoid corresponding warning + cleaning some updates in CohesiveFrictionalPM. Unfortunately, the law still does not work in macroscale simulations... CohesiveFrictionalPM update - add normalization of a quaternion + other few changes Luc Sibille (2): I added the (updated) ThreeDTriaxialEngine, and it is also to see if we managed to make bzr working through an ssh tunnel - update of ThreeDTriaxialEngine with YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY \n - modified ThreeDTriaxialEngine to be able to perform internal compaction (growing particles) \n - modified TriaxialStateRecorder to be able to use it with ThreeDTriaxialEngine Sergei Dorofeenko (37): 1. virtual facets don't have a BoundingVolume (flag noBoundingVolume in utils.facet) 2. new engine ResetRandomPosition (another name?). This engine reset the body position to a random position in specifed (by virtual facets) region. 3. example of using of ResetRandomPosition engine: scripts/test/ResetRandomPosition.py Fix [Bug 485209] 1. adapt VTKRecorder to body removing 2. fix bug with colon separated paths in a profiles. fix bug in scons.profile*: now CPPPATH and LIBPATH is a simple string (not a list) with colon separated paths. Adaptation of viscoelastic model classes and some others to new material/state classes: 1. Add a meta package ViscoelasticPM, which now contains all classes for viscoelastic model. 2. Fix STLImporter, getViscoelasticFromSpheresInteraction 3. Fix bug in utils.sphere, utils._commonBodySetup Adaptation examples/STLImporterTest.py for new viscoelastic classes. Adaptation NewtonDampedLaw to material/state classes Add to NewtonDampedLaw a modified leap-frog algorithm for accurate integration of rotation equation. This is intermideate commit: new algo seems to work, but needs some coupling with previous code. merge clump branch with trunk Add some tests for clumps Fix bug with import facets from stl small optimization of acc.rot.alg; fix velocity and add angVel in VTKRecorder." 1. handle DOFs for new rotation alg.; 2. add new clump-hopper-viscoelastic script merge with clump branch: 1. handle DOFs for new rotation alg.; 2. add new clump-hopper-viscoelastic script; 3. small optimization of acc.rot.alg; fix velocity and add angVel in VTKRecorder. Intergate new acc.rot.alg. to code. Intermediate commit. Rename prevAngMom to angMom revert NewtonDampedLaw to r1817 and rename prevAngMom to angMom Integrate new rotate alg. into code. Intermideate commit integrate a new acc.rot.alg to NewtonDampledLaw framework remove log_trace from NewtonDampedLaw::lfRigidBodyRotate Integrate new rotate integrator into the NewtonDampedLaw framework NewtonDampledLaw: rename functions and remove duplicate code as suggest Vaclav (thanks!) 1. NewtonDampedLaw: rename functions and remove duplicate code as Vaclav suggest (thanks!) 2. Add spheres ids to VTKRecorder 1.fix link with GLU for QGLViewer; 2.fix header for Shop; 3.Add clumpids to VTKRecorder Update ResetRandomPosition STLImporter returns a vector imported facets instead of adding them directly utils._commonBodySetup does not reset body id. small update examples/STLImportedTest.py Fix bug #531394 refixing bug #531394 Reanimation of some examples; fix bug in ymport.stl fix bug in utils.py; consistent signs in ViscoelasticPM fix typo small modify of STLImporterTest.py Fix shear direction damping as Chiara Modenese suggest. And more fixing damping shear direction yet more fixing ViscoelasticPM Add doc for utils.getViscoelasticFromSpheresInteraction Unknown (5): 1. Make all paths given to scons on the command line COLON separated rather than space separated. BACKWARDS INCOMPATIBLE if you used scons in scripts (doesn't affect saved profiles). (Rationale: impossible to save the option in shell and later use it due to quoting issues) 2. Optionally set PATH as argument to scons (you can use scons PATH=$PATH as well) 3. Enhance VTKRecorder to record interactions andsome data on them. 1. Fixes in scons for qt path (hopefully OK now); remove VTKINCDIR, use CPPPATH which alread exists 2. Improve yade-multi web interface (keep it running if --http-wait specified; show total time at the end) 3. Fixed in VTKRecorder and CPM 1. Enhance yade-multi to query running jobs for status (percentage, step number etc), to keep connections, allow more fine-grained thread number control 2. Add some more cpm data (like sigma, sigmaMean, tau) 3. Enhance vtkrecorder to save those cpm data 4. Don't set matplotlib backend in yade.plot automatically, since ti breaks in headless environments 5. Add O.tags.has_key A typo in SConstruct. getClassIndexStatic() member turned to public. Vincent Richefeu (2): - Increase DISTANCE_MAX - use gcc-4.0 (4.3 doesn't work correctly on mac snow leopard) Rewrite KinematicLocalisationAnalyser::DefToFile for vtk format. Václav Šmilauer (264): 1. Hopefully fix vtk libs in SConstruct (?) 2. Add compress parameter to VTKRecorder (doesn't seem to make any difference in the output files, however...?) 3. Add CPM damage to VTKRecorder 4. Move spiralProject to Shop, to be usable from within c++ 5. Add a 2 functions to compute 2d and 3d stresses to yade.eudoxos 1. Enhance VTKRecorder to save more CPM data 2. Add confinement storage to CpmMat; CpmStateUpdater now computes that. 3. Add method to get aabb of Gauss-smoothed domain. 1. Update examples/concrete/uniax.py and add CpmPhysDamageColorizer to renamed classes dictionary with warning. 1. Use colon as separator to all path parameters to scons (PATH, CPPPATH etc), to avoid shell escaping insaneness. NOT BACKWARDS COMPATIBLE if you call scons from scripts with multiple paths. Scons.profile-* files will work. 2. Add PATH parameter to scons, for things like pkg-config that we call during the configure stage (you can propagate whole path by saying scons PATH=$PATH) 3. Extend VTKRecorder to record interactions as well; add some cpm-related parameters. 4. avgStress is now Vector3r 5. Fix openGL-less builds (missing parenthesis in core/SConscript) 1. Remove VTKINCDIR (duplicates already existing CPPPATH) 2. Fix handling of QTDIR (hopefully?) 3. Yade multi now displays total time at the end, takes --jobs (long option for -j), and the http server keeps running as long as the summary page is requested if run with --http-wait 4. Fix computation of sxx, syy, szz in cpm Yade-multi, VTKRecorder enhancements, &c 1. Fix compilation on nfs (unable to delete .nfs* files) 2. remove debug message from the info socket 3. Make SpiralEngine assign velocities to (nondynamic) bodies so that when velocityBins are used, contacts are not missed. 1. Add example of generating randomly-packed tunnel-like scene (6 lines of python code). 2. Add explicit check for physics dispatchers in InteractionDispatcher even in the optimized build. Fix what seems like bug in is2is4scg... 1. Set timeout on infosocket 2. Add velocity bins to uniax.py example 1. New yade.post2d module for 2d post-processing (raw/smooth scalar/vector field plots), with docs and examples 2. Add epydoc brief documentation to all python modules 3. Change constructor of GaussAverage in python to take always the relThreshold parameter 1. New BodyVector written from scratch: supports body removal, intelligently allocates new ids at insertion. Is now default; a few pecent faster than BodyRedirectionVector which will be removed after a while. 2. Remove BodyAssocVector 3. Remove mass-spring for good 4. Add body removal support to InsertionSortCollider 5. Add empty body support to NewtonsDampedLaw, GravityEngine, OpenGLRenderingEngine and a few others 6. Wrap body removal from python 7. scripts/test/remove-body.py to demonstrate continuous dynamic body addition/removal. 1. Remove InteractionHashMap Add 'deprecated' feature which guards code pending removal. To compile those, you have to add 'deprecated' to features. 1. Add infinite axis-aligned planes (Walls), interacting with spheres; I would like to deprecate Boxes soon. scripts/test/wall.py show the functionality, utils.wall create ready-made body. 2. Add Walls to triaxial test as an option to facets and boxes. 3. Unbreak ef2_Spheres_Elastic_ElasticLaw (passing neverErase broke virtual function resolution -> exception) 4. Make Simulation controller always open, closing it quits yade. Generator accessible from controller; player must be accessed from controller by opening generator, closing it (where by main window apprears), then opening player. 5. Change prototype for InteractingGeometry functors, to get some information about the openGL context (scene radius and center, ATM). 1. Remove all deprecated classes as described in the last commit. 2. Start flagging code needing GeometricalModel by YADE_REQUIRE_FEATURE(shape). Once it compiles without shape, affected classes will be removed. Remove GeometricalModel from everywhere, unless you compile with the 'shape' features. Many classes had to be disabled; those who care about them are expected to fix them so that they don't rely on GeometricalModel. I will post on the mailing list on how to do that. Trivial fix. But shape feature is no longer supported, fix such things yourself next time, if you need them. 1. For each interaction, save when it was last seen by the collider. Adapt SpatialQuickSortCollider for that (remove Interaction::cycle), it saves 2 loops over interactions. The deletion is triggered in InteractionDispatcher/InteractionGeometryDispatcher afterwards. This infrastructure is neede for the grid collider. 1. Flatten file hierarchy a little bit. 2. Add MetaEngine{1,2}D and EngineUnit{1,2}D to the MetaEngine.hpp and EngineUnit.hpp instead of having them in separate headers. Remove 'deprecated' features from SCons files since they're not in the codebase anymore. 1. Change syntax of python docstrings to restructured text instead of epytext (for future compatibility) 2. Workaround CPPPATH error saving option 3. Make SpatialQuickSortCollider skip boundless bodies 4. Fix rendering bodies with names (i.e. selectables) Initial commit of new Material and State classes that will replace PhysicalParameters in the future. No changes in functionality. 1. Fix crash when removing bodies with velocityBins and MetaInteractingGeometry2AABB 2. Add option to draw normals for InteractingFacet (off by default); see scripts/test/remove-body.py (commented) Fix compile error introduced in last commit. Rollback point for adding YADE_REQUIRE_FEATURE(physpar) everywhere. rollback point 2 Build core only OK (no gui,python,extra) NewtonsDampedLaw, Clumps, SpatialQuickSortCollider compile. Checkpoint before replacing PhysicalParametersMetaEngine and friends REMOVED PhysicalParameters, add Material and State classes. DISABLED many (most) plugins, I ask the respective authors/users to fix them. 1. A few small leftovers. 1. Initialize dnesity to 4800 in CpmMat 2. Add warning if passing obsolete physParamsClass to utils.{sphere,facet,box,wall} 3. Add Material.cpp to ensure virtual functions work properly (not sure if they didn't, but now they do) 4. Fix uniax.py 1. shared materials; see scripts/test/facet-sphere.py and also py/tests/omega.py. 2. added some regression tests for Omega 3. python iterator over O.bodies silently skips erased bodies now 4. finally rename all MetaBody::transientInteractions to MetaBody::interactions 1. Fix uninitialized memebrs in Material (thans Anton) 2. Add equivalent of dispSe3 to OpenGLRenderingEngine directly 3. Fix pack.py 1. Make the optimized build default (as per Sega's suggestion); it also sets linkStrategy to monolithic (is that OK?) 2. Add some vtk dirs to default CPPPATH 3. Fix periodic boundaries in OpenGL & remove some YADE_SHAPE stuff from there. 4. Fix some warnings 5. Fix pack.randomDensePack **kw 6. Adapt examples/concrete/uniax.py to shared materials 1. Add Material::newAssocState creating State instance that is supposed to go along with given material; wrapped in python. It is used by utils.{sphere,facet,box,wall} functions now (hence by most or all body-construction things in python) 2. Fix py/post2d.py and examples/concrete/uniax-post.py 3. Fix crash for material-less bodies in scripts/test/regular-sphere-pack.py 1. Move import functions from utils to yade.ymport (sorry, import is python keyword and cannot be used ;-) ). yade.utils contains proxy function that warn and call the implementation in ymport. 2. Added virtual book Material::stateTypeOk(State*). 2. MetaBody checks that material--state couples are OK at the first run (like initializers, but not listed among initializers...); throws on error. Added this to regression tests. 3. O.step() now calls MetaBody::moveToNextTimeStep() directly, instead of spawning worker for 1 iteration. 4. Adapt stl import test to yade.ymport (the facets look weird, though?) (forgotten: remove prototypes for incrementCurrentIteration and incrementSimulationTime that are no longer used from Omega.hpp) Regression check that NULL state throws (if there is a material) as well. 1. Merge PeriodicInsertionSortCollider into InsertionSortCollider (periodicity detected automatically); PeriIsoCompressor moved to a separate file. 2. Initialize GranularMat properties (such as posisson't ratio) to arbitrary but non-zero values (avoids NaN's and disappearing bodies, bug #488100) 3. Re-enable clump logic in NewtonsDampedLaw (was #ifdef'd out), fixes bug #488100 4. Change prototypes of Shop::sphere and other methods, to take advantage of shared materials. 5. Change Collider::probeBoundingVolume prototype to return vector instead of storing it in the collider itself. 1. Enable velocityBins in pack.randomDensePack for periodic compression, speedup of about 13% (quite small?) 1. Fix Bruno's compile error pkg/dem/meta/Shop.cpp:281: error: operands to ?: have different types 'boost::shared_ptr' and 'boost::shared_ptr' 2. Fix warning's from out-of-order initializer in State. 1. add #error to DataRecorder so that people don't use it, with explanation. 2. Add Recorder, deriving from PeriodicEngine and taking care of opening file. 3. Derive TriaxialStateRecorder from Recorder. (Anton: do the same for CohesiveStateRPMRecorder, I don't want to edit it since the version would probably diverge if you work on it now) 4. Fix PositionOrientationRecorder (is that one being used at all?) 5. Rewrite Singleton (to work accross different translation units) 6. Remove qt3 from 'exclude'. Enabling opengl requires qt3 automatically now. 7. Remove lib/sqlite3x, which was only used in noew-removed SQLiteRecorder 8. Experimental main in python (not fully functionaly for now) 1. Re-enable temporarily commented code. 1. Re-enable PeriodicPythonEngine and a few other YADE_REQUIRE_FEATURE(PYTHON) that I overlooked 2. Make the python main program work with plugins (RTLD_GLOBAL in both DynLibManager and python); doesn't work with openmp and opengl (investigation ongoing), looks promising otherwise. The program is called yade-trunk-dbg-py and such; not all options of the c++ main is implemented (yet?). 3. (In previous commit) Remove loading preferences.xml, just use QtGUI if possible and enabled, otherwise "only" python console. 1. Remove rests of Preferences. 2. Remove HUP emergency saving (was disabled since long anyway) 1. Add chunkSize option that determines how many plugins will be compiled together. (orthogonal to linkStrategy, that one determines how many will be linked to together). Should avoid issue with monolithic link on machines with less RAM; allows parallel compilation of plugins on machines with lots of RAM. Defaults to 20. 1. Re-enable crash warning in pyboot.cpp 1. Remove implementation of global functions from Tetra.hpp to Tetra.cpp (gave errors on linking multiple objects including that same header.) 2. Add Body().geom as alias for (now deprecated?) Body().mold Make YADE_DEBUG work as expected (set debug leverl with log4cxx); avoid possible crash when logging during early log4cxx initialization. 1. Change prototype for InteractionGeometryMetaEngine to receive const State& instead of const Se3r&. Add const Vector3r& shift2 for peroioditiy (ZERO by default). 1. Fix Sega's and Anton's bug which was introduced in r1820 (keeping return from older version, instead of continue :-| ) 1. Rename EngineUnits to Functors, MetaEngines to Dispatchers (only the 4 types that we will keep). Python scripts should not be affected, except for raising deprecation warnings for the old names 2. Fix corner cases in deprecated names logic in python 1. Rename MetaBody to World (it had to be done at some point, regardless of what the name is) 2. Add Engine::world, set before every call in moveToNextTimestep 3. Change names of a few related methods 1. Fix "rootBody" in FileGenerator saver. 1. Add scan&replace scons builder 2. Get libstdc++ path from the compiler, embed it in main.py; it runs fine 3. Fix temporary filename in Omega (forgotten dir separator) (doesn't compile, will fix in a few minutes; need to transfer between computers now) cleanup of python boot code 1. Add yade.system module containing most startup things 2. yade-trunk-py usable now; startup is _much_ faster than the c++ main :-) (lazy linkage?). If everything works well, the c++ main will be deprecated soon (though still functional) 1. Add YADE_LINK_EXTRA_LIB so that plugin can request to be linked with additional library (used in MicroMacroAnalyser) 2. Add -frounding-math when compiling with CGAL 3. Lot of reorganization of python code. Yade is now fully usable (it seems) with the python main (yade-trunk-py), and also lodable from pure python 1. Fix assertion failure in NewtonsDampedLaw triggered by clumps in debug mode (typo) 2. Fix periodicity for Dem3Dof classes 3. Don't put things to __builtins__ in python, from yade import * will import wrappers as necessary into current global scope instead. 4. Expose Omega as yade.wrapper.O instance in the c++ code directly. 1. Error out if adding the same body twice from python 2. First steps for user tutorial (please do not edit now) 1. Move TesselationWrapper to lib/triangulation. 2. Main program (e.g. yade-trunk) is now in python; the old is yade-trunk-cxx. Most functionality should be the same, but please do report undesired behavior. 3. Adjust ipython configuration to be more friendly. 4. Improve default log4cxx output format 5. rename yade.PythonTCPServer to yade.remote 6. Remove annoying "INFO: sanitize failed" warnings 7. SimulationController now closes on escape or any function key. 1. Rename World to Scene, as Bruno suggested. It feels better, we are no gods to create worlds... 2. Rename BoundingVolume to Bound; BoundingVolumeDispatcher to BoundDispatcher; dtto for Functor 3. The 'shape' feature was renamed to 'geometricalmodel' feature to not conflict with the following: 4. Rename InteractingGeometry to Shape 5. Rename ef2_*_Sphere_Dem3DofGeom to Ig2_*_Sphere_Dem3DofGeom 6. Rename ConstitutiveLaw to LawFunctor, ConstitutiveLawDispatcher to LawDispatcher 1. Fix many warnings in various parts of python code related to renaming. 1. Rename data members to follow types: Body::boundingVolume → Body::bound, Body::interactingGeometry → Body::shape. Old names are still present as references with deprecation warning by the compiler. Regression tests passing. 1. make realVersion to be bzr revision 2. Re-enable Controller at startup always 3. Always rebuild python template files invisibly, since they wouldn't spot revision change otherwise (very fast) 1. Fix the plot example. 1. Add PeriTriaxController, with sample script in scripts/test/periodic-triax.py; works perfectly 2. Fix stress sign in PeriIsoCompressor (summing abs stresses still broken) 3. Handle periodic boundary moves with velocityBins 4. Rename ncb to scene in NewtonsDampedLaw (gradual change) 1. Fix (hopefully) an issue with log4cxx 0.9 reported by build robot. (Python 2.5 fix for robot) 1. Enhance PeriTriaxController for controlling strain/stress in periodic simulations; stress and strains appear to be physically correct now (however, see https://bugs.launchpad.net/yade/+bug/493102) 2. Add examples/concrete/periodic.py, showing uniaxial/biaxial periodic loading. Results are awesome. 3. Fix stiffness computation for Cpm. 4. Add (unpolished) pack.randomPeriPack for generating periodic packings. 5. Add some sphinx doc files (no contents, just skeleton). 1. Change prototype to InterationGeometryFunctor (see https://www.yade-dem.org/index.php/API_Changes) 1. Write some docs 1. Fix PeriTriaxController example 1. Refactor parameter table support (one reader class) 2. Fix yade-multi, add detection of regular exit with log4cxx crash at exit 3. Add --nice option to main.py 4. Make O.exitNoBacktrace output either "Yade: normal exit." (magic for OK exit, detected by yade-multi for instance) or "Yade: error exit". Fix reading parameters from table (thanks Anton for patience) Hopefully fix yade-multi https://bugs.launchpad.net/yade/+bug/493686 now? Please confirm. 1. Add Scene* Functor::scene, update it from all dispatchers at every step. 2. Add NewtonsDampedLaw::homotheticCellResize (0,1,2 for disabled, velocity or position update) (not tested at all) 3. Start removing Scene* ncb and Scene* rootBody etc from Engine::action as I stumble accross them. Please do the same, Engine::scene can be always used instead. 1. Renames as discussed on yade-dev: NewtonsDampedLaw -> NewtonIntegrator, StandAloneEngine -> GlobalEngine, DeusExMachina -> PartialEngine. Regression tests ok. 2. Rename the confusing scons 'pretty' option to 'brief'. Profiles will be updated automatically, both options are valid for now. 1. Finish renaming DeusExMachina -> PartialEngine 1. Enable search engine in doxygen. 1. Fix https://bugs.launchpad.net/bugs/495358 (seems like concurrent access with Anton ;-) ) 2. Add mask check to the collider 3. Initialize Body::id with Body::ID_NONE rather than -1 4. First attempt at doctest (for utils.sphere) 1. Don't call CreateIndex in Materia::Material (see https://bugs.launchpad.net/yade/+bug/495437) 2. Add dipl and rot methods to body, for querying displacement and rotation relative to reference position and orientation (moved from the python wrapper). 3. Add .classIndices to return list of class indices from the instance up to the top-level indexable from python. 1. Rename Sphere (as GeometricalModel) to SphereModel (to facilitate InteractingSphere -> Sphere soon) 2. Initialized density to 1000 in Material, to avoid weird explosions 3. Add scripts/tests/triax-basic.py, a TriaxialTest in python 1. A few renames: Facet → FacetModel, Box → BoxModel, GLDrawSphere → GLDrawSphereModel, GLDrawBox → GLDrawBoxModel 2. Remove shadowVolume functors, since they were not used anywhere in OpenGLRenderingEngine 1. Rename GLDraw* to Gl1_* 2. Scene no longer inherits from Body, some of its properties are "emulated" (bound, shape). Not sure if Shape is really needed, perhaps for periodicity things etc in one place? It can be in the class itself just as well. 3. Remove MetaInteractingGeometry2AABB from all files (no longer needed); backwards-compatibility with python assured. Hotfix for twice-renamed Bo1_SceneShape_Aabb. 1. Add some introspection interfaces to Indexables and dispatchers, as needed for Programmer's manual (https://yade-dem.org/sphinx/prog.html#multiple-dispatch), remove dead code, some cleanups. 1. Move lib/triangulation stuff to CGT namespace as suggested by Bruno in https://lists.launchpad.net/yade-dev/msg02658.html 1. Rename SpheresContactGeometry to ScGeom 2. Rename corresponding functors: InteractingBox2InteractingSphere4SpheresContactGeometry -> Ig2_Box_Sphere_ScGeom InteractingFacet2InteractingSphere4SpheresContactGeometry -> Ig2_Facet_Sphere_ScGeom InteractingSphere2InteractingSphere4SpheresContactGeometry -> Ig2_Sphere_Sphere_ScGeom 1. Rename InteractingBox -> Box, InteractingSphere->Sphere, InteractingFacet->Facet. 1. Fix renaming conflict (InteractingSphere->Sphere shadowed by older Sphere->SphereModel) 1. use stderr for standard startup messages 2. add scripts/test/dispatch-torture.py for visualizing dispatch matrices in html. Add support HTML.py module from the web. 3. call cleanupTemps if exiting; we should leave cruft in /tmp/yade-* only if crashing before trying to exit (unusual) 1. Make MetaInteractingGeometry2AABB warning more descriptive. 1. Remove Scene::{cellMin,cellMax}, use just Scene::cellSize; update all related code and scripts 2. Change python interface: Omega.periodicCell=Vector3 (only size, no more min/max) 3. Add (not yet used) core/Cell.hpp header. Will be accessible as Scene::cell, once used. 1. call centerScene() in GLViewer ctor, bind C to centerScene if no body is selected (was deactivated most likely by mistake, bzr annotate thinks it was me...!?). This should fix bug reported by Chiara for TriaxialTest with UpperCorner=Vector3(12,12,12) Fix missing import in py/post2d.py 1. Use Scene::cell instead of Scene::cellSize; update all code 2. Have O.cellSize (instead of O.periodicCell; add wrapper with warning) and add O.cellShear 3. Add scripts/test/periodic-shear.py (purely for showing the display things, no interactions etc yet!) Do pending renames: * AABB → Aabb * Interacting{Box,Sphere,Facet}2AABB → Bo1_{Box,Sphere,Facet}_Aabb * Wall2AABB → Bo1_Wall_Aabb * GLDrawAABB → Gl1_Aabb 1. Finish implementation of sheared periodic space. 2. Fix bug which might have caused missed asymetric (Facet - Sphere, for instance) in periodic space, when interaction order was reversed. 3. Add possiblity to pass a callable to utils.spheres' material parameter, to avoid shared material properties when called indirectly (pac.randomDensePack) 4. Remove Aabb::{center,halfSize}, since they were used only rarely and were redundant. 1. Remove abstract RenderingEngine 2. Remove SceneShape and related classes 1. Add python2.5 relative module import workaround (hope it works) 2. Move some python accessors from yadeWrapper to their respective classes 3. Half work on periodic cell scaling in the OpenGL renderer 1. Add ctor priorities, but only for gcc >= 4.3 (for early logging and plugins; necessary for the next point) 2. Register Functor core class in the factory (will be done for the rest soon, see https://bugs.launchpad.net/yade/+bug/498337) 3. Wrap Matrix3 class in python, write unit tests for it. 4. Re-enable ForceEngine and FacetTopologyAnalyzer 5. Update a few scripts in test/scripts 1. Implement arbitrary strain for periodic cell (see scripts/test/periodic-shear.py). Most code adapted accordingly. 2. ClassFactory now logs to cerr if YADE_DEBUG env var is defined, not otherwise. This avoids initialization order of plugins vs. ClassFactory itself 1. Fix weird behavior reported by Luc at https://lists.launchpad.net/yade-dev/msg02794.html (numerical issue) 2. Fix crash at body selection (wrong dispatcher arguments) 3. Add warnings about what Luc observed, should it happen again. 1. Allow spaces after YADE_REQUIRE_FEATURE (before parenthesis) and around its argument inside parentheses. 1. Fix https://bugs.launchpad.net/yade/+bug/499697 (sorry, Luc) 1. Rename BexContainer to ForceContainer, O.bex to O.forces etc. Mostly backwards-compatible in python. 2. Add Shop::flipCell which changes shear without affecting interactions (by integral steps), demonstrated in scripts/test/periodic-shear.py (not yet fully tested, but doesn't crash ;-) ) [BROKEN due to recent VELGRAD changed] 3. Add InteractionsContainer::eraseNonReal (Fix unsignificant hasShear mistake in Cell, clean old code there) 1. Make python interaction iterator return only real interactions. (TODO: regression test & check scripts for compat) 1. Add cell strain rate integration to the Scene loop. 2. Remove Cell::Hsize and friends, remove VELGRAD; unify both approaches. 3. Update some scripts, fix Shop::flipCell (demo in scripts/test/periodic-triax-velgrad.py) 1. Use Cell::trsf instead of Cell::strain (which really meant trsf-Id) 2. NewtonIntegrator now precomputes cellTrsfInc for the current step, instead of using Cell::getTrsfInc getting increment from the previous step (!?) 3. Update scripts and other code. 1. fix size computation in cell 2. Save history at exit, incremental history search with arrows up/down 3. Don't return false in Ig2_Box_Sphere_ScGeom for existing intr 1. Separate rotation&shear from scaling in cell. Fix possible error (but also possibly not?) error in collider. Spheres' Aabb's are still probably not correctly enlarged. 1. Forgotten new file. 1. Re-enable error check in InsertionSortCollider, make the explanation clearer 2. Fix sphere's Aabb (hopefully) (Bruno, could you check that?) 3. Worker thread now catches exception from simulation and O.wait() (or O.run()) will rethrow it; avoids crashes from exceptions. 1. Preliminary attempt at https://blueprints.launchpad.net/yade/+spec/c++-numpy-arrays (for postprocessing and similar), example in eudoxos.testNumpy 2. SpherePack::makeCloud can be asked for negative number of spheres (= as much as possible) 1. May fixes for errors found when running larger simulation. 2. Move material properties from Ip2_CpmMat_CpmMat_CpmPhys to CpmMat itself. 3. Some reverts in PeriIsoCompressor (log strain and usage of refSize) 1. Add clone function to python objects, taking optinal python dictionary with changed attributes 2. Fix PeriIsoCompressor for examples/concrete/periodic.py 3. GaussAverage relThreshold argument is now optional in python, as it is in c++ (again) 1. Fix examples/concrete/periodic.py 2. Fix (partially) scaling of periodic cell resize in OpenGL Implement https://blueprints.launchpad.net/yade/+spec/sphere-gl-stripes (weird lighting things). Must be enabled via "Gl1_Sphere(stripes=True)" in python. 1. Fix SpherePack().makeCloud() in python 1. Remove some old docs 2. Attempt at update-alternatives 3. packaging updates 1. FIx core class registration in the factory (fixes inheritance info in python for such classes) 2. Fix debian packaging, use update-alternatives Bulk of consistency renames (hopefully last for long time to come): * ElasticMat → ElastMat * GranularMat → FrictMat * NormalInteraction → NormPhys * NormalShearInteraction → NormShearPhys * ElasticContactInteraction → FrictPhys * SimpleElasticRelationships → Ip2_FrictMat_FrictMat_FrictPhys * ef2_Spheres_Elastic_ElasticLaw → Law2_ScGeom_FrictPhys_Basic * Law2_Dem3Dof_Elastic_Elastic → Law2_Dem3Dof_FrictPhys_Basic 1. Document PeriodicEngine (doxygen comment in the header) 2. Fix runtimePREFIX vs. PREFIX in yade-multi (only affects packages, not regular builds) 1. Fix epydoc generation with python main (thansk Anton for th yade-cxx hint!) 2. Expose O.tmpFilename returning unique filename in temporary dir that is deleted at exit 3. Do not import yade.plot at startup, since it initialized matplotlib to TkAgg, which needs $DISPLAY (and fails later if no $DISPLAY exists, i.e. for headless simulations) 4. Fix shear stress computation in CpmStateUpdater 1. Fix numpy_boost and TesselationWrapper 2. Start moving python registration code inside classes themselves. That should allow proper class hierarchy in python as well as (faster) object.attribute access instead of hacky object['attribute']. Please report errors you might encounter. 3. Resurrect Dem6DofGeom, doesn't work for now. 1. Add new-style python wrapper to most classes that were previously wrapped in yadeWrapper.cpp. Let me know if this breaks something for you. 1. Add YADE_CLASS_BASE_DOC_ATTRS and YADE_CLASS_BASE_DOC_ATTRS_PY macros for python wrapping, including documentation (e.g. https://yade-dem.org/sphinx/yade.wrapper.html#yade.wrapper.Body). All classes should be converted in the future. 2. Remove global functions (diagDiv, componentMinVector, ...) from the wm3 wrapper 1. Add new python wrapper to a few more classes. 2. Make python's executable have real python path in the #! line at the beginning (that is, the same python interpreter used for running scons) 1. Fix body_id_t typedef (add includes) 2. Check body id when accessing ForceContainer from python 3. Override prefix in config.py already if YADE_PREFIX is set 1. Fix python docstring options for boost <=1.35 (hopefully) 1. Classes now warn at startup if they don't register &document attributes with YADE_CLASS_BASE_DOC_ATTRS & friends. 2. Add YADE_CLASS_BASE_DOC_ATTRDECL_CTOR_PY macro that declares, documents and initializes data members. 3. Add NaN to lib/base/yadeWm3Extra.hpp, which is std::numeric_limits::signalingNaN() 4. Fix syntax in a few python modules, away from the old obj['attr'] to obj.attr 1. Add detection & mention workaround for https://bugs.launchpad.net/ubuntu/+source/boost1.38/+bug/457688 1. Convert a few more classes to YADE_CLASS_BASE_DOC_ATTRS 1. Re-disable CInem{CNC,KNC}Engines (sorry, Jerome) 2. don't compile cxx main anymore; delete the executable from installation if present 3. Add help for --threads equali with OMP_NUM_THREADS 1. Moved all (most) unused files to attic/* (such as those that have YADE_REQUIRE_FEATURE(PHYSPAR);). We will not keep them there indefinitely (they are in the history), though. If you want to re-enable some classes, fix them and move them back (using bzr mv) to pkg/*. If I inconsciously moved some file that was being used, please fix it yourself (it is unlikely, though). Get rid of physpas a geometricalshape relicts in non-attic code. 1. Fix class registration macro without attributes (remove "cap" in Rpm LawFunctor as well) 2. Remove StretchPeriodicEngine, it was probably too complicated to be really used; remove yade.plot data reduction which was relying on StretchPeriodicEngine 3. Properly expose PeriodicEngine, PythonPeriodicRunner, VTKRecorder, FileGenerator to python 1. Fix python registration of CohesiveStateRPMRecorder (YADE_PLUGIN was missing for PeriodicEngine and Recorder, it seems). Thanks Anton. 1. Wrap many classes using YADE_CLASS_BASE_DOC_ATTRDECL_CTOR_PY and friends. 2. "Fix" problems with features=all (is rejected now, features must be written by hand) 3. Add |ystatic| sphinx role (for static data memebers) 4. Rename GLDrawCpmPhys to Gl1_CpmPhys 1. Wrap yet more classes with YADE_CLASS_BASE_DOC_ATTRS and friends. I strongly ask people to do the same for "their" classes (like Bruno for TriaxialTest and so on); I will not and it might make those classes unfunctional in the future. 2. Add documentation here and there, where it was lacking 1. Remove wm3 includes from everywhere, use lib/base/Math.hpp instead (in preparation to the eigen switch). Regression tests passed. 1. Remove a few forgotten files. 1. Fix empty display (improperly initialized drawMask) 1. Catch io exceptions in the gui 2. Detect io error and throw in IOFormatManager 3. Set config dir at startup, enabling use of logging.conf etc 4. Fix display issues we had. When not running script/xml from command line, yade doesn't display the controller (press F12 to have it). Let me know if this is OK or not. 5. Fix OpenGL initialization code. 1. Add bin with 0 interactions to _utils.bodyNumInteractionsHistogram, hereby fixing utils.avgNumInteractions as well (thanks, Luc) 1. Update comments in scripts/simple-scene-plot.py (thanks, Chiara) Document registration macros (will move to Programmer's manual later) (Add 2 more hyperlinks to ElasticContactLaw, once it serves as example for docs) 1. Remove some garbage 2. Make code partially compile with the wm3-eigen glue. (more fixes for wm3-eigen compat) 1. Fix compilation for per-class builds 2. Add manual wrapper for wm3 classes instead of the auto-generated one, to ease transition to eigen. Let me know if it broke something. Fix compilation error introduced in last commit; sorry. Fix setting # of OpenMP threads via -j switch 1. do not build miniWm3 at all if not needed 1. Document a few classes. Register TimeStepper with YADE_PLUGIN as it should be (that's the reason it wasn't reported as not being registered with YADE_BASE_DOC_* -- thanks Bruno for pointing that out) 1. Add #ifndef YADE_* feature handling to implicit build scanner (till now, it was only supporting #ifdef YADE_*) rename sphere{From,To}File to {ymport,export}.text for consistency. 1. Add scene->forces.sync() to several places Fix typo (Scene::force vs. Scene::forces). Sorry. Thanks to Chiara for reporting. 1. Add no-alignment macros to compiler command line directly, this fixes compilation with eigen, including the tt.py test and scripts/regression-testss.py 1. Fix plugin registration for CinemCNCEngine, remove some cruft, fix formatting, add hyperlinks. 1. Fix quaternion/vector initializers in NormalInelasticityPhys 2. Fix some eigen related macros 1. Add eudoxos.InteractionLocator and eudoxos.IntrSmooth3 for 3d smoothing of arbitrary quantities defined on interactions. 2. Adjust some docstring formatting 1. Doc fixes 2. Change prototype for Funtor::getFunctor, since it doesn't seem to work from python now (perhaps it's that Functors don't inherit from Functor in python universe, actually?!) 3. Fix some stuff with class indices for GenericSpheresContact. (It doesn't seem to help, though, either) 1. Fix instruction set (march) for debian packages 2. chunkSize=∞ if <= 0 1. Add docs at several places 2. Update debian/rules to run tests 3. Add funnel.py scripts/test/CundallStrackTest.py 4. Add more formats to SnapshotEngine (don't seem to work, though) 1. Add IntrCallback and BodyCallback (not yet really documented), for hooking into interaction loop in InteractionDispatchers and body loop in NewtonIntegrator (suggested by Bruno). Two real callbacks are defined, to compute summary (hence also mean) forces on interactions and bodies. Sample script is scripts/test/callbacks.py, but currently it crashes for reasons beyond my comprehension. 2. Remove Scene* ncb and similar stuff from everywhere, since all Engines have scene declared in the base Engine class and don't need it pass as arguments. Later, the prototype will be changed (Engine::action(void) etc). 3. Add docs here and there. 1. Eninge::action and Engine::isActivated no longer takes Scene* pointer. It must be set beforehand by the caller (done e.g. in moveToNextTimeStep). Please check for suspicious crashes. 2. Remove PartialEngine::applyCondition, replace by action just like other engines (https://blueprints.launchpad.net/yade/+spec/remove-partial-engine-apply-condition) 3. Resurrect JumpChangeSe3 engine 4. add py/_extraDocs.py for documentation of c++ classes/function written conveniently in python strings rather than c++ string literals. 5. Fix bug in Dem3DofGeom_SphereSphere, introduced when avoiding normalization of (0,0,0) vector; is OK now. 1. devirtualize BodyContainer and InteractionContainer (they use implementation from BodyVector and InteractionVecMap). There is some speedup. I ask people (you) to run some simulation with the older and current version and report what they observe on the ML. I had more than 2x faster in some cases (in debug mode, though). 2. Fix chunkSize=-1 linkage (is like setting it to infinity) 1. Set docstring format for yade.qt 1. Code cleanups, docs 2. Make sure we are able to compile with boost::serialization (loading/saving works now as well, but no compression yet; about 3x faster for saving and even more for loading) 3. Enable boost-serialization feature for debian builds 1. Don't create python proxy classes for those not using YADE_CLASS_BASE_DOC_* 2. Remove few deprecated things like O.bex and such. 3. Warn about object['attribute'] syntax 4. Add yade --update option, which will do in-place replace for deprecated class names. Run on scripts/test/*.py 5. Wrap ResetRandomPosition and PositionOrientationRecorder 6. Remove some olden scripts 1. Move SpherePadder from extra to py/pack/SpherePadder 2. Add py/pack directory, to avoid too many files in py 3. Other small fixes 1. Fix crasher in Ip2_FrictMat_FrictMat_FrictPhys (??) 2. Cleanup python code 3. Add feature gl2ps, hitting 'v' in the GL view will save PDF (seems to freeze on large scenes, but works nice on small ones) 4. Add special syntax for deprecated attributes. For testing, renamed Shape::diffuseColor to Shape::color. 1. Fix gl2ps, works even for larger scenes now. 1. Rename many attributes in OpenGLRenderingEngine, using the deprecated attribute framework 2. Add pickling support to Serializables (useless) 3. Fixes of docstrings here and there 1. Disable deprecated attributes handling for gcc<=4.2, which gives errors on that code. 1. Use BSP sort in gl2ps only if len(O.bodies)<100 2. Remove ClumpMemberMover, no longer used anywhere 3. Fix pack.regularHexa bug, reported by Nasibeh http://www.mail-archive.com/yade-users@lists.launchpad.net/msg01424.html 1. Uniformize accumulator interface for open and openmp-less builds. 1. Fix compilation of deprecated attributes for gcc 4.3 (thanks Jerome for reporting) 2. Re-add facet rendering code. 3. Add docs to predicates. 1. TriaixalStressController: originally compilation fix, but Luc was faster; Bruno, I tried to replace on c-array with boost::array; if that works, you could use it for other c-arrays as well 2. Add yield surface query function from python to Law2_..._Cpm 3. Make plot support label translation via yade.plot.labels 4. make chunkSize very small for debian; add strip for the optimized build 1. Fix action(Scene*) vs. action() virtuals (mass replace in attic as well), in TranslationEngine. Thanks to Nasibeh Moradi for reporting. 1. Add doc/references.bib, which can be references from docstring using [Author2008]_ syntax (note the underscore). 2. Added a few bibliography items to test, and changed relevant docstrings -- see e.g. https://www.yade-dem.org/sphinx/yade.wrapper.html#yade.wrapper.NewtonIntegrator.damping Add doc to SimpleViscoelasticPhys, add Jean-Francois' paper to both bibtex and SpherePadder's docs 1. add axis parameter to utils.uniaxialTestFeatures, to force strain direction 1. Import yade.plot when showing graph 2. Fix bibtex entry 3. Handle unseen interaction in InteractionDispatchers differently than with requestErase, as that will not work with certain colliders 4. Add from yade import utils to utils.py docstrings, and show full utils.sphere instead of sphere in session transcripts (thanks to Jerome for pointing that out) 1. Add toy grid-based collider (very slow) 1. Rename viscoelastic classes as discussed on the mailing list 2. FIx some docstrings. Fix weird crash http://www.mail-archive.com/yade-users@lists.launchpad.net/msg01482.html in glGetError() (disable error check) 1. Reorganize engines a little bit, as discussed in http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg03337.html and other messages in the thread (trivial to change, though) 2. Small fixes at different places 1. Fix https://bugs.launchpad.net/yade/+bug/539562 (thanks, Luc) 2. Fix import warning in yade.remote Fix monolithic build (#pragma once for BoundaryController and FieldApplier), sorry 1. Add importing native SpherePadder meshes 2. Fix LSMGenGeo interaction with our own type Sphere (in yade itself and in SpherePadder (HACK!!) 3. Fix sample scripts for GenGeo and SpherePadder 4. Allow both gengeo and GenGeo imports 5. Fix ymport.gengeo (shift vs. moveto) 1. Start filling NEWS for upcoming 0.5: do the same if you have some big things in mind 2. Fix hyperlinks in Gl1_Sphere doc 1. Make python return Vector2r, Vector2r, Vector3i, Vector3r, Quaternionr and Matrix3r by reference rather than by value; fixes http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg03406.html and was introduced by fixing https://bugs.launchpad.net/yade/+bug/539562. See explanation in Serializable.hpp. 1. Replace the ugliest code I've ever written by something more sensible. Still ashamed, though, please forgive me. 1. Completely remove HydraulicForceEngine which didn't exist in sources (removed by Bruno in previous commit) 2. Experimental binary io using boost::serialization 3. Some function in yade.eudoxos 1. Some preliminary work to make boost:;serialization work (MUCH faster) 1. Fix calling {pre,post}ProcessAttribute multiple times with boost::serialization. Fix unchanged name (Bruno, do you use scripts/rename-class.py, right? https://www.yade-dem.org/sphinx/prog.html#renaming-class) 1. Skip yade::ObjectIO for boost::serialization-less builds. (thanks Nasibeh for reporting) Fix Jerome's problem with boost 1.35 (don't compile code uselessly) 1. Fix cached values for cell and facet when modified from python 2. Fix table parsing for lines with 1 character onlyDynamic 1. Clarify error message i Law2 functor is not found (thanks, Chiara) 2. Make static attributes initialized by values provided in YADE_CLASS_BASE_DOC_STATICATTRS 3. documentation fixes here and there 1. Fix yade.plot broken in last commit 2. adjust interpolating-force example script 1. Adjust interpolating-force.py script; present for Chia 1. Fix boost::serialization and postProcessAttributes 2. Add scripts/test/serialization-benchmark.py for comparing serialization time/size (http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg03496.html) 3. Fix bug #557124 (hopefully) 4. Don't call postProcessAttributes on Facet in utils.facet, as that is called automatically when setting vertices now. Some eigen compatibility stuff Some more replaces After some text replaces (IDENTITY etc); removed MarchingCube 1. Replace things for eigen compatibility. See https://www.yade-dem.org/wiki/Wm3%E2%86%92Eigen for details. Code should not be changed functionally. Report if it is. 2. Remove PositionOrientationRecorder from everywhere. 3. Make the timestep entry behave differently: only when enter is pressed, it will change timestep. Fixes bug #394687 1. Forgotten fixes. REALLY fix bad end iterator on InteractionContainer (since r2092!!). UPDATE your code, this makes simulations little wrong (some interaction might be processed twice in one step). (Remove unnecessary aseerts in InteractionContainer.) 1. Remove some ToAxisAngle and FromAxisAngle as per https://www.yade-dem.org/wiki/Wm3%E2%86%92Eigen 2. Fix NewtonIntegrator using [i] on quaternions. 2. Add docs for VTKRecorder 1. Make controller a little more compact 2. JumpChangeSe3->StepDisplacer (does it sound ok, Chia?), MomentEngine->TorqueEngine 3. Fix a few docs 4. Disable building of CapillaryPressureEngine, it cannot work. 1. Change Wm3 interface so that it is eigen-compatible. Please let me know if there are regressions. 2. Fix body selection with python when no onBodySelect callback is defined 1. Some garbage removal 2. Fix assertion in NewtonIntegrator 1. Fixes for Eigen compatibility (compile with features eigen,nowm3) 1. Add forgotten file 1. Add docs for kineticEnergy 2. Complete wrapper for Eigen in Python (will be renamed from miniWm3Wrap to yade.math or similar later), passes scripts/regression-test.py now 1. Rename miniWm3Wrap module to miniEigen. Let me know in case of regressions (shouldn't be, unless you imported that module directly) 2. Add documentation to the eigen wrapper, document operators (https://www.yade-dem.org/sphinx/external.html#module-miniEigen) 3. Add custom converters from sequences for all supported vector types 1. Fix bug with facet import Luc reported (thanks) 2. Add None to separate y1 and y2 axis (instead of |||, which will still work, but is not documented anymore) 3. Add the possibility to plot multiple x axes with the save variable by adding spaces to the name in yade.plots 4. Rename TestWm3Wrapper to TestEigenWrapper 1. Add backward-compat to Cpm model if from external files 2. Complete the eigen wrapper 3. Fix some docstrings. Fix inplace operators. 1. Add Pournin article to references.bib 2. Fix some docstrings (still not clear) Fix DOI for Luc's article 1. Make yade compile with eigen by default. Use 'wm3' feature to compile with Wm3 instead (beware, you still need eigen installed) 2. Disable the possibility of ocmpiling with external wm3. 3. Add Identity, Ones, Zero, Unit{X,Y,Z} to old wm3 wrapper so that they can be used in python. 1. Fix O.tags with keys with spaces (historical relics) 1. Add forgotten ctor with kwargs to classes with static attrs (such as GL functors) 2. Update scripts/test/Dem3DofGeom.py 1. Fix facet wall vertices addition in TriaxialTest. 1. Fix O.tags tag update. Thanks to Anton for spotting the problem. 1. Change O.dt semantics (negative value activates TimeStepper) 2. Rename O.usesTimeStepper to O.dynDt 3. Remove several Omega wrapper functions that really pertain to Scene, adapt code accordingly. 4. Remove bunch of useless files from attic (mostly seem to have equivalents in our tree, or are obsolete WRT code structure) 1. Change O.dt as per http://www.mail-archive.com/yade-users@lists.launchpad.net/msg01767.html + update docs 1. Remove some old garbage code 2. Make Material::id read-only from python 1. Forgotten Scene #include in StepDisplacer, sorry. 1. Partial fix for clump eigen decomposition 1. Fix apparent clumps problems, spheres in the dogbone were getting through. 1. Rename groupMask to mask, change its default value to match that of Body::Body ctor (Bodies with 0 mask would not collide!!!!!!!!!!!!) and add to to waoll and box as well (please keep the interface the same for all 4: sphere, facet, wall, box). 1. Remove old sphinx docs before adding new ones. 1. Merge sphinx docs from https://launchpad.net/~eudoxos/+junk/ydoc/ 1. remove sdecGroupMask from functors (handled by the collider already) -- thanks to Chiara for pointing it out. Fix compilation error (Bruno, you must have been terribly tired today) 1. add explicit qt dependencies. 1. Fix scene pointer in CohesiveFrictionalContactLaw 2. add doc to utils.avgNumContacts. 1. Fix timestepper selection 2. Disable debuggin in Eigen (for higher performance with debug builds) 1. compile with package QGLViewer, if installed (package libqglviewer-qt3-dev) 1. Add Peri3dController, done by Jan and me during a rainy day 2. Implement memoizeDb for pack.randomPeriPack 3. add polar decomposition to Matrix3 in python 4. make the 3d view update even if there are no bodies 1. Fix bibliography path in generated docs 2. Fix bug #582679 hopefully (compile error with clean builds) 3. Add import gts to gts related function in yade.pack, to make the error message more informative 4. Rewrite scripts/debian-prep in python instead of shell 5. Add qglviewer to some versions in debian/control-template 1. Remove pause time from omega, avoids negative realtime 2. Fix some scripts in scripts/test 1. Avoid recompilation of the UI when already compiled 1. Tentative fix for the clumps bug 1. Re-enable PeriIsoCompressor and PeriTriaxController 1. Update docs for Peri3dController 2. Fix compiler warning 1. Adjust debian-related packaging files 2. Remove NullGUI for good 3. Remove non-DISPATCH_CACHE code (not used) 1. Fix a non-critical typo in the script 1. packaging fixes 1. Remove attic (use bzr co lp:yade -r2280 to get it) 2. Remove QGLViewer 3. Remove miniWm3 1. Remove wm3 sources 2. Remove #ifdefs pertaining to Wm3 1. make Body::isDynamic a method (and Body::setDynamic to change it), in preparation towards making dynamic equivalent to State::blockDOFs==State::DOF_ALL 2. make YADE_BOOST_SERIALIZATION and YADE_SERIALIZE_USING_BOOST #defined in all builds (will be removed later once the switch is complete) 1. Replace wm3-compatibility functions (component{Min,Max}Vector, angleAxisFromQuat, diag{Mult,Div}) with their eigen equivalents. 1. Fix stl import with different material ================================================== yade-0.20.2 Sat, Sep 19 21:41:52 2009 +0200 Anton Gladky (34): 1. This is my first test commit 2. Added some initial files for mining rocks classes simulation 1. Some changes in RockPM, still does not work good 1. Some small changes on RockPM.* files 2. Test SVN_2_email 1. Test 2. RockPM.* updated Changes on RockPM.* files 1. RockPM, first variant of "destruction mechanism" 1. Deleted euclid.py 1. delete euclid.py (fised Sconscript) 1. In utils.py alignedFacetBox has been changed to facetBox. It is now possible to create arbitrarily-aligned box composed of facets 2. Updated regular-sphere-pack.py 3. Some small changes on RockPM.cpp 1. RockPM update. Added simple "destruction mechanism" 2. Added scripts/installOnUbuntu.sh to make "oneButton-checkout+compile+install+doxygen+epydoc" script. Not tested yet. Requires corrections. 1. Updated some scripts according to new syntax 1. Added PressTestEngine for simulating presses. Can be used and for PointLoadTest simulations. 1. Updated simple-scene-graph.py according to a new syntax 2. Updated simple-scene-video.py according to a new syntax 1. Changes on PressTestEngine. Now it defines the destruction moment more precisely 2. YADE CONSOLE emblem shows now without upper row shifted. 1. Some small changes 1. All variables initialize in PressTestEngine and RockPm Some changes on News Fix compile error 1. Partly fixed 1. Almost fixed https://bugs.launchpad.net/yade/+bug/412892 Just 1 warning: Some changes in INSTALL file because of migrating to BZR Some changes on one-click-install script Added "warning" in one-click-install script 1. Fixes compiling error without openmp feature. 1. 418107, I guess it is more correctly. Some nonessential changes Blocked some warnings in RockPM.cpp Small changes Press Engine and RockPM changes Added demonstration of buldozer simulation "Thanks" and Thanks to Janek :) Fixes VTK-librabry dependencies for Ubuntu Some small changes on Buldozer 0.20.2 Bruno Chareyre (22): A wrong comment on contact laws in PFC3D is removed. svn update - no real change (in principle) - recovering from erased local file - Fix conflicts and prepare next implementation of isotropic compression - Few files missing in the previous commit. - Add a new class for computing/recording micromechanical data based on tesselation Still recovering from conflicted files... I hope this is the last one. A class with algorithm for analysing contacts-forces-displacements statistics. Using the triangulation lib. 1. Fixed a critical bug in ElasticContactInteraction (kn, was not registered and left undefined after loading a simulation). 2. Test if fn!=0 (i.e. contact exists) before adding kn/ks to the global stiffness. 1. "Water" classes are updated based on the code developped locally (but not commited for a while) by Luc Scholtes. 2. Triangulation code updated as well (not compiled by default). 1. Add a missing class (for the capillarity model), this fixes a compilation error in the previous commit due to the missing files. The "stopSimulation" command in the compression engine is now optional, as sometimes you don't want it to stop at all(1). The default behaviour of the compressionEngine is not affected, with autoStopSimulation=true by default. However, the TriaxialTest IS affected : it sets autoStopSimulation=false by default. 1. Update capillary files and add a new engine for them. 2. Prepare for removing old useless classes (typically some variants of engines with "water" at the end) Remove useless dependency. -Avoid crash when computing fusion number (it was using pointers to deleted interractions) FIXME : no distant meniscii for now due to deletion by the contact law. Base class for the solid-fluid coupling (E. Catalano PhD). -Register "thickness" so that sample dimensions are computed correctly (and not with 0 thickness) Dimensions could be 0 when "updateParameters" was called from TriaxialCompressionEngine before TTController::action Missing declarations in r1836. - cleanup : removing unused (and useless) "water" variants of engines - some cleanup in recorders too Update of the read/write functions for the connection with comsol. (coupling via Berkeley<->Grenoble mail servers! ;)) Missing declarations of member variables. Set default read/write behaviour as in Andrea's version. Feng Chen (1): This is viscous force damping, equation similar to http://en.wikipedia.org/wiki/Damping, damping parameters are controlled by betaNormal and betaShear, it is sometimes more realistic than the non-viscous (or say, local) damping. While using this code, please make a reference to: Janek Kozicki (54): ouch, forgot to mark INSTALL file as outdated. We need to update it. some cleanup in the files fix crashes of this->parentWidget()->parentWidget() in UI yade.cpp: more detailed info about compilation flags. LatticeExample: added material parameters bond zone between steel fibres and cement matrix update to use latest scons 1.0.0 don't refresh display when there's nothing to refresh support for generating multiple file with single NullGUI call add to SimulationController buttons for looking in different directions. The default view direction is now down along the direction of gravity. improved generation of steel fibres in lattice fixed snaphotNames in NullGUI for .xml.gz more configurable MakeItFlat, TriaxialTest can be now a biaxial test as well. small fixes in UIs make it compile with boost 1.35 (I wonder what 1.36 will bring) Fixed OpenGL problems with displaying spheres, which - never occurred on my desktop - I've seen them sometimes on other peoples computers, but never could reproduce them - but finally have appeared on my laptop. up direction on Y release 0.12.1 created nearly empty snow package: pkg-snow Snow stuff - generate grains made of layers according to voxel data read from file. And daraw it. forgot some files - make it compile with boost 1.34 - some snow improvements - another fix. now it really compiles with boost 1.34 1. TriaxialStressController reads radius from interactingGeometry Code wasn't compiling because of #include MicroMacroAnalyser - comment it out. 1. argh, guys. svn HEAD must compile. You didn't check your commits and then I waste 1h to fix that. See this commit, to check what I had to comment out about WATER - added keyboard shortcut '.' that toggles grid subdivision by 10 - fixed error with grid step - grid step is now shown in gl window small snow update another small snow update 1. small snow update 2. fix compilation error by Vaclav (hey, you didn't compile again before commit! ;p ) rename file to avoid case conflict with directory 1. GLViewer - when sth. is selected don't move it to 0,0,0 position, but use its original position. This is done by delaying assignment to the next call of draw() - added extensive comments to the polyhedron code which will be used for collisions small snow update maybe spheres won't disappear anymore? a placeholder for drawing snow interactions changed guards to #pragma once postpone creating a 3d view, until a file is loaded. That should hopefully fix the problem with the primary view being empty. added AUTHORS file, for the purpose of updating file headers. This was copied from http://yade.wikia.com/wiki/Authors Why do I have the impression that I'm adding this file a second time? After all it's referred to in almost all source files "See file LICENSE for details.", right? sort people in alphabetical order sorry for bumping up revisions.... Snow, as it is finished by me. Further work on it will to be done by next post-doc researcher who wants money from EU for working on this :) fix miniwm3 / full wm3 compilation error I forgot to add those, sorry. (I wonder how it could stay unnoticed for so long ;) add option for horizontal or vertical wires in fibre reinforced concrete. 1. correct display of lattice rods on 0th iteration 2. on/off switch for using different stiffness for tension and compression in lattice 3. fixed a bug in BodyRedirectionVector related to deleting of bodies 4. two more lattice examples 5. few more safety checks in lattice code 1. NullGUI was still usin .gz while thay are not supported anymore 2. small lattice update sanitize stupid numers in QtGUI, eg. 0.1299999999999 becomes 0.13 small fix after isNew and isReal are removed I'll update the code to use new contact logic. Add an option to display DOFs and body IDs in the OpenGL window - Lattice uses DOFs now - old implementation is still accessible by setting a flag backward_compatible, so that hundreds of my old FileGenerator files will still work - some improvements to recording strains and forces - fix all my warnings - lattice generator improvements wrt concrete with steel fibres - some improvements wrt to generation of densely packed aggregates and steel fibres in the concrete structure - testing command "bzr commit --fixes lp:414868" - fixing bug 414868 Fix stupid error introduced when we have migrated to bex container 1. get snow code to run, albeit still buggy 2. why dynamic_casts stopped working everywhere, that's a mystery to me 3. interactions isNew doesn't exist anymore, snow code needs update for this Jerome Duriez (9): Added : - Engines for simulating shear tests at constant normal displacement, normal stress or normal rigidity (CinemDNCEngine, CinemCNCEngine and CinemKNCEngine) for samples deriving from SimpleShear PreProcessor (added also, former DirectShearCis) - ContactLaw1 : a contact law with Moment Transfer and inelastic behaviour in compression : see comments. With correspondant Relationships and type of Interactions. NB : sorry for the name : i didn't search too long for a more explicit one but I think personly that the comments in the files (and I tried to put some) are far much better than the one - Add of the paragraph for the CL1Relationships, which was forgotten, in the corresponding SConscript A (last ?) error concerning last revision in the paragraph CL1Relationships : "CL1Interaction" does not exist, that's ContactLaw1Interaction -ContactLaw1 : correction of prototype of action() : it needed a body, whereas now action methods of Engines need a Metabody. This led the simulation to crash and is now fixed - SimpleShear : now all is normaly done so that this preprocessor could be used (with success) with this ContactLaw. Moreover it is now linked to the GlobalStifnessTimeStepper (instead of the ElasticOne) Suppress of some useful comments (sorry for the extra mail) (At last) The good Sconscript file - The GlobalStifnessCounter engine (for correct use of GlobalStifnessTimeStepper) was forgotten in the preprocessor SimpleShear... - Correction of the headers of two files "ContactLaw1Interaction" which were commited by me and not by Bruno - Some features of ContactLaw1Interaction were declared in ElasticContactInteraction. This was a mistake totally not planned (and the fact it was in svn also was not noticed) and is now corrected - End of the job by suppressing also the corresponding lines in .cpp... Luc Sibille (1): I added a new engine "ThreeDTriaxialEngine" to perform triaxial simulations with an independant control in stress or in strain in the three space directions respectively. In this goal, the TriaxialStressControlEngine has been sligtly modified to impose a different stress value or strainrate in each space direction. I hope I have broken nothing! Sergei Dorofeenko (32): 1. A new algorithm for facets. It use only a class Facet, so classes Vertex and Edge are deprecated and has been removed. 2. Add functions to python gui for import geometry from stl and for creating facets. 3. Add Shop::inscribedCircleCenter for calculate position of center of triangle inscribed circle (use it for set facet's se3.position). 4. ForceRecorder now take cary about old data files and renaming them. 5. SimulationPlayer now allow wire body form view tab. 1. ResetPositionEngine is now inherited from PeriodicEngine. 2. Add examples/rod_penetration model and geometry. small fixes 1. New random-access interaction container InteractionVecMap (rewrited from InteractionVecSet) 2. Fixes: default initialization some attributes in SCG and IS2IS4SCG Intermediate commit for SpheresFactory. Don't work yet. 1. New engine SpheresFactory 2. Add function engineByLabel to MetaBody 3. Add members to BroadInteractor. 1.First worked version of SpheresFactory engine. Example in examples/SpheresFactory 2.Added PersistentSAPCollider::probeBoundingVolume function (for using with SpheresFactory) 3.InteractionGeometryMetaEngine::explicitAction has been modified to remove artifical (as me seems) asserts. 4.python import_stl_geometry now return list of body ids instead only their number. 5.import stl geometry now allows import facets without BoundingVolume and InteractingGeometry. 6.Fixed dynamic_cast for BroadInteractor. 1. SpheresFactory allows now to create spheres in a convex volume. 2. SimulationController estimates total simulation time if stopAtIteration>0. 1. SimulationPlayer now allows to reload filters without reloading all simulation. 2. ColorizedVelocityFilter now allows to setup minValue,maxValue without reloading the filter. Fixed bug in RotationEngine: rotationAxis now normalized in action(), not in postProcessAttributes() ColorizedVelocityFilter counts a scale for each frame, without using previous min,max values. Class SimpleViscoelasticInteraction is renamed to ViscoelasticInteraction and is inherited from ElasticContactInteraction now. 1. Convert SimpleViscoelasticContactLaw to ConstitutiveLaw engine unit (Spheres_Viscoelastic_SimpleViscoelasticContactLaw). 2. SimulatonPlayer have now Display tab as one in SimulationController. 1. The experimental widget for drawing a color scale for colorized velocity filter. 2. Convenient python function utils.ColorizedVelocityFilter. Merging utils.*_v2 functions with their "first" analogs. Add two new filters: ColorizedTimeFilter and PythonRunnerFilter Migrate GravityEngines and ConstitutiveLaw to BEX_CONTAINER Convert STLImporterTest to ConstitutiveLaw (SimpleViscoelastic contact model) and NewtonsDampedLaw engine. Fix bug in serialization for ViscoelasticInteraction. Fix compilation error for InteractionHashMap Update contact logic for SpatialQuickSortCollider (hope, it's correct) Fix typo in PersistentSAPCollider 1. Remove zeroPoint 2. Add prefix ef2_ to Spheres_Viscoelastic_SimpleViscoelasticContactLaw Fix link errors fixed and updated some examples in keeping with last modifications Realise InsertionSortCollider::probeBoundingVolume() so SpheresFactory now works SpheresFactory now can create a spheres by python function. See scripts/test/SpheresFactory/model.py for example. Add export python module with VTKWriter class (very initial) to export data from YADE to VTK-based post-processing tools Added a c++ VTKRecorder (for spheres and facets) and new feature 'vtk' needed for it. Add colors rec to VTKRecorder Add default path for VTK Fix VTKRecorder headers Fix VTKRecorder headers Add VTKINCDIR to configure options for directories where to look for VTK headers Unknown (3): I added a new state at the triaxial compression test in order to realize isotropic compression by the walls displacement until a indicated porosity value. These modifications can be seen with generator file "TriaxialCompression" in the last three parameters (added). I corrected my errors on the triaxialtest files.Moreover, i added comments in the TriaxialCompressionEngine.hpp. The isotropic compaction into the TraxialTest is activated: 1)I have deleted the translationspeed parameter (now the translation speed of walls is the strainRate parameter) 2)I have activated the porosity parameter in the TriaxailStressController.cpp file Vincent Richefeu (42): - initialize radius in InteractingSphere constructor. - add new plugins used for membrane modelling. - add GLDraw plugin for BssSweptSphereLineSegment displaying - 'Membrane' (in fact geogrid) has been improved but still doesn't work... - the class GroupRelationData has been add (not used yet) to define interacting parameters such as coefficient of friction or restitution that have nothing to do in the bodies parameters (in my opinion) - forgotten files - add the soft mgpost for DEM simulation post-processing and visualization. - set menus in english mode A very quick guide for mgpost (usage and XML format) a forgotten file in mgpost/doc - add a new tool for sphere packing (still in dev) - some enhancement in mgpost interface - SpherePadder devel... SpherePadder devel... SpherePadder (devel: 5 steps ok) - SpherePadder update - add a basic 'user friend' interface for sphere packing generation. The module can of course be used without this interface. Speed enhacement for the SpherePadder algorithm. Add possibility to make PNG screenshots (using libpng) Add a DataRecoder that generate MGP files (only for Spheres for the moment). The MGP files can then be read with mgpost. - add a class based on CGAL for 3D triangulation. - Packing method enhanced (place 380000 spheres in less than 2 min) Fix some bugs and enhance the display of positive and negative forces Fix some bugs Begin devel. of densification process 2 files that were forgotten Simplify sphere shapes when if there number is increased Bug corrections (min and max radii) - overlap with spheres inserted by user -> bug fixed - Densification begins to work Increase the number of colors for the display of body's groupMasks from 6 to 10 We can now make the packing denser with a stop criterion based on the solid fraction or total number of spheres. Add BasicViscoelasticRelationships: an alternative to SimpleViscoelasticRelationships. It accounts for the effective mass of each contact and considere the parameter cn as a dimensionless ponderation of its critical value (computed for each contact). Parameter cs is set to zero for the moment. Add a boost.python wrapper (module packing) Add a function to SpherePadder_wrapper to pass the result back to python. As Vaclav suggested, it is a list of (x,y,z,R) tuples. (Complet integration into yade is not done yet) - Add 'HistoryRecorder' to save the sample and network state with a given time-step interval. - Correct a small bug due to the fact that a Clump cannot be casted into a GeometricalModel (and I don't know why!) Use the clump mass instead of clump-member mass for the determination of the effective mass. Ooops! There was a bug Add the function NormalRestitution2DampingRate. Add sphere reading for gdm-tk format Remove default linkage with libtiff (png is now prefered) Add an example of python script for SpherePadder Add GroupRelationData serialization (not used yet in *Relationships classes) This class serves to manage parameters between bodies depending on their groupMasks. Here is an example of 'command stream' in xml file to set the parameters: Just try to use GroupRelationData with BasicViscolelasticRelationships. Cast size_t to int in pow(double,int) function to avoid ambiguity for gcc (compilation failled on one of my computer) Some tiny modifications for Mac OS X compatibility (Does not compil yet). Some forgotten tasks replace gcc-3.3 by gcc in the Makefile.macosx of mgpost Václav Šmilauer (313): Move big news to NEWS, ready for release finally (?) Update INSTALL file from wiki (brief instructions only). 1. Reimplement some loop-intensive functions from yade.utils in c++ for better performance (as yade._utils, imported into yade.utils automatically - transparent to the user) 2. Add poisson's ratio and Young's modulus estimation in yade.eudoxos based on linear regressions of position→displacement mapping along different axes 3. Rename Shop::ElasticWaveTimestepEstimate to Shop::PWaveTimeStep, wrapped in yade.utils 1. Add python interface for blocking DOFs: b.phys.blockedDOFs=['z','rx','ry'] It is friendlier than b.phys['blockedDOFs']=1<<2|1<<3|1<<4. The property is read-write. 1. Add code for computing histogram of interaction directions in given plane in _utils. 2. This is code is used by yade.eudoxos.plotDirections() to create the actual (nice) figure. 1. Skip (almost) exactly zero projections, implement masking of bodies. 1. poisson and young estimator now works on a fractional part of the speciment 2. do not switch ui automatically if selected explcitly 3. body::maskOK to check mask 1. eudoxos module cleanups, young estimator arg chages 2. fix harmless compiler warning in _utils.cpp 1. add utility function to compute elastic energy within a volume (the dynamic_cast to NormalShearInteraction still fails; what is going on?) 2. add utils.fractionalBox, an AABB reduced to its fraction 3. fix fixmes in Force and Momentum about unused functions about to be deleted 4. plotting interaction direction histogram now works on contrained volume (to study boundary influence on the distribution) 1. Beginning hijacking SpheresContactGeometry to hold more elaborate geometry characteristics, such as relative shear displacement. By default, those parameters are neither calculated nor displated (exactRot==False; must be set to True in ISphere2ISphere4SpheresContactGeometry to enable it). Test script is in scripts/exact-rot.py 2. Remove deprecated code from UniaxialStrainController 3. Add GLUtils to draw lines, text, numbers -- copid over from Shop 4. Add operator<< for Quatrnions (axis angle) 5. Fix energy calculation in volume (in _utils.cpp) 6. Other fixes here and there... 1. The exactRot code is reasonably verified now to be functional, including rolling correction (SpheresContactGeometry::relocateContactPoints) and will used in brefcom soon. 2. Updated the "testing" script scripts/exact-rot.py, as a showcase as well. 1. Remove GL things from Shop, moved to lib/opengl/GLUtils.hpp 2. Cleanup of SpheresContactGeometry code, rename exactRot to hasShear (I thought most of this was already commited?!) 1. Delete unused IS2IS4DistantSpheresContactGeometry (merged with IS2IS4SCG), adapt existing code 2. Adapt new facet code to updated SpheresContactGeometry (only superficially tested) so that they can interact using BrefcomLaw; add scripts/exact-rot-facet.py to show that. 3. Fix a few missing loggers in others' commits. 4. SimulationController redraws if iteration changes (the +1 button would otherwise not cause redraw) 5. Remove cruft from Brefcom. 6. Fix inheritance (dynamic casts) of NormalShearInteraction and of BrefcomPhysParams 7. Remove cruft from UniaxialStrainer 8. Add some python code to compute stress from stored elastic energy. 1. Move interaction direction distribution pie histograms to utils 2. Add plotting histogram of number of contacts to plotDirections() 1. Omega().bodies.append can take list of bodies now (instead of just one body), returning list of added id's 2. utils.facet can take both tuples and lists for vertex coordinates 1. Add NormalInteraction::normalForce and NormalShearInteraction::normalForce (moved up the hierarchy from ElasticContactInteraction) so that unbalancedForce can be calculated on any subclassed interaction type. 2. Adapt Brefcom for this. 3. Add Shop::unbalancedForce and utils.unbalancedForce 4. Add workaround for saving ipython history as suggested by http://lists.ipython.scipy.org/pipermail/ipython-user/2008-September/005839.html 5. Fix AxialGravityEngine to register parent class attributes. 1. Avoid compiler warning in optimized builds from pyOmega 2. Body containers now allocate the lowest possible ID for each added body. The old behavior was to allocate the first free ID greater than the ID of the body, if it was already set. Please let me know if this is critical for someone. We can do things like: 1. 3d view now has by default a OSD with iteration number, simulation time and virtual time. This can be toggled (all combinations) by pressing 'D' (which used to mean toggling d+ynamic flag...?) and set also from python with GLView.timeMask='rvi' (Real,Virtual,Iteration) and so on. 2. Simulation player displays real time and wall clock loaded from db (insted of bogus values of system clock when the player is being run) 3. new periodic SnapshotEngine that takes snapshots of any GL view to numbered PNG files. 4. new function qt.makeSimulationVideo that makes video _while running the simulation_. 5. qt.createVideo renamed to qt.makePlayerVideo 6. Added Omega method to query computation duration. 7. An example of using qt.makeSimulationVideo is in new file scripts/simple-scene-video.py 1. Add forgotten SnapshotEngine 2. BodyRedirectionVector always really find the lowest unused ID (the same for BodyAssocVector) 3. add Omega().interactions.clear() in python 4. Move the "Less than 500 bodies, moving possible" to LOG_INFO instead of on-screen since it disturbs videos taken during simulation... A few fixes in TriaxialTest: 1. radiusStdDev is a registered attribute parameter 2. skip unloading phase if sigmaLateralConfinement==sigmaIsoCompaction 3. new bool autoUnload, that controls automaticity of going from compaction to unloading; autocompressionActivation controls from unloading to loading. Note: IFacet2IS4SCG is broken, but not yet fixed. 1. TriaxialTest now takes readiusMean argument (by default negative, i.e. disabled); if >0, box size is scaled so that both requested porosity and mean size can be preserved. 2. Attempt to fix computation of stress from stored elastic energy. 1. Fix adding empty engine if record wall stress interval <= 0 in TriaxialTest (bug introduced yesterday) 1. Add Interaction::swapOrder(), for use in EngineUnits that want to avoid calling goReverse() 2. SnapshotEngine can sleep specified number of msecs after shot, which probably can avoid some hw problems (make_current failed in mesa, freezes etc) 3. InteractingFacet2IS4SCG now works "correctly" (not exactly physically, though) with shear 4. DynLibDispatcher should report names of classes if dispatch fails. 1. Add InteractionGeometryMetaEngine::explicitAction and InteractionPhysicsMetaEngine::explicitAction for creating contacts manually using the dispatcher 2. add utils.createInteraction(id1,id2) that requests explicit transient interaction creation 3. Add sample ElasticContactLaw2 (in ElasticContactLaw.cpp) that uses new SpheresContactGeometry code and can be used for "persistent" (transient but not deleted by the collider) contacts. 4. Add Shop::applyForceAtContactPoint (applies contact force at contact point to both bodies (reversed for body2) and moments acting on their cenroids as well) 5. All the previous new functionality is demonstrated in scripts/chain-distant-interactions.py. 1. Add Omega().reload() 2. Create map Omega::memSavedSimulations, where simulations are saved if they begin with special sequence ":memory:" and can be loaded again, within lifetime of Omega. 3. Add Omega().tmpLoad() and Omega().tmpSave() that use the above mentioned thing. 4. add utils.readParamsFromTable that reads any python variables from text file (useful for automatic parametric studies) 5. Add less expensive routine for sontact point relocation in SpheresContactGeometry 1. Separate player into two windows (controller and the 3d view); the controller may be hidden with ::hide() (and ::show()) or with Alt-H from the 3d view. This allows for correctly restoring 3d view size. Closing any of the two closes the player. Please log crashes, if any. 2. Update QtGUI-python.cpp: runPlayerSession 1. Yade now runs TCP server at the first free port above 9000 (accessible from localhost only), which simulates python console. (let me know if you need this over network -- it is DANGEROUS, since someone can delete all your files etc without any authentication). The interpreter has its own namespace. 1. Fix crasher (under special circumstances) in PersistentSAPCollider (deletion invalidating iterator) 2. PeriodicEngine now takes nDo and nDone attributes, limitng number of activations 3. Fix minor things is BrefcomDamageColorizer, add normalized damage to BrefcomPhysParams 4. Fix some indents in Triaxial Fix stupid sign mistake when applying contact force in brefcom. 1. PythonTCPServer now generates random 6-letter cookie (password) at startup and authenticates all connections by that cookie. It can be retrieved from yade.runtime.cookie 1. Add Body().mask in python 2. Add PhysicalParameters().pos and .ori instead of ugly pp['se3'][:3] and pp['se3'][3:] 3. Add dmgPlane plot in brefcom 4. Do not delete renderer if we close the last view (loses all renderer settings) 1. Add a quick implementation of bending and torsion code to SpheresContactGeometry 2. Update ElasticContactLaw2 to use that code; stiffnesses are hard-coded for now. 3. Update scripts/chain-distant-interactions.py to show that that code really works 4. Plot residual strength instead of damage in brefcom 5. Add some functions for spiral projections (not correctly working yet) 6. Fix missing std:: in DisplayParameters 1. Add 2d weighted average smoothing abstract class and its specialization on symmetric gaussian kernel, with python glue of course. 2. Remove .gz support. 3. Fix some bugs in the spiral projection code. 1. Fix errors preventing compilation due to missing TesselationWrapper. !! IMPORTANT !! Introduced new dependency on "python-numpy" package (numpy/ndarrayobject.h header), which is now checked for by scons. Tell me if this is not OK! 1. Add initializers for all SpheresContactGeometry members, to avoid nan's in the .xml file 2. Add code for saving arbitrary python variables within the .xml file, see documentation on utils.saveVars() and utils.loadVars() 3. Fix error (hopefully) caused by dangling symlinks in the symlinked buildDir/include tree 1. Fix algebraic typo in max distance check. 1. Commit simple parametric study interface, documented at http://yade.wikia.com/index.php?title=ScriptParametricStudy and wrapper script to queue jobs, which is installed as yade-trunk-multi, yade-trunk-opt-multi and so on. 2. Examples of such parametric "study" added in scripts/multi.py and scripts/multi.table 3. MetaBody now create Omega().tags['id'] at initialization like '20081028T102950p15498' (date, time, pid) that is unique 1. Changed colors to be random by default on utils.{sphere,box,facet} 1. Make our intelligence-challenged deserializer finally gracefully handle nan, inf, -inf (arbitrary lower-upper case). 2. Fix crash in MembraneTest (leftover in the commit from testing, oh well) 3. Add TriaxialTest::fixedBoxDims to not scale selected box dimensions if sphere mean radius is given (example underway). 1. experimental support for Real==long double (#defines QUAD_PRECISION, scons quad=1). long double is not necessarily quadruple precision (not on IA32, at least) though, but is still more precise than double. (search "long double" on wikipedia) 2. Some preparation to compile with -std=c++0x (not yet functional) WRT and boost::shared_ptr vs. and std::shared_ptr 3. Fixed in yade-multi. 4. New direct oofenm exporter in yade.eudoxos. 5. Don't fiddle with termios in non-interactive sessions. 1. Add INTEGER (besides FLOAT) to the list of wrapped c++ types in python. Fix type detection for long double 2. Fix Real->double conversions in GLDrawBssSweptSphereLineSegment.cpp 1. Body().phys.refPos is directly accessible now (old way Body().phys['refSe3'[0:3]] still works, though) 2. Labeled engines are at load-time or when Omega().engines are modified assigned to variables __builtins__.label; for example Add forgotten file. 1. Add linear templated interpolation function working on 2 lists, t and values 2. Add InterpolatingRotationEngine that changes rotation speed as given by value table 3. Lower info about starting python thread to debug message only. 1. Rename REGISTER_SERIALIZABLE(class,bool) to REGISTER_SERIALIZABLE_GENERIC, add two macros REGISTER_SERIALIZABLE and REGISTER_SERIALIZABLE_FUNDAMENTAL. Changed all uses accordingly. 2. Added REGISTER_CLASS_AND_BASE(class,base) which performs REGISTER_CLASS_NAME and REGISTER_BASE_CLASS_NAME at once. 3. Added REGISTER_ATTRIBUTES (not trailing 'S'), expanding to void registerAttributes(){...}, and REGISTER_ATTRIBUTES_WITH_BASE, which prepends call to baseClass::registerAttributes() (specified as the first argument). 1. Added Se3Interpolator engine, with scripts/test/Se3Interpolator.py 2. Added from math import * to PythonUI_rc.py so that math functions are readily accessible everywhere 3. Implemented stopStrain in UniaxialStrainControlledTest 4. other small fixes 1. Modify REGISTER_ATTRIBUTES macro so that it work with or without base class given. Change all headers in core to use that. It should help us if we ever make the transition to boost::serialization. 2. User REGISTER_CLASS_AND_BASE instead of REGISTER_CLASS_NAME and REGISTER_BASE_CLASS in core and at a few other places. 1. Removed cerr garbage from glviewer (use LOG_DEBUG if needed) 1. Fix warnings in GLViewer 2. Add (35.4%)-style counter if stopAtIteration is set to the OSD in gl view 3. Add utils.downCast to downcast object to its derived class and copying all attributes. 4. Add utils.SpherePWaveTimeStep to compute critical dt from a few parameters only 5. Add routine to compute overall kinetic energy to Shop (indirectly to utils as well) 6. Add routine to sum torque (momentum) with respect to an axis from forces and torques on given set of bodies. Fix typo (compilation error in debug mode) in Shop::kineticEnergy 1. Fix a bug in rotation ode in SpheresContactGeometry. Now the code gives the same results as almost-for-sure-correct FEM code regarding strain computation. 2. Add label attribute to StandAloneEngine (inherits from Engine) omg (code cleanup, no functional changes) Exit once the simulation finishes; do not rely on simulation exiting itself. 1. SpiralEngine that does both rotation and translation along the same axis 2. InterpolatingSpiralEngine for variable rotation+translation speed (replaces InterpolationgRotationEngine) 3. scripts/test-spiral.py for rudimentary functionality testing. 1. Un-disallow (bug) having all dimensions scalable in triaxial if particle radius is fixed. 2. Don't record anything by default to file in UniaxialStrainer (only useful for debugging) 1. Add a few functions for integrating piecewise-linear functions in new module yade.linterpolation 1. fix damage colorizer (removed dynamic_cast causing segfaults on non-spheres) 2. InterpolatingSpiralEngine now takes bool wrap rather than Real period. 3. qt.makePlayerVideo takse startWait argument, which waits for Backspace before starting (useful for setting up the view manually); postLoadHook gets run afterwards now. 1. Add algorithm for pushing sphere always to the same side when in contact with facet, even under extreme stress where the sphere geometrically passes to the other side. 2. Add bool SpheresContactGeometry::initContactOnPositiveFacetSide for that 3. Add test/demo script for that. 4. Re-enabled GLDrawSphere::glutUse (cosurgi?) 5. Renamed yade.runtime.args to argv, to be consistent with sys.argv 6. Allow passing sys.argv (arguments to scripts) through QtGUI as well 1. Fix clip plane orientation inversion as well as wheel normal movement. 2. Clip planes not displayed at all unless one of the clip planes is being manupulated. 1. Unbreak bad type (list) for sys.argv[0], broken recently 2. Color bodies by residual strength rather than damage parameter (smoother) 3. Make player messages (maybe) better formatted omg... 1. Make player reuse existing renderer if there is one (allows setting Draw_mask etc before running player) 2. Add initRun parameter to PeriodicEngine (false by default), to run at the very fist run. 1. Make BrefcomDamageColorizer run at 0th iteration as well 2. Make player set stopAtIter to last iteration in db so that percentage is displayed in the output. Fix previous commit, overlooked. sorry. 1. Number lines in parameter table for multijobs from 1 (as text editors do) 2. Print short summary at the end of job log (when started, when finished, exit status, duration, commandline) 1. Fix logic typo in QtGUI (warning when there shouldn't be and vice versa) 1. logarithmic strain for Brefcom. 2. change sphere-facet algorithm such that it works on corners. Maybe no longer necessary, but it doesn't hurt now. scripts/test-sphere-facet-corner.py as provided by sega demonstrates that. 3. "from __future__ import division" in python init such that 3/2==1.5 and 3//2=1 (is default since python 2.6) 4. Global GL lock to avoid crashes/freezes with GL accessed from multiple threads concurrently. scripts/gl-test.py (which used to crash) now works with one view; 5. Properly lock/unlock on all gl ops in QtGUI-python.cpp, like setting view direction, resizing etc. 6. Fix wrong assertion in SQLite player 7. add Omega().resetTime to reset iteration number, virtual and real time. 8. Changed utils.loadVars/saveVars code to be more reliable. 9. Added utils.aabbExtrema2d 1. Lock GL when closing view. Seems to fix crashes / delays at exit 1. Contact sphere-facet must be deleted by the constitutive law once created. Let me know if that is a problem -- I think it is the way it should be in the future everywhere, though. 2. Fixes for boost 1.37 (boost::thread not fully compatible) 3. utils.basidDEMEngines (not tested yet) 4. Fix warning in GroupRelationData 5. add march switch to scons ('native' is default, but not supported by older compilers) 6. Prepend default CXXFLAGS so that user-defined ones (like warning suppression) come after the default ones and override those. 1. Tentative fix for newer scons, which links empty files (dummy plugins) with plain gcc and doesn't find default c++ libs to link with. 1. File not needed. 1. Beautify no-debug code in main 2. SpiralEngine now saves angle it has turned so far 3. Remove failing assertion from IFacet2ISphere4SCG (why it fails? it was a (I->isReal&&I->interactionGeometry)||(!I->isReal&&!I->interactionGeometry)...) 4. Improve the utils.spiralproject function to specify period (moderately tested, but seems to work) 5. Adjust locks in GLViewer. Fixes my crashes on nvidia for both player and 3d view (didn't dare to try 2nd view). Next step will be to move this lock to Omega and lock it when loading/resetting simulation etc. 6. Change theora video quality to 63 (maximum) instead of medium 32 in utils.encodeVideoFromFrames. Makes the video about 3x bigger. Two BIG changes: 1. Add ef2_Spheres_Brefcom_BrefcomLaw, is faster (!) 2. Fix locking in Omega, we don't get crashes when loading simulation with the 3D view enabled anymore (please report any further crashes in OpenGLRenderingEngine, that should be fixed) 3. Automatic update of Doxygen configuration file 4. Dem3DofContactGeometry, which should be in near future parent of SpheresContactGeometry and other new geometries providing normal and shear strains (SphereFacetContactGeometry, in my mind) 5. Add convenience function to apply force to contact point between two particles. (remove no-warn for c++0x since that flag is not known to gcc-3.4) 1. Add possibility to change container types from python (for benchmarks) -- code not yet tested! 2. Possible optimization in PhysicalActionVectorVector, now disabled. collider mistake hotfix 1. Make triaxial stop if !autoCompressionActivation and already unloaded. If this breaks something, please let me know, we can do it otherwise, but, for Cundall's sake, can we keep the same behavior for at least 6 months?? 2. SpatialQuickSortCollider will not delete real contacts, even if bodies don't collide. 3. Remove redundant attribute registration from SpheresContactGeometry fix typo in collider 1. removed persistentInteraction from most places; they are still present in MetaBody, but not serialized any more, most importantly (avoids warnings) and not GL-drawn. 2. Plugin loading loginc completely changes, the underlying macro YADE_PLUGIN has still the same interface. We used __attribute__((constructor)), __attribute__((visibility("internal"))) and anonymous namespace magic to get there. This will make it possible to put multiple plugins to a single shared library without touching the source, only fiddling with SConscript's. 3. PythonUI is interactive by default (it was not?? weird.) 1. Add new non-generic Bex container. For non-optimized build, it increased the speed by about 11% (9:35 vs. 8:49) as compared to PhysicalActionVectorVector. Users willling to go with the slower PhysicalActionContainer can compile with scons CXXFLAGS=-DNO_BEX now to get the old behavior. 1. Adapted TriaxialTest and ElasticContactLaw to BexContainer (switchable at compile-time). 2. Adapter GlobalStiffnessTimeStepper to BexContainer (GlobalStiffnessCounter code put to a function inside this one, hence that engine is not needed anymore). 3. Adapted Shop::Bex to BexContainer (probably not needed anymore?) 4. Exception is thrown in PhysicalActionVectorVector is used && built with BEX_CONTAINER (would most likely crash anyway). 5. transientInteractions and persistentInteractions are only references to MetaBody::interactions now. Removed extra loops in InteractionPhysicsMetaEngine and InteractionGeometryMetaEngine. 6. Remove including qglviewer into miniWm3, as it breaks compilation if using miniWm3 separately from yade (for testing purposes). 1. Define Janek's functions to convert from/to QGLViewer vector where they are used. 1. Add BexContainer (same interface, but separate implementation) in openMP flavor. 2. openmp=0 is the default for scons now (for some time), since openMP BexContainer gives about 7% slowdown and thus is not useful before at least some engines are parallelized as well. 3. Removed getting references to Force/Torque from BexContainer, since that breaks concurrency. Instead, addForce/addTorque must be used. If you need to read back with getForce/getTorque, you have to call sync() (expensive!!) beforehand, which will compute summary values for all bodies; if you forget, exception will be thrown. Note that sync() is invalidated at next write operation. 4. Adapted a few constitutive laws and other engines for the changes mentiones here. 1. Add time-profiling classes. See http://yade.wikia.com/wiki/Speed_profiling_using_TimingInfo_and_TimingDeltas_classes for details. It is accessible from python as well. 2. SimulationController no longer asks for output format. It just uses XML, the only available one. 3. Engine, EngineUnit have timingInfo member and pointer to optional timingDeltas. Timing is disabled by default, but it may still have some overhead in the order <1% perhaps (will test) 1. Forgotten file with yade.timing.stats() that pretty-prints some numbers. 1. Move all container to core, remove linking with them since it is not necessary 2. Fix things so that everything compiles (at least) both with and without BexContainer 3. Parallelize ConstitutiveLawDispatcher, InteracionPhysicsMetaEngine and InteractionGeometryMetaEngine with openMP if enabled on command-line 4. Make InteractionVecMap default container for interactions; necessary for parallel code. 1. New InteractionDispatchers class that has one common loop for InteractionGeometryMetaEngine, InteractionPhysicsMetaEngine and ConstitutiveLawDispatcher. It can be used from python like this: 1. Adapt ForceEngine to BexContainer 2. Add BEX_CONTAINER and YADE_OPENMP flags to be reported by -h. 1. Add two more forgotten headers. They are not used anywhere, though, and will be removed later. 1. Enhancement of utils.box from Marco. 1. Make Shop load 4/5/6 columns text files for spheres (and skip 5-cols) 2. Change evaluation of args in readParamsFromTable to be able to pass strings better (single quotes) and consistently 3. Parameters passed as env. vars by yade-multi are prefixed with ! 4. fix typo in timing for resetting timers. 1. Make the yade-multi scheduler multithread-aware. 2. Add the collider performance test as example 3. added utils.replaceCollider(anotherCollider) for convenience 4. added Omega().isChildClassOf(classNameChild,classNameParent) 1. Fix collider-perf (TriaxialTest has hardcoded dt=0.001 !!!!), set timestep by hand at first 2. Fix Shop:: loading spheres from file (regression from yesterday) 3. Add functorCache to Interaction and to InteractionDispatchers. About 5% improvement, but not yet finished. 4. Add DynLibDispatcher::getFunctor2D 5. Add BexContainer::sync() to other places in triaxial (thrown otherwise) 1. Fix old rename of runtime.args to runtime.argv in default-test.py. Should run OK now. 1. Fix for the compile error in snow for OrthogonalPlaneFit3. It still misses pkg/snow/Engine/ElawSnowLayersDeformation.cpp in the repo. Compile with exclude=...,snow as workaround. 1. Rename BroadInteractor to Collider. 2. Move some part of the contact logic to this common base class. The Collider::handleExistingInteraction is subject to discussion and not yet used. 1. Small fix in the collider code. 1. Remove SAPCollider completely 2. Make yade log4cxx 0.10 compatibile 3. Other minor fixes 1. Fix linking of realtime-rigidbody WRT PersistentSAPCollider 1. change default xiShear to 0 instead of NaN (is not used anyway) 2. Fix linking of mass-spring in cliean build 1. Fix #include's that include files not in the current source directory via "". 2. Add scripts/linkdeps.py that can automatically determine what plugin links to what other plugins, which can be once used for configurable monolithic/pluggable builds etc. 1. Fix crashed in TriaxialTest introduced by me a few days ago (referencing engine before being created) 2. Add simple (working?) memory usage query to utils and collider perf test. 1. Fixed collider performance benchmark 2. Added script to generate graph from log files (like http://yade.wikia.com/wiki/Colliders_performace) 1. Added SpheresContactGeometry::updateShearForce, will be used (not activated though yet) by ElasticContactLaw and other. hotfix related to last commit 1. Initial checkout for the DemXDofGeom classes (will contain the hasShear code from SpheresContactGeometry and more eventually). 1. Preliminary version for sphere-facet collisions with total formulation (moderately tested). 2. Same for sphere-sphere collision. 3. test script for facet-sphere collision geometry. 1. Use local foreach.hpp if not found in the system 2. Use local file defining boost::python::len for boost<1.34 1. remove explicit linkage to boost_python in gui/SConscript Forgotten empty file. 1. Remove logger from ClassFactory 2. Cleanup logging stuff in main (use constructor function, among other) 3. Cleanup system exit from python in PythonUI_rc.py 4. Add SpheresContactGeometry::updateShear that can be optionally used with ElasticContactLaw to update shear displacement instead of updating shearForce. triax-identical-results.py show quite large difference between both implementations, but I am not able to tell which one is correct. scripts/test/shear.py shown almost no difference for 2-sphere scenarios, modulo differences at 15th decimal place or so. 5. Remove debug output from BexContainer 6. Remove warning about meniscus data from CapillaryCohesiveLaw (warning is given in postProcessAttributes now, i.e. iff the class is actually used) 7. Add logger to snow. 8. Removed shear computation code in ElasticContactLaw, use SpheresContactGeometry::updateShearForce. 9. Fix scons deprecation warnings 1. Add functions to augment forces/torques in BexContainer. 1. Remove some garbage from SpheresContactGeometry 2. Verify that SCG_SHEAR doesn't alter behavior if ElasticContactLaw::useShear is false 3. Implement SCG_SHEAR for sphere-box interactions 4. sphere-box interactions no longer call goReverse, but swap interaction order instead, as facets do. 5. Fix triax-idnetical-results.py to reload generated initial config to avoid rounding issues of sphere coords in text file. Minifix: link core with librt (clock_gettime) for platforms that require it 1. Add rate-dependent damage to normal and viscoplasticity to shear components of Brefcom (not yet tested, just compiles); other cleanups there. 1. add addF and addT to legacy ActionContainer Add label attribute to engine units. Python wrapper updated. 1. Rate-dependent fixes (more to come) in brefcom. 1. Remove MetaBody::physicalActions if compiling with BEX_CONTAINER (default) 2. Make everything work with both BexContainer and deprecated PhysicalActionContainer 3. Change PhysicalActionDamper, PhysicalActionDamperUnit, PhysicalActionApplier and PhysicalActionApplierUnit to dispatch only according to PhysicalParameters (not PhysicalAction anymore). That means that only one unit will be called for each body and that NewtonsMomentumLaw has to do the job of NewtonsForceLaw as well (same for CundallNonViscousMomentumDamping). 4. Fix (finally) defaultDt computation in TriaxialTest (forgotten assignment to defaultDt in the GlobalStiffnessTimeStepper) 5. Fix (finally?) timestep manipulation form within the QtGUI. If reloading the same file, timestep settings will be preserved, otherwise those saved in the XML are used. 1. Create ef2_Spheres_Elastic_ElasticLaw that has the ElasticContactLaw algorithm 2. ElasticContactLaw now merely calls ef2_Spheres_Elastic_ElasticLaw. 3. TriaxialTest::parallel controls whether to use InteractionDispatchers or not. 4. Added examples/triax-perf to show the impact of that. Also see http://yade.wikia.com/wiki/Triaxial_Test_Parallel 5. Fix a few compilation issues. 6. Flush stdout before exiting from main, so that in case of crash upon exit (log4cxx?) we have all messages output. 1. Hotfix for 2 issues with ElasticContactLaw 1. Remove all traces of physical actions: 1. Remove Shop::Bex (no longer necessary) 2. Add InterpolatingDirectedForceEngine for Roger (not yet tested!) 1. Fix linking of ForceEngine with interpolation 2. Random rate-dependent things. 3. Typo in BexContainer docs 1. A few fixes in Brefcom. 2. Make python wrapper correctly handle long long attributes. 3. Added test script for InterpolatingDirectedForceEngine 1. MAJOR change in python syntax (backwards-compatible, though): through small bit of very dirty code, classes can be instantiated as python objects with keyowrd arguments, i.e. instead of 1. cleanup UniaxialStrainer code, add vars to control length of the acceleration phase and the ability to set absolute speed 2. EngineUnits within InteractionDispatchers can be labeled and accessed from python now. 3. A few minor things in the plot module 1. Remove cruft from brefcom, a few fixes there 2. Add gnuplot grid to gnuplot by default 3. Fix speed in USCT 4. Fix InteractionDispatchers traversal in pyOmega 1. Fix weird python problem if LIBS is not defined by distuils (?) 1. Add working version of facet adjacency finder (to get their mutual angle at edge) 1. Parallelize initial bound filling in PersistentSAPCollider. Gives almost 3x speedup for the first step. 2. Fix missing headers so that it compiles with g++-4.4 (in QGLViewer) 3. FacetTopologyAnalyzer works (not tested extensively), questions of where to put topology data for InteractingFacet (will be raised on yade-dev) 4. Test script for FacetTopologyAnalyzer. 1. Remove leftover var in PersistentSAPCollider 1. Add preliminary gnuplot plots merging facility to yade-multi 2. Fix yade.log module so that it also works without log4cxx (and gives 1 warning) 3. Switch to new syntax in scripts/plot.py 1. Fix race condition in brefcom (omp critical section) 2. Remove -ffast-math from optimized build, since NaNs do not work properly (e.g. isnan(NaN)==false!) 1. Fix bug in FacetTopologyAnalyzer algorithm 2. Add angle info to InteractingFacet (not yet used) 3. Add triangulated sphere test for FacetTopoloyAnalyzer to facet-topo.py 4. Fixes in rate-dep in brefcom 1. Add approximate viscosity equations to brefcom (not working) 2. Fixes in yade-multi 1. Finish implementation of Dof3DofGeom_FacetSphere (with plastic slip as well) 2. Adapt Brefcom optionally to Dem3DofGeom 3. Add d0fixup to SpheresContactGeometry to get correct normal strain in sphere-facet contact with fictive sphere (zero for sphere-sphere) 4. Finish FacetTopologyAnalyzer; angle usage in Dem4DofGeom_FacetSphere not yet tested. 1. Remove cruft from UniaxialStrainer, add the ability to set initial velocities to suppress inertia at the simulation beginning 2. Jobs in yade-multi can be automatically named after variables suffixed with ! 3. yade-multi now shows and updates automatically some statistic on localhost:9080 using http 1. Finish Dem3Dof for both spheres and facets, migrate Brefcom. Removing stuff from SpheresContactGeometry is on schedule, once thorough testing is finished. 2. Fix attribute inheritance for a few engine units 3. Add ef2_Dem3Dof_Elastic_ElasticLaw, which works like ElasticContactLaw (but faster ;-) ) 4. Remove BrefcomLaw, keep just the constitutive law as functor. Adapt sample generators for that. 5. Add hydrostatic confinement to brefcom (isoPrestress), remove viscApprox. 6. Add interface for querying and setting (doesn't work yet) number of openMP threads 7. Job description is taken from columns suffixed with ! or by combining all parameters 8. Add function for plotting yeild surface of brefcom to the eudoxos module 9. Oofem export now uses reference (starting) positions of particles as it should 10. Add "-" before profile name when generating default variant suffix in scons (which is expected) Fix comp9ilation error for Janek. 1. Add python wrapper for clumps, see scripts/test/clump.py on how to use it (O.bodies.appendClumped) 2. Fix clump support in NewtonsDampedLaw (damping is quite wrong, it seems...; Bruno, any ideas on that?) 3. Move clump to pkg-dem (even though it depends on extra/Shop) 4. Remove absolute shear computation from SpheresContactGeometry, as Dem3Dof works fine now and Brefcom will not use SCG anymore; adapt a few other classes to that; remove ElasticContactLaw2 that was using it. 5. 1. Warn in --version if -ffast-math was used 1. Fixing bug in TriaxialCompressionEngine (introduced by luc apparently). Big changes: Handle boundingVolume-less bodies gracefully in InsertionSortCollider 1. Add utils.regularSphereOrthoPack by Anoton Forgotten showcase. 1. Add InteractionContainer::requestErase to hint colliders that wouldn't otherwise see !isReal interactions. 2. Use this logic in InsertionSortCollider, PersistentSAPCollider, SpatialQuickSortCollider (noop in the last one) 3. Add InsertionSortCollider::sortThenCollide to make it behave as non-persistent collider (for debugging only?) 4. Add Interaction::reset() that has common initialization code. 5. Assign zero inertia to utils.facet (better than uninitialized binary garbage) 6. Fix contact logic in Brefcom, finally I get the same results with InsertionSortCollider as with SpatialQuickSortCollider on large simulation (more fixes to come) 7. Do not install pkg-config; fixes compilation error reported by the build bot. 1. Use bitfield instead of bools in InsertsionSortCollider 2. Revert accidental changes in insertion-sort-collider.py 3. Add function for using renamed classes from python with warning Getting rid of the Brefcom name, classes renamed as follows (moving files around will follow) 1. Add logic to scons to delete files that will not be installed in this run but are on-disk. This should make it unnecessary to remove files by hand. In the same way, disable implicit target cache which was making problems if files shuffle around. 2. Remove Brefcom* files, move to pkg/dem/ConcretePM.?pp. (not sure what other place, since it contains Engines, DataClasses etc in one file that I would refuse to break.). 3. Add detailed comments on ConcretePM to the ConcretePM.hpp 4. Remove extra/usct, moveUniaxialStrainer and put to pkg/dem; move SimpleScene from extra to pkg/dem 5. Remove core/yadeExceptions.* 6. Remove Preferences::dynLibDirectores and Preferences::version. Omega now recursively searches the lib directory for plugins and loads them. preferences.xml has only defaultGUILibName now. Finally. Remove baseDirs and other cruft from DynLibManager. 2 forgotten files (separated from UniaxialStrainer before) 1. Fix hopefully last relict of pkg-config 2. Degrade deleting non-existent interaction from fatal erro to warning only (not sure where that can come from, though.) Solve the cause of nonexistent interactions being deleted (after O.interactions.clear()). Make warning fatal error again. 1. Remove Interaction::isNew, Interaction::isReal. Add Interaction::isReal() which test for presence of _both_ interactionGeometry and interactionPhysics and Interaction::isFresh() which checks the interaction creation timestamp against current iteration. Updated all code for that. Please verify that your stuff works, it is possible I made some mistakes! 2. All code saying isReal=false replaced by interaction->requestErase(id1,id2) 3. make requestErase thread-safe 4. Add interace for traversing interactions pending erase (template) 5. Add TriaxialTest::noFiles and TriaxialCompressionEngine::noFiles to not generate any files (default: off) 6. Add predicate utils.ptInAABB(p,minPt,maxPt) 7. utils.spheresToFile return number of spheres written (instead of None) 8. Add examples/concrete/pack to generate packing; other stuff in concrete will follow, with simplified version of the cpm model in ConcretePM. 1. Syntax fixes in ConcretePM model 2. Interactions will be deleted also if the ye4xist, but geometry functor fails (returns false) 3. Add utils.approxSectionArea, utils.spheresFromFileUnixial (get some parameters useful for uniaxial tests from the sphere packing, such as cross-section, principal axis, etc) 4. Add lib/computational-geometry/Hull2d.hpp for computing convex hull in 2d using Graham scan algorithm (I know it is in CGAL already, but I don't want to depend on that commercial stuff) 5. Remove some unused stuff from utils. 1. Add epsNPl to Cpm 2. Replace vector by Vector2 and make it properly serializable (should be faster) 3. Add function to compute forces on interactions crossing plane. 4. Replace custom xcombine function by itertools.product in grid sphere packing Fixes and cleanups in the CPM code. Add new 'feature' to scons called openGL, which is on by default. Qt3 GUI will not be built without openGL. YADE_OPENGL is defined in openGL-enabled builds. Sconscript files adapted to skip GL plugins or GL parts of plugins. 1. Fix missing libs for linkage 2. Fix a few typos 1. Don't link core with glut (is there a reason for that?) Do not include X11 headers if without opengl 1. Move all python modules to PREFIX/lib/yadeSUFFIX/py/yade instead of */gui/yade 2. Add pack module for generating regular packings (thanks to Anton Gladky for his ideas & code) 3. Add _packPredicates module for solid inclusion testing. 4. Update regular-sphere-pack.py to test new packing features. Remove leftover reularSpheresOrthoPack from utils. Is in yade.pack now. Add pack.inHyperboloid predicate. Should be useful for cylindric specimen in uniaxial tension, but with the middle part having smaller diameter. Added to the test script as well. 1. Fix (hopefully) clump damping 2. Remove unused code from InsertionSortCollider 3. Make SimulationController NOT change timestep (rounding) by just opening it (!!) 4. Fix paths in PythonUI and lib/SConscript for $PREFIX/yade$SUFFIX/py/yade instead of $PREFIX/yade$SUFFIX/gui/yade 1. Add resetting interactionGeometry and interactionPhysics to Interaction::reset(), as it should be... 2. Small things in CPM 3. Add GaussAverage.data method to python (for debugging and plotting) Include Python.h in PythonRunnerFilter. Build this plugin only with EMBED_PYTHON. A few changes to allow run primarily python with qt3 on the top of that (open, close etc as needed). This paves way to running main yade process in python ;-) (just kidding, for now) 1. Handle groupMasks of bodies in InteractionDispatchers directly (not in geometry functors etc). 2. Fixes for qt3 started from within python 3. Add Body().dynamic flag to the wrapper, instead of using Body()['isDynamic'] all the time. Anton's new things: axis-aligned ellipsoid predicate and fix in pack.regularHexa. 1. Add external euclid.py module (suggested by Anton, thanks!) to our installation 1. Propose *.sqlite ending for saved simulations instead of * in the player Fix error-tolerant law which uses no interactionPhysics: add void Interaction physics in the geometry functor if returning true, to make Interaction::isReal return true. (Shouldn't we remove ErrorTolerant...? Does it have some serious use?) 1. Remove constructor priority for log4cxx to avoid syntax unsupported by gcc<=4.0. 2. Remove some commented cruft from FrictionLessElasticContactLaw 1. Add boolean operators on solid predicates (&,|,^,-), shown in scripts/test/regular-sphere-pack.py 2. Add notch predicate (not functional yet) 3. Add utils.alignedFacetBox to create hollow box from facets. Shown in new file scripts/test/facet-box.py 1. Update simulation filename in controller periodically 2. Fix notInNotch predicate, use infinite AABB for unbounded solids and raise exception in the packing generator if such is encountered. 3. Add notch to the head of regular-sphere-pack.py guy 1. Add checks for GTS (optional) 2. Add pyGTS to our tree (built only if needed), since no packages are available. 1. Fix corner case in InsertionSortCollider related to instability of std::sort (quicksort) and bodies having the same upper and lower bounds (facet in the xy plane, for example). Thanks to Anton for providing the crasher. Fix feature macro definitions (typos) 1. Add GTS surface predicate 2. Add example of sphere horse falling onto facet horse in scripts/test/gts.py (try it!) 3. Predicate difference now takes padding in the inverse sense for the second predicate (logical) 4. Attempt to enable lightning on facets (no effect :-( ) 1. Add coarsened horse geometry for the example gts.py 1. Rename ef2_Dem3Dof_Elastic_ElasticLaw to Law2_Dem3Dof_Elastic_Elastic (in scripts as well) 1. Make virtual methods on pack.Predicate work in python (inGtsSurface, for instance). Add scripts/test/gts-operators.py to show that. 2. Move scripts/test/gts.py to gts-horse.py 3. Add a few functions to pack for constructing triangulated revolution surfaces from meridians. 1. Padding support (though slow and not very precise) for pack.inGtsSurface 1. Fix crashers in InteractingMyTetrahedron* classes (introduced by me when updating interaction logic) 2. Reimplement inGtsSurface in c/c++ which makes it faster due to pygts interface limitations (addressed on pygts mailing list meanwhile), but is dirty programming. 3. Set CCOMSTR to correspond to CXXCOMSTR in SConstruct (to show nice line when compiling c source file, for pygts) 4. Set good-looking timestep in the TetrahedronsTest generator 1. Add triaxial packing generator, with optional memoization to sqlite database to avoid generating packing if there are suitable ones (same parameters/scalable to same parameters) available. Sample script will be provided soon. This allows for filling arbitrary (gts-defined, for example) volumes with irregular, high-quality sphere packing. 2. Add python-wrapped class SpherePack for manipulating sphere packings (loading, saving, spatial transformations, iterating) 3. Add shared_ptr Omega::rootBodyAnother to be used with Omega().switchWorld() 4. Move some stuff from gui/py to lib/py, which is more logical hopefully 5. If negative value is specified for TriaxialTest::thickness, wall thickness will correspond to the mean sphere radius (avoids spheres going through the walls during compaction for some radii) 1. Add automatic converter from python::tuple to Vector3r and vice versa. Wrapped functions can take/return Vector3r directly instead of manual conversion. Clean code that had to do that. Let me know if something breaks, the changes should not touch any python code. 2. Some preliminary work on wrapping Vector+Quaternion classes in python via py++ (not enabled, just the files are there) 3. Add forgotten _packSphere.cpp, thanks to Vincent for reporting. 1. Add scripts/test/gts-traix-pack.py to demonstrate triaxial packing generator. Remove useless include in GlobalStiffnessTimeStepper. 1. Fix STUPID (my fault, sorry!!) mistake in setting Interaction::iterMadeReal, which cause ElasticContactLaw to function wrong. It concerns a few other contact laws calling isFresh, which would return true as well. Sorry again. 1. Shuffling stuff around, moving most python things to py/ 2. Wrapping Vector3r, Quaternionr and Vector2r in python directly, see scripts/wm3-wrap.py 3. Change the way utils.box, utils.sphere and utils.facet works: arguments to physical parameters are passed as keywords, not as dictionary now (update your old code by passing **dict instead of dict as the last argument) 4. Fix a bug with useShear, now getting almost identical results for triaxial again. 5. Preliminary Triaxial::facetWalls, to be able to used Dem3DofGeom with Triaxial. (not fully functional yet) 6. TriaxialStressController::thickness is -1 by default now (get thickness from box width), as 0 is real value for Facets. Doesn't change beahvior in any way. 1. Update triax-perf.py 2. Add Omega().tmpToString returning string of :memory: saved simluation 1. add yade.plot.resetData(), which unlike reset() resets just data 2. Add scripts/test/compare-identical.py to run 2 simulations at the same time and check at every step (configurable) if they differ or not. 3. Add active=active line to GlobalStiffnessTimeStepper, which for some reason causes two same simulations to be the same. Any explanation someone?? 1. Add forgotten py/SConscript (sorry!) 1. Fix absolute path generated by py++ 1. Dump XML in ConcretePM in case of problems (nan's) 2. InteractingFacet::postProcessAttributes gives FATAL message if there are coincident vertices 3. Update triax-perf, add script and openoffice sheet to make table 4. InsertionSortCollider is used in TriaxialTest always (not only with fast) now. 1. Change prototype of Engine::isActivated() to Engine::isActivate(MetaBody*) 2. Add maxVelocitySq to NewtonsDampedLaw for analysis purposes 3. Add BoundingVolumeMetaEngine::sweepTime and ::sweepDist to sweep bounding volume by given predicted motion over time or by given absolute distance. 4. Add strided run support to InsertionSortCollider (using sweeping) 5. Add scripts/test/collider-stride-triax.py to play with the strategies of sweeping based on strides 6. Add O.interactions.countReal() 1. Fix collider-stride.py to match changed parameters. (it is quite useless now, anyway 1. Make NewtonsDampedLaw compute maxVlocitySq at every step anew. 2. Make InsertionSortCollider find NewtonsDampedLaw and get max speed from there. Together with InsertionSortColider::sweepLength, this makes stride adapted automatically to maxVelocitySq; this will described at http://yade.wikia.com/wiki/Insertion_Sort_Collider_Stride. 3. Update test script for that. 1. Handle clumps in a better way in NewtonsDampedLaw (only if asked by the clump itself) -- future parallelization work. (related to bug #398086) 2. InsertionSortCollider now knows when to run based on maximum distance the fastest body could have travelled. (It is actually the physical meaning of sweepDistance). Handle varying maxVelocitySq in a constitent way. 3. Add InteractionContainer::serializeSorted to sort interactions by id1 and id2 before serializing (useful for comparing XML files). Added Interaction::operator< to compare 2 interactions in that way. 4. Fix openMP strategy in InteractionDispatchers to "guided" (as per https://blueprints.launchpad.net/yade/+spec/omp-schedule-strategy) 1. Remove doc/removed, it is in SVN history 2. Tune debian scripts to install docs+examples+scripts instead of headers (targets https://bugs.launchpad.net/yade/+bug/398174, but not yet finished) 3. Add depends on python-numpy instead of python-scientific packages for debian 4. Add ../py directory to doxygen (targets bug #398190) 1. Change NewtonsDampedLaw to a StandAloneEngine 2. add .updateExistingKeys (perhaps should be updateExistingAttributes) to all python-wrapped yade objects, which will change only existing attributes from given dictionary 3. Adapt STLImporterTest to new nicer syntax. 1. Add virtual destructors to all EngineUnits so that they can by dynamic_cast'ed to. This fixes possible crash from python, bug #398255 2. Rename updateExistingKeys to updateExistingAttrs, add updateAttrs. 3. Add forgotten script to demonstrate predicate operators 4. The default debug level is -ggdb2 (instead of -ggdb3). Libs are about 60% in size and still give the same debug information. 1. Rename scons option arcs to PGO (profile=guided optimizations) 2. Install only binaries by default (no docs, must be requested from cmd line via path) 1. Various fixes related to generating debian packages 1. Fix EngineUnits linkage for SImpleViscoelasticRelationships 1. Add velocity binning for collision optimization: requires cooperation of NewtonsDampedLaw, BoundingVolumeMetaEngine and InsertionSortCollider. 2. Remove time-based sweeping from BoundingVOlumeMetaEngine. 3. QtGUI doesn't show annoying warning when run from python session anymore. 1. Parallelized NewtonsDampedLaw (scales very well) 2. Parallelized VelocityBins 3. Add const modifier to BodyContainer::size 4. Add virtual dtors to PhysicalAction{Damper,Applier}Unit (for dynamic_cast'ing) 1. Move NewtonsDampedLaw to StandAloneEngine directory 2. Add omp critical to ConcretePM 3. Remove SphericalDEMSimulator 1. Add sweepLength to TriaxialTest if fast==true 2. Remove euclid from the pack module, since we use wrapped wm3 now. 3. Add _packObb.cpp to compute minimal oriented bounding box on cloud of points 4. inGtsSurface predicate with triaxialPack will work on the minimum OBB 5. Add check for engine to prevent crash as per https://bugs.launchpad.net/yade/+bug/399810 6. Enhance the pack.inSpace predicate to work as expected. Custom center can be given to the ctor 1. Fix non-tuple in graph specification 2. Allow plotting agains the y2 axis, after a special parameter '|||'. 1. Remove mutex from requestErase (should be verified to compile on non-openMP machine!) 2. Add mutex to PhysicalParameters, so that body state can be locked while updating from the interaction loop. 3. Add linking with EngineUnits to Tetra (thans Emanuelle) why..?? 1. Adapt simple-scene-graph.py to new instance syntax 2. Add support to y2axis to saved gnuplot plots 3. Change interface for yade.plot.addData to take **kw instead of straight dict (still backwards-compatible) 1. Do not use REGISTER_ATTRIBUTE anymore, use REGISTER_ATTRIBUTES instead everywhere. This generates (in addition to serialization code) also some python code and makes python independent on the yade serialization framework (Janek, if you want to try boost::serialization, I have no objections now). 1. Remove garbage from doc 2. Instruct getopt to not shuffle command-line arguments, so that their order is preserved 3. Add epydoc documentation for all python classes and functions 1. Fix linking logic for _packPredicates (fixes https://bugs.launchpad.net/yade/+bug/401029) 2. Make gts-horse coarse original horse automatically Fix small bug in Velocity bins related to max sweep length (should improve performance as well). Still some incorrect things WRT bboxes, it seems. 1. Fix mathematical error with VelocityBins, verified by new script scripts/test/collider-sweep-simple.py to be correct 2. Add py/ directory to skipped dirs for linkdeps.py so that it works on current trunk 1. BIG CHANGE: pkg/ no longer have SConscript files but are scanned at startup for plugins. See http://yade.wikia.com/wiki/ImplicitBuilds for some details. Let me know if there are some problems. add boost-serialization and boost-program-options to debian. 1. Move STILimport to pkg/dem, as it depends on dem 2. update RockPM with the new-old version (probably svn didn't update the moved version? what a deal. We should definitely move to bzr...) 1. Fix unreported version for the debian build 1. Fix snow compilation by #including Voxel/* files in SnowVoxeslLoader and noc compiling them directly (sorry) 2. STLReader is a pure-header import lib now, tolerance is passed as regular data member. 3. Fix all warnings in ConcretePM. 4. Merge lib/yade-* into lib/yade-support. 1. Fix monolithic compilation even with fem. All modules can now be compiled that way. fix compilation? Fix TetraTestGen crasher (functionally still brokne, though) Remove SDECLinkGeometry, replaced by SpheresContactGeometry at a few places. Not checked for functionality. This avoid many warnings. 1. Fix linking with full Wm3 library 2. Automatically add /usr/include/wm3 to CPPPATH if useMiniWm3=False 1. Hopefully fix https://bugs.launchpad.net/yade/+bug/402098 2. Fast in TriaxialTest uses nBins==5 and binCoeff==2 for VelocityBins 1. Fix SnapshotEngine and simple-scene-video.py to run. It doesn't work, though, because of the makeCurrent() failed error (probably getting snapshot from another thread...) 1. Add GLViewer::nextFrameSnapshotFilename to save frame in postDraw 2. Adjust SnapshotEngine to take advantage of that. This should solve https://bugs.launchpad.net/yade/+bug/396023 3. utils.encodeVideoFromFrames can take list of files (instead of just wildcard). Backwards-compatible. 4. scons doc skips debian/ directory (would mess up if deb package was build) 1. Fix for https://bugs.launchpad.net/yade/+bug/406343 (at least for me) 1. Add GenericSpheresContactClass to unit radius1, radius2 and normal between SpheresContactGeometry and Dem3DofGeom (to make it work with GlobalSitffnessTimeStepper). Partially solves https://bugs.launchpad.net/yade/+bug/399963 1. Add docstrings to all wrapper.Omega() methods 2. Fix a few warnings. Fix has_map warning and one more in FlowEngine. 1. Add infrastructure for getting temporary filenames in a secure manner to Omega 2. move selectedBOyd to MetaBody; initialize it properly to avoid possible crash. Remove leftover SConscripts. 1. Change syntax of YADE_PLUGIN("Plugin1","Plugin2") to YADE_PLUGIN((Plugin1)(Plugin2)) (replaced everywhere) 2. Add some perliminary and not-enabled by default support for boost::serialization (see ClassFactory.hpp) 3. Add boost::serialization code for Se3r, Vector2r, Vector2, Quaternionr 4. Do not reset BexContainer's moves and rotations uselessly (i.e. if not used) 5. Use Omega's mutex in SimulationController to prevent loading-related crashes 1. Don't use __COUNTER__ to generate plugin registration function names, as they wre added in gcc 4.3 Use the name of the first plugin instead. 2. Dem3Dof_SphereSphere takes touching distance as equilibrium if distanceFactor is <=1. The initial position otherwise (was the default everytime until now) 1. Generate proxy constructors to all classes deriving only from Serializable in python (like GLDrawBox and similar). 2. Fix scripts to have the new syntax everywhere, since e.g. EngineUnit is just abstract class that cannot be instantiated from python. 3. Add check fro valid data before saving plot to gnuplot; raise comprehensible exception if there is nothing to save. 4. Remove leftover scripts/pch.py 1. Add an example of uniaxial tension-compression test for concrete (ready long time ago...) 1. All different yade types are real python types now. They have their properties defined at startup. One can say O.bodies[0].shape.diffuseColor instead of O.bodies[0].shape['diffuseColor'] now. It also works much better with ipython tab-completion. It is not sure whether we will be able ever to deprecate the old object['attribute'] syntax. 2. Wrap ParallelEngine in python, and finish Dispatcher wraps as well. 1. Reset interaction radius after the initial contacts have been created. Fix FileGenerator wrapper in PythonUI_rc.py (has different name in c++ (FileGenerator) and python (Preprocessor). 1. Rename Preprocessor in python to FileGenerator, to be consistent with c++. Preprocessor is never used directly, anyway. The old deprecated name put in the deprecation table. 2. Manage crash at exit in defaut-test gracefully 3. Fix serialization of pairs (overlooked replace) 1. Initial attempt at regression tests (only the python wrapper so far); run scripts/regression-tests.py 2. Fix a few bugs discovered that way :-) 1. Replace PersistentSAPCollider and DistantPersistentSAPCollider by InsertionSortCollider everywhere. The two are still in the sources, but are not compiled. Will be removed in near future. Added to deprecated table in python so that old scripts still work. 2. Add some more regression tests for the python wrapper. 3. Fix timestep in HangingCloth (it does some weird things, can someone check it or just remove mass-spring from the tree?) 1. Be more tolerant to specifying invalid GUI at the command line 2. Throw exception about unopenable $DISPLAY rather than letting QApplication abort() 1. Fix https://bugs.launchpad.net/bugs/409254 https://bugs.launchpad.net/yade/+bug/409254 take 2 Maybe fix https://bugs.launchpad.net/yade/+bug/409365 1. Fix (?) https://bugs.launchpad.net/yade/+bug/409254 by moving ClumpTestGen out of Clump.hpp 2. Avoid warnings in STL import code (return values _should_ be checked, though!) 3. Avoid warning in yade.cpp in optimized build 1. Infrastructure for periodic collision handling. Not at all functional at this moment, don't even try to use. 1. Beta version of periodic boundary conditions (try scripts/test/periodic-simple.py 1. Assign new function O.exitNoBacktrace to sys.exit. Fixes partially https://bugs.launchpad.net/yade/+bug/410250 2. Add some more comments to periodic stuff. 1. Script that shrinks the periodic cell progressively (reveals bugs in the collider, though ;-) ) 2. Add function to compute total force in volume from interactions to Shop, wrapped in _utils as well. 1. Working periodic collider, yay!! scripts/test/periodic-grow.py shows that 2. A few changes related to that. 1. Add PeriIsoCompressor for periodic isotropic compression; see scripts/test/periodic-compress.py. Not so much slower than regular triax, nice surprise. 2. Make SpherePack standalone class (previously just in python's _packSpheres), add the function to generate cloud of spheres, both periodic and non-periodic. _packSpheres wrapper is update, but otherwise not changed. 3. Fix python-less compilation for se3 interpolator engine 4. Add Omega().runEngine() 5. Fix some compilation/linking issues. 1. Fix missing vtable for GenericSphereContact (crasher with debugging) 2. Fix collider stride for TriaxialTest with unspecified radius 1. Try to fix locking with boost-1.35, possibly fixes https://bugs.launchpad.net/yade/+bug/411572 (please confirm) 2. Add periodic repetition function to SpherePack 1. Fix linkage for boost<=1.34 (hopefully) 1. Fix a few things in SpherePack 2. Remove TriaxialTest::GenerateCloud, replaced by SpherePack::makeCloud 3. Fix crash in BoundingVolumeMetaEngine, if MetaBody has no boundingVolume 4. Improve sorting operator, remove workarounds for std::sort wrapping minima/maxima (https://bugs.launchpad.net/yade/+bug/402098) 5. Limit minimum cell width in PeriIsoCompressor, to not crash. 6. Add code for periodic packs in pack.triaxialPack (not yet fully functional) 1. Add #pragma once to SpherePack.hpp (possibly cause of https://bugs.launchpad.net/bugs/412442) 2. Fix crash in TetraTestGen (finally, I think), closing https://bugs.launchpad.net/bugs/408422 3. Add highlight parameter to utils.{facet,sphere,box}, passed to Body::geometricalModel 1. Fix assertion is 2d dispatch code, add indices to RpmPhys, RpmMat, CpmPhys, CpmMat (would break dispatching if using more classes derived from the same base in the dispatch matrix) 1. Remove {,Distant}PersistentSAPCollider and Fixed{Position,Orientation}Engine classes 2. Add test script for generating packing 1. Summarize important changes since the last release. Add your own things, if they are important for everybody (svn log has the small details) 1. Add scripts/rename-class.py for renaming classes (replaces in code, moves files with bzr, adds rename record to python). Not very well tested, though. 2. Remove core/StandAloneSimulator.*pp (not used anymore) Add ignore patterns so that bzr st doesn't show (some) generated files 1. Merged upstream changes. 1. Clen the plugin loading logic a little (no nominal win32 support), support YADE_PREFIX for changing prefix (should be runtime-detected inthe future, anyway) 2. Use $ORIGIN in rpath to make yade relocatable; it can be fragile, let me know if there are troubles! 3. Add make check to the debian package (will be tested soon) 1. Add compatibility for hardy 2. Fix missing newlines (hardy compiler gives warning) Adjust rpath for the main executable (ugly hack) Run tests in debian package (not failing if the test crashes, though, for now) 1. IMPORTANT! All features are lower-cased now (avoids mess: openGL or OpenGL etc). This will probably break your profile files. 2. IMPORTANT! openmp is one of features, no longer a separate options. Adjust your profiles 3. Rename LOG4CXX to YADE_LOG4CXX; all features now #define YADE_FEATURE macros 4. Better $ORIGIN syntax in scons 5. Abort yade if running PythonUI_rc.py fails 6. Adjust pbuilder script 1. Add wrapper for running tests, to trap exit segfault at squeeze 2. Use the wrapper for tests in debian/control 3. Add wrapper for vector Make the test script report what distribution failed (currently only karmic). Fix GTS features (thanks for spotting that; we need regression tests for all the modules) 1. Skip more stuff in doxygen, a few warnings 2. Add debugging code to DynLibDispatcher (disabled) 1. Rewrite 2d dispatching code from scratch 2. Expose classIndex to python for indexable classes 3. scripts/test-sphere-facet.py shows how the dispatch matrix fills with data Add python 2.5 compatibility hack Avoid error in pack.triaxialTest if compiled without GTS. 1. PeriIsoCompressor: add keepProportions parameter (on by default), decrease global updates interval. 2. Omega: startSimulationLoop warns if there is no simulationLoop (how can that happen? It somehow can) 3. SpherePack: resets periodicity (and warns) if being rotated; cellSize is writable now. 4. pack.triaxialPack: renamed to pack.randomDensePack; fix loads of stuff in that; rename radiusStDev parameter to rRelFuzz; add epydoc documentation; fix erroneous detection of inGtsSurface being defined 5. wrapper: lock renderer when adding list of bodies; Omega().resetThisWorld to reset current world only. 6. Fix scripts/test/{gts-random-pack.py,gts-random-obb.py} ef2_Sphere_Sphere_Dem3Dof: change meaning of distanceFactor, see docs (if < 0, equilibrium is sum of radii, otherwise the initial distance; defaults to -1). Renamed to distFactor, to break old code intentionally InteractingSphere2AABB: allow negative aabbEnlargeFactor, which doesn't scale aabb at all (same as if it is 1.) yade-multi: use the first non-blank line as column headings (not necessarily the first line of the file, as is used to be) SpatialQuickSortCollider: fix clearing interaction with openMP examples/concrete/uniaxial: move files around, add confinement and docs; remove examples/concrete/pack since not in the pack module (an example should be given, though) examples/collider-perf: remove PersistentSAPCollider, add InsertionSortCollide with strides, but commented out since no effect at hthe beginning of simulation PeriodicInsertionSortCollider: remove unnecessary (hopefully) condition that would abort in scripts/test/periodic-simple.py PeriIsoCompressor: fix absolute displacements changing proportions, operate on averages instead pack.randomDensePack: fix proportions in periodic packs; change residual stress to 1e8 instead of 1e9 SConstruct: remove obsolete (unused) standalone openmp option yadeWrapper: Fix compilation with boost<1.35 (again) (now?) 1. Fix startup crash if no $DISPLAY set at all miniWm3Wrap: update with newer py++; still errors out at karmic spirit: avoid warning with newer boost versions Add gts to depends on the script. Remove unnecessary inclusion of indexing_suite which breaks compilation for boost<1.34 (or something like that). utils.uniaxialTestFeatures: fix compat with py2.5 SConstruct: fix compilation issues with older symlinks in include dirs Fix OperationalError, reported by Janek in https://bugs.launchpad.net/yade/+bug/416906 SConstruct: add doc for pretty, fix a few lib checks on karmic Fix version detection on systems where version is not specified by hand or in RELEASE file and bzr is not installed main: disable SIGHUP handler (emergency save) and automatic loading. 1. Remove garbage from examples. 2. Fix SpheresFactory, fix examples/SpheresFactory/model.py move SpheresFactor to scripts/test as it doesn't work. Add notes to changelog and news. Forgotten file Mark release version Add mill script mimicking http://www.youtube.com/watch?v=005rdDBoe4w Some changes in qt interface (useless) Add series to package version to allow same version for multiple series in the ppa (0.20-1~hardy, 0.20-1~karmic etc) Added script for http://www.youtube.com/watch?v=KUv26xlh89I 1. Fix facet lighting, mill shown with wire=False now (looks better) 2. Revert recent useless change in QtGUI-python 1. Enabling O.timingEnabled when running will not produce garbage values for current engine anymore 2. Add maxRefRelStep to VelocityBins, to limit speed fo maximum velocity changes 3. Fix epydoc format for utils.encodeVideoFromFrames and utils.uniaxialTestFeatures 1. Do not save potential-only interactions to the XML; do not save pendingErase interactions (are only potential) 2. Do not save interactions in SQLiteRecorder by default (saveInteractions=True if you want the old behavior) 3. Add slider to the simulation player, in the "snaps" tab 1. Add scene that has been sitting here for a few days (should be run for comparison with pfc3d) Workaround bug #416335; static members of Vector3 work only on instance, e.g. Vector3.ZERO will not work, you have to use Vector3().ZERO; changed all occurences in the code accordingly, update your scripts as well.\n2.Some undocumented and untested enhancements for parameter table (backwards compatible) ================================================== yade-0.20.0 Sat, Sep 19 21:41:52 2009 +0200 Anton Gladky (33): 1. This is my first test commit 2. Added some initial files for mining rocks classes simulation 1. Some changes in RockPM, still does not work good 1. Some small changes on RockPM.* files 2. Test SVN_2_email 1. Test 2. RockPM.* updated Changes on RockPM.* files 1. RockPM, first variant of "destruction mechanism" 1. Deleted euclid.py 1. delete euclid.py (fised Sconscript) 1. In utils.py alignedFacetBox has been changed to facetBox. It is now possible to create arbitrarily-aligned box composed of facets 2. Updated regular-sphere-pack.py 3. Some small changes on RockPM.cpp 1. RockPM update. Added simple "destruction mechanism" 2. Added scripts/installOnUbuntu.sh to make "oneButton-checkout+compile+install+doxygen+epydoc" script. Not tested yet. Requires corrections. 1. Updated some scripts according to new syntax 1. Added PressTestEngine for simulating presses. Can be used and for PointLoadTest simulations. 1. Updated simple-scene-graph.py according to a new syntax 2. Updated simple-scene-video.py according to a new syntax 1. Changes on PressTestEngine. Now it defines the destruction moment more precisely 2. YADE CONSOLE emblem shows now without upper row shifted. 1. Some small changes 1. All variables initialize in PressTestEngine and RockPm Some changes on News Fix compile error 1. Partly fixed 1. Almost fixed https://bugs.launchpad.net/yade/+bug/412892 Just 1 warning: Some changes in INSTALL file because of migrating to BZR Some changes on one-click-install script Added "warning" in one-click-install script 1. Fixes compiling error without openmp feature. 1. 418107, I guess it is more correctly. Some nonessential changes Blocked some warnings in RockPM.cpp Small changes Press Engine and RockPM changes Added demonstration of buldozer simulation "Thanks" and Thanks to Janek :) Fixes VTK-librabry dependencies for Ubuntu Some small changes on Buldozer Bruno Chareyre (16): 1. Fixed a critical bug in ElasticContactInteraction (kn, was not registered and left undefined after loading a simulation). 2. Test if fn!=0 (i.e. contact exists) before adding kn/ks to the global stiffness. 1. "Water" classes are updated based on the code developped locally (but not commited for a while) by Luc Scholtes. 2. Triangulation code updated as well (not compiled by default). 1. Add a missing class (for the capillarity model), this fixes a compilation error in the previous commit due to the missing files. The "stopSimulation" command in the compression engine is now optional, as sometimes you don't want it to stop at all(1). The default behaviour of the compressionEngine is not affected, with autoStopSimulation=true by default. However, the TriaxialTest IS affected : it sets autoStopSimulation=false by default. 1. Update capillary files and add a new engine for them. 2. Prepare for removing old useless classes (typically some variants of engines with "water" at the end) Remove useless dependency. -Avoid crash when computing fusion number (it was using pointers to deleted interractions) FIXME : no distant meniscii for now due to deletion by the contact law. Base class for the solid-fluid coupling (E. Catalano PhD). -Register "thickness" so that sample dimensions are computed correctly (and not with 0 thickness) Dimensions could be 0 when "updateParameters" was called from TriaxialCompressionEngine before TTController::action Missing declarations in r1836. - cleanup : removing unused (and useless) "water" variants of engines - some cleanup in recorders too Update of the read/write functions for the connection with comsol. (coupling via Berkeley<->Grenoble mail servers! ;)) Missing declarations of member variables. Set default read/write behaviour as in Andrea's version. Feng Chen (1): This is viscous force damping, equation similar to http://en.wikipedia.org/wiki/Damping, damping parameters are controlled by betaNormal and betaShear, it is sometimes more realistic than the non-viscous (or say, local) damping. While using this code, please make a reference to: Janek Kozicki (40): created nearly empty snow package: pkg-snow Snow stuff - generate grains made of layers according to voxel data read from file. And daraw it. forgot some files - make it compile with boost 1.34 - some snow improvements - another fix. now it really compiles with boost 1.34 1. TriaxialStressController reads radius from interactingGeometry Code wasn't compiling because of #include MicroMacroAnalyser - comment it out. 1. argh, guys. svn HEAD must compile. You didn't check your commits and then I waste 1h to fix that. See this commit, to check what I had to comment out about WATER - added keyboard shortcut '.' that toggles grid subdivision by 10 - fixed error with grid step - grid step is now shown in gl window small snow update another small snow update 1. small snow update 2. fix compilation error by Vaclav (hey, you didn't compile again before commit! ;p ) rename file to avoid case conflict with directory 1. GLViewer - when sth. is selected don't move it to 0,0,0 position, but use its original position. This is done by delaying assignment to the next call of draw() - added extensive comments to the polyhedron code which will be used for collisions small snow update maybe spheres won't disappear anymore? a placeholder for drawing snow interactions changed guards to #pragma once postpone creating a 3d view, until a file is loaded. That should hopefully fix the problem with the primary view being empty. added AUTHORS file, for the purpose of updating file headers. This was copied from http://yade.wikia.com/wiki/Authors Why do I have the impression that I'm adding this file a second time? After all it's referred to in almost all source files "See file LICENSE for details.", right? sort people in alphabetical order sorry for bumping up revisions.... Snow, as it is finished by me. Further work on it will to be done by next post-doc researcher who wants money from EU for working on this :) fix miniwm3 / full wm3 compilation error I forgot to add those, sorry. (I wonder how it could stay unnoticed for so long ;) add option for horizontal or vertical wires in fibre reinforced concrete. 1. correct display of lattice rods on 0th iteration 2. on/off switch for using different stiffness for tension and compression in lattice 3. fixed a bug in BodyRedirectionVector related to deleting of bodies 4. two more lattice examples 5. few more safety checks in lattice code 1. NullGUI was still usin .gz while thay are not supported anymore 2. small lattice update sanitize stupid numers in QtGUI, eg. 0.1299999999999 becomes 0.13 small fix after isNew and isReal are removed I'll update the code to use new contact logic. Add an option to display DOFs and body IDs in the OpenGL window - Lattice uses DOFs now - old implementation is still accessible by setting a flag backward_compatible, so that hundreds of my old FileGenerator files will still work - some improvements to recording strains and forces - fix all my warnings - lattice generator improvements wrt concrete with steel fibres - some improvements wrt to generation of densely packed aggregates and steel fibres in the concrete structure - testing command "bzr commit --fixes lp:414868" - fixing bug 414868 Fix stupid error introduced when we have migrated to bex container 1. get snow code to run, albeit still buggy 2. why dynamic_casts stopped working everywhere, that's a mystery to me 3. interactions isNew doesn't exist anymore, snow code needs update for this Jerome Duriez (2): - Correction of the headers of two files "ContactLaw1Interaction" which were commited by me and not by Bruno - Some features of ContactLaw1Interaction were declared in ElasticContactInteraction. This was a mistake totally not planned (and the fact it was in svn also was not noticed) and is now corrected - End of the job by suppressing also the corresponding lines in .cpp... Luc Sibille (1): I added a new engine "ThreeDTriaxialEngine" to perform triaxial simulations with an independant control in stress or in strain in the three space directions respectively. In this goal, the TriaxialStressControlEngine has been sligtly modified to impose a different stress value or strainrate in each space direction. I hope I have broken nothing! Sergei Dorofeenko (28): Intermediate commit for SpheresFactory. Don't work yet. 1. New engine SpheresFactory 2. Add function engineByLabel to MetaBody 3. Add members to BroadInteractor. 1.First worked version of SpheresFactory engine. Example in examples/SpheresFactory 2.Added PersistentSAPCollider::probeBoundingVolume function (for using with SpheresFactory) 3.InteractionGeometryMetaEngine::explicitAction has been modified to remove artifical (as me seems) asserts. 4.python import_stl_geometry now return list of body ids instead only their number. 5.import stl geometry now allows import facets without BoundingVolume and InteractingGeometry. 6.Fixed dynamic_cast for BroadInteractor. 1. SpheresFactory allows now to create spheres in a convex volume. 2. SimulationController estimates total simulation time if stopAtIteration>0. 1. SimulationPlayer now allows to reload filters without reloading all simulation. 2. ColorizedVelocityFilter now allows to setup minValue,maxValue without reloading the filter. Fixed bug in RotationEngine: rotationAxis now normalized in action(), not in postProcessAttributes() ColorizedVelocityFilter counts a scale for each frame, without using previous min,max values. Class SimpleViscoelasticInteraction is renamed to ViscoelasticInteraction and is inherited from ElasticContactInteraction now. 1. Convert SimpleViscoelasticContactLaw to ConstitutiveLaw engine unit (Spheres_Viscoelastic_SimpleViscoelasticContactLaw). 2. SimulatonPlayer have now Display tab as one in SimulationController. 1. The experimental widget for drawing a color scale for colorized velocity filter. 2. Convenient python function utils.ColorizedVelocityFilter. Merging utils.*_v2 functions with their "first" analogs. Add two new filters: ColorizedTimeFilter and PythonRunnerFilter Migrate GravityEngines and ConstitutiveLaw to BEX_CONTAINER Convert STLImporterTest to ConstitutiveLaw (SimpleViscoelastic contact model) and NewtonsDampedLaw engine. Fix bug in serialization for ViscoelasticInteraction. Fix compilation error for InteractionHashMap Update contact logic for SpatialQuickSortCollider (hope, it's correct) Fix typo in PersistentSAPCollider 1. Remove zeroPoint 2. Add prefix ef2_ to Spheres_Viscoelastic_SimpleViscoelasticContactLaw Fix link errors fixed and updated some examples in keeping with last modifications Realise InsertionSortCollider::probeBoundingVolume() so SpheresFactory now works SpheresFactory now can create a spheres by python function. See scripts/test/SpheresFactory/model.py for example. Add export python module with VTKWriter class (very initial) to export data from YADE to VTK-based post-processing tools Added a c++ VTKRecorder (for spheres and facets) and new feature 'vtk' needed for it. Add colors rec to VTKRecorder Add default path for VTK Fix VTKRecorder headers Fix VTKRecorder headers Add VTKINCDIR to configure options for directories where to look for VTK headers Unknown (1): The isotropic compaction into the TraxialTest is activated: 1)I have deleted the translationspeed parameter (now the translation speed of walls is the strainRate parameter) 2)I have activated the porosity parameter in the TriaxailStressController.cpp file Vincent Richefeu (38): - add the soft mgpost for DEM simulation post-processing and visualization. - set menus in english mode A very quick guide for mgpost (usage and XML format) a forgotten file in mgpost/doc - add a new tool for sphere packing (still in dev) - some enhancement in mgpost interface - SpherePadder devel... SpherePadder devel... SpherePadder (devel: 5 steps ok) - SpherePadder update - add a basic 'user friend' interface for sphere packing generation. The module can of course be used without this interface. Speed enhacement for the SpherePadder algorithm. Add possibility to make PNG screenshots (using libpng) Add a DataRecoder that generate MGP files (only for Spheres for the moment). The MGP files can then be read with mgpost. - add a class based on CGAL for 3D triangulation. - Packing method enhanced (place 380000 spheres in less than 2 min) Fix some bugs and enhance the display of positive and negative forces Fix some bugs Begin devel. of densification process 2 files that were forgotten Simplify sphere shapes when if there number is increased Bug corrections (min and max radii) - overlap with spheres inserted by user -> bug fixed - Densification begins to work Increase the number of colors for the display of body's groupMasks from 6 to 10 We can now make the packing denser with a stop criterion based on the solid fraction or total number of spheres. Add BasicViscoelasticRelationships: an alternative to SimpleViscoelasticRelationships. It accounts for the effective mass of each contact and considere the parameter cn as a dimensionless ponderation of its critical value (computed for each contact). Parameter cs is set to zero for the moment. Add a boost.python wrapper (module packing) Add a function to SpherePadder_wrapper to pass the result back to python. As Vaclav suggested, it is a list of (x,y,z,R) tuples. (Complet integration into yade is not done yet) - Add 'HistoryRecorder' to save the sample and network state with a given time-step interval. - Correct a small bug due to the fact that a Clump cannot be casted into a GeometricalModel (and I don't know why!) Use the clump mass instead of clump-member mass for the determination of the effective mass. Ooops! There was a bug Add the function NormalRestitution2DampingRate. Add sphere reading for gdm-tk format Remove default linkage with libtiff (png is now prefered) Add an example of python script for SpherePadder Add GroupRelationData serialization (not used yet in *Relationships classes) This class serves to manage parameters between bodies depending on their groupMasks. Here is an example of 'command stream' in xml file to set the parameters: Just try to use GroupRelationData with BasicViscolelasticRelationships. Cast size_t to int in pow(double,int) function to avoid ambiguity for gcc (compilation failled on one of my computer) Some tiny modifications for Mac OS X compatibility (Does not compil yet). Some forgotten tasks replace gcc-3.3 by gcc in the Makefile.macosx of mgpost Václav Šmilauer (269): 1. Add linear templated interpolation function working on 2 lists, t and values 2. Add InterpolatingRotationEngine that changes rotation speed as given by value table 3. Lower info about starting python thread to debug message only. 1. Rename REGISTER_SERIALIZABLE(class,bool) to REGISTER_SERIALIZABLE_GENERIC, add two macros REGISTER_SERIALIZABLE and REGISTER_SERIALIZABLE_FUNDAMENTAL. Changed all uses accordingly. 2. Added REGISTER_CLASS_AND_BASE(class,base) which performs REGISTER_CLASS_NAME and REGISTER_BASE_CLASS_NAME at once. 3. Added REGISTER_ATTRIBUTES (not trailing 'S'), expanding to void registerAttributes(){...}, and REGISTER_ATTRIBUTES_WITH_BASE, which prepends call to baseClass::registerAttributes() (specified as the first argument). 1. Added Se3Interpolator engine, with scripts/test/Se3Interpolator.py 2. Added from math import * to PythonUI_rc.py so that math functions are readily accessible everywhere 3. Implemented stopStrain in UniaxialStrainControlledTest 4. other small fixes 1. Modify REGISTER_ATTRIBUTES macro so that it work with or without base class given. Change all headers in core to use that. It should help us if we ever make the transition to boost::serialization. 2. User REGISTER_CLASS_AND_BASE instead of REGISTER_CLASS_NAME and REGISTER_BASE_CLASS in core and at a few other places. 1. Removed cerr garbage from glviewer (use LOG_DEBUG if needed) 1. Fix warnings in GLViewer 2. Add (35.4%)-style counter if stopAtIteration is set to the OSD in gl view 3. Add utils.downCast to downcast object to its derived class and copying all attributes. 4. Add utils.SpherePWaveTimeStep to compute critical dt from a few parameters only 5. Add routine to compute overall kinetic energy to Shop (indirectly to utils as well) 6. Add routine to sum torque (momentum) with respect to an axis from forces and torques on given set of bodies. Fix typo (compilation error in debug mode) in Shop::kineticEnergy 1. Fix a bug in rotation ode in SpheresContactGeometry. Now the code gives the same results as almost-for-sure-correct FEM code regarding strain computation. 2. Add label attribute to StandAloneEngine (inherits from Engine) omg (code cleanup, no functional changes) Exit once the simulation finishes; do not rely on simulation exiting itself. 1. SpiralEngine that does both rotation and translation along the same axis 2. InterpolatingSpiralEngine for variable rotation+translation speed (replaces InterpolationgRotationEngine) 3. scripts/test-spiral.py for rudimentary functionality testing. 1. Un-disallow (bug) having all dimensions scalable in triaxial if particle radius is fixed. 2. Don't record anything by default to file in UniaxialStrainer (only useful for debugging) 1. Add a few functions for integrating piecewise-linear functions in new module yade.linterpolation 1. fix damage colorizer (removed dynamic_cast causing segfaults on non-spheres) 2. InterpolatingSpiralEngine now takes bool wrap rather than Real period. 3. qt.makePlayerVideo takse startWait argument, which waits for Backspace before starting (useful for setting up the view manually); postLoadHook gets run afterwards now. 1. Add algorithm for pushing sphere always to the same side when in contact with facet, even under extreme stress where the sphere geometrically passes to the other side. 2. Add bool SpheresContactGeometry::initContactOnPositiveFacetSide for that 3. Add test/demo script for that. 4. Re-enabled GLDrawSphere::glutUse (cosurgi?) 5. Renamed yade.runtime.args to argv, to be consistent with sys.argv 6. Allow passing sys.argv (arguments to scripts) through QtGUI as well 1. Fix clip plane orientation inversion as well as wheel normal movement. 2. Clip planes not displayed at all unless one of the clip planes is being manupulated. 1. Unbreak bad type (list) for sys.argv[0], broken recently 2. Color bodies by residual strength rather than damage parameter (smoother) 3. Make player messages (maybe) better formatted omg... 1. Make player reuse existing renderer if there is one (allows setting Draw_mask etc before running player) 2. Add initRun parameter to PeriodicEngine (false by default), to run at the very fist run. 1. Make BrefcomDamageColorizer run at 0th iteration as well 2. Make player set stopAtIter to last iteration in db so that percentage is displayed in the output. Fix previous commit, overlooked. sorry. 1. Number lines in parameter table for multijobs from 1 (as text editors do) 2. Print short summary at the end of job log (when started, when finished, exit status, duration, commandline) 1. Fix logic typo in QtGUI (warning when there shouldn't be and vice versa) 1. logarithmic strain for Brefcom. 2. change sphere-facet algorithm such that it works on corners. Maybe no longer necessary, but it doesn't hurt now. scripts/test-sphere-facet-corner.py as provided by sega demonstrates that. 3. "from __future__ import division" in python init such that 3/2==1.5 and 3//2=1 (is default since python 2.6) 4. Global GL lock to avoid crashes/freezes with GL accessed from multiple threads concurrently. scripts/gl-test.py (which used to crash) now works with one view; 5. Properly lock/unlock on all gl ops in QtGUI-python.cpp, like setting view direction, resizing etc. 6. Fix wrong assertion in SQLite player 7. add Omega().resetTime to reset iteration number, virtual and real time. 8. Changed utils.loadVars/saveVars code to be more reliable. 9. Added utils.aabbExtrema2d 1. Lock GL when closing view. Seems to fix crashes / delays at exit 1. Contact sphere-facet must be deleted by the constitutive law once created. Let me know if that is a problem -- I think it is the way it should be in the future everywhere, though. 2. Fixes for boost 1.37 (boost::thread not fully compatible) 3. utils.basidDEMEngines (not tested yet) 4. Fix warning in GroupRelationData 5. add march switch to scons ('native' is default, but not supported by older compilers) 6. Prepend default CXXFLAGS so that user-defined ones (like warning suppression) come after the default ones and override those. 1. Tentative fix for newer scons, which links empty files (dummy plugins) with plain gcc and doesn't find default c++ libs to link with. 1. File not needed. 1. Beautify no-debug code in main 2. SpiralEngine now saves angle it has turned so far 3. Remove failing assertion from IFacet2ISphere4SCG (why it fails? it was a (I->isReal&&I->interactionGeometry)||(!I->isReal&&!I->interactionGeometry)...) 4. Improve the utils.spiralproject function to specify period (moderately tested, but seems to work) 5. Adjust locks in GLViewer. Fixes my crashes on nvidia for both player and 3d view (didn't dare to try 2nd view). Next step will be to move this lock to Omega and lock it when loading/resetting simulation etc. 6. Change theora video quality to 63 (maximum) instead of medium 32 in utils.encodeVideoFromFrames. Makes the video about 3x bigger. Two BIG changes: 1. Add ef2_Spheres_Brefcom_BrefcomLaw, is faster (!) 2. Fix locking in Omega, we don't get crashes when loading simulation with the 3D view enabled anymore (please report any further crashes in OpenGLRenderingEngine, that should be fixed) 3. Automatic update of Doxygen configuration file 4. Dem3DofContactGeometry, which should be in near future parent of SpheresContactGeometry and other new geometries providing normal and shear strains (SphereFacetContactGeometry, in my mind) 5. Add convenience function to apply force to contact point between two particles. (remove no-warn for c++0x since that flag is not known to gcc-3.4) 1. Add possibility to change container types from python (for benchmarks) -- code not yet tested! 2. Possible optimization in PhysicalActionVectorVector, now disabled. collider mistake hotfix 1. Make triaxial stop if !autoCompressionActivation and already unloaded. If this breaks something, please let me know, we can do it otherwise, but, for Cundall's sake, can we keep the same behavior for at least 6 months?? 2. SpatialQuickSortCollider will not delete real contacts, even if bodies don't collide. 3. Remove redundant attribute registration from SpheresContactGeometry fix typo in collider 1. removed persistentInteraction from most places; they are still present in MetaBody, but not serialized any more, most importantly (avoids warnings) and not GL-drawn. 2. Plugin loading loginc completely changes, the underlying macro YADE_PLUGIN has still the same interface. We used __attribute__((constructor)), __attribute__((visibility("internal"))) and anonymous namespace magic to get there. This will make it possible to put multiple plugins to a single shared library without touching the source, only fiddling with SConscript's. 3. PythonUI is interactive by default (it was not?? weird.) 1. Add new non-generic Bex container. For non-optimized build, it increased the speed by about 11% (9:35 vs. 8:49) as compared to PhysicalActionVectorVector. Users willling to go with the slower PhysicalActionContainer can compile with scons CXXFLAGS=-DNO_BEX now to get the old behavior. 1. Adapted TriaxialTest and ElasticContactLaw to BexContainer (switchable at compile-time). 2. Adapter GlobalStiffnessTimeStepper to BexContainer (GlobalStiffnessCounter code put to a function inside this one, hence that engine is not needed anymore). 3. Adapted Shop::Bex to BexContainer (probably not needed anymore?) 4. Exception is thrown in PhysicalActionVectorVector is used && built with BEX_CONTAINER (would most likely crash anyway). 5. transientInteractions and persistentInteractions are only references to MetaBody::interactions now. Removed extra loops in InteractionPhysicsMetaEngine and InteractionGeometryMetaEngine. 6. Remove including qglviewer into miniWm3, as it breaks compilation if using miniWm3 separately from yade (for testing purposes). 1. Define Janek's functions to convert from/to QGLViewer vector where they are used. 1. Add BexContainer (same interface, but separate implementation) in openMP flavor. 2. openmp=0 is the default for scons now (for some time), since openMP BexContainer gives about 7% slowdown and thus is not useful before at least some engines are parallelized as well. 3. Removed getting references to Force/Torque from BexContainer, since that breaks concurrency. Instead, addForce/addTorque must be used. If you need to read back with getForce/getTorque, you have to call sync() (expensive!!) beforehand, which will compute summary values for all bodies; if you forget, exception will be thrown. Note that sync() is invalidated at next write operation. 4. Adapted a few constitutive laws and other engines for the changes mentiones here. 1. Add time-profiling classes. See http://yade.wikia.com/wiki/Speed_profiling_using_TimingInfo_and_TimingDeltas_classes for details. It is accessible from python as well. 2. SimulationController no longer asks for output format. It just uses XML, the only available one. 3. Engine, EngineUnit have timingInfo member and pointer to optional timingDeltas. Timing is disabled by default, but it may still have some overhead in the order <1% perhaps (will test) 1. Forgotten file with yade.timing.stats() that pretty-prints some numbers. 1. Move all container to core, remove linking with them since it is not necessary 2. Fix things so that everything compiles (at least) both with and without BexContainer 3. Parallelize ConstitutiveLawDispatcher, InteracionPhysicsMetaEngine and InteractionGeometryMetaEngine with openMP if enabled on command-line 4. Make InteractionVecMap default container for interactions; necessary for parallel code. 1. New InteractionDispatchers class that has one common loop for InteractionGeometryMetaEngine, InteractionPhysicsMetaEngine and ConstitutiveLawDispatcher. It can be used from python like this: 1. Adapt ForceEngine to BexContainer 2. Add BEX_CONTAINER and YADE_OPENMP flags to be reported by -h. 1. Add two more forgotten headers. They are not used anywhere, though, and will be removed later. 1. Enhancement of utils.box from Marco. 1. Make Shop load 4/5/6 columns text files for spheres (and skip 5-cols) 2. Change evaluation of args in readParamsFromTable to be able to pass strings better (single quotes) and consistently 3. Parameters passed as env. vars by yade-multi are prefixed with ! 4. fix typo in timing for resetting timers. 1. Make the yade-multi scheduler multithread-aware. 2. Add the collider performance test as example 3. added utils.replaceCollider(anotherCollider) for convenience 4. added Omega().isChildClassOf(classNameChild,classNameParent) 1. Fix collider-perf (TriaxialTest has hardcoded dt=0.001 !!!!), set timestep by hand at first 2. Fix Shop:: loading spheres from file (regression from yesterday) 3. Add functorCache to Interaction and to InteractionDispatchers. About 5% improvement, but not yet finished. 4. Add DynLibDispatcher::getFunctor2D 5. Add BexContainer::sync() to other places in triaxial (thrown otherwise) 1. Fix old rename of runtime.args to runtime.argv in default-test.py. Should run OK now. 1. Fix for the compile error in snow for OrthogonalPlaneFit3. It still misses pkg/snow/Engine/ElawSnowLayersDeformation.cpp in the repo. Compile with exclude=...,snow as workaround. 1. Rename BroadInteractor to Collider. 2. Move some part of the contact logic to this common base class. The Collider::handleExistingInteraction is subject to discussion and not yet used. 1. Small fix in the collider code. 1. Remove SAPCollider completely 2. Make yade log4cxx 0.10 compatibile 3. Other minor fixes 1. Fix linking of realtime-rigidbody WRT PersistentSAPCollider 1. change default xiShear to 0 instead of NaN (is not used anyway) 2. Fix linking of mass-spring in cliean build 1. Fix #include's that include files not in the current source directory via "". 2. Add scripts/linkdeps.py that can automatically determine what plugin links to what other plugins, which can be once used for configurable monolithic/pluggable builds etc. 1. Fix crashed in TriaxialTest introduced by me a few days ago (referencing engine before being created) 2. Add simple (working?) memory usage query to utils and collider perf test. 1. Fixed collider performance benchmark 2. Added script to generate graph from log files (like http://yade.wikia.com/wiki/Colliders_performace) 1. Added SpheresContactGeometry::updateShearForce, will be used (not activated though yet) by ElasticContactLaw and other. hotfix related to last commit 1. Initial checkout for the DemXDofGeom classes (will contain the hasShear code from SpheresContactGeometry and more eventually). 1. Preliminary version for sphere-facet collisions with total formulation (moderately tested). 2. Same for sphere-sphere collision. 3. test script for facet-sphere collision geometry. 1. Use local foreach.hpp if not found in the system 2. Use local file defining boost::python::len for boost<1.34 1. remove explicit linkage to boost_python in gui/SConscript Forgotten empty file. 1. Remove logger from ClassFactory 2. Cleanup logging stuff in main (use constructor function, among other) 3. Cleanup system exit from python in PythonUI_rc.py 4. Add SpheresContactGeometry::updateShear that can be optionally used with ElasticContactLaw to update shear displacement instead of updating shearForce. triax-identical-results.py show quite large difference between both implementations, but I am not able to tell which one is correct. scripts/test/shear.py shown almost no difference for 2-sphere scenarios, modulo differences at 15th decimal place or so. 5. Remove debug output from BexContainer 6. Remove warning about meniscus data from CapillaryCohesiveLaw (warning is given in postProcessAttributes now, i.e. iff the class is actually used) 7. Add logger to snow. 8. Removed shear computation code in ElasticContactLaw, use SpheresContactGeometry::updateShearForce. 9. Fix scons deprecation warnings 1. Add functions to augment forces/torques in BexContainer. 1. Remove some garbage from SpheresContactGeometry 2. Verify that SCG_SHEAR doesn't alter behavior if ElasticContactLaw::useShear is false 3. Implement SCG_SHEAR for sphere-box interactions 4. sphere-box interactions no longer call goReverse, but swap interaction order instead, as facets do. 5. Fix triax-idnetical-results.py to reload generated initial config to avoid rounding issues of sphere coords in text file. Minifix: link core with librt (clock_gettime) for platforms that require it 1. Add rate-dependent damage to normal and viscoplasticity to shear components of Brefcom (not yet tested, just compiles); other cleanups there. 1. add addF and addT to legacy ActionContainer Add label attribute to engine units. Python wrapper updated. 1. Rate-dependent fixes (more to come) in brefcom. 1. Remove MetaBody::physicalActions if compiling with BEX_CONTAINER (default) 2. Make everything work with both BexContainer and deprecated PhysicalActionContainer 3. Change PhysicalActionDamper, PhysicalActionDamperUnit, PhysicalActionApplier and PhysicalActionApplierUnit to dispatch only according to PhysicalParameters (not PhysicalAction anymore). That means that only one unit will be called for each body and that NewtonsMomentumLaw has to do the job of NewtonsForceLaw as well (same for CundallNonViscousMomentumDamping). 4. Fix (finally) defaultDt computation in TriaxialTest (forgotten assignment to defaultDt in the GlobalStiffnessTimeStepper) 5. Fix (finally?) timestep manipulation form within the QtGUI. If reloading the same file, timestep settings will be preserved, otherwise those saved in the XML are used. 1. Create ef2_Spheres_Elastic_ElasticLaw that has the ElasticContactLaw algorithm 2. ElasticContactLaw now merely calls ef2_Spheres_Elastic_ElasticLaw. 3. TriaxialTest::parallel controls whether to use InteractionDispatchers or not. 4. Added examples/triax-perf to show the impact of that. Also see http://yade.wikia.com/wiki/Triaxial_Test_Parallel 5. Fix a few compilation issues. 6. Flush stdout before exiting from main, so that in case of crash upon exit (log4cxx?) we have all messages output. 1. Hotfix for 2 issues with ElasticContactLaw 1. Remove all traces of physical actions: 1. Remove Shop::Bex (no longer necessary) 2. Add InterpolatingDirectedForceEngine for Roger (not yet tested!) 1. Fix linking of ForceEngine with interpolation 2. Random rate-dependent things. 3. Typo in BexContainer docs 1. A few fixes in Brefcom. 2. Make python wrapper correctly handle long long attributes. 3. Added test script for InterpolatingDirectedForceEngine 1. MAJOR change in python syntax (backwards-compatible, though): through small bit of very dirty code, classes can be instantiated as python objects with keyowrd arguments, i.e. instead of 1. cleanup UniaxialStrainer code, add vars to control length of the acceleration phase and the ability to set absolute speed 2. EngineUnits within InteractionDispatchers can be labeled and accessed from python now. 3. A few minor things in the plot module 1. Remove cruft from brefcom, a few fixes there 2. Add gnuplot grid to gnuplot by default 3. Fix speed in USCT 4. Fix InteractionDispatchers traversal in pyOmega 1. Fix weird python problem if LIBS is not defined by distuils (?) 1. Add working version of facet adjacency finder (to get their mutual angle at edge) 1. Parallelize initial bound filling in PersistentSAPCollider. Gives almost 3x speedup for the first step. 2. Fix missing headers so that it compiles with g++-4.4 (in QGLViewer) 3. FacetTopologyAnalyzer works (not tested extensively), questions of where to put topology data for InteractingFacet (will be raised on yade-dev) 4. Test script for FacetTopologyAnalyzer. 1. Remove leftover var in PersistentSAPCollider 1. Add preliminary gnuplot plots merging facility to yade-multi 2. Fix yade.log module so that it also works without log4cxx (and gives 1 warning) 3. Switch to new syntax in scripts/plot.py 1. Fix race condition in brefcom (omp critical section) 2. Remove -ffast-math from optimized build, since NaNs do not work properly (e.g. isnan(NaN)==false!) 1. Fix bug in FacetTopologyAnalyzer algorithm 2. Add angle info to InteractingFacet (not yet used) 3. Add triangulated sphere test for FacetTopoloyAnalyzer to facet-topo.py 4. Fixes in rate-dep in brefcom 1. Add approximate viscosity equations to brefcom (not working) 2. Fixes in yade-multi 1. Finish implementation of Dof3DofGeom_FacetSphere (with plastic slip as well) 2. Adapt Brefcom optionally to Dem3DofGeom 3. Add d0fixup to SpheresContactGeometry to get correct normal strain in sphere-facet contact with fictive sphere (zero for sphere-sphere) 4. Finish FacetTopologyAnalyzer; angle usage in Dem4DofGeom_FacetSphere not yet tested. 1. Remove cruft from UniaxialStrainer, add the ability to set initial velocities to suppress inertia at the simulation beginning 2. Jobs in yade-multi can be automatically named after variables suffixed with ! 3. yade-multi now shows and updates automatically some statistic on localhost:9080 using http 1. Finish Dem3Dof for both spheres and facets, migrate Brefcom. Removing stuff from SpheresContactGeometry is on schedule, once thorough testing is finished. 2. Fix attribute inheritance for a few engine units 3. Add ef2_Dem3Dof_Elastic_ElasticLaw, which works like ElasticContactLaw (but faster ;-) ) 4. Remove BrefcomLaw, keep just the constitutive law as functor. Adapt sample generators for that. 5. Add hydrostatic confinement to brefcom (isoPrestress), remove viscApprox. 6. Add interface for querying and setting (doesn't work yet) number of openMP threads 7. Job description is taken from columns suffixed with ! or by combining all parameters 8. Add function for plotting yeild surface of brefcom to the eudoxos module 9. Oofem export now uses reference (starting) positions of particles as it should 10. Add "-" before profile name when generating default variant suffix in scons (which is expected) Fix comp9ilation error for Janek. 1. Add python wrapper for clumps, see scripts/test/clump.py on how to use it (O.bodies.appendClumped) 2. Fix clump support in NewtonsDampedLaw (damping is quite wrong, it seems...; Bruno, any ideas on that?) 3. Move clump to pkg-dem (even though it depends on extra/Shop) 4. Remove absolute shear computation from SpheresContactGeometry, as Dem3Dof works fine now and Brefcom will not use SCG anymore; adapt a few other classes to that; remove ElasticContactLaw2 that was using it. 5. 1. Warn in --version if -ffast-math was used 1. Fixing bug in TriaxialCompressionEngine (introduced by luc apparently). Big changes: Handle boundingVolume-less bodies gracefully in InsertionSortCollider 1. Add utils.regularSphereOrthoPack by Anoton Forgotten showcase. 1. Add InteractionContainer::requestErase to hint colliders that wouldn't otherwise see !isReal interactions. 2. Use this logic in InsertionSortCollider, PersistentSAPCollider, SpatialQuickSortCollider (noop in the last one) 3. Add InsertionSortCollider::sortThenCollide to make it behave as non-persistent collider (for debugging only?) 4. Add Interaction::reset() that has common initialization code. 5. Assign zero inertia to utils.facet (better than uninitialized binary garbage) 6. Fix contact logic in Brefcom, finally I get the same results with InsertionSortCollider as with SpatialQuickSortCollider on large simulation (more fixes to come) 7. Do not install pkg-config; fixes compilation error reported by the build bot. 1. Use bitfield instead of bools in InsertsionSortCollider 2. Revert accidental changes in insertion-sort-collider.py 3. Add function for using renamed classes from python with warning Getting rid of the Brefcom name, classes renamed as follows (moving files around will follow) 1. Add logic to scons to delete files that will not be installed in this run but are on-disk. This should make it unnecessary to remove files by hand. In the same way, disable implicit target cache which was making problems if files shuffle around. 2. Remove Brefcom* files, move to pkg/dem/ConcretePM.?pp. (not sure what other place, since it contains Engines, DataClasses etc in one file that I would refuse to break.). 3. Add detailed comments on ConcretePM to the ConcretePM.hpp 4. Remove extra/usct, moveUniaxialStrainer and put to pkg/dem; move SimpleScene from extra to pkg/dem 5. Remove core/yadeExceptions.* 6. Remove Preferences::dynLibDirectores and Preferences::version. Omega now recursively searches the lib directory for plugins and loads them. preferences.xml has only defaultGUILibName now. Finally. Remove baseDirs and other cruft from DynLibManager. 2 forgotten files (separated from UniaxialStrainer before) 1. Fix hopefully last relict of pkg-config 2. Degrade deleting non-existent interaction from fatal erro to warning only (not sure where that can come from, though.) Solve the cause of nonexistent interactions being deleted (after O.interactions.clear()). Make warning fatal error again. 1. Remove Interaction::isNew, Interaction::isReal. Add Interaction::isReal() which test for presence of _both_ interactionGeometry and interactionPhysics and Interaction::isFresh() which checks the interaction creation timestamp against current iteration. Updated all code for that. Please verify that your stuff works, it is possible I made some mistakes! 2. All code saying isReal=false replaced by interaction->requestErase(id1,id2) 3. make requestErase thread-safe 4. Add interace for traversing interactions pending erase (template) 5. Add TriaxialTest::noFiles and TriaxialCompressionEngine::noFiles to not generate any files (default: off) 6. Add predicate utils.ptInAABB(p,minPt,maxPt) 7. utils.spheresToFile return number of spheres written (instead of None) 8. Add examples/concrete/pack to generate packing; other stuff in concrete will follow, with simplified version of the cpm model in ConcretePM. 1. Syntax fixes in ConcretePM model 2. Interactions will be deleted also if the ye4xist, but geometry functor fails (returns false) 3. Add utils.approxSectionArea, utils.spheresFromFileUnixial (get some parameters useful for uniaxial tests from the sphere packing, such as cross-section, principal axis, etc) 4. Add lib/computational-geometry/Hull2d.hpp for computing convex hull in 2d using Graham scan algorithm (I know it is in CGAL already, but I don't want to depend on that commercial stuff) 5. Remove some unused stuff from utils. 1. Add epsNPl to Cpm 2. Replace vector by Vector2 and make it properly serializable (should be faster) 3. Add function to compute forces on interactions crossing plane. 4. Replace custom xcombine function by itertools.product in grid sphere packing Fixes and cleanups in the CPM code. Add new 'feature' to scons called openGL, which is on by default. Qt3 GUI will not be built without openGL. YADE_OPENGL is defined in openGL-enabled builds. Sconscript files adapted to skip GL plugins or GL parts of plugins. 1. Fix missing libs for linkage 2. Fix a few typos 1. Don't link core with glut (is there a reason for that?) Do not include X11 headers if without opengl 1. Move all python modules to PREFIX/lib/yadeSUFFIX/py/yade instead of */gui/yade 2. Add pack module for generating regular packings (thanks to Anton Gladky for his ideas & code) 3. Add _packPredicates module for solid inclusion testing. 4. Update regular-sphere-pack.py to test new packing features. Remove leftover reularSpheresOrthoPack from utils. Is in yade.pack now. Add pack.inHyperboloid predicate. Should be useful for cylindric specimen in uniaxial tension, but with the middle part having smaller diameter. Added to the test script as well. 1. Fix (hopefully) clump damping 2. Remove unused code from InsertionSortCollider 3. Make SimulationController NOT change timestep (rounding) by just opening it (!!) 4. Fix paths in PythonUI and lib/SConscript for $PREFIX/yade$SUFFIX/py/yade instead of $PREFIX/yade$SUFFIX/gui/yade 1. Add resetting interactionGeometry and interactionPhysics to Interaction::reset(), as it should be... 2. Small things in CPM 3. Add GaussAverage.data method to python (for debugging and plotting) Include Python.h in PythonRunnerFilter. Build this plugin only with EMBED_PYTHON. A few changes to allow run primarily python with qt3 on the top of that (open, close etc as needed). This paves way to running main yade process in python ;-) (just kidding, for now) 1. Handle groupMasks of bodies in InteractionDispatchers directly (not in geometry functors etc). 2. Fixes for qt3 started from within python 3. Add Body().dynamic flag to the wrapper, instead of using Body()['isDynamic'] all the time. Anton's new things: axis-aligned ellipsoid predicate and fix in pack.regularHexa. 1. Add external euclid.py module (suggested by Anton, thanks!) to our installation 1. Propose *.sqlite ending for saved simulations instead of * in the player Fix error-tolerant law which uses no interactionPhysics: add void Interaction physics in the geometry functor if returning true, to make Interaction::isReal return true. (Shouldn't we remove ErrorTolerant...? Does it have some serious use?) 1. Remove constructor priority for log4cxx to avoid syntax unsupported by gcc<=4.0. 2. Remove some commented cruft from FrictionLessElasticContactLaw 1. Add boolean operators on solid predicates (&,|,^,-), shown in scripts/test/regular-sphere-pack.py 2. Add notch predicate (not functional yet) 3. Add utils.alignedFacetBox to create hollow box from facets. Shown in new file scripts/test/facet-box.py 1. Update simulation filename in controller periodically 2. Fix notInNotch predicate, use infinite AABB for unbounded solids and raise exception in the packing generator if such is encountered. 3. Add notch to the head of regular-sphere-pack.py guy 1. Add checks for GTS (optional) 2. Add pyGTS to our tree (built only if needed), since no packages are available. 1. Fix corner case in InsertionSortCollider related to instability of std::sort (quicksort) and bodies having the same upper and lower bounds (facet in the xy plane, for example). Thanks to Anton for providing the crasher. Fix feature macro definitions (typos) 1. Add GTS surface predicate 2. Add example of sphere horse falling onto facet horse in scripts/test/gts.py (try it!) 3. Predicate difference now takes padding in the inverse sense for the second predicate (logical) 4. Attempt to enable lightning on facets (no effect :-( ) 1. Add coarsened horse geometry for the example gts.py 1. Rename ef2_Dem3Dof_Elastic_ElasticLaw to Law2_Dem3Dof_Elastic_Elastic (in scripts as well) 1. Make virtual methods on pack.Predicate work in python (inGtsSurface, for instance). Add scripts/test/gts-operators.py to show that. 2. Move scripts/test/gts.py to gts-horse.py 3. Add a few functions to pack for constructing triangulated revolution surfaces from meridians. 1. Padding support (though slow and not very precise) for pack.inGtsSurface 1. Fix crashers in InteractingMyTetrahedron* classes (introduced by me when updating interaction logic) 2. Reimplement inGtsSurface in c/c++ which makes it faster due to pygts interface limitations (addressed on pygts mailing list meanwhile), but is dirty programming. 3. Set CCOMSTR to correspond to CXXCOMSTR in SConstruct (to show nice line when compiling c source file, for pygts) 4. Set good-looking timestep in the TetrahedronsTest generator 1. Add triaxial packing generator, with optional memoization to sqlite database to avoid generating packing if there are suitable ones (same parameters/scalable to same parameters) available. Sample script will be provided soon. This allows for filling arbitrary (gts-defined, for example) volumes with irregular, high-quality sphere packing. 2. Add python-wrapped class SpherePack for manipulating sphere packings (loading, saving, spatial transformations, iterating) 3. Add shared_ptr Omega::rootBodyAnother to be used with Omega().switchWorld() 4. Move some stuff from gui/py to lib/py, which is more logical hopefully 5. If negative value is specified for TriaxialTest::thickness, wall thickness will correspond to the mean sphere radius (avoids spheres going through the walls during compaction for some radii) 1. Add automatic converter from python::tuple to Vector3r and vice versa. Wrapped functions can take/return Vector3r directly instead of manual conversion. Clean code that had to do that. Let me know if something breaks, the changes should not touch any python code. 2. Some preliminary work on wrapping Vector+Quaternion classes in python via py++ (not enabled, just the files are there) 3. Add forgotten _packSphere.cpp, thanks to Vincent for reporting. 1. Add scripts/test/gts-traix-pack.py to demonstrate triaxial packing generator. Remove useless include in GlobalStiffnessTimeStepper. 1. Fix STUPID (my fault, sorry!!) mistake in setting Interaction::iterMadeReal, which cause ElasticContactLaw to function wrong. It concerns a few other contact laws calling isFresh, which would return true as well. Sorry again. 1. Shuffling stuff around, moving most python things to py/ 2. Wrapping Vector3r, Quaternionr and Vector2r in python directly, see scripts/wm3-wrap.py 3. Change the way utils.box, utils.sphere and utils.facet works: arguments to physical parameters are passed as keywords, not as dictionary now (update your old code by passing **dict instead of dict as the last argument) 4. Fix a bug with useShear, now getting almost identical results for triaxial again. 5. Preliminary Triaxial::facetWalls, to be able to used Dem3DofGeom with Triaxial. (not fully functional yet) 6. TriaxialStressController::thickness is -1 by default now (get thickness from box width), as 0 is real value for Facets. Doesn't change beahvior in any way. 1. Update triax-perf.py 2. Add Omega().tmpToString returning string of :memory: saved simluation 1. add yade.plot.resetData(), which unlike reset() resets just data 2. Add scripts/test/compare-identical.py to run 2 simulations at the same time and check at every step (configurable) if they differ or not. 3. Add active=active line to GlobalStiffnessTimeStepper, which for some reason causes two same simulations to be the same. Any explanation someone?? 1. Add forgotten py/SConscript (sorry!) 1. Fix absolute path generated by py++ 1. Dump XML in ConcretePM in case of problems (nan's) 2. InteractingFacet::postProcessAttributes gives FATAL message if there are coincident vertices 3. Update triax-perf, add script and openoffice sheet to make table 4. InsertionSortCollider is used in TriaxialTest always (not only with fast) now. 1. Change prototype of Engine::isActivated() to Engine::isActivate(MetaBody*) 2. Add maxVelocitySq to NewtonsDampedLaw for analysis purposes 3. Add BoundingVolumeMetaEngine::sweepTime and ::sweepDist to sweep bounding volume by given predicted motion over time or by given absolute distance. 4. Add strided run support to InsertionSortCollider (using sweeping) 5. Add scripts/test/collider-stride-triax.py to play with the strategies of sweeping based on strides 6. Add O.interactions.countReal() 1. Fix collider-stride.py to match changed parameters. (it is quite useless now, anyway 1. Make NewtonsDampedLaw compute maxVlocitySq at every step anew. 2. Make InsertionSortCollider find NewtonsDampedLaw and get max speed from there. Together with InsertionSortColider::sweepLength, this makes stride adapted automatically to maxVelocitySq; this will described at http://yade.wikia.com/wiki/Insertion_Sort_Collider_Stride. 3. Update test script for that. 1. Handle clumps in a better way in NewtonsDampedLaw (only if asked by the clump itself) -- future parallelization work. (related to bug #398086) 2. InsertionSortCollider now knows when to run based on maximum distance the fastest body could have travelled. (It is actually the physical meaning of sweepDistance). Handle varying maxVelocitySq in a constitent way. 3. Add InteractionContainer::serializeSorted to sort interactions by id1 and id2 before serializing (useful for comparing XML files). Added Interaction::operator< to compare 2 interactions in that way. 4. Fix openMP strategy in InteractionDispatchers to "guided" (as per https://blueprints.launchpad.net/yade/+spec/omp-schedule-strategy) 1. Remove doc/removed, it is in SVN history 2. Tune debian scripts to install docs+examples+scripts instead of headers (targets https://bugs.launchpad.net/yade/+bug/398174, but not yet finished) 3. Add depends on python-numpy instead of python-scientific packages for debian 4. Add ../py directory to doxygen (targets bug #398190) 1. Change NewtonsDampedLaw to a StandAloneEngine 2. add .updateExistingKeys (perhaps should be updateExistingAttributes) to all python-wrapped yade objects, which will change only existing attributes from given dictionary 3. Adapt STLImporterTest to new nicer syntax. 1. Add virtual destructors to all EngineUnits so that they can by dynamic_cast'ed to. This fixes possible crash from python, bug #398255 2. Rename updateExistingKeys to updateExistingAttrs, add updateAttrs. 3. Add forgotten script to demonstrate predicate operators 4. The default debug level is -ggdb2 (instead of -ggdb3). Libs are about 60% in size and still give the same debug information. 1. Rename scons option arcs to PGO (profile=guided optimizations) 2. Install only binaries by default (no docs, must be requested from cmd line via path) 1. Various fixes related to generating debian packages 1. Fix EngineUnits linkage for SImpleViscoelasticRelationships 1. Add velocity binning for collision optimization: requires cooperation of NewtonsDampedLaw, BoundingVolumeMetaEngine and InsertionSortCollider. 2. Remove time-based sweeping from BoundingVOlumeMetaEngine. 3. QtGUI doesn't show annoying warning when run from python session anymore. 1. Parallelized NewtonsDampedLaw (scales very well) 2. Parallelized VelocityBins 3. Add const modifier to BodyContainer::size 4. Add virtual dtors to PhysicalAction{Damper,Applier}Unit (for dynamic_cast'ing) 1. Move NewtonsDampedLaw to StandAloneEngine directory 2. Add omp critical to ConcretePM 3. Remove SphericalDEMSimulator 1. Add sweepLength to TriaxialTest if fast==true 2. Remove euclid from the pack module, since we use wrapped wm3 now. 3. Add _packObb.cpp to compute minimal oriented bounding box on cloud of points 4. inGtsSurface predicate with triaxialPack will work on the minimum OBB 5. Add check for engine to prevent crash as per https://bugs.launchpad.net/yade/+bug/399810 6. Enhance the pack.inSpace predicate to work as expected. Custom center can be given to the ctor 1. Fix non-tuple in graph specification 2. Allow plotting agains the y2 axis, after a special parameter '|||'. 1. Remove mutex from requestErase (should be verified to compile on non-openMP machine!) 2. Add mutex to PhysicalParameters, so that body state can be locked while updating from the interaction loop. 3. Add linking with EngineUnits to Tetra (thans Emanuelle) why..?? 1. Adapt simple-scene-graph.py to new instance syntax 2. Add support to y2axis to saved gnuplot plots 3. Change interface for yade.plot.addData to take **kw instead of straight dict (still backwards-compatible) 1. Do not use REGISTER_ATTRIBUTE anymore, use REGISTER_ATTRIBUTES instead everywhere. This generates (in addition to serialization code) also some python code and makes python independent on the yade serialization framework (Janek, if you want to try boost::serialization, I have no objections now). 1. Remove garbage from doc 2. Instruct getopt to not shuffle command-line arguments, so that their order is preserved 3. Add epydoc documentation for all python classes and functions 1. Fix linking logic for _packPredicates (fixes https://bugs.launchpad.net/yade/+bug/401029) 2. Make gts-horse coarse original horse automatically Fix small bug in Velocity bins related to max sweep length (should improve performance as well). Still some incorrect things WRT bboxes, it seems. 1. Fix mathematical error with VelocityBins, verified by new script scripts/test/collider-sweep-simple.py to be correct 2. Add py/ directory to skipped dirs for linkdeps.py so that it works on current trunk 1. BIG CHANGE: pkg/ no longer have SConscript files but are scanned at startup for plugins. See http://yade.wikia.com/wiki/ImplicitBuilds for some details. Let me know if there are some problems. add boost-serialization and boost-program-options to debian. 1. Move STILimport to pkg/dem, as it depends on dem 2. update RockPM with the new-old version (probably svn didn't update the moved version? what a deal. We should definitely move to bzr...) 1. Fix unreported version for the debian build 1. Fix snow compilation by #including Voxel/* files in SnowVoxeslLoader and noc compiling them directly (sorry) 2. STLReader is a pure-header import lib now, tolerance is passed as regular data member. 3. Fix all warnings in ConcretePM. 4. Merge lib/yade-* into lib/yade-support. 1. Fix monolithic compilation even with fem. All modules can now be compiled that way. fix compilation? Fix TetraTestGen crasher (functionally still brokne, though) Remove SDECLinkGeometry, replaced by SpheresContactGeometry at a few places. Not checked for functionality. This avoid many warnings. 1. Fix linking with full Wm3 library 2. Automatically add /usr/include/wm3 to CPPPATH if useMiniWm3=False 1. Hopefully fix https://bugs.launchpad.net/yade/+bug/402098 2. Fast in TriaxialTest uses nBins==5 and binCoeff==2 for VelocityBins 1. Fix SnapshotEngine and simple-scene-video.py to run. It doesn't work, though, because of the makeCurrent() failed error (probably getting snapshot from another thread...) 1. Add GLViewer::nextFrameSnapshotFilename to save frame in postDraw 2. Adjust SnapshotEngine to take advantage of that. This should solve https://bugs.launchpad.net/yade/+bug/396023 3. utils.encodeVideoFromFrames can take list of files (instead of just wildcard). Backwards-compatible. 4. scons doc skips debian/ directory (would mess up if deb package was build) 1. Fix for https://bugs.launchpad.net/yade/+bug/406343 (at least for me) 1. Add GenericSpheresContactClass to unit radius1, radius2 and normal between SpheresContactGeometry and Dem3DofGeom (to make it work with GlobalSitffnessTimeStepper). Partially solves https://bugs.launchpad.net/yade/+bug/399963 1. Add docstrings to all wrapper.Omega() methods 2. Fix a few warnings. Fix has_map warning and one more in FlowEngine. 1. Add infrastructure for getting temporary filenames in a secure manner to Omega 2. move selectedBOyd to MetaBody; initialize it properly to avoid possible crash. Remove leftover SConscripts. 1. Change syntax of YADE_PLUGIN("Plugin1","Plugin2") to YADE_PLUGIN((Plugin1)(Plugin2)) (replaced everywhere) 2. Add some perliminary and not-enabled by default support for boost::serialization (see ClassFactory.hpp) 3. Add boost::serialization code for Se3r, Vector2r, Vector2, Quaternionr 4. Do not reset BexContainer's moves and rotations uselessly (i.e. if not used) 5. Use Omega's mutex in SimulationController to prevent loading-related crashes 1. Don't use __COUNTER__ to generate plugin registration function names, as they wre added in gcc 4.3 Use the name of the first plugin instead. 2. Dem3Dof_SphereSphere takes touching distance as equilibrium if distanceFactor is <=1. The initial position otherwise (was the default everytime until now) 1. Generate proxy constructors to all classes deriving only from Serializable in python (like GLDrawBox and similar). 2. Fix scripts to have the new syntax everywhere, since e.g. EngineUnit is just abstract class that cannot be instantiated from python. 3. Add check fro valid data before saving plot to gnuplot; raise comprehensible exception if there is nothing to save. 4. Remove leftover scripts/pch.py 1. Add an example of uniaxial tension-compression test for concrete (ready long time ago...) 1. All different yade types are real python types now. They have their properties defined at startup. One can say O.bodies[0].shape.diffuseColor instead of O.bodies[0].shape['diffuseColor'] now. It also works much better with ipython tab-completion. It is not sure whether we will be able ever to deprecate the old object['attribute'] syntax. 2. Wrap ParallelEngine in python, and finish Dispatcher wraps as well. 1. Reset interaction radius after the initial contacts have been created. Fix FileGenerator wrapper in PythonUI_rc.py (has different name in c++ (FileGenerator) and python (Preprocessor). 1. Rename Preprocessor in python to FileGenerator, to be consistent with c++. Preprocessor is never used directly, anyway. The old deprecated name put in the deprecation table. 2. Manage crash at exit in defaut-test gracefully 3. Fix serialization of pairs (overlooked replace) 1. Initial attempt at regression tests (only the python wrapper so far); run scripts/regression-tests.py 2. Fix a few bugs discovered that way :-) 1. Replace PersistentSAPCollider and DistantPersistentSAPCollider by InsertionSortCollider everywhere. The two are still in the sources, but are not compiled. Will be removed in near future. Added to deprecated table in python so that old scripts still work. 2. Add some more regression tests for the python wrapper. 3. Fix timestep in HangingCloth (it does some weird things, can someone check it or just remove mass-spring from the tree?) 1. Be more tolerant to specifying invalid GUI at the command line 2. Throw exception about unopenable $DISPLAY rather than letting QApplication abort() 1. Fix https://bugs.launchpad.net/bugs/409254 https://bugs.launchpad.net/yade/+bug/409254 take 2 Maybe fix https://bugs.launchpad.net/yade/+bug/409365 1. Fix (?) https://bugs.launchpad.net/yade/+bug/409254 by moving ClumpTestGen out of Clump.hpp 2. Avoid warnings in STL import code (return values _should_ be checked, though!) 3. Avoid warning in yade.cpp in optimized build 1. Infrastructure for periodic collision handling. Not at all functional at this moment, don't even try to use. 1. Beta version of periodic boundary conditions (try scripts/test/periodic-simple.py 1. Assign new function O.exitNoBacktrace to sys.exit. Fixes partially https://bugs.launchpad.net/yade/+bug/410250 2. Add some more comments to periodic stuff. 1. Script that shrinks the periodic cell progressively (reveals bugs in the collider, though ;-) ) 2. Add function to compute total force in volume from interactions to Shop, wrapped in _utils as well. 1. Working periodic collider, yay!! scripts/test/periodic-grow.py shows that 2. A few changes related to that. 1. Add PeriIsoCompressor for periodic isotropic compression; see scripts/test/periodic-compress.py. Not so much slower than regular triax, nice surprise. 2. Make SpherePack standalone class (previously just in python's _packSpheres), add the function to generate cloud of spheres, both periodic and non-periodic. _packSpheres wrapper is update, but otherwise not changed. 3. Fix python-less compilation for se3 interpolator engine 4. Add Omega().runEngine() 5. Fix some compilation/linking issues. 1. Fix missing vtable for GenericSphereContact (crasher with debugging) 2. Fix collider stride for TriaxialTest with unspecified radius 1. Try to fix locking with boost-1.35, possibly fixes https://bugs.launchpad.net/yade/+bug/411572 (please confirm) 2. Add periodic repetition function to SpherePack 1. Fix linkage for boost<=1.34 (hopefully) 1. Fix a few things in SpherePack 2. Remove TriaxialTest::GenerateCloud, replaced by SpherePack::makeCloud 3. Fix crash in BoundingVolumeMetaEngine, if MetaBody has no boundingVolume 4. Improve sorting operator, remove workarounds for std::sort wrapping minima/maxima (https://bugs.launchpad.net/yade/+bug/402098) 5. Limit minimum cell width in PeriIsoCompressor, to not crash. 6. Add code for periodic packs in pack.triaxialPack (not yet fully functional) 1. Add #pragma once to SpherePack.hpp (possibly cause of https://bugs.launchpad.net/bugs/412442) 2. Fix crash in TetraTestGen (finally, I think), closing https://bugs.launchpad.net/bugs/408422 3. Add highlight parameter to utils.{facet,sphere,box}, passed to Body::geometricalModel 1. Fix assertion is 2d dispatch code, add indices to RpmPhys, RpmMat, CpmPhys, CpmMat (would break dispatching if using more classes derived from the same base in the dispatch matrix) 1. Remove {,Distant}PersistentSAPCollider and Fixed{Position,Orientation}Engine classes 2. Add test script for generating packing 1. Summarize important changes since the last release. Add your own things, if they are important for everybody (svn log has the small details) 1. Add scripts/rename-class.py for renaming classes (replaces in code, moves files with bzr, adds rename record to python). Not very well tested, though. 2. Remove core/StandAloneSimulator.*pp (not used anymore) Add ignore patterns so that bzr st doesn't show (some) generated files 1. Merged upstream changes. 1. Clen the plugin loading logic a little (no nominal win32 support), support YADE_PREFIX for changing prefix (should be runtime-detected inthe future, anyway) 2. Use $ORIGIN in rpath to make yade relocatable; it can be fragile, let me know if there are troubles! 3. Add make check to the debian package (will be tested soon) 1. Add compatibility for hardy 2. Fix missing newlines (hardy compiler gives warning) Adjust rpath for the main executable (ugly hack) Run tests in debian package (not failing if the test crashes, though, for now) 1. IMPORTANT! All features are lower-cased now (avoids mess: openGL or OpenGL etc). This will probably break your profile files. 2. IMPORTANT! openmp is one of features, no longer a separate options. Adjust your profiles 3. Rename LOG4CXX to YADE_LOG4CXX; all features now #define YADE_FEATURE macros 4. Better $ORIGIN syntax in scons 5. Abort yade if running PythonUI_rc.py fails 6. Adjust pbuilder script 1. Add wrapper for running tests, to trap exit segfault at squeeze 2. Use the wrapper for tests in debian/control 3. Add wrapper for vector Make the test script report what distribution failed (currently only karmic). Fix GTS features (thanks for spotting that; we need regression tests for all the modules) 1. Skip more stuff in doxygen, a few warnings 2. Add debugging code to DynLibDispatcher (disabled) 1. Rewrite 2d dispatching code from scratch 2. Expose classIndex to python for indexable classes 3. scripts/test-sphere-facet.py shows how the dispatch matrix fills with data Add python 2.5 compatibility hack Avoid error in pack.triaxialTest if compiled without GTS. 1. PeriIsoCompressor: add keepProportions parameter (on by default), decrease global updates interval. 2. Omega: startSimulationLoop warns if there is no simulationLoop (how can that happen? It somehow can) 3. SpherePack: resets periodicity (and warns) if being rotated; cellSize is writable now. 4. pack.triaxialPack: renamed to pack.randomDensePack; fix loads of stuff in that; rename radiusStDev parameter to rRelFuzz; add epydoc documentation; fix erroneous detection of inGtsSurface being defined 5. wrapper: lock renderer when adding list of bodies; Omega().resetThisWorld to reset current world only. 6. Fix scripts/test/{gts-random-pack.py,gts-random-obb.py} ef2_Sphere_Sphere_Dem3Dof: change meaning of distanceFactor, see docs (if < 0, equilibrium is sum of radii, otherwise the initial distance; defaults to -1). Renamed to distFactor, to break old code intentionally InteractingSphere2AABB: allow negative aabbEnlargeFactor, which doesn't scale aabb at all (same as if it is 1.) yade-multi: use the first non-blank line as column headings (not necessarily the first line of the file, as is used to be) SpatialQuickSortCollider: fix clearing interaction with openMP examples/concrete/uniaxial: move files around, add confinement and docs; remove examples/concrete/pack since not in the pack module (an example should be given, though) examples/collider-perf: remove PersistentSAPCollider, add InsertionSortCollide with strides, but commented out since no effect at hthe beginning of simulation PeriodicInsertionSortCollider: remove unnecessary (hopefully) condition that would abort in scripts/test/periodic-simple.py PeriIsoCompressor: fix absolute displacements changing proportions, operate on averages instead pack.randomDensePack: fix proportions in periodic packs; change residual stress to 1e8 instead of 1e9 SConstruct: remove obsolete (unused) standalone openmp option yadeWrapper: Fix compilation with boost<1.35 (again) (now?) 1. Fix startup crash if no $DISPLAY set at all miniWm3Wrap: update with newer py++; still errors out at karmic spirit: avoid warning with newer boost versions Add gts to depends on the script. Remove unnecessary inclusion of indexing_suite which breaks compilation for boost<1.34 (or something like that). utils.uniaxialTestFeatures: fix compat with py2.5 SConstruct: fix compilation issues with older symlinks in include dirs Fix OperationalError, reported by Janek in https://bugs.launchpad.net/yade/+bug/416906 SConstruct: add doc for pretty, fix a few lib checks on karmic Fix version detection on systems where version is not specified by hand or in RELEASE file and bzr is not installed main: disable SIGHUP handler (emergency save) and automatic loading. 1. Remove garbage from examples. 2. Fix SpheresFactory, fix examples/SpheresFactory/model.py move SpheresFactor to scripts/test as it doesn't work. Add notes to changelog and news. Forgotten file Mark release version Add mill script mimicking http://www.youtube.com/watch?v=005rdDBoe4w Some changes in qt interface (useless) Add series to package version to allow same version for multiple series in the ppa (0.20-1~hardy, 0.20-1~karmic etc) Added script for http://www.youtube.com/watch?v=KUv26xlh89I 1. Fix facet lighting, mill shown with wire=False now (looks better) 2. Revert recent useless change in QtGUI-python 1. Enabling O.timingEnabled when running will not produce garbage values for current engine anymore 2. Add maxRefRelStep to VelocityBins, to limit speed fo maximum velocity changes 3. Fix epydoc format for utils.encodeVideoFromFrames and utils.uniaxialTestFeatures 1. Do not save potential-only interactions to the XML; do not save pendingErase interactions (are only potential) 2. Do not save interactions in SQLiteRecorder by default (saveInteractions=True if you want the old behavior) 3. Add slider to the simulation player, in the "snaps" tab 1. Add scene that has been sitting here for a few days (should be run for comparison with pfc3d) Workaround bug #416335; static members of Vector3 work only on instance, e.g. Vector3.ZERO will not work, you have to use Vector3().ZERO; changed all occurences in the code accordingly, update your scripts as well.\n2.Some undocumented and untested enhancements for parameter table (backwards compatible) ================================================== yade-0.12.1 Sat, Nov 22 22:48:27 2008 +0000 Bruno Chareyre (6): A wrong comment on contact laws in PFC3D is removed. svn update - no real change (in principle) - recovering from erased local file - Fix conflicts and prepare next implementation of isotropic compression - Few files missing in the previous commit. - Add a new class for computing/recording micromechanical data based on tesselation Still recovering from conflicted files... I hope this is the last one. A class with algorithm for analysing contacts-forces-displacements statistics. Using the triangulation lib. Janek Kozicki (14): ouch, forgot to mark INSTALL file as outdated. We need to update it. some cleanup in the files fix crashes of this->parentWidget()->parentWidget() in UI yade.cpp: more detailed info about compilation flags. LatticeExample: added material parameters bond zone between steel fibres and cement matrix update to use latest scons 1.0.0 don't refresh display when there's nothing to refresh support for generating multiple file with single NullGUI call add to SimulationController buttons for looking in different directions. The default view direction is now down along the direction of gravity. improved generation of steel fibres in lattice fixed snaphotNames in NullGUI for .xml.gz more configurable MakeItFlat, TriaxialTest can be now a biaxial test as well. small fixes in UIs make it compile with boost 1.35 (I wonder what 1.36 will bring) Fixed OpenGL problems with displaying spheres, which - never occurred on my desktop - I've seen them sometimes on other peoples computers, but never could reproduce them - but finally have appeared on my laptop. up direction on Y release 0.12.1 Jerome Duriez (7): Added : - Engines for simulating shear tests at constant normal displacement, normal stress or normal rigidity (CinemDNCEngine, CinemCNCEngine and CinemKNCEngine) for samples deriving from SimpleShear PreProcessor (added also, former DirectShearCis) - ContactLaw1 : a contact law with Moment Transfer and inelastic behaviour in compression : see comments. With correspondant Relationships and type of Interactions. NB : sorry for the name : i didn't search too long for a more explicit one but I think personly that the comments in the files (and I tried to put some) are far much better than the one - Add of the paragraph for the CL1Relationships, which was forgotten, in the corresponding SConscript A (last ?) error concerning last revision in the paragraph CL1Relationships : "CL1Interaction" does not exist, that's ContactLaw1Interaction -ContactLaw1 : correction of prototype of action() : it needed a body, whereas now action methods of Engines need a Metabody. This led the simulation to crash and is now fixed - SimpleShear : now all is normaly done so that this preprocessor could be used (with success) with this ContactLaw. Moreover it is now linked to the GlobalStifnessTimeStepper (instead of the ElasticOne) Suppress of some useful comments (sorry for the extra mail) (At last) The good Sconscript file - The GlobalStifnessCounter engine (for correct use of GlobalStifnessTimeStepper) was forgotten in the preprocessor SimpleShear... Sergei Dorofeenko (4): 1. A new algorithm for facets. It use only a class Facet, so classes Vertex and Edge are deprecated and has been removed. 2. Add functions to python gui for import geometry from stl and for creating facets. 3. Add Shop::inscribedCircleCenter for calculate position of center of triangle inscribed circle (use it for set facet's se3.position). 4. ForceRecorder now take cary about old data files and renaming them. 5. SimulationPlayer now allow wire body form view tab. 1. ResetPositionEngine is now inherited from PeriodicEngine. 2. Add examples/rod_penetration model and geometry. small fixes 1. New random-access interaction container InteractionVecMap (rewrited from InteractionVecSet) 2. Fixes: default initialization some attributes in SCG and IS2IS4SCG Unknown (2): I added a new state at the triaxial compression test in order to realize isotropic compression by the walls displacement until a indicated porosity value. These modifications can be seen with generator file "TriaxialCompression" in the last three parameters (added). I corrected my errors on the triaxialtest files.Moreover, i added comments in the TriaxialCompressionEngine.hpp. Vincent Richefeu (4): - initialize radius in InteractingSphere constructor. - add new plugins used for membrane modelling. - add GLDraw plugin for BssSweptSphereLineSegment displaying - 'Membrane' (in fact geogrid) has been improved but still doesn't work... - the class GroupRelationData has been add (not used yet) to define interacting parameters such as coefficient of friction or restitution that have nothing to do in the bodies parameters (in my opinion) - forgotten files Václav Šmilauer (44): Move big news to NEWS, ready for release finally (?) Update INSTALL file from wiki (brief instructions only). 1. Reimplement some loop-intensive functions from yade.utils in c++ for better performance (as yade._utils, imported into yade.utils automatically - transparent to the user) 2. Add poisson's ratio and Young's modulus estimation in yade.eudoxos based on linear regressions of position→displacement mapping along different axes 3. Rename Shop::ElasticWaveTimestepEstimate to Shop::PWaveTimeStep, wrapped in yade.utils 1. Add python interface for blocking DOFs: b.phys.blockedDOFs=['z','rx','ry'] It is friendlier than b.phys['blockedDOFs']=1<<2|1<<3|1<<4. The property is read-write. 1. Add code for computing histogram of interaction directions in given plane in _utils. 2. This is code is used by yade.eudoxos.plotDirections() to create the actual (nice) figure. 1. Skip (almost) exactly zero projections, implement masking of bodies. 1. poisson and young estimator now works on a fractional part of the speciment 2. do not switch ui automatically if selected explcitly 3. body::maskOK to check mask 1. eudoxos module cleanups, young estimator arg chages 2. fix harmless compiler warning in _utils.cpp 1. add utility function to compute elastic energy within a volume (the dynamic_cast to NormalShearInteraction still fails; what is going on?) 2. add utils.fractionalBox, an AABB reduced to its fraction 3. fix fixmes in Force and Momentum about unused functions about to be deleted 4. plotting interaction direction histogram now works on contrained volume (to study boundary influence on the distribution) 1. Beginning hijacking SpheresContactGeometry to hold more elaborate geometry characteristics, such as relative shear displacement. By default, those parameters are neither calculated nor displated (exactRot==False; must be set to True in ISphere2ISphere4SpheresContactGeometry to enable it). Test script is in scripts/exact-rot.py 2. Remove deprecated code from UniaxialStrainController 3. Add GLUtils to draw lines, text, numbers -- copid over from Shop 4. Add operator<< for Quatrnions (axis angle) 5. Fix energy calculation in volume (in _utils.cpp) 6. Other fixes here and there... 1. The exactRot code is reasonably verified now to be functional, including rolling correction (SpheresContactGeometry::relocateContactPoints) and will used in brefcom soon. 2. Updated the "testing" script scripts/exact-rot.py, as a showcase as well. 1. Remove GL things from Shop, moved to lib/opengl/GLUtils.hpp 2. Cleanup of SpheresContactGeometry code, rename exactRot to hasShear (I thought most of this was already commited?!) 1. Delete unused IS2IS4DistantSpheresContactGeometry (merged with IS2IS4SCG), adapt existing code 2. Adapt new facet code to updated SpheresContactGeometry (only superficially tested) so that they can interact using BrefcomLaw; add scripts/exact-rot-facet.py to show that. 3. Fix a few missing loggers in others' commits. 4. SimulationController redraws if iteration changes (the +1 button would otherwise not cause redraw) 5. Remove cruft from Brefcom. 6. Fix inheritance (dynamic casts) of NormalShearInteraction and of BrefcomPhysParams 7. Remove cruft from UniaxialStrainer 8. Add some python code to compute stress from stored elastic energy. 1. Move interaction direction distribution pie histograms to utils 2. Add plotting histogram of number of contacts to plotDirections() 1. Omega().bodies.append can take list of bodies now (instead of just one body), returning list of added id's 2. utils.facet can take both tuples and lists for vertex coordinates 1. Add NormalInteraction::normalForce and NormalShearInteraction::normalForce (moved up the hierarchy from ElasticContactInteraction) so that unbalancedForce can be calculated on any subclassed interaction type. 2. Adapt Brefcom for this. 3. Add Shop::unbalancedForce and utils.unbalancedForce 4. Add workaround for saving ipython history as suggested by http://lists.ipython.scipy.org/pipermail/ipython-user/2008-September/005839.html 5. Fix AxialGravityEngine to register parent class attributes. 1. Avoid compiler warning in optimized builds from pyOmega 2. Body containers now allocate the lowest possible ID for each added body. The old behavior was to allocate the first free ID greater than the ID of the body, if it was already set. Please let me know if this is critical for someone. We can do things like: 1. 3d view now has by default a OSD with iteration number, simulation time and virtual time. This can be toggled (all combinations) by pressing 'D' (which used to mean toggling d+ynamic flag...?) and set also from python with GLView.timeMask='rvi' (Real,Virtual,Iteration) and so on. 2. Simulation player displays real time and wall clock loaded from db (insted of bogus values of system clock when the player is being run) 3. new periodic SnapshotEngine that takes snapshots of any GL view to numbered PNG files. 4. new function qt.makeSimulationVideo that makes video _while running the simulation_. 5. qt.createVideo renamed to qt.makePlayerVideo 6. Added Omega method to query computation duration. 7. An example of using qt.makeSimulationVideo is in new file scripts/simple-scene-video.py 1. Add forgotten SnapshotEngine 2. BodyRedirectionVector always really find the lowest unused ID (the same for BodyAssocVector) 3. add Omega().interactions.clear() in python 4. Move the "Less than 500 bodies, moving possible" to LOG_INFO instead of on-screen since it disturbs videos taken during simulation... A few fixes in TriaxialTest: 1. radiusStdDev is a registered attribute parameter 2. skip unloading phase if sigmaLateralConfinement==sigmaIsoCompaction 3. new bool autoUnload, that controls automaticity of going from compaction to unloading; autocompressionActivation controls from unloading to loading. Note: IFacet2IS4SCG is broken, but not yet fixed. 1. TriaxialTest now takes readiusMean argument (by default negative, i.e. disabled); if >0, box size is scaled so that both requested porosity and mean size can be preserved. 2. Attempt to fix computation of stress from stored elastic energy. 1. Fix adding empty engine if record wall stress interval <= 0 in TriaxialTest (bug introduced yesterday) 1. Add Interaction::swapOrder(), for use in EngineUnits that want to avoid calling goReverse() 2. SnapshotEngine can sleep specified number of msecs after shot, which probably can avoid some hw problems (make_current failed in mesa, freezes etc) 3. InteractingFacet2IS4SCG now works "correctly" (not exactly physically, though) with shear 4. DynLibDispatcher should report names of classes if dispatch fails. 1. Add InteractionGeometryMetaEngine::explicitAction and InteractionPhysicsMetaEngine::explicitAction for creating contacts manually using the dispatcher 2. add utils.createInteraction(id1,id2) that requests explicit transient interaction creation 3. Add sample ElasticContactLaw2 (in ElasticContactLaw.cpp) that uses new SpheresContactGeometry code and can be used for "persistent" (transient but not deleted by the collider) contacts. 4. Add Shop::applyForceAtContactPoint (applies contact force at contact point to both bodies (reversed for body2) and moments acting on their cenroids as well) 5. All the previous new functionality is demonstrated in scripts/chain-distant-interactions.py. 1. Add Omega().reload() 2. Create map Omega::memSavedSimulations, where simulations are saved if they begin with special sequence ":memory:" and can be loaded again, within lifetime of Omega. 3. Add Omega().tmpLoad() and Omega().tmpSave() that use the above mentioned thing. 4. add utils.readParamsFromTable that reads any python variables from text file (useful for automatic parametric studies) 5. Add less expensive routine for sontact point relocation in SpheresContactGeometry 1. Separate player into two windows (controller and the 3d view); the controller may be hidden with ::hide() (and ::show()) or with Alt-H from the 3d view. This allows for correctly restoring 3d view size. Closing any of the two closes the player. Please log crashes, if any. 2. Update QtGUI-python.cpp: runPlayerSession 1. Yade now runs TCP server at the first free port above 9000 (accessible from localhost only), which simulates python console. (let me know if you need this over network -- it is DANGEROUS, since someone can delete all your files etc without any authentication). The interpreter has its own namespace. 1. Fix crasher (under special circumstances) in PersistentSAPCollider (deletion invalidating iterator) 2. PeriodicEngine now takes nDo and nDone attributes, limitng number of activations 3. Fix minor things is BrefcomDamageColorizer, add normalized damage to BrefcomPhysParams 4. Fix some indents in Triaxial Fix stupid sign mistake when applying contact force in brefcom. 1. PythonTCPServer now generates random 6-letter cookie (password) at startup and authenticates all connections by that cookie. It can be retrieved from yade.runtime.cookie 1. Add Body().mask in python 2. Add PhysicalParameters().pos and .ori instead of ugly pp['se3'][:3] and pp['se3'][3:] 3. Add dmgPlane plot in brefcom 4. Do not delete renderer if we close the last view (loses all renderer settings) 1. Add a quick implementation of bending and torsion code to SpheresContactGeometry 2. Update ElasticContactLaw2 to use that code; stiffnesses are hard-coded for now. 3. Update scripts/chain-distant-interactions.py to show that that code really works 4. Plot residual strength instead of damage in brefcom 5. Add some functions for spiral projections (not correctly working yet) 6. Fix missing std:: in DisplayParameters 1. Add 2d weighted average smoothing abstract class and its specialization on symmetric gaussian kernel, with python glue of course. 2. Remove .gz support. 3. Fix some bugs in the spiral projection code. 1. Fix errors preventing compilation due to missing TesselationWrapper. !! IMPORTANT !! Introduced new dependency on "python-numpy" package (numpy/ndarrayobject.h header), which is now checked for by scons. Tell me if this is not OK! 1. Add initializers for all SpheresContactGeometry members, to avoid nan's in the .xml file 2. Add code for saving arbitrary python variables within the .xml file, see documentation on utils.saveVars() and utils.loadVars() 3. Fix error (hopefully) caused by dangling symlinks in the symlinked buildDir/include tree 1. Fix algebraic typo in max distance check. 1. Commit simple parametric study interface, documented at http://yade.wikia.com/index.php?title=ScriptParametricStudy and wrapper script to queue jobs, which is installed as yade-trunk-multi, yade-trunk-opt-multi and so on. 2. Examples of such parametric "study" added in scripts/multi.py and scripts/multi.table 3. MetaBody now create Omega().tags['id'] at initialization like '20081028T102950p15498' (date, time, pid) that is unique 1. Changed colors to be random by default on utils.{sphere,box,facet} 1. Make our intelligence-challenged deserializer finally gracefully handle nan, inf, -inf (arbitrary lower-upper case). 2. Fix crash in MembraneTest (leftover in the commit from testing, oh well) 3. Add TriaxialTest::fixedBoxDims to not scale selected box dimensions if sphere mean radius is given (example underway). 1. experimental support for Real==long double (#defines QUAD_PRECISION, scons quad=1). long double is not necessarily quadruple precision (not on IA32, at least) though, but is still more precise than double. (search "long double" on wikipedia) 2. Some preparation to compile with -std=c++0x (not yet functional) WRT and boost::shared_ptr vs. and std::shared_ptr 3. Fixed in yade-multi. 4. New direct oofenm exporter in yade.eudoxos. 5. Don't fiddle with termios in non-interactive sessions. 1. Add INTEGER (besides FLOAT) to the list of wrapped c++ types in python. Fix type detection for long double 2. Fix Real->double conversions in GLDrawBssSweptSphereLineSegment.cpp 1. Body().phys.refPos is directly accessible now (old way Body().phys['refSe3'[0:3]] still works, though) 2. Labeled engines are at load-time or when Omega().engines are modified assigned to variables __builtins__.label; for example Add forgotten file. ================================================== yade-0.12.0 Wed, Aug 20 14:37:02 2008 +0000 Janek Kozicki (8): testing if SVN commit messages can go to launchpad eliminate crash on simulation reload. commented out line 241 in QtFileGenerator.cpp some small bugfixes that allow all non-broken filegenerators to run. Those based on SDECLinks will never work, so just put "return false;" there to indicate failure. use NDEBUG to detect optimized builds in FEMBeam and HangingCloth small changes in Lattice small bugfix in scons (by Vaclav) No idea why dynamic_cast fails while static_cast works in TriaxialCompressionEngine:275 and GlobalStiffnessCounter:63 when casting to NormalShearInteraction. We will use static_cast for now... New ChangeLog format. Now I will update with older revisions. But next time it's ALL OF YOU who will write this ChangeLog. It's not nice to write 200 entries once per year. Release 0.12 is ready Sergei Dorofeenko (1): Fixed small bugs and misprints Václav Šmilauer (22): 1. Remove unused GLViewer4 2. Add fairly straightforward GLViewer wrapper (manually wrapped) 3. Fix scripts/simple-scene-player.py that generates video 4. yade.qt module is now in python and imports * from yade._qt for the binary wrappers 5. importing qt if qt not running raises ImportError 6. utils.qtCreateVideo moved to qt.CreateVideo 7. Exponential softening in brefcom (untested) 1. DECREASED Mathr::ZERO_TOLERANCE to 1e-20 so that we don't get identity quaternions for small rotation in ToAxisAngle (!!) 2. Add glue for GLViewer, currently may crash, probably concurrency issues there 3. added yade.plot.reset() 4. add data smoothing (moving averages &c) function to yade.eudoxos 5. Omega().run(num#,wait=False): if the bool is True, it is equivalent to o.run(20); o.wait() for convenience 1. Fix file generator to properly return bool. This fixes some of default-test.py. Change python interface to throw on generator error rather than return bool. 2. Added python glue to set logging levels for individual loggers (from yade import log; log.setLevel('TriaxialTest',log.DEBUG) ) 3. Configuration file for logging is not monitored anymore, since changes from python would be lost 4. Added PhysicalParameters BrefcomPhysParams to prepare for storing volumetric strain; adapted utils.sphere and utils.box to take physParamsClass argument to determine what class to actually create (was always BodyMacroParameters, which is the default now) 5. Brefcom now computes unbalanced force (which is apparently broken as far as the numbers go) and volumetric strain. Many cleanups in Brefcom as well. 6. The collider now properly deletes interactions !I->isReal && !I->isNew && haveDistantTransient. More discussion is needed on that, though. 1. Fix USCTGen so that it works within default-test.py 2. Minor fixes as usual. 1. Fix all crashing preprocessors - for the price of SDECLinkedSpheres and ThreePointBending not really working - InteractingSphere2InteractingSphere4SpheresContactGoemetry only handles SpheresContactGeometry (and not SDECLinkGeometry), OTOH CohesiveContactLaw works only on SDECLinkGeometry. scripts/default-test.py passes now all preprocessors. 2. SDECLinkGeometry marked as deprecated. 1. Permit non-zero integeres as bool - sometimes the serializaer confuses bool with int; give warning to console about that. 2. the -opt profile (and optimize=1) generates instruction set for the current machine (gcc: -march=native) which means that the code may not run on different processor (e.g. core2 code will not run on Pentium IV). Please let me know if this is problem for someone. 1. Fix error with newer ipython coming from the fact that sys.argv wasn't defined in the embedded python env. 2. Fixes in brefcom. 3. stopSimulationLoop in TriaxialCompressionEngine if we enter LIMBO state. 1. Fix refresh period: use it for regular GL rendering as well 2. Make "open automatically" open generated simulation even if a simulation is already loaded 3. Fix crasher (on some machines) the close() was emitted 2× for QtFileGenerato 1. Fix a typo causing crash in the renderer. Fix another crash - rendering interaction that were, meanwhile, deleted during simulation being loaded. A more proper solution (like having a mutex on the whole rootBody that would be locked during loading) is welcome. 1. Remove draw mutex when loading simulation introduced a few days ago (may throw boost::lock_error under some conditions) 2. Restore default signal handlers before exit from main; set SEGV handler to nullHandler since on i386 we (on lenny consistently) get crashes in some log4cxx destructor. WARNING! This version crashes - but I don't know why and I please for help. Summary follows. 1. Fix GUI "crash" when trying to run python console without terminal (running by clicking an icon, for example): if no $TERM, run non-interactively 2. Select QtGUI over PythonUI if no $TERM set 1. Do not propagate exception to c++ (-> crash) if there is python exception in the script being run from command-line. Just print traceback and drop to the python console (unless stop after execution specified). 1. Kill building threads if the master thread is interruped in multi-builds (profile=a,b) Fix physical action index. test commit (whitespace) test commit 2 (whitespace) test commit (whitespace) 1. Fix catching all (including SystemExit) exceptions in python scripts. If nonInteractive or stopAfter, exit immediately, otherwise just print traceback and drop to the python shell. Reveals many unfunctional generators suddenly. 1. Fix nan's in SpheresContactGeometry 2. Fix ThreePointBending returning false on success (?!) 3. Add Preprocessor().load() method to python wrapper that generates to tempfile and loads it immediately. 1. Fix SDECLinkedSpheres returning false on succes (?!). ================================================== yade-0.12.0rc1 Sun, Jul 27 10:52:50 2008 +0000 Bruno Chareyre (69): Modifications in the equations of "non-viscous" damping. The equations are now as defined by Cundall. Engines are now compiled in a different order, with DeusExMachinas compiled last. The full DEM package has been compiled successfully after thuis change. IsotropicCompressionEngine removed from SVN. TriaxialTest do the same thing (i.e. isot. compression) better, and do more. The damping equations are reverted to their original expressions, with independant damping of each DOF. It looks like the convergence to equilibrium is faster with these equations. Squared distances are now compared instead of simple distances (faster) to decide if two grains are in contact. In addition, InteractionDetectionFactor is added as member data. The default value is 1, a value greater than one will allow the geometry of contacts to be created as soon as the distance is less than Factor*SumOfRadii. Usefull for interactions at longer distances (like capillary effects). A simple definition of contact stiffness based on E and nu : kn = E*size of sphere (so that apparent stiffness will be independent of size) ks = nu*kn A lot of small changes in triaxial classes, impossible to comment all of them; but note that : - TriaxialCompressionEngine can compress a sample to a dense isotropic state (either by moving walls or increasing the size of the spheres), - then change the confining pressure if needed (for running tests with different confining pressure on the same sample), - then start a triaxial compression test at constant zz strain rate and constant xx and yy stress (when the sample is considered stable based on StabilityCriterion). - The transitions between the different phases are (in principle) very smooth. Revert erroneous (and unexpected) changes in this pro file. Minor changes in the computation of the critical timestep. All files related to capillary law. Update of all classes related to dry and unsaturated triaxial tests. Modified definition of the interpenetration for box-spheres interractions. The previous definition was inconsistent. Correction of a wrong formula introduced in the last revision (the position of the contact point was wrong). Some changes in the computation of critical timestep so that the triaxial samples do not explode when dt is set to the automatic value. The change mostly affects the first steps of a simulation. Now, dt is computed at each timestep during the first steps, whatever the value of the user-defined variable "timeStepUpdateInterval", until a relevant value is found. Cosmetic changes in TriaxialTest. Initial zoom in the simulation player is set to a more reasonable value. UnbalancedForce member data was not defined in the constructor of TriaxialCompressionEngine, it was causing a crash when loading a TriaxialTest.xml. -TriaxialTest now includes a recorder to write stress history to a file. -safety factor is set to a smaller value in the timestepper as the computed value was still a bit too large in some cases. -UnbalancedForce is defined in TriaxialCompressionEngine() to avoid errors when loading a xml. Link TriaxialTest with WallStressRecorder in SConscript This commit contains new classes in order to simulate cohesive interactions with transient interactions. The new SAPCollider does set IsReal=false at each time step, neither do the Sphere2Sphere4Distant... engine. The user must set isReal=false in another engine (here the CohesiveFrictionalContactLaw engine) in order to have the interactions removed from the DistantPersistentSAPCollider list. All new engines are used in the CohesiveTriaxialTest. A REGISTER_ATTRIBUTE was missing in the previous commit. Some new classes related to the coupling with comsol (main author Andrea Cortis). FIXED : TriaxialCompressionEngine was stopping the simulation at each time step... 1- New contact law and related classes : CohesiveFrictionalContactLaw. It will be the most general contac law in Yade soon probably (TODO : include rotational effects like MomentRotation law). 2- New Stress-Strain recorder : TriaxialStateRecorder, autodetect the TrixialCompressionEngine of a MetaBody and write the parameters from it in a text file. 3- TriaxialCompressionEngine and TriaxialStressController are modified in order to compute stress and strain on demand. Modification in the usage of default values in GlobalStiffnessTimestepper. Change in dt default values in the preprocessors. Added some comments (doxygen friendly) and corrected the author in some of the source files related to the triaxial test example. In Yade.cpp : conditional compilation in order to compile with boost 1.33 In TriaxialTest.cpp : instanciation of a SimpleElasticRelationship object before adding it to engines (to avoid a crash). Vaçlav please, what is going on here?O Few "cerr" are back... Different fixes, including -TimeStepper : previousDt is now a registerable parameter, which can be used after saving/loading. New feature implemented : dt can be increased at a steady rate : dt=1.5*dt each time maximum (to prevent sudden increases and explosions). Comments added. -TriaxialTest : The timestepper is moved to a earlier location in the list of engines, so that the timestep is set before the stressController call. REMARK : REGISTERABLE dt IN THE TIMESTEPPER MAY BE REDUNDANT WITH THE "RECOVER TIME STEP" FEATURE OF YADE, DO WE NEED THIS ONE? -StressController : revert a small mistake in last commit. Fix the bug with BrefCom in GlobalStiffnessCounter. Samll optimizations. r1263 is +25% slower than r1264 based on tests on 2 different computers. Added NewtonsDampedLaw : The test on penetrationDepth is moved to a different line : no need for a "new SpheresContactGeometry()" when interaction->isReal will be false. A registered parameter (finalMaxMultiplier) was not set for the relevant engine. Fixed now. Parameters are adapted to the last modifications in TriaxialStressCompressionEngine. TriaxialStateRecorder : add the unbalanced force in 8th column. TriaxialTest : revert order of creation of spheres and boxes (boxes first), to prevent numbering problems in SAPcollider when using HydraulicTest. HydraulicTest : search engines and modify their parameters (desactivate stress control/activate gravity) dem/SConscript : link HydraulicTest with few more libs Safety coefficient on critical dt is changed to 1 (was 0.25 before). 0.25 was far too conservative. A bit (lot) of cleaning in TriaxialTest. Useless recorders inherited from the early ages of Yade are no longer present. Fixed interpolation for the case P=0. Added minimalist documentation. 1. TriaxialCompressionEngine is now saving at the end of compaction rather than at the begining of compression test, so that the simulation is saved when autoCompression is not activated (before this change, the simulation was going in LIMBO state without even saving, which means it was lost). Some cleaning. A link was missing between TriaxialTest and the NewtonsDampedLaw (new engine doing the same as the 6 previous integrating engines). A lot of fixes to make this engine work correctly regarding transitions between different states, including situations with saving/editing/loading. This commit contains an experimental version of the collider based on the triangulation package of CGAL.org. Compilation is disabled for the moment, but uncommenting few lines will enable compilation if CGAL and my (me=Bruno) own libs are available for linker. Contact law based on voronoi tesselation (using CGAL). Not included in compiling process now, this is for JF Jerier. This reverts a previous change in IGMetaEngine from Janek (interactions were set "new" when not real - problem was that non-distant interactions are ALWAYS "not real" when starting IG dispatching - so they were set new and reseted at each timestep, which disabled friction). What was supposed to be done in IGMetaengine is now replaced by something almost equivalent in the SAPcollider (the difference is that if an interaction is not real before being reseted by the collider, it really means that it is not-overlaping and not-physicaly-interacting). Again few changes in the behaviour of this engine, it should now handle correctly any manual change in the xml file (still needs a fix : there is still a part of the code that is done only at first iteration, which means that a modification of sigma_iso by editing the xml will give a different result than the same modification from PythonUI). Timestep safety coefficient is back to 0.25. - ks is registered in ElasticContactInteraction (it was not, which was a bug, but it was not affecting computation because initialKs was used to set ks=initialKs at each timestep). Added code for computing porosity in TriaxialStateRecorder and titles for colums in output history file (porosity is in the 9th column). 1+2 : added "Key" string in filenames. 3 : missed that hpp in previous commit. A small cast mistake. Corrected a local #include path. Added a function that can modify friction of all bodies/interactions. Usefull to compact at low friction and then perform the compression test with normal (higher) friction. Modify slightly the way shear displacement is computed to prevent "ratcheting" (see comment) Same modif as in ElasticContactLaw (previous revision) to prevent "ratcheting". Added a code that will be common to all output filenames to help sorting different simulation results. Some code for triangulation/tesselation using CGAL, it is experimental and not included in the build process for the moment. Fixed a bug due to a wrong macro definition in CGAL (CGAL_LIB_CREATE sould be "ar cr" instead of "ar cr ''"). This macro is not used now. - epsilonMax added to compressionEngine to stop simulation. - data files for Triangulation removed from svn - bool "isNeighbor" added to interactions, used in triangulationCollider. - Modified numerical scheme to reproduce a standard 2nd order finite difference scheme integration (more stable). - TimeStepSafetyCoefficient can be set to 1 rather than 0.25. - same change still to be done in the separate LeapFrog engines (the default TimeStepSafetyCoefficient is 0.25 in the meantime to prevent explosions with preprocessors using those separate engines). NewtonsDampedLaw : fixing a small mistake and cleaning the code. IMPORTANT NOTE : Forces/Moments are not affected by damping now, only accelerations are modified. The result is the same in terms of damping, but users can now get the exact values of forces/moments on bodies at any point during a timestep. Mostly small changes and fixes from previous weeks. Sorry for such poor comments... ks is added to registered parameters. Fix a problem resulting in VectSet (default) and HashMap being used simultaneously for transient/persistent interactions in the same simulation (which for unknown reasons is not good). Janek Kozicki (82): added info where are the pictures for the user manual can be undeleted from the history if anybody needs that directories for Czesiu and Tiziano to work on yade packages: debian and gentoo. later we can add directories for .rpm, etc.... - better DynLib error reporting - new Lattice, only 2D - triaxial test from Bruno - deleted unused QGLThread Fixed some problems with yade-flat deleted yade-lib-time, and using boost::posix_time instead - it is possible to select (shift click) and 'm'ove bodies in the simulation view window. a dirty implementation. Needs major refactoring. - the "display" tab now offers the ability to set 'display refresh rate' in [ms] so it's like the priority of draw. renaming SimulationRunner -> ThreadRunner SimulationFlow -> ThreadWorker renaming done. FileGenerator now does not block whole GUI when generating. And can be stopped if function generate() calls somewhere in the loops: small fixes to ThreadWorker Graphics display can be now synchronized with the calculation without problems, and without blocking GUI - more improvements in ThreadRunner, ThreadWorker::~ThreadWorker and SimulationController - fiddling with lattice: angle between beams is now calculated in 3D not 2D, with tracking of positive/negative angle. So the angle is between -180 and 180 deg, while arcus cosinus can only give a result between 0 and 180 degrees. Finally deleted swiftpp and qhull. Now we have less license problems. There is still license problem with math library, though. ... ... Some cleaning, involving changing variable names, like Body::interactingGeometry. Which caused almost all the files to be modified. oops, forgot to commit MyTetrahedronLaw renaming: ElasticContactParameters ElasticContactInteraction renaming cd... renaming finished: ElasticContactParameters ElasticContactInteraction added GLDrawStateFunctor. So now it is possible to see bodies' velocity, acceleration, angularVelocity, angularAcceleration. And other State attributes of a body. =========-----------------============ -------------------------------------- NullGUI allows to call a FileGenerator Omega throws when loading bad simulation file ----------- SimulationController catches that error from Omega :) (when loading bad file) 'C' key centers scene on selected body 'D' sets the 'isDynamic' flag of selected body. (select it twice to unset this flag). -- flag that allows to enable/disable calculating of torsion LatticeExample FileGenerator can now generate a 3D tetrahedral regular grid. (before there was only orthogonal grid) Added drawMask to OpenGLRenderingEngine, it is now possible to see only bodies that have a certain groupMask Added non-working scripts that can compile yade using waf. At least they are not working for me. -- removed invMass and invInertia. Removed special handling for division by zero. mass shouldn't be zero anyway. Matrix3 patch from Vaclav - FileGenerator reports how long the generation took - yade.cpp takes PREFIX and POSTFIX as #define /some/path , without " - small change to lattice generation method - Makefile cleans after scons - SConstruct: removed \" from defines in PREFIX and POSTFIX line 147 added -pthread for g++ 3.3 moved env.Append(CXXFLAGS=['-pipe','-Wall','-pthread']) before invoking the tests changed "nor" to "not", line 271 removed PATH, becuase I couldn't get it to work. so instead I set CXX='distcc g++-3.3' - FileGenerator shows generation time, and saving time - QtFileGenerator remembers save file name (so it is not always ../data/scene.xml), this was done in previous commit. A small bugfix here - OpenGLRenderingEngine didn't draw Body when it's groupMask was 0 - some changes in lattice. - I added GeometricalModelForceColorizer. It is another hacky Engine that I have added (along with Quadrilaterals). I did it, because I wanted to see spheres colored according to force acting on them. This is a hack because the GLDraw mechanism is currently very limited, and has to be extended to allow things like this. So currently it works, but not in a way it should be done. GLDraw* changes are coming ... soon :) In this commit I made Interactions drawable by GLDraw*, and I added three example GLDraws for Interactions: - in GLViewer new keys: 'o' and 'p' to change the field of view. Useful for changing the perspective. IMPORTANT: In this sommit I have added a third parameter to GLDrawInteractingGeometryFunctor, which means that all GLDrawInteracting* classes had to be changed. If you have your own classes that draw interacting geometry you must modify them as well. The extra paramater added is 'bool wireFrame'. I think it will be useful :) - a more prominent warning when PREFIX was not defined during compilation - ThreePointBending does not crash when there is not file to load - some fiddling with lattice moved some obsolete scripts to doc/removed - Updated trunk/ChangeLog - new icon - fix several warnings, - merge latest version of lattice from my PhD - todo: serialization problems with findType in NodeRecorder and FEMBeam, remove ErrorTolerant, fix collistions in rigid body - removed ErrorTolerant, - SConscript uses md5sum instead of timestamp. Tetrahedron modification to std::vector - fixed crash in SDECLinkedSpheres example - there must me a dynamic cast in InteractingSphere2InteractingSphere4SpheresContactGeometry.cpp until the containers are rewritten. - fixed RotatingBox and BoxStack examples - and accidental mistake in SAPCollider - timestepper is set correctly when loading file in GUI (I hope!) - no need to reload second time - FileGenerator does not open SimulationController if it already exists - introduced body_id_t(ype) so that bodies are not numbered as an int, but as a body_id_t - added center 'scene button' on first tab of simulation controller trunk on SVN is deprecated now undeprecating trunk. Now I'll apply diffs from BZR back here. BZR revno: 983 committer: vsmilauer Fix scons to handle boost.*-mt well, some other cleanups. BZR revno: 989 committer: VĂĄclav Ĺ milauer message: Modify debian builds so that making source packages for release versions work as well. BZR revno: 991 committer: Janek Kozicki message: - Tetra2TetraBang returns before it starts (to avoid crashes in the release) - fixed some crashing of HangingCloth, but I see that there is still some problem. Tracking it down is a waste of time, currently, because new containers will enforce refactoring here and fixing this problem. - FileGenerators try to set the timestep when TimeStepper is not used. But it is still not working when simulation is running during the generation. This means, that 'dt' should not be in Omega, but inside a simulation itself. At last there is a clear answer for this dilemma. OK, I think that migration back from BZR is complete :-) Ooops, previous commit did break SCDECLinkedSpheres example and HangingCloth... I hope that it's fixed now. Also removed warnings from Capillary law... again. HangingCloth finally is fixed, and is not crashing in optimized build. The dynamic cast ought to be in HangingCloth.cpp FileGenerator ;) Added RELEASE file in tags/yade-0.11.0 more descriptive error message when directory ../data/ doesn't exist (usually happens at start...) - update yade icon, by Vaclav's suggestion (the red spheres are not so vividly red, so looks a bit better) - scons will create the installation directory if it doesn't exist - incorporated Bruno's fixes into 0.11 release - Updated RELEASE info in yade.cpp, although the best would be if sons will #define RELEASE update changelog Preparinf 0.11.1 release. Updated INSTALL file. ForceRecorder now checks if a body exists. changed char* yadePluginClasses[]= to const char* yadePluginClasses[]= to eliminate possible misuse updated release 0.11.1 looks like ready to ship Some fixes in lattice regarding yade::serialization problems (function findType()) that started to occur when using g++ newer than 3.4 The offending code was commented because it wasn't working. Now I uncommented and modified it, so it works. deleted unused class AAInteractingBox2InteractingSphere4ClosestFeatures Use lattice model for simulation of concrete with steel fibres reinforcement. SConstruct is now working on debian etch, exclude multimethods in Doxyfile 1. Fix FUNCTOR2D mistake in CundallNonViscousMomentumDamping 2. make it compile with python2.4 and qt3 (which sucks) NOTE: python-scientific requires boost 1.34 recent changes in Dispatcher seemingly broke adding InteractingSphere2InteractingSphere4DistantSpheresContactGeometry and InteractingBox2InteractingSphere4SpheresContactGeometry as strings. Need to create class instance first, then add it as a variable (not as string). I must assign something to avoid "nan" when loading dt. When recover=false, those can be "nan" and lead to crash. - draw linked interactions only if isReal. Added StaticAttractionEngine, which help to fasten a little the initial stage of compression - removing the central void. But it is in fact too slow, for bigger usage. That's because everything is attracted to everything. I don't know what's up with Brefcom, but I need yade to compile, because those guys who will sell us 16-core machine will be using this SVN revision for their benchmarks. dang! I just want the latest SVN revision to compile. yade.cpp give info about cmdGui -N name : specify the user interface (available: NullGUI, cmdGui, QtGUI) FileGenerator catches exceptions. Moment law. 1. moment law: some cleaning 2. GLDrawSphere - draws circles faster (wireframe) 3. yadeControl - fix compilation error with optimized builds: YADE_PTR_CAST -> dynamic_pointer_cast in previous commit, when optimizing the circle, I committed by accident a filled version. It's just a bool to toggle between filled and not filled, but, it's not possible to change from GUI... yet. Use / * - + for front cutting plane: 1. added new class YadeCamera : public qglviewer::Camera 2. ovverride virtual function which calculates the front cutting plane 3. it's possible that GLViewer4 will have to be modified - to use YadeCamera to have this new feature - front cutting plane. I didn't touch it. Ask the FileGenerator for the filename. - flag 'active' in DisplacementEngine - CapillaryCohesiveLaw now complains to stderr (could use LOG_WARN as well, but didn't compile) - flag 'always_use_moment_law' in CohesiveFrictionalContactLaw (so is possible to use even for broken contacts) - added comment about the contact law from PFC-3D (I used it for comparison with Wenjie) - started snow creep test. - added optional creep in CohesiveFrictionalContactLaw Jerome Duriez (1): - A new Preprocessor (DirectShearCis) allowing to simulate ... direct shear tests with the Engine associated to let move correctly the box (CinemCisEngine) Sergei Dorofeenko (17): Add linear viscoelastic contact model 1. Main commit: import a geometry of walls from a STL file. Translate comments to english. 1. Fix orientation. Now one can rotate the STL geometry. 2. Added rotation kinematics to STLImporterTest preprocessor 3. Bugs fix. 4. Added another example of STL file in examples directory. 1. Python wrapper for STLImporter 2. Example python preprocessor STLImporterTest.py 3. Small fixes 1. Added attribute zeroPoint to RigidBodyParameters and RotationEngine. This attribute defines the rotation center of kinematic body. 2. For ElasticContactLaw added accounting rotation of kinematic body around its zeroPoint. 3. Added phase flag "cycle" to Interaction. SpatialQuickSortCollider is modified so interaction's cycle flag is used to mark stale contacts instead isReal flag. 4. Small changed InteractingSphere2InteractingSphere4SpheresContactGeometry and GLDrawElasticContactInteraction. I think, towards an improvement. If there are objections, changes must be reverted. 5. pyOmega.save allows recovery 6. STLImporter allows multiple files to import consistently. 7. Bugs fix. reverting condition c->isReal 1. Add engine ResetPositionEngine for the return of bodies at their initilal positions. 2. small fixes. Small fixes Fix relative path in SimulationPlayer small fix 1. ResetPositionEngine: added import/export initial positions from file 2. GLSimulationPlayerViewer: skip bodies which does not have a geometrical model 3. QtGeneratedSimulationPlayer: small fixes layout and sizePolicy. 4. utils.py: agreement spheresToFile and spheresFromFile In PositionOrientationRecorder and GLSimulationPlayerViewer pass the bodies without geometrical model Small fixes in PositionOrientationRecorder 1. Added new engines: - FiltrEngine is a base engine for a scene filtration before visualization (both for a player and for a controller). The filtration is activated through GUI (now only for SimulationPlayer). - ColorizedLayerFilter allocates with colour a layer of bodies - ColorizedVelocityFilter allocates with colour a velocity of bodies 2. Add Omega::setCurrentIteration to allow current simulation time from a player 3. ResetPositionEngine allows onlyDynamic (without save subscribed bodies ids) small fixes fix errors in previous commits Fix in SimulationPlayer: search filters and updateGL after loading simulation Unknown (2): Fixed some typos. Modified Doxyfile not to show lib/ and to optimize for C++ Václav Šmilauer (208): Multiple changes. Add logging.hpp which I forgot in the previous commit. Remove printing headers being linked, add help for cleaning. Tried scons on a cleanly checked-out trunk and it worked. Sorry for the traffic. 1. Two sets of files were named StiffnessMatrixTimeStepper, of which the other one was in directory Global StiffnessTimestepper. Since it was not used (not compiled by default), I renamed the second set to match the directory name. If it breaks something, let me know. 2. Updated the scons script, scons now compiles yade completely, including header installation. It is yet to be tuned to be lot more fast, but works fine already. 3. Cleaning up messages at startup, (almost) everything is piped through the LOG_* stuff. 4. Included sample logging.conf.sample file, log4cxx is amazingly flexible and easy to use. Give it a try! 5. Lot of debugging since after the last change of allowing regular files to be plugin-loaded, yade would try to load garbage (like the file foobar.baz transformed to libbar.so and the like) giving spurious errors. Everything should work properly now, you can have whatever you like in the plugins directories. It will not even crash on short files (amazing fragility...). 6. Removed the message from ResultantForceEngine constructor, to not to pollute the console every time. Dtto for StiffnessMatrixTimeStepper. 7. Added one ; in yade.cpp that broke compilation without LOG4CXX. The non-log4cxx macros are now enclosed within {} just as their log4cxx counter parts. This should eliminate the need for separately building both configurations. First commit from the wm3 convergence set. Header files were modified to allow compilation with old methods with deprecation warnings from the compiler. This is the second changeset. Yade now compiles without any single warning about deprecated functions. For fixing your own code, I will upload a script to automatize that process shortly. As time goes by, deprecated functions and (slowly) wm3 itself will be removed from yade's sources. Provided script hackett-warn-replace.py is for eventually helping you with replacing deprecated wm3 methods by the good ones. hackett.py was used to insert deprecated wrapper to headers and will probably never used as such anymore. Deleted old erskine2* stuff, since it is superseded by erskine3* and scons. This commit marks properly all headers as well as methods that were deprecated during the transition to the official wm3 library. Next commit will follow shortly and will fix all deprecated headers warnings. It is (and will be for a while) to compile in with USE_BASTARDIZED_WM3 to use the old headers, but expect many warnings during the build. - Bastardized wm3 library ejected from the tree. From now on, you need to install wm3 separately. Will update README shortly on how to proceed. Basically, add "-I/usr/local/include/wm3" to CXXFLAGS if you use qmake. Includes and linking was adjusted in c++ and .pro files. - DOUBLE_PRECISION removed in favor of SINGLE_PRECISION. Therefore, the default is to define Reals as doubles now. SINGLE_PRECISION will be removed very soon anyway. - Removed yade-lib-algorithms, since it is not used. Once someone needs it, it can be found in svn history. - Created yade-lib-base, that for now contains 1. Logging.hpp: moved from yade-core to avoid circular dependency), 2. yadeWm3.hpp: typedefs for Vector3r Vecrtor3, definition of Real. This header will be removed soon, since it will not be needed. 3. yadeWm3Extra.hpp: things that were added to the bastardized wm3, like a few operators and functions. You almost certainly want to include it in your code if you get undefined references (and link with yade-lib-base). - Omega now reports undefined symbols demangled. Re-enable workaround for scons: create install directories beforehand. Cause of that is to be inspected yet. Disable DEBUG messages for non-log4cxx builds so that Janek's screen is nicer ;-) (sorry for these scattered commits, hopefully this is the last one). Exceptions from the FileGenerator thread are now properly caught; it means for example that if you pass an invalid classname in createActors, yade will tell yo +u what class it wasn't able to construct instead of hanging infinitely. Massive update of scons, which I now recommend for building. It has some autodetection support as well. Please report any bugs (?) / RFEs to me. Brief instruction are given in INSTALL. Quick fix for recently discovered segfault. Wondering why it didn't surface before. Valgrind still complains about PhysicalActionVectorVectorIterator::increment using an unitialized value, but that may be unrelated (probably is) to this one. SCons update, please use it and report any problems to yade-dev or yade-users. Thanks. Iterations/sec display added to simulation controller (someone more sensible may redesign the layout in the future). Line ending changed from CRLF to CR. Scons accepts additional POSTFIX parameter, which will alter installation so that PREFIX/{bin,lib}/yade becomes PREFIX/{bin,lib}/yadePOSTFIX (similar to EXTRAVERSION of Linux). Further, configuration files will be searched for in ~/.yadePOSTFIX instead of ~/.yade. Unfortunately, headers installed in PREFIX will still be overwritten by newer version, even with different POSTFIX, since most files do something like #include<...>. This is meant to ease simultaneous installations of different variants of yade. To achieve full independence, PREFIX and POSTFIX should be different. Note that you don't need to set LD_LIBRARY_PATH, since scons uses linker's -rpath option (hint: man ld). If someone has better solution, please let me know. Microchange to comment on naming of scons configuration options. SConscruct file update - make it work with older scons, remove -floop-optimize2 that doesn't exist for older gcc (<4.0). Hunted down the bugwith node enumeration, now should be reliable. Added some checks so that configuration is not done when cleaning, likewise for installable nodes (so we do NOT uninstall upon cleaning). If you use g++-3.3, you need to set e.g. CXX="distcc g++-3.3 -pthread". This will be fixed perhaps in the future but for now the default is to keep it simple. Other fix for sarge (0.96.1) version of scons. It is a variant to be removed. For some features (especially the srcdir keyword), sonner or later we will mandate 0.96.94 to build yade, but that can be a few months in the future, though. Fix node enumeration for newer scons's (isfile() is true only if the file already exists, which is contrary to what I thought). Microchanges: fix rpath quoting, fix ctags indexing non-c++ files (local bug? --language=c++ would make all files (including .o, for example), being indexed. Plugin loader now handles multi-class plugins, provided that they define "char* yadePluginClasses[]" symbol containing list of class names (sentinel=NULL) that the plugin contains. Regular one-class-per-file plugins work normally. Fix build process for older versions of scons that break if there is a target that has no sources. Added a dummy empty file to the loki library to do that, modified project file. Do not forget to delete yade-libs/yade-lib-loki before running scons again to regenerate SConscript files. 1. Include IsotropicCompressionTest in dem's preprocessors project so that it gets compiled 2. Improve erskine to indent SConscripts in a nice way 1. Fixed Omega::scanPlugins so that it loads plugins that were linked without -rpath for their dependencies. Everything is in #ifdef STUPID_DLL 2. Removed again IsotropicCompressionTest since needed headers are missing. Bruno, please add them back (they were removed in the 1045 commit.) and then enable IsotropicCompressionTest in yade-packages/yade-package-dem/src/PreProcessor/PreProcessor.pro again. Default preferences.xml doesn't neglect the last plugin dir (off-by-one error) Simulation may be (which is the default) loaded after generation automatically now. Prepare framework for "high-level clumps". Everything is withing #ifdef HIGHLEVEL_CLUMPS, hence shouldn't change anything unless compiled with that option (don't try at the moment, it doesn't work). More information at http://beta.arcig.cz/~eudoxos/phd/index.cgi/YaDe/HighLevelClumps . 1. provide Doxyfile, running "cd yade-doc; doxygen" will produce html reference documentation 2. initial (non-functional) implementation of high-level clumps, along with some cleanup of the changes done elsewhere 3. erskine now can be given scons variables (namely, $PREFIX) that will be unexpanded in generated SConscript's 4. SConscruct #defines HIGHLEVEL_CLUMPS, since other people probably don't use scons (yet) 5. New method Body::byId, new typedef Body::id_t, new constant Body::ID_NONE (jailed in HIGHLEVEL_CLUMPS for now, that will be removed sooner or later) 1. Clump code completed, but totally untested so far. 2. Added target 'doc' to Makefile that runs doxygen 3. New tracing macro TRWM3QUAT for quaternions 1. Clump::subBodies are now a std::map, subSe3s removed. 2. Sample clump generator ClumpTestGen written; works, but yade crashes because of dispatchers being setup incorrectly. 3. Omega::setRootBody added so that rootBody can be temporarily set during filegeneration, which is necessary for Body::byId. 1. Fixes in the clump code 2. InteractionGeometryMetaEngine doesn't crash if a body doesn't have interactingGeometry (like Clump) 3. Fixes in the collider, related to the clump code 4. ClumpSubBodyMover is now a DeuxExMachina 5. discovered bug in Wm3::Matrix3::EigenDecomposition 6. ClumpTestGen generates a usable testcase (either a random one, or with one-sphere clump and an equivalent sphere) for testing purposes. Parameters etc. are physically wrong, but at least there are no crashes. 7. ClumpTestGen temporarily sets rootBody in Omega so that Body::byId is usable 1. Clump code is not (hopefully) correct physically - translational, rotational and potential energies give constant sum over time (more or less) 2. ClumpTestGen generates a useful scenario of standalone sphere, {1,2,3,4}-sphere clump. 3. Inertia calculation fallback for cases with NaNs from EigenDecomposition. 4. acceleration and angularAcceleration reset after every position update for clump. 5. Body::{isClump,isClumpMember,isStandalone} added. 6. Gravity engine skips clump members (applied to the whole clump only). 1. Clump code cleanup 2. Python may now be embedded in yade: (i) SConscruct checks for it and #defines EMBED_PYTHON if present. (ii) main sets up the interpreter. One disadvantage is that Python runs in its own thread, so pressing ^C during simulation doesn't quit yade (^\ still works). 3. New class PythonRecorder that evaluates arbitrary expression when activated. 4. Pyade interface that makes it possible to retrieve some values from yade in Python. For example, you can now record body #5 z-velocity and z-angularVelocity every 10 iterations by setting PythonRecorder::expression="if (S.i%10==0): print B[5].v[2],B[5].w[2]". Retrievable attributes are documented in the source (or the Doxygen documentation). 1. selection in the renderer are now saved in Omega::selectedBodies (GUI to that list is in the future yet) 2. PythonRecorder now supports retrieving selected bodies; it redirects stdout to file if specified. 3. pyade now required scientific python to be installed - this permits to do vector and quaternion arithmetics in python. General cleanup. 4. pyadeDummy.py module added - for testing pyade without yade Microchange to catch exception from distutils in python detection. 1. Scons changes, node enumeration gotten rid of, now uses proper Install in SConscript's. Should eliminate scons version problems we've had. 2. Some new make targets: for repetitive compilation (with -j2) and first personalizaed target: eudoxos. 3. Selecting clump member in GLViewer now selects the whole clump; it is moved and redrawn as well (only with HIGHLEVEL_CLUMPS). 4. An attempts at escaping special characters beforce XML serialization (\",\n,\t,\\), doesn't work - commented out. 5. Project files cleaned from nonexistent include directories. 1. OK, the floats floating around for colors drove me nuts, so I replace all of that garbage by doubles. Since for one particular case (glMaterialv) the corresponding function taking double (glMaterialdv) is not defined in mesa (and perhaps not in most other gl libs), for that one the argument was converted explicitly. 2. New Shop class, that defines static methods for easy things, along with a dictionary of default parameters for some useful stuff: like getting a rootbody with reasonable set of actors, sphere body, box body. That's all for the moment. Add your own stuff. Filegenerators may shrink considerably this way. 3. Clump::subBodies renamed to Clump::members, Clump::moveSubBodies to Clump::moveMembers, ClumpSubBodyMover to ClumpMemberMover - to be consistent with Body::isClumpMember. Clump still not moved to DEM, that will wait till later - at the moment, QGLViewer depends on Clump (for moving clump when selected and moved with mouse). Many extensive changes: 1. renamed Chagelog to ChangeLog, will be generated autmatically from svn chamgelog 2. removed waf script (wscript), not used 3. scons now installs everything with '-version-postfix' appended, like yade-svn1072-debug 4. scons builds different variants (version and postfix) in separate directories 1. Clump member velocities are calculated in ClumpMemberMover. This may create problems since velocity will always be lagged by one iteration. 2. removed cyclic dependency of Clump and Shop. 1. Debugging mode now #defines YADE_DEBUG in addition to DEBUG, which seems to be #undef'ed by some header. Lazy to trace down. 2. Removed #ifdef DEBUG messages from dynlib &co (now under #if 0); use LOG_TRACE if you need those messages 3. Signal handler now handles SIGSEGV (segmentation fault) and SIGABRT (failed assertions, among other) in debugging mode: gdb is run, attached to the current process and backtrace of all threads is printed. Python fixes: 1. load pyade.py from path given by PREFIX and POSTFIX (we really need to define that somewhere in a unified manner: not by using BOOST_PP_STRINGIZE everywhere! - config.hpp...?) 2. velocity and angularVelocity are vectors now (returned only the x component by mistake) Attempt to access interactions from Python, commeted out for the moment. May disappear later. Not used anywhere. Do not use. 1. Cleanup of clump includes 2. Scons now puts buildDir include directory first so that it shadows eventually installed versions 3. jobs=x added to scons, like -j3, but is saved accross runs 4. Archive modifications (shuffling includes around) so that compiling with recent g++ (4.1) works - was preprocessor problem. Fixed error in yesterday's commit, should compile really fine with g++4.1 now. SCons cleanup. Now supports buildPrefix (defaults to '..') so that build is completely separate from sources. commit before mass-replacing Dymanic_cast. This will not compile, used only as wayback for me. New commit shortly. dynamic_cast replaced by YADE_CAST where appropriate: i.e. the result of the cast is not checked to verify whether the conversion was successful as condition for further flow branching. The consequence is that you have to #define YADE_CAST in CXXFLAGS by hand as either dynamic_cast (original version) or static_cast (for optimized builds) when using make. dynamic_pointer_cast replaced by YADE_PTR_CAST as appropriate. It must be defined on compiler command-line (-DYADE_PTR_CAST=dynamic_pointer_cast or -DYADE_PTR_CAST=static_pointer_cast). Scons builds get this automatically. Doxygen settings from yade-flat imported. New file tracking removed elements. Merged the scons-layout branch to trunk. 1. PythonRecorder runs optimized byte-compiled expression, optionally translated to machine-code by psyco 2. Serialization lib now properly escapes and unescapes XML-unfriendly charcters (\n,\t,<,>,",\\)->(\\n,\\t,\[,\],\',\\\\) 1. Remove cyclic plugin loading forever (undefined STUPID_DLL) 2. Tetrahedron has vector v instead of Vector3r v1,v2,v3,v4; (fem will probably not compile because of this for now - will be fixed) 3. Added experimental tetra class & friends. ough... put actual data in. Next commit will rename files as they should be (stupid svn...). Renamed files. 1. gdbCrashBatch moved to Omega (was emptry when a different thread thatn the main one crashed?!) 2. Shop generates tetrahedra properly now, including dispatchers 3. Tetrahedra rendering and linking fixed 4. Added an icon to the main window (not serious ;-) ) 5. commented out STUPID_DLL overflowing loader 6. log4cxx has level set to INFO by default (was DEBUG, lot of garbage on screen) 1. Some type fixes (signed vs. unsigned). The Body ID mess needs to be cleaned up!!! 2. More tetrahedron stuff; will not compile for now, though. 3. Icon update ;-) 1. remove vector from tetrahedra code, replace simply by Vector3r[4] 2. implement 4h-4h intersection peroperly, without relying on wm3. Compiles, not tested for correctness at all. Make compilation proper when python is not found (no errors, just disable what should be disabled). #define MINIWM3 when using miniWm3 don't exclude lattice with miniWm3 (lattice needs to be modified to not use undefined functions from full Wm3 in this case (Delaunay!) Adjust QTDIR to gentoo, too Configure-time decision whether to link against QGLViewer or 3dviewer. use -mt variants of boost byt preference if both exist useMiniWm3 by default 1. Fix fedora/centos etc compilation ( in the .ui file mentioning nonexistent file) 2. Other scons cleanup 1. Fix soname on shared libs (no soname at all; bug with "" in the name previously). Is it good for something? 2. Add 'features' option to scons, which can enable/disable python and log4cxx at compile-time (extensible) 1. Correct 'all' value for features 2. Add a few signed/unsigned typecasts 3. Check clump code 1. Fix uninitialized se3 in one-member clump handling 2. Fix syntax error in SConstruct introduced in previous commit. If RELEASE file exists, get yade version from there, instead of from svn. Remove wildmagic-dev from debian deps. fixed qt3 detection (used deprecated qapp.h header instead of qapplication.h). Adjust debian package generation back to svn. frontend cleanups, eperimental python console ui. Convenience functions for serialization - experimental. fix qualifiers in constructor of AttrAccess 1. rename ThreadWorker::message() to ThreadWorker::getStatus, ThreadWorker::setMessage() to ThreadWorker::setStatus (and private ThreadWorker::m_message to m_status) 2. add public: std::string FileGenerator::message that holds exit value description 3. FileGenerator::generate returns now bool (if the generation was successful); description in ::message 4. Adapted all generators and UIs for the above changes (except NullGUI - is that needed?) Adjust other components for FileGenerator changes. Add wrapper for preprocessor in python. 1. SCons will download new version of itself if older thatn 0.96.93 and will proxy all calls to it transparently (hopefully) 2. Revamped python wrappers, now all attributes are settable as dicionary entries in respective instances from python 3. added example of python script that generates and runs BoxStack 4. Do not #define DEBUG, since it is used in log4cxx (as log4cxx::Levels::DEBUG). YADE_DEBUG is used everywhere. If you ever get weird errors about that, #undef DEBUG after including qt3 headers. 5. Some code cleanups. Fix argv[0] for scons proxy. Don't warn on amd64 about limited type range in comparison. Initial .spec file for fedora 6 spec file works on fedora 6 now 1. Add screw example (this is really my personal one...) 2. Fix Shop::tetra (tetra interacting geometry still incorrect or incorrectly drawn... why???) 3. Remove python finalization, boost should take care of that. 4. Possibly fix plugin loader bug (first plugin after one with yadePluginClasses "inherits" them unless it has its own yadePluginClasses defined). Sync SConstruct with sid packages (lib for qglviewer is not in capitals there) 1. Tetrahedron fixes (intersections are correct now, but interaction still wrong - crashes??!) 2. Fix scons to work with versions > .97 (no syntax errors; didn't try if it compiles 1. Scons now updates itself to 0.97.0d20070918 (for testing purposes etc) 2. fix crash in ElasticContactLaw and ElasticCohesiveLaw if interaction is not SpheresContactGeometry and ElasticContactInteraction; this fixes tetrahedra interaction. 3. other tetrahedron fixes (still not fully functional yet) 4. mark attributes in class factory as __attribute__((unused)) to avoid warnings 1. Correct typo in comment in SConstruct 2. Correct formulas for 4hedron inertia, testcase passes 3. Switch to fixed timestep when timestep is being changed by user in the qt3 ui 1. Change default timestep to 1e-8, should prevent weidness onthe first run. 2. Fix cmdGui to handle gracefully reading/assigning nonexistent attributes (not crash, but caught exception) 3. Fix char* / const char * warnings from g++-4.2 in main() and OpenGLRenderingEngine. 4. Cleanup of triaxial test, added parameter noLateralConfinement (not yet used). 1. Default scons to latest snapshot (should be a bit faster) 2. Don't autocreate plugin path entries for paths that are not installed 3. Turn TriaxialStressEngine into state machine, while preserving the possibility of changing some values by hand in .xml. (should be tested). 4. Exclude Loki:: from doxygen docs. 1. Remove relicts of old Omega::logMessage &c 2. Remove duplicated Wm3 headers in core (is already in lib-yade-base) 3. Update python scripting (object.attribute is shorthand for object['attribute'] now) 4. Cleanups in triaxial, adding STATE_UNINITIALIZED 1. BIG update of python wrappers - enagines can be created, added, modified from python now. Examples will be provided very soon. 2. fix plugin loader for multi-plugins: YADE_PLUGIN() macro should be used in all plugins, otherwise due to linking symbol overrides a multi-plugin will shadow classes in the plugin actually being loaded (better solution?!) 3. Add experimental BREakable Frictional COhesive Moment-blocking material (brefcom for short), not yet fully done. 4. PersistentSAPCollider now can be parametrized to permit distant contacts (is not the default, though), incorporating Bruno's changes in DistantPersistentSAPCollider 5. Uniaxial strain-controlled test (USCT), a quite simple implementation. Used primarily for brefcom testing now. 6. Fix SConstruct so that it is backward-compatible with python2.4 1. Remove MetaEngine, inherit MetaDispatchingEngine directly 2. Fix unbalanced force reporting (thanks for complaining, Bruno) 3. EngineUnits now declare their types with FUNCTOR1D(.) or FUNCTOR2D(.,.) macros, dispatchers will ask for their types automagically. Old syntax still supported, once all engines have those types declared, it will be obsoleted and removed (like e->add("InteractingSphere","InteractingSphere","InteractingSphere2InteractingSphere4SpheresContactGeometry"); Shop and USCTGen usethe new syntax now. 4. Brefcom law passes some rudimentary tests and appears to work (normal force and damage for now; we miss shear force and blocked rotations) 5. Brefcom contact can be drawn with opengl, damage signified by color. 6. Updated Python wrapper. 1. Remove the old prototype for adding EngineUnits to dispatchers add(string,string,string) 2. All EngineUnits now have FUNCTOR1D(...) or FUNCTOR2D(...,...) in their headers. 1. Preliminary recovery of simulation accross runs (try sending SIGHUP to yade) 2. Python wrapper for body parameters. 3. Misc fixes of engines. 4. Allow Omega to stop at predefined iteration number (for regression tests, I work on that ;-) ) 5. ... Fix lefover of experimental code in TriaxialCompressionEngine (creating sohesive links after compaction. Updated brefcom, with undisclosable parts moved outside the tree. Fix typo breaking compilation on different machines than mine. 1. Remove "../data", replace by "./" (cwd) or "". 2. Some other stuff I don't remember. 1. HUGE update of python, it wraps almost all yade classes now (except PhysicalActionContainer and InteractionContainer). Documentation is lacking as well. 2. Move most of init stuff of python from cmdGui::run to cmdGuiInit.py (which I forgot to "svn add", will commit shortly) 3. Run ipython shell (or python shell with history and tab completion as fallback) inside yade Adding init code as advertised in last commit. Passing exclude='qt3' to scons will disable qt3 checks and everything related to qt3. Note that the default GUI is still QtGUI unless you change that in your config file or at command line with -N. Avoid using boost1.34 python/stl_iterator.hpp, should compile with 1.33 now (debian etch, ubuntu feisty) Fixes and addendum for openSuse based on comments by Sega 1. Test suite for all preprocessors 2. Added assumeElasticSpheres attribute to GlobalStiffnessCounter; if set to false, dynamic_casts are used to properly determine type of contact between spheres (used in USCTGen now) 3. Debugger now dumps backtrace without interruption and exits immediately (core is still dumped) 1. cmdGui now exports yade binary name (to allow spawning subprocesses) 2. default-test.py handles crashing simulations gracefully (by executing them in a subprocess) 3. Omega retains original argc and argv from the command line. 1. Remove NaN's in PersistentSAPCollider for bodies that don't have bounding box: use zero-size degenerate box at its position instead. (fixes warning when running ClumpTestGen) 2. Remove check for scientific python from scons as we don't use it now. 1. BIG: Moved latest upstream qglviewer to our tree. If you REALLY need to use the packaged version, let me know. As of now, there is no way to do that. 2. BIG: Removed many (unfunctional) parts of the qt3 GUI, in the view of qt4 migration which will probably not happen. Maybe I removed too much (simulation player -- does it work?!), let me know in that case. 3. Experimental GLViewer support in python, disabled. (broken and needs qt4) 4. Misc fixes related to that and other small stuff. Previous commit didn't compile on clean environment, fixed now. HOTFIX: final fix for the libqglviewer linking issue.... I hate qt3, I hate uic, I hate moc. It works now, please test on you machines and let me know if there are any regressions. Forgotten files, build crashed on foreign machine. Fixed now. (This stuff is not tested, do not use!) OK, now QGLViewer REALLY builds. Was bug in scons: file.ext1.ext2 is not handled properly with the qt3 tool. Created symlinks replacing first dot with _. Add tags, doc and clean "targets" to scons do their job, short-circuit the rest of building process and exit. Clean only removes builddir, _not_ installed files as -c would do. (LP: #202067) 1. Resurredced and un-crapped simulation player (for making videos). Updated howto is http://yade.wikia.com/wiki/New:Making_videos#Using_Simulation_Player_with_svn.3E1281 1. Include fracture strain calibration routines in brefcom. 2. Add BrecomDamageColorizer - changes colora ccording to average cohesive interactions the body has. 3. Delete non-cohesive interactions from inside BrefcomLaw when spheres become distant. 4. Documentation updates. 1. MAJOR improvements of the python wrappers (constructors take attributes etc.) 2. FIRST proof-of-implementation simulation completely created in python: scripts/simple-scene.py. This file will be commented abundantly shortly. 3. Add default values to some bool params so that there is no serializer error if they are uninitialized. 4. Add aabbEnlargeFactor to InteractingSphere2AABB (should be added to InteractingBox2AABB as well?) (not tested yet) 5. rename InteractionDetectionFactor to interactinDetectionFactor 6. Serialization now registers only attributes that have not yet been registered (there were problems with python because of that: at first save, attributes were duplicated and the xml file was less readble, although loadable) 7. Scan .tpp and .ipp for c++ tags as well 8. Some documentation. 1. New engine attracting bodies towards a fixed axis (constant force, points towards the axis everywhere) 2. some fixes in python wrapper (run initializers if needed; the logic in yade itself is currently broken however) 3. New python "example" for creating cylindrical packing of spheres 1. allow saving spheres (format like small.sdec.xyz) from python 2. PositionOrientationRecorder can optionally record RGB color of each body as well now 3. SimulationPlayer now can change colors of bodies, if the .rgb file exists 4. Bunch of fixes if brefcom, in UniaxialStrainControlledTest 5. dt moved from Omega to MetaBody for good; this allows preprocessor to set timestep that will be used when the simulation is loaded. 6. Code cleanups here and there. Update debian control to possibly fix deb package builds Fix header scanner if there are extra headers in the tree. 1. PROTOTYPE CHANGE: Engine::action(Body*) changed to Engine::action(MetaBody*); all engines adapted 2. MetaBody::miscParams can be used to set static variables at deserialization (used for GLDrawBrefcomContact now) 3. allow serialization of shared_ptr (only pointers to derived classes were enabled until now) 4. big fixes inside brefcom 5. enhancements of python interface (Generic class, fixes) 6. added Shop::GLDrawLine, Shop::GLDrawArrow, Shop::GLDrawNum 7. fixed QGLViewer #defining DEBUG (qt3) by #undef'ing it after qt3 headers inclusion 1. Add many checks to see where XML and BIN serializers take each other's work (non-intrusive). 2. reorganization of cmdGui (will be renamed - perhaps - to pyUi or similar) 3. BINFormatManager is now optional and _disabled by default_. feature 'binfmt' must be enabled to build the plugin. 4. Added utils classes in python, examples are much simplified now. Fix python2.4 compatibility fix of the previous fix. 1. Commit before other changes. Renamed cmdGui to PythonUI. Tests seem to be working now. 1. Define macro NEEDS_BEX() that engines can use to advertise what physical actions they need. This avoids the necessity of passing that to PhysicalActionContainerInitializer. The change is backwards-compatible, all present engines were adapted however. 2. Fix BrefcomTestGen and USCTGen: don't crash anymore. 3. Small fixes in python code. Svn wants to commit before moving files... :-| Refactored MetaDispatchingEngine to MetaEngine (everywhere) Support saving to .xml, .xml.gz and .xml.bz2. Loading works as well. 1. Added heavy comments to simple-scene.py, started functionally equal code in extra/SimpleScene.{c,h}pp 2. Added dependency on boost::iostreams to debian template (for gzip/bzip2 streams). Hotfix for file loading logic. 1. Ignore ^C in PythonUI (gives crashes) 2. Shop::Bex caches physical action indices in static variables (not yet benchmarked) 3. Check for boost/foreach.hpp in scons and suggest how to install it. 4. Fixes in Brefcom 5. Set initial qglview size to 550x550 Big scons updates: Fix compilation problems and some warnings in the previous commit. 1. BOOST_FOREACH now works with InteractionContainer and BodyContainer and is #defined as foreach. 1. GUI change in qt3: make the simulation controller to take _much_ less space (no LCD displays, notably) and allow more place for 3d views. If someone is not happy with that, gui/qt3 can be reverted. 2. UniaxialStrainController now measures and records transversal strain. 3. Add attempt at smart command-line completion for ipython console. 4. Improved the class index cache in Shop::Bex (benchmarks needed) 1. Added MetaBody* as optional argument to Body::byId, to avoid Omega::instance().getRootBody() lookups - took a few percent of time in valgrind-profiled run. 2. Completed SimpleScene, a script to generate commented source py2wiki.py and put results on http://yade.wikia.com/wiki/SimpleSceneTutorial 3. Swap argument order in utils.sphere and utils.box to match Shop::sphere and Shop::box (center first, then radius/extents and not vice versa as it used to be) Make the GUI loader/saver a bit less intelligent. .yade, .xml, .xml.gz, .xml.bz2 are accepted when both loading and saving (hopefully). 1. Fix tabs in SConstruct. 1. Rudimentary plotting support through python; see http://yade.wikia.com/wiki/PythonPlotting and scripts/simple-scene-graph.py for details 2. Updates in examples/cmdGui1.py 1. QtGUI now integrated PythonUI if available. This means simulation can be controlled both from the QtGUi and the console. The + standalone PythonUI is available as well. 2. Changed form workspace to MDI windows; main window is menu-only thing that hides when simulation is open. 3. other minor changes. 1. Replace foreach with FOREACH, based on discussion with Janek. 2. Fix FileGenerateor message crash without workspace. 3. Fix TimeStepper choosable at the same time as fixed timestep. There is some problem with switching back to timestepper, use Omega().usesTimeStepper=True/False from python for now, please. 1. Merging containers and iterators and iteratorpointers to one .hpp. (Proxy headers created, no existign code affected) 2. Moving default containers for interactions, bodies and physicalAction to core; therefore, omega is constructed with out-of-the-box usable Metabody. (no code affected, though some initializations are now redundant) 3. Dropped workspace mode of QtGUI, since for some weeks no-one complained. 4. Big simplification of QtGUI (no dynamic menus and the like), to allow Views to be opened from python, independently of the simulation controller and so on. 5. Initial wrapper for gui stuff in python, in module yade.qt (View(),Controller(),center()) 6. Exiting the python interpreted (^D, quit()) will close yade main window as well. 7. Moved python wrapper helpers to gui/py/pyAttrUtils.hpp to be usable from elsewhere. Fix: move files properly (with svn) Forgotten add. MetaBody still needs InteractingGeometry, BoundingVolume and PhysicalParameters initialized. But that would mean moving more classes to core, which is questionable. For now, fix that in Python and still rely on user init in other code (as before, but less). 1. Fix passing .py to PythonUI (local vars shadowing global ones); fixes default-test.py as well. 2. Fallback to PythonUI automatically if $DISPLAY is not defined in shell 3. Ignore closing YadeQtMainWindow if it doesnt exist instead of throwing exception 1. Arguments can be passed to scripts, propagated as yade.runtime.args 2. default-test more robust, with e-mail report Update testing script for automated tests Micro fix in python script. Cleanups for ubuntu package builds. 1. Other fixes related to deb packages (jobs=1 because of fakeroot :-( ) 2. transversal strain sensors max speed can only be positive in USCT Fix for crashing from python-constructed rootbody. Hopfully other things are not broken. Fix player crashes (dialogs should have no parents) Fix setting timeStepper / fixed timestep from the qt3 ui Build qt3 with python disabled cleanly. 1. Add std::string Engine::label, which user can set to identify an engine by arbitrary label 2. Fix warnings in SpatialQuickSortCollider 3. Set isDynamic in rootBody by default 4. Remove PlotDataGetter, superseded by PeriodicPythonRunner 5. New abstract class for running things in predefined periods PeriodicEngine Forgotten file. 1. Fix sync mode in qt3 ui. 2. Fix real time display in qt3 ui. 3. Fix resizing of controller in qt3 ui (childs expand now) 4. Remove deprecated PythonRecorder (superseded by PeriodicPythonRunner) 5. Initialize Omega timers also at construction-time rather than simulation-loading only as it used to be. 6. Don't print bogus values of iters/sec in controller at startup. 1. Fix the priodic engine. 2. Add layout to the main windows with 4 buttons. 3. Fix PeriodicPythonRunner plugin installation 4. Update simple-scene-graph.py so that it works after latest plotting changes. 1. Add the possibility to save as gnuplot figure to the plotting interface 2. Add PeriodicEngine (fixed period) as opposed to RangePeriodicEngine (variable period) 3. Make BrefcomDamageColorizer subclass of PeriodicEngine instead of doing Omega::instance().getIteration()%interval==0 4. Change some icons in the UI 5. Add 'scale' parameter to loading spheres from file 1. Fix segfault in GUI exception trap 2. Handle .xml.gz and .xml.bz2 (in addition to .xml) as command-line argument in QtGUI Small fixes here and there. Merged from https://code.launchpad.net/~yade-team/yade/t2. All changes here: 1. Add list MetaBody::tags, which hold metadata in the key=value format; this is to workaround current serialization that errors out on map in findType. 2. Add meanStress and vlumetricStrain to Triaxial for python access 3. add neverDamage flag to Brefcom which forces elastic behavior regardless off strain magnitude. 4. Fix some warnings in STLImporter regarding signedness 5. add __attribute__((unused)) to a variable in Wm3Matrix3 that was not used during optimized builds - to avoid warning. 1. Fix tagging, do it as list; must NOT contain spaces! 2. Adapt python to that (replaces spaces automatically and so on) Forgotten variable after move Fixes for g++-4.3 compatibility (still some warnings, may need -fpermissive to compile) 1. Small fixes here and there 2. In brefcom, make the parameter set richer 3. PythonUI now may be run in non-interactive mode (batch processing) 4. new function Omega().interactions.nth(n) for getting random interaction Microfix: unitialized diffuseColor in boundingVolume 1. Remove failing and unused screw generator. 2. Add rate-dependence variables to brefcom 3. Add raw attribute access from python, like this: gm=GeometricalModel("Facet") gm.setRaw('vertices',"[{1 2 3} {4 5 6} {7 8 9}]") to provide access to attributes the current wrapper doesn't wrap properly (i.e. anything beyond numbers, bools, strings and flat arrays of numbers: e.g. vector, as in Facet). The format of the raw string is that of XMLFormatManager. 1. Triaxial now calculates thickness of the walls automatically (from the extents of the first wall) 2. Add flags to scons, for the gold linker (doesn't link plugins, oh well) 3. Many fixes in brefcom 4. flag needsInitializers moved into MetaBody and it is checked at every iteration; assigning initializers from python sets this flag. It is set to true in MetaBody constructor. 5. Added wrapper for postProcessAttributes in python, for Facets. Serializable::postProcessAttributes was made public due to that (don't kill me). 6. A few things added to yade.utils 7. SimulationController now correctly handles decreasing timestep mantissa from 1 (goes to 9 and exponent is decreased by 1) and increasing it from 9. 1. Parallel engine that runs engines in parallel; python wrapper for that 2. Added simple-scene-parallel.py for an example (sppedup of 16% over simple-scene.py) 3. Added openmp flags to scons (enabled by default) 4. Simultaneous builds of multiple profiles: scons profile=default,opt will run all the machinery 5. Refactored grid-drawing code; press 'x','y','z' to have grids with that normal 6. Ported some things from GLViewer to GLSimulationPlayerViewer (grid and mouse events) 1. Fix the simple-scene-parallel.py (interactionGeometry and interactionPhysics may _not_ be run in parallel) 2. Fix the #pragma clause in ParallelEngine (it did not run in parallel before, but still there were performance gains ?!) 3. When saving simulation, set the filename so that it can be reloaded from the GUI 1. PositionOrientationRecorder save to bzip2'ed files now; player is able to read both compressed and uncompressed files for backward compatibility. 2. Unsucessful try to use glut for drawing spheres; left as an option that is disabled by default, however. 3. Fixes in brefcom 4. Simulation player now has progress window and supports strides when loading files. 5. Fix wrong timestamp format in saveGnuplot in gui/py/plot.py (%m instead of %M) 1. Implemented clipping planes in the GL viewer and GL renderer 2. Moving body is now consistent with mouse bindings for moving scene Remove duplicated code in GLSimulationPlayerViewer, subclass from GLViewer. Median centering routine (for cases where one body went nuts and centerScene will make the whole a small point) - activated with Alt-C (both controller and viewer) 1. Added displacement and rotation scaling to the OpenGLRenderingEngine (accessible from the renderer config). Documentation missing as of now. Displacements from reference point will be scaled in the rendering. At this moment, only geometrical model and a few other elements of the GL display are scaled. 1. Double-click aligns clipping planes if manipulated, x,y,z aligns normal with axis. 2. Default number of clipping planes is 3 instead of 2 now. 2. Fix compilation error in ResetPositionEngine (missing logger) 1. sqlite3-dev is now required for yade (checked by scons) 2. sqlite3x c++ sqlite3 wrapper is in our tree (5 files, about 60kb of code), built by scons 3. Check for boost::regex 4. Experimental SQLiteRecorder (the player side is not yet supported at all!) 5. Remove messages at startup about singletons (define YADE_DEBUG env var to get them again) 6. StretchPeriodicEngine that will eventually replace the overdesigned RangePeriodicEngine Fix logger error at startup. 1. Remove some warnings about persistentInteractions initialization (initialization is done in MetaBody constructor anyway, it can not break anything); 2. Remove long obsolete pyade 3. Add Omega::getComputationTime 4. Add Omega::saveSimulationToStream and Omega::loadSimulationFromStream 5. Improve the SQLiteRecorder: put simulation into the db, create table with pointers to other tables, declare column types. The recording part is almost done. Implementation in player is to be done. 1. Move FiltrEngine from core to common (I know this is arguable, given that DeusExMachina and StandAloneEngine are in core as well. I think, however, that common is a more appropriate place since these engines are not as important...) 2. Completed the recording sqlite part 3. Completed the player part of sqlite (in player) 4. Added libsqlite3-dev to debian build depends 5. PeriodicEngine now is activated when the priod is reached, not afterwards (> vs. >=) Other fixes. Please not in GLSimulationPlayerViewer I had to comment one line that I didn't know how to make compile (dynamic-Cast). 1. Set iteration number with sqlite as well 1. Views, Player, Controller and Generator can be opened asynchronously from python now. 2. Revamped the player UI, hopefully making it better. 3. Added Alt-S for saving viewer state (camera etc) 4. Added runPlayer to python for aotomatized replay. The file contains instructions for offscreen thereof rendering as well. Re-enable sega's code that doesn't compile here. 1. qtCreateVideo creates video from the replay snapshots directly (using gstreamer) 2. qt.{Player,Generator,Controller} now take an optional bool; if true (_not_ default), they will not return until the requested window will have been created and ready. 3. runPlayer return wildcard and list of snapshot files now 4. Adapted simple-scene-player.py to reflect that. Fix linking issue. 1. new class DisplayParameters is a string->string "hash map" for holding various configurations. 2. Multiple display parameters (i.e. QGLViewer config and OpenGLRenderingEngine config) are stored in Metabody. 4. stopAtIteration moved to MetaBody so that it is saved and reloaded (MetaBody::recover hack is gone) 5. Remove unnecessary persistentInteraction initializers so that we have less warnings 6. Remove deprecated RangePeriodicEngine, plotting uses StretchPeriodicEngine instead. 7. Add the ability to load from stream and save to stream to IOFormatManager (afterwards, I discovered there were actually_identical_ functions loadArchive and saveArchive; those were deleted since unused elsewhere) 8. GLViewer can now load and save state from/to string 9. in GLViewer, keys 7,8,9 load display config #0,1,2 and Alt-{7,8,9} saves current view to #0,1,2. Those are saved in MetaBody. BUG: after loading such config, the QtGUI-generated OpenGLRenderingEngine config dialog doesn't work anymore (probably some issue with archives, not sure). 9. Hopefully all xml-parser-offensive characters are escaped at string serialization (and unescaped at deserialization). We use standard SGML escapes (newline=&br; tab=&tab; <=< and so on) now. This allows to save XML-as-string in the xml itself (used for DisplayParameters). 10. GLViewer now properly saves what XYZ planes are displayed (using custom DOM element) 11. Some fixes in Brefcom, more to come. 1. Fixes in Brefcom 2. Add docstrings to QtGUI-python functions; 3. StretchPeriodicEngine adjusts both limit and period if one of them is nonzero 4. Other fixes in python interface Sync with upstream QGLViewer 2.3.0 1. Experimental scale drawing in GLViewer (disabled by default) 2. Fix (?) race conditions (?) in Omega and python 3. Other fixes in plotting, works now again (remove numpy.array, not needed) 1. Merge all gravity engines (central, axial, directional (the old one)) into 1 header 2. Cleanups of pkg/common/SConstript 3. Add more brefcom accessors (Fs, Fn, ...) 4. Fix (hopefully) threading issues with python; Omega().pause and other now use Py_BEGIN_ALLOW_THREADS to avoid deadlock of the interpreter if called from c++ interpreting python code 1. Add private functions to eudoxos.py 2. Fix a few broken includes Fix #includes in affected files. Forgotten file. Second file that was forgotten :-| 1. Omega().interactions.nth returns n-th real interaction 2. Export more brefcom data to python 3. Make LOG_DEBUG and LOG_TRACE no-op in NDEBUG (optimized) builds 4. Change linebreaks from CR+LF to unix LF in a few random diles 5. Make DeusExMachina registerAttributes of Engine 6. Serializer prints offending value if bad_lexical_cast. 7. Attempt to catch exception if reading bool written as int (254 etc) and consider that "true" (doesn't work?) 8. JumpChangeSe3 can set (angular)velocity if requested instead of plain moving 1. Move refSe3 and dispSe3 to PhysicalParameters; this should speed up the renderer (clipping is done only once etc) and make it possible to apply clipping (via PhysicalParameters::isDisplayed) in GL functors for interactions as well. 2. Add button for setting reference positionts to the controller 3. Remove warnings in NewtonsDampedLaw 1. Cleanups in OpenGLRenderingEngine, use systematically clipping and scaling 2. Merge GL functor abstract class headers in one (GLDrawFunctors.hpp) and fix files using them 3. Make qt-serialization layout a bit more space-conservative. 1. Fix default test to report errors during simulation loading as well 2. Fix preprocessors derived from triaxial to not initializa transienInteractions, preventing crash discussed with Bruno: containes for transient and persistent must be the same, for unknown reason. 3. Fix preprocessors using brefcom to define all variables, otherwise we have nan's in XML which crashes the deserializer. Add script for making release Improved the release script. 1. Add the ability to block individual DOFs on every body in PhysicalParameters and implement relevant code in both NewtonsDampedLaw and LeapFrog integrators 2. Add that to UniaxialStrainer 3. Put both CundallNonViscous damping classes in one file (cleanup), adapt all files to that 1. Make the -x flag to PythonUI stop even if no script is provided. Fix missing lib (error at startup) ================================================== yade-0.10.0 Tue Jul 11 13:17:04 2006 +0000 Janek Kozicki (55): small correction in INSTALL, renamed ayde-data to yade-examples, and tagged it. added schedule added some more instructions to INSTALL file I am committing new version of docs, checked by my sister. And briefly checked by me. Olivier, now you can work on it, and remember to copy & paste lots of text and explanations from the article! directory for creating packages with yade. directory for Czesiu to work on debian packages for yade. later we can add directories for .rpm or gentoo, etc.... Fixed some broken symlinks. Removed unnecessary int i from MetaBody loops added missing -lglut yade is compiling with boost 1.33, but I had to make some modifications in ErrorTolerantLaw <- it is compiling, but I'm sure that it Jacobian is WRONG !! - Oliver it's your code, only you can fix that. some small changes, before I start something bigger ClassFactory is one step closer to windows version I have started changes that will make yade compilable on windows another step closer to compile yade on windows: to compile yade on windows we have to remove symlinks. I started doing that, but it's not finished. I have to commit in the middle still removing symlinks... symlinks removed. but it is NOT compiling now deleted all useless directories modyfing all .pro files and Makefiles so that it will compile maybe it is compiling... so symlinks are now removed, and it is compiling and installing exactly like before. So I have started compiling it on windows, and I stopped on the problem that linker cannot link serialization with factory. General cleaning of all header files. Now they are much more readable, and more coherent with C++ coding standards. added SDECMovingWall FileGenerator contributed by Andreas Plesch. You have decided to rename class: Box2AABB to a new name: InteractingBox2AABB You have decided to rename class: Sphere2AABB to a new name: InteractingSphere2AABB D yade-packages/yade-package-common/src/Engine/EngineUnit/Box2AABB/Box2AABB.pro D yade-packages/yade-package-common/src/Engine/EngineUnit/Box2AABB/Box2AABB.cpp D yade-packages/yade-package-common/src/Engine/EngineUnit/Box2AABB/Box2AABB.hpp A yade-packages/yade-package-common/src/Engine/EngineUnit/Box2AABB/InteractingBox2AABB.pro A yade-packages/yade-package-common/src/Engine/EngineUnit/Box2AABB/InteractingBox2AABB.cpp A yade-packages/yade-package-common/src/Engine/EngineUnit/Box2AABB/InteractingBox2AABB.hpp D yade-packages/yade-package-common/src/Engine/EngineUnit/Sphere2AABB/Sphere2AABB.cpp D yade-packages/yade-package-common/src/Engine/EngineUnit/Sphere2AABB/Sphere2AABB.hpp A yade-packages/yade-package-common/src/Engine/EngineUnit/Sphere2AABB/InteractingSphere2AABB.pro A yade-packages/yade-package-common/src/Engine/EngineUnit/Sphere2AABB/InteractingSphere2AABB.cpp A yade-packages/yade-package-common/src/Engine/EngineUnit/Sphere2AABB/InteractingSphere2AABB.hpp D yade-packages/yade-package-common/src/Engine/EngineUnit/Sphere2AABB/Sphere2AABB.pro I hope that scripts to rename classess are still working okay :> ErrorTolerantContactModel -> ErrorTolerantContact AABox2Sphere4ClosestFeatures -> AAInteractingBox2InteractingSphere4ClosestFeatures Box2Box4ClosestFeatures -> InteractingBox2InteractingBox4ClosestFeatures Box2Sphere4ClosestFeatures -> InteractingBox2InteractingSphere4ClosestFeatures Box2Sphere4ErrorTolerant -> InteractingBox2InteractingSphere4ErrorTolerantContact Box2Sphere4MacroMicroContactGeometry -> InteractingBox2InteractingSphere4SpheresContactGeometry Sphere2Sphere4ClosestFeatures -> InteractingSphere2InteractingSphere4ClosestFeatures Sphere2Sphere4ErrorTolerant -> InteractingSphere2InteractingSphere4ErrorTolerantContact Sphere2Sphere4MacroMicroContactGeometry -> InteractingSphere2InteractingSphere4SpheresContactGeometry continued... this renaming is DONE GLDrawInteractionBox -> GLDrawInteractingBox GLDrawInteractionGeometryFunctor -> GLDrawInteractingGeometryFunctor GLDrawInteractionSphere -> GLDrawInteractingSphere GLDrawInteractionGeometrySet -> GLDrawMetaInteractingGeometry renaming continued.. renamig DONE Serialization::registerAttributes() is now protected, as it should be. renamed MetaBody::actors to engines added: QtEngineEditor is not working - doesn't detect correctly StandAloneEngines - can save simulation from simulation controller - can change background color of the simulation displayed binary serialization for yade - looks like it is working :) fixed one bug in BINFormatManager fixed savig ElasticContactParameters and SpheresContactGeometry, so that after loading the simulation is not going crazy added several try/catch blocks removed GLAPI and GLAPIENTRY from OpenGLWrapper XMLSaxParser is now better at counting lines I have just enabled commit-email.pl for SVN. we should get info about commits for yade-dev, I wonder it if works :) not so small bugfixes and imprvements: - fixed serious bug in bool BodyRedirectionVector::erase(unsigned int); - added function bool exists() const; to BodyContainer - graphical display now has reversed meaning of scrollwheel, so it is now similar to behaviour of blender and autocad - SDECLinkedSpheres is working after some (surprise!) quick hack. That part is still waiting for total rewrite. - big improvements in lattice model. beam bending works (but not always) with axis+angle notation. maybe with quaternions it will be better. There is a problem that shows itself when using regular triangular grid. - added function Quaternion::power(RealType) - lattice bending works now in 2d (X-Y plane), using angles. not vectors or quaternions. I will do 3d later. - 'cancel' when loading filegenerator is not crashing now - started non-local model for lattice - hopefully 2d lattice beams are now okay. middle button in 3d view is now "PAN" command, not "ZOOM" as it used to be. It's more similar to AutoCAD 'yade -h' will now display compilation flags (currently only DOUBLE_PRECISION - how about adding long double ;) ?) small fix so yade works with lates kubuntu: Threadable class has been removed: - when yade is idle 0% of CPU is consumed by the display, - when simulation is ran it is in separate thread, second processor (if present) is drawing on the screen, - with two processors theoretically QtGUI should have speed equal to NullGUI, - drawing on the screen is not synchronized, so some bodies are from previous iteration, some are from next iteration (later there will be an option to turn synchronization ON - it will slow down computations a bit) Renaming SimulationLoop to SimulationRunner. renaming finished. SimulationLoop -> SimulationRunner deleted yade-lib-threads, added SimulationRunner, that can start/stop or perform singleLoop of simulation in separate thread. final touches to SimulationRunner compilation fix yade-flat now allows to debug yade from inside kdevelop SimulationController is now updating iterations/time and sets time step correctly. updated INSTALL file (before release). Olivier Galizzi (10): Corrected one missing include into yade-package-lattice so that it is compiling Added new yade-spherical-dem-simulator plugin. It is compiling but I have not tested it for now. This plugin will be used to compare yade performances to a dedicated simulator that can only run simulation on spheres and which is not extensible. Corrected some symlinks (forgot to call symlinks -rcs) Improvement into SphericalDEMSimulator SphericalDEMSimulator is now working. But maybe an error remains because for now it is 10x faster than yade !! Started to add SimulationPlayer plugin to QtGUI Some small optimisation of Math library. Some if statement where remaining after an assert that were doing the same check. Improvement into SphericalDEMSimulator and QtSimulationPlayer. SimulationPlayer is now working; but there is no check to see is the files exists or not, so it is up to the user to be carefull (at least for now) Minor changes into NullGUI. ================================================== yade-0.09.0 Sun Aug 21 20:41:37 2005 +0000 Janek Kozicki (34): fixed some broken symlinks removed inifinite loop when loading plugins fixed setDebug and setRelease scripts. Set everything to debug. added yade-flat - it is very useful for debugging, because command: fixed some Makefiles - changed make to $(MAKE) corrected invalid usage of postfix increment++ changed Makefiles, so that qmake respects INSTALL_DIR and PREFIX_DIR corrected a mistake another correction in Makefiles still fixind Makefiles, should be OK now... So now I think that Makefiles are OK. But I've discovered a mistake in .pro, when trying to install to totally custom directory (for example /home/joe/work ). So I'm committing this before fixing that. so by default /usr/local/include is searched for include files. INSTALL_DIR and PREFIX_DIR modify this path automatically. So that there is no problem to install yade as a normal non root user, in home directory. all Makefiles are tested and are working. following commmands were tested (launched from trunk/ directory) I started renaming SpheresContactGeometry to MacroMicroContactGeometry, and also I am testing new fixed renaming scripts! still testing renaming scripts... after this commit I'll know if scripts are correct fixing item no. 35 in yade-core/.todo fixing item no. 35 in yade-core/.todo Finished fixing item no. 35 in yade-core/.todo renaming: SDECTimeStepper ElasticCriterionTimeStepper SDECTimeStepper -> ElasticCriterionTimeStepper finished SDECTimeStepper -> ElasticCriterionTimeStepper InteractionDescriptionSet2AABB -> MetaInteractingGeometry2AABB ./yade-scripts/renameClassFilenames InteractionDescriptionSet2AABB MetaInteractingGeometry2AABB ./yade-scripts/renameClassDirectories InteractionDescriptionSet2AABB MetaInteractingGeometry2AABB updated Changelog M trunk/Changelog D tags/yade-0.1 M trunk/Changelog preparing for release. is compiling with DOUBLE_PRECISION corrected instructions in INSTALLs text files. ok, I think that this version is ready for release added dependencies diagram started tagging releases. renemed top directory QtGUI to yade-gui-qt. Just like XMLFormatManager tagged all new releases! Olivier Galizzi (19): Better YadeQtMainWindow. Now menus are displayed in menu bar in the same order they are added in the program. Added preferences for QtGUI. Now it remembers size and position and exit. Now it is possible to choose time step from GUI. Created directory yade-plugins to store all yade unfisnished plugins Added iteratortest to test iterator on polymorphic container Improved version of polymorphic iterator Splitted files in iteratortest so there is one class per file I have introduced iterators for all types of containers in order to remove the dirty gotoFirst, gotoNext, hasNext and notAtEnd methods. Now it looks like more like stl iterators. It is compiling but unfortunately it is segfaulting at runtime, probably some problems in ++,* operators. Yade is now working with iterator. At least all configurations generated by some FileGenerator are working. Added some improvement into GLEngineEditor. For that I have rewritten a big part of yade-lib-opengl because it was not possible to delete windows without corrupting the id of the others windows. Added Makefile to compile and install all packages at once. Better design : added class related to MetaEngine. Removed all references to Serialization stuff into yade-lib-multimethod. They are now into newly added classes. Some cleaning in MetaEngine hpp and cpp. Some improvement into QtEngineEditor Improvements into QtEngineEditor. Now it is olamost possible to create graphically a simultation loop.Now I have to make something to set parameter of MetaEngines. Improvement into QtEngineEditor Moved REGISTER_CLASS_NAME from Serializable to Factorable and started to add REGSITER_BASE_CLASS_NAME to all Factorable classes. With those two macro we'll be able to build into Omega for example the class tree and then reuse it everywhere it is needed. For example it will be usefull to create GUI that want to deal only with this or this type of class. Now all classes register their base class name. Removed unused classes. Fixed some compiletion errors. Added Makefile to compile the whole trunk at once. Improvement int QtEngineEditor. Now only correct EngineUnit and base base are displayed thank's to the REGISTER_BASE_CLASS_NAME macro. Simulation loop editing is now working. There are still some random crashes to fix and for now it is not possible to load a simulation loop. ================================================== yade-0.08.7 Thu Jul 7 11:14:08 2005 +0000 Janek Kozicki (10): renamed mscv to msvc first version of Makefile for yade-lib-loki Makefiles are better added Makefile for all libs Makefiles uninstall correctly make install works for all yade-libs (weel, actually oinly three of them now) looks like commands: small correction in docs small fix for make clean after name change of libXMLManager we had to correct Makefile Olivier Galizzi (77): Created yade-libs directoryt to clean a little the directory tree Created directory yade-packages Created directory yade-empties Created yade-empties directory Removed directories yade-lib-rendering-engine-opengl and yade-lib-gui-qt because they now have no reasons to be there Renaming directory yade to yade-core Modified yade-empty-lib directory structure Added Makefile in yade-empty-lib Added README file into yade-empty-lib/doc/ Created yade-lib-qhull Created yade-lib-loki Added symlinks for yade-lib-loki Created yade-lib-wm3-math Making symlinks relative Created lib yade-lib-threads and yade-lib-time The lib yade-lib-factory was also created but is not working because it needs the lib-loki to be installed Creaed libs yade-lib-swiftpp, yade-lib-multimethods. Corrected yade-lib-time, yade-lib-factory Created libs yade-lib-opengl and yade-lib-algorithms Created libs yade-lib-serialization and yade-lib-computational-geometry Created libs yade-lib-serialization-xml and yade-lib-serialization-qt Corrected #include statements to point to yade/yade-lib-* instead of just yade-lib* removed old yade-empty-package Added new yade-empty-package which is simpler than previous one Started to add yade/ in all include statements Finished to change #include statements Sub-Project libraries removed from yade-core Yade is now compiling with separate libraries projects Yade is now compiling AND running !! :) Changed yade-empty-package so that all subdirectories contain not plural names. Added empty kdevelop project into yade-empty-lib Added script changeLibName into yade-empty-lib, which allow the user to change the name of kdevelop project, this is easier when you wnat to start to develop a library Added script into yade-empties so that it is easier to start to develop a new package of lib. Added yade-empty-gui Improved version of scripts that change the name of empties. Started to make yade-core clean (without all plugins) Making yade-core clean. Making yade-core clean yade-core is clean. When asking for default gui, QtGUI is choosen when return is pressed. Created project yade-guis/QtGUI Modified make clean to remove kdevelop temp file Cleaning yade-packages before splitting First version of yade-package-common with containers and DataClasses ok, but for Terrain which is not compiling Moved Terrain to sandbox because it is absolutely not finished yet. Some cleaning in yade-tmp Added PersistentSAPCollider and SAPCollider to yade-package-common Engine Created yade-package-fem and yade-package-dem Intermediate commit because I have put Ellastic*Law into Engine and not Engine/StandAloneEngine Continuing splitting of yade. Removed unused directories Created package yade-package-realtime-rigidbody, yade-package-lattice, yade-package-mass-spring All data classes are almost splitted Prepocessor are all splitted, so as DataClasses removed useless directories Splitted all InteractionSolver Added forgottent LatticeLaw StandAloneEngine Removed unused directories All MetaEngine are now splitted Removed unused directories Splitted engine unit to yade-common Moved directory previously moved to wrong place Temporary commit because of wrong svn mv Moved directories that were in wrong place All BodyEngineUnit are now splitted Removed unused directories Temp commit because of error Everything is splitted but RenderingEngine and NarrowInteractionGeometryEngineUnit Removed unused directories Everything is now splitted but RenderingEngine Removed unused directories Splitting yade-core finished. Maybe some changes will be needed in the future. Of course now we have to make compile the new projects ! Removed unused directory. Fixed symlinks error into yade-core yade-core and yade-common are compiling Yade-package-dem is compiling yade-package-fem is compiling yade-package-lattice is compiling yade-package-mass-spring is compiling yade-package-rigid-body is compiling So all packages are now compiling, but I still have to check for build order. Yade is now compiling and running Changed build order of yade-package-common so that it is compiling on the first try. ================================================== yade-0.08.6 Fri Jul 1 15:36:47 2005 +0000 Olivier Galizzi (14): Added some functions into yade-lib-computational-geometry Started to and graphical interface for buliding simulation loop and initializer list Added ommitted files QtEngineEditor.* Added unused class MetaEngine, MetaDispatchingEngine2D and MetaDispatchingEngine1D. I wanted to make something easier for the user but it is not working now. Updates into QtGeneratedCodeGenerator.ui. Started to implement the GUI Updates in Omega : now foreach plugins we store if it is indexable, factorable or serializable. Improved code generation : Data class, engine and dispatching engine works. No stuff is done for generation of kdevelop projects. All libs use now $(YADEDYNLIBPATH)/yade-libs directory as output path. Some changes had to be made in most of the .pro files. Added a preference editor in QTGUI Attempt to use Yade without environnement variable. I am closer to the solution but it is still not working. Small change so that yade is compiling with qglviewer 2.0 No there is no need to set up and environnement variable to run yade. Of course because the libs are still into a local dir your LD_LIBRARY_PATH should point to this local folder. Yade is now working and compiling. Started to move yade-lib-gui-qt back to plugins yade-lib-gui-qt moved back to plugins Yade is now compiling fine. I removed qyade and nyade since they are not needed anymore. Added user manual without pictures. But .tex is compiling well. ================================================== yade-0.08.5 Sun Jun 19 23:01:35 2005 +0000 Janek Kozicki (5): it's compiling now with gcc 3.3 added warining in Omega.cpp when trying to scan non existing directory for dynlibs added missing 'virtual' to destructors of some classess - I had random compiler/startup errors because of that. openGL problem fixed - yade must link with -lglut, and display works. Lattice works with rods, but dirty, of course - as always when something is implemented for the first time :> Olivier Galizzi (6): All EngineUnit now link with their corresponding MetaEngine otherwise findType doesn't work ! Why ... I don't know ! :) Because EngineUnit only use the abstract class contained inside corresponding MetaEngine dynlib and nothing else ... To make yade deserialization working I had to modify PointerHandler.tpp around line 90. Basically I just remplaced a dynamic_cast by a reinterpret_cast. We have to find why dynamic_cast is not working anymore ! Added some dynlibs for handling swept sphere volume. Tetrahedron are almost working. A bug into SWIFT is still causing troubles. Some changes into SweptSphere and Tetrahedron Putting some stupid name for 2 enum in Typelist.hpp (l 518 and 520) so that yade is compiling with gcc 4. Gcc 4 do not accept anymore anonymous enum type ! ================================================== yade-0.08.4 Mon May 23 12:51:50 2005 +0000 Janek Kozicki (1): added -lpthread in some places, so it is compiling with g++ 3.3 Olivier Galizzi (17): Removing MarchingCube GeometricalModel (because it is not a GeometricalModel !) Renaming PhysicalActionEngineUnit to PhysicalActionDamperUnit and PhysicalActionApplierUnit Added class Preferences that contain directory to dynlibs. Modification of library yade-lib-factory so that it is using multiple directories to look for requested dynlib Removing remaining directory toolboxes Started to split include files of libraries into different directories. Started to change all #include "lib" to #include Corrected some wrong #include stuff All include files from plugins/pre and post processor are now into include/yade-common. This is not final destination but it is closer to want we want. All #include stuff are modified according to this new structure. Added script countNbLines that count the number of lines of code of the project Starting renaming SimpleSpringLaw to FrictionLessElasticContactLaw Renaming SimpleSpringLaw to FrictionLessElasticContactLaw Renaming SimpleSpringLaw to FrictionLessElasticContactLaw SimpleSpringLaw renamed to FrictionLessElasticContactLaw. Yade is compiling. Improved documentation : added introduction to YADE Improved documentation Added librarie swift++ and qhull. Modified scripts so that they works with .h and .c files. Added MarchingCube algorithm into yade-lib-computationnal-geometry Created lib yade-lib-algorithms were to gather algorithms of different type : for now there is only a PerlinNoise algorithm, but we can put here sorting algorithm ... Moving, renaming some directories before splitting Added new file generator Funnel and TetrahedronsTest Added new interactingGeometry PolyhedralSweptSphere Added new NarrowInteractionGeometryEngine SwiftPolyhedronProximityModeler that will use SWIFT++ library and PolyhedralSweptSphere Added EngineUnit Tetrahedron2PolyhedralSweptSphere and Box2PolyhedralSweptSphere that will build InteractingGeometry ================================================== yade-0.08.3 Tue May 10 08:40:39 2005 +0000: Olivier Galizzi (32): Renaming ActionParameter to PhysicalAction Renaming ActionParameter to PhysicalAction finished Renaming ActionParameterForce/Momentum to Force/Momentum adn ActionParameterInitilizer/Reseter to PhysicalActionContainerInitializer/Reseter Renaming ActionParameterForce/Momentum to Force/Momentum adn ActionParameterInitilizer/Reseter to PhysicalActionContainerInitializer/Reseter ... Renaming ActionParameterForce/Momentum to Force/Momentum adn ActionParameterInitilizer/Reseter to PhysicalActionContainerInitializer/Reseter Renaming ActionParameterVectorVector to PhysicalActionVectorVector ... Renaming ActionParameterVectorVector to PhysicalActionVectorVector ... Yade is now compiling ... Moving NullGUI to yade core and renaming QtGUI to yade-qt-gui Moving yade-gui-gt from extensions/Frontend to gui Still moving yade-qt-gui Moving XMLManager from extensions/IOManager to serialization Renaming back yade-qt-gui to QtGUI to try to make yade compile first ... Renaming back yade-qt-gui to QtGUI to try to make yade compile first finished Forgot to re-ad QtGUI to kdevelop project Changing yade-empty-package directory tree Changing build order Moving all MetaEngine stored inside yade core to plugin/engine/metaengine ... Moving MetaEngine from yade to plugins Moving MetaEngine from yade to plugins Moving MetaEngine from yade to plugins... Modifications so that yade is compiling with new directory tree Creating library yade-lib-serialization-qt and yade-lib-time Changing build order and moving XMLManager to libraries Changing build order and removing unused directory serialization Renaming XMLManager to yade-lib-serialization-xml Moving gui/QtGUI to libraries/yade-lib-gui-qt Changing build order and finishing renaming of XMLManager and QtGUI Changing the way QtGUI load OpenGLRenderingEngine so that QtGUI doesn't need anymore to link with OpenGLRenderingEngine library. Making yade main application with flat directory structure Making yade main application with flat directory structure Removing all references to libraries Interactions, Body, Engine than no longer exist. Yade should now compile. Splitted ElasticContactLaw into 2 : ElasticContactLaw and ElasticCohesiveLaw. Autocollision for hanging cloth is working without hack. ================================================== yade-0.08.2 Fri May 6 15:57:05 2005 +0000 Olivier Galizzi (75): Starting creating new directory structure Directory renaming ... renaming directories ... Directory renaming ... Directory renaming ... Directory renaming ... Directory renaming ... Directory renaming ... Directory renaming ... Directory renaming ... Directory tree redesign ... Directory tree redesign ... Directory tree redesign ... s D yade/src/plugins/Engine/ActionParameterFunctor D yade/src/plugins/Engine/PhysicalAction Directory tree redesign ... Directory tree redesign ... Directory tree redesign ... Directory tree redesign ... Directory tree redesign ... Directory tree redesign ... Directory tree redesign ... Directory tree redesign ... Directory tree redesign ... Directory tree redesign ... Directory tree redesign ... Directory tree redesign ... Directory tree redesign ... Directory tree redesign ... Directory tree redesign ... Directory tree redesign ... Directory tree redesign ... Finishing directory tree redesign ... not compiling yet Now starting to rename files and some directories Renaming files ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes ... Renaming classes is almost finished and yade is now compiling ! Renaming libraries to yade-lib-* Renaming libraries to yade-lib-* ... Renaming libraries to yade-lib-* Renaming libraries to yade-lib-* Renaming libraries to yade-lib-* Renaming libraries to yade-lib-* done. Yade is now compiling. Moving DataStructure to plugins ... Moving DataStructure to plugins finished Yade is now compiling on the first try. I removed initialization in constructor of bodyContainer, InteractionContainer ... because now container are in plugins and so compiled after yade itself. Changing name Dispatcher/funtor to MetaEngine/EngineUnit Changing names Dispatcher/Functor to MetaEngine/EngineUnit ... Changing names Dispatcher/Functor to MetaEngine/EngineUnit ... Changing names Dispatcher/Functor to MetaEngine/EngineUnit ... Changing names Dispatcher/Functor to MetaEngine/EngineUnit ... Changing names Dispatcher/Functor to MetaEngine/EngineUnit ... Changing names Dispatcher/Functor to MetaEngine/EngineUnit ... Changing names Dispatcher/Functor to MetaEngine/EngineUnit ... Changing names Dispatcher/Functor to MetaEngine/EngineUnit ... Changing names Dispatcher/Functor to MetaEngine/EngineUnit finished ================================================== yade-0.08.1 Wed Apr 27 16:51:17 2005 +0000 Janek Kozicki (348): deleted file makeSymLink, and corrected calling scripts, when current directory is not in $PATH - just added ./ everywhere better scripts - easier to use better script to switch dynlib on/off, but still not good enough removed spaces at the end of line Multimethods work! but class Factorable MUST be added, to clean mess with CollisionFunctor correcten compile dependencies - builds again from command line corrected (again) compile dependencies removed couple of compiler warnings added yade/scripts/setDebug yade/scripts/setRelease added FIXME about serialization, and Omega constructor tells about -rdynamic flag added comments into MAIN LOOP (currently inside NonConnexBody) scripts now check if YADEPATH was set scripts now checking if YADEPATH set, othervise tell user to set it moving GUI to frontend moved GUI to FrontEnd added FactoryExceptions so that ClassFactory is reusable fixed ArchiveTypes.hpp:FIXME : change SMART_POINTER to POINTER and STL_CONTAINER to CONTAINER added ClassFactory snippet, in order to clean it and make reusable ClassFactory now should be really reusable starting work with Serialization (spirit) preparing yade to use reusable snippets - do not modify those files inside yade! do it in snippets instead now yade uses exactly the same files as snippets. DO NOT MODIFY THEM, modify snippets first, then copy here. now yade uses boost::spirit, DO NOT MODIFY, work on snippets instead little cleanup, before making resetable rootBody corrected spirit. DO NOT MODIFY, please test on snippets first. now hanging cloth uses fundamental variable [ {1 {2 3 4}} {1 {2 3 4}} ... ] we started adding SDEC element. now SDECTestExample works. but not rotating box. and we need to clean stuff SDECDynamicEngine starts to work with contact law moving CollisionModel into CollisionGeometry changing *PhaseCollider into *Collider changing *PhaseCollider into *Collider (2) changing *PhaseCollider into *Collider (3) changed *PhaseCollider into *Collider, now starting with qmake static libraries inside yade directory now yade accepts more arguments on input: filename, timestep, maxiter added benchmark - we can easily test speed changes of yade CollllisionFunctor does NOT need to derive from Indexable!, rearranging subprojects changes in Math directory... more changes in directory tree (I must commit between changes...) more changes in directory tree (I must commit between changes... 2) moving files around ...still not compiling.. i must commit before I move directories.. looks like I've found a solution for qmake... looks like I've found a solution for qmake...2 finally! rearrangement of qmake/yade subtree. Serialization must be a dynlib!! it is absolutely not working as a static library!!, Omega must be freed from dependency on Vector3, this causes lots of problems (4hours to find it), 12h total, wheeeew. I Hope this work is not useless... CollisionFunctor derived or not, from Indexable? (in g++3.3 if YES - it's faster, but rather uncorrect...) now compiles with g++3.3, that was darn difficult to figure out, and is not slower than 94 svn status -q :) correction in SDECDynamicEngine with PermanentLinks, and Quaternion precise rotation added tetrahedron with permanent links, and -a flag, to say if we want autostart computations added NullGUI, and -p flag SDECBenchmark8k.xml is working now. added two more examples not working moment law - just after implementing it with JP wtf with euler angle on y direction??? added SDECMoreTetrahedronsWithLinksMDEM3D.xml this one works stable, but bad: data/SDECPermanentChainRotated.xml corrected SDECRotatingBoxWithTetrahedrons.xml and FileGenerator/RotatingBox/RotatingBox.cpp added LinkedSpheres filegenerator, small note inside Translatro.cpp - so that we can reproduce strange bahaviour changed order of REGISTER_ATTRIBUTES in NonConnexBody - interactions are first SDECDynamiCEngine has damping 0.3 now (should be attribute!!) added SDECCollision.xml - looks really good with timestep 0.003(FIXME - should be inside .xml) and moment law uncommented(FIXME) in SDECDynamicEngine XMLManager says line number of .xml if serialization fails, at least sometimes... Serializtion now supports: std::map, Loki::AssocVector, std::list, std::deque, std::set, std::vector, std::pair, boost::tuple1/2/3/4/5 corrected all .pro files to include toolboxes/Libraries/AssocVector - so that yade now compiles and runs good with all that new serialization stuff createIncludes script corrected, Makefile removed this version of file is used to make comparision of results with Jean Patrick corrected - works with current (unfinished) containers moved Singleton.hpp to toolboxes/Libraries/Singleton - place where it belongs now yade works with new serialization - added beforeSerialization, afterSerialization, beforeDeserialization, afterDesrialization removed class Contact, in prepare for interactionContainer added InteractionContainer (not integrated yet) InteractionContainer integrated into yade InteractioContainer eraseCurrent() useful for SAPColider BodyContainer starts to work BodyContainer with ids works, now I havr to move it into yade/Body, yade/Interaction InteractionContainer and BodyContainer integration completed. but container classes quality/speed is not good (and tested) yet InteractionVecSet and BodyVector FIXED threading on multi-processor machine (not real multiprocessor, just hyper threading...) rename BodyVector to BodyRedirectionVector corrected BodyRedirectionVector, added comment in Singleton scripts that allow easy switching between relative paths and paths in environemnt YADE*PATH variables threads are now crashing little less often... (only when clicking "new view" "start" "stop") XMLManager writes pointers in a shorter way, with _className_ preProcessAttributes postProcessAttributes converted SDECBenchmark8k.xml NullGUI works - for benchmars of Vector3 not in Serializable, etc.. scripts are checking all Environement Variables - more safety fixed missing is_base_and_derived in Indexable.hpp started with OpenGLWrapper and removed extra tabs in serialization OpenGLWrapper starts to work - now to write all those functions from gl.h OpenGLWrapper 50% done - and #DOUBLE_PRECISION works! (float/double) improved SDECLinkedSpheres (momwnt law is not workingsvn status -q) SDECCollision.xml is loading correctly, but is not working!!! - it was working previously!! SDECCollision.xml works for dt=0.003 SDECCollision.xml and SDECTetrahedronWithLinks.xml work for dt=0.003 SDECLinkedSpheres example now is much more interesteing, with dt=0.003 fixed hack in PointerHandler, fixed SDECBenchmark8k, some .pro were release, not debug ok, this problem in IOManager.cpp is strange... rearranging directories. changing directories cd... changing directories cd... changing directories cd... Finished rearranging subdirectories. Now we have directory extensions (we can rename it, if there is a better name), and ClassFactory is in toolbox/Libraries, Multimethods (once there are done) should go there too, because MultiMethods have nothing to do with yade. yade is now compiling (and works) with g++ 3.3 all .xml examples except ErrorTolerant, are now working NullGUI is now saving results during computations. Those results can be opened with QtGUI and we can see what is computed. added filegenerator that can import data files from SDEC hack, which must be corrected just after adding Action, allows to measure forces during simulation InteractionVecSet is corrected and working, yade is now compiling withi double (there was some mistake with float), but all the examples are now broken! yade is now crashing less often, so I hope that we will never again see that error: again was not compiling with double.... corrected some threading problems, removed MyEngine2 from DynamicEngine.pro, because it doesn't exist added SopeTest in SimulationController -pthreads -lpthreads are required for yade to compile with 3.3!! don`t remove them!!!! added some comments to code regarding integration with new multimethods started integration of multimethods integrating new multimethods, continued... 1D, 2D MultiMethods are working in yade. but there is a bug in DynLibDispatcher, current workaround is done with a hack added some comments to working multimethods, hack is little better, but not removed, yet Multimethods are now working, clean, checked with valgrind, and results from older version are compared with kompare. added two postprocessors - recording forces, and average position. but why they crash Omega.loadDynLibs(), when I use ofstream??? force recorder is not modifying data anymore, but anyway it`s dirty and must use Action, and work like real sensors!! SDECImport uses new dialog box changes into Interaction and Interaction container: version 0.1.5, with many changes: - moment rotation law added, mess inside SDECDynamicEngine (three enegines in one!) - Serialization now supports almost all std, boost and Loki containers and more - math classes are separate from serialization, and done with templates (but with wild-magic license) - for storing Bodies and Interactions we now use polymorphic classes InteractionContainer and BodyContainer - yade uses threads now, but still not fully stable - switch at compile time to select float/double precision of calculation - displayed objects are now casting really cool shadows - some examples are not updated, and therefor not working. it is guaranteed that SDECBenchmark8k will always work. - BoundingVolume optimized for each kind of GeometricalModel makes computation almost twice faster - new very generic MultiMethods are added, allowing multivirtual call with extra parameters, and easy code reuse added changelog small correction in Interaction constructor putting Real in all places where it is used for calculation was not compiling because of stupid .pro problems renamed DynLibLauncher to FunctorWrapper changing name from SDECContactModel to SDECContactModel - but not tested yet - I must commit between subversion operations SDECContactModel renamed to SDECContactGeometry, OK renaming BroadCollider, NarrowCollider to BroadInteractor, NarrowInteractor, part 1 still renaming finished renaming BroadCollider, NarrowCollider to BroadInteractor, NarrowInteractor changed color of sphere number 1 and 10 - this is for checking the shearForce between those spheres (as we had numerically different results for float and double) some cleaning before ActionContainer some .pro conflicts, now it's compiling, still before ActionContainer added empty class ActionVecVec I added empty classes ActionForce and ActionMomentum, because I need something that ActionContainer can store classes are empty now. So, now all classes are added: Action, ActionVecVec, ActionContainer, ActionForce, ActionMomentum, etc.. but they are empty. And it is compiling abstract interface for ActionContainer is specified, now to fill in the class ActionVecVec .... work inside ActionVecVec - not done yet, but is compiling corrected compilation order (except for CollisionGeometrySet, which is a sign bigger design flaw, than just a compilation order) and xorrected SDECBenchmark8k.xml so that it is running with latest modifications ActionContainer->reset() - resetting actions without deleting all the pointers - faster changed the way in which ActionContainer works, now all fields are never empty. DynamicEngine (or some other actor?), when if(first) must call ActionContainer->prepare(), and then ActionContainer works much faster. added flat kdevelop project, this is for debugging - I don't know why, but alleyoop is not showing line numbers inside dynlibs, now... finad() and getCurrent() in containers are now returning references, as it should be faster Body is Indexable, but we have to register SDECDiscreteElement to dispatcher, not RigidBody... it's a bug in Indexable class, or somewhere there... Multimethods now support inheritance in Indexable objects, I had to modify in Indexable class: possibly faster DynLibDispatcher, I was also trying to fix problem that Singleton is not deleted at end, but finally I made only some improvement, but it is still not fixed. renaming CollisionFunctor to InteractionFunctor, part 1 renaming, part 2 renaming, part 4 renaming, part 5 renaming, part 6 finished renaming of InteractionFunctor, and I also corrected colors in qt dialog, and qt simulation-controller window. But I'm not sure about colors in qt dialog. small change in ActionDispatcher.cpp, is faster, but if Action was holding body's id it is possible that it can be faster corrected SDECBenchmark8k.xml, and I've checked that visually simulation is the same as previous version renaming... moving stuff around moving stuff around moving stuff around cd.. moving stuff around... now I'll try to compile... still trying to compile... it is almost compiling so it is compiling, except for CollisionGeometrySet problem OpenGL display works with strange static_cast inside DynLibDispatcher started with PositionOrientationRecorder changed double to Real in few remaining places. small fixes in multimethods. remove ParticleBallisticEngine BallisticDynamicEngine renamed geometricalModel, interactionGeometry, boundingVolume before renaming class name of CollisionGeometry to InteractionGeometry renaming collistion to interaction, cd... renaming cd... renaming... renaming... renaming... renaming... still renaming collision to interaction... still renaming collision to interaction... still renaming collision to interaction... still renaming collision to interaction... still renaming collision to interaction... renaming mess.. classes aggregated by Body have a prefix 'Body' in their name, to reduce confusion of class names: fixed OpenGL display of cloth, and still renaming classess aggregated by Body Loki library in single place, but it should be renamed to SmallLoki, or YadeLoki, because this is not an exact copy of Loki library. added FactoryFunctors and UpdatorFunctors for BoundingVolume, GeometricalModel, etc... They are empty for now Loki ok (just should be SmallLoki, or YadeLoki), BodyAssocVec -> BodyAssocVector because of name conflict between Body::InteractionGeometry and Interaction::InteractionGeometry, maybe name Body::InteractionDescription will be ok? this is what I've renamed in this commit so now we have (arrow <- means 'aggregates'): renaming cd.. renaming cd.. renaming cd.. before renaming InteractionFunctor-s to InteractionGeometryFunctor-s little renaming/cleaning is finished. problem with InteractionDescriptionSet is solved, and now yade just compiles without any errors! I have done some general cleaning - removed unnecessary constructors, deleted unused postProcessAttributes, etc.. OK/Cancel works now in file selection dialog, ActionForce2RigidBody was deleted, because ActionForce2Particle does the same job now I'm staring to work on updating GeometricalModel of Mesh2D, so that cloth will be displayed properly changed names RigidBody to RigidBodyParameters and so on before making correct display of cloth geometrical model I have to move Geometry into Body, because Body owns geometry, and it will not compile if I don;t move it there. all renaming finished for now. so I'll start with proper update of geometrical model for cloth. update of GeometricalModel for cloth is working is compiling now with g++ 3.3, and with double FunctorWrapper is Serializable, now - because we want Dispatcher to work with serialization, so that Functors can get extra arguments from .xml Functors are serializable, so now I'm working on DynLibDispatcher to support this serialization of functors Serializable functors are working, so now I'll separate damping from SDECDynamicEngine. It will be a functor, with parameters. preaparations for ActionDampingFunctor, corrected SDECBenchmark8k.xml damping is separated from SDECDynamicEngine and works, strange is that ActionDampingDispatcher and ActionApplyDispatcher are exactly the same!! so they should be merged into one dispatcher. maybe Action2BodyPhysicalParametersDispatcher damping works quite good added ActionReset - it is not inside SDECDynamicEngine - because for cloth example we have two/three engines, so they can't do a reset - because they will delete results from other engine renamed: stared with RotatingBox with simplespring, filegenerator... RotatingBox example with spheres and boxes inside is working quite good - with SimpleSpringDynamicEngine BoxStack example is working quite good. meybe it should be renamed to WallImpact, or something like that... the real name for damping is: Cundall Non Viscous Local Damping TimeStepper is working quite nice, and now - even SDECLinkedSpheres example is stable! SDECParameters is now holding shearingAngle, young modulus and posiions ratio - as it should. internal shearing angle is added, and yade is ready to compare results with sdec, although force recorder is little dirty, because it is releasing the bug ball some small corrections, before comparing results with sdec splitting leapfrom integrator into two parts.... added velocity recorder, and timeintegrator is split in two parts started with lattice model Lattice model generation starts to work. SDECImport can also create walls made of spheres Body::group changed into Body::groupMask (so bodies can belong to many groups - max. 16 groups, because we have 16 bits here) supid error everywhere!!! volume of a spohere was 4/3*PI*radius*radius, EVERYWHERE!!!. the volume of a sphere should be calculated in ONLY one place!!! so now we will make another comparision with SDEC, after sphere volume was fixed renaming DynamicEngine to InteractionLaw renaming KinematicEngine to KinematicMotion DynamicEngine -> InteractionLaw KinematicEngine -> KinematicMotion renaming DynamicEngine is ConstitutiveLaw ApplyActionForce2Particle -> NewtonsForceLaw ApplyActionMomentum2RigidBody -> NewtonsMomentumLaw started nice class diagram better (but not finished) class diagram version used for training with Julien, Frederic, and Luc yadeExampleTimeLoop.dia (xml) almost finished renaming Action to ActionParameter renaming cd... renaming cd... renamed Action to ActionParameter separating gravity to GravityForceFunctor - it is necessery because I'm preparing code for courses. some filegeneratr examples now have zero gravity, and empty ActionParameterContainer, that is easy to fix with ActionParameterInitializer, when doing ActionParameterInitializer, also ActionParameterReset must be done correctly and split from ActionReset. Then we have to add ActionParameter displacement, position and angularDisplacement, so that ImposeKinematicConditions will work correctly (AngularDisplacementFunctor, DisplacementFunctor (it was Rotor and Translator)) some cleaning stared ActionParameterInitializer and ActionParameterReset started LeapFrogOrientationIntegratorFunctor and LeapFrogPositionIntegratorFunctor LeapFrogOrientationIntegratorFunctor LeapFrogPositionIntegratorFunctor done renaming KinematicMotion to COndition renaming KinematicMotion to Condition renaming KinematicMotion to Condition ForceCondition GravityCondition RotationCondition TranslationCondition, are OK renaming.. renaming.. renaming.. renaming.. renaming.. renaming.. renaming.. renaming.. renamed: SDECParameters -> BodyMacroParameters SDECContactGeometry -> MacroMicroContactGeometry, and all functors SDECMacroMicroElasticRelationships -> MacroMicroElasticRelationships SDECContactPhysics -> ElasticContactParameters SDECLaw -> ElasticContactLaw added empty classess: added empty FEMSetTextLoaderFunctor FEMBeam load the file correctly FEM bodies inherit from BodyPhysicalParameters scripts to rename classess, hopefully working correctly I'm testing the renaming scripts: I'm testing the scripts: I'm testing the scripts scripts should work now, with small human intervention I'm testing scripts again ./renameClassFilenames FEMTetrahedronParameters FEMTetrahedronData ./renameClassDirectories FEMTetrahedronParameters FEMTetrahedronData ComplexBody has now actors and initializers, and thanks to that FEMSetTextLoaderFunctor is working. FEM is half done - generation works. and other stuff. Only Constitutive Law for FEM is empty - waiting to be written. But there is a compilation problem we have to compile twice now, because of linker errors in fem loader. FEM works!! GLDrawTetrahedron is now drawing solid tetrahedrons. but sometimes it is drawing not correctly.... corrected some comments in FEMLaw FEM stuff is compiling correctly, some cleaning. created directory A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-fem created created created A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-qt A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-wm3math A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-loki A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-serialization A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-multimethods A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-factory A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-threads A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-opengl A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-computationalgeometry A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-massspring A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-realtime-rigidbody A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-computational-geometry D svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-computationalgeometry A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-wm3-math D svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-wm3math A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-mass-spring D svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-massspring A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-empty A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-sandbox A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-serialization-xml A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-dem-fem D svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-femdem better openGL tetrahedron display A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-time A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-gui-qt D svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-qt A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-rendering-engine-opengl A trunk/yade-package-fem A trunk/yade-package-fem-dem D trunk/yade-mass-spring A trunk/yade-package-realtime-rigidbody D trunk/yade-dem D trunk/yade-fem D trunk/yade-dem-fem D trunk/yade-realtime-rigidbody A trunk/yade-package-lattice D trunk/yade-lattice A trunk/yade-package-mass-spring A trunk/yade-package-dem A trunk/yade-lib-wm3-math A trunk/yade-lib-loki D trunk/yade-rendering-engine-opengl A trunk/yade-lib-factory A trunk/yade-lib-computational-geometry D trunk/yade-multimethods A trunk/yade=lib-time A trunk/yade-lib-opengl D trunk/yade-threads D trunk/yade-wm3-math D trunk/yade-time D trunk/yade-loki A trunk/yade-lib-rendering-engine-opengl D trunk/yade-factory D trunk/yade-computational-geometry A trunk/yade-lib-multimethods D trunk/yade-opengl A trunk/yade-lib-threads A trunk/yade-lib-time D trunk/yade-serialization-xml D trunk/yade-serialization A trunk/yade-lib-serialization-xml A trunk/yade-lib-serialization D trunk/yade=lib-time fem-dem coupling ... disabled stuff in QtGeneratedSimulationController changed todo changed something in interactions ./renameClassFirst InteractionDescription InteractingGeometry ./renameClassFilenames InteractionDescription InteractingGeometry D yade/src/yade/Body/InteractionDescription A yade/src/yade/Body/InteractingGeometry D yade/projects/kdevelop/yade/Body/InteractionDescription A yade/projects/kdevelop/yade/Body/InteractingGeometry A yade/projects/kdevelop/yade/Body/InteractingGeometry/InteractingGeometry.pro M yade/projects/kdevelop/yade.kdevelop SimpleBody deleted renameClassFirst ComplexBody MetaBody ./renameClassFilenames ComplexBody MetaBody D yade/src/plugins/Body/InteractionDescription A yade/src/plugins/Body/InteractingGeometry D yade/src/plugins/Body/InteractionDescriptionFunctor A yade/src/plugins/Body/InteractingGeometryFunctor D yade/projects/kdevelop/plugins/Body/InteractionDescription A yade/projects/kdevelop/plugins/Body/InteractingGeometry D yade/projects/kdevelop/plugins/Body/InteractionDescriptionFunctor A yade/projects/kdevelop/plugins/Body/InteractingGeometryFunctor M yade/projects/kdevelop/plugins/Body/Body.pro M yade/projects/kdevelop/yade.kdevelop D yade/projects/kdevelop/plugins/Body/InteractingGeometry/InteractionDescription.pro A yade/projects/kdevelop/plugins/Body/InteractingGeometry/InteractingGeometry.pro D yade/projects/kdevelop/plugins/Body/InteractingGeometryFunctor/InteractionDescriptionFunctor.pro A yade/projects/kdevelop/plugins/Body/InteractingGeometryFunctor/InteractingGeometryFunctor.pro DeusExMachina /renameClassFilenames Condition DeusExMachina Condition DeusExMachina Condition DeusExMachina ./renameClassFirst InteractionSolver ConstitutiveLaw ./renameClassFilenames InteractionSolver ConstitutiveLaw InteractionSolver ConstitutiveLaw InteractionSolver ConstitutiveLaw Actor - Engine Actor - Engine BodyPhysicalParameters PhysicalParameters BodyPhysicalParameters PhysicalParameters BodyPhysicalParameters PhysicalParameters BodyPhysicalParameters PhysicalParameters ... ... ... ... ... ... ... ... A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-empty-lib A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-package D svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-empty A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-empty-package D svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-package updated todo A svn+ssh://svn.berlios.de/svnroot/repos/yade/trunk/yade-lib-serialization-contrib we have made a great yade-empty directory structure!! Olivier Galizzi (147): removing ui file from CORBA IDL section and problem with moc resolved by removing trailing slash at the end of YADEPATH moving everything into subdirectory yade (part 1) moving everything into subdirectory yade (part 2) changed README - better quick-guide renaming function collisionModelisationPhase to narrowCollisionPhase smalls changes into ContactModel, CollisionModel, Body for preparing to multimethods. Class Indexable added. Splitting collision function into dynlibs Multimethod implemented but not tested yet! Indexable class not working (can't shared_dynamic_cast Serializable to Indexable) New classes added (Factorable,Interaction,InteractionModel) Rewriting class Factorable and InteractionModel because subversion delete their content during last commit ??? Add some toolboxes (M3D,M2D,Rand,Constants) Some unused files were removed. The content of some files was again erased by an unknown reason? All serialization stuff are now into a dynlib Putting build order in the correct order Toolboxes Distances and Intersections created shared_dynamic_cast was changed to dynamic_pointer_cast Adding new class for cloth simulation. There is some mess with serialization. starting adding cloth simulation Cloth simulation is working but some stuff are dirty Cloth and spheres are working together but in a dirty way Starting adding FEMBody and renaming Cloth to MassSpringBody Putting all GUI stuff into a dynlib and new class QtGUIGenerator (that generate a qt widget from a serializable object) added Correct some little error in QtGUIGenerator subproject Changing build order Minor changes + adding boxes into RotatingBox Better tuning of rotatingBox simulation Added not working BoxStack, and createDynamicEngine script New SDECDiscreteElement and SDECDynamicEngine added New simple example for SDEC added Some minor changes in SDECDynamicEngine - but it is still not working with RotatingBox New multimethod design (moved from omega to nonconnexbody) Some include of Omega were missing in previous commit Improved detection of new and old interactions (we hope it is faster) We change the way we remember contacts from previous time step (new geometrical old physical) Added Actor so we can choose order of main loop modules. Started to add permanent links Added new ErrorTolerant classes SDECTestPermanentLink.xml is now working Added ErrorTolerant classes round 2 Added todo file, corrected examples, corrected permanents links, started to add jean patrick law Moment law is now working better but there are still some problems Moment law is now using Quaternion instead of weird modulo loop for computing dBeta (but still some problem) Moment law seems now to work or at least it is much more stable Added Translator kinematic engine Continuing ErrorTolerantDynamicEngine and added CollisionFunctor for him LCP solver using bi-conjugate gradient is implemented but is not working yet Starting moving libraries AssocVector, Frontend, IOManager to correct places added /home/evasion/galizzi/devel/yade/yade/include, libraries in correct places now modified todo, removed some junk Change all declaration of Math stuff so that it is using new template Vector3, Matrix3 ... Yade is now working with new serialization of vector ... Removed output when class are registered Added some todo stuff QtGUIGenerator is now able to (de)-serialize all fundamentals into a serializable Add QtFileGenerator, for automatic file generation with Qt GUI (not completely working yet) QtGuiGenerator and QtFileGenerator are now working Added improvements into QtGUIGenerator and QtFileGenerator All Qt libraries are now in one library. Improved version of QtGUIGenerator Removed directory QtFileGenerator and QtGUIGenerator Created new qt controller for simulation and new opengl library New SimulationController is now working Started moving simulation loop from glViewer to a specific thread Added ThreadSynchronizer. Yade is now working with external simulation loop Improved thread management. Multiple views are now working Improved GUI. Is ThreadSynchronizer really working ? Improved version of Threads library Added omitted Thread* files Changes into ThreadSynchronizer Much better version of Thread library and multithreaded QGLViewer Reenabling GUI updater thread Now we use InteractionHashMap by default because InteractionVecSet is not ready yet Added RenderingEngines Changing build order Shadow added but not working yet because of problems with stencil buffer Shadows are working but not when they overlap Changing stencil function solved the problem with overlapping shadows Better lighting parameters Faster shadow. Only 1 rendering instead of 3 and use of QUAD_STRIP Improved QtGUI Improved QtGUI some changes in shadows Improved SDECSpheresPlanes Improved fast shadow volumes Added new classes for bounding volume management (not used yet) Bounding volume are now both indexalbe and a GeometricalModel BoundingVolume update is now done into an actor Improved version of GLWindowManager library Improved GUI with (de)-serialization of RenderingEngine into SimulationController Improved version of QtGUIGenerator. Now boolean are represented by checkboxes instead of linedits Better handling of start,stop and reload simulation. Thread now terminate when associated window is closed Update in BoundingVolume updating. Now it is working for rootBody through it CollisionGeometrySet. Scene is now dynamically centered when file is loaded Changes into FileGenerator Fixed some problems with FileGenerators Boxes are now casting shadows Boxes are now casting shadows Better handling of thread into GUI. But they are still problems especially if you close the first GLWindows because it contain the GLContext where the GL lists are stored Improved stability Threads improvement Somes changes into Thread and GUI Mush better handling of threads, open/close ... it is never crashing on my laptop at least Now yade is no more segfaulting on exit Display list are now builded at each new creation of RenderingEngine Changes into threads Added createDynlib script Added Messagedialog Fix error when reloading simulation and display list are now not built several times Redesigned the way we use boost::lock Added mutex into Threadable sleep method Added changes from snippets Thread Better handling of real simulation duration Improved GUI Persistent SAPCollider is now working. Added PersistantSAPCollider files that were missing in previous revision Added script addClassToDynLib Fix crash with permanent links. Added clas InteractionPhysics Added subproject InteractionPhysics Renamed subproject InteractionModel to InterationGeometry Added into SVN repository omitted files InteractionPhysics Problem with InteractionPhysics Corrected kdevelop mistakes due to introduction of InteractionPhysics Added SDECContactPhysics and SDECPermanentLinkPhysics Fix mistake into SDECPermentLink : Some attributes were not registered Implemented InteractionPhysics and InteractionGeometry Updated todo list : Switch all possible dynamic_pointer_cast to PointedType * p = static_cast(shared_p.get()) Added Action, ActionContainer, SDECLinearContactModel, PhysicalInteractor. We started redesign to introduce Action which are the response of a DynamicEngine to an Interaction and acts on body. Adding factorable macros into Action and ActionContainer Add function add,sub and reset into Action classes. Almost finished action container. You have to call createIndex() from constructor of all Indexable class. Before adding displatcher for applying Actions. Added ActionDispatcher. Now we want to use it. Now ActionDispatcher is working. Added omitted files from previous commit. Added single step button in QtGUI Better SpheresPlanes FileGenerator Started to rename and move SimpleNarrowCollider and classes related to InteractionPhysics InteractionPhysicsDispatcher starts to works. But we have to make BodyPhysics HangingCloth is working again but it is designed using Yade framework Small changes into MassSpring so that it is faster Added BodyPhysics class and moved all type of bodies into subdirectory BodyPhysics To add BodyPhysicalParameter we have to make OpenGLDispatchers. So we started to add all of them. OpenGL continued... Stuff with BodyPhysicalParameters is compiling . Corrected some bugs due to introduction of BodyPhysicalParameters Created TimeIntegratorFunctor and Dispatcher. BallisticDynamicEngine is now LeapFrogIntegrator Corrected KinematicEngine. MassSpring cloth is now working : but we still have to update geometricalModel Added layout and scrollview to QTGUI corrected function name into Quaternion Added file yade.sxw which contain concept and spirit of yade Added tree file to rename files and directories Added some concepts into yade.sxw trunk-2017.01a/INSTALL000066400000000000000000000003461304022710500142160ustar00rootroot00000000000000Installation instructions are updating regularly. The most actual instruction can be found on the website: http://www.yade-dem.org/doc/installation.html which is generated from the following file: doc/sphinx/installation.rst trunk-2017.01a/LICENSE000066400000000000000000000432541304022710500141770ustar00rootroot00000000000000 GNU GENERAL PUBLIC LICENSE Version 2, June 1991 Copyright (C) 1989, 1991 Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. Preamble The licenses for most software are designed to take away your freedom to share and change it. By contrast, the GNU General Public License is intended to guarantee your freedom to share and change free software--to make sure the software is free for all its users. This General Public License applies to most of the Free Software Foundation's software and to any other program whose authors commit to using it. (Some other Free Software Foundation software is covered by the GNU Lesser General Public License instead.) You can apply it to your programs, too. When we speak of free software, we are referring to freedom, not price. Our General Public Licenses are designed to make sure that you have the freedom to distribute copies of free software (and charge for this service if you wish), that you receive source code or can get it if you want it, that you can change the software or use pieces of it in new free programs; and that you know you can do these things. To protect your rights, we need to make restrictions that forbid anyone to deny you these rights or to ask you to surrender the rights. These restrictions translate to certain responsibilities for you if you distribute copies of the software, or if you modify it. For example, if you distribute copies of such a program, whether gratis or for a fee, you must give the recipients all the rights that you have. You must make sure that they, too, receive or can get the source code. And you must show them these terms so they know their rights. We protect your rights with two steps: (1) copyright the software, and (2) offer you this license which gives you legal permission to copy, distribute and/or modify the software. Also, for each author's protection and ours, we want to make certain that everyone understands that there is no warranty for this free software. If the software is modified by someone else and passed on, we want its recipients to know that what they have is not the original, so that any problems introduced by others will not reflect on the original authors' reputations. Finally, any free program is threatened constantly by software patents. We wish to avoid the danger that redistributors of a free program will individually obtain patent licenses, in effect making the program proprietary. To prevent this, we have made it clear that any patent must be licensed for everyone's free use or not licensed at all. The precise terms and conditions for copying, distribution and modification follow. GNU GENERAL PUBLIC LICENSE TERMS AND CONDITIONS FOR COPYING, DISTRIBUTION AND MODIFICATION 0. This License applies to any program or other work which contains a notice placed by the copyright holder saying it may be distributed under the terms of this General Public License. The "Program", below, refers to any such program or work, and a "work based on the Program" means either the Program or any derivative work under copyright law: that is to say, a work containing the Program or a portion of it, either verbatim or with modifications and/or translated into another language. (Hereinafter, translation is included without limitation in the term "modification".) Each licensee is addressed as "you". Activities other than copying, distribution and modification are not covered by this License; they are outside its scope. The act of running the Program is not restricted, and the output from the Program is covered only if its contents constitute a work based on the Program (independent of having been made by running the Program). Whether that is true depends on what the Program does. 1. You may copy and distribute verbatim copies of the Program's source code as you receive it, in any medium, provided that you conspicuously and appropriately publish on each copy an appropriate copyright notice and disclaimer of warranty; keep intact all the notices that refer to this License and to the absence of any warranty; and give any other recipients of the Program a copy of this License along with the Program. You may charge a fee for the physical act of transferring a copy, and you may at your option offer warranty protection in exchange for a fee. 2. You may modify your copy or copies of the Program or any portion of it, thus forming a work based on the Program, and copy and distribute such modifications or work under the terms of Section 1 above, provided that you also meet all of these conditions: a) You must cause the modified files to carry prominent notices stating that you changed the files and the date of any change. b) You must cause any work that you distribute or publish, that in whole or in part contains or is derived from the Program or any part thereof, to be licensed as a whole at no charge to all third parties under the terms of this License. c) If the modified program normally reads commands interactively when run, you must cause it, when started running for such interactive use in the most ordinary way, to print or display an announcement including an appropriate copyright notice and a notice that there is no warranty (or else, saying that you provide a warranty) and that users may redistribute the program under these conditions, and telling the user how to view a copy of this License. (Exception: if the Program itself is interactive but does not normally print such an announcement, your work based on the Program is not required to print an announcement.) These requirements apply to the modified work as a whole. If identifiable sections of that work are not derived from the Program, and can be reasonably considered independent and separate works in themselves, then this License, and its terms, do not apply to those sections when you distribute them as separate works. But when you distribute the same sections as part of a whole which is a work based on the Program, the distribution of the whole must be on the terms of this License, whose permissions for other licensees extend to the entire whole, and thus to each and every part regardless of who wrote it. Thus, it is not the intent of this section to claim rights or contest your rights to work written entirely by you; rather, the intent is to exercise the right to control the distribution of derivative or collective works based on the Program. In addition, mere aggregation of another work not based on the Program with the Program (or with a work based on the Program) on a volume of a storage or distribution medium does not bring the other work under the scope of this License. 3. You may copy and distribute the Program (or a work based on it, under Section 2) in object code or executable form under the terms of Sections 1 and 2 above provided that you also do one of the following: a) Accompany it with the complete corresponding machine-readable source code, which must be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, b) Accompany it with a written offer, valid for at least three years, to give any third party, for a charge no more than your cost of physically performing source distribution, a complete machine-readable copy of the corresponding source code, to be distributed under the terms of Sections 1 and 2 above on a medium customarily used for software interchange; or, c) Accompany it with the information you received as to the offer to distribute corresponding source code. (This alternative is allowed only for noncommercial distribution and only if you received the program in object code or executable form with such an offer, in accord with Subsection b above.) The source code for a work means the preferred form of the work for making modifications to it. For an executable work, complete source code means all the source code for all modules it contains, plus any associated interface definition files, plus the scripts used to control compilation and installation of the executable. However, as a special exception, the source code distributed need not include anything that is normally distributed (in either source or binary form) with the major components (compiler, kernel, and so on) of the operating system on which the executable runs, unless that component itself accompanies the executable. If distribution of executable or object code is made by offering access to copy from a designated place, then offering equivalent access to copy the source code from the same place counts as distribution of the source code, even though third parties are not compelled to copy the source along with the object code. 4. You may not copy, modify, sublicense, or distribute the Program except as expressly provided under this License. Any attempt otherwise to copy, modify, sublicense or distribute the Program is void, and will automatically terminate your rights under this License. However, parties who have received copies, or rights, from you under this License will not have their licenses terminated so long as such parties remain in full compliance. 5. You are not required to accept this License, since you have not signed it. However, nothing else grants you permission to modify or distribute the Program or its derivative works. These actions are prohibited by law if you do not accept this License. Therefore, by modifying or distributing the Program (or any work based on the Program), you indicate your acceptance of this License to do so, and all its terms and conditions for copying, distributing or modifying the Program or works based on it. 6. Each time you redistribute the Program (or any work based on the Program), the recipient automatically receives a license from the original licensor to copy, distribute or modify the Program subject to these terms and conditions. You may not impose any further restrictions on the recipients' exercise of the rights granted herein. You are not responsible for enforcing compliance by third parties to this License. 7. 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If the distribution and/or use of the Program is restricted in certain countries either by patents or by copyrighted interfaces, the original copyright holder who places the Program under this License may add an explicit geographical distribution limitation excluding those countries, so that distribution is permitted only in or among countries not thus excluded. In such case, this License incorporates the limitation as if written in the body of this License. 9. The Free Software Foundation may publish revised and/or new versions of the General Public License from time to time. Such new versions will be similar in spirit to the present version, but may differ in detail to address new problems or concerns. Each version is given a distinguishing version number. If the Program specifies a version number of this License which applies to it and "any later version", you have the option of following the terms and conditions either of that version or of any later version published by the Free Software Foundation. If the Program does not specify a version number of this License, you may choose any version ever published by the Free Software Foundation. 10. If you wish to incorporate parts of the Program into other free programs whose distribution conditions are different, write to the author to ask for permission. For software which is copyrighted by the Free Software Foundation, write to the Free Software Foundation; we sometimes make exceptions for this. Our decision will be guided by the two goals of preserving the free status of all derivatives of our free software and of promoting the sharing and reuse of software generally. NO WARRANTY 11. BECAUSE THE PROGRAM IS LICENSED FREE OF CHARGE, THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF ALL NECESSARY SERVICING, REPAIR OR CORRECTION. 12. IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MAY MODIFY AND/OR REDISTRIBUTE THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS), EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF SUCH DAMAGES. END OF TERMS AND CONDITIONS How to Apply These Terms to Your New Programs If you develop a new program, and you want it to be of the greatest possible use to the public, the best way to achieve this is to make it free software which everyone can redistribute and change under these terms. To do so, attach the following notices to the program. It is safest to attach them to the start of each source file to most effectively convey the exclusion of warranty; and each file should have at least the "copyright" line and a pointer to where the full notice is found. Copyright (C) This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA. Also add information on how to contact you by electronic and paper mail. If the program is interactive, make it output a short notice like this when it starts in an interactive mode: Gnomovision version 69, Copyright (C) year name of author Gnomovision comes with ABSOLUTELY NO WARRANTY; for details type `show w'. This is free software, and you are welcome to redistribute it under certain conditions; type `show c' for details. The hypothetical commands `show w' and `show c' should show the appropriate parts of the General Public License. Of course, the commands you use may be called something other than `show w' and `show c'; they could even be mouse-clicks or menu items--whatever suits your program. You should also get your employer (if you work as a programmer) or your school, if any, to sign a "copyright disclaimer" for the program, if necessary. Here is a sample; alter the names: Yoyodyne, Inc., hereby disclaims all copyright interest in the program `Gnomovision' (which makes passes at compilers) written by James Hacker. , 1 April 1989 Ty Coon, President of Vice This General Public License does not permit incorporating your program into proprietary programs. If your program is a subroutine library, you may consider it more useful to permit linking proprietary applications with the library. If this is what you want to do, use the GNU Lesser General Public License instead of this License. trunk-2017.01a/README.rst000066400000000000000000000032621304022710500146540ustar00rootroot00000000000000=================================== YADE - Yet Another Dynamic Engine =================================== Extensible open-source framework for discrete numerical models, focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, allowing independent implementation of new algorithms and interfaces. Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging. **Documentation:** - https://www.yade-dem.org/doc/ (includes c++ and python reference) - https://yade-dem.org/doc/Yade.pdf (PDF-file with documentation) - https://yade-dem.org/doc/Yade.epub (EPUB-file with documentation) **Downloads:** - Packages for Ubuntu and Debian: - https://yade-dem.org/doc/installation.html#packages - External packages: https://launchpad.net/~yade-users/+archive/external - Tarballs of different versions: - https://github.com/yade/trunk/tags - Repository on github.com: https://github.com/yade - Repository on git.debian.org: http://git.debian.org/?p=debian-science/packages/yade.git **Teams involved:** - General users: https://launchpad.net/~yade-users - Developers and advanced users: https://launchpad.net/~yade-dev - Infrastructure maintainers: https://launchpad.net/~yade-pkg **Miscellaneous:** - `Yade buildbot `_ - `Yade page on ohloh-project `_ - `Yade on Debian PTS `_ - `Yade in Ubuntu `_ - `Home page `_ - `Wiki `_ - `Screenshots `_ trunk-2017.01a/RELEASE000066400000000000000000000000111304022710500141550ustar00rootroot000000000000002017.01a trunk-2017.01a/cMake/000077500000000000000000000000001304022710500142025ustar00rootroot00000000000000trunk-2017.01a/cMake/CombineSources.cmake000066400000000000000000000017411304022710500201270ustar00rootroot00000000000000# include several source files (in SRCS) in one or more # combined files; each combined file holds maximally # MAXNUM files. # BASE gives basename for created files; # files corresponding to the pattern are deleted # first, so that there are no relicts from previous runs # with possibly different MAXNUM MACRO(COMBINE_SOURCES BASE SRCS MAXNUM) LIST(LENGTH SRCS SRCS_LENGTH) SET(COMB_COUNTER 0) FILE(GLOB EXISTING "${BASE}.*.cpp") IF("$EXISTING") FILE(REMOVE ${EXISTING}) ENDIF() SET(OUT "${BASE}.${COMB_COUNTER}.cpp") FILE(WRITE ${OUT}) SET(COUNTER 0) FOREACH(SRC ${SRCS}) if(${SRC} MATCHES "^/.*$") # absolute filename FILE(APPEND ${OUT} "#include<${SRC}>\n") else() FILE(APPEND ${OUT} "#include<${CMAKE_SOURCE_DIR}/${SRC}>\n") endif() MATH(EXPR COUNTER "${COUNTER}+1") IF(${COUNTER} EQUAL ${MAXNUM}) SET(COUNTER 0) MATH(EXPR COMB_COUNTER ${COMB_COUNTER}+1) SET(OUT "${BASE}.${COMB_COUNTER}.cpp") FILE(WRITE ${OUT}) ENDIF() ENDFOREACH() ENDMACRO() trunk-2017.01a/cMake/FindCGAL.cmake000066400000000000000000000026751304022710500165250ustar00rootroot00000000000000# http://code.google.com/p/pixelstruct/source/browse/trunk/cmake/FindCGAL.cmake?r=29 # # - Find CGAL # adapted from # # Find the CGAL includes and client library # This module defines # CGAL_DEFINITIONS: compiler flags for compiling with CGAL # CGAL_INCLUDE_DIR: where to find CGAL.h # CGAL_LIBRARIES: the libraries needed to use CGAL # CGAL_FOUND: if false, do not try to use CGAL IF(CGAL_INCLUDE_DIR AND CGAL_LIBRARIES) SET(CGAL_FOUND TRUE) ELSE(CGAL_INCLUDE_DIR AND CGAL_LIBRARIES) FIND_PATH(CGAL_INCLUDE_DIR basic.h /usr/include/CGAL /usr/local/include/CGAL $ENV{ProgramFiles}/CGAL/*/include/CGAL $ENV{SystemDrive}/CGAL/*/include/CGAL ) FIND_LIBRARY(CGAL_LIBRARIES NAMES CGAL libCGAL PATHS /usr/lib /usr/local/lib /usr/lib/CGAL /usr/lib64 /usr/local/lib64 /usr/lib64/CGAL $ENV{ProgramFiles}/CGAL/*/lib/ms $ENV{SystemDrive}/CGAL/*/lib/ms ) IF(CGAL_INCLUDE_DIR AND CGAL_LIBRARIES) SET(CGAL_FOUND TRUE) MESSAGE(STATUS "Found CGAL: ${CGAL_INCLUDE_DIR}, ${CGAL_LIBRARIES}") ELSE(CGAL_INCLUDE_DIR AND CGAL_LIBRARIES) SET(CGAL_FOUND FALSE) MESSAGE(STATUS "CGAL not found.") ENDIF(CGAL_INCLUDE_DIR AND CGAL_LIBRARIES) MARK_AS_ADVANCED(CGAL_INCLUDE_DIR CGAL_LIBRARIES) ENDIF(CGAL_INCLUDE_DIR AND CGAL_LIBRARIES) trunk-2017.01a/cMake/FindCLP.cmake000077500000000000000000000024601304022710500164300ustar00rootroot00000000000000IF(CLP_INCLUDE_DIR AND CLP2_INCLUDE_DIR AND CLP_LIBRARY AND CLP2_LIBRARY AND CLP3_LIBRARY) SET(CLP_FOUND TRUE) ELSE(CLP_INCLUDE_DIR AND CLP2_INCLUDE_DIR AND CLP_LIBRARY AND CLP2_LIBRARY AND CLP3_LIBRARY) FIND_LIBRARY(CLP_LIBRARY NAMES Clp PATHS /usr/lib/x86_64-linux-gnu ) FIND_LIBRARY(CLP2_LIBRARY NAMES OsiClp PATHS /usr/lib/x86_64-linux-gnu ) FIND_LIBRARY(CLP3_LIBRARY NAMES CoinUtils PATHS /usr/lib/x86_64-linux-gnu ) FIND_PATH( CLP_INCLUDE_DIR ClpSimplexDual.hpp PATHS /usr/include/coin ) FIND_PATH( CLP2_INCLUDE_DIR coinutils.pc PATHS /usr/lib/x86_64-linux-gnu/pkgconfig ) IF(CLP_INCLUDE_DIR AND CLP2_INCLUDE_DIR AND CLP_LIBRARY AND CLP2_LIBRARY AND CLP3_LIBRARY) SET(CLP_FOUND TRUE) MESSAGE(STATUS "Found CLP: ${CLP_INCLUDE_DIR}, ${CLP_LIBRARY}") ELSE(CLP_INCLUDE_DIR AND CLP2_INCLUDE_DIR AND CLP_LIBRARY AND CLP2_LIBRARY AND CLP3_LIBRARY) SET(CLP_FOUND FALSE) MESSAGE(STATUS "CLP not found.") ENDIF(CLP_INCLUDE_DIR AND CLP2_INCLUDE_DIR AND CLP_LIBRARY AND CLP2_LIBRARY AND CLP3_LIBRARY) MARK_AS_ADVANCED(CLP_INCLUDE_DIR CLP2_INCLUDE_DIR CLP_LIBRARY CLP2_LIBRARY CLP3_LIBRARY) ENDIF(CLP_INCLUDE_DIR AND CLP2_INCLUDE_DIR AND CLP_LIBRARY AND CLP2_LIBRARY AND CLP3_LIBRARY) trunk-2017.01a/cMake/FindCholmod.cmake000066400000000000000000000027411304022710500173760ustar00rootroot00000000000000# - Try to find CHOLMOD # This will define # # CHOLMOD_FOUND - system has CHOLMOD # CHOLMOD_LIBRARIES - library to link against to use Cholmod # CHOLMOD_INCLUDE_DIR - where to find cholmod.h, etc. # AMD_LIBRARY - needed by CHOLMOD # COLAMD_LIBRARY - needed by CHOLMOD # CCOLAMD_LIBRARY - needed by CHOLMOD # CAMD_LIBRARY - needed by CHOLMOD FIND_LIBRARY(CHOLMOD_LIBRARIES NAMES cholmod libcholmod PATHS /usr/lib /usr/local/lib /usr/lib/CGAL /usr/lib64 /usr/local/lib64 /usr/lib64/CGAL ) FIND_LIBRARY(AMD_LIBRARY NAMES amd PATHS /usr/lib /usr/local/lib /usr/lib/CGAL /usr/lib64 /usr/local/lib64 /usr/lib64/CGAL) FIND_LIBRARY(CAMD_LIBRARY NAMES camd PATHS /usr/lib /usr/local/lib /usr/lib/CGAL /usr/lib64 /usr/local/lib64 /usr/lib64/CGAL) FIND_LIBRARY(COLAMD_LIBRARY NAMES colamd PATHS /usr/lib /usr/local/lib /usr/lib/CGAL /usr/lib64 /usr/local/lib64 /usr/lib64/CGAL) FIND_LIBRARY(CCOLAMD_LIBRARY NAMES ccolamd PATHS /usr/lib /usr/local/lib /usr/lib/CGAL /usr/lib64 /usr/local/lib64 /usr/lib64/CGAL) FIND_PATH(CHOLMOD_INCLUDE_DIR cholmod.h PATH /usr/include /usr/include/suitesparse) INCLUDE(FindPackageHandleStandardArgs) FIND_PACKAGE_HANDLE_STANDARD_ARGS(Cholmod DEFAULT_MSG CHOLMOD_LIBRARIES CHOLMOD_INCLUDE_DIR AMD_LIBRARY CAMD_LIBRARY COLAMD_LIBRARY CCOLAMD_LIBRARY) MARK_AS_ADVANCED(CHOLMOD_LIBRARIES CHOLMOD_INCLUDE_DIR AMD_LIBRARY CAMD_LIBRARY COLAMD_LIBRARY CCOLAMD_LIBRARY) trunk-2017.01a/cMake/FindEigen3.cmake000066400000000000000000000056621304022710500171300ustar00rootroot00000000000000# - Try to find Eigen3 lib # # This module supports requiring a minimum version, e.g. you can do # find_package(Eigen3 3.1.2) # to require version 3.1.2 or newer of Eigen3. # # Once done this will define # # EIGEN3_FOUND - system has eigen lib with correct version # EIGEN3_INCLUDE_DIR - the eigen include directory # EIGEN3_VERSION - eigen version # Copyright (c) 2006, 2007 Montel Laurent, # Copyright (c) 2008, 2009 Gael Guennebaud, # Copyright (c) 2009 Benoit Jacob # Redistribution and use is allowed according to the terms of the 2-clause BSD license. if(NOT Eigen3_FIND_VERSION) if(NOT Eigen3_FIND_VERSION_MAJOR) set(Eigen3_FIND_VERSION_MAJOR 2) endif(NOT Eigen3_FIND_VERSION_MAJOR) if(NOT Eigen3_FIND_VERSION_MINOR) set(Eigen3_FIND_VERSION_MINOR 91) endif(NOT Eigen3_FIND_VERSION_MINOR) if(NOT Eigen3_FIND_VERSION_PATCH) set(Eigen3_FIND_VERSION_PATCH 0) endif(NOT Eigen3_FIND_VERSION_PATCH) set(Eigen3_FIND_VERSION "${Eigen3_FIND_VERSION_MAJOR}.${Eigen3_FIND_VERSION_MINOR}.${Eigen3_FIND_VERSION_PATCH}") endif(NOT Eigen3_FIND_VERSION) macro(_eigen3_check_version) file(READ "${EIGEN3_INCLUDE_DIR}/Eigen/src/Core/util/Macros.h" _eigen3_version_header) string(REGEX MATCH "define[ \t]+EIGEN_WORLD_VERSION[ \t]+([0-9]+)" _eigen3_world_version_match "${_eigen3_version_header}") set(EIGEN3_WORLD_VERSION "${CMAKE_MATCH_1}") string(REGEX MATCH "define[ \t]+EIGEN_MAJOR_VERSION[ \t]+([0-9]+)" _eigen3_major_version_match "${_eigen3_version_header}") set(EIGEN3_MAJOR_VERSION "${CMAKE_MATCH_1}") string(REGEX MATCH "define[ \t]+EIGEN_MINOR_VERSION[ \t]+([0-9]+)" _eigen3_minor_version_match "${_eigen3_version_header}") set(EIGEN3_MINOR_VERSION "${CMAKE_MATCH_1}") set(EIGEN3_VERSION ${EIGEN3_WORLD_VERSION}.${EIGEN3_MAJOR_VERSION}.${EIGEN3_MINOR_VERSION}) if(${EIGEN3_VERSION} VERSION_LESS ${Eigen3_FIND_VERSION}) set(EIGEN3_VERSION_OK FALSE) else(${EIGEN3_VERSION} VERSION_LESS ${Eigen3_FIND_VERSION}) set(EIGEN3_VERSION_OK TRUE) endif(${EIGEN3_VERSION} VERSION_LESS ${Eigen3_FIND_VERSION}) if(NOT EIGEN3_VERSION_OK) message(STATUS "Eigen3 version ${EIGEN3_VERSION} found in ${EIGEN3_INCLUDE_DIR}, " "but at least version ${Eigen3_FIND_VERSION} is required") endif(NOT EIGEN3_VERSION_OK) endmacro(_eigen3_check_version) if (EIGEN3_INCLUDE_DIR) # in cache already _eigen3_check_version() set(EIGEN3_FOUND ${EIGEN3_VERSION_OK}) else (EIGEN3_INCLUDE_DIR) find_path(EIGEN3_INCLUDE_DIR NAMES signature_of_eigen3_matrix_library PATHS ${CMAKE_INSTALL_PREFIX}/include ${KDE4_INCLUDE_DIR} PATH_SUFFIXES eigen3 eigen ) if(EIGEN3_INCLUDE_DIR) _eigen3_check_version() endif(EIGEN3_INCLUDE_DIR) include(FindPackageHandleStandardArgs) find_package_handle_standard_args(Eigen3 DEFAULT_MSG EIGEN3_INCLUDE_DIR EIGEN3_VERSION_OK) mark_as_advanced(EIGEN3_INCLUDE_DIR) endif(EIGEN3_INCLUDE_DIR) trunk-2017.01a/cMake/FindGL2PS.cmake000066400000000000000000000030501304022710500166320ustar00rootroot00000000000000# https://unihub.ru/tools/ofservice/browser/trunk/1.7/ThirdParty-1.7.1/paraview-3.8.0/VTK/CMake/FindGL2PS.cmake?rev=2 # - Find GL2PS library # Find the native GL2PS includes and library # This module defines # GL2PS_INCLUDE_DIR, where to find tiff.h, etc. # GL2PS_LIBRARIES, libraries to link against to use GL2PS. # GL2PS_FOUND, If false, do not try to use GL2PS. # also defined, but not for general use are # GL2PS_LIBRARY, where to find the GL2PS library. #============================================================================= # Copyright 2009 Kitware, Inc. # Copyright 2009 Mathieu Malaterre # # Distributed under the OSI-approved BSD License (the "License"); # see accompanying file Copyright.txt for details. # # This software is distributed WITHOUT ANY WARRANTY; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. # See the License for more information. #============================================================================= # (To distributed this file outside of CMake, substitute the full # License text for the above reference.) FIND_PATH(GL2PS_INCLUDE_DIR gl2ps.h) FIND_LIBRARY(GL2PS_LIBRARY NAMES gl2ps ) # handle the QUIETLY and REQUIRED arguments and set GL2PS_FOUND to TRUE if # all listed variables are TRUE INCLUDE(FindPackageHandleStandardArgs) FIND_PACKAGE_HANDLE_STANDARD_ARGS(GL2PS DEFAULT_MSG GL2PS_LIBRARY GL2PS_INCLUDE_DIR) IF(GL2PS_FOUND) SET( GL2PS_LIBRARIES ${GL2PS_LIBRARY} ) ENDIF(GL2PS_FOUND) MARK_AS_ADVANCED(GL2PS_INCLUDE_DIR GL2PS_LIBRARY) trunk-2017.01a/cMake/FindGMP.cmake000066400000000000000000000016201304022710500164270ustar00rootroot00000000000000# http://liris.cnrs.fr/dgtal/cgi-bin/trac.cgi/browser/trunk/cmake/FindGMP.cmake # # Try to find the GMP librairies # GMP_FOUND - system has GMP lib # GMP_INCLUDE_DIR - the GMP include directory # GMP_LIBRARIES - Libraries needed to use GMP # Copyright (c) 2006, Laurent Montel, # # Redistribution and use is allowed according to the terms of the BSD license. # For details see the accompanying COPYING-CMAKE-SCRIPTS file. if (GMP_INCLUDE_DIR AND GMP_LIBRARIES) # Already in cache, be silent set(GMP_FIND_QUIETLY TRUE) endif (GMP_INCLUDE_DIR AND GMP_LIBRARIES) find_path(GMP_INCLUDE_DIR NAMES gmp.h ) find_library(GMP_LIBRARIES NAMES gmp libgmp ) find_library(GMPXX_LIBRARIES NAMES gmpxx libgmpxx ) MESSAGE(STATUS "GMP libs: " ${GMP_LIBRARIES} " " ${GMPXX_LIBRARIES} ) include(FindPackageHandleStandardArgs) FIND_PACKAGE_HANDLE_STANDARD_ARGS(GMP DEFAULT_MSG GMP_INCLUDE_DIR GMP_LIBRARIES) trunk-2017.01a/cMake/FindGMPXX.cmake000066400000000000000000000016311304022710500167110ustar00rootroot00000000000000# https://svn.zib.de/lenne3d/lib/qpl_cgal/3.5.1/cmake/modules/FindGMPXX.cmake # # Try to find the GMPXX libraries # GMPXX_FOUND - system has GMPXX lib # GMPXX_INCLUDE_DIR - the GMPXX include directory # GMPXX_LIBRARIES - Libraries needed to use GMPXX # TODO: support Windows and MacOSX # GMPXX needs GMP find_package( GMP QUIET ) if(GMP_FOUND) if (GMPXX_INCLUDE_DIR AND GMPXX_LIBRARIES) # Already in cache, be silent set(GMPXX_FIND_QUIETLY TRUE) endif() find_path(GMPXX_INCLUDE_DIR NAMES gmpxx.h PATHS ${GMP_INCLUDE_DIR_SEARCH} DOC "The directory containing the GMPXX include files" ) find_library(GMPXX_LIBRARIES NAMES gmpxx PATHS ${GMP_LIBRARIES_DIR_SEARCH} DOC "Path to the GMPXX library" ) find_package_handle_standard_args(GMPXX "DEFAULT_MSG" GMPXX_LIBRARIES GMPXX_INCLUDE_DIR ) endif() trunk-2017.01a/cMake/FindGTS.cmake000066400000000000000000000125511304022710500164460ustar00rootroot00000000000000# http://code.google.com/p/booststl/source/browse/trunk/Modules/FindGTS.cmake?r=25 # Try to find gnu triangulation library GTS # See # http://gts.sf.net # # Once run this will define: # # GTS_FOUND = system has GTS lib # # GTS_LIBRARIES = full path to the libraries # on Unix/Linux with additional linker flags from "gts-config --libs" # # CMAKE_GTS_CXX_FLAGS = Unix compiler flags for GTS, essentially "`gts-config --cxxflags`" # # GTS_INCLUDE_DIR = where to find headers # # GTS_LINK_DIRECTORIES = link directories, useful for rpath on Unix # GTS_EXE_LINKER_FLAGS = rpath on Unix # # # GTS modyfication by # A.Khalatyan 05/2009 # # www.aip.de/~arm2arm # # This script is based on GSL script by # Felix Woelk 07/2004 # and Jan Woetzel # www.mip.informatik.uni-kiel.de # -------------------------------- IF(WIN32) # JW tested with gsl-1.8, Windows XP, MSVS 7.1, MSVS 8.0 SET(GTS_POSSIBLE_ROOT_DIRS ${GTS_ROOT_DIR} $ENV{GTS_ROOT_DIR} ${GTS_DIR} ${GTS_HOME} $ENV{GTS_DIR} $ENV{GTS_HOME} $ENV{EXTERN_LIBS_DIR}/gts $ENV{EXTRA} # "C:/home/arm2arm/SOFTWARE/gts-0.7.6" ) FIND_PATH(GTS_INCLUDE_DIR NAMES gts.h gtsconfig.h PATHS ${GTS_POSSIBLE_ROOT_DIRS} PATH_SUFFIXES include DOC "GTS header include dir" ) FIND_LIBRARY(GTS_GTS_LIBRARY NAMES gts libgts PATHS ${GTS_POSSIBLE_ROOT_DIRS} PATH_SUFFIXES lib DOC "GTS library dir" ) # FIND_LIBRARY(GTS_GLIB_LIBRARY # NAMES glib libgslcblas # PATHS ${GSL_POSSIBLE_ROOT_DIRS} # PATH_SUFFIXES lib # DOC "GSL cblas library dir" ) SET(GTS_LIBRARIES ${GTS_GTS_LIBRARY}) #MESSAGE("DBG\n" # "GSL_GSL_LIBRARY=${GSL_GSL_LIBRARY}\n" # "GSL_GSLCBLAS_LIBRARY=${GSL_GSLCBLAS_LIBRARY}\n" # "GSL_LIBRARIES=${GSL_LIBRARIES}") ELSE(WIN32) IF(UNIX) SET(GSL_CONFIG_PREFER_PATH "$ENV{GTS_DIR}/bin" "$ENV{GTS_DIR}" "$ENV{GTS_HOME}/bin" "$ENV{GTS_HOME}" CACHE STRING "preferred path to GTS (gts-config)") FIND_PROGRAM(GTS_CONFIG gts-config ${GTS_CONFIG_PREFER_PATH} /work2/arm2arm/SOFTWARE/bin/ ) #MESSAGE("DBG GTS_CONFIG ${GTS_CONFIG}") IF (GTS_CONFIG) MESSAGE(STATUS "GTS using gts-config ${GTS_CONFIG}") # set CXXFLAGS to be fed into CXX_FLAGS by the user: EXEC_PROGRAM(${GTS_CONFIG} ARGS --cflags OUTPUT_VARIABLE GTS_CXX_FLAGS ) #SET(GTS_CXX_FLAGS "`${GTS_CONFIG} --cflags`") SET(CMAKE_GTS_CXX_FLAGS ${GTS_CXX_FLAGS}) # MESSAGE("DBG ${GTS_CXX_FLAGS}") # set INCLUDE_DIRS to prefix+include EXEC_PROGRAM(${GTS_CONFIG} ARGS --prefix OUTPUT_VARIABLE GTS_PREFIX) SET(GTS_INCLUDE_DIR ${GTS_PREFIX}/include CACHE STRING INTERNAL) # set link libraries and link flags #SET(GSL_LIBRARIES "`${GSL_CONFIG} --libs`") # extract link dirs for rpath EXEC_PROGRAM(${GTS_CONFIG} ARGS --libs OUTPUT_VARIABLE GTS_CONFIG_LIBS ) SET(GTS_LIBRARIES "${GTS_CONFIG_LIBS}") # split off the link dirs (for rpath) # use regular expression to match wildcard equivalent "-L*" # with is a space or a semicolon STRING(REGEX MATCHALL "[-][L]([^ ;])+" GTS_LINK_DIRECTORIES_WITH_PREFIX "${GTS_CONFIG_LIBS}" ) # MESSAGE("DBG GSL_LINK_DIRECTORIES_WITH_PREFIX=${GSL_LINK_DIRECTORIES_WITH_PREFIX}") # remove prefix -L because we need the pure directory for LINK_DIRECTORIES IF (GTS_LINK_DIRECTORIES_WITH_PREFIX) STRING(REGEX REPLACE "[-][L]" "" GTS_LINK_DIRECTORIES ${GTS_LINK_DIRECTORIES_WITH_PREFIX} ) ENDIF (GTS_LINK_DIRECTORIES_WITH_PREFIX) SET(GTS_EXE_LINKER_FLAGS "-Wl,-rpath,${GTS_LINK_DIRECTORIES}" CACHE STRING INTERNAL) # MESSAGE("DBG GSL_LINK_DIRECTORIES=${GSL_LINK_DIRECTORIES}") # MESSAGE("DBG GSL_EXE_LINKER_FLAGS=${GSL_EXE_LINKER_FLAGS}") # ADD_DEFINITIONS("-DHAVE_GSL") # SET(GSL_DEFINITIONS "-DHAVE_GSL") MARK_AS_ADVANCED( GTS_CXX_FLAGS GTS_INCLUDE_DIR GTS_LIBRARIES GTS_LINK_DIRECTORIES GTS_DEFINITIONS ) MESSAGE(STATUS "Using GTS from ${GTS_PREFIX}") ELSE(GTS_CONFIG) INCLUDE(UsePkgConfig) #needed for PKGCONFIG(...) MESSAGE(STATUS "GSL using pkgconfig") # PKGCONFIG(gsl includedir libdir linkflags cflags) PKGCONFIG(gts GTS_INCLUDE_DIR GTS_LINK_DIRECTORIES GTS_LIBRARIES GTS_CXX_FLAGS) IF(GTS_INCLUDE_DIR) MARK_AS_ADVANCED( GTS_CXX_FLAGS GTS_INCLUDE_DIR GTS_LIBRARIES GTS_LINK_DIRECTORIES ) ELSE(GTS_INCLUDE_DIR) MESSAGE("FindGTS.cmake: gts-config/pkg-config gts not found. Please set it manually. GTS_CONFIG=${GTS_CONFIG}") ENDIF(GTS_INCLUDE_DIR) ENDIF(GTS_CONFIG) ENDIF(UNIX) ENDIF(WIN32) IF(GTS_LIBRARIES) IF(GTS_INCLUDE_DIR OR GTS_CXX_FLAGS) SET(GTS_FOUND 1) ENDIF(GTS_INCLUDE_DIR OR GTS_CXX_FLAGS) ENDIF(GTS_LIBRARIES) # ========================================== IF(NOT GTS_FOUND) # make FIND_PACKAGE friendly IF(NOT GTS_FIND_QUIETLY) IF(GTS_FIND_REQUIRED) MESSAGE(FATAL_ERROR "GTS required, please specify it's location.") ELSE(GTS_FIND_REQUIRED) MESSAGE(STATUS "ERROR: GTS was not found.") ENDIF(GTS_FIND_REQUIRED) ENDIF(NOT GTS_FIND_QUIETLY) ENDIF(NOT GTS_FOUND) trunk-2017.01a/cMake/FindLoki.cmake000066400000000000000000000010761304022710500167070ustar00rootroot00000000000000# - Find Loki library # # This module defines # LOKI_INCLUDE_DIR, where to find loki/Typelist.h, etc. # LOKI_LIBRARY, libraries to link against to use GL2PS. # LOKI_FOUND, If false, do not try to use GL2PS. FIND_PATH(LOKI_INCLUDE_DIR loki/Typelist.h) FIND_LIBRARY(LOKI_LIBRARY NAMES loki ) # handle the QUIETLY and REQUIRED arguments and set LOKI_FOUND to TRUE if # all listed variables are TRUE INCLUDE(FindPackageHandleStandardArgs) FIND_PACKAGE_HANDLE_STANDARD_ARGS(Loki DEFAULT_MSG LOKI_INCLUDE_DIR LOKI_LIBRARY) MARK_AS_ADVANCED(LOKI_INCLUDE_DIR LOKI_LIBRARY) trunk-2017.01a/cMake/FindMetis.cmake000066400000000000000000000011621304022710500170660ustar00rootroot00000000000000# - Find Metis library # # This module defines # METIS_INCLUDE_DIR, where to find loki/Typelist.h, etc. # METIS_LIBRARY, libraries to link against to use GL2PS. # METIS_FOUND, If false, do not try to use GL2PS. FIND_PATH(METIS_INCLUDE_DIR metis.h PATHS /usr/include/metis) FIND_LIBRARY(METIS_LIBRARY NAMES metis parmetis PATHS /usr/lib) # handle the QUIETLY and REQUIRED arguments and set LOKI_FOUND to TRUE if # all listed variables are TRUE INCLUDE(FindPackageHandleStandardArgs) FIND_PACKAGE_HANDLE_STANDARD_ARGS(Metis DEFAULT_MSG METIS_INCLUDE_DIR METIS_LIBRARY) MARK_AS_ADVANCED(METIS_INCLUDE_DIR METIS_LIBRARY) trunk-2017.01a/cMake/FindNumPy.cmake000066400000000000000000000072411304022710500170610ustar00rootroot00000000000000# https://github.com/ContinuumIO/dynd-python/blob/master/FindNumPy.cmake # - Find the NumPy libraries # This module finds if NumPy is installed, and sets the following variables # indicating where it is. # # TODO: Update to provide the libraries and paths for linking npymath lib. # # NUMPY_FOUND - was NumPy found # NUMPY_VERSION - the version of NumPy found as a string # NUMPY_VERSION_MAJOR - the major version number of NumPy # NUMPY_VERSION_MINOR - the minor version number of NumPy # NUMPY_VERSION_PATCH - the patch version number of NumPy # NUMPY_VERSION_DECIMAL - e.g. version 1.6.1 is 10601 # NUMPY_INCLUDE_DIRS - path to the NumPy include files #============================================================================ # Copyright 2012 Continuum Analytics, Inc. # # MIT License # # Permission is hereby granted, free of charge, to any person obtaining # a copy of this software and associated documentation files # (the "Software"), to deal in the Software without restriction, including # without limitation the rights to use, copy, modify, merge, publish, # distribute, sublicense, and/or sell copies of the Software, and to permit # persons to whom the Software is furnished to do so, subject to # the following conditions: # # The above copyright notice and this permission notice shall be included # in all copies or substantial portions of the Software. # # THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS # OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, # FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL # THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR # OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, # ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR # OTHER DEALINGS IN THE SOFTWARE. # #============================================================================ # Finding NumPy involves calling the Python interpreter if(NumPy_FIND_REQUIRED) find_package(PythonInterp REQUIRED) else() find_package(PythonInterp) endif() if(NOT PYTHONINTERP_FOUND) set(NUMPY_FOUND FALSE) return() endif() execute_process(COMMAND "${PYTHON_EXECUTABLE}" "-c" "import numpy as n; print(n.__version__); print(n.get_include());" RESULT_VARIABLE _NUMPY_SEARCH_SUCCESS OUTPUT_VARIABLE _NUMPY_VALUES ERROR_VARIABLE _NUMPY_ERROR_VALUE OUTPUT_STRIP_TRAILING_WHITESPACE) if(NOT _NUMPY_SEARCH_SUCCESS MATCHES 0) if(NumPy_FIND_REQUIRED) message(FATAL_ERROR "NumPy import failure:\n${_NUMPY_ERROR_VALUE}") endif() set(NUMPY_FOUND FALSE) return() endif() # Convert the process output into a list string(REGEX REPLACE ";" "\\\\;" _NUMPY_VALUES ${_NUMPY_VALUES}) string(REGEX REPLACE "\n" ";" _NUMPY_VALUES ${_NUMPY_VALUES}) list(GET _NUMPY_VALUES 0 NUMPY_VERSION) list(GET _NUMPY_VALUES 1 NUMPY_INCLUDE_DIRS) # Make sure all directory separators are '/' string(REGEX REPLACE "\\\\" "/" NUMPY_INCLUDE_DIRS ${NUMPY_INCLUDE_DIRS}) # Get the major and minor version numbers string(REGEX REPLACE "\\." ";" _NUMPY_VERSION_LIST ${NUMPY_VERSION}) list(GET _NUMPY_VERSION_LIST 0 NUMPY_VERSION_MAJOR) list(GET _NUMPY_VERSION_LIST 1 NUMPY_VERSION_MINOR) list(GET _NUMPY_VERSION_LIST 2 NUMPY_VERSION_PATCH) string(REGEX MATCH "[0-9]*" NUMPY_VERSION_PATCH ${NUMPY_VERSION_PATCH}) math(EXPR NUMPY_VERSION_DECIMAL "(${NUMPY_VERSION_MAJOR} * 10000) + (${NUMPY_VERSION_MINOR} * 100) + ${NUMPY_VERSION_PATCH}") find_package_message(NUMPY "Found NumPy: version \"${NUMPY_VERSION}\" ${NUMPY_INCLUDE_DIRS}" "${NUMPY_INCLUDE_DIRS}${NUMPY_VERSION}") set(NUMPY_FOUND TRUE) trunk-2017.01a/cMake/FindOpenBlas.cmake000066400000000000000000000007771304022710500175230ustar00rootroot00000000000000# - Find OpenBlas library # # This module defines # OPENBLAS_LIBRARY, libraries to link against to use Openblas. # OPENBLAS_FOUND, If false, do not try to use Openblas. FIND_LIBRARY(OPENBLAS_LIBRARY NAMES openblas blas PATHS /usr/lib/openblas-base ) # handle the QUIETLY and REQUIRED arguments and set LOKI_FOUND to TRUE if # all listed variables are TRUE INCLUDE(FindPackageHandleStandardArgs) FIND_PACKAGE_HANDLE_STANDARD_ARGS(OpenBlas DEFAULT_MSG OPENBLAS_LIBRARY) MARK_AS_ADVANCED(OPENBLAS_LIBRARY) trunk-2017.01a/cMake/FindPythonModule.cmake000066400000000000000000000015551304022710500204420ustar00rootroot00000000000000# http://www.cmake.org/pipermail/cmake/2011-January/041666.html # # - Find Python Module FUNCTION(find_python_module module) STRING(TOUPPER ${module} module_upper) IF(ARGC GREATER 1 AND ARGV1 STREQUAL "REQUIRED") SET(${module}_FIND_REQUIRED TRUE) ENDIF(ARGC GREATER 1 AND ARGV1 STREQUAL "REQUIRED") EXECUTE_PROCESS(COMMAND "${PYTHON_EXECUTABLE}" "-c" "import re, ${module}; print re.compile('/__init__.py.*').sub('',${module}.__file__)" RESULT_VARIABLE _${module}_status OUTPUT_VARIABLE _${module}_location ERROR_QUIET OUTPUT_STRIP_TRAILING_WHITESPACE) IF(_${module}_status MATCHES 0) SET(PY_${module} ${_${module}_location} CACHE STRING "Location of Python module ${module}") ENDIF(_${module}_status MATCHES 0) FIND_PACKAGE_HANDLE_STANDARD_ARGS(${module} DEFAULT_MSG PY_${module}) ENDFUNCTION(find_python_module) trunk-2017.01a/cMake/FindQGLVIEWER-qt4.cmake000066400000000000000000000013461304022710500200640ustar00rootroot00000000000000# - Try to find QGLViewer # Once done this will define # # QGLVIEWER_FOUND - system has QGLViewer # QGLVIEWER_INCLUDE_DIR - the QGLViewer include directory # QGLVIEWER_LIBRARIES - Link these to use QGLViewer find_path(QGLVIEWER_INCLUDE_DIR NAMES qglviewer.h PATHS /usr/include/QGLViewer ) find_library(QGLVIEWER_LIBRARIES NAMES QGLViewer QGLViewer-qt4 ) IF(QGLVIEWER_INCLUDE_DIR AND QGLVIEWER_LIBRARIES) SET(QGLVIEWER_FOUND TRUE) SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DQGLVIEWER_FOUND") ENDIF(QGLVIEWER_INCLUDE_DIR AND QGLVIEWER_LIBRARIES) include(FindPackageHandleStandardArgs) FIND_PACKAGE_HANDLE_STANDARD_ARGS(QGLVIEWER-qt4 DEFAULT_MSG QGLVIEWER_INCLUDE_DIR QGLVIEWER_LIBRARIES) trunk-2017.01a/cMake/FindQGLVIEWER-qt5.cmake000066400000000000000000000013461304022710500200650ustar00rootroot00000000000000# - Try to find QGLViewer # Once done this will define # # QGLVIEWER_FOUND - system has QGLViewer # QGLVIEWER_INCLUDE_DIR - the QGLViewer include directory # QGLVIEWER_LIBRARIES - Link these to use QGLViewer find_path(QGLVIEWER_INCLUDE_DIR NAMES qglviewer.h PATHS /usr/include/QGLViewer ) find_library(QGLVIEWER_LIBRARIES NAMES QGLViewer QGLViewer-qt5 ) IF(QGLVIEWER_INCLUDE_DIR AND QGLVIEWER_LIBRARIES) SET(QGLVIEWER_FOUND TRUE) SET(CMAKE_CXX_FLAGS "${CMAKE_CXX_FLAGS} -DQGLVIEWER_FOUND") ENDIF(QGLVIEWER_INCLUDE_DIR AND QGLVIEWER_LIBRARIES) include(FindPackageHandleStandardArgs) FIND_PACKAGE_HANDLE_STANDARD_ARGS(QGLVIEWER-qt5 DEFAULT_MSG QGLVIEWER_INCLUDE_DIR QGLVIEWER_LIBRARIES) trunk-2017.01a/cMake/Findglib2.cmake000066400000000000000000000135241304022710500170110ustar00rootroot00000000000000# Downloaded from http://opensource.bolloretelecom.eu/projects/boc-wimax/browser/cmake/modules/FindGLIB2.cmake?rev=8f5b254534bd304923d4cc7bc7e9d6552c119ea2 # - Try to find GLib2 # Once done this will define # # GLIB2_FOUND - system has GLib2 # GLIB2_INCLUDE_DIRS - the GLib2 include directory # GLIB2_LIBRARIES - Link these to use GLib2 # # HAVE_GLIB_GREGEX_H glib has gregex.h header and # supports g_regex_match_simple # # Copyright (c) 2006 Andreas Schneider # Copyright (c) 2006 Philippe Bernery # Copyright (c) 2007 Daniel Gollub # Copyright (c) 2007 Alban Browaeys # Copyright (c) 2008 Michael Bell # Copyright (c) 2008 Bjoern Ricks # # Redistribution and use is allowed according to the terms of the New # BSD license. # For details see the accompanying COPYING-CMAKE-SCRIPTS file. # IF (GLIB2_LIBRARIES AND GLIB2_INCLUDE_DIRS ) # in cache already SET(GLIB2_FOUND TRUE) ELSE (GLIB2_LIBRARIES AND GLIB2_INCLUDE_DIRS ) INCLUDE(FindPkgConfig) ## Glib IF ( GLIB2_FIND_REQUIRED ) SET( _pkgconfig_REQUIRED "REQUIRED" ) ELSE ( GLIB2_FIND_REQUIRED ) SET( _pkgconfig_REQUIRED "" ) ENDIF ( GLIB2_FIND_REQUIRED ) IF ( GLIB2_MIN_VERSION ) PKG_SEARCH_MODULE( GLIB2 ${_pkgconfig_REQUIRED} glib-2.0>=${GLIB2_MIN_VERSION} ) ELSE ( GLIB2_MIN_VERSION ) PKG_SEARCH_MODULE( GLIB2 ${_pkgconfig_REQUIRED} glib-2.0 ) ENDIF ( GLIB2_MIN_VERSION ) IF ( PKG_CONFIG_FOUND ) IF ( GLIB2_FOUND ) SET ( GLIB2_CORE_FOUND TRUE ) ELSE ( GLIB2_FOUND ) SET ( GLIB2_CORE_FOUND FALSE ) ENDIF ( GLIB2_FOUND ) ENDIF ( PKG_CONFIG_FOUND ) # Look for glib2 include dir and libraries w/o pkgconfig IF ( NOT GLIB2_FOUND AND NOT PKG_CONFIG_FOUND ) FIND_PATH( _glibconfig_include_DIR NAMES glibconfig.h PATHS /opt/gnome/lib64 /opt/gnome/lib /opt/lib/ /opt/local/lib /sw/lib/ /usr/lib64 /usr/lib /usr/local/include ${CMAKE_LIBRARY_PATH} PATH_SUFFIXES glib-2.0/include ) FIND_PATH( _glib2_include_DIR NAMES glib.h PATHS /opt/gnome/include /opt/local/include /sw/include /usr/include /usr/local/include PATH_SUFFIXES glib-2.0 ) #MESSAGE(STATUS "Glib headers: ${_glib2_include_DIR}") FIND_LIBRARY( _glib2_link_DIR NAMES glib-2.0 glib PATHS /opt/gnome/lib /opt/local/lib /sw/lib /usr/lib /usr/local/lib ) IF ( _glib2_include_DIR AND _glib2_link_DIR ) SET ( _glib2_FOUND TRUE ) ENDIF ( _glib2_include_DIR AND _glib2_link_DIR ) IF ( _glib2_FOUND ) SET ( GLIB2_INCLUDE_DIRS ${_glib2_include_DIR} ${_glibconfig_include_DIR} ) SET ( GLIB2_LIBRARIES ${_glib2_link_DIR} ) SET ( GLIB2_CORE_FOUND TRUE ) ELSE ( _glib2_FOUND ) SET ( GLIB2_CORE_FOUND FALSE ) ENDIF ( _glib2_FOUND ) # Handle dependencies # libintl IF ( NOT LIBINTL_FOUND ) FIND_PATH(LIBINTL_INCLUDE_DIR NAMES libintl.h PATHS /opt/gnome/include /opt/local/include /sw/include /usr/include /usr/local/include ) FIND_LIBRARY(LIBINTL_LIBRARY NAMES intl PATHS /opt/gnome/lib /opt/local/lib /sw/lib /usr/local/lib /usr/lib ) IF (LIBINTL_LIBRARY AND LIBINTL_INCLUDE_DIR) SET (LIBINTL_FOUND TRUE) ENDIF (LIBINTL_LIBRARY AND LIBINTL_INCLUDE_DIR) ENDIF ( NOT LIBINTL_FOUND ) # libiconv IF ( NOT LIBICONV_FOUND ) FIND_PATH(LIBICONV_INCLUDE_DIR NAMES iconv.h PATHS /opt/gnome/include /opt/local/include /opt/local/include /sw/include /sw/include /usr/local/include /usr/include PATH_SUFFIXES glib-2.0 ) FIND_LIBRARY(LIBICONV_LIBRARY NAMES iconv PATHS /opt/gnome/lib /opt/local/lib /sw/lib /usr/lib /usr/local/lib ) IF (LIBICONV_LIBRARY AND LIBICONV_INCLUDE_DIR) SET (LIBICONV_FOUND TRUE) ENDIF (LIBICONV_LIBRARY AND LIBICONV_INCLUDE_DIR) ENDIF ( NOT LIBICONV_FOUND ) IF (LIBINTL_FOUND) SET (GLIB2_LIBRARIES ${GLIB2_LIBRARIES} ${LIBINTL_LIBRARY}) SET (GLIB2_INCLUDE_DIRS ${GLIB2_INCLUDE_DIRS} ${LIBINTL_INCLUDE_DIR}) ENDIF (LIBINTL_FOUND) IF (LIBICONV_FOUND) SET (GLIB2_LIBRARIES ${GLIB2_LIBRARIES} ${LIBICONV_LIBRARY}) SET (GLIB2_INCLUDE_DIRS ${GLIB2_INCLUDE_DIRS} ${LIBICONV_INCLUDE_DIR}) ENDIF (LIBICONV_FOUND) ENDIF ( NOT GLIB2_FOUND AND NOT PKG_CONFIG_FOUND ) ## IF (GLIB2_CORE_FOUND AND GLIB2_INCLUDE_DIRS AND GLIB2_LIBRARIES) SET (GLIB2_FOUND TRUE) ENDIF (GLIB2_CORE_FOUND AND GLIB2_INCLUDE_DIRS AND GLIB2_LIBRARIES) IF (GLIB2_FOUND) IF (NOT GLIB2_FIND_QUIETLY) MESSAGE (STATUS "Found GLib2: ${GLIB2_LIBRARIES} ${GLIB2_INCLUDE_DIRS}") ENDIF (NOT GLIB2_FIND_QUIETLY) ELSE (GLIB2_FOUND) IF (GLIB2_FIND_REQUIRED) MESSAGE (SEND_ERROR "Could not find GLib2") ENDIF (GLIB2_FIND_REQUIRED) ENDIF (GLIB2_FOUND) # show the GLIB2_INCLUDE_DIRS and GLIB2_LIBRARIES variables only in the advanced view MARK_AS_ADVANCED(GLIB2_INCLUDE_DIRS GLIB2_LIBRARIES) MARK_AS_ADVANCED(LIBICONV_INCLUDE_DIR LIBICONV_LIBRARY) MARK_AS_ADVANCED(LIBINTL_INCLUDE_DIR LIBINTL_LIBRARY) ENDIF (GLIB2_LIBRARIES AND GLIB2_INCLUDE_DIRS) IF ( GLIB2_FOUND ) # Check if system has a newer version of glib # which supports g_regex_match_simple INCLUDE( CheckIncludeFiles ) SET( CMAKE_REQUIRED_INCLUDES ${GLIB2_INCLUDE_DIRS} ) CHECK_INCLUDE_FILES ( glib/gregex.h HAVE_GLIB_GREGEX_H ) # Reset CMAKE_REQUIRED_INCLUDES SET( CMAKE_REQUIRED_INCLUDES "" ) ENDIF( GLIB2_FOUND ) trunk-2017.01a/cMake/GNUInstallDirs.cmake000066400000000000000000000163451304022710500200170ustar00rootroot00000000000000# - Define GNU standard installation directories # Provides install directory variables as defined for GNU software: # http://www.gnu.org/prep/standards/html_node/Directory-Variables.html # Inclusion of this module defines the following variables: # CMAKE_INSTALL_ - destination for files of a given type # CMAKE_INSTALL_FULL_ - corresponding absolute path # where is one of: # BINDIR - user executables (bin) # SBINDIR - system admin executables (sbin) # LIBEXECDIR - program executables (libexec) # SYSCONFDIR - read-only single-machine data (etc) # SHAREDSTATEDIR - modifiable architecture-independent data (com) # LOCALSTATEDIR - modifiable single-machine data (var) # LIBDIR - object code libraries (lib or lib64 or lib/ on Debian) # INCLUDEDIR - C header files (include) # OLDINCLUDEDIR - C header files for non-gcc (/usr/include) # DATAROOTDIR - read-only architecture-independent data root (share) # DATADIR - read-only architecture-independent data (DATAROOTDIR) # INFODIR - info documentation (DATAROOTDIR/info) # LOCALEDIR - locale-dependent data (DATAROOTDIR/locale) # MANDIR - man documentation (DATAROOTDIR/man) # DOCDIR - documentation root (DATAROOTDIR/doc/PROJECT_NAME) # Each CMAKE_INSTALL_ value may be passed to the DESTINATION options of # install() commands for the corresponding file type. If the includer does # not define a value the above-shown default will be used and the value will # appear in the cache for editing by the user. # Each CMAKE_INSTALL_FULL_ value contains an absolute path constructed # from the corresponding destination by prepending (if necessary) the value # of CMAKE_INSTALL_PREFIX. #============================================================================= # Copyright 2011 Nikita Krupen'ko # Copyright 2011 Kitware, Inc. # # Distributed under the OSI-approved BSD License (the "License"); # see accompanying file Copyright.txt for details. # # This software is distributed WITHOUT ANY WARRANTY; without even the # implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. # See the License for more information. #============================================================================= # (To distribute this file outside of CMake, substitute the full # License text for the above reference.) # Installation directories # if(NOT DEFINED CMAKE_INSTALL_BINDIR) set(CMAKE_INSTALL_BINDIR "bin" CACHE PATH "user executables (bin)") endif() if(NOT DEFINED CMAKE_INSTALL_SBINDIR) set(CMAKE_INSTALL_SBINDIR "sbin" CACHE PATH "system admin executables (sbin)") endif() if(NOT DEFINED CMAKE_INSTALL_LIBEXECDIR) set(CMAKE_INSTALL_LIBEXECDIR "libexec" CACHE PATH "program executables (libexec)") endif() if(NOT DEFINED CMAKE_INSTALL_SYSCONFDIR) set(CMAKE_INSTALL_SYSCONFDIR "etc" CACHE PATH "read-only single-machine data (etc)") endif() if(NOT DEFINED CMAKE_INSTALL_SHAREDSTATEDIR) set(CMAKE_INSTALL_SHAREDSTATEDIR "com" CACHE PATH "modifiable architecture-independent data (com)") endif() if(NOT DEFINED CMAKE_INSTALL_LOCALSTATEDIR) set(CMAKE_INSTALL_LOCALSTATEDIR "var" CACHE PATH "modifiable single-machine data (var)") endif() if(NOT DEFINED CMAKE_INSTALL_LIBDIR) set(_LIBDIR_DEFAULT "lib") # Override this default 'lib' with 'lib64' iff: # - we are on Linux system but NOT cross-compiling # - we are NOT on debian # - we are on a 64 bits system # reason is: amd64 ABI: http://www.x86-64.org/documentation/abi.pdf # For Debian with multiarch, use 'lib/${CMAKE_LIBRARY_ARCHITECTURE}' if # CMAKE_LIBRARY_ARCHITECTURE is set (which contains e.g. "i386-linux-gnu" # See http://wiki.debian.org/Multiarch if((CMAKE_SYSTEM_NAME MATCHES "Linux|kFreeBSD" OR CMAKE_SYSTEM_NAME STREQUAL "GNU") AND NOT CMAKE_CROSSCOMPILING) if (EXISTS "/etc/debian_version") # is this a debian system ? if(CMAKE_LIBRARY_ARCHITECTURE) set(_LIBDIR_DEFAULT "lib/${CMAKE_LIBRARY_ARCHITECTURE}") endif() else() # not debian, rely on CMAKE_SIZEOF_VOID_P: if(NOT DEFINED CMAKE_SIZEOF_VOID_P) message(AUTHOR_WARNING "Unable to determine default CMAKE_INSTALL_LIBDIR directory because no target architecture is known. " "Please enable at least one language before including GNUInstallDirs.") else() if("${CMAKE_SIZEOF_VOID_P}" EQUAL "8") set(_LIBDIR_DEFAULT "lib64") endif() endif() endif() endif() set(CMAKE_INSTALL_LIBDIR "${_LIBDIR_DEFAULT}" CACHE PATH "object code libraries (${_LIBDIR_DEFAULT})") endif() if(NOT DEFINED CMAKE_INSTALL_INCLUDEDIR) set(CMAKE_INSTALL_INCLUDEDIR "include" CACHE PATH "C header files (include)") endif() if(NOT DEFINED CMAKE_INSTALL_OLDINCLUDEDIR) set(CMAKE_INSTALL_OLDINCLUDEDIR "/usr/include" CACHE PATH "C header files for non-gcc (/usr/include)") endif() if(NOT DEFINED CMAKE_INSTALL_DATAROOTDIR) set(CMAKE_INSTALL_DATAROOTDIR "share" CACHE PATH "read-only architecture-independent data root (share)") endif() #----------------------------------------------------------------------------- # Values whose defaults are relative to DATAROOTDIR. Store empty values in # the cache and store the defaults in local variables if the cache values are # not set explicitly. This auto-updates the defaults as DATAROOTDIR changes. if(NOT CMAKE_INSTALL_DATADIR) set(CMAKE_INSTALL_DATADIR "" CACHE PATH "read-only architecture-independent data (DATAROOTDIR)") set(CMAKE_INSTALL_DATADIR "${CMAKE_INSTALL_DATAROOTDIR}") endif() if(NOT CMAKE_INSTALL_INFODIR) set(CMAKE_INSTALL_INFODIR "" CACHE PATH "info documentation (DATAROOTDIR/info)") set(CMAKE_INSTALL_INFODIR "${CMAKE_INSTALL_DATAROOTDIR}/info") endif() if(NOT CMAKE_INSTALL_LOCALEDIR) set(CMAKE_INSTALL_LOCALEDIR "" CACHE PATH "locale-dependent data (DATAROOTDIR/locale)") set(CMAKE_INSTALL_LOCALEDIR "${CMAKE_INSTALL_DATAROOTDIR}/locale") endif() if(NOT CMAKE_INSTALL_MANDIR) set(CMAKE_INSTALL_MANDIR "" CACHE PATH "man documentation (DATAROOTDIR/man)") set(CMAKE_INSTALL_MANDIR "${CMAKE_INSTALL_DATAROOTDIR}/man") endif() if(NOT CMAKE_INSTALL_DOCDIR) set(CMAKE_INSTALL_DOCDIR "" CACHE PATH "documentation root (DATAROOTDIR/doc/PROJECT_NAME)") set(CMAKE_INSTALL_DOCDIR "${CMAKE_INSTALL_DATAROOTDIR}/doc/${PROJECT_NAME}") endif() #----------------------------------------------------------------------------- mark_as_advanced( CMAKE_INSTALL_BINDIR CMAKE_INSTALL_SBINDIR CMAKE_INSTALL_LIBEXECDIR CMAKE_INSTALL_SYSCONFDIR CMAKE_INSTALL_SHAREDSTATEDIR CMAKE_INSTALL_LOCALSTATEDIR CMAKE_INSTALL_LIBDIR CMAKE_INSTALL_INCLUDEDIR CMAKE_INSTALL_OLDINCLUDEDIR CMAKE_INSTALL_DATAROOTDIR CMAKE_INSTALL_DATADIR CMAKE_INSTALL_INFODIR CMAKE_INSTALL_LOCALEDIR CMAKE_INSTALL_MANDIR CMAKE_INSTALL_DOCDIR ) # Result directories # foreach(dir BINDIR SBINDIR LIBEXECDIR SYSCONFDIR SHAREDSTATEDIR LOCALSTATEDIR LIBDIR INCLUDEDIR OLDINCLUDEDIR DATAROOTDIR DATADIR INFODIR LOCALEDIR MANDIR DOCDIR ) if(NOT IS_ABSOLUTE ${CMAKE_INSTALL_${dir}}) set(CMAKE_INSTALL_FULL_${dir} "${CMAKE_INSTALL_PREFIX}/${CMAKE_INSTALL_${dir}}") else() set(CMAKE_INSTALL_FULL_${dir} "${CMAKE_INSTALL_${dir}}") endif() endforeach() trunk-2017.01a/cMake/GetVersion.cmake000066400000000000000000000035331304022710500172750ustar00rootroot00000000000000# Define version or set it from git IF (NOT YADE_VERSION) IF (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/RELEASE ) #Release file is found SET(READFILE cat) exec_program( ${READFILE} ${CMAKE_CURRENT_SOURCE_DIR} ARGS "RELEASE" OUTPUT_VARIABLE YADE_VERSION ) ELSEIF (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/.git/config) #Use git for version defining exec_program( "git" ${CMAKE_CURRENT_SOURCE_DIR} ARGS "log" ARGS "-n1" ARGS "--pretty=oneline" ARGS "|" ARGS "cut" ARGS "-c1-7" OUTPUT_VARIABLE VERSION_GIT ) exec_program( "git" ${CMAKE_CURRENT_SOURCE_DIR} ARGS "log" ARGS "-n1" ARGS "--pretty=fuller" ARGS "--date=iso" ARGS "|" ARGS "grep" ARGS "AuthorDate" ARGS "|" ARGS "cut" ARGS "-c13-22" OUTPUT_VARIABLE VERSION_DATE ) SET(YADE_VERSION "${VERSION_DATE}.git-${VERSION_GIT}") #git log -n1 --pretty=format:"%ai_%h" ELSEIF (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/.bzr/branch/last-revision) #Use bzr for version defining exec_program( "less" ${CMAKE_CURRENT_SOURCE_DIR}/.bzr/branch/ ARGS "last-revision" ARGS "|" ARGS "cut" ARGS "-c13-20" OUTPUT_VARIABLE VERSION_GIT ) exec_program( "bzr" ${CMAKE_CURRENT_SOURCE_DIR} ARGS "log" ARGS "-l" ARGS "1" ARGS "--gnu-changelog" ARGS "|" ARGS "head" ARGS "-n1" ARGS "|" ARGS "cut" ARGS "-c1-10" OUTPUT_VARIABLE VERSION_DATE ) SET(YADE_VERSION "${VERSION_DATE}.git-${VERSION_GIT}") ELSE (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/.git/config ) SET (YADE_VERSION "Unknown") ENDIF (EXISTS ${CMAKE_CURRENT_SOURCE_DIR}/RELEASE ) ENDIF (NOT YADE_VERSION) MESSAGE (STATUS "Version is set to " ${YADE_VERSION}) trunk-2017.01a/core/000077500000000000000000000000001304022710500141125ustar00rootroot00000000000000trunk-2017.01a/core/Body.cpp000066400000000000000000000027231304022710500155170ustar00rootroot00000000000000 #include #include #include #include //! This could be -1 if id_t is re-typedef'ed as `int' const Body::id_t Body::ID_NONE=Body::id_t(-1); const shared_ptr& Body::byId(Body::id_t _id, Scene* rb){return (*((rb?rb:Omega::instance().getScene().get())->bodies))[_id];} const shared_ptr& Body::byId(Body::id_t _id, shared_ptr rb){return (*(rb->bodies))[_id];} // return list of interactions of this particle boost::python::list Body::py_intrs(){ boost::python::list ret; for(Body::MapId2IntrT::iterator it=this->intrs.begin(),end=this->intrs.end(); it!=end; ++it) { //Iterate over all bodie's interactions if(!(*it).second->isReal()) continue; ret.append((*it).second); } return ret; } // return list of interactions of this particle const unsigned int Body::coordNumber() const { unsigned int intrSize = 0; for(auto it=this->intrs.begin(),end=this->intrs.end(); it!=end; ++it) { //Iterate over all bodie's interactions if(!(*it).second->isReal()) continue; intrSize++; } return intrSize; } bool Body::maskOk(int mask) const { return (mask==0 || ((groupMask & mask) != 0)); } bool Body::maskCompatible(int mask) const { return (groupMask & mask) != 0; } #ifdef YADE_MASK_ARBITRARY bool Body::maskOk(const mask_t& mask) const { return (mask==0 || ((groupMask & mask) != 0)); } bool Body::maskCompatible(const mask_t& mask) const { return (groupMask & mask) != 0; } #endif trunk-2017.01a/core/Body.hpp000066400000000000000000000162701304022710500155260ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include "Shape.hpp" #include "Bound.hpp" #include "State.hpp" #include "Material.hpp" #include #include #include class Scene; class Interaction; class Body: public Serializable{ public: // numerical types for storing ids using id_t = int ; // internal structure to hold some interaction of a body; used by InteractionContainer; using MapId2IntrT = std::map >; // groupMask type // bits for Body::flags enum { FLAG_BOUNDED=1, FLAG_ASPHERICAL=2 }; /* add powers of 2 as needed */ //! symbolic constant for body that doesn't exist. static const Body::id_t ID_NONE; //! get Body pointer given its id. static const shared_ptr& byId(Body::id_t _id,Scene* rb=NULL); static const shared_ptr& byId(Body::id_t _id,shared_ptr rb); //! Whether this Body is a Clump. //! @note The following is always true: \code (Body::isClump() XOR Body::isClumpMember() XOR Body::isStandalone()) \endcode bool isClump() const {return clumpId!=ID_NONE && id==clumpId;} //! Whether this Body is member of a Clump. bool isClumpMember() const {return clumpId!=ID_NONE && id!=clumpId;} //! Whether this body is standalone (neither Clump, nor member of a Clump) bool isStandalone() const {return clumpId==ID_NONE;} //! Whether this body has all DOFs blocked // inline accessors // logic: http://stackoverflow.com/questions/47981/how-do-you-set-clear-and-toggle-a-single-bit-in-c bool isDynamic() const { assert(state); return state->blockedDOFs!=State::DOF_ALL; } void setDynamic(bool d){ assert(state); if(d){ state->blockedDOFs=State::DOF_NONE; } else { state->blockedDOFs=State::DOF_ALL; state->vel=state->angVel=Vector3r::Zero(); } } bool isBounded() const {return flags & FLAG_BOUNDED; } void setBounded(bool d){ if(d) flags|=FLAG_BOUNDED; else flags&=~(FLAG_BOUNDED); } bool isAspherical() const {return flags & FLAG_ASPHERICAL; } void setAspherical(bool d){ if(d) flags|=FLAG_ASPHERICAL; else flags&=~(FLAG_ASPHERICAL); } /*! Hook for clump to update position of members when user-forced reposition and redraw (through GUI) occurs. * This is useful only in cases when engines that do that in every iteration are not active - i.e. when the simulation is paused. * (otherwise, GLViewer would depend on Clump and therefore Clump would have to go to core...) */ virtual void userForcedDisplacementRedrawHook(){return;} boost::python::list py_intrs(); Body::id_t getId() const {return id;}; const unsigned int coordNumber() const; // Number of neighboring particles const mask_t getGroupMask() const {return groupMask; }; bool maskOk(int mask) const; bool maskCompatible(int mask) const; #ifdef YADE_MASK_ARBITRARY bool maskOk(const mask_t& mask) const; bool maskCompatible(const mask_t& mask) const; #endif // only BodyContainer can set the id of a body friend class BodyContainer; YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Body,Serializable,"A particle, basic element of simulation; interacts with other bodies.", ((Body::id_t,id,Body::ID_NONE,Attr::readonly,"Unique id of this body.")) ((mask_t,groupMask,1,,"Bitmask for determining interactions.")) ((int,flags,FLAG_BOUNDED,Attr::readonly,"Bits of various body-related flags. *Do not access directly*. In c++, use isDynamic/setDynamic, isBounded/setBounded, isAspherical/setAspherical. In python, use :yref:`Body.dynamic`, :yref:`Body.bounded`, :yref:`Body.aspherical`.")) ((shared_ptr,material,,,":yref:`Material` instance associated with this body.")) ((shared_ptr,state,new State,,"Physical :yref:`state`.")) ((shared_ptr,shape,,,"Geometrical :yref:`Shape`.")) ((shared_ptr,bound,,,":yref:`Bound`, approximating volume for the purposes of collision detection.")) ((MapId2IntrT,intrs,,Attr::hidden,"Map from otherId to Interaction with otherId, managed by InteractionContainer. NOTE: (currently) does not contain all interactions with this body (only those where otherId>id), since performance issues with such data duplication have not yet been investigated.")) ((int,clumpId,Body::ID_NONE,Attr::readonly,"Id of clump this body makes part of; invalid number if not part of clump; see :yref:`Body::isStandalone`, :yref:`Body::isClump`, :yref:`Body::isClumpMember` properties. \n\nNot meant to be modified directly from Python, use :yref:`O.bodies.appendClumped` instead.")) ((long,chain,-1,,"Id of chain to which the body belongs.")) ((long,iterBorn,-1,,"Step number at which the body was added to simulation.")) ((Real,timeBorn,-1,,"Time at which the body was added to simulation.")) , /* ctor */, /* py */ // .def_readwrite("mat",&Body::material,"Shorthand for :yref:`Body::material`") .add_property("dynamic",&Body::isDynamic,&Body::setDynamic,"Whether this body will be moved by forces. (In c++, use ``Body::isDynamic``/``Body::setDynamic``) :ydefault:`true`") .add_property("bounded",&Body::isBounded,&Body::setBounded,"Whether this body should have :yref:`Body.bound` created. Note that bodies without a :yref:`bound ` do not participate in collision detection. (In c++, use ``Body::isBounded``/``Body::setBounded``) :ydefault:`true`") .add_property("aspherical",&Body::isAspherical,&Body::setAspherical,"Whether this body has different inertia along principal axes; :yref:`NewtonIntegrator` makes use of this flag to call rotation integration routine for aspherical bodies, which is more expensive. :ydefault:`false`") .add_property("mask",boost::python::make_getter(&Body::groupMask,boost::python::return_value_policy()),boost::python::make_setter(&Body::groupMask,boost::python::return_value_policy()),"Shorthand for :yref:`Body::groupMask`") .add_property("isStandalone",&Body::isStandalone,"True if this body is neither clump, nor clump member; false otherwise.") .add_property("isClumpMember",&Body::isClumpMember,"True if this body is clump member, false otherwise.") .add_property("isClump",&Body::isClump,"True if this body is clump itself, false otherwise.") .add_property("iterBorn",&Body::iterBorn,"Returns step number at which the body was added to simulation.") .add_property("timeBorn",&Body::timeBorn,"Returns time at which the body was added to simulation.") .def_readwrite("chain",&Body::chain,"Returns Id of chain to which the body belongs.") .def("intrs",&Body::py_intrs,"Return all interactions in which this body participates.") ); }; REGISTER_SERIALIZABLE(Body); trunk-2017.01a/core/BodyContainer.cpp000066400000000000000000000040731304022710500173620ustar00rootroot00000000000000// 2010 © Václav Šmilauer #include "Scene.hpp" #include "Body.hpp" #include "BodyContainer.hpp" #include "Clump.hpp" #ifdef YADE_OPENMP #include #endif CREATE_LOGGER(BodyContainer); void BodyContainer::clear(){ body.clear(); } Body::id_t BodyContainer::insert(shared_ptr b){ const shared_ptr& scene=Omega::instance().getScene(); b->iterBorn=scene->iter; b->timeBorn=scene->time; b->id=body.size(); scene->doSort = true; body.push_back(b); // Notify ForceContainer about new id scene->forces.addMaxId(b->id); return b->id; } bool BodyContainer::erase(Body::id_t id, bool eraseClumpMembers){//default is false (as before) if(!body[id]) return false; const shared_ptr& b=Body::byId(id); if ((b) and (b->isClumpMember())) { const shared_ptr clumpBody=Body::byId(b->clumpId); const shared_ptr clump=YADE_PTR_CAST(clumpBody->shape); Clump::del(clumpBody, b); if (clump->members.size()==0) this->erase(clumpBody->id,false); //Clump has no members any more. Remove it } if ((b) and (b->isClump())){ //erase all members if eraseClumpMembers is true: const shared_ptr& clump=YADE_PTR_CAST(b->shape); std::map& members = clump->members; std::vector idsToRemove; for(const auto mm : members) idsToRemove.push_back(mm.first); // Prepare an array of ids, which need to be removed. for(Body::id_t memberId : idsToRemove){ if (eraseClumpMembers) { this->erase(memberId,false); // erase members } else { //when the last members is erased, the clump will be erased automatically, see above Body::byId(memberId)->clumpId=Body::ID_NONE; // make members standalones } } body[id].reset(); return true; } const shared_ptr& scene=Omega::instance().getScene(); for(auto it=b->intrs.begin(), end=b->intrs.end(); it!=end; ++it) { //Iterate over all body's interactions scene->interactions->requestErase((*it).second); } b->id=-1;//else it sits in the python scope without a chance to be inserted again body[id].reset(); return true; } trunk-2017.01a/core/BodyContainer.hpp000066400000000000000000000061171304022710500173700ustar00rootroot00000000000000// 2004 © Olivier Galizzi // 2004 © Janek Kozicki // 2010 © Václav Šmilauer #pragma once #include #include class Body; class InteractionContainer; #if YADE_OPENMP #define YADE_PARALLEL_FOREACH_BODY_BEGIN(b_,bodies) const Body::id_t _sz(bodies->size()); _Pragma("omp parallel for") for(Body::id_t _id=0; _id<_sz; _id++){ if(!(*bodies)[_id]) continue; b_((*bodies)[_id]); #define YADE_PARALLEL_FOREACH_BODY_END() } #else #define YADE_PARALLEL_FOREACH_BODY_BEGIN(b,bodies) FOREACH(b,*(bodies)){ #define YADE_PARALLEL_FOREACH_BODY_END() } #endif /* Container of bodies implemented as flat std::vector. It handles body removal and intelligently reallocates free ids for newly added ones. The nested iterators and the specialized FOREACH_BODY macros above will silently skip null body pointers which may exist after removal. The null pointers can still be accessed via the [] operator. Any alternative implementation should use the same API. */ class BodyContainer: public Serializable{ private: using ContainerT = std::vector > ; using MemberMap = std::map ; ContainerT body; public: friend class InteractionContainer; // accesses the body vector directly //An iterator that will automatically jump slots with null bodies class smart_iterator : public ContainerT::iterator { public: ContainerT::iterator end; smart_iterator& operator++() { ContainerT::iterator::operator++(); while (!(this->operator*()) && end!=(*this)) ContainerT::iterator::operator++(); return *this;} smart_iterator operator++(int) {smart_iterator temp(*this); operator++(); return temp;} smart_iterator& operator=(const ContainerT::iterator& rhs) {ContainerT::iterator::operator=(rhs); return *this;} smart_iterator& operator=(const smart_iterator& rhs) {ContainerT::iterator::operator=(rhs); end=rhs.end; return *this;} smart_iterator() {} smart_iterator(const ContainerT::iterator& source) {(*this)=source;} smart_iterator(const smart_iterator& source) {(*this)=source; end=source.end;} }; using iterator = smart_iterator ; using const_iterator = const smart_iterator ; BodyContainer() {}; virtual ~BodyContainer() {}; Body::id_t insert(shared_ptr); void clear(); iterator begin() { iterator temp(body.begin()); temp.end=body.end(); return (body.begin()==body.end() || *temp)?temp:++temp;} iterator end() { iterator temp(body.end()); temp.end=body.end(); return temp; } const size_t size() const { return body.size(); } shared_ptr& operator[](unsigned int id){ return body[id];} const shared_ptr& operator[](unsigned int id) const { return body[id]; } const bool exists(Body::id_t id) const { return ((id>=0) && ((size_t)id #include #include #include /*! Interface for approximate body locations in space Note: the min and max members refer to shear coordinates, in periodic and sheared space, not cartesian coordinates in the physical space. */ class Bound: public Serializable, public Indexable{ public: YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Bound,Serializable,"Object bounding part of space taken by associated body; might be larger, used to optimalize collision detection", ((int,lastUpdateIter,0,Attr::readonly,"record iteration of last reference position update |yupdate|")) ((Vector3r,refPos,Vector3r(NaN,NaN,NaN),Attr::readonly,"Reference position, updated at current body position each time the bound dispatcher update bounds |yupdate|")) // ((bool,isBounding,false,Attr::readonly,"A flag used to tell when the body moves out of bounds - only used if oriVerlet striding is active :yref:`BoundDispatcher::updatingDispFactor`>0 |yupdate|")) ((Real,sweepLength,0, Attr::readonly,"The length used to increase the bounding boxe size, can be adjusted on the basis of previous displacement if :yref:`BoundDispatcher::targetInterv`>0. |yupdate|")) ((Vector3r,color,Vector3r(1,1,1),,"Color for rendering this object")) ((Vector3r,min,Vector3r(NaN,NaN,NaN),(Attr::noSave | Attr::readonly),"Lower corner of box containing this bound (and the :yref:`Body` as well)")) ((Vector3r,max,Vector3r(NaN,NaN,NaN),(Attr::noSave | Attr::readonly),"Upper corner of box containing this bound (and the :yref:`Body` as well)")) , /* ctor*/, /*py*/ YADE_PY_TOPINDEXABLE(Bound) ); REGISTER_INDEX_COUNTER(Bound); }; REGISTER_SERIALIZABLE(Bound); trunk-2017.01a/core/Cell.cpp000066400000000000000000000032171304022710500155000ustar00rootroot00000000000000 #include CREATE_LOGGER(Cell); void Cell::integrateAndUpdate(Real dt){ //incremental displacement gradient _trsfInc=dt*velGrad; // total transformation; M = (Id+G).M = F.M trsf+=_trsfInc*trsf; _invTrsf=trsf.inverse(); // hSize contains colums with updated base vectors prevHSize=hSize; _vGradTimesPrevH = velGrad*prevHSize; hSize+=_trsfInc*hSize; if(hSize.determinant()==0){ throw runtime_error("Cell is degenerate (zero volume)."); } // lengths of transformed cell vectors, skew cosines Matrix3r Hnorm; // normalized transformed base vectors for(int i=0; i<3; i++){ Vector3r base(hSize.col(i)); _size[i]=base.norm(); base/=_size[i]; //base is normalized now Hnorm(0,i)=base[0]; Hnorm(1,i)=base[1]; Hnorm(2,i)=base[2];}; // skew cosines for(int i=0; i<3; i++){ int i1=(i+1)%3, i2=(i+2)%3; // sin between axes is cos of skew _cos[i]=(Hnorm.col(i1).cross(Hnorm.col(i2))).squaredNorm(); } // pure shear trsf: ones on diagonal _shearTrsf=Hnorm; // pure unshear transformation _unshearTrsf=_shearTrsf.inverse(); // some parts can branch depending on presence/absence of shear _hasShear=(hSize(0,1)!=0 || hSize(0,2)!=0 || hSize(1,0)!=0 || hSize(1,2)!=0 || hSize(2,0)!=0 || hSize(2,1)!=0); // OpenGL shear matrix (used frequently) fillGlShearTrsfMatrix(_glShearTrsfMatrix); } void Cell::fillGlShearTrsfMatrix(double m[16]){ m[0]=_shearTrsf(0,0); m[4]=_shearTrsf(0,1); m[8]=_shearTrsf(0,2); m[12]=0; m[1]=_shearTrsf(1,0); m[5]=_shearTrsf(1,1); m[9]=_shearTrsf(1,2); m[13]=0; m[2]=_shearTrsf(2,0); m[6]=_shearTrsf(2,1); m[10]=_shearTrsf(2,2);m[14]=0; m[3]=0; m[7]=0; m[11]=0; m[15]=1; } trunk-2017.01a/core/Cell.hpp000066400000000000000000000407221304022710500155070ustar00rootroot00000000000000// 2009 © Václav Šmilauer /*! Periodic cell parameters and routines. Usually instantiated as Scene::cell. The Cell has current box configuration represented by the parallelepiped's base vectors (*hSize*). Lengths of the base vectors can be accessed via *size*. * Matrix3r *trsf* is "deformation gradient tensor" F (http://en.wikipedia.org/wiki/Finite_strain_theory) * Matrix3r *velGrad* is "velocity gradient tensor" (http://www.cs.otago.ac.nz/postgrads/alexis/FluidMech/node7.html) The transformation is split between "normal" part and "rotation/shear" part for contact detection algorithms. The shearPt, unshearPt, getShearTrsf etc functions refer to both shear and rotation. This decomposition is frame-dependant and does not correspond to the rotation/stretch decomposition of mechanics (with stretch further decomposed into isotropic and deviatoric). Therefore, using the shearPt family in equations of mechanics is not recommended. Similarly, attributes assuming the existence of a "reference" state are considered deprecated (refSize, hSize0). It is better to not use them since there is no guarantee that the so-called "reference state" will be maintained consistently in the future. */ #pragma once #include #include //#include class Cell: public Serializable{ public: //! Get/set sizes of cell base vectors const Vector3r& getSize() const { return _size; } void setSize(const Vector3r& s){for (int k=0;k<3;k++) hSize.col(k)*=s[k]/hSize.col(k).norm(); refHSize=hSize; postLoad(*this);} //! Return copy of the current size (used only by the python wrapper) Vector3r getSize_copy() const { return _size; } //! return vector of consines of skew angle in yz, xz, xy planes between respective transformed base vectors const Vector3r& getCos() const {return _cos;} //! transformation matrix applying pure shear&rotation (scaling removed) const Matrix3r& getShearTrsf() const { return _shearTrsf; } //! inverse of getShearTrsfMatrix(). const Matrix3r& getUnshearTrsf() const {return _unshearTrsf;} //! transformation increment matrix applying arbitrary field (remove if not used in NewtonIntegrator! ) // const Matrix3r& getTrsfInc() const { return _trsfInc; } /*! return pointer to column-major OpenGL 4x4 matrix applying pure shear. This matrix is suitable as argument for glMultMatrixd. Note: the order of OpenGL transoformations matters; for instance, if you draw sheared wire box of size *size*, centered at *center*, the order is: 1. translation: glTranslatev(center); 3. shearing: glMultMatrixd(scene->cell->getGlShearTrsfMatrix()); 2. scaling: glScalev(size); 4. draw: glutWireCube(1); See also http://www.songho.ca/opengl/gl_transform.html#matrix . */ const double* getGlShearTrsfMatrix() const { return _glShearTrsfMatrix; } //! Whether any shear (non-diagonal) component of the strain matrix is nonzero. bool hasShear() const {return _hasShear; } // caches; private private: Matrix3r _invTrsf; Matrix3r _trsfInc; Matrix3r _vGradTimesPrevH; Vector3r _size, _cos; Vector3r _refSize; bool _hasShear; Matrix3r _shearTrsf, _unshearTrsf; double _glShearTrsfMatrix[16]; void fillGlShearTrsfMatrix(double m[16]); public: DECLARE_LOGGER; //! "integrate" velGrad, update cached values used by public getter. void integrateAndUpdate(Real dt); /*! Return point inside periodic cell, even if shear is applied */ Vector3r wrapShearedPt(const Vector3r& pt) const { return shearPt(wrapPt(unshearPt(pt))); } /*! Return point inside periodic cell, even if shear is applied; store cell coordinates in period. */ Vector3r wrapShearedPt(const Vector3r& pt, Vector3i& period) const { return shearPt(wrapPt(unshearPt(pt),period)); } /*! Apply inverse shear on point; to put it inside (unsheared) periodic cell, apply wrapPt on the returned value. */ Vector3r unshearPt(const Vector3r& pt) const { return _unshearTrsf*pt; } //! Apply shear on point. Vector3r shearPt(const Vector3r& pt) const { return _shearTrsf*pt; } /*! Wrap point to inside the periodic cell; don't compute number of periods wrapped */ Vector3r wrapPt(const Vector3r& pt) const { Vector3r ret; for(int i=0;i<3;i++) ret[i]=wrapNum(pt[i],_size[i]); return ret;} /*! Wrap point to inside the periodic cell; period will contain by how many cells it was wrapped. */ Vector3r wrapPt(const Vector3r& pt, Vector3i& period) const { Vector3r ret; for(int i=0; i<3; i++){ ret[i]=wrapNum(pt[i],_size[i],period[i]); } return ret;} /*! Wrap number to interval 0…sz */ static Real wrapNum(const Real& x, const Real& sz) { Real norm=x/sz; return (norm-floor(norm))*sz;} /*! Wrap number to interval 0…sz; store how many intervals were wrapped in period */ static Real wrapNum(const Real& x, const Real& sz, int& period) { Real norm=x/sz; period=(int)floor(norm); return (norm-period)*sz;} // relative position and velocity for interaction accross multiple cells Vector3r intrShiftPos(const Vector3i& cellDist) const { return hSize*cellDist.cast(); } Vector3r intrShiftVel(const Vector3i& cellDist) const { return _vGradTimesPrevH*cellDist.cast(); } // return body velocity while taking away mean field velocity (coming from velGrad) if the mean field velocity is applied on velocity Vector3r bodyFluctuationVel(const Vector3r& pos, const Vector3r& vel, const Matrix3r& prevVelGrad) const { return (vel-prevVelGrad*pos); } // get/set current shape; setting resets trsf to identity Matrix3r getHSize() const { return hSize; } void setHSize(const Matrix3r& m){ hSize=refHSize=m; postLoad(*this); } // set current transformation; has no influence on current configuration (hSize); sets display refHSize as side-effect Matrix3r getTrsf() const { return trsf; } void setTrsf(const Matrix3r& m){ trsf=m; postLoad(*this); } Matrix3r getVelGrad() const { return velGrad; } void setVelGrad(const Matrix3r& m){ nextVelGrad=m; velGradChanged=true;} //BEGIN Deprecated (see refSize property) // get undeformed shape Matrix3r getHSize0() const { return _invTrsf*hSize; } // edge lengths of the undeformed shape Vector3r getRefSize() const { Matrix3r h=getHSize0(); return Vector3r(h.col(0).norm(),h.col(1).norm(),h.col(2).norm()); } // temporary, will be removed in favor of more descriptive setBox(...) void setRefSize(const Vector3r& s){ // if refSize is set to the current size and the cell is a box (used in older scripts), say it is not necessary Matrix3r hSizeEigen3=hSize.diagonal().asDiagonal(); //Eigen3 support if(s==_size && hSize==hSizeEigen3){ LOG_WARN("Setting O.cell.refSize=O.cell.size is useless, O.trsf=Matrix3.Identity is enough now."); } else {LOG_WARN("Setting Cell.refSize is deprecated, use Cell.setBox(...) instead.");} setBox(s); postLoad(*this); } //END Deprecated // set box shape of the cell void setBox(const Vector3r& size){ setHSize(size.asDiagonal()); trsf=Matrix3r::Identity(); postLoad(*this); } void setBox3(const Real& s0, const Real& s1, const Real& s2){ setBox(Vector3r(s0,s1,s2)); } // return current cell volume Real getVolume() const {return hSize.determinant();} void postLoad(Cell&){ integrateAndUpdate(0); } // to resolve overloads Vector3r wrapShearedPt_py(const Vector3r& pt) const { return wrapShearedPt(pt);} Vector3r wrapPt_py(const Vector3r& pt) const { return wrapPt(pt);} // strain measures Matrix3r getDefGrad() { return trsf; } Matrix3r getSmallStrain() { return .5*(trsf+trsf.transpose()) - Matrix3r::Identity(); } Matrix3r getRCauchyGreenDef() { return trsf.transpose()*trsf; } Matrix3r getLCauchyGreenDef() { return trsf*trsf.transpose(); } Matrix3r getLagrangianStrain() { return .5*(getRCauchyGreenDef()-Matrix3r::Identity()); } Matrix3r getEulerianAlmansiStrain() { return .5*(Matrix3r::Identity()-getLCauchyGreenDef().inverse()); } void computePolarDecOfDefGrad(Matrix3r& R, Matrix3r& U) { Matrix_computeUnitaryPositive(trsf,&R,&U); } boost::python::tuple getPolarDecOfDefGrad(){ Matrix3r R,U; computePolarDecOfDefGrad(R,U); return boost::python::make_tuple(R,U); } Matrix3r getRotation() { Matrix3r R,U; computePolarDecOfDefGrad(R,U); return R; } Matrix3r getLeftStretch() { Matrix3r R,U; computePolarDecOfDefGrad(R,U); return U; } Matrix3r getRightStretch() { Matrix3r R,U; computePolarDecOfDefGrad(R,U); return trsf*R.transpose(); } Vector3r getSpin() {Matrix3r R=.5*(velGrad-velGrad.transpose()); return Vector3r(-R(1,2),R(0,2),-R(0,1));} // stress measures //Matrix3r getStress() { return Shop::getStress(); } //Matrix3r getCauchyStress() { Matrix3r s=getStress(); return .5*(s+s.transpose()); } enum { HOMO_NONE=0, HOMO_POS=1, HOMO_VEL=2, HOMO_VEL_2ND=3 }; YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Cell,Serializable,"Parameters of periodic boundary conditions. Only applies if O.isPeriodic==True.", /* overridden below to be modified by getters/setters because of intended side-effects */ ((Matrix3r,trsf,Matrix3r::Identity(),,"[overridden]")) //"Current transformation matrix of the cell, which defines how far is the current cell geometry (:yref:`hSize`) from the reference configuration. Changing trsf will not change :yref:`hSize`, it serves only as accumulator for transformations applied via :yref:`velGrad`.")) ((Matrix3r,refHSize,Matrix3r::Identity(),,"Reference cell configuration, only used with :yref:`OpenGLRenderer.dispScale`. Updated automatically when :yref:`hSize` or :yref:`trsf` is assigned directly; also modified by :yref:`yade.utils.setRefSe3` (called e.g. by the ``Reference`` button in the UI).")) ((Matrix3r,hSize,Matrix3r::Identity(),,"[overridden below]")) ((Matrix3r,prevHSize,Matrix3r::Identity(),Attr::readonly,":yref:`hSize` from the previous step, used in the definition of relative velocity across periods.")) /* normal attributes */ ((Matrix3r,velGrad,Matrix3r::Zero(),,"[overridden below]")) ((Matrix3r,nextVelGrad,Matrix3r::Zero(),Attr::readonly,"see :yref:`Cell.velGrad`.")) ((Matrix3r,prevVelGrad,Matrix3r::Zero(),Attr::readonly,"Velocity gradient in the previous step.")) ((int,homoDeform,2,,"If >0, deform (:yref:`velGrad`) the cell homothetically by adjusting positions and velocities of bodies. The velocity change is obtained by deriving the expression v=∇v.x, where ∇v is the macroscopic velocity gradient, giving in an incremental form: Δv=Δ ∇v x + ∇v Δx. As a result, velocities are modified as soon as ``velGrad`` changes, according to the first term: Δv(t)=Δ ∇v x(t), while the 2nd term reflects a convective term: Δv'= ∇v v(t-dt/2). The second term is neglected if homoDeform=1. All terms are included if homoDeform=2 (default)")) ((bool,velGradChanged,false,Attr::readonly,"true when velGrad has been changed manually (see also :yref:`Cell.nextVelGrad`)")), /*ctor*/ _invTrsf=Matrix3r::Identity(); integrateAndUpdate(0), /*py*/ // override some attributes above .add_property("hSize",&Cell::getHSize,&Cell::setHSize,"Base cell vectors (columns of the matrix), updated at every step from :yref:`velGrad` (:yref:`trsf` accumulates applied :yref:`velGrad` transformations). Setting *hSize* during a simulation is not supported by most contact laws, it is only meant to be used at iteration 0 before any interactions have been created.") .add_property("size",&Cell::getSize_copy,&Cell::setSize,"Current size of the cell, i.e. lengths of the 3 cell lateral vectors contained in :yref:`Cell.hSize` columns. Updated automatically at every step. Assigning a value will change the lengths of base vectors (see :yref:`Cell.hSize`), keeping their orientations unchanged.") .add_property("refSize",&Cell::getRefSize,&Cell::setRefSize,"Reference size of the cell (lengths of initial cell vectors, i.e. column norms of :yref:`hSize`).\n\n.. note::\n\t Modifying this value is deprecated, use :yref:`setBox` instead.") // useful properties .add_property("trsf",&Cell::getTrsf,&Cell::setTrsf,"Current transformation matrix of the cell, obtained from time integration of :yref:`Cell.velGrad`.") .add_property("velGrad",&Cell::getVelGrad,&Cell::setVelGrad,"Velocity gradient of the transformation; used in :yref:`NewtonIntegrator`. Values of :yref:`velGrad` accumulate in :yref:`trsf` at every step.\n\n NOTE: changing velGrad at the beginning of a simulation loop would lead to inacurate integration for one step, as it should normaly be changed after the contact laws (but before Newton). To avoid this problem, assignment is deferred automatically. The target value typed in terminal is actually stored in :yref:`Cell.nextVelGrad` and will be applied right in time by Newton integrator. \n\n.. note::\n\t Assigning individual components of velGrad is not possible (it will not return any error but it will have no effect). Instead, you can assign to :yref:`Cell.nextVelGrad`, as in O.cell.nextVelGrad[1,2]=1.") .def_readonly("size",&Cell::getSize_copy,"Current size of the cell, i.e. lengths of the 3 cell lateral vectors contained in :yref:`Cell.hSize` columns. Updated automatically at every step.") .add_property("volume",&Cell::getVolume,"Current volume of the cell.") // functions .def("setBox",&Cell::setBox,"Set :yref:`Cell` shape to be rectangular, with dimensions along axes specified by given argument. Shorthand for assigning diagonal matrix with respective entries to :yref:`hSize`.") .def("setBox",&Cell::setBox3,"Set :yref:`Cell` shape to be rectangular, with dimensions along $x$, $y$, $z$ specified by arguments. Shorthand for assigning diagonal matrix with the respective entries to :yref:`hSize`.") // debugging only .def("wrap",&Cell::wrapShearedPt_py,"Transform an arbitrary point into a point in the reference cell") .def("unshearPt",&Cell::unshearPt,"Apply inverse shear on the point (removes skew+rot of the cell)") .def("shearPt",&Cell::shearPt,"Apply shear (cell skew+rot) on the point") .def("wrapPt",&Cell::wrapPt_py,"Wrap point inside the reference cell, assuming the cell has no skew+rot.") .def("getDefGrad",&Cell::getDefGrad,"Returns deformation gradient tensor $\\mat{F}$ of the cell deformation (http://en.wikipedia.org/wiki/Finite_strain_theory)") .def("getSmallStrain",&Cell::getSmallStrain,"Returns small strain tensor $\\mat{\\varepsilon}=\\frac{1}{2}(\\mat{F}+\\mat{F}^T)-\\mat{I}$ of the cell (http://en.wikipedia.org/wiki/Finite_strain_theory)") .def("getRCauchyGreenDef",&Cell::getRCauchyGreenDef,"Returns right Cauchy-Green deformation tensor $\\mat{C}=\\mat{F}^T\\mat{F}$ of the cell (http://en.wikipedia.org/wiki/Finite_strain_theory)") .def("getLCauchyGreenDef",&Cell::getLCauchyGreenDef,"Returns left Cauchy-Green deformation tensor $\\mat{b}=\\mat{F}\\mat{F}^T$ of the cell (http://en.wikipedia.org/wiki/Finite_strain_theory)") .def("getLagrangianStrain",&Cell::getLagrangianStrain,"Returns Lagrangian strain tensor $\\mat{E}=\\frac{1}{2}(\\mat{C}-\\mat{I})=\\frac{1}{2}(\\mat{F}^T\\mat{F}-\\mat{I})=\\frac{1}{2}(\\mat{U}^2-\\mat{I})$ of the cell (http://en.wikipedia.org/wiki/Finite_strain_theory)") .def("getEulerianAlmansiStrain",&Cell::getEulerianAlmansiStrain,"Returns Eulerian-Almansi strain tensor $\\mat{e}=\\frac{1}{2}(\\mat{I}-\\mat{b}^{-1})=\\frac{1}{2}(\\mat{I}-(\\mat{F}\\mat{F}^T)^{-1})$ of the cell (http://en.wikipedia.org/wiki/Finite_strain_theory)") .def("getPolarDecOfDefGrad",&Cell::getPolarDecOfDefGrad,"Returns orthogonal matrix $\\mat{R}$ and symmetric positive semi-definite matrix $\\mat{U}$ as polar decomposition of deformation gradient $\\mat{F}$ of the cell ( $\\mat{F}=\\mat{RU}$ )") .def("getRotation",&Cell::getRotation,"Returns rotation of the cell (orthogonal matrix $\\mat{R}$ from polar decomposition $\\mat{F}=\\mat{RU}$ )") .def("getLeftStretch",&Cell::getLeftStretch,"Returns left (spatial) stretch tensor of the cell (matrix $\\mat{U}$ from polar decomposition $\\mat{F}=\\mat{RU}$ )") .def("getRightStretch",&Cell::getRightStretch,"Returns right (material) stretch tensor of the cell (matrix $\\mat{V}$ from polar decomposition $\\mat{F}=\\mat{RU}=\\mat{VR}\\ \\rightarrow\\ \\mat{V}=\\mat{FR}^T$ )") .def("getSpin",&Cell::getSpin,"Returns the spin defined by the skew symmetric part of :yref:`velGrad`") .def_readonly("shearTrsf",&Cell::_shearTrsf,"Current skew+rot transformation (no resize)") .def_readonly("unshearTrsf",&Cell::_unshearTrsf,"Inverse of the current skew+rot transformation (no resize)") .add_property("hSize0",&Cell::getHSize0,"Value of untransformed hSize, with respect to current :yref:`trsf` (computed as :yref:`trsf` ⁻¹ × :yref:`hSize`.") ); }; REGISTER_SERIALIZABLE(Cell); trunk-2017.01a/core/Clump.cpp000066400000000000000000000556061304022710500157120ustar00rootroot00000000000000// (c) 2007-2010 Vaclav Smilauer #include"Clump.hpp" #include #include #include #include YADE_PLUGIN((Clump)); CREATE_LOGGER(Clump); boost::python::dict Clump::members_get(){ boost::python::dict ret; FOREACH(MemberMap::value_type& b, members){ ret[b.first]=boost::python::make_tuple(b.second.position,b.second.orientation); } return ret; } void Clump::add(const shared_ptr& clumpBody, const shared_ptr& subBody){ Body::id_t subId=subBody->getId(); const shared_ptr clump=YADE_PTR_CAST(clumpBody->shape); if(clump->members.count(subId)!=0) throw std::invalid_argument(("Body #"+boost::lexical_cast(subId)+" is already part of this clump #"+boost::lexical_cast(clumpBody->id)).c_str()); if(subBody->isClumpMember()) throw std::invalid_argument(("Body #"+boost::lexical_cast(subId)+" is already a clump member of #"+boost::lexical_cast(subBody->clumpId)).c_str()); else if(subBody->isClump()){ const shared_ptr subClump=YADE_PTR_CAST(subBody->shape); FOREACH(const MemberMap::value_type& mm, subClump->members){ const Body::id_t& memberId=mm.first; Scene* scene(Omega::instance().getScene().get()); // get scene const shared_ptr& member=Body::byId(memberId,scene); assert(member->isClumpMember()); member->clumpId=clumpBody->id; clump->members[memberId]=Se3r();// meaningful values will be put in by Clump::updateProperties //LOG_DEBUG("Added body #"<id<<" to clump #"<id); } //LOG_DEBUG("Clump #"<id<<" will be erased.");// see addToClump() in yadeWrapper.cpp } else{ // subBody must be a standalone! clump->members[subId]=Se3r();// meaningful values will be put in by Clump::updateProperties subBody->clumpId=clumpBody->id; } clumpBody->clumpId=clumpBody->id; // just to make sure clumpBody->setBounded(false); // disallow collisions with the clump itself if(subBody->isStandalone()){LOG_DEBUG("Added body #"<id<<" to clump #"<id);} } void Clump::del(const shared_ptr& clumpBody, const shared_ptr& subBody){ // erase the subBody; removing body that is not part of the clump throws const shared_ptr clump=YADE_PTR_CAST(clumpBody->shape); if(clump->members.erase(subBody->id)!=1) throw std::invalid_argument(("Body #"+boost::lexical_cast(subBody->id)+" not part of clump #"+boost::lexical_cast(clumpBody->id)+"; not removing.").c_str()); subBody->clumpId=Body::ID_NONE; LOG_DEBUG("Removed body #"<id<<" from clump #"<id); } void Clump::addForceTorqueFromMembers(const State* clumpState, Scene* scene, Vector3r& F, Vector3r& T){ FOREACH(const MemberMap::value_type& mm, members){ const Body::id_t& memberId=mm.first; const shared_ptr& member=Body::byId(memberId,scene); assert(member->isClumpMember()); State* memberState=member->state.get(); const Vector3r& f=scene->forces.getForce(memberId); const Vector3r& t=scene->forces.getTorque(memberId); F+=f; T+=t+(memberState->pos-clumpState->pos).cross(f); } } /*! Clump's se3 will be updated (origin at centroid and axes coincident with principal inertia axes) and subSe3 modified in such a way that members positions in world coordinates will not change. Note: velocities and angularVelocities of constituents are zeroed. OLD DOCS (will be cleaned up): -# Clump::members values and Clump::physicalParameters::se3 are invalid from this point -# M=0; S=vector3r(0,0,0); I=zero tensor; (ALL calculations are in world coordinates!) -# loop over Clump::members (position x_i, mass m_i, inertia at subBody's centroid I_i) [this loop will be replaced by numerical integration (rasterization) for the intersecting case; the rest will be the same] - M+=m_i - S+=m_i*x_i (local static moments are zero (centroid) - get inertia tensor of subBody in world coordinates, by rotating the principal (local) tensor against subBody->se3->orientation; then translate it to world origin (parallel axes theorem), then I+=I_i_world -# clumpPos=S/M -# translate aggregate's inertia tensor; parallel axes on I (R=clumpPos): I^c_jk=I'_jk-M*(delta_jk R.R - R_j*R_k) [http://en.wikipedia.org/wiki/Moments_of_inertia#Parallel_axes_theorem] -# eigen decomposition of I, get principal inertia and rotation matrix of the clump -# se3->orientation=quaternion(rotation_matrix); se3->position=clumpPos -# update subSe3s */ void Clump::updateProperties(const shared_ptr& clumpBody, unsigned int discretization){ LOG_DEBUG("Updating clump #"<id<<" parameters"); const shared_ptr state(clumpBody->state); const shared_ptr clump(YADE_PTR_CAST(clumpBody->shape)); if(clump->members.empty()){ throw std::runtime_error("Clump::updateProperties: clump has zero members."); } // trivial case if(clump->members.size()==1){ LOG_DEBUG("Clump of size one will be treated specially.") MemberMap::iterator I=clump->members.begin(); shared_ptr subBody=Body::byId(I->first); //const shared_ptr& subRBP(YADE_PTR_CAST(subBody->physicalParameters)); State* subState=subBody->state.get(); // se3 of the clump as whole is the same as the member's se3 state->pos=subState->pos; state->ori=subState->ori; // relative member's se3 is identity I->second.position=Vector3r::Zero(); I->second.orientation=Quaternionr::Identity(); state->inertia=subState->inertia; state->mass=subState->mass; state->vel=Vector3r::Zero(); state->angVel=Vector3r::Zero(); return; } //check for intersections: bool intersecting = false; shared_ptr sph (new Sphere); int Sph_Index = sph->getClassIndexStatic(); // get sphere index for checking if bodies are spheres if (discretization>0){ FOREACH(MemberMap::value_type& mm, clump->members){ const shared_ptr subBody1=Body::byId(mm.first); FOREACH(MemberMap::value_type& mm, clump->members){ const shared_ptr subBody2=Body::byId(mm.first); if ((subBody1->shape->getClassIndex() == Sph_Index) && (subBody2->shape->getClassIndex() == Sph_Index) && (subBody1!=subBody2)){//clump members should be spheres Vector3r dist = subBody1->state->pos - subBody2->state->pos; const Sphere* sphere1 = YADE_CAST (subBody1->shape.get()); const Sphere* sphere2 = YADE_CAST (subBody2->shape.get()); Real un = (sphere1->radius+sphere2->radius) - dist.norm(); if (un > 0.001*min(sphere1->radius,sphere2->radius)) {intersecting = true; break;} } } if (intersecting) break; } } /* quantities suffixed by g: global (world) coordinates s: local subBody's coordinates c: local clump coordinates */ Real M=0; // mass Real dens=0;//density Vector3r Sg(0,0,0); // static moment, for getting clump's centroid Matrix3r Ig(Matrix3r::Zero()), Ic(Matrix3r::Zero()); // tensors of inertia; is upper triangular, zeros instead of symmetric elements /** algorithm for estimation of volumes and inertia tensor from clumps using summation/integration scheme with regular grid spacing (some parts copied from woo: http://bazaar.launchpad.net/~eudoxos/woo/trunk/view/head:/pkg/dem/Clump.cpp) */ if(intersecting){ //get boundaries of clump: AlignedBox3r aabb; FOREACH(MemberMap::value_type& mm, clump->members){ const shared_ptr subBody = Body::byId(mm.first); if (subBody->shape->getClassIndex() == Sph_Index){//clump member should be a sphere const Sphere* sphere = YADE_CAST (subBody->shape.get()); aabb.extend(subBody->state->pos + Vector3r::Constant(sphere->radius)); aabb.extend(subBody->state->pos - Vector3r::Constant(sphere->radius)); } } Real rMin=min(aabb.diagonal()[0],min(aabb.diagonal()[1],aabb.diagonal()[2])); //get volume and inertia tensor using regular cubic cell array inside bounding box of the clump: Real dx = rMin/discretization; //edge length of cell Real dv = pow(dx,3); //volume of cell long nCells=(aabb.sizes()/dx).prod(); if(nCells>1e7) LOG_WARN("Clump::updateProperties: Cell array has "<members){ const shared_ptr subBody = Body::byId(mm.first); if (subBody->shape->getClassIndex() == Sph_Index){//clump member should be a sphere dens = subBody->material->density; const Sphere* sphere = YADE_CAST (subBody->shape.get()); if((x-subBody->state->pos).squaredNorm() < pow(sphere->radius,2)){ Real m = dens*dv; M += m; Sg += m*x; //inertia I = sum_i( mass_i*dist^2 + I_s) ) //steiners theorem Ig += m*( x.dot(x)*Matrix3r::Identity()-x*x.transpose())/*dist^2*/+Matrix3r(Vector3r::Constant(dv*pow(dx,2)/6.).asDiagonal())/*I_s/m = d^2: along princial axes of dv; perhaps negligible?*/; break; } } } } } } } else {//not intersecting FOREACH(MemberMap::value_type& mm, clump->members){ // mm.first is Body::id_t, mm.second is Se3r of that body const shared_ptr subBody=Body::byId(mm.first); dens = subBody->material->density; if (subBody->shape->getClassIndex() == Sph_Index){//clump member should be a sphere State* subState=subBody->state.get(); const Sphere* sphere = YADE_CAST (subBody->shape.get()); Real vol = (4./3.)*Mathr::PI*pow(sphere->radius,3.); Real m = dens*vol; M+=m; Sg+=m*subState->pos; Ig+=Clump::inertiaTensorTranslate(Vector3r::Constant((2/5.)*m*pow(sphere->radius,2)).asDiagonal(),m,-1.*subState->pos); } else { // non-spherical bodies State* subState = subBody->state.get(); const Real& m = subState->mass; const Vector3r& inertia = subState->inertia; const Vector3r& pos = subState->pos; const Quaternionr& ori = subState->ori; M += m; Sg += m*pos; Ig += inertiaTensorTranslate(inertiaTensorRotate(inertia.asDiagonal(),ori),m,-pos); } } } assert(M>0); LOG_TRACE("M=\n"<pos=Sg/M; // this will calculate translation only, since rotation is zero Matrix3r Ic_orientG=inertiaTensorTranslate(Ig, -M /* negative mass means towards centroid */, state->pos); // inertia at clump's centroid but with world orientation LOG_TRACE("Ic_orientG=\n"< decomposed(Ic_orientG); const Matrix3r& R_g2c(decomposed.eigenvectors()); // has NaNs for identity matrix?? LOG_TRACE("R_g2c=\n"<ori=Quaternionr(R_g2c); state->ori.normalize(); state->inertia=decomposed.eigenvalues(); state->mass=M; // TODO: these might be calculated from members... but complicated... - someone needs that?! state->vel=state->angVel=Vector3r::Zero(); clumpBody->setAspherical(state->inertia[0]!=state->inertia[1] || state->inertia[0]!=state->inertia[2]); // update subBodySe3s; subtract clump orientation (=apply its inverse first) to subBody's orientation FOREACH(MemberMap::value_type& I, clump->members){ shared_ptr subBody=Body::byId(I.first); State* subState=subBody->state.get(); I.second.orientation=state->ori.conjugate()*subState->ori; I.second.position=state->ori.conjugate()*(subState->pos-state->pos); } } void Clump::updatePropertiesNonSpherical(const shared_ptr& clumpBody, bool intersecting,shared_ptr rb){ //FIXME //LOG_DEBUG("Updating clump #"<0); const shared_ptr state(clumpBody->state); const shared_ptr clump(YADE_PTR_CAST(clumpBody->shape)); // trivial case if(clump->members.size()==1){ LOG_DEBUG("Clump of size one will be treated specially.") MemberMap::iterator I=clump->members.begin(); shared_ptr subBody=Body::byId(I->first,rb); //const shared_ptr& subRBP(YADE_PTR_CAST(subBody->physicalParameters)); State* subState=subBody->state.get(); // se3 of the clump as whole is the same as the member's se3 state->pos=subState->pos; state->ori=subState->ori; // relative member's se3 is identity I->second.position=Vector3r::Zero(); I->second.orientation=Quaternionr::Identity(); state->inertia=subState->inertia; state->mass=subState->mass; state->vel=Vector3r::Zero(); state->angVel=Vector3r::Zero(); return; } /* quantities suffixed by g: global (world) coordinates s: local subBody's coordinates c: local clump coordinates */ double M=0; // mass Vector3r Sg(0,0,0); // static moment, for getting clump's centroid Matrix3r Ig(Matrix3r::Zero()), Ic(Matrix3r::Zero()); // tensors of inertia; is upper triangular, zeros instead of symmetric elements if(intersecting){ LOG_WARN("Self-intersecting clumps not yet implemented, intersections will be ignored."); intersecting=false; } // begin non-intersecting loop here if(!intersecting){ FOREACH(MemberMap::value_type& I, clump->members){ // I.first is Body::id_t, I.second is Se3r of that body shared_ptr subBody=Body::byId(I.first,rb); State* subState=subBody->state.get(); M+=subState->mass; Sg+=subState->mass*subState->pos; // transform from local to global coords Quaternionr subState_ori_conjugate=subState->ori.conjugate(); Matrix3r Imatrix=Matrix3r::Zero(); Imatrix.diagonal()=subState->inertia; // TRWM3MAT(Imatrix); TRWM3QUAT(subRBP_orientation_conjugate); Ig+=Clump::inertiaTensorTranslate(Clump::inertiaTensorRotate(Imatrix,subState_ori_conjugate),subState->mass,-1.*subState->pos); //TRWM3MAT(Clump::inertiaTensorRotate(Matrix3r(subRBP->inertia),subRBP_orientation_conjugate)); } } //TRVAR1(M); TRWM3MAT(Ig); TRWM3VEC(Sg); assert(M>0); state->pos=Sg/M; // clump's centroid // this will calculate translation only, since rotation is zero Matrix3r Ic_orientG=Clump::inertiaTensorTranslate(Ig, -M /* negative mass means towards centroid */, state->pos); // inertia at clump's centroid but with world orientation //TRWM3MAT(Ic_orientG); Matrix3r R_g2c(Matrix3r::Zero()); //rotation matrix Ic_orientG(1,0)=Ic_orientG(0,1); Ic_orientG(2,0)=Ic_orientG(0,2); Ic_orientG(2,1)=Ic_orientG(1,2); // symmetrize //TRWM3MAT(Ic_orientG); matrixEigenDecomposition(Ic_orientG,R_g2c,Ic); /*! @bug eigendecomposition might be wrong. see http://article.gmane.org/gmane.science.physics.yade.devel/99 for message. It is worked around below, however. */ // has NaNs for identity matrix! //TRWM3MAT(R_g2c); // set quaternion from rotation matrix state->ori=Quaternionr(R_g2c); state->ori.normalize(); // now Ic is diagonal state->inertia=Ic.diagonal(); state->mass=M; // this block will be removed once EigenDecomposition works for diagonal matrices //#if 1 // if(isnan(R_g2c(0,0))||isnan(R_g2c(0,1))||isnan(R_g2c(0,2))||isnan(R_g2c(1,0))||isnan(R_g2c(1,1))||isnan(R_g2c(1,2))||isnan(R_g2c(2,0))||isnan(R_g2c(2,1))||isnan(R_g2c(2,2))){ // throw std::logic_error("Clump::updateProperties: NaNs in eigen-decomposition of inertia matrix?!"); // } //#endif //TRWM3VEC(state->inertia); // TODO: these might be calculated from members... but complicated... - someone needs that?! state->vel=state->angVel=Vector3r::Zero(); clumpBody->setAspherical(state->inertia[0]!=state->inertia[1] || state->inertia[0]!=state->inertia[2]); // update subBodySe3s; subtract clump orientation (=apply its inverse first) to subBody's orientation FOREACH(MemberMap::value_type& I, clump->members){ // now, I->first is Body::id_t, I->second is Se3r of that body shared_ptr subBody=Body::byId(I.first,rb); //const shared_ptr& subRBP(YADE_PTR_CAST(subBody->physicalParameters)); State* subState=subBody->state.get(); I.second.orientation=state->ori.conjugate()*subState->ori; I.second.position=state->ori.conjugate()*(subState->pos-state->pos); } } void Clump::updatePropertiesNonSpherical(const shared_ptr& clumpBody, bool intersecting){ //FIXME //LOG_DEBUG("Updating clump #"<0); const shared_ptr state(clumpBody->state); const shared_ptr clump(YADE_PTR_CAST(clumpBody->shape)); // trivial case if(clump->members.size()==1){ LOG_DEBUG("Clump of size one will be treated specially.") MemberMap::iterator I=clump->members.begin(); shared_ptr subBody=Body::byId(I->first); //const shared_ptr& subRBP(YADE_PTR_CAST(subBody->physicalParameters)); State* subState=subBody->state.get(); // se3 of the clump as whole is the same as the member's se3 state->pos=subState->pos; state->ori=subState->ori; // relative member's se3 is identity I->second.position=Vector3r::Zero(); I->second.orientation=Quaternionr::Identity(); state->inertia=subState->inertia; state->mass=subState->mass; state->vel=Vector3r::Zero(); state->angVel=Vector3r::Zero(); return; } /* quantities suffixed by g: global (world) coordinates s: local subBody's coordinates c: local clump coordinates */ double M=0; // mass Vector3r Sg(0,0,0); // static moment, for getting clump's centroid Matrix3r Ig(Matrix3r::Zero()), Ic(Matrix3r::Zero()); // tensors of inertia; is upper triangular, zeros instead of symmetric elements if(intersecting){ LOG_WARN("Self-intersecting clumps not yet implemented, intersections will be ignored."); intersecting=false; } // begin non-intersecting loop here if(!intersecting){ FOREACH(MemberMap::value_type& I, clump->members){ // I.first is Body::id_t, I.second is Se3r of that body shared_ptr subBody=Body::byId(I.first); State* subState=subBody->state.get(); M+=subState->mass; Sg+=subState->mass*subState->pos; // transform from local to global coords Quaternionr subState_ori_conjugate=subState->ori.conjugate(); Matrix3r Imatrix=Matrix3r::Zero(); Imatrix.diagonal()=subState->inertia; // TRWM3MAT(Imatrix); TRWM3QUAT(subRBP_orientation_conjugate); Ig+=Clump::inertiaTensorTranslate(Clump::inertiaTensorRotate(Imatrix,subState_ori_conjugate),subState->mass,-1.*subState->pos); //TRWM3MAT(Clump::inertiaTensorRotate(Matrix3r(subRBP->inertia),subRBP_orientation_conjugate)); } } //TRVAR1(M); TRWM3MAT(Ig); TRWM3VEC(Sg); assert(M>0); state->pos=Sg/M; // clump's centroid // this will calculate translation only, since rotation is zero Matrix3r Ic_orientG=Clump::inertiaTensorTranslate(Ig, -M /* negative mass means towards centroid */, state->pos); // inertia at clump's centroid but with world orientation //TRWM3MAT(Ic_orientG); Matrix3r R_g2c(Matrix3r::Zero()); //rotation matrix Ic_orientG(1,0)=Ic_orientG(0,1); Ic_orientG(2,0)=Ic_orientG(0,2); Ic_orientG(2,1)=Ic_orientG(1,2); // symmetrize //TRWM3MAT(Ic_orientG); matrixEigenDecomposition(Ic_orientG,R_g2c,Ic); /*! @bug eigendecomposition might be wrong. see http://article.gmane.org/gmane.science.physics.yade.devel/99 for message. It is worked around below, however. */ // has NaNs for identity matrix! //TRWM3MAT(R_g2c); // set quaternion from rotation matrix state->ori=Quaternionr(R_g2c); state->ori.normalize(); // now Ic is diagonal state->inertia=Ic.diagonal(); state->mass=M; // this block will be removed once EigenDecomposition works for diagonal matrices //#if 1 // if(isnan(R_g2c(0,0))||isnan(R_g2c(0,1))||isnan(R_g2c(0,2))||isnan(R_g2c(1,0))||isnan(R_g2c(1,1))||isnan(R_g2c(1,2))||isnan(R_g2c(2,0))||isnan(R_g2c(2,1))||isnan(R_g2c(2,2))){ // throw std::logic_error("Clump::updateProperties: NaNs in eigen-decomposition of inertia matrix?!"); // } //#endif //TRWM3VEC(state->inertia); // TODO: these might be calculated from members... but complicated... - someone needs that?! state->vel=state->angVel=Vector3r::Zero(); clumpBody->setAspherical(state->inertia[0]!=state->inertia[1] || state->inertia[0]!=state->inertia[2]); // update subBodySe3s; subtract clump orientation (=apply its inverse first) to subBody's orientation FOREACH(MemberMap::value_type& I, clump->members){ // now, I->first is Body::id_t, I->second is Se3r of that body shared_ptr subBody=Body::byId(I.first); //const shared_ptr& subRBP(YADE_PTR_CAST(subBody->physicalParameters)); State* subState=subBody->state.get(); I.second.orientation=state->ori.conjugate()*subState->ori; I.second.position=state->ori.conjugate()*(subState->pos-state->pos); } } void Clump::addNonSpherical(const shared_ptr& clumpBody, const shared_ptr& subBody){ //FIXME Body::id_t subId=subBody->getId(); if(subBody->clumpId!=Body::ID_NONE) throw std::invalid_argument(("Body #"+boost::lexical_cast(subId)+" is already in clump #"+boost::lexical_cast(subBody->clumpId)).c_str()); const shared_ptr clump=YADE_PTR_CAST(clumpBody->shape); if(clump->members.count(subId)!=0) throw std::invalid_argument(("Body #"+boost::lexical_cast(subId)+" is already part of this clump #"+boost::lexical_cast(clumpBody->id)).c_str()); clump->members[subId]=Se3r(); // meaningful values will be put in by Clump::updateProperties subBody->clumpId=clumpBody->id; clumpBody->clumpId=clumpBody->id; // just to make sure clumpBody->setBounded(false); // disallow collisions with the clump itself //LOG_DEBUG("Added body #"< #pragma once #include #include #include #include /*! Body representing clump (rigid aggregate) composed by other existing bodies. Clump is one of bodies that reside in scene->bodies. When an existing body is added to ::Clump, it's ::Body::dynamic flag is set to false (it is still subscribed to all its engines, to make it possible to remove it from the clump again). All forces acting on Clump::members are made to act on the clump itself, which will ensure that they influence all Clump::members as if the clump were a rigid particle. What are clump requirements so that they function? -# Given any body, tell - if it is a clump member: Body::isClumpMember() - if it is a clump: Body:: isClump(). (Correct result is assured at each call to Clump::add). (we could use RTTI instead? Would that be more reliable?) - if it is a standalone Body: Body::isStandalone() - what is it's clump id (Body::clumpId) -# given the root body, tell - what clumps it contains (enumerate all bodies and filter clumps, see above) -# given a clump, tell - what bodies it contains (keys of ::Clump::members) - what are se3 of these bodies (values of ::Clump::members) -# add/delete bodies from/to clump (::Clump::add, ::Clump::del) - This includes saving se3 of the subBody: it \em must be in clump's local coordinates so that it is constant. The transformation from global to local is given by clump's se3 at the moment of addition. Clump's se3 is initially (origin,identity) -# Update clump's physical properties (Clump::updateProperties) - This \em must reposition members so that they have the same se3 globally -# Apply forces acting on members to the clump instead (done in NewtonsForceLaw, NewtonsMomentumLaw) - uses world coordinates to calculate effect on the clump's centroid -# Integrate position and orientation of the clump - LeapFrogPositionIntegrator and LeapFrogOrientationIntegrator move clump as whole - clump members are skipped, since they have Body::dynamic==false. - ClumpMemberMover is an engine that updates positions of the clump memebers in each timestep (calls Clump::moveSubBodies internally) Some more information can be found http://beta.arcig.cz/~eudoxos/phd/index.cgi/YaDe/HighLevelClumps For an example how to generate a clump, see ClumpTestGen::createOneClump. @todo GravityEngine should be applied to members, not to clump as such?! Still not sure. Perhaps Clumps should have mass and inertia set to zeros so that engines unaware of clumps do not act on it. It would have some private mass and insertia that would be used in NewtonsForceLaw etc for clumps specially... @note Collider::mayCollide (should be used by all colliders) bypasses Clumps explicitly. This no longer depends on the absence of bound. @note Clump relies on its id being assigned (as well as id of its components); therefore, only bodies that have already been inserted to the container may be added to Clump which has been itself already added to the container. We further requier that clump id is greater than ids of clumped bodies */ class NewtonIntegrator; class Clump: public Shape { public: typedef std::map MemberMap; static void add(const shared_ptr& clump, const shared_ptr& subBody); static void del(const shared_ptr& clump, const shared_ptr& subBody); //! Recalculate physical properties of Clump. static void updateProperties(const shared_ptr& clump, unsigned int discretization); static void updatePropertiesNonSpherical(const shared_ptr& clump, bool intersecting,shared_ptr rb);//FIXME static void updatePropertiesNonSpherical(const shared_ptr& clump, bool intersecting);//FIXME //! Calculate positions and orientations of members based on relative Se3; newton pointer (if non-NULL) calls NewtonIntegrator::saveMaximaVelocity // done as template to avoid cross-dependency between clump and newton (not necessary if all plugins are linked together) template static void moveMembers(const shared_ptr& clumpBody, Scene* scene, IntegratorT* integrator=NULL){ const shared_ptr& clump=YADE_PTR_CAST(clumpBody->shape); const shared_ptr& clumpState=clumpBody->state; FOREACH(MemberMap::value_type& B, clump->members){ // B.first is Body::id_t, B.second is local Se3r of that body in the clump const shared_ptr& b = Body::byId(B.first,scene); const shared_ptr& subState=b->state; const Vector3r& subPos(B.second.position); const Quaternionr& subOri(B.second.orientation); // position update subState->pos=clumpState->pos+clumpState->ori*subPos; subState->ori=clumpState->ori*subOri; // velocity update subState->vel=clumpState->vel+clumpState->angVel.cross(subState->pos-clumpState->pos); subState->angVel=clumpState->angVel; if(integrator) integrator->saveMaximaDisplacement(b); } } static void addNonSpherical(const shared_ptr& clump, const shared_ptr& subBody); //FIXME //! update member positions after clump being moved by mouse (in case simulation is paused and engines will not do that). void userForcedDisplacementRedrawHook(){ throw runtime_error("Clump::userForcedDisplacementRedrawHook not yet implemented (with Clump as subclass of Shape).");} //! get force and torque on the clump itself, from forces/torques on members; does not include force on clump itself void addForceTorqueFromMembers(const State* clumpState, Scene* scene, Vector3r& F, Vector3r& T); //! Recalculates inertia tensor of a body after translation away from (default) or towards its centroid. static Matrix3r inertiaTensorTranslate(const Matrix3r& I,const Real m, const Vector3r& off); //! Recalculate body's inertia tensor in rotated coordinates. static Matrix3r inertiaTensorRotate(const Matrix3r& I, const Matrix3r& T); //! Recalculate body's inertia tensor in rotated coordinates. static Matrix3r inertiaTensorRotate(const Matrix3r& I, const Quaternionr& rot); boost::python::dict members_get(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Clump,Shape,"Rigid aggregate of bodies", ((MemberMap,members,,Attr::hidden,"Ids and relative positions+orientations of members of the clump (should not be accessed directly)")) ((vector,ids,,Attr::readonly,"Ids of constituent particles (only informative; direct modifications will have no effect).")) //FIXME ,/*ctor*/ createIndex(); ,/*py*/ .add_property("members",&Clump::members_get,"Return clump members as {'id1':(relPos,relOri),...}") ); DECLARE_LOGGER; REGISTER_CLASS_INDEX(Clump,Shape); }; REGISTER_SERIALIZABLE(Clump); trunk-2017.01a/core/Dispatcher.hpp000066400000000000000000000245231304022710500167170ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include // real base class for all dispatchers (the other one are templates) class Dispatcher: public Engine{ public: // these functions look to be completely unused...? virtual string getFunctorType() { throw; }; virtual int getDimension() { throw; }; virtual string getBaseClassType(unsigned int ) { throw; }; // virtual ~Dispatcher() {}; YADE_CLASS_BASE_DOC(Dispatcher,Engine,"Engine dispatching control to its associated functors, based on types of argument it receives. This abstract base class provides no functionality in itself.") }; REGISTER_SERIALIZABLE(Dispatcher); /* Each real dispatcher derives from Dispatcher1D or Dispatcher2D (both templates), which in turn derive from Dispatcher (an Engine) and DynLibDispatcher (the dispatch logic). Because we need literal functor and class names for registration in python, we provide macro that creates the real dispatcher class with everything needed. */ #define _YADE_DISPATCHER1D_FUNCTOR_ADD(FunctorT,f) virtual void addFunctor(shared_ptr f){ add1DEntry(f->get1DFunctorType1(),f); } #define _YADE_DISPATCHER2D_FUNCTOR_ADD(FunctorT,f) virtual void addFunctor(shared_ptr f){ add2DEntry(f->get2DFunctorType1(),f->get2DFunctorType2(),f); } #define _YADE_DIM_DISPATCHER_FUNCTOR_DOC_ATTRS_CTOR_PY(Dim,DispatcherT,FunctorT,doc,attrs,ctor,py) \ typedef FunctorT FunctorType; \ void updateScenePtr(){ FOREACH(shared_ptr f, functors){ f->scene=scene; }} \ void postLoad(DispatcherT&){ clearMatrix(); FOREACH(shared_ptr f, functors) add(YADE_PTR_CAST(f)); } \ virtual void add(FunctorT* f){ add(shared_ptr(f)); } \ virtual void add(shared_ptr f){ bool dupe=false; string fn=f->getClassName(); FOREACH(const shared_ptr& f, functors) { if(fn==f->getClassName()) dupe=true; } if(!dupe) functors.push_back(f); addFunctor(f); } \ BOOST_PP_CAT(_YADE_DISPATCHER,BOOST_PP_CAT(Dim,D_FUNCTOR_ADD))(FunctorT,f) \ boost::python::list functors_get(void) const { boost::python::list ret; FOREACH(const shared_ptr& f, functors){ ret.append(f); } return ret; } \ void functors_set(const vector >& ff){ functors.clear(); FOREACH(const shared_ptr& f, ff) add(f); postLoad(*this); } \ void pyHandleCustomCtorArgs(boost::python::tuple& t, boost::python::dict& d){ if(boost::python::len(t)==0)return; if(boost::python::len(t)!=1) throw invalid_argument("Exactly one list of " BOOST_PP_STRINGIZE(FunctorT) " must be given."); typedef std::vector > vecF; vecF vf=boost::python::extract(t[0])(); functors_set(vf); t=boost::python::tuple(); } \ YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(DispatcherT,Dispatcher,"Dispatcher calling :yref:`functors<" BOOST_PP_STRINGIZE(FunctorT) ">` based on received argument type(s).\n\n" doc, \ ((vector >,functors,,,"Functors active in the dispatch mechanism [overridden below].")) /*additional attrs*/ attrs, \ /*ctor*/ ctor, /*py*/ py .add_property("functors",&DispatcherT::functors_get,&DispatcherT::functors_set,"Functors associated with this dispatcher." " :yattrtype:`vector >` ") \ .def("dispMatrix",&DispatcherT::dump,boost::python::arg("names")=true,"Return dictionary with contents of the dispatch matrix.").def("dispFunctor",&DispatcherT::getFunctor,"Return functor that would be dispatched for given argument(s); None if no dispatch; ambiguous dispatch throws."); \ ) #define YADE_DISPATCHER1D_FUNCTOR_DOC_ATTRS_CTOR_PY(DispatcherT,FunctorT,doc,attrs,ctor,py) _YADE_DIM_DISPATCHER_FUNCTOR_DOC_ATTRS_CTOR_PY(1,DispatcherT,FunctorT,doc,attrs,ctor,py) #define YADE_DISPATCHER2D_FUNCTOR_DOC_ATTRS_CTOR_PY(DispatcherT,FunctorT,doc,attrs,ctor,py) _YADE_DIM_DISPATCHER_FUNCTOR_DOC_ATTRS_CTOR_PY(2,DispatcherT,FunctorT,doc,attrs,ctor,py) // HELPER FUNCTIONS /*! Function returning class name (as string) for given index and topIndexable (top-level indexable, such as Shape, Material and so on) This function exists solely for debugging, is quite slow: it has to traverse all classes and ask for inheritance information. It should be used primarily to convert indices to names in Dispatcher::dictDispatchMatrix?D; since it relies on Omega for RTTI, this code could not be in Dispatcher itself. s*/ template std::string Dispatcher_indexToClassName(int idx){ boost::scoped_ptr top(new topIndexable); std::string topName=top->getClassName(); typedef std::pair classItemType; FOREACH(classItemType clss, Omega::instance().getDynlibsDescriptor()){ if(Omega::instance().isInheritingFrom_recursive(clss.first,topName) || clss.first==topName){ // create instance, to ask for index shared_ptr inst=YADE_PTR_DYN_CAST(ClassFactory::instance().createShared(clss.first)); assert(inst); if(inst->getClassIndex()<0 && inst->getClassName()!=top->getClassName()){ throw logic_error("Class "+inst->getClassName()+" didn't use REGISTER_CLASS_INDEX("+inst->getClassName()+","+top->getClassName()+") and/or forgot to call createIndex() in the ctor. [[ Please fix that! ]]"); } if(inst->getClassIndex()==idx) return clss.first; } } throw runtime_error("No class with index "+boost::lexical_cast(idx)+" found (top-level indexable is "+topName+")"); } //! Return class index of given indexable template int Indexable_getClassIndex(const shared_ptr i){return i->getClassIndex();} //! Return sequence (hierarchy) of class indices of given indexable; optionally convert to names template boost::python::list Indexable_getClassIndices(const shared_ptr i, bool convertToNames){ int depth=1; boost::python::list ret; int idx0=i->getClassIndex(); if(convertToNames) ret.append(Dispatcher_indexToClassName(idx0)); else ret.append(idx0); if(idx0<0) return ret; // don't continue and call getBaseClassIndex(), since we are at the top already while(true){ int idx=i->getBaseClassIndex(depth++); if(convertToNames) ret.append(Dispatcher_indexToClassName(idx)); else ret.append(idx); if(idx<0) return ret; } } template < class FunctorType, bool autoSymmetry=true> class Dispatcher1D : public Dispatcher, public DynLibDispatcher < TYPELIST_1(typename FunctorType::DispatchType1) // base classes for dispatch , FunctorType // class that provides multivirtual call , typename FunctorType::ReturnType // return type , typename FunctorType::ArgumentTypes , autoSymmetry > { public : typedef typename FunctorType::DispatchType1 baseClass; typedef baseClass argType1; typedef FunctorType functorType; typedef DynLibDispatcher dispatcherBase; shared_ptr getFunctor(shared_ptr arg){ return dispatcherBase::getExecutor(arg); } boost::python::dict dump(bool convertIndicesToNames){ boost::python::dict ret; FOREACH(const DynLibDispatcher_Item1D& item, dispatcherBase::dataDispatchMatrix1D()){ if(convertIndicesToNames){ string arg1=Dispatcher_indexToClassName(item.ix1); ret[boost::python::make_tuple(arg1)]=item.functorName; } else ret[boost::python::make_tuple(item.ix1)]=item.functorName; } return ret; } int getDimension() { return 1; } virtual string getFunctorType(){ shared_ptr eu(new FunctorType); return eu->getClassName(); } virtual string getBaseClassType(unsigned int i){ if (i==0) { shared_ptr bc(new baseClass); return bc->getClassName(); } else return ""; } public: REGISTER_ATTRIBUTES(Dispatcher,); REGISTER_CLASS_AND_BASE(Dispatcher1D,Dispatcher DynLibDispatcher); }; template < class FunctorType, bool autoSymmetry=true> class Dispatcher2D : public Dispatcher, public DynLibDispatcher < TYPELIST_2(typename FunctorType::DispatchType1,typename FunctorType::DispatchType2) // base classes for dispatch , FunctorType // class that provides multivirtual call , typename FunctorType::ReturnType // return type , typename FunctorType::ArgumentTypes // argument of engine unit , autoSymmetry > { public : typedef typename FunctorType::DispatchType1 baseClass1; typedef typename FunctorType::DispatchType2 baseClass2; typedef baseClass1 argType1; typedef baseClass2 argType2; typedef FunctorType functorType; typedef DynLibDispatcher dispatcherBase; shared_ptr getFunctor(shared_ptr arg1, shared_ptr arg2){ return dispatcherBase::getExecutor(arg1,arg2); } boost::python::dict dump (bool convertIndicesToNames) { boost::python::dict ret; FOREACH(const DynLibDispatcher_Item2D& item, dispatcherBase::dataDispatchMatrix2D()){ if(convertIndicesToNames){ string arg1=Dispatcher_indexToClassName(item.ix1), arg2=Dispatcher_indexToClassName(item.ix2); ret[boost::python::make_tuple(arg1,arg2)]=item.functorName; } else ret[boost::python::make_tuple(item.ix1,item.ix2)]=item.functorName; } return ret; } virtual int getDimension() { return 2; } virtual string getFunctorType(){ shared_ptr eu(new FunctorType); return eu->getClassName(); } virtual string getBaseClassType(unsigned int i){ if (i==0){ shared_ptr bc(new baseClass1); return bc->getClassName(); } else if (i==1){ shared_ptr bc(new baseClass2); return bc->getClassName();} else return ""; } public: REGISTER_ATTRIBUTES(Dispatcher,); REGISTER_CLASS_AND_BASE(Dispatcher2D,Dispatcher DynLibDispatcher); }; trunk-2017.01a/core/DisplayParameters.hpp000066400000000000000000000033031304022710500202530ustar00rootroot00000000000000#pragma once /* Class for storing set of display parameters. * * The interface sort of emulates map string->string (which is not handled by yade-serialization). * * The "keys" (called displayTypes) are intended to be "OpenGLRenderer" or "GLViewer" (and perhaps other). * The "values" are intended to be XML representation of display parameters, obtained either by yade-serialization * with OpenGLRenderer and saveStateToStream with QGLViewer (and GLViewer). * */ class DisplayParameters: public Serializable{ private: std::vector values; std::vector displayTypes; public: //! Get value of given display type and put it in string& value and return true; if there is no such display type, return false. bool getValue(std::string displayType, std::string& value){assert(values.size()==displayTypes.size()); vector::iterator I=std::find(displayTypes.begin(),displayTypes.end(),displayType); if(I==displayTypes.end()) return false; value=values[std::distance(displayTypes.begin(),I)]; return true;} //! Set value of given display type; if such display type exists, it is overwritten, otherwise a new one is created. void setValue(std::string displayType, std::string value){assert(values.size()==displayTypes.size()); vector::iterator I=std::find(displayTypes.begin(),displayTypes.end(),displayType); if(I==displayTypes.end()){displayTypes.push_back(displayType); values.push_back(value);} else {values[std::distance(displayTypes.begin(),I)]=value;};} DisplayParameters(){} virtual ~DisplayParameters(){} REGISTER_ATTRIBUTES(Serializable,(displayTypes)(values)); REGISTER_CLASS_AND_BASE(DisplayParameters,Serializable); }; REGISTER_SERIALIZABLE(DisplayParameters); trunk-2017.01a/core/EnergyTracker.hpp000066400000000000000000000067231304022710500174000ustar00rootroot00000000000000#pragma once #include #include namespace py=boost::python; class EnergyTracker: public Serializable{ public: ~EnergyTracker(); void findId(const std::string& name, int& id, bool reset=false, bool newIfNotFound=true){ if(id>0) return; // the caller should have checked this already if(names.count(name)) id=names[name]; else if(newIfNotFound) { #ifdef YADE_OPENMP #pragma omp critical #endif { energies.resize(energies.size()+1); id=energies.size()-1; resetStep.resize(id+1); resetStep[id]=reset; names[name]=id; assert(id<(int)energies.size()); assert(id>=0); } } } // set value of the accumulator; note: must NOT be called from parallel sections! void set(const Real& val, const std::string& name, int &id){ if(id<0) findId(name,id,/* do not reset value that is set directly */ false); energies.set(id,val); } // add value to the accumulator; safely called from parallel sections void add(const Real& val, const std::string& name, int &id, bool reset=false){ if(id<0) findId(name,id,reset); energies.add(id,val); } Real getItem_py(const std::string& name){ int id=-1; findId(name,id,false,false); if (id<0) {PyErr_SetString(PyExc_KeyError,("Unknown energy name '"+name+"'.").c_str()); py::throw_error_already_set(); } return energies.get(id); } void setItem_py(const std::string& name, Real val){ int id=-1; set(val,name,id); } void clear(){ energies.clear(); names.clear(); resetStep.clear();} void resetResettables(){ size_t sz=energies.size(); for(size_t id=0; id > dta=energies.getPerThreadData(); FOREACH(pairStringInt p,names) ret[p.first]=dta[p.second]; return ret; }; typedef std::map mapStringInt; typedef std::pair pairStringInt; YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(EnergyTracker,Serializable,"Storage for tracing energies. Only to be used if :yref:`O.trackEnergy` is True.", ((OpenMPArrayAccumulator,energies,,,"Energy values, in linear array")) ((mapStringInt,names,,Attr::hidden,"Associate textual name to an index in the energies array.")) ((vector,resetStep,,Attr::hidden,"Whether the respective energy value should be reset at every step.")) ,/*ctor*/ ,/*py*/ .def("__getitem__",&EnergyTracker::getItem_py,"Get energy value for given name.") .def("__setitem__",&EnergyTracker::setItem_py,"Set energy value for given name (will create a non-resettable item, if it does not exist yet).") .def("clear",&EnergyTracker::clear,"Clear all stored values.") .def("keys",&EnergyTracker::keys_py,"Return defined energies.") .def("items",&EnergyTracker::items_py,"Return contents as list of (name,value) tuples.") .def("total",&EnergyTracker::total,"Return sum of all energies.") .add_property("_perThreadData",&EnergyTracker::perThreadData,"Contents as dictionary, where each value is tuple of individual threads' values (for debugging)") ) }; REGISTER_SERIALIZABLE(EnergyTracker); trunk-2017.01a/core/Engine.hpp000066400000000000000000000072611304022710500160360ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include class Body; class Scene; CREATE_LOGGER(Engine); class Engine: public Serializable{ public: // pointer to the simulation, set at every step by Scene::moveToNextTimeStep Scene* scene; //! high-level profiling information; not serializable TimingInfo timingInfo; //! precise profiling information (timing of fragments of the engine) shared_ptr timingDeltas; virtual ~Engine() {}; virtual bool isActivated() { return true; }; virtual void action() { LOG_FATAL("Engine "<(new TimingDeltas); #endif , /* py */ .add_property("execTime",&Engine::timingInfo_nsec_get,&Engine::timingInfo_nsec_set,"Cummulative time this Engine took to run (only used if :yref:`O.timingEnabled`\\ ==\\ ``True``).") .add_property("execCount",&Engine::timingInfo_nExec_get,&Engine::timingInfo_nExec_set,"Cummulative count this engine was run (only used if :yref:`O.timingEnabled`\\ ==\\ ``True``).") .def_readonly("timingDeltas",&Engine::timingDeltas,"Detailed information about timing inside the Engine itself. Empty unless enabled in the source code and :yref:`O.timingEnabled`\\ ==\\ ``True``.") .def("__call__",&Engine::explicitAction) ); }; REGISTER_SERIALIZABLE(Engine); trunk-2017.01a/core/FileGenerator.cpp000066400000000000000000000047531304022710500173550ustar00rootroot00000000000000/************************************************************************* * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include #include #include #include #include"FileGenerator.hpp" CREATE_LOGGER(FileGenerator); bool FileGenerator::generate(std::string& msg){ throw invalid_argument("Calling abstract FileGenerator::generate() does not make sense."); } bool FileGenerator::generateAndSave(const string& outputFileName, string& message) { bool status; message=""; boost::posix_time::ptime now = boost::posix_time::second_clock::local_time(); try { status=generate(message); // will modify message } catch(std::exception& e){ LOG_FATAL("Unhandled exception: "< #include #include "Scene.hpp" #include "ThreadWorker.hpp" class FileGenerator: public Serializable { protected: shared_ptr scene; public: bool generateAndSave(const string& outFile, string& message); protected : //! Returns whether the generation was successful; message for user is in FileGenerator::message virtual bool generate(std::string& msg); void pyGenerate(const string& out); void pyLoad(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(FileGenerator,Serializable,"Base class for scene generators, preprocessors.", /*attrs*/, /*ctor*/ , .def("generate",&FileGenerator::pyGenerate,(boost::python::arg("out")),"Generate scene, save to given file") .def("load",&FileGenerator::pyLoad,"Generate scene, save to temporary file and load immediately"); ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(FileGenerator); trunk-2017.01a/core/ForceContainer.hpp000066400000000000000000000124651304022710500175340ustar00rootroot00000000000000// 2009 © Václav Šmilauer #pragma once #include #include #include // make sure that (void*)&vec[0]==(void*)&vec BOOST_STATIC_ASSERT(sizeof(Vector3r)==3*sizeof(Real)); #ifdef YADE_OPENMP #include #endif /*! Container for Body External Variables (forces), typically forces and torques from interactions. * Values should be reset at every iteration by calling ForceContainer::reset(); * If you want to add your own force type, you need to: * * 1. Create storage vector * 2. Create accessor function * 3. Update the resize function * 4. Update the reset function * 5. update the sync function (for the multithreaded implementation) * * This class exists in two flavors: non-parallel and parallel. The parallel one stores * force increments separately for every thread and sums those when sync() is called. * The reason of this design is that the container is not truly random-access, but rather * is written to everywhere in one phase and read in the next one. Adding to force/torque * marks the container as dirty and sync() must be performed before reading the stored data. * Calling getForce/getTorque when the container is not synchronized throws an exception. * * It is intentional that sync() needs to be called exlicitly, since syncs are expensive and * the programmer should be aware of that. Sync is however performed only if the container * is dirty. Every full sync increments the syncCount variable, that should ideally equal * the number of steps (one per step). * * The number of threads (omp_get_max_threads) may not change once ForceContainer is constructed. * * The non-parallel flavor has the same interface, but sync() is no-op and synchronization * is not enforced at all. */ //! This is the parallel flavor of ForceContainer class ForceContainer { private: typedef std::vector vvector; #ifdef YADE_OPENMP std::vector _forceData; std::vector _torqueData; std::vector _moveData; std::vector _rotData; std::vector _maxId; std::vector sizeOfThreads; void ensureSize(Body::id_t id, int threadN); #else void ensureSize(Body::id_t id); Body::id_t _maxId=0; #endif vvector _force, _torque, _move, _rot, _permForce, _permTorque; size_t size = 0; bool syncedSizes = true; int nThreads; bool synced = true; bool moveRotUsed = false; bool permForceUsed = false; boost::mutex globalMutex; const Vector3r _zero = Vector3r::Zero(); void ensureSynced(); // dummy function to avoid template resolution failure friend class boost::serialization::access; template void serialize(ArchiveT & ar, unsigned int version){} public: unsigned long syncCount = 0; long lastReset = 0; ForceContainer(); const Vector3r& getForce(Body::id_t id); void addForce(Body::id_t id, const Vector3r& f); const Vector3r& getTorque(Body::id_t id); void addTorque(Body::id_t id, const Vector3r& t); const Vector3r& getMove(Body::id_t id); void addMove(Body::id_t id, const Vector3r& m); const Vector3r& getRot(Body::id_t id); void addRot(Body::id_t id, const Vector3r& r); void addMaxId(Body::id_t id); void setPermForce(Body::id_t id, const Vector3r& f); void setPermTorque(Body::id_t id, const Vector3r& t); const Vector3r& getPermForce(Body::id_t id); const Vector3r& getPermTorque(Body::id_t id); /*! Function to allow friend classes to get force even if not synced. Used for clumps by NewtonIntegrator. * Dangerous! The caller must know what it is doing! (i.e. don't read after write * for a particular body id. */ const Vector3r& getForceUnsynced (Body::id_t id); const Vector3r& getTorqueUnsynced(Body::id_t id); void addForceUnsynced(Body::id_t id, const Vector3r& f); void addTorqueUnsynced(Body::id_t id, const Vector3r& m); /* To be benchmarked: sum thread data in getForce/getTorque upon request for each body individually instead of by the sync() function globally */ // this function is used from python so that running simulation is not slowed down by sync'ing on occasions // since Vector3r writes are not atomic, it might (rarely) return wrong value, if the computation is running meanwhile const Vector3r getForceSingle (Body::id_t id); const Vector3r getTorqueSingle(Body::id_t id); const Vector3r getMoveSingle (Body::id_t id); const Vector3r getRotSingle (Body::id_t id); #ifdef YADE_OPENMP void syncSizesOfContainers(); void resize(size_t newSize, int threadN); #else void resize(size_t newSize); #endif /* Sum contributions from all threads, save to _force&_torque. * Locks globalMutex, since one thread modifies common data (_force&_torque). * Must be called before get* methods are used. Exception is thrown otherwise, since data are not consistent. */ void sync(); void resizePerm(size_t newSize); /*! Reset all resetable data, also reset summary forces/torques and mark the container clean. If resetAll, reset also user defined forces and torques*/ // perhaps should be private and friend Scene or whatever the only caller should be void reset(long iter, bool resetAll=false); //! say for how many threads we have allocated space const int getNumAllocatedThreads() const; const bool getMoveRotUsed() const; const bool getPermForceUsed() const; }; trunk-2017.01a/core/ForceContainerParallel.cpp000066400000000000000000000166021304022710500212010ustar00rootroot00000000000000#include void ForceContainer::ensureSynced() { if(!synced) throw runtime_error("ForceContainer not thread-synchronized; call sync() first!"); } void ForceContainer::addForceUnsynced(Body::id_t id, const Vector3r& f) { assert ((size_t)id void ForceContainer::ensureSize(Body::id_t id, int threadN) { assert(nThreads>omp_get_thread_num()); const Body::id_t idMaxTmp = max(id, _maxId[threadN]); _maxId[threadN] = 0; if (threadN<0) { resizePerm(min((size_t)1.5*(idMaxTmp+100),(size_t)(idMaxTmp+2000))); } else if (sizeOfThreads[threadN]<=(size_t)idMaxTmp) { resize(min((size_t)1.5*(idMaxTmp+100),(size_t)(idMaxTmp+2000)),threadN); } } ForceContainer::ForceContainer() { nThreads=omp_get_max_threads(); for(int i=0; i 0) { synced = false;} } if(synced) return; boost::mutex::scoped_lock lock(globalMutex); if(synced) return; // if synced meanwhile for(int i=0; i 0) { ensureSize(_maxId[i],i);} } syncSizesOfContainers(); for(long id=0; id<(long)size; id++){ Vector3r sumF(Vector3r::Zero()), sumT(Vector3r::Zero()); for(int thread=0; thread ForceContainer::ForceContainer() {}; void ForceContainer::ensureSize(Body::id_t id) { const Body::id_t idMaxTmp = max(id, _maxId); _maxId = 0; if(size<=(size_t)idMaxTmp) { resize(min((size_t)1.5*(idMaxTmp+100),(size_t)(idMaxTmp+2000))); }; } const Vector3r& ForceContainer::getForce(Body::id_t id) { ensureSize(id); return _force[id]; } void ForceContainer::addForce(Body::id_t id,const Vector3r& f) { ensureSize(id); _force[id]+=f; } const Vector3r& ForceContainer::getTorque(Body::id_t id) { ensureSize(id); return _torque[id]; } void ForceContainer::addTorque(Body::id_t id,const Vector3r& t) { ensureSize(id); _torque[id]+=t; } const Vector3r& ForceContainer::getMove(Body::id_t id) { ensureSize(id); return _move[id]; } void ForceContainer::addMove(Body::id_t id,const Vector3r& f) { ensureSize(id); moveRotUsed=true; _move[id]+=f; } const Vector3r& ForceContainer::getRot(Body::id_t id) { ensureSize(id); return _rot[id]; } void ForceContainer::addRot(Body::id_t id,const Vector3r& f) { ensureSize(id); moveRotUsed=true; _rot[id]+=f; } void ForceContainer::addMaxId(Body::id_t id) { _maxId=id; } void ForceContainer::setPermForce(Body::id_t id, const Vector3r& f) { ensureSize(id); _permForce[id]=f; permForceUsed=true; } void ForceContainer::setPermTorque(Body::id_t id, const Vector3r& t) { ensureSize(id); _permTorque[id]=t; permForceUsed=true; } const Vector3r& ForceContainer::getPermForce(Body::id_t id) { ensureSize(id); return _permForce[id]; } const Vector3r& ForceContainer::getPermTorque(Body::id_t id) { ensureSize(id); return _permTorque[id]; } const Vector3r& ForceContainer::getForceUnsynced (Body::id_t id) { return getForce(id); } const Vector3r& ForceContainer::getTorqueUnsynced(Body::id_t id) { return getForce(id); } const Vector3r ForceContainer::getForceSingle (Body::id_t id) { ensureSize(id); if (permForceUsed) { return _force [id] + _permForce[id]; } else { return _force [id]; } } const Vector3r ForceContainer::getTorqueSingle(Body::id_t id) { ensureSize(id); if (permForceUsed) { return _torque[id] + _permTorque[id]; } else { return _torque[id]; } } const Vector3r ForceContainer::getMoveSingle(Body::id_t id) { ensureSize(id); return _move [id]; } const Vector3r ForceContainer::getRotSingle(Body::id_t id) { ensureSize(id); return _rot[id]; } void ForceContainer::sync() { if (_maxId>0) { ensureSize(_maxId); _maxId=0; } if (permForceUsed) { for(long id=0; id<(long)size; id++) { _force[id]+=_permForce[id]; _torque[id]+=_permTorque[id]; } } return; } void ForceContainer::reset(long iter, bool resetAll) { memset(&_force [0],0,sizeof(Vector3r)*size); memset(&_torque[0],0,sizeof(Vector3r)*size); if(moveRotUsed){ memset(&_move [0],0,sizeof(Vector3r)*size); memset(&_rot [0],0,sizeof(Vector3r)*size); moveRotUsed=false; } if (resetAll){ memset(&_permForce [0], 0,sizeof(Vector3r)*size); memset(&_permTorque[0], 0,sizeof(Vector3r)*size); permForceUsed = false; } lastReset=iter; } void ForceContainer::resize(size_t newSize) { _force.resize(newSize,Vector3r::Zero()); _torque.resize(newSize,Vector3r::Zero()); _permForce.resize(newSize,Vector3r::Zero()); _permTorque.resize(newSize,Vector3r::Zero()); _move.resize(newSize,Vector3r::Zero()); _rot.resize(newSize,Vector3r::Zero()); size=newSize; } const int ForceContainer::getNumAllocatedThreads() const {return 1;} const bool ForceContainer::getMoveRotUsed() const {return moveRotUsed;} const bool ForceContainer::getPermForceUsed() const {return permForceUsed;} #endif trunk-2017.01a/core/FrontEnd.hpp000066400000000000000000000016161304022710500163460ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include "Omega.hpp" #include class FrontEnd : public Factorable { public : FrontEnd () {}; virtual ~FrontEnd () {}; virtual int run(int , char * []) { return -1;}; // called before actually invoking it virtual bool available(){return false;} REGISTER_CLASS_AND_BASE(FrontEnd,Factorable); }; REGISTER_FACTORABLE(FrontEnd); trunk-2017.01a/core/Functor.hpp000066400000000000000000000117621304022710500162520ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include class TimingDeltas; class Scene; class Functor: public Serializable { public: virtual vector getFunctorTypes(){throw;} shared_ptr timingDeltas; //! updated before every dispatch loop by the dispatcher; DO NOT ABUSE access to scene, except for getting global variables like scene->dt. Scene* scene; virtual ~Functor() {}; // defined in Dispatcher.cpp YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Functor,Serializable,"Function-like object that is called by Dispatcher, if types of arguments match those the Functor declares to accept.", ((string,label,,,"Textual label for this object; must be a valid python identifier, you can refer to it directly from python.")), /*ctor*/ #ifdef USE_TIMING_DELTAS timingDeltas=shared_ptr(new TimingDeltas); #endif , .def_readonly("timingDeltas",&Functor::timingDeltas,"Detailed information about timing inside the Dispatcher itself. Empty unless enabled in the source code and O.timingEnabled==True.") .add_property("bases",&Functor::getFunctorTypes,"Ordered list of types (as strings) this functor accepts.") ); }; REGISTER_SERIALIZABLE(Functor); template < class _DispatchType1, class _ReturnType, class _ArgumentTypes > class Functor1D: public Functor, public FunctorWrapper<_ReturnType, _ArgumentTypes> { public: typedef _DispatchType1 DispatchType1; typedef _ReturnType ReturnType; typedef _ArgumentTypes ArgumentTypes; #define FUNCTOR1D(type1) public: std::string get1DFunctorType1(void){return string(#type1);} int checkArgTypes(const shared_ptr& arg1){ return (bool)YADE_PTR_DYN_CAST(arg1)?1:0; } virtual std::string get1DFunctorType1(void){throw runtime_error("Class "+this->getClassName()+" did not use FUNCTOR1D to declare its argument type?"); } virtual vector getFunctorTypes(void){vector ret; ret.push_back(get1DFunctorType1()); return ret;}; // check that the object can be correctly cast to the derived class handled by the functor (will be used if ever utils.createInteraction can be called with list of functors only) // virtual bool checkArgTypes(const shared_ptr& arg1){ throw runtime_error("Class "+this->getClassName()+" did not use FUNCTOR1D to declare its argument type?"); } REGISTER_CLASS_AND_BASE(Functor1D,Functor FunctorWrapper); /* do not REGISTER_ATTRIBUTES here, since we are template; derived classes should call REGISTER_ATTRIBUTES(Functor,(their)(own)(attributes)), bypassing Functor1D */ }; template < class _DispatchType1, class _DispatchType2, class _ReturnType, class _ArgumentTypes > class Functor2D: public Functor, public FunctorWrapper<_ReturnType, _ArgumentTypes> { public: typedef _DispatchType1 DispatchType1; typedef _DispatchType2 DispatchType2; typedef _ReturnType ReturnType; typedef _ArgumentTypes ArgumentTypes; #define FUNCTOR2D(type1,type2) public: std::string get2DFunctorType1(void){return string(#type1);}; std::string get2DFunctorType2(void){return string(#type2);}; int checkArgTypes(const shared_ptr& arg1, const shared_ptr& arg2){ if(YADE_PTR_DYN_CAST(arg1)&&YADE_PTR_DYN_CAST(arg2)) return 1; if(YADE_PTR_DYN_CAST(arg2)&&YADE_PTR_DYN_CAST(arg1)) return -1; return 0; } virtual std::string get2DFunctorType1(void){throw logic_error("Class "+this->getClassName()+" did not use FUNCTOR2D to declare its argument types?");} virtual std::string get2DFunctorType2(void){throw logic_error("Class "+this->getClassName()+" did not use FUNCTOR2D to declare its argument types?");} virtual vector getFunctorTypes(){vector ret; ret.push_back(get2DFunctorType1()); ret.push_back(get2DFunctorType2()); return ret;}; // check that objects can be correctly cast to derived classes handled by the functor (see comment in Functor1D:: checkArgTypes) // virtual bool checkArgTypes(const shared_ptr&, const shared_ptr&){ throw logic_error("Class "+this->getClassName()+" did not use FUNCTOR2D to declare its argument types?"); } REGISTER_CLASS_AND_BASE(Functor2D,Functor FunctorWrapper); /* do not REGISTER_ATTRIBUTES here, since we are template; derived classes should call REGISTER_ATTRIBUTES(Functor,(their)(own)(attributes)), bypassing Functor2D */ }; trunk-2017.01a/core/GLConfig.hpp000066400000000000000000000030511304022710500162520ustar00rootroot00000000000000// code not yet for use (6/12/2009); if long here uselessly, delete. // // 2009 © Václav Šmilauer #include /*! Storage for general 3d view settings. Is saved along with simulation and passed to every call to render(...). Contains more or less what used to be inside OpenGLRenderer. */ class GLConfig: public Serializable{ Vector3r lightPos,bgColor; Body::id_t currSel; bool dof,id,bbox,geom,wire,intrGeom,intrPhys; int mask; bool scaleDisplacements,scaleRotations; Vector3r displacementScale; Real rotationScale; vector clipPlaneSe3; vector clipPlaneActive; // should be bool, but serialization doesn't handle vector // not saved Vector3r highlightEmission0; Vector3r highlightEmission1; // normalized saw signal with given periodicity, with values ∈ 〈0,1〉 */ Real normSaw(Real t, Real period){ Real xi=(t-period*((int)(t/period)))/period; /* normalized value, (0-1〉 */ return (xi<.5?2*xi:2-2*xi); } Real normSquare(Real t, Real period){ Real xi=(t-period*((int)(t/period)))/period; /* normalized value, (0-1〉 */ return (xi<.5?0:1); } //! wrap number to interval x0…x1 Real wrapCell(const Real x, const Real x0, const Real x1); //! wrap point to inside Scene's cell (identity if !Scene::isPeriodic) Vector3r wrapCellPt(const Vector3r& pt, Scene* rb); void drawPeriodicCell(Scene*); REGISTER_ATTRIBUTES(Serializable,(dof)(id)(bbox)(geom)(wire)(intrGeom)(intrPhys)(mask)(scaleDisplacements)(scaleRotations)(displacementScale)(rotationScale)(clipPlaneSe3)(clipPlaneActive)); }; trunk-2017.01a/core/GlobalEngine.hpp000066400000000000000000000014511304022710500171520ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include "Engine.hpp" class GlobalEngine: public Engine{ public : virtual ~GlobalEngine() {}; YADE_CLASS_BASE_DOC(GlobalEngine,Engine,"Engine that will generally affect the whole simulation (contrary to PartialEngine)."); }; REGISTER_SERIALIZABLE(GlobalEngine); trunk-2017.01a/core/IGeom.hpp000066400000000000000000000017201304022710500156230ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include class IGeom : public Serializable, public Indexable { YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(IGeom,Serializable,"Geometrical configuration of interaction", /*no attrs*/, /*ctor*/, /*py*/ YADE_PY_TOPINDEXABLE(IGeom) ); REGISTER_INDEX_COUNTER(IGeom); }; REGISTER_SERIALIZABLE(IGeom); trunk-2017.01a/core/IPhys.hpp000066400000000000000000000017441304022710500156650ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include class IPhys : public Serializable, public Indexable { YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(IPhys,Serializable,"Physical (material) properties of :yref:`interaction`.", /*attrs*/, /*ctor*/, /*py*/YADE_PY_TOPINDEXABLE(IPhys) ); REGISTER_INDEX_COUNTER(IPhys); }; REGISTER_SERIALIZABLE(IPhys); trunk-2017.01a/core/Interaction.cpp000066400000000000000000000025651304022710500171050ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include"Interaction.hpp" #include Interaction::Interaction(Body::id_t newId1,Body::id_t newId2): id1(newId1), id2(newId2), cellDist(Vector3i(0,0,0)){ reset(); } bool Interaction::isFresh(Scene* rb){ return iterMadeReal==rb->iter;} void Interaction::init(){ iterMadeReal=-1; functorCache.geomExists=true; isActive=true; } void Interaction::reset(){ geom=shared_ptr(); phys=shared_ptr(); functorCache.geom = nullptr; functorCache.phys = nullptr; functorCache.constLaw = nullptr; init(); } void Interaction::swapOrder(){ if(geom || phys){ throw std::logic_error("Bodies in interaction cannot be swapped if they have geom or phys."); } std::swap(id1,id2); cellDist*=-1; } trunk-2017.01a/core/Interaction.hpp000066400000000000000000000076611304022710500171140ustar00rootroot00000000000000#pragma once #include // keep those two here, template instantiation & boost::python gets broken otherwise, e.g. https://bugs.launchpad.net/bugs/618766 #include #include #include class IGeomFunctor; class IPhysFunctor; class LawFunctor; class Scene; class Interaction: public Serializable{ private: friend class IPhysDispatcher; friend class InteractionLoop; public: bool isReal() const {return (bool)geom && (bool)phys;} //! If this interaction was just created in this step (for the constitutive law, to know that it is the first time there) bool isFresh(Scene* rb); bool isActive; Interaction(Body::id_t newId1,Body::id_t newId2); const Body::id_t& getId1() const {return id1;}; const Body::id_t& getId2() const {return id2;}; //! swaps order of bodies within the interaction void swapOrder(); bool operator<(const Interaction& other) const { return getId1() geom = nullptr; shared_ptr phys = nullptr; shared_ptr constLaw = nullptr; } functorCache; //! Reset interaction to the intial state (keep only body ids) void reset(); //! common initialization called from both constructor and reset() void init(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Interaction,Serializable,"Interaction between pair of bodies.", ((Body::id_t,id1,0,Attr::readonly,":yref:`Id` of the first body in this interaction.")) ((Body::id_t,id2,0,Attr::readonly,":yref:`Id` of the second body in this interaction.")) ((long,iterMadeReal,-1,,"Step number at which the interaction was fully (in the sense of geom and phys) created. (Should be touched only by :yref:`IPhysDispatcher` and :yref:`InteractionLoop`, therefore they are made friends of Interaction")) ((long,iterLastSeen,-1,(Attr::noSave|Attr::hidden),"At which step this interaction was last detected by the collider. InteractionLoop will remove it if InteractionContainer::iterColliderLastRun==scene->iter, InteractionContainer::iterColliderLastRun is positive (some colliders manage interaction deletion themselves, such as :yref:`InsertionSortCollider`) and iterLastSeeniter.")) ((shared_ptr,geom,,,"Geometry part of the interaction.")) ((shared_ptr,phys,,,"Physical (material) part of the interaction.")) ((Vector3i,cellDist,Vector3i(0,0,0),,"Distance of bodies in cell size units, if using periodic boundary conditions; id2 is shifted by this number of cells from its :yref:`State::pos` coordinates for this interaction to exist. Assigned by the collider.\n\n.. warning::\n\t(internal) cellDist must survive Interaction::reset(), it is only initialized in ctor. Interaction that was cancelled by the constitutive law, was reset() and became only potential must have thepriod information if the geometric functor again makes it real. Good to know after few days of debugging that :-)")) ((int,linIx,-1,(Attr::noSave|Attr::hidden),"Index in the linear interaction container. For internal use by InteractionContainer only.")) ((long,iterBorn,-1,,"Step number at which the interaction was added to simulation.")) , /* ctor */ init(), /*py*/ .add_property("isReal",&Interaction::isReal,"True if this interaction has both geom and phys; False otherwise.") .def_readwrite("isActive",&Interaction::isActive,"True if this interaction is active. Otherwise the forces from this interaction will not be taken into account. True by default.") ); }; REGISTER_SERIALIZABLE(Interaction); trunk-2017.01a/core/InteractionContainer.cpp000066400000000000000000000117351304022710500207470ustar00rootroot00000000000000// 2008 © Sergei Dorofeenko // 2009,2010 © Václav Šmilauer #include "InteractionContainer.hpp" #include "Scene.hpp" #ifdef YADE_OPENMP #include #endif CREATE_LOGGER(InteractionContainer); // begin internal functions bool InteractionContainer::insert(const shared_ptr& i){ assert(bodies); boost::mutex::scoped_lock lock(drawloopmutex); Body::id_t id1=i->getId1(); Body::id_t id2=i->getId2(); if (id1>id2) swap(id1,id2); assert((Body::id_t)bodies->size()>id1); // the bodies must exist already assert((Body::id_t)bodies->size()>id2); const shared_ptr& b1=(*bodies)[id1]; const shared_ptr& b2=(*bodies)[id2]; if(!b1->intrs.insert(Body::MapId2IntrT::value_type(id2,i)).second) return false; // already exists if(!b2->intrs.insert(Body::MapId2IntrT::value_type(id1,i)).second) return false; linIntrs.resize(++currSize); // currSize updated linIntrs[currSize-1]=i; // assign last element i->linIx=currSize-1; // store the index back-reference in the interaction (so that it knows how to erase/move itself) const shared_ptr& scene=Omega::instance().getScene(); i->iterBorn=scene->iter; return true; } void InteractionContainer::clear(){ assert(bodies); boost::mutex::scoped_lock lock(drawloopmutex); FOREACH(const shared_ptr& b, *bodies) { if (b) b->intrs.clear(); } linIntrs.clear(); currSize=0; dirty=true; } bool InteractionContainer::erase(Body::id_t id1,Body::id_t id2, int linPos){ assert(bodies); boost::mutex::scoped_lock lock(drawloopmutex); if (id1>id2) swap(id1,id2); if(id2>=(Body::id_t)bodies->size()) return false; const shared_ptr& b1((*bodies)[id1]); const shared_ptr& b2((*bodies)[id2]); int linIx=-1; if(!b1) linIx=linPos; else { Body::MapId2IntrT::iterator I(b1->intrs.find(id2)); if(I==b1->intrs.end()) linIx=linPos; else { linIx=I->second->linIx; assert(linIx==linPos); //erase from body, we also erase from linIntrs below b1->intrs.erase(I); if (b2) { Body::MapId2IntrT::iterator I2(b2->intrs.find(id1)); if (not(I2==b2->intrs.end())) { b2->intrs.erase(I2); } } } } if(linIx<0) { LOG_ERROR("InteractionContainer::erase: attempt to delete interaction with a deleted body (the definition of linPos in the call to erase() should fix the problem) for ##"+boost::lexical_cast(id1)+"+"+boost::lexical_cast(id2)); return false;} // iid is not the last element; we have to move last one to its place if (linIx<(int)currSize-1) { linIntrs[linIx]=linIntrs[currSize-1]; linIntrs[linIx]->linIx=linIx; // update the back-reference inside the interaction } // in either case, last element can be removed now linIntrs.resize(--currSize); // currSize updated return true; } const shared_ptr& InteractionContainer::find(Body::id_t id1,Body::id_t id2){ assert(bodies); if (id1>id2) swap(id1,id2); // those checks could be perhaps asserts, but pyInteractionContainer has no access to the body container... if(id2>=(Body::id_t)bodies->size()){ empty=shared_ptr(); return empty; } const shared_ptr& b1((*bodies)[id1]); if(!b1) { empty=shared_ptr(); return empty; } Body::MapId2IntrT::iterator I(b1->intrs.find(id2)); if (I!=b1->intrs.end()) return I->second; else { empty=shared_ptr(); return empty; } } bool InteractionContainer::insert(Body::id_t id1,Body::id_t id2) { shared_ptr i(new Interaction(id1,id2) ); return insert(i); } void InteractionContainer::requestErase(Body::id_t id1, Body::id_t id2){ const shared_ptr I=find(id1,id2); if(!I) return; I->reset(); } void InteractionContainer::requestErase(const shared_ptr& I){ I->reset(); } void InteractionContainer::requestErase(Interaction* I){ I->reset(); } void InteractionContainer::eraseNonReal(){ FOREACH(const shared_ptr& i, *this) if(!i->isReal()) this->erase(i->getId1(),i->getId2(),i->linIx); } // compare interaction based on their first id struct compPtrInteraction{ bool operator() (const shared_ptr& i1, const shared_ptr& i2) const { return (*i1)<(*i2); } }; void InteractionContainer::preSave(InteractionContainer&){ for(const shared_ptr& I : *this) { if(I->geom || I->phys) interaction.push_back(I); // since requestErase'd interactions have no interaction physics/geom, they are not saved } if(serializeSorted) std::sort(interaction.begin(),interaction.end(),compPtrInteraction()); } void InteractionContainer::postSave(InteractionContainer&){ interaction.clear(); } void InteractionContainer::preLoad(InteractionContainer&){ interaction.clear(); } void InteractionContainer::postLoad__calledFromScene(const shared_ptr& bb){ bodies=&bb->body; clear(); FOREACH(const shared_ptr& I, interaction){ Body::id_t id1=I->getId1(), id2=I->getId2(); if (!(*bodies)[id1] || !(*bodies)[id2]) { return; } else { insert(I); } } interaction.clear(); } trunk-2017.01a/core/InteractionContainer.hpp000066400000000000000000000155641304022710500207600ustar00rootroot00000000000000// 2004 © Olivier Galizzi // 2004 © Janek Kozicki // 2010 © Václav Šmilauer #pragma once #include #include #ifdef YADE_OPENMP #include #endif #include #include /* This InteractionContainer implementation has reference to the body container and stores interactions in 2 places: * Internally in a std::vector; that allows for const-time linear traversal. Each interaction internally holds back-reference to the position in this container in Interaction::linIx. * Inside Body::intrs (in the body with min(id1,id2)). Both must be kep in sync, which is handled by insert & erase methods. It was originally written by 2008 © Sergei Dorofeenko , later devirtualized and put here. Alternative implementations of InteractionContainer should implement the same API. Due to performance reasons, no base class with virtual methods defining such API programatically is defined (it could be possible to create class template for this, though). Future (?): * the linear vector might be removed; in favor of linear traversal of bodies by their subdomains, then traversing the map in each body. If the previous point would come to realization, half of the interactions would have to be skipped explicitly in such a case. */ class InteractionContainer: public Serializable{ private: typedef vector > ContainerT; // linear array of container interactions ContainerT linIntrs; // pointer to body container, since each body holds (some) interactions // this must always point to scene->bodies->body const BodyContainer::ContainerT* bodies; // always in sync with intrs.size(), to avoid that function call size_t currSize; shared_ptr empty; // used only during serialization/deserialization vector > interaction; public: // flag for notifying the collider that persistent data should be invalidated bool dirty; // required by the class factory... :-| InteractionContainer(): currSize(0),dirty(false),serializeSorted(false),iterColliderLastRun(-1){ bodies=NULL; } void clear(); // iterators typedef ContainerT::iterator iterator; typedef ContainerT::const_iterator const_iterator; iterator begin(){return linIntrs.begin();} iterator end() {return linIntrs.end();} const_iterator begin() const {return linIntrs.begin();} const_iterator end() const {return linIntrs.end();} // insertion/deletion bool insert(Body::id_t id1,Body::id_t id2); bool insert(const shared_ptr& i); //3rd parameter is used to remove I from linIntrs (in conditionalyEraseNonReal()) when body b1 has been removed bool erase(Body::id_t id1,Body::id_t id2,int linPos); const shared_ptr& find(Body::id_t id1,Body::id_t id2); inline bool found(const Body::id_t& id1,const Body::id_t& id2){ assert(bodies); if(id2>=(Body::id_t)bodies->size() or (id1 == id2)) { return false; } else { if (id1>id2) { return (*bodies)[id2]->intrs.count(id1); } else { return (*bodies)[id1]->intrs.count(id2); } } } // index access shared_ptr& operator[](size_t id){return linIntrs[id];} const shared_ptr& operator[](size_t id) const { return linIntrs[id];} size_t size(){ return currSize; } // simulation API //! Erase all non-real (in term of Interaction::isReal()) interactions void eraseNonReal(); // mutual exclusion to avoid crashes in the rendering loop boost::mutex drawloopmutex; // sort interactions before serializations; useful if comparing XML files from different runs (false by default) bool serializeSorted; // iteration number when the collider was last run; set by the collider, if it wants interactions that were not encoutered in that step to be deleted by InteractionLoop (such as SpatialQuickSortCollider). Other colliders (such as InsertionSortCollider) set it it -1, which is the default long iterColliderLastRun; //! Ask for erasing the interaction given (from the constitutive law); this resets the interaction (to the initial=potential state) and collider should traverse potential interactions to decide whether to delete them completely or keep them potential void requestErase(Body::id_t id1, Body::id_t id2); void requestErase(const shared_ptr& I); void requestErase(Interaction* I); /*! Traverse all interactions and erase them if they are not real and the (T*)->shouldBeErased(id1,id2) return true, or if body(id1) has been deleted Class using this interface (which is presumably a collider) must define the bool shouldBeErased(Body::id_t, Body::id_t) const */ template size_t conditionalyEraseNonReal(const T& t, Scene* rb){ // beware iterators here, since erase is invalidating them. We need to iterate carefully, and keep in mind that erasing one interaction is moving the last one to the current position. // For the parallel flavor we build the list to be erased in parallel, then it is erased sequentially. Still significant speedup since checking bounds is the most expensive part. #ifdef YADE_OPENMP if (omp_get_max_threads()<=1) { #endif size_t initSize=currSize; for (size_t linPos=0; linPos& i=linIntrs[linPos]; if(!i->isReal() && t.shouldBeErased(i->getId1(),i->getId2(),rb)) erase(i->getId1(),i->getId2(),linPos); else linPos++;} return initSize-currSize; #ifdef YADE_OPENMP } else { unsigned nThreads= omp_get_max_threads(); assert(nThreads>0); std::vector >toErase; toErase.resize(nThreads,std::vector()); for (unsigned kk=0; kk& i=linIntrs[linPos]; if(!i->isReal() && t.shouldBeErased(i->getId1(),i->getId2(),rb)) toErase[omp_get_thread_num()].push_back(Vector3i(i->getId1(),i->getId2(),linPos)) ; } for (int kk=nThreads-1; kk>=0; kk--) for (int ii(toErase[kk].size()-1); ii>=0;ii--) erase(toErase[kk][ii][0],toErase[kk][ii][1],toErase[kk][ii][2]); return initSize-currSize; } #endif } // we must call Scene's ctor (and from Scene::postLoad), since we depend on the existing BodyContainer at that point. void postLoad__calledFromScene(const shared_ptr&); void preLoad(InteractionContainer&); void preSave(InteractionContainer&); void postSave(InteractionContainer&); REGISTER_ATTRIBUTES(Serializable,(interaction)(serializeSorted)(dirty)); REGISTER_CLASS_AND_BASE(InteractionContainer,Serializable); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(InteractionContainer); trunk-2017.01a/core/Material.cpp000066400000000000000000000016261304022710500163610ustar00rootroot00000000000000#include #include #include const shared_ptr Material::byId(int id, Scene* w_){ Scene* w=w_?w_:Omega::instance().getScene().get(); assert(id>=0 && (size_t)idmaterials.size()); assert(w->materials[id]->id == id); return w->materials[id]; } const shared_ptr Material::byLabel(const std::string& label, Scene* w_){ Scene* w=w_?w_:Omega::instance().getScene().get(); FOREACH(const shared_ptr& m, w->materials){ if(m->label == label) return m; } throw std::runtime_error(("No material labeled `"+label+"'.").c_str()); } const int Material::byLabelIndex(const std::string& label, Scene* w_){ Scene* w=w_?w_:Omega::instance().getScene().get(); size_t iMax=w->materials.size(); for(size_t i=0; imaterials[i]->label==label) return i; } throw std::runtime_error(("No material labeled `"+label+"'.").c_str()); } trunk-2017.01a/core/Material.hpp000066400000000000000000000053741304022710500163720ustar00rootroot00000000000000// 2009 © Václav Šmilauer #pragma once #include #include #include #include class Scene; /*! Material properties associated with a body. Historical note: this used to be part of the PhysicalParameters class. The other data are now in the State class. */ class Material: public Serializable, public Indexable{ public: virtual ~Material() {}; //! Function to return empty default-initialized instance of State that // is supposed to go along with this Material. Don't override unless you need // something else than basic State. virtual shared_ptr newAssocState() const { return shared_ptr(new State); } /*! Function that returns true if given State instance is what this material expects. Base Material class has no requirements, but the check would normally look like this: return (bool)dynamic_cast state; */ virtual bool stateTypeOk(State*) const { return true; } static const shared_ptr byId(int id, Scene* scene=NULL); static const shared_ptr byId(int id, shared_ptr scene) {return byId(id,scene.get());} static const shared_ptr byLabel(const std::string& label, Scene* scene=NULL); static const shared_ptr byLabel(const std::string& label, shared_ptr scene) {return byLabel(label,scene.get());} // return index of material, given its label static const int byLabelIndex(const std::string& label, Scene* scene=NULL); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Material,Serializable,"Material properties of a :yref:`body`.", ((int,id,((void)"not shared",-1),Attr::readonly,"Numeric id of this material; is non-negative only if this Material is shared (i.e. in O.materials), -1 otherwise. This value is set automatically when the material is inserted to the simulation via :yref:`O.materials.append`. (This id was necessary since before boost::serialization was used, shared pointers were not tracked properly; it might disappear in the future)")) ((string,label,,,"Textual identifier for this material; can be used for shared materials lookup in :yref:`MaterialContainer`.")) ((Real,density,1000,,"Density of the material [kg/m³]")), /* ctor */, /*py*/ .def("newAssocState",&Material::newAssocState,"Return new :yref:`State` instance, which is associated with this :yref:`Material`. Some materials have special requirement on :yref:`Body::state` type and calling this function when the body is created will ensure that they match. (This is done automatically if you use utils.sphere, … functions from python).") YADE_PY_TOPINDEXABLE(Material) ); REGISTER_INDEX_COUNTER(Material); }; REGISTER_SERIALIZABLE(Material); trunk-2017.01a/core/Omega.cpp000066400000000000000000000234321304022710500156520ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "Omega.hpp" #include "Scene.hpp" #include "TimeStepper.hpp" #include "ThreadRunner.hpp" #include #include #include #include #include #include #include #include class RenderMutexLock: public boost::mutex::scoped_lock{ public: RenderMutexLock(): boost::mutex::scoped_lock(Omega::instance().renderMutex){} ~RenderMutexLock(){} }; CREATE_LOGGER(Omega); SINGLETON_SELF(Omega); const map& Omega::getDynlibsDescriptor(){return dynlibs;} const shared_ptr& Omega::getScene(){return scenes.at(currentSceneNb);} void Omega::resetCurrentScene(){ RenderMutexLock lock; scenes.at(currentSceneNb) = shared_ptr(new Scene);} void Omega::resetScene(){ resetCurrentScene(); } void Omega::resetAllScenes(){ RenderMutexLock lock; scenes.resize(1); scenes[0] = shared_ptr(new Scene); currentSceneNb=0; } int Omega::addScene(){ scenes.push_back(shared_ptr(new Scene)); return scenes.size()-1; } void Omega::switchToScene(int i) { if (i<0 || i>=int(scenes.size())) { LOG_ERROR("Scene "<(tmpFileCounter++); } void Omega::reset(){ stop(); init(); } void Omega::init(){ sceneFile=""; resetAllScenes(); sceneAnother=shared_ptr(new Scene); timeInit(); createSimulationLoop(); } void Omega::timeInit(){ startupLocalTime=boost::posix_time::microsec_clock::local_time(); } void Omega::createSimulationLoop(){ simulationLoop=shared_ptr(new ThreadRunner(&simulationFlow_)); } void Omega::stop(){ LOG_DEBUG(""); if (simulationLoop&&simulationLoop->looping())simulationLoop->stop(); if (simulationLoop) simulationLoop=shared_ptr(); } /* WARNING: even a single simulation step is run asynchronously; the call will return before the iteration is finished. */ void Omega::step(){ if (simulationLoop){ simulationLoop->spawnSingleAction(); } } void Omega::run(){ if(!simulationLoop){LOG_ERROR("No Omega::simulationLoop? Creating one (please report bug)."); createSimulationLoop(); } if (simulationLoop && !simulationLoop->looping()){ simulationLoop->start(); } } void Omega::pause(){ if (simulationLoop && simulationLoop->looping()){ simulationLoop->stop(); } } bool Omega::isRunning(){ if(simulationLoop) return simulationLoop->looping(); else return false; } void Omega::buildDynlibDatabase(const vector& dynlibsList){ LOG_DEBUG("called with "< pythonables; FOREACH(string name, dynlibsList){ shared_ptr f; try { LOG_DEBUG("Factoring plugin "<(f)).get()!=0); for(int i=0;igetBaseClassNumber();i++){ dynlibs[name].baseClasses.insert(f->getBaseClassName(i)); } if(dynlibs[name].isSerializable) pythonables.push_back(name); } catch (std::runtime_error& e){ /* FIXME: this catches all errors! Some of them are not harmful, however: * when a class is not factorable, it is OK to skip it; */ } } // handle Serializable specially //Serializable().pyRegisterClass(wrapperScope); /* python classes must be registered such that base classes come before derived ones; for now, just loop until we succeed; proper solution will be to build graphs of classes and traverse it from the top. It will be done once all classes are pythonable. */ for(int i=0; i<100 && pythonables.size()>0; i++){ if(getenv("YADE_DEBUG")) cerr< done; for(std::list::iterator I=pythonables.begin(); I!=pythonables.end(); ){ shared_ptr s=boost::static_pointer_cast(ClassFactory::instance().createShared(*I)); try{ if(getenv("YADE_DEBUG")) cerr<<"{{"<<*I<<"}}"; s->pyRegisterClass(wrapperScope); std::list::iterator prev=I++; pythonables.erase(prev); } catch (...){ if(getenv("YADE_DEBUG")){ cerr<<"["<<*I<<"]"; PyErr_Print(); } boost::python::handle_exception(); I++; } } } map::iterator dli = dynlibs.begin(); map::iterator dliEnd = dynlibs.end(); for( ; dli!=dliEnd ; ++dli){ set::iterator bci = (*dli).second.baseClasses.begin(); set::iterator bciEnd = (*dli).second.baseClasses.end(); for( ; bci!=bciEnd ; ++bci){ string name = *bci; if (name=="Dispatcher1D" || name=="Dispatcher2D") (*dli).second.baseClasses.insert("Dispatcher"); else if (name=="Functor1D" || name=="Functor2D") (*dli).second.baseClasses.insert("Functor"); else if (name=="Serializable") (*dli).second.baseClasses.insert("Factorable"); else if (name!="Factorable" && name!="Indexable") { shared_ptr f = ClassFactory::instance().createShared(name); for(int i=0;igetBaseClassNumber();i++) dynlibs[name].baseClasses.insert(f->getBaseClassName(i)); } } } } bool Omega::isInheritingFrom(const string& className, const string& baseClassName){ return (dynlibs[className].baseClasses.find(baseClassName)!=dynlibs[className].baseClasses.end()); } bool Omega::isInheritingFrom_recursive(const string& className, const string& baseClassName){ if (dynlibs[className].baseClasses.find(baseClassName)!=dynlibs[className].baseClasses.end()) return true; FOREACH(const string& parent,dynlibs[className].baseClasses){ if(isInheritingFrom_recursive(parent,baseClassName)) return true; } return false; } void Omega::loadPlugins(vector pluginFiles){ FOREACH(const string& plugin, pluginFiles){ LOG_DEBUG("Loading plugin "<& plugins(ClassFactory::instance().pluginClasses); plugins.sort(); plugins.unique(); buildDynlibDatabase(vector(plugins.begin(),plugins.end())); } void Omega::loadSimulation(const string& f, bool quiet){ bool isMem=boost::algorithm::starts_with(f,":memory:"); if(!isMem && !boost::filesystem::exists(f)) throw runtime_error("Simulation file to load doesn't exist: "+f); if(isMem && memSavedSimulations.count(f)==0) throw runtime_error("Cannot load nonexistent memory-saved simulation "+f); if(!quiet) LOG_INFO("Loading file "+f); shared_ptr& scene = scenes[currentSceneNb]; { stop(); // stop current simulation if running resetScene(); RenderMutexLock lock; if(isMem){ istringstream iss(memSavedSimulations[f]); yade::ObjectIO::load(iss,"scene",scene); } else { yade::ObjectIO::load(f,"scene",scene); } } if(scene->getClassName()!="Scene") throw logic_error("Wrong file format (scene is not a Scene!?) in "+f); sceneFile=f; timeInit(); //Add zero-force to the youngest body to be sure ForceContainer is large enough. const int _sz = scene->bodies->size(); for(Body::id_t _id=0; _id<_sz; _id++) { if((&scene->bodies)[_id]) { scene->forces.addForce(_id, Vector3r::Zero()); break; } } if(!quiet) LOG_DEBUG("Simulation loaded"); } void Omega::saveSimulation(const string& f, bool quiet){ if(f.size()==0) throw runtime_error("f of file to save has zero length."); if(!quiet) LOG_INFO("Saving file " << f); shared_ptr& scene = scenes[currentSceneNb]; if(boost::algorithm::starts_with(f,":memory:")){ if(memSavedSimulations.count(f)>0 && !quiet) LOG_INFO("Overwriting in-memory saved simulation "<(oss,"scene",scene); memSavedSimulations[f]=oss.str(); } else { yade::ObjectIO::save(f,"scene",scene); } sceneFile=f; } trunk-2017.01a/core/Omega.hpp000066400000000000000000000067601304022710500156640ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include #include #include #include #include #include #include "SimulationFlow.hpp" #ifndef FOREACH # define FOREACH BOOST_FOREACH #endif class Scene; class ThreadRunner; struct DynlibDescriptor{ set baseClasses; bool isSerializable; }; class Omega: public Singleton{ shared_ptr simulationLoop; SimulationFlow simulationFlow_; map dynlibs; // FIXME : should store that in ClassFactory ? void buildDynlibDatabase(const vector& dynlibsList); // FIXME - maybe in ClassFactory ? vector > scenes; int currentSceneNb; shared_ptr sceneAnother; // used for temporarily running different simulation, in Omega().switchscene() boost::posix_time::ptime startupLocalTime; map memSavedSimulations; // to avoid accessing simulation when it is being loaded (should avoid crashes with the UI) boost::mutex loadingSimulationMutex; boost::mutex tmpFileCounterMutex; long tmpFileCounter; std::string tmpFileDir; public: // management, not generally useful void init(); void reset(); void timeInit(); void initTemps(); void cleanupTemps(); const map& getDynlibsDescriptor(); void loadPlugins(vector pluginFiles); bool isInheritingFrom(const string& className, const string& baseClassName ); bool isInheritingFrom_recursive(const string& className, const string& baseClassName ); void createSimulationLoop(); bool hasSimulationLoop(){return (bool)(simulationLoop);} string gdbCrashBatch; char** origArgv; int origArgc; // do not change by hand /* Mutex for: * 1. GLViewer::paintGL (deffered lock: if fails, no GL painting is done) * 2. other threads that wish to manipulate GL * 3. Omega when substantial changes to the scene are being made (bodies being deleted, simulation loaded etc) so that GL doesn't access those and crash */ boost::try_mutex renderMutex; void run(); void pause(); void step(); void stop(); // resets the simulationLoop bool isRunning(); std::string sceneFile; // updated at load/save automatically void loadSimulation(const string& name, bool quiet=false); void saveSimulation(const string& name, bool quiet=false); void resetScene(); void resetCurrentScene(); void resetAllScenes(); const shared_ptr& getScene(); int addScene(); void switchToScene(int i); //! Return unique temporary filename. May be deleted by the user; if not, will be deleted at shutdown. string tmpFilename(); Real getRealTime(); boost::posix_time::time_duration getRealTime_duration(); // configuration directory used for logging config and possibly other things std::string confDir; DECLARE_LOGGER; Omega(){ LOG_DEBUG("Constructing Omega."); } ~Omega(){} FRIEND_SINGLETON(Omega); friend class pyOmega; }; trunk-2017.01a/core/PartialEngine.hpp000066400000000000000000000017431304022710500173520ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include class PartialEngine: public Engine{ public: virtual ~PartialEngine() {}; YADE_CLASS_BASE_DOC_ATTRS(PartialEngine,Engine,"Engine affecting only particular bodies in the simulation, defined by :yref:`ids attribute`.", ((std::vector,ids,,,":yref:`Ids` list of bodies affected by this PartialEngine.")) ); }; REGISTER_SERIALIZABLE(PartialEngine); trunk-2017.01a/core/Scene.cpp000066400000000000000000000212001304022710500156460ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include"Scene.hpp" #include #include #include #include #include #include #include #include #include namespace py=boost::python; YADE_PLUGIN((Scene)); CREATE_LOGGER(Scene); // should be elsewhere, probably bool TimingInfo::enabled=false; void Scene::fillDefaultTags(){ // fill default tags struct passwd* pw; char hostname[hostNameMax]; gethostname(hostname,hostNameMax); pw=getpwuid(geteuid()); if(!pw) throw runtime_error("getpwuid(geteuid()) failed!"); // a few default tags // real name: will have all non-ASCII characters replaced by ? since serialization doesn't handle that // the standard GECOS format is Real Name,,, - first comma and after will be discarded string gecos(pw->pw_gecos), gecos2; size_t p=gecos.find(","); if(p!=string::npos) boost::algorithm::erase_tail(gecos,gecos.size()-p); for(size_t i=0;ipw_name)+"@"+hostname+")"," ","~")); tags.push_back(string("isoTime="+boost::posix_time::to_iso_string(boost::posix_time::second_clock::local_time()))); string id=boost::posix_time::to_iso_string(boost::posix_time::second_clock::local_time())+"p"+boost::lexical_cast(getpid()); tags.push_back("id="+id); tags.push_back("d.id="+id); tags.push_back("id.d="+id); // tags.push_back("revision="+py::extract(py::import("yade.config").attr("revision"))());; } void Scene::postLoad(Scene&){ // update the interaction container; must be done in Scene ctor as well; important! interactions->postLoad__calledFromScene(bodies); // this might be removed at some point, since it is checked by regression tests now FOREACH(const shared_ptr& b, *bodies){ if(!b || !b->material || b->material->id<0) continue; // not a shared material if(b->material!=materials[b->material->id]) throw std::logic_error("Scene::postLoad: Internal inconsistency, shared materials not preserved when loaded; please report bug."); } } void Scene::moveToNextTimeStep(){ if(runInternalConsistencyChecks){ runInternalConsistencyChecks=false; checkStateTypes(); } // substepping or not, update engines from _nextEngines, if defined, at the beginning of step // subStep can be 0, which happens if simulations is saved in the middle of step (without substepping) // this assumes that prologue will not set _nextEngines, which is safe hopefully if(!_nextEngines.empty() && (subStep<0 || (subStep<=0 && !subStepping))){ engines=_nextEngines; _nextEngines.clear(); // hopefully this will not break in some margin cases (subStepping with setting _nextEngines and such) subStep=-1; } if(!subStepping && subStep<0){ /* set substep to 0 during the loop, so that engines/nextEngines handler know whether we are inside the loop currently */ subStep=0; // ** 1. ** prologue if(isPeriodic) cell->integrateAndUpdate(dt); //forces.reset(); // uncomment if ForceResetter is removed const bool TimingInfo_enabled=TimingInfo::enabled; // cache the value, so that when it is changed inside the step, the engine that was just running doesn't get bogus values TimingInfo::delta last=TimingInfo::getNow(); // actually does something only if TimingInfo::enabled, no need to put the condition here // ** 2. ** engines FOREACH(const shared_ptr& e, engines){ e->scene=this; if(e->dead || !e->isActivated()) continue; e->action(); if(TimingInfo_enabled) {TimingInfo::delta now=TimingInfo::getNow(); e->timingInfo.nsec+=now-last; e->timingInfo.nExec+=1; last=now;} } // ** 3. ** epilogue // Calculation speed if (iter==0) { //For the first time prevTime = boost::posix_time::microsec_clock::local_time(); } else { boost::posix_time::ptime timeNow = boost::posix_time::microsec_clock::local_time(); boost::posix_time::time_duration duration = timeNow - prevTime; long dif = duration.total_microseconds(); SpeedElements(iter%nSpeedIter,0)=1000000.0 / dif; speed = SpeedElements.mean(); prevTime = timeNow; } iter++; time+=dt; subStep=-1; } else { /* IMPORTANT: take care to copy EXACTLY the same sequence as is in the block above !! */ if(TimingInfo::enabled){ TimingInfo::enabled=false; LOG_INFO("O.timingEnabled disabled, since O.subStepping is used."); } if(subStep<-1 || subStep>(int)engines.size()){ LOG_ERROR("Invalid value of Scene::subStep ("<=-1 && subs<=(int)engines.size()); // ** 1. ** prologue if(subs==-1){ if(isPeriodic) cell->integrateAndUpdate(dt); } // ** 2. ** engines else if(subs>=0 && subs<(int)engines.size()){ const shared_ptr& e(engines[subs]); e->scene=this; if(!e->dead && e->isActivated()) e->action(); } // ** 3. ** epilogue else if(subs==(int)engines.size()){ iter++; time+=dt; /* gives -1 along with the increment afterwards */ subStep=-2; } // (?!) else { /* never reached */ assert(false); } } subStep++; // if not substepping, this will make subStep=-2+1=-1, which is what we want } } shared_ptr Scene::engineByName(const string& s){ FOREACH(shared_ptr e, engines){ if(e->getClassName()==s) return e; } return shared_ptr(); } bool Scene::timeStepperPresent(){ int n=0; FOREACH(const shared_ptr&e, engines){ if(dynamic_cast(e.get())) n++; } if(n>1) throw std::runtime_error(string("Multiple ("+boost::lexical_cast(n)+") TimeSteppers in the simulation?!").c_str()); return n>0; } bool Scene::timeStepperActive(){ int n=0; bool ret=false; FOREACH(const shared_ptr&e, engines){ TimeStepper* ts=dynamic_cast(e.get()); if(ts) { ret=ts->active; n++; } } if(n>1) throw std::runtime_error(string("Multiple ("+boost::lexical_cast(n)+") TimeSteppers in the simulation?!").c_str()); return ret; } bool Scene::timeStepperActivate(bool a){ int n=0; FOREACH(const shared_ptr e, engines){ TimeStepper* ts=dynamic_cast(e.get()); if(ts) { ts->setActive(a); n++; } } if(n>1) throw std::runtime_error(string("Multiple ("+boost::lexical_cast(n)+") TimeSteppers in the simulation?!").c_str()); return n>0; } void Scene::checkStateTypes(){ FOREACH(const shared_ptr& b, *bodies){ if(!b || !b->material) continue; if(b->material && !b->state) throw std::runtime_error("Body #"+boost::lexical_cast(b->getId())+": has Body::material, but NULL Body::state."); if(!b->material->stateTypeOk(b->state.get())){ throw std::runtime_error("Body #"+boost::lexical_cast(b->getId())+": Body::material type "+b->material->getClassName()+" doesn't correspond to Body::state type "+b->state->getClassName()+" (should be "+b->material->newAssocState()->getClassName()+" instead)."); } } } void Scene::updateBound(){ if(!bound) bound=shared_ptr(new Bound); const Real& inf=std::numeric_limits::infinity(); Vector3r mx(-inf,-inf,-inf); Vector3r mn(inf,inf,inf); FOREACH(const shared_ptr& b, *bodies){ if(!b) continue; if(b->bound){ for(int i=0; i<3; i++){ if(!std::isinf(b->bound->max[i])) mx[i]=max(mx[i],b->bound->max[i]); if(!std::isinf(b->bound->min[i])) mn[i]=min(mn[i],b->bound->min[i]); } } else { mx=mx.cwiseMax(b->state->pos); mn=mn.cwiseMin(b->state->pos); } } bound->min=mn; bound->max=mx; } trunk-2017.01a/core/Scene.hpp000066400000000000000000000144511304022710500156650ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include #include #include #include #include #include #ifdef YADE_OPENMP #include #endif class Bound; #ifdef YADE_OPENGL class OpenGLRenderer; #endif class Scene: public Serializable{ const unsigned int hostNameMax = 255; public: //! Adds material to Scene::materials. It also sets id of the material accordingly and returns it. int addMaterial(shared_ptr m){ materials.push_back(m); m->id=(int)materials.size()-1; return m->id; } //! Checks that type of Body::state satisfies Material::stateTypeOk. Throws runtime_error if not. (Is called from BoundDispatcher the first time it runs) void checkStateTypes(); //! update our bound; used directly instead of a BoundFunctor, since we don't derive from Body anymore void updateBound(); // neither serialized, nor accessible from python (at least not directly) ForceContainer forces; // initialize tags (author, date, time) void fillDefaultTags(); // advance by one iteration by running all engines void moveToNextTimeStep(); /* Functions operating on TimeStepper; they all throw exception if there is more than 1 */ // return whether a TimeStepper is present bool timeStepperPresent(); // true if TimeStepper is present and active, false otherwise bool timeStepperActive(); // (de)activate TimeStepper; returns whether the operation was successful (i.e. whether a TimeStepper was found) bool timeStepperActivate(bool activate); static const int nSpeedIter = 10; //Number of iterations, which are taking into account for speed calculation Eigen::Matrix SpeedElements; //Array for saving speed-values for last "nSpeedIter"-iterations shared_ptr engineByName(const string& s); #ifdef YADE_LIQMIGRATION OpenMPVector addIntrs; //Array of added interactions, needed for liquid migration. OpenMPVector > delIntrs; //Array of deleted interactions, needed for liquid migration. #endif #ifdef YADE_OPENGL shared_ptr renderer; #endif void postLoad(Scene&); boost::posix_time::ptime prevTime; //Time value on the previous step YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Scene,Serializable,"Object comprising the whole simulation.", ((Real,dt,1e-8,,"Current timestep for integration.")) ((long,iter,0,Attr::readonly,"Current iteration (computational step) number")) ((bool,subStepping,false,,"Whether we currently advance by one engine in every step (rather than by single run through all engines).")) ((int,subStep,-1,Attr::readonly,"Number of sub-step; not to be changed directly. -1 means to run loop prologue (cell integration), 0…n-1 runs respective engines (n is number of engines), n runs epilogue (increment step number and time.")) ((Real,time,0,Attr::readonly,"Simulation time (virtual time) [s]")) ((Real,speed,0,Attr::readonly,"Current calculation speed [iter/s]")) ((long,stopAtIter,0,,"Iteration after which to stop the simulation.")) ((Real,stopAtTime,0,,"Time after which to stop the simulation")) ((bool,isPeriodic,false,Attr::readonly,"Whether periodic boundary conditions are active.")) ((bool,trackEnergy,false,Attr::readonly,"Whether energies are being traced.")) ((bool,doSort,false,Attr::readonly,"Used, when new body is added to the scene.")) ((bool,runInternalConsistencyChecks,true,Attr::hidden,"Run internal consistency check, right before the very first simulation step.")) ((Body::id_t,selectedBody,-1,,"Id of body that is selected by the user")) ((list,tags,,,"Arbitrary key=value associations (tags like mp3 tags: author, date, version, description etc.)")) ((vector >,engines,,Attr::hidden,"Engines sequence in the simulation.")) ((vector >,_nextEngines,,Attr::hidden,"Engines to be used from the next step on; is returned transparently by O.engines if in the middle of the loop (controlled by subStep>=0).")) // NOTE: bodies must come before interactions, since InteractionContainer is initialized with a reference to BodyContainer::body ((shared_ptr,bodies,new BodyContainer,Attr::hidden,"Bodies contained in the scene.")) ((shared_ptr,interactions,new InteractionContainer,Attr::hidden,"All interactions between bodies.")) ((shared_ptr,energy,new EnergyTracker,Attr::hidden,"Energy values, if energy tracking is enabled.")) ((vector >,materials,,Attr::hidden,"Container of shared materials. Add elements using Scene::addMaterial, not directly. Do NOT remove elements from here unless you know what you are doing!")) ((shared_ptr,bound,,Attr::hidden,"Bounding box of the scene (only used for rendering and initialized if needed).")) ((shared_ptr,cell,new Cell,Attr::hidden,"Information on periodicity; only should be used if Scene::isPeriodic.")) ((vector >,miscParams,,Attr::hidden,"Store for arbitrary Serializable objects; will set static parameters during deserialization (primarily for GLDraw functors which otherwise have no attribute access)")) ((vector >,dispParams,,Attr::hidden,"'hash maps' of display parameters (since yade::serialization had no support for maps, emulate it via vector of strings in format key=value)")) , /*ctor*/ fillDefaultTags(); interactions->postLoad__calledFromScene(bodies); SpeedElements.Zero(); , /* py */ ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Scene); trunk-2017.01a/core/Shape.hpp000066400000000000000000000030531304022710500156640ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #define BV_FUNCTOR_CACHE class BoundFunctor; class InternalForceFunctor; class Shape: public Serializable, public Indexable { public: virtual ~Shape() {}; // vtable #ifdef BV_FUNCTOR_CACHE shared_ptr boundFunctor; #endif //! cache functor that are called for this type of DeformableElement. Used by FEInternalForceEngine shared_ptr internalforcefunctor; YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Shape,Serializable,"Geometry of a body", ((Vector3r,color,Vector3r(1,1,1),,"Color for rendering (normalized RGB).")) ((bool,wire,false,,"Whether this Shape is rendered using color surfaces, or only wireframe (can still be overridden by global config of the renderer).")) ((bool,highlight,false,,"Whether this Shape will be highlighted when rendered.")), /*ctor*/, /*py*/ YADE_PY_TOPINDEXABLE(Shape) ); REGISTER_INDEX_COUNTER(Shape); }; REGISTER_SERIALIZABLE(Shape); trunk-2017.01a/core/SimulationFlow.cpp000066400000000000000000000022071304022710500175730ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include #include "SimulationFlow.hpp" #include "Scene.hpp" #include "Omega.hpp" CREATE_LOGGER(SimulationFlow); void SimulationFlow::singleAction() { Scene* scene=Omega::instance().getScene().get(); if (!scene) throw logic_error("SimulationFlow::singleAction: no Scene object?!"); if(scene->subStepping) { LOG_INFO("Sub-stepping disabled when running simulation continuously."); scene->subStepping=false; } scene->moveToNextTimeStep(); if(scene->stopAtIter>0 && scene->iter==scene->stopAtIter) setTerminate(true); if(scene->stopAtTime>0 && scene->time==scene->stopAtTime) setTerminate(true); }; trunk-2017.01a/core/SimulationFlow.hpp000066400000000000000000000012451304022710500176010ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include "ThreadWorker.hpp" class SimulationFlow : public ThreadWorker { public: virtual void singleAction(); DECLARE_LOGGER; }; trunk-2017.01a/core/State.cpp000066400000000000000000000021201304022710500156710ustar00rootroot00000000000000// 2009 © Václav Šmilauer #include CREATE_LOGGER(State); void State::setDOFfromVector3r(Vector3r disp,Vector3r rot){ blockedDOFs=((disp[0]==1.0)?DOF_X :0)| ((disp[1]==1.0)?DOF_Y :0)| ((disp[2]==1.0)?DOF_Z :0)| ((rot [0]==1.0)?DOF_RX:0)| ((rot [1]==1.0)?DOF_RY:0)| ((rot [2]==1.0)?DOF_RZ:0); } std::string State::blockedDOFs_vec_get() const { std::string ret; #define _SET_DOF(DOF_ANY,ch) if((blockedDOFs & State::DOF_ANY)!=0) ret.push_back(ch); _SET_DOF(DOF_X,'x'); _SET_DOF(DOF_Y,'y'); _SET_DOF(DOF_Z,'z'); _SET_DOF(DOF_RX,'X'); _SET_DOF(DOF_RY,'Y'); _SET_DOF(DOF_RZ,'Z'); #undef _SET_DOF return ret; } void State::blockedDOFs_vec_set(const std::string& dofs){ blockedDOFs=0; for(char c : dofs) { #define _GET_DOF(DOF_ANY,ch) if(c==ch) { blockedDOFs|=State::DOF_ANY; continue; } _GET_DOF(DOF_X,'x'); _GET_DOF(DOF_Y,'y'); _GET_DOF(DOF_Z,'z'); _GET_DOF(DOF_RX,'X'); _GET_DOF(DOF_RY,'Y'); _GET_DOF(DOF_RZ,'Z'); #undef _GET_DOF } } trunk-2017.01a/core/State.hpp000066400000000000000000000116001304022710500157010ustar00rootroot00000000000000// 2009 © Václav Šmilauer #pragma once #include #include #include class State: public Serializable, public Indexable{ public: /// linear motion (references to inside se3) Vector3r& pos; /// rotational motion (reference to inside se3) Quaternionr& ori; //! mutex for updating the parameters from within the interaction loop (only used rarely) boost::mutex updateMutex; // bits for blockedDOFs enum {DOF_NONE=0,DOF_X=1,DOF_Y=2,DOF_Z=4,DOF_RX=8,DOF_RY=16,DOF_RZ=32}; //! shorthand for all DOFs blocked static const unsigned DOF_ALL=DOF_X|DOF_Y|DOF_Z|DOF_RX|DOF_RY|DOF_RZ; //! shorthand for all displacements blocked static const unsigned DOF_XYZ=DOF_X|DOF_Y|DOF_Z; //! shorthand for all rotations blocked static const unsigned DOF_RXRYRZ=DOF_RX|DOF_RY|DOF_RZ; //! Return DOF_* constant for given axis∈{0,1,2} and rotationalDOF∈{false(default),true}; e.g. axisDOF(0,true)==DOF_RX static unsigned axisDOF(int axis, bool rotationalDOF=false){return 1<<(axis+(rotationalDOF?3:0));} //! set DOFs according to two Vector3r arguments (blocked is when disp[i]==1.0 or rot[i]==1.0) void setDOFfromVector3r(Vector3r disp,Vector3r rot=Vector3r::Zero()); //! Getter of blockedDOFs for list of strings (e.g. DOF_X | DOR_RX | DOF_RZ → 'xXZ') std::string blockedDOFs_vec_get() const; //! Setter of blockedDOFs from string ('xXZ' → DOF_X | DOR_RX | DOF_RZ) void blockedDOFs_vec_set(const std::string& dofs); //! Return displacement (current-reference position) const Vector3r displ() const {return pos-refPos;} //! Return rotation (current-reference orientation, as Vector3r) const Vector3r rot() const { Quaternionr relRot=refOri.conjugate()*ori; AngleAxisr aa(relRot); return aa.axis()*aa.angle(); } // python access functions: pos and ori are references to inside Se3r and cannot be pointed to directly const Vector3r pos_get() const {return pos;} void pos_set(const Vector3r p) {pos=p;} const Quaternionr ori_get() const {return ori; } void ori_set(const Quaternionr o){ori=o;} YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(State,Serializable,"State of a body (spatial configuration, internal variables).", ((Se3r,se3,Se3r(Vector3r::Zero(),Quaternionr::Identity()),,"Position and orientation as one object.")) ((Vector3r,vel,Vector3r::Zero(),,"Current linear velocity.")) ((Real,mass,0,,"Mass of this body")) ((Vector3r,angVel,Vector3r::Zero(),,"Current angular velocity")) ((Vector3r,angMom,Vector3r::Zero(),,"Current angular momentum")) ((Vector3r,inertia,Vector3r::Zero(),,"Inertia of associated body, in local coordinate system.")) ((Vector3r,refPos,Vector3r::Zero(),,"Reference position")) ((Quaternionr,refOri,Quaternionr::Identity(),,"Reference orientation")) ((unsigned,blockedDOFs,,,"[Will be overridden]")) ((bool,isDamped,true,,"Damping in :yref:`Newtonintegrator` can be deactivated for individual particles by setting this variable to FALSE. E.g. damping is inappropriate for particles in free flight under gravity but it might still be applicable to other particles in the same simulation.")) ((Real,densityScaling,1,,"|yupdate| see :yref:`GlobalStiffnessTimeStepper::targetDt`.")) #ifdef YADE_SPH ((Real,rho, -1.0,, "Current density (only for SPH-model)")) // [Mueller2003], (12) ((Real,rho0,-1.0,, "Rest density (only for SPH-model)")) // [Mueller2003], (12) ((Real,press,0.0,, "Pressure (only for SPH-model)")) // [Mueller2003], (12) #endif #ifdef YADE_LIQMIGRATION ((Real,Vf, 0.0,, "Individual amount of liquid")) ((Real,Vmin, 0.0,, "Minimal amount of liquid")) #endif , /* additional initializers */ ((pos,se3.position)) ((ori,se3.orientation)), /* ctor */, /*py*/ YADE_PY_TOPINDEXABLE(State) .add_property("blockedDOFs",&State::blockedDOFs_vec_get,&State::blockedDOFs_vec_set,"Degress of freedom where linear/angular velocity will be always constant (equal to zero, or to an user-defined value), regardless of applied force/torque. String that may contain 'xyzXYZ' (translations and rotations).") // references must be set using wrapper funcs .add_property("pos",&State::pos_get,&State::pos_set,"Current position.") .add_property("ori",&State::ori_get,&State::ori_set,"Current orientation.") .def("displ",&State::displ,"Displacement from :yref:`reference position` (:yref:`pos` - :yref:`refPos`)") .def("rot",&State::rot,"Rotation from :yref:`reference orientation` (as rotation vector)") #ifdef YADE_SPH .add_property("rho", &State::rho, "Returns the current density (only for SPH-model).") .add_property("rho0", &State::rho0,"Returns the rest density (only for SPH-model).") .add_property("press",&State::press,"Returns the pressure (only for SPH-model).") #endif ); REGISTER_INDEX_COUNTER(State); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(State); trunk-2017.01a/core/ThreadRunner.cpp000066400000000000000000000054641304022710500172300ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include #include "ThreadRunner.hpp" #include "ThreadWorker.hpp" #include #include #include CREATE_LOGGER(ThreadRunner); void ThreadRunner::run() { // this is the body of execution of separate thread boost::mutex::scoped_lock lock(m_runmutex); try{ workerThrew=false; while(looping()) { call(); if(m_thread_worker->shouldTerminate()){ stop(); return; } } } catch (std::exception& e){ LOG_FATAL("Exception occured: "<setTerminate(false); m_thread_worker->callSingleAction(); } void ThreadRunner::pleaseTerminate() { stop(); m_thread_worker->setTerminate(true); } void ThreadRunner::spawnSingleAction() { boost::mutex::scoped_lock boollock(m_boolmutex); boost::mutex::scoped_lock calllock(m_callmutex); if(m_looping) return; boost::function0 call( boost::bind( &ThreadRunner::call , this ) ); boost::thread th(call); } void ThreadRunner::start() { boost::mutex::scoped_lock lock(m_boolmutex); if(m_looping) return; m_looping=true; boost::function0 run( boost::bind( &ThreadRunner::run , this ) ); boost::thread th(run); } void ThreadRunner::stop() { if(!m_looping) return; boost::mutex::scoped_lock lock(m_boolmutex); m_looping=false; } bool ThreadRunner::looping() { boost::mutex::scoped_lock lock(m_boolmutex); return m_looping; } ThreadRunner::~ThreadRunner() { pleaseTerminate(); boost::mutex::scoped_lock runlock(m_runmutex); boost::mutex::scoped_lock calllock(m_callmutex); } trunk-2017.01a/core/ThreadRunner.hpp000066400000000000000000000053121304022710500172250ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include /*! \brief ThreadRunner takes care of starting/stopping (executing) the ThreadWorker in the separate thread. It is achieved by either: - one execution of { ThreadWorker::singleAction(); } in separate thread - a loop { while(looping() ) ThreadWorker::singleAction(); } in separate thread Lifetime of ThreadRunner is guaranteed to be longer or equal to the lifetime of the separate thread of execution. The ThreadRunner owner must make sure that ThreadWorker has longer or equal lifetime than instance of ThreadRunner. Otherwise ThreadRunner will try to execute a dead object, which will lead to crash. Do not destroy immediately after call to singleAction(). Destructor can kick in before a separate thread starts, which will lead to a crash. User can explicitly ask the running thread to terminate execution. If the thread supports it, it will terminate. \note This code is reentrant. Simultaneous requests from other threads to start/stop or perform singleAction() are expected. So ThreadWorker(s) are running, while the user is interacting with the UI frontend (doesn't matter whether the UI is graphical, ncurses or any other). */ class ThreadWorker; class ThreadRunner { private : ThreadWorker* m_thread_worker; bool m_looping; boost::mutex m_boolmutex; boost::mutex m_callmutex; boost::mutex m_runmutex; void run(); void call(); DECLARE_LOGGER; public : ThreadRunner(ThreadWorker* c) : m_thread_worker(c), m_looping(false), workerThrew(false) {}; ~ThreadRunner(); /// perform ThreadWorker::singleAction() in separate thread void spawnSingleAction(); /// start doing singleAction() in a loop in separate thread void start(); /// stop the loop (changes the flag checked by looping() ) void stop(); /// kindly ask the separate thread to terminate void pleaseTerminate(); /// precondition for the loop started with start(). bool looping(); //! if true, workerException is copy of the exception thrown by the worker bool workerThrew; //! last exception thrown by the worker, if any std::exception workerException; }; trunk-2017.01a/core/ThreadWorker.cpp000066400000000000000000000032371304022710500172240ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "ThreadWorker.hpp" void ThreadWorker::setTerminate(bool b) { boost::mutex::scoped_lock lock(m_mutex); m_should_terminate=b; }; bool ThreadWorker::shouldTerminate() { boost::mutex::scoped_lock lock(m_mutex); return m_should_terminate; }; void ThreadWorker::setProgress(float i) { boost::mutex::scoped_lock lock(m_mutex); m_progress=i; }; void ThreadWorker::setStatus(std::string s) { boost::mutex::scoped_lock lock(m_mutex); m_status=s; }; float ThreadWorker::progress() { boost::mutex::scoped_lock lock(m_mutex); return m_progress; }; std::string ThreadWorker::getStatus() { boost::mutex::scoped_lock lock(m_mutex); return m_status; }; void ThreadWorker::setReturnValue(boost::any a) { boost::mutex::scoped_lock lock(m_mutex); m_val = a; }; boost::any ThreadWorker::getReturnValue() { boost::mutex::scoped_lock lock(m_mutex); return m_val; }; bool ThreadWorker::done() { boost::mutex::scoped_lock lock(m_mutex); return m_done; }; void ThreadWorker::callSingleAction() { { boost::mutex::scoped_lock lock(m_mutex); m_done = false; } this->singleAction(); { boost::mutex::scoped_lock lock(m_mutex); m_done = true; } }; trunk-2017.01a/core/ThreadWorker.hpp000066400000000000000000000045541304022710500172340ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include class ThreadRunner; /*! \brief ThreadWorker contains information about tasks to be performed when the separate thread is executed. */ class ThreadWorker // perhaps simulation steps, or stage? as it is a single stage // of the simulation, that consists of several steps // Update: it is more general now. simulation stages perhaps will be derived from this class { private: /// You should check out ThreadRunner, it is used for execution control of this class friend class ThreadRunner; bool m_should_terminate; bool m_done; boost::mutex m_mutex; boost::any m_val; float m_progress; std::string m_status; void callSingleAction(); protected: void setTerminate(bool); /// singleAction() can check whether someone asked for termination, and terminate if/when possible bool shouldTerminate(); /// if something must be returned, set the result using this method void setReturnValue(boost::any); /// if you feel monitored for progress, you can set it here: a value between 0.0 and 1.0 void setProgress(float); /// if you feel being monitored for what currently is done, set the message here void setStatus(std::string); /// derived classes must define this method, that's what is executed in separate thread virtual void singleAction() = 0; public: ThreadWorker() : m_should_terminate(false), m_done(false), m_progress(0) {}; virtual ~ThreadWorker() {}; /// Returns a value between 0.0 and 1.0. Useful for updating a progress bar. float progress(); // get_progress ? (pick a naming convention, efngh) /// You can display a message in GUI about what is the current work status std::string getStatus(); /// Check whether execution is finished, bool done(); /// then get the result. boost::any getReturnValue(); }; trunk-2017.01a/core/TimeStepper.hpp000066400000000000000000000023461304022710500170710ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include "Interaction.hpp" #include "GlobalEngine.hpp" #include "Scene.hpp" class Body; class TimeStepper: public GlobalEngine{ public: virtual void computeTimeStep(Scene* ) { throw; }; virtual bool isActivated() {return (active && (scene->iter % timeStepUpdateInterval == 0));}; virtual void action() { computeTimeStep(scene);} ; void setActive(bool a, int nb=-1) {active = a; if (nb>0) {timeStepUpdateInterval = (unsigned int)nb;}} YADE_CLASS_BASE_DOC_ATTRS( TimeStepper,GlobalEngine,"Engine defining time-step (fundamental class)", ((bool,active,true,,"is the engine active?")) ((unsigned int,timeStepUpdateInterval,1,,"dt update interval"))); }; REGISTER_SERIALIZABLE(TimeStepper); trunk-2017.01a/core/Timing.hpp000066400000000000000000000027671304022710500160660ustar00rootroot00000000000000// 2009 © Václav Šmilauer #pragma once #include struct TimingInfo{ typedef unsigned long long delta; long nExec; delta nsec; TimingInfo():nExec(0),nsec(0){} static delta getNow(bool evenIfDisabled=false) { if(!enabled && !evenIfDisabled) return 0L; #ifdef __APPLE__ std::cerr << "ERROR: Time profiling (TimingInfo) not implemented on Apples." << std::endl; return 0L; #else struct timespec ts; clock_gettime(CLOCK_MONOTONIC,&ts); return delta(1e9*ts.tv_sec+ts.tv_nsec); #endif } static bool enabled; }; /* Create TimingDeltas object, then every call to checkpoint() will add * (or use existing) TimingInfo to data. It increases its nExec by 1 * and nsec by time elapsed since construction or last checkpoint. */ class TimingDeltas{ TimingInfo::delta last; size_t i; public: vector data; vector labels; TimingDeltas():i(0){} void start(){if(!TimingInfo::enabled)return; i=0;last=TimingInfo::getNow();} void checkpoint(const string& label){ if(!TimingInfo::enabled) return; if(data.size()<=i) { data.resize(i+1); labels.resize(i+1); labels[i]=label;} TimingInfo::delta now=TimingInfo::getNow(); data[i].nExec+=1; data[i].nsec+=now-last; last=now; i++; } void reset(){ data.clear(); labels.clear(); } // python access boost::python::list pyData(){ boost::python::list ret; for(size_t i=0; i // make core classes known to the class factory #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include // these two are not accessible from python directly (though they should be in the future, perhaps) BOOST_CLASS_EXPORT_IMPLEMENT(BodyContainer); BOOST_CLASS_EXPORT_IMPLEMENT(InteractionContainer); YADE_PLUGIN((Body)(Bound)(Cell)(Dispatcher)(EnergyTracker)(Engine)(FileGenerator)(Functor)(GlobalEngine)(Interaction)(IGeom)(IPhys)(Material)(PartialEngine)(Shape)(State)(TimeStepper)); EnergyTracker::~EnergyTracker(){} trunk-2017.01a/core/main/000077500000000000000000000000001304022710500150365ustar00rootroot00000000000000trunk-2017.01a/core/main/main.py.in000077500000000000000000000316161304022710500167530ustar00rootroot00000000000000#!${pyExecutable} # encoding: utf-8 # syntax:python import sys,os,os.path,time try: import _io except ImportError: import io # Add search path for yade Python-modules # It allows to use both Yade-versions (packaged and self-compiled one). # See LP:1254708 for more details # https://bugs.launchpad.net/yade/+bug/1254708 sys.path.insert(1,'${runtimePREFIX}/${LIBRARY_OUTPUT_PATH}/yade${SUFFIX}/py') # get yade path (allow YADE_PREFIX to override) prefix,suffix='${runtimePREFIX}' if not os.environ.has_key('YADE_PREFIX') else os.environ['YADE_PREFIX'],'${SUFFIX}' # duplicate some items from yade.config here, so that we can increase verbosity when the c++ part is booting features,version,debugbuild='${CONFIGURED_FEATS}'.split(' '),'${realVersion}',' ${debugbuild}' if (features[0]==''): features=features[1:] libPATH='${LIBRARY_OUTPUT_PATH}' if (libPATH[1:] == '{LIBRARY_OUTPUT_PATH}'): libPATH='lib' ## find available builds libDir=prefix+'/'+libPATH+'/yade'+suffix if not (os.path.exists(libDir+'/py/yade/__init__.py')): raise RuntimeError('Libraries are not found! ('+libDir+'/py/yade/__init__.py, /py/yade/__init__.py)') # handle command-line options first try: import argparse except ImportError: # argparse not present, print error message raise RuntimeError("\n\nPlease install 'python-argparse' package.\n") prog = os.path.basename(sys.argv[0]) par=argparse.ArgumentParser(usage='%s [options] [ simulation.xml[.bz2] | script.py [script options]]'%prog, prog=prog,description="Yade: open-source platform for dynamic compuations. It\ is an extensible open-source framework for discrete numerical models, focused\ on Discrete Element Method. The computation parts are written in c++ using\ flexible object model, allowing independent implementation of new algorithms\ and interfaces. Python is used for rapid and concise scene construction, \ simulation control, postprocessing and debugging.\ Available features: %s.\ Homepage http://www.yade-dem.org, code hosted at http://www.launchpad.net/yade."%features ) par.add_argument('-v','--version',help='Print version and exit.',dest='version',action='store_true') par.add_argument('-j','--threads',help='Number of OpenMP threads to run; defaults to 1. Equivalent to setting OMP_NUM_THREADS environment variable.',dest='threads',type=int) par.add_argument('--cores',help='Set number of OpenMP threads (as \-\-threads) and in addition set affinity of threads to the cores given. Please provide a string with comma-separated core-ids.',dest='cores',type=str) par.add_argument('--update',help='Update deprecated class names in given script(s) using text search & replace. Changed files will be backed up with ~ suffix. Exit when done without running any simulation.',dest='updateScripts',nargs='+') par.add_argument('--nice',help='Increase nice level (i.e. decrease priority) by given number.',dest='nice',type=int) par.add_argument('-x',help='Exit when the script finishes',dest='exitAfter',action='store_true') par.add_argument('-n',help="Run without graphical interface (equivalent to unsetting the DISPLAY environment variable)",dest='nogui',action='store_true') par.add_argument('--test',help="Run regression test suite and exit; the exists status is 0 if all tests pass, 1 if a test fails and 2 for an unspecified exception.",dest="test",action='store_true') par.add_argument('--checks',help='Run a series of user-defined check tests as described in /yade/scripts/checks-and-tests/checks/README',dest='checks',action='store_true') par.add_argument('--performance',help='Starts a test to measure the productivity',dest='performance',action='store_true') par.add_argument('script',nargs='?',default='',type=str,help=argparse.SUPPRESS) par.add_argument('args',nargs=argparse.REMAINDER,help=argparse.SUPPRESS) # see argparse doc, par.disable_interspersed_args() from optargs module par.add_argument('-l',help='import libraries at startup before importing yade libs. May be used when the ordering of imports matter (see e.g. https://bugs.launchpad.net/yade/+bug/1183402/comments/3). The option can be use multiple times, as in "yade -llib1 -llib2"',default=None,action='append',dest='impLibraries',type=str) opts=par.parse_args() args = opts.args if opts.impLibraries: sys.path.append('.') for lib in opts.impLibraries: __import__(lib) if opts.version: print 'Yade version: %s%s'%(version,debugbuild) sys.exit(0) if opts.script: args.insert(0,opts.script) # for compatibility with userSession(), could be modified in the future ## remove later ## python2.5 relative module imports workaround v=sys.version_info if v[0]==2 and v[1]<=5: for submodule in ('yade','gts','yade/tests'): sys.path.append(os.path.join(libDir,'py',submodule)) sys.path.append(os.path.join(libDir,'py')) # run regression test suite and exit if opts.test: import yade.tests try: result=yade.tests.testAll() except: print 20*'*'+' UNEXPECTED EXCEPTION WHILE RUNNING TESTS '+20*'*' print 20*'*'+' '+str(sys.exc_info()[0]) print 20*'*'+" Please report bug at http://bugs.launchpad.net/yade providing the following traceback:" import traceback; traceback.print_exc() print 20*'*'+' Thank you '+20*'*' sys.exit(2) if (os.path.exists('./DirSearchYade')): os.remove('./DirSearchYade') if (os.path.exists('./MicroMacroAnalysis')): os.remove('./MicroMacroAnalysis') if result.wasSuccessful(): print "*** ALL TESTS PASSED ***" sys.exit(0) else: print 20*'*'+' SOME TESTS FAILED '+20*'*' sys.exit(1) if not 'OpenMP' in features and (opts.cores or (opts.threads and opts.threads>1)): print 'WARNING: compiled without OpenMP, -j/--threads/--cores have no effect.' # OpenMP env variables must be set before loading yade libs ("import yade" below) # changes have no effect after libgomp initializes if opts.cores: if opts.threads: print 'WARNING: --threads ignored, since --cores specified.' try: cores=[int(i) for i in opts.cores.split(',')] except ValueError: raise ValueError('Invalid --cores specification %s, should be a comma-separated list of non-negative integers'%opts.cores) opts.nthreads=len(cores) os.environ['GOMP_CPU_AFFINITY']=' '.join([str(c) for c in cores]) os.environ['OMP_NUM_THREADS']=str(len(cores)) elif opts.threads: os.environ['OMP_NUM_THREADS']=str(opts.threads) else: os.environ['OMP_NUM_THREADS']='1' if __name__ == "__main__": # do not print this while importing yade in other python application sys.stdout.write('Welcome to Yade '+version+debugbuild+'\n') # initialization and c++ plugins import import yade # other parts we will need soon import yade.config import yade.wrapper import yade.system import yade.runtime # continue option processing if opts.updateScripts: yade.system.updateScripts(args) sys.exit(0) # modify sys.argv in-place so that it can be handled by userSession sys.argv=yade.runtime.argv=args yade.runtime.opts=opts from yade import utils, pack from yade.utils import * from yade.pack import * from math import * # Run the check tests listed in scripts/checks-and-tests/checks/checkList.py if opts.checks: checksPath=libDir+'/py/yade/tests/checks' execfile(checksPath+'/checkList.py') # Run performance check test if opts.performance: checksPath=libDir+'/py/yade/tests/checks/performance' execfile(checksPath+'/checkPerf.py') def userSession(gui='none',qapp=None): # prepare nice namespace for users import yade.runtime import sys if __name__ != "__main__": # for importing as python module return # start non-blocking qt4 app here; need to ask on the mailing list on how to make it functional ## with ipython 0.11, start the even loop early (impossible with 0.10, which is thread-based) #if qt4 and yade.runtime.ipython_version==11: # import IPython # IPython.appstart_qt4(qapp) if len(sys.argv)>0: arg0=sys.argv[0] if (gui<>'none'): yade.qt.Controller(); if sum(bool(arg0.endswith(ext)) for ext in ('.xml','.xml.bz2','.xml.gz','.yade','.yade.gz','.yade.bz2','.bin','.bin.gz','.bin.bz2'))>0: if len(sys.argv)>1: raise RuntimeError('Extra arguments to saved simulation to run: '+' '.join(sys.argv[1:])) sys.stderr.write("Running simulation "+arg0+'\n') if arg0.endswith('.py'): def runScript(script): sys.stderr.write("Running script "+arg0+'\n') try: execfile(script,globals()) except SystemExit: raise except: # all other exceptions import traceback traceback.print_exc() if yade.runtime.opts.exitAfter: sys.exit(1) if yade.runtime.opts.exitAfter: sys.exit(0) runScript(arg0) if yade.runtime.opts.exitAfter: sys.exit(0) # common ipython configuration banner='[[ ^L clears screen, ^U kills line. '+', '.join((['F12 controller','F11 3d view (use h-key for showing help)','F10 both','F9 generator'] if (gui<>'none') else [])+['F8 plot'])+'. ]]' ipconfig=dict( # ipython options, see e.g. http://www.cv.nrao.edu/~rreid/casa/tips/ipy_user_conf.py prompt_in1='Yade [\#]: ', prompt_in2=' .\D.: ', prompt_out=" -> [\#]: ", separate_in='',separate_out='',separate_out2='', #execfile=[prefix+'/lib/yade'+suffix+'/py/yade/ipython.py'], readline_parse_and_bind=[ 'tab: complete', # only with the gui; the escape codes might not work on non-linux terminals. ] +(['"\e[24~": "\C-Uyade.qt.Controller();\C-M"','"\e[23~": "\C-Uyade.qt.View();\C-M"','"\e[21~": "\C-Uyade.qt.Controller(), yade.qt.View();\C-M"','"\e[20~": "\C-Uyade.qt.Generator();\C-M"'] if (gui<>'none') else []) #F12,F11,F10,F9 +['"\e[19~": "\C-Uimport yade.plot; yade.plot.plot();\C-M"', #F8 '"\e[A": history-search-backward', '"\e[B": history-search-forward', # incremental history forward/backward ] ) # show python console # handle both ipython 0.10 and 0.11 (incompatible API) if yade.runtime.ipython_version==10: from IPython.Shell import IPShellEmbed ipshell=IPShellEmbed(banner=banner,rc_override=ipconfig) ipshell() # save history -- a workaround for atexit handlers not being run (why?) # http://lists.ipython.scipy.org/pipermail/ipython-user/2008-September/005839.html import IPython.ipapi IPython.ipapi.get().IP.atexit_operations() elif yade.runtime.ipython_version==11: from IPython.frontend.terminal.embed import InteractiveShellEmbed # use the dict to set attributes for k in ipconfig: setattr(InteractiveShellEmbed,k,ipconfig[k]) InteractiveShellEmbed.banner1=banner+'\n' # called banner1 here, not banner anymore ipshell=InteractiveShellEmbed() ipshell() elif yade.runtime.ipython_version>=12: if yade.runtime.ipython_version>=100: from IPython.terminal.embed import InteractiveShellEmbed else: from IPython.frontend.terminal.embed import InteractiveShellEmbed if yade.runtime.ipython_version>=500: from traitlets.config.loader import Config cfg = Config() prompt_config = cfg.TerminalInteractiveShell.prompts_class else: from IPython.config.loader import Config cfg = Config() prompt_config = cfg.PromptManager prompt_config.in_template = ipconfig['prompt_in1'] prompt_config.in2_template = ipconfig['prompt_in2'] prompt_config.out_template = ipconfig['prompt_out'] import readline for k in ipconfig['readline_parse_and_bind']: readline.parse_and_bind(k) InteractiveShellEmbed.config=cfg InteractiveShellEmbed.banner1=banner+'\n' ipshell=InteractiveShellEmbed() ipshell() ## run userSession in a way corresponding to the features we use: gui=None yade.runtime.hasDisplay=False # this is the default initialized in the module, anyway if 'GUI' in features: gui='qt4' if 'GUI-Qt5' in features: gui='qt5' if opts.nogui: gui=None if gui: import Xlib.display # PyQt4's QApplication does exit(1) if it is unable to connect to the display # we however want to handle this gracefully, therefore # we test the connection with bare xlib first, which merely raises DisplayError try: # contrary to display.Display, _BaseDisplay does not check for extensions and that avoids spurious message "Xlib.protocol.request.QueryExtension" (bug?) Xlib.display._BaseDisplay(); yade.runtime.hasDisplay=True except: # usually Xlib.error.DisplayError, but there can be Xlib.error.XauthError etc as well # let's just pretend any exception means the display would not work gui=None print 'Warning: no X rendering available (see https://bbs.archlinux.org/viewtopic.php?id=13189)' # run remote access things, before actually starting the user session (not while imported by other python application) if __name__ == "__main__": from yade import remote if (gui=='qt4' or gui=='qt5'): yade.remote.useQThread=True yade.remote.gui=gui yade.remote.runServers() if gui==None: userSession() elif gui=='qt4': ## we already tested that DISPLAY is available and can be opened ## otherwise Qt4 might crash at this point import PyQt4 from PyQt4 import QtGui from PyQt4.QtCore import * import yade.qt # this yade.qt is different from the one that comes with qt3 qapp=QtGui.QApplication(sys.argv) userSession(gui=gui,qapp=qapp) elif gui=='qt5': import PyQt5 from PyQt5 import QtGui from PyQt5.QtCore import * from PyQt5.QtWidgets import * import yade.qt qapp=QApplication(sys.argv) userSession(gui=gui,qapp=qapp) if __name__ == "__main__": O.exitNoBacktrace() trunk-2017.01a/core/main/pyboot.cpp000066400000000000000000000030251304022710500170560ustar00rootroot00000000000000#include #include #include #ifdef YADE_DEBUG void crashHandler(int sig){ switch(sig){ case SIGABRT: case SIGSEGV: signal(SIGSEGV,SIG_DFL); signal(SIGABRT,SIG_DFL); // prevent loops - default handlers cerr<<"SIGSEGV/SIGABRT handler called; gdb batch file is `"<(getpid())<<"\nset pagination off\nthread info\nthread apply all backtrace\ndetach\nquit\n"; gdbBatch.close(); signal(SIGABRT,crashHandler); signal(SIGSEGV,crashHandler); #endif vector ppp; for(int i=0; i(pp[i])); Omega::instance().loadPlugins(ppp); } void yadeFinalize(){ Omega::instance().cleanupTemps(); } BOOST_PYTHON_MODULE(boot){ boost::python::scope().attr("initialize")=&yadeInitialize; boost::python::scope().attr("finalize")=&yadeFinalize; //,"Finalize yade (only to be used internally).") } trunk-2017.01a/core/main/yade-batch.in000077500000000000000000000707521304022710500174050ustar00rootroot00000000000000#!${pyExecutable} # encoding: utf-8 # # vim: syntax=python # portions © 2008 Václav Šmilauer import os, sys, thread, time, logging, pipes, socket, xmlrpclib, re, shutil, random # Add search path for yade Python-modules # It allows to use both Yade-versions (packaged and self-compiled one). # See LP:1254708 for more details # https://bugs.launchpad.net/yade/+bug/1254708 sys.path.insert(1,'${runtimePREFIX}/${LIBRARY_OUTPUT_PATH}/yade${SUFFIX}/py') #socket.setdefaulttimeout(10) ## replaced by scons automatically prefix,suffix='${runtimePREFIX}' if not os.environ.has_key('YADE_PREFIX') else os.environ['YADE_PREFIX'],'${SUFFIX}' libPATH='${LIBRARY_OUTPUT_PATH}' if (libPATH[1:] == '{LIBRARY_OUTPUT_PATH}'): libPATH='lib' libDir=prefix+'/'+libPATH+'/yade'+suffix # run the batch always in non-debug mode (the spawned processes do honor debuggin flag, however) docDir=prefix+'/share/doc/yade'+suffix imageLogo = docDir+'/img/yade-logo-note.png' sys.path.append(os.path.join(libDir,'py')) executable=os.path.join(prefix,'bin','yade'+suffix) ## we just need this ... import yade, yade.utils, yade.config, yade.remote class JobInfo(): def __init__(self,num,id,command,hrefCommand,log,nCores,script,table,lineNo,affinity): self.started,self.finished,self.duration,self.durationSec,self.exitStatus=None,None,None,None,None # duration is a string, durationSec is a number self.command=command; self.hrefCommand=hrefCommand; self.num=num; self.log=log; self.id=id; self.nCores=nCores; self.cores=set(); self.infoSocket=None self.script=script; self.table=table; self.lineNo=lineNo; self.affinity=affinity self.hasXmlrpc=False self.status='PENDING' self.threadNum=None self.plotsLastUpdate,self.plotsFile=0.,yade.Omega().tmpFilename()+'.'+yade.remote.plotImgFormat def saveInfo(self): log=file(self.log,'a') log.write(""" =================== JOB SUMMARY ================ id : %s status : %d (%s) duration: %s command : %s started : %s finished: %s """%(self.id,self.exitStatus,'OK' if self.exitStatus==0 else 'FAILED',self.duration,self.command,time.asctime(time.localtime(self.started)),time.asctime(time.localtime(self.finished)))); log.close() #Show notification messasge if (pynotifyAvailable): statusString = '' if (self.exitStatus==0): statusString = 'Finished.' else: statusString = 'FAILED!' n = pynotify.Notification("Yade", "The job %d/%d is %s Duration %s"%(self.num+1, len(jobs), statusString, self.duration), imageLogo) n.show() def ensureXmlrpc(self): 'Attempt to establish xmlrpc connection to the job (if it does not exist yet). If the connection could not be established, as magic line was not found in the log, return False.' if self.hasXmlrpc: return True for l in open(self.log,'r'): if not l.startswith('XMLRPC info provider on'): continue url=l[:-1].split()[4] self.xmlrpcConn=xmlrpclib.ServerProxy(url,allow_none=True) self.hasXmlrpc=True return True if not self.hasXmlrpc: return False # catches the case where the magic line is not in the log yet def getInfoDict(self): if self.status!='RUNNING': return None if not self.ensureXmlrpc(): return None return self.xmlrpcConn.basicInfo() def updatePlots(self): global opts if self.status!='RUNNING': return if not self.ensureXmlrpc(): return if time.time()-self.plotsLastUpdate0: ret+='%2.2f%% done
step %d/%d'%(info['iter']*100./info['stopAtIter'],info['iter'],info['stopAtIter']) finishTime = str(time.ctime(time.time()+int((round(info['stopAtIter'] - info['iter'])/info['speed'])))) ret+='
%s finishes
'%finishTime else: ret+='step %d'%(info['iter']) if info['realtime']!=0: ret+='
speed %g/sec'%(info['speed']) ret+='
%d bodies
%d intrs'%(info['numBodies'],info['numIntrs']) ret+='' else: ret+=' (no info) ' ret+='%d%s'%(self.nCores,(' ('+','.join([str(c) for c in self.cores])+')') if self.cores and self.status=='RUNNING' else '') # TODO: make clickable so that it can be served full-size if os.path.exists(self.plotsFile): img='[plots]'%(self.num) ret+='%s'%(self.num,img) else: ret+=' (no plots) ' ret+='%s'%self.hrefCommand ret+='' return ret def stopJob(self): if self.status!='RUNNING': return None if not self.ensureXmlrpc(): return None self.xmlrpcConn.stop() return ("The job #%s is stopped
Return back to statistic page"%(self.num)) def t2hhmmss(dt): return '%02d:%02d:%02d'%(dt//3600,(dt%3600)//60,(dt%60)) def totalRunningTime(): tt0,tt1=[j.started for j in jobs if j.started],[j.finished for j in jobs if j.finished]+[time.time()] # it is safe to suppose that if len(tt0)==0: return 0 # no job has been started at all return max(tt1)-min(tt0) def globalHtmlStats(): t0=min([j.started for j in jobs if j.started!=None]) unfinished=len([j for j in jobs if j.status!='DONE']) nUsedCores=sum([j.nCores for j in jobs if j.status=='RUNNING']) global maxJobs if unfinished: ret='

Running for %s, since %s.

'%(t2hhmmss(totalRunningTime()),time.ctime(t0)) else: failed=len([j for j in jobs if j.exitStatus!=0]) lastFinished=max([j.finished for j in jobs]) # FIXME: do not report sum of runnign time of all jobs, only the real timespan ret='

Finished, idle for %s, running time %s since %s.

'%('red' if failed else 'lime',t2hhmmss(time.time()-lastFinished),t2hhmmss(sum([j.finished-j.started for j in jobs if j.started is not None])),time.ctime(t0)) ret+='

Pid %d'%(os.getpid()) if opts.globalLog: ret+=', log %s'%(opts.globalLog) ret+='

' allCores,busyCores=set(range(0,maxJobs)),set().union(*(j.cores for j in jobs if j.status=='RUNNING')) ret+='

%d cores available, %d used + %d free.

'%(maxJobs,nUsedCores,maxJobs-nUsedCores) # show busy and free cores; gives nonsense if not all jobs have CPU affinity set # '([%s] = [%s] + [%s])'%(','.join([str(c) for c in allCores]),','.join([str(c) for c in busyCores]),','.join([str(c) for s in (allCores-busyCores)])) ret+='

Jobs

' nFailed=len([j for j in jobs if j.status=='DONE' and j.exitStatus!=0]) ret+='

%d total, %d running, %d done%s

'%(len(jobs),len([j for j in jobs if j.status=='RUNNING']), len([j for j in jobs if j.status=='DONE']),' (%d failed)'%nFailed if nFailed>0 else '') return ret from BaseHTTPServer import BaseHTTPRequestHandler,HTTPServer import socket,re class HttpStatsServer(BaseHTTPRequestHandler): favicon=None # binary favicon, created when first requested def do_GET(self): if not self.path or self.path=='/': self.sendGlobal() else: if self.path=='/favicon.ico': if not self.__class__.favicon: import base64 self.__class__.favicon=base64.b64decode(yade.remote.b64favicon) self.sendHttp(self.__class__.favicon,contentType='image/vnd.microsoft.icon') return elif self.path=='/log' and opts.globalLog: self.sendTextFile(opts.globalLog,refresh=opts.refresh) return jobMatch=re.match('/jobs/([0-9]+)/(.*)',self.path) if not jobMatch: self.send_error(404,self.path); return jobId=int(jobMatch.group(1)) if jobId>=len(jobs): self.send_error(404,self.path); return job=jobs[jobId] rest=jobMatch.group(2) if rest=='plots': job.updatePlots() # internally checks for last update time self.sendFile(job.plotsFile,contentType=yade.remote.plotImgMimetype,refresh=(0 if job.status=='DONE' else opts.refresh)) elif rest=='log': if not os.path.exists(job.log): self.send_error(404,self.path); return ## once we authenticate properly, send the whole file ## self.sendTextFile(jobs[jobId].log,refresh=opts.refresh) ## now we have to filter away the cookie cookieRemoved=False; data='' for l in open(job.log): if not cookieRemoved and l.startswith('TCP python prompt on'): ii=l.find('auth cookie `'); l=l[:ii+13]+'******'+l[ii+19:]; cookieRemoved=True data+=l self.sendHttp(data,contentType='text/plain;charset=utf-8;',refresh=(0 if job.status=='DONE' else opts.refresh)) elif rest=='script': self.sendPygmentizedFile(job.script,linenostep=5) elif rest=='table': if not job.table: return self.sendPygmentizedFile(job.table,hl_lines=[job.lineNo],linenostep=1) elif rest=='stop': self.sendHttp(job.stopJob(),contentType='text/html',refresh=(0 if job.status=='DONE' else opts.refresh)) elif rest=='askforstop': self.sendHttp('Are you sure, you want to stop job #%d?
Stop
Cancel'%(job.num,job.num),contentType='text/html',refresh=(0 if job.status=='DONE' else opts.refresh)) else: self.send_error(404,self.path) return def log_request(self,req): pass def sendGlobal(self): html='Yade-batch at %s overview\n'%(socket.gethostname()) html+=globalHtmlStats() html+='\n' for j in jobs: html+=j.htmlStats()+'\n' html+='
idstatusinfocoresplotscommand
' self.sendHttp(html,contentType='text/html',refresh=opts.refresh) # refresh sent as header def sendTextFile(self,fileName,**headers): if not os.path.exists(fileName): self.send_error(404); return import codecs f=codecs.open(fileName,encoding='utf-8') self.sendHttp(f.read(),contentType='text/plain;charset=utf-8;',**headers) def sendFile(self,fileName,contentType,**headers): if not os.path.exists(fileName): self.send_error(404); return f=open(fileName) self.sendHttp(f.read(),contentType=contentType,**headers) def sendHttp(self,data,contentType,**headers): "Send file over http, using appropriate content-type. Headers are converted to strings. The *refresh* header is handled specially: if the value is 0, it is not sent at all." self.send_response(200) self.send_header('Content-type',contentType) if 'refresh' in headers and headers['refresh']==0: del headers['refresh'] for h in headers: self.send_header(h,str(headers[h])) self.end_headers() self.wfile.write(data) global httpLastServe httpLastServe=time.time() def sendPygmentizedFile(self,f,**kw): if not os.path.exists(f): self.send_error(404); return try: import codecs from pygments import highlight from pygments.lexers import PythonLexer from pygments.formatters import HtmlFormatter data=highlight(codecs.open(f,encoding='utf-8').read(),PythonLexer(),HtmlFormatter(linenos=True,full=True,encoding='utf-8',title=os.path.abspath(f),**kw)) self.sendHttp(data,contentType='text/html;charset=utf-8;') except ImportError: self.sendTextFile(f) def runHttpStatsServer(): maxPort=11000; port=9080 while port0: job.exitStatus=0 job.finished=time.time() dt=job.finished-job.started; job.durationSec=dt job.duration=t2hhmmss(dt) strStatus='done ' if job.exitStatus==0 else 'FAILED ' job.status='DONE' havePlot=False if os.path.exists(job.plotsFile): f=(job.log[:-3] if job.log.endswith('.log') else job.log+'.')+yade.remote.plotImgFormat shutil.copy(job.plotsFile,f) job.plotsFile=f havePlot=True print "#%d (%s%s) %s (exit status %d), duration %s, log %s%s"%(job.num,job.id,'' if job.nCores==1 else '/%d'%job.nCores,strStatus,job.exitStatus,job.duration,job.log,(', plot %s'%(job.plotsFile) if havePlot else '')) job.saveInfo() def runJobs(jobs,numCores): running,pending=0,len(jobs) inf=1000000 while (running>0) or (pending>0): pending,running,done=sum([j.nCores for j in jobs if j.status=='PENDING']),sum([j.nCores for j in jobs if j.status=='RUNNING']),sum([j.nCores for j in jobs if j.status=='DONE']) numFreeCores=numCores-running minRequire=min([inf]+[j.nCores for j in jobs if j.status=='PENDING']) if minRequire==inf: minRequire=0 #print pending,'pending;',running,'running;',done,'done;',numFreeCores,'free;',minRequire,'min' overloaded=False if minRequire>numFreeCores and running==0: overloaded=True # a job wants more cores than the total we have pendingJobs=[j for j in jobs if j.status=='PENDING'] if opts.randomize: random.shuffle(pendingJobs) for j in pendingJobs: if j.nCores<=numFreeCores or overloaded: freeCores=set(range(0,numCores))-set().union(*(j.cores for j in jobs if j.status=='RUNNING')) #print 'freeCores:',freeCores,'numFreeCores:',numFreeCores,'overloaded',overloaded if not overloaded: # only set cores if CPU affinity is desired; otherwise, just numer of cores is used if j.affinity: j.cores=list(freeCores)[0:j.nCores] # take required number of free cores # if overloaded, do not assign cores directly thread.start_new_thread(runJob,(j,)) break time.sleep(.5) sys.stdout.flush() import sys,re,os try: import argparse except ImportError: # argparse not present, print error message raise RuntimeError("\n\nPlease install 'python-argparse' package.\n") def getNumCores(): nCpu=1 try: nCpu=len([l for l in open('/proc/cpuinfo','r') if l.find('processor')==0]) except: print 'WARNING: No cpuinfo available! Setting the maximal number of processors 1' pass if os.environ.has_key("OMP_NUM_THREADS"): return min(int(os.environ['OMP_NUM_THREADS']),nCpu) return nCpu numCores=getNumCores() maxOmpThreads=numCores if 'OpenMP' in yade.config.features else 1 features,version='${CONFIGURED_FEATS}'.split(','),'${realVersion}' if (features[0]==''): features=features[1:] prog = os.path.basename(sys.argv[0]) parser=argparse.ArgumentParser(usage='%s [options] [ TABLE [SIMULATION.py] | SIMULATION.py[/nCores] [...] ]'%prog,description='%s runs yade simulation multiple times with different parameters.\n\nSee https://yade-dem.org/sphinx/user.html#batch-queuing-and-execution-yade-batch for details.\n\nBatch can be specified either with parameter table TABLE (must not end in .py), which is either followed by exactly one SIMULATION.py (must end in .py), or contains !SCRIPT column specifying the simulation to be run. The second option is to specify multiple scripts, which can optionally have /nCores suffix to specify number of cores for that particular simulation (corresponds to !THREADS column in the parameter table), e.g. sim.py/3.'%prog) parser.add_argument('-j','--jobs',dest='maxJobs',type=int,help="Maximum number of simultaneous threads to run (default: number of cores, further limited by OMP_NUM_THREADS if set by the environment: %d)"%numCores,metavar='NUM',default=numCores) parser.add_argument('-v','--version',help='Print version and exit.',dest='version',action='store_true') parser.add_argument('--job-threads',dest='defaultThreads',type=int,help="Default number of threads for one job; can be overridden by per-job with !THREADS (or !OMP_NUM_THREADS) column. Defaults to 1.",metavar='NUM',default=1) parser.add_argument('--force-threads',action='store_true',dest='forceThreads',help='Force jobs to not use more cores than the maximum (see \-j), even if !THREADS colums specifies more.') parser.add_argument('--log',dest='logFormat',help='Format of job log files: must contain a $, %% or @, which will be replaced by script name, line number or by description column respectively (default: $.@.log)',metavar='FORMAT',default='$.@.log') parser.add_argument('--global-log',dest='globalLog',help='Filename where to redirect output of yade-batch itself (as opposed to \-\-log); if not specified (default), stdout/stderr are used',metavar='FILE') parser.add_argument('-l','--lines',dest='lineList',help='Lines of TABLE to use, in the format 2,3-5,8,11-13 (default: all available lines in TABLE)',metavar='LIST') parser.add_argument('--nice',dest='nice',type=int,help='Nice value of spawned jobs (default: 10)',default=10) parser.add_argument('--cpu-affinity',dest='affinity',action='store_true',help='Bind each job to specific CPU cores; cores are assigned in a quasi-random order, depending on availability at the moment the jobs is started. Each job can override this setting by setting AFFINE column.') parser.add_argument('--executable',dest='executable',help='Name of the program to run (default: %s). Jobs can override with !EXEC column.'%executable,default=executable,metavar='FILE') parser.add_argument('--gnuplot',dest='gnuplotOut',help='Gnuplot file where gnuplot from all jobs should be put together',default=None,metavar='FILE') parser.add_argument('--dry-run',action='store_true',dest='dryRun',help='Do not actually run (useful for getting gnuplot only, for instance)',default=False) parser.add_argument('--http-wait',action='store_true',dest='httpWait',help='Do not quit if still serving overview over http repeatedly',default=False) parser.add_argument('--plot-update',type=int,dest='plotAlwaysUpdateTime',help='Interval (in seconds) at which job plots will be updated even if not requested via HTTP. Non-positive values will make the plots not being updated and saved unless requested via HTTP (see \-\-plot-timeout for controlling maximum age of those). Plots are saved at exit under the same name as the log file, with the .log extension removed. (default: 120 seconds)',metavar='TIME',default=120) parser.add_argument('--plot-timeout',type=int,dest='plotTimeout',help='Maximum age (in seconds) of plots served over HTTP; they will be updated if they are older. (default: 30 seconds)',metavar='TIME',default=30) parser.add_argument('--refresh',type=int,dest='refresh',help='Refresh rate of automatically reloaded web pages (summary, logs, ...).',metavar='TIME',default=30) parser.add_argument('--timing',type=int,dest='timing',default=0,metavar='COUNT',help='Repeat each job COUNT times, and output a simple table with average/variance/minimum/maximum job duration; used for measuring how various parameters affect execution time. Jobs can override the global value with the !COUNT column.') parser.add_argument('--timing-output',type=str,metavar='FILE',dest='timingOut',default=None,help='With \-\-timing, save measured durations to FILE, instead of writing to standard output.') parser.add_argument('--randomize',action='store_true',dest='randomize',help='Randomize job order (within constraints given by assigned cores).') parser.add_argument('--disable-pynotify',action='store_true',dest='disablePynotify',help='Disable screen notifications') parser.add_argument('args',nargs=argparse.REMAINDER,help=argparse.SUPPRESS) # see argparse doc, par.disable_interspersed_args() from optargs module #parser.add_argument('--serial',action='store_true',dest='serial',default=False,help='Run all jobs serially, even if there are free cores opts=parser.parse_args() args = opts.args logFormat,lineList,maxJobs,nice,executable,gnuplotOut,dryRun,httpWait,globalLog=opts.logFormat,opts.lineList,opts.maxJobs,opts.nice,opts.executable,opts.gnuplotOut,opts.dryRun,opts.httpWait,opts.globalLog if opts.version: print 'Yade version: %s, features: %s'%(version,','.join(features)) sys.exit(0) if globalLog: print 'Redirecting all output to',globalLog sys.stderr=open(globalLog,"w") sys.stdout=sys.stderr if len([1 for a in args if re.match('.*\.py(/[0-9]+)?',a)])==len(args) and len(args)!=0: # if all args end in .py, they are simulations that we will run table=None; scripts=args elif len(args)==2: table,scripts=args[0],[args[1]] elif len(args)==1: table,scripts=args[0],[] else: parser.print_help() sys.exit(1) pynotifyAvailable = False n = 0; if not opts.disablePynotify: try: import pynotify pynotifyAvailable = True pynotify.init("Yade") except ImportError: pynotifyAvailable = False print "Will run simulation(s) %s using `%s', nice value %d, using max %d cores."%(scripts,executable,nice,maxJobs) if table: reader=yade.utils.TableParamReader(table) params=reader.paramDict() availableLines=params.keys() print "Will use table `%s', with available lines"%(table),', '.join([str(i) for i in availableLines])+'.' if lineList: useLines=[] def numRange2List(s): ret=[] for l in s.split(','): if "-" in l: ret+=range(*[int(s) for s in l.split('-')]); ret+=[ret[-1]+1] else: ret+=[int(l)] return ret useLines0=numRange2List(lineList) for l in useLines0: if l not in availableLines: logging.warn('Skipping unavailable line %d that was requested from the command line.'%l) else: useLines+=[l] else: useLines=availableLines print "Will use lines ",', '.join([str(i)+' (%s)'%params[i]['description'] for i in useLines])+'.' else: print "Running %d stand-alone simulation(s) in batch mode."%(len(scripts)) useLines=[] params={} for i,s in enumerate(scripts): fakeLineNo=-i-1 useLines.append(fakeLineNo) params[fakeLineNo]={'description':'default','!SCRIPT':s} # fix script and set threads if script.py/num m=re.match('(.*)(/[0-9]+)$',s) if m: params[fakeLineNo]['!SCRIPT']=m.group(1) params[fakeLineNo]['!THREADS']=int(m.group(2)[1:]) jobs=[] executables=set() logFiles=[] for i,l in enumerate(useLines): script=scripts[0] if len(scripts)>0 else None envVars=[] nCores=opts.defaultThreads jobExecutable=executable jobAffinity=opts.affinity jobCount=opts.timing for col in params[l].keys(): if col[0]!='!': continue val=params[l][col] if col=='!OMP_NUM_THREADS' or col=='!THREADS': nCores=int(val) elif col=='!EXEC': jobExecutable=val elif col=='!SCRIPT': script=val elif col=='!AFFINITY': jobAffinity=eval(val) elif col=='!COUNT': jobCount=eval(val) else: envVars+=['%s=%s'%(head[1:],values[l][col])] if not script: raise ValueError('When only batch table is given without script to run, it must contain !SCRIPT column with simulation to be run.') logFile=logFormat.replace('$',script).replace('%',str(l)).replace('@',params[l]['description']) if (len(logFile)>230): #For very long files, to prevent system errors. logFile = logFile[0:230]+'_'+str(l)+logFile[-4:] #l is added to prevent name duplications. if nCores>maxJobs: if opts.forceThreads: logging.info('Forcing job #%d to use only %d cores (max available) instead of %d requested'%(i,maxJobs,nCores)) nCores=maxJobs else: logging.warning('WARNING: job #%d will use %d cores but only %d are available'%(i,nCores,maxJobs)) if 'OpenMP' not in yade.config.features and nCores>1: logging.warning('Job #%d will be uselessly run with %d threads (compiled without OpenMP support).'%(i,nCores)) executables.add(jobExecutable) # compose command-line: build the hyper-linked variant, then strip HTML tags (ugly, but ensures consistency) for j in range(0,opts.timing if opts.timing>0 else 1): jobNum=len(jobs) logFile2=logFile+('.%d'%j if opts.timing>0 else '') # append numbers to log file if it already exists, to prevent overwriting if logFile2 in logFiles: i=0; while logFile2+'.%d'%i in logFiles: i+=1 logFile2+='.%d'%i logFiles.append(logFile2) env='YADE_BATCH=' if table: env+='%s:%d'%(jobNum,table,l) # keep YADE_BATCH empty (but still defined) if running a single simulation env+=' DISPLAY= %s '%(' '.join(envVars)) cmd='%s%s [threadspec] %s -x %s'%(jobExecutable,'','--nice=%s'%nice if nice!=None else '',i,script) log='> %s 2>&1'%(jobNum,pipes.quote(logFile2)) hrefCmd=env+cmd+log fullCmd=re.sub('(]+">|)','',hrefCmd) desc=params[l]['description'] if '!SCRIPT' in params[l].keys(): desc=script+'.'+desc # prepend filename if script is specified explicitly if opts.timing>0: desc+='[%d]'%j jobs.append(JobInfo(jobNum,desc,fullCmd,hrefCmd,logFile2,nCores,script=script,table=table,lineNo=l,affinity=jobAffinity)) print "Master process pid",os.getpid() print "Job summary:" for job in jobs: print ' #%d (%s%s):'%(job.num,job.id,'' if job.nCores==1 else '/%d'%job.nCores),job.command sys.stdout.flush() httpLastServe=0 runHttpStatsServer() if opts.plotAlwaysUpdateTime>0: # update plots periodically regardless of whether they are requested via HTTP def updateAllPlots(): time.sleep(opts.plotAlwaysUpdateTime) for job in jobs: job.updatePlots() thread.start_new_thread(updateAllPlots,()) # OK, go now if not dryRun: runJobs(jobs,maxJobs) print 'All jobs finished, total time ',t2hhmmss(totalRunningTime()) plots=[] for j in jobs: if not os.path.exists(j.plotsFile): continue plots.append(j.plotsFile) if plots: print 'Plot files:',' '.join(plots) # for easy grepping in logfiles: print 'Log files:',' '.join([j.log for j in jobs]) # write timing table if opts.timing>0: if opts.timingOut: print 'Writing gathered timing information to',opts.timingOut try: out=open(opts.timingOut,'w') except IOError: logging.warn('Unable to open file %s for timing output, writing to stdout.'%opts.timingOut) out=sys.stdout else: print 'Gathered timing information:' out=sys.stdout # write header out.write('## timing data, written '+time.asctime()+' with arguments\n## '+' '.join(sys.argv)+'\n##\n') paramNames=params[params.keys()[0]].keys(); paramNames.sort() out.write('## line\tcount\tavg\tdev\trelDev\tmin\tmax\t|\t'+'\t'.join(paramNames)+'\n') import math for i,l in enumerate(useLines): jobTimes=[j.durationSec for j in jobs if j.lineNo==l and j.durationSec!=None] tSum=sum(jobTimes); tAvg=tSum/len(jobTimes) tMin,tMax=min(jobTimes),max(jobTimes) tDev=math.sqrt(sum((t-tAvg)**2 for t in jobTimes)/len(jobTimes)) tRelDev=tDev/tAvg out.write('%d\t%d\t%.2f\t%.2f\t%.3g\t%.2f\t%.2f\t|\t'%(l,len(jobTimes),tAvg,tDev,tRelDev,tMin,tMax)+'\t'.join([params[l][p] for p in paramNames])+'\n') if not gnuplotOut: print 'Bye.' else: print 'Assembling gnuplot files…' for job in jobs: for l in file(job.log): if l.startswith('gnuplot '): job.plot=l.split()[1] break preamble,plots='',[] for job in jobs: if not 'plot' in job.__dict__: print "WARN: No plot found for job "+job.id continue for l in file(job.plot): if l.startswith('plot'): # attempt to parse the plot line ll=l.split(' ',1)[1][:-1] # rest of the line, without newline # replace title 'something' with title 'description: something' ll,nn=re.subn(r'title\s+[\'"]([^\'"]*)[\'"]',r'title "'+job.id+r': \1"',ll) if nn==0: logging.error("Plot line in "+job.plot+" not parsed (skipping): "+ll) plots.append(ll) break if not plots: # first plot, copy all preceding lines preamble+=l gp=file(gnuplotOut,'w') gp.write(preamble) gp.write('plot '+','.join(plots)) print "gnuplot",gnuplotOut print "Plot written, bye." if httpWait and time.time()-httpLastServe<30: print "(continue serving http until no longer requested as per --http-wait)" while time.time()-httpLastServe<30: time.sleep(1) yade.Omega().exitNoBacktrace() trunk-2017.01a/doc/000077500000000000000000000000001304022710500137275ustar00rootroot00000000000000trunk-2017.01a/doc/README000066400000000000000000000002521304022710500146060ustar00rootroot00000000000000All documentation is at http://www.yade-dem.org, in particular see https://yade-dem.org/index.php/Reference_documentation To generate documentation see sphinx/README trunk-2017.01a/doc/citing_yade.bib000066400000000000000000000023011304022710500166600ustar00rootroot00000000000000@book{yade:doc2, altnote = "\\url{http://yade-dem.org/doc/}", author = "V. \v{S}milauer and others", doi = "10.5281/zenodo.34073", note = "http://yade-dem.org/doc/", title = "{{Y}ade {D}ocumentation 2nd ed}", publisher = "{The {Y}ade Project}", year = "2015" } @incollection{yade:manual2, altnote = "\\url{http://yade-dem.org/doc/}", author = "V. \v{S}milauer and others", doi = "10.5281/zenodo.34043", booktitle = "{Y}ade {D}ocumentation 2nd ed", note = "http://yade-dem.org/doc/", publisher = "{The {Y}ade Project}", title = "Using and Programming", year = "2015" } @incollection{yade:background2, altnote = "\\url{http://yade-dem.org/doc/}", author = "V. \v{S}milauer and B. Chareyre", doi = "10.5281/zenodo.34044", booktitle = "{Y}ade {D}ocumentation 2nd ed", note = "http://yade-dem.org/doc/", publisher = "{The {Y}ade Project}", title = "DEM formulation", year = "2015" } @incollection{yade:reference2, altnote = "\\url{http://yade-dem.org/doc/}", author = "V. \v{S}milauer and others", doi = "10.5281/zenodo.34045", booktitle = "{Y}ade {D}ocumentation 2nd ed", note = "http://yade-dem.org/doc/", publisher = "{The {Y}ade Project}", title = "Reference Manual", year = "2015" } trunk-2017.01a/doc/how-to-release.md000066400000000000000000000010571304022710500171070ustar00rootroot00000000000000* Create RELEASE file in the root folder with the version number in it * Add new changelog entries to Changelog using "git shortlog PREVVERSION.." * Create branch using the following command and format "git checkout -b YYYY.MM" * Tag release "git tag -as YYYY.MMa -m"YYYY.MMa" * Return to master branch and remove RELEASE file * Push master, new branch and tags to github * Download tar.gz * Create asc-file (signature): gpg --armor --sign --detach-sig tarball.tar.gz * Upload new tarball on Launchpad * Make announcement on mailing list and on Launchpad trunk-2017.01a/doc/logging.conf.sample000066400000000000000000000032371304022710500175110ustar00rootroot00000000000000# This is example logging configuration file for yade. # # Place it in ~/.yade/logging.conf if you want it to be loaded and watched for changes during execution as well. # # log4cxx homepage is http://logging.apache.org/log4cxx/ # of particular interest is instroduction (http://logging.apache.org/log4cxx/manual/Introduction.html) # and pattern description (http://logging.apache.org/log4cxx/manual/classlog4cxx_1_1PatternLayout.html) # # Set root logger level to DEBUG, one appender for console and other to a file log4j.rootLogger=DEBUG,console,logfile log4j.appender.console=org.apache.log4j.ConsoleAppender # A1 uses PatternLayout. log4j.appender.console.layout=org.apache.log4j.PatternLayout #log4j.appender.console.layout.ConversionPattern=%-4r %-5p %c %x - %m%n # this is the default log4j.appender.console.layout.ConversionPattern=%-5p %-10c %m%n # this appender creates logfile that is being rotated following a size criterion # better would be to rotate it at every execution, but I am not sure if that exists in log4cxx... log4j.appender.logfile=org.apache.log4j.RollingFileAppender log4j.appender.logfile.File=/tmp/yade.log log4j.appender.logfile.MaxFileSize=10MB log4j.appender.logfile.MaxBackupIndex=1 # Keep one backup file log4j.appender.logfile.layout=org.apache.log4j.PatternLayout log4j.appender.logfile.layout.ConversionPattern=%-5p %t %-10c %m%n # Minimum level of messages you want to see # Childs inherit from their parents, unless overridden explicitly, therefore # the following disables DEBUG messages by default (everywhere) log4j.logger.yade=INFO # except for the classes where requested: #log4j.logger.yade.Omega=DEBUG log4j.logger.yade.DynLibManager=DEBUG trunk-2017.01a/doc/references.bib000066400000000000000000001000651304022710500165300ustar00rootroot00000000000000*************************** This file contains publications references from docstrings (as [Author2008]\_) of classes, in bibtex format. When adding new entries: 1. Keep entries in the form Author2008 (Author is the first author), Author2008b if repeated 2. Try to fill mandatory fields for given type of citations (http://en.wikipedia.org/wiki/Bibtex\\\\\#Entry\\\\\_Types) 3. Do not use {\'i} funny escapes for accents, put everything in straight utf-8 Thanks. *************************** @Article{ Bertrand2008, title = "Discrete element method (DEM) numerical modeling of double-twisted hexagonal mesh ", author = "D. Bertrand and F. Nicot and P. Gotteland and S. Lambert", journal = "Canadian Geotechnical Journal", pages = "1104--1117", volume = "45", number = "8", year = "2008" } @Article{ Bertrand2005, title = "Modelling a geo-composite cell using discrete analysis", author = "D. Bertrand and F. Nicot and P. Gotteland and S. Lambert", journal = "Computers and Geotechnics", pages = "564--577", volume = "32", number = "8", year = "2005" } @Article{ Chan2011, title = "Film drainage and coalescence between deformable drops and bubbles.", author = "D. Chan and E. Klaseboer and R. Manica", journal = "Soft Matter", pages = "2235-2264", volume = "7", number = "6", year = "2011" } @Article{ Chareyre2002a, title = "Theoretical versus experimental modeling of the anchorage capacity of geotextiles in trenches.", author = "B. Chareyre and L. Briancon and P. Villard", journal = "Geosynthet. Int.", pages = "97--123", volume = "9", number = "2", year = "2002" } @Article{ Chareyre2005, author = "Bruno Chareyre and Pascal Villard", title = "Dynamic Spar Elements and Discrete Element Methods in Two Dimensions for the Modeling of Soil-Inclusion Problems", publisher = "ASCE", year = "2005", journal = "Journal of Engineering Mechanics", volume = "131", number = "7", pages = "689--698", url = "https://yade-dem.org/wiki/File:Chareyre%26Villard2005_licensed.pdf", doi = "10.1061/(ASCE)0733-9399(2005)131:7(689)" } @PhDThesis{ Chareyre2003, author = "Bruno Chareyre", title = "Modélisation du comportement d'ouvrages composites sol-géosynthétique par éléments discrets - Application aux tranchées d'ancrage en tête de talus.", school = "Grenoble University", year = "2003", url = "http://tel.archives-ouvertes.fr/tel-00486807/fr/" } @InProceedings{ Chareyre2002b, title = "Discrete element modeling of curved geosynthetic anchorages with known macro-properties.", author = "B. Chareyre and P. Villard", booktitle = "Proc., First Int. PFC Symposium, Gelsenkirchen, Germany", year = "2002", pages = "197--203" } @Article{ Villard2004a, title = "Design methods for geosynthetic anchor trenches on the basis of true scale experiments and discrete element modelling", author = "P. Villard and B. Chareyre", journal = "Canadian Geotechnical Journal", pages = "1193--1205", volume = "41", year = "2004" } @Article{ Lu1998, author = "Ya Yan Lu", title = "Computing the Logarithm of a Symmetric Positive Definite Matrix", journal = "Appl. Numer. Math", year = "1998", volume = "26", pages = "483--496", doi = "10.1016/S0168-9274(97)00103-7", url = "http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.37.759&rep=rep1&type=pdf" } @InProceedings{ Alonso2004, title = "Micro-mechanical investigation of the granular ratcheting", author = "F. Alonso-Marroquin and R. Garcia-Rojo and H.J. Herrmann", booktitle = "Cyclic Behaviour of Soils and Liquefaction Phenomena", publisher = "Taylor \& Francis", year = "2004", month = "april", isbn = "9058096203", pages = "3--10", editor = "T. Triantafyllidis", url = "http://www.comphys.ethz.ch/hans/p/334.pdf" } @Article{ McNamara2008, title = "Microscopic origin of granular ratcheting", author = "S. McNamara and R. García-Rojo and H. J. Herrmann", journal = "Physical Review E", year = "2008", number = "3", volume = "77", doi = "11.1103/PhysRevE.77.031304" } @InProceedings{ GarciaRojo2004, author = "R. García-Rojo and S. McNamara and H. J. Herrmann", title = "Discrete element methods for the micro-mechanical investigation of granular ratcheting", booktitle = "Proceedings ECCOMAS 2004", year = "2004", address = "Jyvaskyla", url = "http://www.ica1.uni-stuttgart.de/publications/2004/GMH04" } @Book{ Allen1989, author = "M. P. Allen and D. J. Tildesley", title = "Computer simulation of liquids", year = "1989", isbn = "0-19-855645-4", publisher = "Clarendon Press", address = "New York, NY, USA" } @Proceedings{ DeghmReport2006, title = "Annual Report 2006", year = "2006", editor = "F. V. Donzé", organization = "Discrete Element Group for Hazard Mitigation", publisher = "Université Joseph Fourier, Grenoble", url = " http://geo.hmg.inpg.fr/frederic/Discrete_Element_Group_FVD.html " } @Article{ Pournin2001, title = "Molecular-dynamics force models for better control of energy dissipation in numerical simulations of dense granular media", author = "L. Pournin and Th. M. Liebling and A. Mocellin", journal = "Phys. Rev. E", volume = "65", number = "1", pages = "011302", numpages = "7", year = "2001", month = "Dec", doi = "10.1103/PhysRevE.65.011302", publisher = "American Physical Society" } @Article{ Jung1997, author = "Derek Jung and Kamal K. Gupta", title = "Octree-based hierarchical distance maps for collision detection", journal = "Journal of Robotic Systems", volume = "14", number = "11", pages = "789--806", year = "1997", doi = "10.1002/(SICI)1097-4563(199711)14:11<789::AID-ROB3>3.0.CO;2-Q" } @Article{ Hubbard1996, author = "Philip M. Hubbard", title = "Approximating polyhedra with spheres for time-critical collision detection", journal = "ACM Trans. Graph.", volume = "15", number = "3", year = "1996", issn = "0730-0301", pages = "179--210", doi = "10.1145/231731.231732", publisher = "ACM", address = "New York, NY, USA" } @Article{ Klosowski1998, author = "James T. Klosowski and Martin Held and Joseph S. B. Mitchell and Henry Sowizral and Karel Zikan", title = "Efficient Collision Detection Using Bounding Volume Hierarchies of k-DOPs", journal = "IEEE Transactions on Visualization and Computer Graphics", year = "1998", volume = "4", pages = "21--36", url = "http://citeseerx.ist.psu.edu/viewdoc/download?doi=10.1.1.105.6555&rep=rep1&type=pdf" } @Article{ Munjiza2006, Author = "A. Munjiza and E. Rougier and N. W. M. John", Title = "MR linear contact detection algorithm", journal = "International Journal for Numerical Methods in Engineering", volume = "66", number = "1", pages = "46--71", year = "2006", publisher = "John Wiley \& Sons, Ltd.", doi = "10.1002/nme.1538", abstract = "Large-scale discrete element simulations, as well as a whole range of related problems, involve contact of a large number of separate bodies and an efficient and robust contact detection algorithm is necessary. There has been a number of contact detection algorithms with total detection time proportional to N ln(N) (where N is the total number of separate bodies) reported in the past. In more recent years algorithms with total CPU time proportional to N have been developed. In this work, a novel contact detection algorithm with total detection time proportional to N is proposed. The performance of the algorithm is not influenced by packing density, while memory requirements are insignificant. The algorithm is applicable to systems comprising bodies of a similar size. The algorithm is named MR (Munjiza-Rougier: Munjiza devised the algorithm, Rougier implemented it). In the second part of the paper the algorithm is extended to particles of different sizes. The new algorithm is called MMR (multi-step MR) algorithm." } @Article{ Munjiza1998, Author = "A. Munjiza and K. R. F. Andrews", Title = "NBS contact detection algorithm for bodies of similar size", journal = "International Journal for Numerical Methods in Engineering", volume = "43", number = "1", pages = "131--149", year = "1998", publisher = "John Wiley \& Sons, Ltd.", doi = "10.1002/(SICI)1097-0207(19980915)43:1<131::AID-NME447>3.0.CO;2-S", abstract = "Large-scale discrete element simulations, as well as a whole range of related problems, involve contact of a large number of separate bodies. In this context an efficient and robust contact detection algorithm is necessary. There has been a number of contact detection algorithms with total detection time (CPU time needed to detect all couples close to each other) proportional to Nln(N) (where N is the total number of separate bodies) reported in recent years. In this work a contact detection algorithm with total detection time proportional to N is reported. The algorithm is termed NBS, which stands for no binary search. In other words, the proposed algorithm involves no binary search at any stage. In addition the performance of the algorithm in terms of total detection time is not influenced by packing density, while memory requirements are insignificant. The only limitation of the algorithm is its applicability to the systems comprising bodies of similar size." } @Article{ Verlet1967, title = "Computer ``Experiments'' on Classical Fluids. I. Thermodynamical Properties of Lennard-Jones Molecules", author = "Loup Verlet", journal = "Phys. Rev.", volume = "159", number = "1", pages = "98", year = "1967", month = "Jul", doi = "10.1103/PhysRev.159.98", publisher = "American Physical Society" } @InProceedings{ Luding2008, author = "Stefan Luding", title = "Introduction to discrete element methods", booktitle = "European Journal of Environmental and Civil Engineering", publisher = "Lavoisier", year = "2008", isbn = "978-2-7462-2258-8", pages = "785--826", editor = "Félix Darve and Jean-Pierre Ollivier" } @Article{ Wang2009, title = "A new algorithm to model the dynamics of 3-D bonded rigid bodies with rotations", author = "Yucang Wang", journal = "Acta Geotechnica", publisher = "Springer Berlin / Heidelberg", issn = "1861-1125 (Print) 1861-1133 (Online)", url = "http://www.springerlink.com/content/l2306412v1004871/", abstract = "In this paper we propose a new algorithm to simulate the dynamics of 3-D interacting rigid bodies. Six degrees of freedom are introduced to describe a single 3-D body or particle, and six relative motions and interactions are permitted between bonded bodies. We develop a new decomposition technique for 3-D rotation and pay particular attention to the fact that an arbitrary relative rotation between two coordinate systems or two rigid bodies can not be decomposed into three mutually independent rotations around three orthogonal axes. However, it can be decomposed into two rotations, one pure axial rotation around the line between the centers of two bodies, and another rotation on a specified plane controlled by another parameter. These two rotations, corresponding to the relative axial twisting and bending in our model, are sequence-independent. Therefore all interactions due to the relative translational and rotational motions between linked bodies can be uniquely determined using such a two-step decomposition technique. A complete algorithm for one such simulation is presented. Compared with existing methods, this algorithm is physically more reliable and has greater numerical accuracy.", number = "2", pages = "117--127", volume = "4", doi = "10.1007/s11440-008-0072-1", year = "2009", keywords = "Bonded rigid-bodies - Decomposition of 3-D finite rotations - Quaternion", month = "July" } @Article{ Omelyan1999, title = "A New Leapfrog Integrator of Rotational Motion. The Revised Angular-Momentum Approach", author = "Igor P. Omelyan", journal = "Molecular Simulation", volume = "22", number = "3", year = "1999", doi = "10.1080/08927029908022097", url = "http://arxiv.org/pdf/physics/9901025" } @Article{ Neto2006, author = "Natale Neto and Luca Bellucci", title = "A new algorithm for rigid body molecular dynamics", journal = "Chemical Physics", volume = "328", number = "1--3", pages = "259--268", year = "2006", issn = "0301-0104", doi = "10.1016/j.chemphys.2006.07.009" } @Article{ Johnson2008, author = "Scott M. Johnson and John R. Williams and Benjamin K. Cook", title = "Quaternion-based rigid body rotation integration algorithms for use in particle methods", journal = "International Journal for Numerical Methods in Engineering", volume = "74", number = "8", pages = "1303--1313", year = "2008", doi = "10.1002/nme.2210" } @InProceedings{ Addetta2001, author = "G.A. {D'Addetta} and F. {Kun} and E. {Ramm} and H.J. {Herrmann}", title = "{From solids to granulates - Discrete element simulations of fracture and fragmentation processes in geomaterials.}", booktitle = "Continuous and Discontinuous Modelling of Cohesive-Frictional Materials", year = 2001, series = "Lecture Notes in Physics, Berlin Springer Verlag", volume = 568, editor = "{P.A. Vermeer, S. Diebels, W. Ehlers, H.J. Herrmann, S. Luding, E. Ramm}", pages = "231--+", url = "http://www.comphys.ethz.ch/hans/p/267.pdf" } @Book{ Pfc3dManual30, author = "ICG", title = "PFC3D (Particle Flow Code in 3D) Theory and Background Manual, version 3.0", publisher = "Itasca Consulting Group", year = "2003" } @PhDThesis{ Hentz2003, Author = "Séebastien Hentz", Title = "Modélisation d'une Structure en Béton Armé Soumise à un Choc par la méthode des Eléments Discrets", School = "Université Grenoble 1 -- Joseph Fourier", Year = "2003", Month = "October" } @InProceedings{ Price2007, Author = "Mathew Price and Vasile Murariu and Garry Morrison", title = "Sphere clump generation and trajectory comparison for real particles", booktitle = "Proceedings of Discrete Element Modelling 2007", year = "2007", url = "http://www.cogency.co.za/images/info/dem2007_sphereclump.pdf" } @InProceedings{ Kuhl2001, title = "Microplane modelling and particle modelling of cohesive-frictional materials", author = "E. Kuhl and G. A. D'Addetta and M. Leukart and E. Ramm", booktitle = "Continuous and Discontinuous Modelling of Cohesive-Frictional Materials", publisher = "Springer Berlin / Heidelberg", issn = "1616-6361", isbn = "978-3-540-41525-1", url = "http://www.springerlink.com/content/e50544266r506615", abstract = "This paper aims at comparing the microplane model as a particular representative of the class of continuous material models with a discrete particle model which is of discontinuous nature. Thereby, the constitutive equations of both approaches will be based onVoigtshypothesis defining the strain state on the individual microplanes as well as the relative particle displacements. Through an appropriate constitutive assumption, the microplane stresses and the contact forces can be determined. In both cases, the equivalence of microscopic and macroscopic virtual work yields the overall stress strain relation. An elastic and an elasto-plastic material characterization of the microplane model and the particle model are derived and similarities of both approaches are illustrated.", volume = "568", series = "Lecture Notes in Physics", year = "2001", pages = "31--46", doi = "10.1007/3-540-44424-6\_3" } @Article{ Thornton1991, title = "Impact of elastic spheres with and without adhesion", author = "Colin Thornton and K. K. Yin", year = "1991", journal = "Powder technology", volume = "65", pages = "153--166", doi = "10.1016/0032-5910(91)80178-L" } @Article{ Thornton2000, title = "Numerical simulations of deviatoric shear deformation of granular media", author = "Colin Thornton", journal = "Géotechnique", pages = "43--53", volume = "50", year = "2000", number = "1", doi = "10.1680/geot.2000.50.1.43" } @Article{ CundallStrack1979, author = "P.A. Cundall and O.D.L. Strack", title = "A discrete numerical model for granular assemblies", journal = "Geotechnique", volume = "", number = "29", pages = "47--65", year = "1979", doi = "10.1680/geot.1979.29.1.47" } @Article{ cgal, Author = "Jean-Daniel Boissonnat and Olivier Devillers and Sylvain Pion and Monique Teillaud and Mariette Yvinec", Title = "Triangulations in CGAL", Journal = "Computational Geometry: Theory and Applications", Volume = "22", Pages = "5--19", Year = "2002" } @InProceedings{ Satake1982, title = "Fabric tensor in granular materials.", author = "M. Satake", booktitle = "Proc., IUTAM Symp. on Deformation and Failure of Granular materials, Delft, The Netherlands", year = "1982", pages = "63--68" } @article{Hentz2004a, title = {Discrete element modelling of concrete submitted to dynamic loading at high strain rates}, author = {S. Hentz and F.V. Donzé and L.Daudeville}, doi = {10.1016/j.compstruc.2004.05.016 }, journal = {Computers and Structures}, pages = {2509--2524}, volume = {82}, number = {29--30}, year = {2004} } @article{Hentz2004b, title = {Identification and Validation of a Discrete Element Model for Concrete}, author = {S. Hentz and L. Daudeville and F.V. Donzé}, doi = {10.1061/(ASCE)0733-9399(2004)130:6(709)}, journal = {ASCE Journal of Engineering Mechanics}, pages = {709--719}, volume = {130}, number = {6}, year = {2004} } @article{Camborde2000a, title = {Numerical study of rock and Concrete behaviour by discrete element modelling}, author = {F. Camborde and C. Mariotti and F.V. Donzé}, journal = {Computers and Geotechnics}, pages = {225--247}, volume = {27}, year = {2000} } @article{Donze1999a, title = {Study of the behavior of concrete at high strain rate compressions by a discrete element method}, author = {F.V. Donzé and S.A. Magnier and L. Daudeville and C. Mariotti and L. Davenne}, doi = {10.1016/S0266-352X(00)00013-6}, journal = {ASCE J. of Eng. Mech}, pages = {1154--1163}, volume = {125}, number = {10}, year = {1999} } @article{Magnier1998a, title = {Numerical simulation of impacts using a discrete element method}, author = {S.A. Magnier and F.V. Donzé}, doi = {10.1002/(SICI)1099-1484(199807)3:3<257::AID-CFM50>3.0.CO;2-Z}, journal = {Mech. Cohes.-frict. Mater.}, pages = {257--276}, volume = {3}, year = {1998} } @article{Donze1995a, title = {Formulation of a three-dimensional numerical model of brittle behavior}, author = {F.V. Donzé and S.A. Magnier}, journal = {Geophys. J. Int.}, pages = {790--802}, volume = {122}, year = {1995} } @article{Donze1994a, title = {Numerical simulation of faults and shear zones}, author = {F.V. Donzé and P. Mora and S.A. Magnier}, journal = {Geophys. J. Int.}, pages = {46--52}, volume = {116}, year = {1994} } @article{Hentz2005a, title = {Discrete elements modeling of a reinforced concrete structure submitted to a rock impact}, author = {S. Hentz and F.V. Donzé and L.Daudeville}, journal = {Italian Geotechnical Journal}, pages = {83--94}, volume = {XXXIX}, number = {4}, year = {2005} } @article{Donze2004a, title = {Simulation of the Blasting Patterns in Shaft Sinking Using a Discrete Element Method}, author = {F.V. Donzé and P. Bernasconi}, journal = {Electronic Journal of Geotechnical Engineering}, pages = {1--44}, volume = {9}, number = {B}, year = {2004} } @InProceedings{Kettner2011, AUTHOR = {Lutz Kettner and Andreas Meyer and Afra Zomorodian}, BOOKTITLE = {{CGAL} User and Reference Manual}, PUBLISHER = {{CGAL Editorial Board}}, TITLE = {Intersecting Sequences of {dD} Iso-oriented Boxes}, YEAR = {2011}, EDITION = {{3.9}}, url = {http://www.cgal.org/Manual/3.9/doc_html/cgal_manual/packages.html#Pkg:BoxIntersectionD} } @InProceedings{Pion2011, AUTHOR = {Sylvain Pion and Monique Teillaud}, BOOKTITLE = {{CGAL} User and Reference Manual}, PUBLISHER = {{CGAL Editorial Board}}, TITLE = {{3D} Triangulations}, YEAR = {2011}, EDITION = {{3.9}}, url = {http://www.cgal.org/Manual/3.9/doc_html/cgal_manual/packages.html#Pkg:Triangulation3} } @article{Calvetti1997, title={Experimental micromechanical analysis of a 2D granular material: relation between structure evolution and loading path}, author={Calvetti, F. and Combe, G. and Lanier, J.}, journal={Mechanics of Cohesive-frictional Materials}, volume={2}, number={2}, pages={121--163}, year={1997} } @article{Bagi2006, title = {Analysis of microstructural strain tensors for granular assemblies}, journal = {International Journal of Solids and Structures}, volume = {43}, number = {10}, pages = {3166 - 3184}, year = {2006}, doi = {10.1016/j.ijsolstr.2005.07.016}, author = {Katalin Bagi} } @article {Weigert1999, author = {Weigert, Tom and Ripperger, Siegfried}, title = {Calculation of the Liquid Bridge Volume and Bulk Saturation from the Half-filling Angle}, journal = {Particle & Particle Systems Characterization}, volume = {16}, number = {5}, publisher = {WILEY-VCH Verlag GmbH}, issn = {1521-4117}, url = {http://dx.doi.org/10.1002/(SICI)1521-4117(199910)16:5<238::AID-PPSC238>3.0.CO;2-E}, doi = {10.1002/(SICI)1521-4117(199910)16:5<238::AID-PPSC238>3.0.CO;2-E}, pages = {238--242}, year = {1999}, } @article{Willett2000, author = {Willett, Christopher D. and Adams, Michael J. and Johnson, Simon A. and Seville, Jonathan P. 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Šmilauer and E. Catalano and B. Chareyre and S. Dorofeenko and J. Duriez and A. Gladky and J. Kozicki and C. Modenese and L. Scholtès and L. Sibille and J. Stránský and K. Thoeni", ALTEDITOR = "Václav Šmilauer", EDITION = "{1st}", NOTE = "{http://yade-dem.org/doc/}", ALTNOTE = "\\url{http://yade-dem.org/doc/}" } @incollection{ yade:manual, author={V. Šmilauer and A. Gladky and J. Kozicki and C. Modenese and J. Stránský}, booktitle={Yade {D}ocumentation}, editor={V. Šmilauer}, publisher={The Yade Project}, title={Yade, Using and Programming}, year={2010}, edition={1st}, url={https://yade-dem.org/w/images/0/09/YadeManuals.pdf}, note={http://yade-dem.org/doc/} } @incollection{ yade:background, title = "{Y}ade DEM Formulation", author = "V. Šmilauer and B. Chareyre", booktitle = "{Y}ade {D}ocumentation", editor = "V. 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It implements the hierarchical multiscale model (FEMxDEM) for simulating the boundary value problem (BVP) of granular media. FEM is used to discretize the problem domain. Each Gauss point of the FEM mesh is embedded a representative volume element (RVE) packing simulated by DEM which returns local material constitutive responses to FEM. Typically, hundreds to thousands of RVEs are involved in a medium-sized problem which is critically time consuming. Hence parallelization is achieved in the code through either multiprocessing on a supercomputer or mpi4py on a HPC cluster (require MPICH or Open MPI). The MPI implementation in the code is quite experimental. The "mpipool.py" is contributed by Lisandro Dalcin, the author of mpi4py package. Please refer to the examples for the usage of the code. Work on the YADE side ^^^^^^^^^^^^^^^^^^^^^^^^ The version of YADE should be at least rev3682 in which Bruno added the stringToScene function. Before installation, I added some functions to the source code (in "yade" subfolder). But only one function ("Shop::getStressAndTangent" in "./pkg/dem/Shop.cpp") is necessary for the FEMxDEM coupling, which returns the stress tensor and the tangent operator of a discrete packing. The former is homogenized using the Love's formula and the latter is homogenized as the elastic modulus. After installation and we get the executable file: yade-versionNo. We then generate a .py file linked to the executable file by "ln yade-versionNo yadeimport.py". This .py file will serve as a wrapped library of YADE. Later on, we will import all YADE functions into the python script through "from yadeimport import \*" (see simDEM.py file). Open a python terminal. Make sure you can run :: import sys sys.path.append('where you put yadeimport.py') from yadeimport import * Omega().load('your initial RVE packing, e.g. 0.yade.gz') If you are successful, you should also be able to run :: from simDEM import * Work on the Escript side ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ No particular requirement. But make sure the modules are callable in python, which means the main folder of Escript should be in your PYTHONPATH and LD_LIBRARY_PATH. The modules are wrapped as a class in msFEM\*.py. Open a python terminal. Make sure you can run:: from esys.escript import * from esys.escript.linearPDEs import LinearPDE from esys.finley import Rectangle (Note: Escript is used for the current implementation. It can be replaced by any other FEM package provided with python bindings, e.g. FEniCS (http://fenicsproject.org). But the interface files "msFEM\*.py" need to be modified.) Example tests ^^^^^^^^^^^^^^^^ After Steps 1 & 2, one should be able to run all the scripts for the multiscale analysis. The initial RVE packing (default name "0.yade.gz") should be provided by the user (e.g. using YADE to prepare a consolidated packing), which will be loaded by simDEM.py when the problem is initialized. The sample is initially uniform as long as the same RVE packing is assigned to all the Gauss points in the problem domain. It is also possible for the user to specify different RVEs at different Gauss points to generate an inherently inhomogeneous sample. While simDEM.py is always required, only one msFEM\*.py is needed for a single test. For example, in a 2D (3D) dry test, msFEM2D.py (msFEM3D.py) is needed; similarly for a coupled hydro-mechanical problem (2D only, saturated), msFEMup.py is used which incorporates the u-p formulation. Multiprocessing is used by default. To try MPI parallelization, please set useMPI=True when constructing the problem in the main script. Example tests given in the "example" subfolder are listed below. Note: The initial RVE packing (named 0.yade.gz by default) needs to be generated, e.g. using prepareRVE.py in "example" subfolder for a 2D packing (similarly for 3D). #. **2D drained biaxial compression test on dry dense sand** (biaxialSmooth.py) *Note*: Test description and result were presented in [Guo2014]_ and [Guo2014c]_. #. **2D passive failure under translational mode of dry sand retained by a rigid and frictionless wall** (retainingSmooth.py) *Note:* Rolling resistance model (CohFrictMat) is used in the RVE packing. Test description and result were presented in [Guo2015]_. #. **2D half domain footing settlement problem with mesh generated by Gmsh** (footing.py, footing.msh) *Note:* Rolling resistance model (CohFrictMat) is used in the RVE packing. Six-node triangle element is generated by Gmsh with three Gauss points each. Test description and result were presented in [Guo2015]_. #. **3D drained conventional triaxial compression test on dry dense sand using MPI parallelism** (triaxialRough.py) *Note 1:* The simulation is very time consuming. It costs ~4.5 days on one node using multiprocessing (16 processes, 2.0 GHz CPU). When useMPI is switched to True (as in the example script) and four nodes are used (80 processes, 2.2 GHz CPU), the simulation costs less than 24 hours. The speedup is about 4.4 in our test. *Note 2:* When MPI is used, mpi4py is required to be installed. The MPI implementation can be either MPICH or Open MPI. The file "mpipool.py" should also be placed in the main folder. Our test is based on openmpi-1.6.5. This is an on-going work. Test description and result will be presented later. #. **2D globally undrained biaxial compression test on saturated dense sand with changing permeability using MPI parallelism** (undrained.py) *Note:* This is an on-going work. Test description and result will be presented later. Disclaim ^^^^^^^^^^^^ This work extensively utilizes and relies on some third-party packages as mentioned above. Their contributions are acknowledged. Feel free to use and redistribute the code. But there is NO warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. trunk-2017.01a/doc/sphinx/README000066400000000000000000000031451304022710500161230ustar00rootroot00000000000000Generating yade documentation =============================== 1. Get sphinx 1.0 (development snapshots are fine) either from * packages at https://launchpad.net/~yade-users/+archive/external ** sudo apt-add-repository ppa:yade-users/external; sudo apt-get update; sudo apt-get install python-sphinx python-bibtex * from its repository: ** hg clone http://bitbucket.org/birkenfeld/sphinx/ ** optionally apply the patch (only avoids warnings) from http://bitbucket.org/birkenfeld/sphinx/issue/407/patch-do-not-inspect-boost-python-functions ** run python setup.py install 2. Python default encoding must be set to utf-8. As it is not the default, PYTHONPATH=. is used to make Python import local sitecustomize.py file at startup which changes this setting. (The value cannot be set after startup, from within the script) 3. Run (from the current directory, replacing PREFIX by the yade install path) PYTHONPATH=. yade yadeSphinx.py [optional outDir; _build by default] It will be create/update $outDir/{html,latex}. The latex file (Yade.tex) is to be processed with xelatex (rather than latex). See README.latex for details. ==== ipython_console_highlighting.py is copied from matplotlib's trunk/matplotlib/lib/matplotlib/sphinxext Generating yade documentation as a book (for the official chapter references) ============================================================================= First run yadeSphinx.py as explained above. It will generate modules documentation and other things that we use for generating the book. Second run yadeBookSphinx.py (same command as above, adding 'Book' in the script name) trunk-2017.01a/doc/sphinx/bib2rst.py000066400000000000000000000077021304022710500171670ustar00rootroot00000000000000#!/usr/bin/python # encoding: utf-8 try: import _bibtex as bib import _recode as bibRecode except ImportError: raise ImportError("Unable to import _bibtex and/or _recode; install the python-bibtex package.") import sys def readBib(filename): ## _bibtex has horrible interface bibfile=bib.open_file(filename,1) # 2nd argument: strict mode db={} #rq=bibRecode.request('latex..latin1') while True: entry=bib.next(bibfile) if entry is None: break key,type,dta=entry[0],entry[1],entry[4] item={'type':type} for field in dta.keys(): expanded=bib.expand(bibfile,dta[field],-1) #conv=bibRecode.recode(rq,expanded[2]) item[field]=expanded[2].strip() db[key]=item ## now we don't need _bibtex anymore, everything is in our dicts return db def dumpBib(db): for k in db.keys(): print k,db[k] def formatRest(db): ret=[] keys=db.keys(); keys.sort() for key in keys: i=db[key]; type=i['type'] line=r'.. [%s] \ '%key ## ← HACK: explicit space to prevent docutils from using abbreviated first name (e.g. "F.") as enumeration item; it works!! if i.has_key('author'): author=i['author'].replace(' and ',', ') # the module does not handle this..? # required fields from http://en.wikipedia.org/wiki/Bibtex # in some cases, they are not present, anyway if type=='article': if i.has_key('author'): line+='%s '%author if i.has_key('year'): line+='(%s), '%i['year'] line+='**%s**. *%s*'%(i['title'],i['journal']) if i.has_key('issue'): line+=i['issue'] if i.has_key('volume'): line+=' (%s)'%i['volume'] if i.has_key('pages'): line+=', pages %s'%i['pages'] line+='.' elif type=='book': if i.has_key('author'): line+='%s '%author if i.has_key('year'): line+='(%s), '%i['year'] line+='**%s**.'%i['title'] if i.has_key('publisher'): line+=' %s.'%i['publisher'] elif type=='inproceedings': line+='%s (%s), **%s**. In *%s*.'%(author,i['year'],i['title'],i['booktitle'] if i.has_key('booktitle') else i['journal']) elif type=='incollection': line+='%s (%s), **%s**. In *%s* '%(author,i['year'],i['title'],i['booktitle'] if i.has_key('booktitle') else i['journal']) if i.has_key('editor'): line+='( %s'%i['editor']+', ed.),' if i.has_key('publisher'): line+=' %s'%i['publisher']+' ,' if i.has_key('edition'): line+=' %s ed.'%i['edition'] elif type=='phdthesis': line+='%s (%s), **%s**. PhD thesis at *%s*.'%(author,i['year'],i['title'],i['school']) elif type=='mastersthesis': typeThesis = 'Master thesis' if i.has_key('note'): typeThesis = i['note'] line+='%s (%s), **%s**. %s at *%s*.'%(author,i['year'],i['title'],typeThesis,i['school']) elif type=='proceedings': if i.has_key('editor'): line+='%s (ed.), '%i['editor'] line+='**%s** (%s).'%(i['title'],i['year']) if i.has_key('organization'): line+=' *%s*.'%i['organization'] if i.has_key('publisher'): line+=' %s'%i['publisher'] elif type=='misc': if i.has_key('author'): line+=author if i.has_key('year'): line+=' %s'%i['year'] if i.has_key('title'): line+=' **%s**'%i['title'] # add doi and url to everything, if present ## ReST uses <..> to delimit URL, therefore < and > must be encoded in the URL (http://www.blooberry.com/indexdot/html/topics/urlencoding.htm) def escapeUrl(url): return url.replace('<','%3c').replace('>','%3e') if i.has_key('doi'): line+=' DOI `%s `_'%(i['doi'],escapeUrl(i['doi'])) if i.has_key('url'): line+=' `(fulltext) <%s>`__'%escapeUrl(i['url']) if (i.has_key('note') and type<>'mastersthesis'): line+=' (%s)'%i['note'] ret.append(line) return [l.replace('@tilde@','~') for l in ret] def bib2rst(filename): """Return string representing all items in given bibtex file, formatted as ReST.""" import tempfile,shutil,os.path d=tempfile.mkdtemp() bib=d+'/'+os.path.basename(filename) open(bib,'w').write(open(filename).read().replace('~','@tilde@')) db=readBib(bib) shutil.rmtree(d) return '\n\n'.join(formatRest(db)) if __name__=='__main__': import sys print bib2rst(sys.argv[1]) trunk-2017.01a/doc/sphinx/book/000077500000000000000000000000001304022710500161725ustar00rootroot00000000000000trunk-2017.01a/doc/sphinx/book/confBook.py000066400000000000000000000720021304022710500203050ustar00rootroot00000000000000# -*- coding: utf-8 -*- # # Yade documentation build configuration file, created by # sphinx-quickstart on Mon Nov 16 21:49:34 2009. # # This file is execfile()d with the current directory set to its containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # relevant posts to sphinx ML # http://groups.google.com/group/sphinx-dev/browse_thread/thread/b4fbc8d31d230fc4 # http://groups.google.com/group/sphinx-dev/browse_thread/thread/118598245d5f479b ##################### ## custom yade roles ##################### ## ## http://docutils.sourceforge.net/docs/howto/rst-roles.html import sys, os, re from docutils import nodes from sphinx import addnodes from sphinx.roles import XRefRole import docutils # # needed for creating hyperlink targets. # it should be cleand up and unified for both LaTeX and HTML via # the pending_xref node which gets resolved to real link target # by sphinx automatically once all docs have been processed. # # xrefs: http://groups.google.com/group/sphinx-dev/browse_thread/thread/d719d19307654548 # # import __builtin__ if 'latex' in sys.argv: __builtin__.writer='latex' elif 'html' in sys.argv: __builtin__.writer='html' elif 'epub' in sys.argv: __builtin__.writer='epub' else: raise RuntimeError("Must have either 'latex' or 'html' on the command line (hack for reference styles)") sys.path.append(os.path.abspath('./..')) def yaderef_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :yref:`` role, by making hyperlink to yade.wrapper.*. It supports :yref:`Link text` syntax, like usual hyperlinking roles." id=rawtext.split(':',2)[2][1:-1] txt=id; explicitText=False m=re.match('(.*)\s*<(.*)>\s*',id) if m: explicitText=True txt,id=m.group(1),m.group(2) id=id.replace('::','.') #node=nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='http://beta.arcig.cz/~eudoxos/yade/doxygen/?search=%s'%id,**options) #node=nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='yade.wrapper.html#yade.wrapper.%s'%id,**options) return [mkYrefNode(id,txt,rawtext,role,explicitText,lineno,options)],[] def yadesrc_role(role,rawtext,lineno,inliner,options={},content=[]): "Handle the :ysrc:`` role, making hyperlink to git repository webpage with that path. Supports :ysrc:`Link text` syntax, like usual hyperlinking roles. If target ends with ``/``, it is assumed to be a directory." id=rawtext.split(':',2)[2][1:-1] txt=id m=re.match('(.*)\s*<(.*)>\s*',id) if m: txt,id=m.group(1),m.group(2) return [nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='https://github.com/yade/trunk/blob/master/%s'%id)],[] ### **options should be passed to nodes.reference as well # map modules to their html (rst) filenames. Used for sub-modules, where e.g. SpherePack is yade._packSphere.SpherePack, but is documented from yade.pack.rst moduleMap={ 'yade._packPredicates':'yade.pack', 'yade._packSpheres':'yade.pack', 'yade._packObb':'yade.pack' } class YadeXRefRole(XRefRole): #def process_link def process_link(self, env, refnode, has_explicit_title, title, target): print 'TARGET:','yade.wrapper.'+target return '[['+title+']]','yade.wrapper.'+target def mkYrefNode(target,text,rawtext,role,explicitText,lineno,options={}): """Create hyperlink to yade target. Targets starting with literal 'yade.' are absolute, but the leading 'yade.' will be stripped from the link text. Absolute tergets are supposed to live in page named yade.[module].html, anchored at #yade.[module2].[rest of target], where [module2] is identical to [module], unless mapped over by moduleMap. Other targets are supposed to live in yade.wrapper (such as c++ classes).""" writer=__builtin__.writer # to make sure not shadowed by a local var import string if target.startswith('yade.'): module='.'.join(target.split('.')[0:2]) module2=(module if module not in moduleMap.keys() else moduleMap[module]) if target==module: target='' # to reference the module itself uri=('%%%s#%s'%(module2,target) if writer=='latex' else '%s.html#%s'%(module2,target)) if not explicitText and module!=module2: text=module2+'.'+'.'.join(target.split('.')[2:]) text=string.replace(text,'yade.','',1) elif target.startswith('external:'): exttarget=target.split(':',1)[1] if not explicitText: text=exttarget target=exttarget if '.' in exttarget else 'module-'+exttarget uri=(('%%external#%s'%target) if writer=='latex' else 'external.html#%s'%target) else: uri=(('%%yade.wrapper#yade.wrapper.%s'%target) if writer=='latex' else 'yade.wrapper.html#yade.wrapper.%s'%target) #print writer,uri if 0: refnode=addnodes.pending_xref(rawtext,reftype=role,refexplicit=explicitText,reftarget=target) #refnode.line=lineno #refnode+=nodes.literal(rawtext,text,classes=['ref',role]) return [refnode],[] #ret.rawtext,reftype=role, else: return nodes.reference(rawtext,docutils.utils.unescape(text),refuri=uri,**options) #return [refnode],[] def ydefault_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :ydefault:`something` role. fixSignature handles it now in the member signature itself, this merely expands to nothing." return [],[] def yattrtype_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :yattrtype:`something` role. fixSignature handles it now in the member signature itself, this merely expands to nothing." return [],[] # FIXME: should return readable representation of bits of the number (yade.wrapper.AttrFlags enum) def yattrflags_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :yattrflags:`something` role. fixSignature handles it now in the member signature itself." return [],[] from docutils.parsers.rst import roles def yaderef_role_2(type,rawtext,text,lineno,inliner,options={},content=[]): return YadeXRefRole()('yref',rawtext,text,lineno,inliner,options,content) roles.register_canonical_role('yref', yaderef_role) roles.register_canonical_role('ysrc', yadesrc_role) roles.register_canonical_role('ydefault', ydefault_role) roles.register_canonical_role('yattrtype', yattrtype_role) roles.register_canonical_role('yattrflags', yattrflags_role) ## http://sphinx.pocoo.org/config.html#confval-rst_epilog rst_epilog = """ .. |yupdate| replace:: *(auto-updated)* .. |ycomp| replace:: *(auto-computed)* .. |ystatic| replace:: *(static)* """ import collections def customExclude(app, what, name, obj, skip, options): if name=='clone': if 'Serializable.clone' in str(obj): return False return True #escape crash on non iterable __doc__ in some qt object if hasattr(obj,'__doc__') and obj.__doc__ and not isinstance(obj.__doc__, collections.Iterable): return True if hasattr(obj,'__doc__') and obj.__doc__ and ('|ydeprecated|' in obj.__doc__ or '|yhidden|' in obj.__doc__): return True #if re.match(r'\b(__init__|__reduce__|__repr__|__str__)\b',name): return True if name.startswith('_'): if name=='__init__': # skip boost classes with parameterless ctor (arg1=implicit self) if obj.__doc__=="\n__init__( (object)arg1) -> None": return True # skip undocumented ctors if not obj.__doc__: return True # skip default ctor for serializable, taking dict of attrs if obj.__doc__=='\n__init__( (object)arg1) -> None\n\nobject __init__(tuple args, dict kwds)': return True #for i,l in enumerate(obj.__doc__.split('\n')): print name,i,l,'##' return False return True return False def isBoostFunc(what,obj): return what=='function' and obj.__repr__().startswith('.*$',doc1): return None,docc if doc1.endswith(':'): doc1=doc1[:-1] strippedDoc=doc.split('\n')[2:] # check if all lines are padded allLinesHave4LeadingSpaces=True for l in strippedDoc: if l.startswith(' '): continue allLinesHave4LeadingSpaces=False; break # remove the padding if so if allLinesHave4LeadingSpaces: strippedDoc=[l[4:] for l in strippedDoc] for i in range(len(strippedDoc)): # fix signatures inside docstring (one function with multiple signatures) strippedDoc[i],n=re.subn(r'([a-zA-Z_][a-zA-Z0-9_]*\() \(object\)arg1(, |)',r'\1',strippedDoc[i].replace('->','→')) # inspect dosctring after mangling if 'getViscoelasticFromSpheresInteraction' in name and False: print name print strippedDoc print '======================' for l in strippedDoc: print l print '======================' sig=doc1.split('(',1)[1] if removeSelf: # remove up to the first comma; if no comma present, then the method takes no arguments # if [ precedes the comma, add it to the result (ugly!) try: ss=sig.split(',',1) if ss[0].endswith('['): sig='['+ss[1] else: sig=ss[1] except IndexError: # grab the return value try: sig=') -> '+sig.split('->')[-1] #if 'Serializable' in name: print 1000*'#',name except IndexError: sig=')' return '('+sig,strippedDoc def fixSignature(app, what, name, obj, options, signature, return_annotation): #print what,name,obj,signature#,dir(obj) if what=='attribute': doc=unicode(obj.__doc__) ret='' m=re.match('.*:ydefault:`(.*?)`.*',doc) if m: typ='' #try: # clss='.'.join(name.split('.')[:-1]) # instance=eval(clss+'()') # typ='; '+getattr(instance,name.split('.')[-1]).__class__.__name__ # if typ=='; NoneType': typ='' #except TypeError: ##no registered converted # typ='' dfl=m.group(1) m2=re.match(r'\s*\(\s*\(\s*void\s*\)\s*\"(.*)\"\s*,\s*(.*)\s*\)\s*',dfl) if m2: dfl="%s, %s"%(m2.group(2),m2.group(1)) if dfl!='': ret+=' (='+dfl+'%s)'%typ else: ret+=' (=uninitalized%s)'%typ #m=re.match('.*\[(.{,8})\].*',doc) #m=re.match('.*:yunit:`(.?*)`.*',doc) #if m: # units=m.group(1) # print '@@@@@@@@@@@@@@@@@@@@@',name,units # ret+=' ['+units+']' return ret,None elif what=='class': ret=[] if len(obj.__bases__)>0: base=obj.__bases__[0] while base.__module__!='Boost.Python': ret+=[base.__name__] if len(base.__bases__)>0: base=base.__bases__[0] else: break if len(ret): return ' (inherits '+u' → '.join(ret)+')',None else: return None,None elif isBoostFunc(what,obj): sig=boostFuncSignature(name,obj)[0] or ' (wrapped c++ function)' return sig,None elif isBoostMethod(what,obj): sig=boostFuncSignature(name,obj,removeSelf=True)[0] return sig,None #else: print what,name,obj.__repr__() #return None,None from sphinx import addnodes def parse_ystaticattr(env,attr,attrnode): m=re.match(r'([a-zA-Z0-9_]+)\.(.*)\(=(.*)\)',attr) if not m: print 100*'@'+' Static attribute %s not matched'%attr attrnode+=addnodes.desc_name(attr,attr) klass,name,default=m.groups() #attrnode+=addnodes.desc_type('static','static') attrnode+=addnodes.desc_name(name,name) plist=addnodes.desc_parameterlist() if default=='': default='unspecified' plist+=addnodes.desc_parameter('='+default,'='+default) attrnode+=plist attrnode+=addnodes.desc_annotation(' [static]',' [static]') return klass+'.'+name ############################# ## set tab size ################### ## http://groups.google.com/group/sphinx-dev/browse_thread/thread/35b8071ffe9a8feb def setup(app): from sphinx.highlighting import lexers from pygments.lexers.compiled import CppLexer lexers['cpp'] = CppLexer(tabsize=3) lexers['c++'] = CppLexer(tabsize=3) from pygments.lexers.agile import PythonLexer lexers['python'] = PythonLexer(tabsize=3) app.connect('source-read',fixSrc) app.connect('autodoc-skip-member',customExclude) app.connect('autodoc-process-signature',fixSignature) app.connect('autodoc-process-docstring',fixDocstring) app.add_description_unit('ystaticattr',None,objname='static attribute',indextemplate='pair: %s; static method',parse_node=parse_ystaticattr) import sys, os # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. #sys.path.append(os.path.abspath('.')) # -- General configuration ----------------------------------------------------- # Add any Sphinx extension module names here, as strings. They can be extensions # coming with Sphinx (named 'sphinx.ext.*') or your custom ones. # # HACK: change ipython console regexp from ipython_console_highlighting.py import re sys.path.append(os.path.abspath('.')) import yade.config if 1: if yade.runtime.ipython_version<12: import ipython_directive as id else: if 12<=yade.runtime.ipython_version<13: import ipython_directive012 as id elif 13<=yade.runtime.ipython_version<200: import ipython_directive013 as id elif 200<=yade.runtime.ipython_version<500: import ipython_directive200 as id else: import ipython_directive500 as id #The next four lines are for compatibility with IPython 0.13.1 ipython_rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*') ipython_rgxout=re.compile(r'(?:Out| -> )\[(\d+)\]:\s?(.*)\s*') ipython_promptin ='Yade [%d]:' ipython_promptout=' -> [%d]: ' ipython_cont_spaces=' ' #For IPython <=0.12, the following lines are used id.rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*') id.rgxout=re.compile(r'(?:Out| -> )\[(\d+)\]:\s?(.*)\s*') id.rgxcont=re.compile(r'(?: +)\.\.+:\s?(.*)\s*') id.fmtin ='Yade [%d]:' id.fmtout =' -> [%d]: ' # for some reason, out and cont must have the trailing space id.fmtcont=' .\D.: ' id.rc_override=dict(prompt_in1="Yade [\#]:",prompt_in2=" .\D.:",prompt_out=r" -> [\#]: ") if yade.runtime.ipython_version<12: id.reconfig_shell() import ipython_console_highlighting as ich ich.IPythonConsoleLexer.input_prompt = re.compile("(Yade \[[0-9]+\]: )") ich.IPythonConsoleLexer.output_prompt = re.compile("(( -> |Out)|\[[0-9]+\]: )") ich.IPythonConsoleLexer.continue_prompt = re.compile("\s+\.\.\.+:") extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.autosummary', 'sphinx.ext.coverage', 'sphinx.ext.pngmath', 'sphinx.ext.graphviz', 'sphinx.ext.viewcode', 'sphinx.ext.inheritance_diagram', 'matplotlib.sphinxext.plot_directive', 'matplotlib.sphinxext.only_directives', #'matplotlib.sphinxext.mathmpl', 'ipython_console_highlighting', 'youtube', 'sphinx.ext.todo', ] if yade.runtime.ipython_version<12: extensions.append('ipython_directive') else: if 12<=yade.runtime.ipython_version<13: extensions.append('ipython_directive012') elif 13<=yade.runtime.ipython_version<200: extensions.append('ipython_directive013') elif 200<=yade.runtime.ipython_version<500: extensions.append('ipython_directive200') else: extensions.append('ipython_directive500') # the sidebar extension if False: if writer=='html': extensions+=['sphinx.ext.sidebar'] sidebar_all=True sidebar_relling=True #sidebar_abbrev=True sidebar_tocdepth=3 ## http://trac.sagemath.org/sage_trac/attachment/ticket/7549/trac_7549-doc_inheritance_underscore.patch # GraphViz includes dot, neato, twopi, circo, fdp. graphviz_dot = 'dot' inheritance_graph_attrs = { 'rankdir' : 'BT' } inheritance_node_attrs = { 'height' : 0.5, 'fontsize' : 12, 'shape' : 'oval' } inheritance_edge_attrs = {} my_latex_preamble=r''' \usepackage{euler} % must be loaded before fontspec for the whole doc (below); this must be kept for pngmath, however \usepackage{hyperref} \usepackage{amsmath} \usepackage{amsbsy} %\usepackage{mathabx} \usepackage{underscore} \usepackage[all]{xy} \usepackage{multicol} % Metadata of the pdf output \hypersetup{pdftitle={Yade Documentation}} \hypersetup{pdfauthor={Vaclav Smilauer; Emanuele Catalano; Bruno Chareyre; Sergei Dorofeenko; Jerome Duriez; Nolan Dyck; Jan Elias; Burak Er; Alexander Eulitz; Anton Gladky; Ning Guo; Christian Jakob; Francois Kneib; Janek Kozicki; Donia Marzougui; Raphael Maurin; Chiara Modenese; Luc Scholtes; Luc Sibille; Jan Stransky; Thomas Sweijen; Klaus Thoeni; Chao Yuan}} \hypersetup{pdfkeywords={Discrete element method; dem; yade; documentation; manual; python; c++; git, hydromechanical coupling}} % symbols \let\mat\boldsymbol % matrix \let\vec\boldsymbol % vector \let\tens\boldsymbol % tensor \def\normalized#1{\widehat{#1}} \def\locframe#1{\widetilde{#1}} % timestep \def\Dt{\Delta t} \def\Dtcr{\Dt_{\rm cr}} % algorithm complexity \def\bigO#1{\ensuremath{\mathcal{O}(#1)}} % variants for greek symbols \let\epsilon\varepsilon \let\theta\vartheta \let\phi\varphi % shorthands \let\sig\sigma \let\eps\epsilon % variables at different points of time \def\prev#1{#1^-} \def\pprev#1{#1^\ominus} \def\curr#1{#1^{\circ}} \def\nnext#1{#1^\oplus} \def\next#1{#1^+} % shorthands for geometry \def\currn{\curr{\vec{n}}} \def\currC{\curr{\vec{C}}} \def\uT{\vec{u}_T} \def\curruT{\curr{\vec{u}}_T} \def\prevuT{\prev{\vec{u}}_T} \def\currn{\curr{\vec{n}}} \def\prevn{\prev{\vec{n}}} % motion \def\pprevvel{\pprev{\dot{\vec{u}}}} \def\nnextvel{\nnext{\dot{\vec{u}}}} \def\curraccel{\curr{\ddot{\vec{u}}}} \def\prevpos{\prev{\vec{u}}} \def\currpos{\curr{\vec{u}}} \def\nextpos{\next{\vec{u}}} \def\curraaccel{\curr{\dot{\vec{\omega}}}} \def\pprevangvel{\pprev{\vec{\omega}}} \def\nnextangvel{\nnext{\vec{\omega}}} \def\loccurr#1{\curr{\locframe{#1}}} \def\numCPU{n_{\rm cpu}} \DeclareMathOperator{\Align}{Align} \DeclareMathOperator{\sign}{sgn} % sorting algorithms \def\isleq#1{\currelem{#1}\ar@/^/[ll]^{\leq}} \def\isnleq#1{\currelem{#1}\ar@/^/[ll]^{\not\leq}} \def\currelem#1{\fbox{$#1$}} \def\sortSep{||} \def\sortInv{\hbox{\phantom{||}}} \def\sortlines#1{\xymatrix@=3pt{#1}} \def\crossBound{||\mkern-18mu<} ''' pngmath_latex_preamble=r'\usepackage[active]{preview}'+my_latex_preamble pngmath_use_preview=True # Add any paths that contain templates here, relative to this directory. templates_path = ['templates'] # The suffix of source filenames. source_suffix = '.rst' # The encoding of source files. #source_encoding = 'utf-8' # The master toctree document. master_doc = 'index-toctree-book' # General information about the project. project = u'Yade' copyright = u'2009, Václav Šmilauer' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. version = '2nd ed.' # The full version, including alpha/beta/rc tags. release = '2nd ed.' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. #language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: #today = '' # Else, today_fmt is used as the format for a strftime call. #today_fmt = '%B %d, %Y' # List of documents that shouldn't be included in the build. #unused_docs = [] # List of directories, relative to source directory, that shouldn't be searched # for source files. exclude_trees = ['_build','../_build'] # The reST default role (used for this markup: `text`) to use for all documents. #default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. #add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). #add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. show_authors = True # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. modindex_common_prefix = ['yade.'] # -- Options for HTML output --------------------------------------------------- # The theme to use for HTML and HTML Help pages. Major themes that come with # Sphinx are currently 'default' and 'sphinxdoc'. html_theme = 'default' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. html_theme_options = {'stickysidebar':'true','collapsiblesidebar':'true','rightsidebar':'false'} # Add any paths that contain custom themes here, relative to this directory. #html_theme_path = [] # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". #html_title = None # A shorter title for the navigation bar. Default is the same as html_title. #html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. html_logo = '../fig/yade-logo.png' # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. html_favicon = '../fig/yade-favicon.ico' # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['static-html'] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. #html_last_updated_fmt = '%b %d, %Y' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. html_use_smartypants = True # Custom sidebar templates, maps document names to template names. #html_sidebars = {} html_index='index.html' # Additional templates that should be rendered to pages, maps page names to # template names. html_additional_pages = { 'index':'index.html'} # If false, no module index is generated. #html_use_modindex = True # If false, no index is generated. #html_use_index = True # If true, the index is split into individual pages for each letter. #html_split_index = False # If true, links to the reST sources are added to the pages. #html_show_sourcelink = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. #html_use_opensearch = '' # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml"). #html_file_suffix = '' # Output file base name for HTML help builder. htmlhelp_basename = 'Yadedoc' # -- Options for LaTeX output -------------------------------------------------- my_maketitle=r''' \begin{titlepage} \begin{flushright} \hrule{} % Upper part of the page \begin{flushright} \includegraphics[width=0.15\textwidth]{yade-logo.png}\par \end{flushright} \vspace{20 mm} \text{\sffamily\bfseries\Huge Yade Documentation}\\ \vspace{20 mm} %\vspace{70 mm} \begin{sffamily}\bfseries\Large V\'{a}clav \v{S}milauer, Emanuele Catalano, Bruno Chareyre, Sergei Dorofeenko, J\'er\^ome Duriez, Nolan Dyck, Jan Eli\'{a}\v{s}, Burak Er, Alexander Eulitz, Anton Gladky, Ning Guo, Christian Jakob, Fran\c{c}ois Kneib, Janek Kozicki, Donia Marzougui, Rapha\"el Maurin, Chiara Modenese, Luc Scholt\`{e}s, Luc Sibille, Jan Str\'{a}nsk\'{y}, Thomas Sweijen, Klaus Thoeni, Chao Yuan \end{sffamily} \vspace{20 mm} \hrule{} \vfill \textit{\large Yade Documentation 2nd edition, 2015}\\ \textit{based on Yade 1.14.0}\\ \end{flushright} \end{titlepage} \text{\sffamily\bfseries\Large Authors} \begin{multicols}{2} \begin{itemize} \item \text{\sffamily\bfseries\normalsize V\'{a}clav \v{S}milauer}\\ \text{\sffamily\small Freelance consultant (http://woodem.eu)} \item \text{\sffamily\bfseries\normalsize Emanuele Catalano}\\ \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR} \item \text{\sffamily\bfseries\normalsize Bruno Chareyre}\\ \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR} \item \text{\sffamily\bfseries\normalsize Sergei Dorofeenko}\\ \text{\sffamily\small IPCP RAS, Chernogolovka} \item \text{\sffamily\bfseries\normalsize J\'er\^ome Duriez}\\ \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR} \item \text{\sffamily\bfseries\normalsize Nolan Dyck}\\ \text{\sffamily\small Univ. of Western Ontario} \item \text{\sffamily\bfseries\normalsize Jan Eliáš}\\ \text{\sffamily\small Brno University of Technology} \item \text{\sffamily\bfseries\normalsize Burak Er}\\ \text{\sffamily\small Bursa Technical University} \item \text{\sffamily\bfseries\normalsize Alexander Eulitz}\\ \text{\sffamily\small TU Berlin / Institute for Machine Tools}\\ \text{\sffamily\small and Factory Management} \item \text{\sffamily\bfseries\normalsize Anton Gladky}\\ \text{\sffamily\small TU Bergakademie Freiberg} \item \text{\sffamily\bfseries\normalsize Ning Guo}\\ \text{\sffamily\small Hong Kong Univ. of Science and Tech.} \item \text{\sffamily\bfseries\normalsize Christian Jakob}\\ \text{\sffamily\small TU Bergakademie Freiberg} \item \text{\sffamily\bfseries\normalsize François Kneib}\\ \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR / Irstea Grenoble} \item \text{\sffamily\bfseries\normalsize Janek Kozicki}\\ \text{\sffamily\small Gdansk University of Technology} \item \text{\sffamily\bfseries\normalsize Donia Marzougui}\\ \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR} \item \text{\sffamily\bfseries\normalsize Raphaël Maurin}\\ \text{\sffamily\small Irstea Grenoble} \item \text{\sffamily\bfseries\normalsize Chiara Modenese}\\ \text{\sffamily\small University of Oxford} \item \text{\sffamily\bfseries\normalsize Luc Scholt\`{e}s}\\ \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR} \item \text{\sffamily\bfseries\normalsize Luc Sibille}\\ \text{\sffamily\small University of Nantes, lab. GeM} \item \text{\sffamily\bfseries\normalsize Jan Str\'{a}nsk\'{y}}\\ \text{\sffamily\small CVUT Prague} \item \text{\sffamily\bfseries\normalsize Thomas Sweijen}\\ \text{\sffamily\small Utrecht University} \item \text{\sffamily\bfseries\normalsize Klaus Thoeni}\\ \text{\sffamily\small The University of Newcastle (Australia)} \item \text{\sffamily\bfseries\normalsize Chao Yuan} \\ \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR} \end{itemize} \end{multicols} \text{\sffamily\bfseries\large Citing this document:}\\ \v{S}milauer V. et al. (2015). Yade Documentation 2nd ed. doi:10.5281/zenodo.34073. http://yade-dem.org\\ See also http://yade-dem/doc/citing.html. ''' latex_elements=dict( papersize='a4paper', fontpkg=r''' \usepackage{euler} \usepackage{fontspec,xunicode,xltxtra} %\setmainfont[BoldFont={LMRoman10 Bold}]{CMU Concrete} %% CMU Concrete must be installed by hand as otf ''', utf8extra='', fncychap='', preamble=my_latex_preamble, footer='', inputenc='', fontenc='', maketitle=my_maketitle, ) # The paper size ('letter' or 'a4'). #latex_paper_size = 'letter' # The font size ('10pt', '11pt' or '12pt'). #latex_font_size = '10pt' # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ ('index-toctree-book', 'YadeBook.tex', u'Yade documentation', u'Václav Šmilauer et al.', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. latex_logo = '../fig/yade-logo.png' # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. latex_use_parts = True # Additional stuff for the LaTeX preamble. #latex_preamble = '' # Documents to append as an appendix to all manuals. #latex_appendices = [] # If false, no module index is generated. #latex_use_modindex = True trunk-2017.01a/doc/sphinx/book/confManual.py000066400000000000000000000634101304022710500206330ustar00rootroot00000000000000# -*- coding: utf-8 -*- # # Yade documentation build configuration file, created by # sphinx-quickstart on Mon Nov 16 21:49:34 2009. # # This file is execfile()d with the current directory set to its containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # relevant posts to sphinx ML # http://groups.google.com/group/sphinx-dev/browse_thread/thread/b4fbc8d31d230fc4 # http://groups.google.com/group/sphinx-dev/browse_thread/thread/118598245d5f479b ##################### ## custom yade roles ##################### ## ## http://docutils.sourceforge.net/docs/howto/rst-roles.html import sys, os, re from docutils import nodes from sphinx import addnodes from sphinx.roles import XRefRole import docutils # # needed for creating hyperlink targets. # it should be cleand up and unified for both LaTeX and HTML via # the pending_xref node which gets resolved to real link target # by sphinx automatically once all docs have been processed. # # xrefs: http://groups.google.com/group/sphinx-dev/browse_thread/thread/d719d19307654548 # # import __builtin__ if 'latex' in sys.argv: __builtin__.writer='latex' elif 'html' in sys.argv: __builtin__.writer='html' elif 'epub' in sys.argv: __builtin__.writer='epub' else: raise RuntimeError("Must have either 'latex' or 'html' on the command line (hack for reference styles)") sys.path.append(os.path.abspath('./..')) def yaderef_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :yref:`` role, by making hyperlink to yade.wrapper.*. It supports :yref:`Link text` syntax, like usual hyperlinking roles." id=rawtext.split(':',2)[2][1:-1] txt=id; explicitText=False m=re.match('(.*)\s*<(.*)>\s*',id) if m: explicitText=True txt,id=m.group(1),m.group(2) id=id.replace('::','.') #node=nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='http://beta.arcig.cz/~eudoxos/yade/doxygen/?search=%s'%id,**options) #node=nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='yade.wrapper.html#yade.wrapper.%s'%id,**options) return [mkYrefNode(id,txt,rawtext,role,explicitText,lineno,options)],[] def yadesrc_role(role,rawtext,lineno,inliner,options={},content=[]): "Handle the :ysrc:`` role, making hyperlink to git repository webpage with that path. Supports :ysrc:`Link text` syntax, like usual hyperlinking roles. If target ends with ``/``, it is assumed to be a directory." id=rawtext.split(':',2)[2][1:-1] txt=id m=re.match('(.*)\s*<(.*)>\s*',id) if m: txt,id=m.group(1),m.group(2) return [nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='https://github.com/yade/trunk/blob/master/%s'%id)],[] ### **options should be passed to nodes.reference as well # map modules to their html (rst) filenames. Used for sub-modules, where e.g. SpherePack is yade._packSphere.SpherePack, but is documented from yade.pack.rst moduleMap={ 'yade._packPredicates':'yade.pack', 'yade._packSpheres':'yade.pack', 'yade._packObb':'yade.pack' } class YadeXRefRole(XRefRole): #def process_link def process_link(self, env, refnode, has_explicit_title, title, target): print 'TARGET:','yade.wrapper.'+target return '[['+title+']]','yade.wrapper.'+target def mkYrefNode(target,text,rawtext,role,explicitText,lineno,options={}): """Create hyperlink to yade target. Targets starting with literal 'yade.' are absolute, but the leading 'yade.' will be stripped from the link text. Absolute tergets are supposed to live in page named yade.[module].html, anchored at #yade.[module2].[rest of target], where [module2] is identical to [module], unless mapped over by moduleMap. Other targets are supposed to live in yade.wrapper (such as c++ classes).""" writer=__builtin__.writer # to make sure not shadowed by a local var import string if target.startswith('yade.'): module='.'.join(target.split('.')[0:2]) module2=(module if module not in moduleMap.keys() else moduleMap[module]) if target==module: target='' # to reference the module itself uri=('%%%s#%s'%(module2,target) if writer=='latex' else '%s.html#%s'%(module2,target)) if not explicitText and module!=module2: text=module2+'.'+'.'.join(target.split('.')[2:]) text=string.replace(text,'yade.','',1) elif target.startswith('external:'): exttarget=target.split(':',1)[1] if not explicitText: text=exttarget target=exttarget if '.' in exttarget else 'module-'+exttarget uri=(('%%external#%s'%target) if writer=='latex' else 'external.html#%s'%target) else: uri=(('%%yade.wrapper#yade.wrapper.%s'%target) if writer=='latex' else 'yade.wrapper.html#yade.wrapper.%s'%target) #print writer,uri return nodes.reference(rawtext,docutils.utils.unescape(text),refuri=uri,**options) #return [refnode],[] def ydefault_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :ydefault:`something` role. fixSignature handles it now in the member signature itself, this merely expands to nothing." return [],[] def yattrtype_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :yattrtype:`something` role. fixSignature handles it now in the member signature itself, this merely expands to nothing." return [],[] # FIXME: should return readable representation of bits of the number (yade.wrapper.AttrFlags enum) def yattrflags_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :yattrflags:`something` role. fixSignature handles it now in the member signature itself." return [],[] from docutils.parsers.rst import roles def yaderef_role_2(type,rawtext,text,lineno,inliner,options={},content=[]): return YadeXRefRole()('yref',rawtext,text,lineno,inliner,options,content) roles.register_canonical_role('yref', yaderef_role) roles.register_canonical_role('ysrc', yadesrc_role) roles.register_canonical_role('ydefault', ydefault_role) roles.register_canonical_role('yattrtype', yattrtype_role) roles.register_canonical_role('yattrflags', yattrflags_role) ## http://sphinx.pocoo.org/config.html#confval-rst_epilog rst_epilog = """ .. |yupdate| replace:: *(auto-updated)* .. |ycomp| replace:: *(auto-computed)* .. |ystatic| replace:: *(static)* """ import collections def customExclude(app, what, name, obj, skip, options): if name=='clone': if 'Serializable.clone' in str(obj): return False return True #escape crash on non iterable __doc__ in some qt object if hasattr(obj,'__doc__') and obj.__doc__ and not isinstance(obj.__doc__, collections.Iterable): return True if hasattr(obj,'__doc__') and obj.__doc__ and ('|ydeprecated|' in obj.__doc__ or '|yhidden|' in obj.__doc__): return True #if re.match(r'\b(__init__|__reduce__|__repr__|__str__)\b',name): return True if name.startswith('_'): if name=='__init__': # skip boost classes with parameterless ctor (arg1=implicit self) if obj.__doc__=="\n__init__( (object)arg1) -> None": return True # skip undocumented ctors if not obj.__doc__: return True # skip default ctor for serializable, taking dict of attrs if obj.__doc__=='\n__init__( (object)arg1) -> None\n\nobject __init__(tuple args, dict kwds)': return True #for i,l in enumerate(obj.__doc__.split('\n')): print name,i,l,'##' return False return True return False def isBoostFunc(what,obj): return what=='function' and obj.__repr__().startswith('.*$',doc1): return None,docc if doc1.endswith(':'): doc1=doc1[:-1] strippedDoc=doc.split('\n')[2:] # check if all lines are padded allLinesHave4LeadingSpaces=True for l in strippedDoc: if l.startswith(' '): continue allLinesHave4LeadingSpaces=False; break # remove the padding if so if allLinesHave4LeadingSpaces: strippedDoc=[l[4:] for l in strippedDoc] for i in range(len(strippedDoc)): # fix signatures inside docstring (one function with multiple signatures) strippedDoc[i],n=re.subn(r'([a-zA-Z_][a-zA-Z0-9_]*\() \(object\)arg1(, |)',r'\1',strippedDoc[i].replace('->','→')) # inspect dosctring after mangling if 'getViscoelasticFromSpheresInteraction' in name and False: print name print strippedDoc print '======================' for l in strippedDoc: print l print '======================' sig=doc1.split('(',1)[1] if removeSelf: # remove up to the first comma; if no comma present, then the method takes no arguments # if [ precedes the comma, add it to the result (ugly!) try: ss=sig.split(',',1) if ss[0].endswith('['): sig='['+ss[1] else: sig=ss[1] except IndexError: # grab the return value try: sig=') -> '+sig.split('->')[-1] #if 'Serializable' in name: print 1000*'#',name except IndexError: sig=')' return '('+sig,strippedDoc def fixSignature(app, what, name, obj, options, signature, return_annotation): #print what,name,obj,signature#,dir(obj) if what=='attribute': doc=unicode(obj.__doc__) ret='' m=re.match('.*:ydefault:`(.*?)`.*',doc) if m: typ='' #try: # clss='.'.join(name.split('.')[:-1]) # instance=eval(clss+'()') # typ='; '+getattr(instance,name.split('.')[-1]).__class__.__name__ # if typ=='; NoneType': typ='' #except TypeError: ##no registered converted # typ='' dfl=m.group(1) m2=re.match(r'\s*\(\s*\(\s*void\s*\)\s*\"(.*)\"\s*,\s*(.*)\s*\)\s*',dfl) if m2: dfl="%s, %s"%(m2.group(2),m2.group(1)) if dfl!='': ret+=' (='+dfl+'%s)'%typ else: ret+=' (=uninitalized%s)'%typ #m=re.match('.*\[(.{,8})\].*',doc) #m=re.match('.*:yunit:`(.?*)`.*',doc) #if m: # units=m.group(1) # print '@@@@@@@@@@@@@@@@@@@@@',name,units # ret+=' ['+units+']' return ret,None elif what=='class': ret=[] if len(obj.__bases__)>0: base=obj.__bases__[0] while base.__module__!='Boost.Python': ret+=[base.__name__] if len(base.__bases__)>0: base=base.__bases__[0] else: break if len(ret): return ' (inherits '+u' → '.join(ret)+')',None else: return None,None elif isBoostFunc(what,obj): sig=boostFuncSignature(name,obj)[0] or ' (wrapped c++ function)' return sig,None elif isBoostMethod(what,obj): sig=boostFuncSignature(name,obj,removeSelf=True)[0] return sig,None #else: print what,name,obj.__repr__() #return None,None from sphinx import addnodes def parse_ystaticattr(env,attr,attrnode): m=re.match(r'([a-zA-Z0-9_]+)\.(.*)\(=(.*)\)',attr) if not m: print 100*'@'+' Static attribute %s not matched'%attr attrnode+=addnodes.desc_name(attr,attr) klass,name,default=m.groups() #attrnode+=addnodes.desc_type('static','static') attrnode+=addnodes.desc_name(name,name) plist=addnodes.desc_parameterlist() if default=='': default='unspecified' plist+=addnodes.desc_parameter('='+default,'='+default) attrnode+=plist attrnode+=addnodes.desc_annotation(' [static]',' [static]') return klass+'.'+name ############################# ## set tab size ################### ## http://groups.google.com/group/sphinx-dev/browse_thread/thread/35b8071ffe9a8feb def setup(app): from sphinx.highlighting import lexers from pygments.lexers.compiled import CppLexer lexers['cpp'] = CppLexer(tabsize=3) lexers['c++'] = CppLexer(tabsize=3) from pygments.lexers.agile import PythonLexer lexers['python'] = PythonLexer(tabsize=3) app.connect('source-read',fixSrc) app.connect('autodoc-skip-member',customExclude) app.connect('autodoc-process-signature',fixSignature) app.connect('autodoc-process-docstring',fixDocstring) app.add_description_unit('ystaticattr',None,objname='static attribute',indextemplate='pair: %s; static method',parse_node=parse_ystaticattr) import sys, os # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. #sys.path.append(os.path.abspath('.')) # -- General configuration ----------------------------------------------------- # Add any Sphinx extension module names here, as strings. They can be extensions # coming with Sphinx (named 'sphinx.ext.*') or your custom ones. # # HACK: change ipython console regexp from ipython_console_highlighting.py import re sys.path.append(os.path.abspath('.')) import yade.config if 1: if yade.runtime.ipython_version<12: import ipython_directive as id else: if 12<=yade.runtime.ipython_version<13: import ipython_directive012 as id elif 13<=yade.runtime.ipython_version<200: import ipython_directive013 as id elif 200<=yade.runtime.ipython_version<500: import ipython_directive200 as id else: import ipython_directive500 as id #The next four lines are for compatibility with IPython 0.13.1 ipython_rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*') ipython_rgxout=re.compile(r'(?:Out| -> )\[(\d+)\]:\s?(.*)\s*') ipython_promptin ='Yade [%d]:' ipython_promptout=' -> [%d]: ' ipython_cont_spaces=' ' #For IPython <=0.12, the following lines are used id.rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*') id.rgxout=re.compile(r'(?:Out| -> )\[(\d+)\]:\s?(.*)\s*') id.rgxcont=re.compile(r'(?: +)\.\.+:\s?(.*)\s*') id.fmtin ='Yade [%d]:' id.fmtout =' -> [%d]: ' # for some reason, out and cont must have the trailing space id.fmtcont=' .\D.: ' id.rc_override=dict(prompt_in1="Yade [\#]:",prompt_in2=" .\D.:",prompt_out=r" -> [\#]: ") if yade.runtime.ipython_version<12: id.reconfig_shell() import ipython_console_highlighting as ich ich.IPythonConsoleLexer.input_prompt = re.compile("(Yade \[[0-9]+\]: )") ich.IPythonConsoleLexer.output_prompt = re.compile("(( -> |Out)|\[[0-9]+\]: )") ich.IPythonConsoleLexer.continue_prompt = re.compile("\s+\.\.\.+:") extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.autosummary', 'sphinx.ext.coverage', 'sphinx.ext.pngmath', 'sphinx.ext.graphviz', 'sphinx.ext.viewcode', 'sphinx.ext.inheritance_diagram', 'matplotlib.sphinxext.plot_directive', 'matplotlib.sphinxext.only_directives', #'matplotlib.sphinxext.mathmpl', 'ipython_console_highlighting', 'youtube', 'sphinx.ext.todo', ] if yade.runtime.ipython_version<12: extensions.append('ipython_directive') else: if 12<=yade.runtime.ipython_version<13: extensions.append('ipython_directive012') elif 13<=yade.runtime.ipython_version<200: extensions.append('ipython_directive013') elif 200<=yade.runtime.ipython_version<500: extensions.append('ipython_directive200') else: extensions.append('ipython_directive500') # the sidebar extension if False: if writer=='html': extensions+=['sphinx.ext.sidebar'] sidebar_all=True sidebar_relling=True #sidebar_abbrev=True sidebar_tocdepth=3 ## http://trac.sagemath.org/sage_trac/attachment/ticket/7549/trac_7549-doc_inheritance_underscore.patch # GraphViz includes dot, neato, twopi, circo, fdp. graphviz_dot = 'dot' inheritance_graph_attrs = { 'rankdir' : 'BT' } inheritance_node_attrs = { 'height' : 0.5, 'fontsize' : 12, 'shape' : 'oval' } inheritance_edge_attrs = {} my_latex_preamble=r''' \usepackage{euler} % must be loaded before fontspec for the whole doc (below); this must be kept for pngmath, however \usepackage{hyperref} \usepackage{amsmath} \usepackage{amsbsy} %\usepackage{mathabx} \usepackage{underscore} \usepackage[all]{xy} % Metadata of the pdf output \hypersetup{pdftitle={Using and Programming}} \hypersetup{pdfauthor={Vaclav Smilauer; Bruno Chareyre; Jerome Duriez; Alexander Eulitz; Anton Gladky; Ning Guo; Christian Jakob; Janek Kozicki; Francois Kneib; Chiara Modenese; Jan Stransky; Klaus Thoeni}} \hypersetup{pdfkeywords={Discrete element method; dem; yade; documentation; manual; python; c++; git}} % symbols \let\mat\boldsymbol % matrix \let\vec\boldsymbol % vector \let\tens\boldsymbol % tensor \def\normalized#1{\widehat{#1}} \def\locframe#1{\widetilde{#1}} % timestep \def\Dt{\Delta t} \def\Dtcr{\Dt_{\rm cr}} % algorithm complexity \def\bigO#1{\ensuremath{\mathcal{O}(#1)}} % variants for greek symbols \let\epsilon\varepsilon \let\theta\vartheta \let\phi\varphi % shorthands \let\sig\sigma \let\eps\epsilon % variables at different points of time \def\prev#1{#1^-} \def\pprev#1{#1^\ominus} \def\curr#1{#1^{\circ}} \def\nnext#1{#1^\oplus} \def\next#1{#1^+} % shorthands for geometry \def\currn{\curr{\vec{n}}} \def\currC{\curr{\vec{C}}} \def\uT{\vec{u}_T} \def\curruT{\curr{\vec{u}}_T} \def\prevuT{\prev{\vec{u}}_T} \def\currn{\curr{\vec{n}}} \def\prevn{\prev{\vec{n}}} % motion \def\pprevvel{\pprev{\dot{\vec{u}}}} \def\nnextvel{\nnext{\dot{\vec{u}}}} \def\curraccel{\curr{\ddot{\vec{u}}}} \def\prevpos{\prev{\vec{u}}} \def\currpos{\curr{\vec{u}}} \def\nextpos{\next{\vec{u}}} \def\curraaccel{\curr{\dot{\vec{\omega}}}} \def\pprevangvel{\pprev{\vec{\omega}}} \def\nnextangvel{\nnext{\vec{\omega}}} \def\loccurr#1{\curr{\locframe{#1}}} \def\numCPU{n_{\rm cpu}} \DeclareMathOperator{\Align}{Align} \DeclareMathOperator{\sign}{sgn} % sorting algorithms \def\isleq#1{\currelem{#1}\ar@/^/[ll]^{\leq}} \def\isnleq#1{\currelem{#1}\ar@/^/[ll]^{\not\leq}} \def\currelem#1{\fbox{$#1$}} \def\sortSep{||} \def\sortInv{\hbox{\phantom{||}}} \def\sortlines#1{\xymatrix@=3pt{#1}} \def\crossBound{||\mkern-18mu<} ''' pngmath_latex_preamble=r'\usepackage[active]{preview}'+my_latex_preamble pngmath_use_preview=True # Add any paths that contain templates here, relative to this directory. templates_path = ['templates'] # The suffix of source filenames. source_suffix = '.rst' # The encoding of source files. #source_encoding = 'utf-8' # The master toctree document. master_doc = 'index-toctree-manuals' # General information about the project. project = u'Yade' copyright = u'2009, Václav Šmilauer' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. version = 'Yade documentation 2nd ed.' # The full version, including alpha/beta/rc tags. release = 'Yade documentation 2nd ed.' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. #language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: #today = '' # Else, today_fmt is used as the format for a strftime call. #today_fmt = '%B %d, %Y' # List of documents that shouldn't be included in the build. #unused_docs = [] # List of directories, relative to source directory, that shouldn't be searched # for source files. exclude_trees = ['_build','../_build'] # The reST default role (used for this markup: `text`) to use for all documents. #default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. #add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). #add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. #show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. modindex_common_prefix = ['yade.'] # -- Options for HTML output --------------------------------------------------- # The theme to use for HTML and HTML Help pages. Major themes that come with # Sphinx are currently 'default' and 'sphinxdoc'. html_theme = 'default' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. html_theme_options = {'stickysidebar':'true','collapsiblesidebar':'true','rightsidebar':'false'} # Add any paths that contain custom themes here, relative to this directory. #html_theme_path = [] # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". #html_title = None # A shorter title for the navigation bar. Default is the same as html_title. #html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. html_logo = '../fig/yade-logo.png' # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. html_favicon = '../fig/yade-favicon.ico' # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['static-html'] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. #html_last_updated_fmt = '%b %d, %Y' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. html_use_smartypants = True # Custom sidebar templates, maps document names to template names. #html_sidebars = {} html_index='index.html' # Additional templates that should be rendered to pages, maps page names to # template names. html_additional_pages = { 'index':'index.html'} # If false, no module index is generated. #html_use_modindex = True # If false, no index is generated. #html_use_index = True # If true, the index is split into individual pages for each letter. #html_split_index = False # If true, links to the reST sources are added to the pages. #html_show_sourcelink = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. #html_use_opensearch = '' # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml"). #html_file_suffix = '' # Output file base name for HTML help builder. htmlhelp_basename = 'Yadedoc' # -- Options for LaTeX output -------------------------------------------------- my_maketitle=r''' \begin{titlepage} \begin{flushright} \hrule{} % Upper part of the page \begin{flushright} \includegraphics[width=0.15\textwidth]{yade-logo.png}\par \end{flushright} \vspace{20 mm} \text{\sffamily\bfseries\Huge Using and Programming}\\ \vspace{20 mm} %\vspace{70 mm} \begin{sffamily}\bfseries\Large V\'{a}clav \v{S}milauer, Bruno Chareyre, J\'er\^ome Duriez, Alexander Eulitz, Anton Gladky, Ning Guo, Christian Jakob, Janek Kozicki, Fran\c{c}ois Kneib, Chiara Modenese, Jan Str\'{a}nsk\'{y}, Klaus Thoeni \end{sffamily} \vspace{20 mm} \hrule{} \vfill \textit{\large Yade Documentation 2nd edition, 2015}\\ \textit{based on Yade 1.14.0}\\ \end{flushright} \end{titlepage} \text{\sffamily\bfseries\large Citing this document:}\\ \v{S}milauer V. et al. (2015). Using and Programming. In:\textit{Yade Documentation 2nd ed.} doi:10.5281/zenodo.34043. http://yade-dem.org\\ See also http://yade-dem/doc/citing.html. ''' latex_elements=dict( papersize='a4paper', fontpkg=r''' \usepackage{euler} \usepackage{fontspec,xunicode,xltxtra} %\setmainfont[BoldFont={LMRoman10 Bold}]{CMU Concrete} %% CMU Concrete must be installed by hand as otf ''', utf8extra='', fncychap='', preamble=my_latex_preamble, footer='', inputenc='', fontenc='', maketitle=my_maketitle, ) # The paper size ('letter' or 'a4'). #latex_paper_size = 'letter' # The font size ('10pt', '11pt' or '12pt'). #latex_font_size = '10pt' # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ ('index-toctree-manuals', 'YadeManuals.tex', u'Using and Programming', u'Václav Šmilauer et al.', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. latex_logo = '../fig/yade-logo.png' # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. latex_use_parts = False # Additional stuff for the LaTeX preamble. #latex_preamble = '' # Documents to append as an appendix to all manuals. #latex_appendices = [] # If false, no module index is generated. #latex_use_modindex = True trunk-2017.01a/doc/sphinx/book/confReference.py000066400000000000000000000640521304022710500213170ustar00rootroot00000000000000# -*- coding: utf-8 -*- # # Yade documentation build configuration file, created by # sphinx-quickstart on Mon Nov 16 21:49:34 2009. # # This file is execfile()d with the current directory set to its containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # relevant posts to sphinx ML # http://groups.google.com/group/sphinx-dev/browse_thread/thread/b4fbc8d31d230fc4 # http://groups.google.com/group/sphinx-dev/browse_thread/thread/118598245d5f479b ##################### ## custom yade roles ##################### ## ## http://docutils.sourceforge.net/docs/howto/rst-roles.html import sys, os, re from docutils import nodes from sphinx import addnodes from sphinx.roles import XRefRole import docutils # # needed for creating hyperlink targets. # it should be cleand up and unified for both LaTeX and HTML via # the pending_xref node which gets resolved to real link target # by sphinx automatically once all docs have been processed. # # xrefs: http://groups.google.com/group/sphinx-dev/browse_thread/thread/d719d19307654548 # # import __builtin__ if 'latex' in sys.argv: __builtin__.writer='latex' elif 'html' in sys.argv: __builtin__.writer='html' elif 'epub' in sys.argv: __builtin__.writer='epub' else: raise RuntimeError("Must have either 'latex' or 'html' on the command line (hack for reference styles)") sys.path.append(os.path.abspath('./..')) def yaderef_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :yref:`` role, by making hyperlink to yade.wrapper.*. It supports :yref:`Link text` syntax, like usual hyperlinking roles." id=rawtext.split(':',2)[2][1:-1] txt=id; explicitText=False m=re.match('(.*)\s*<(.*)>\s*',id) if m: explicitText=True txt,id=m.group(1),m.group(2) id=id.replace('::','.') #node=nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='http://beta.arcig.cz/~eudoxos/yade/doxygen/?search=%s'%id,**options) #node=nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='yade.wrapper.html#yade.wrapper.%s'%id,**options) return [mkYrefNode(id,txt,rawtext,role,explicitText,lineno,options)],[] def yadesrc_role(role,rawtext,lineno,inliner,options={},content=[]): "Handle the :ysrc:`` role, making hyperlink to git repository webpage with that path. Supports :ysrc:`Link text` syntax, like usual hyperlinking roles. If target ends with ``/``, it is assumed to be a directory." id=rawtext.split(':',2)[2][1:-1] txt=id m=re.match('(.*)\s*<(.*)>\s*',id) if m: txt,id=m.group(1),m.group(2) return [nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='https://github.com/yade/trunk/blob/master/%s'%id)],[] ### **options should be passed to nodes.reference as well # map modules to their html (rst) filenames. Used for sub-modules, where e.g. SpherePack is yade._packSphere.SpherePack, but is documented from yade.pack.rst moduleMap={ 'yade._packPredicates':'yade.pack', 'yade._packSpheres':'yade.pack', 'yade._packObb':'yade.pack' } class YadeXRefRole(XRefRole): #def process_link def process_link(self, env, refnode, has_explicit_title, title, target): print 'TARGET:','yade.wrapper.'+target return '[['+title+']]','yade.wrapper.'+target def mkYrefNode(target,text,rawtext,role,explicitText,lineno,options={}): """Create hyperlink to yade target. Targets starting with literal 'yade.' are absolute, but the leading 'yade.' will be stripped from the link text. Absolute tergets are supposed to live in page named yade.[module].html, anchored at #yade.[module2].[rest of target], where [module2] is identical to [module], unless mapped over by moduleMap. Other targets are supposed to live in yade.wrapper (such as c++ classes).""" writer=__builtin__.writer # to make sure not shadowed by a local var import string if target.startswith('yade.'): module='.'.join(target.split('.')[0:2]) module2=(module if module not in moduleMap.keys() else moduleMap[module]) if target==module: target='' # to reference the module itself uri=('%%%s#%s'%(module2,target) if writer=='latex' else '%s.html#%s'%(module2,target)) if not explicitText and module!=module2: text=module2+'.'+'.'.join(target.split('.')[2:]) text=string.replace(text,'yade.','',1) elif target.startswith('external:'): exttarget=target.split(':',1)[1] if not explicitText: text=exttarget target=exttarget if '.' in exttarget else 'module-'+exttarget uri=(('%%external#%s'%target) if writer=='latex' else 'external.html#%s'%target) else: uri=(('%%yade.wrapper#yade.wrapper.%s'%target) if writer=='latex' else 'yade.wrapper.html#yade.wrapper.%s'%target) #print writer,uri return nodes.reference(rawtext,docutils.utils.unescape(text),refuri=uri,**options) #return [refnode],[] def ydefault_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :ydefault:`something` role. fixSignature handles it now in the member signature itself, this merely expands to nothing." return [],[] def yattrtype_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :yattrtype:`something` role. fixSignature handles it now in the member signature itself, this merely expands to nothing." return [],[] # FIXME: should return readable representation of bits of the number (yade.wrapper.AttrFlags enum) def yattrflags_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :yattrflags:`something` role. fixSignature handles it now in the member signature itself." return [],[] from docutils.parsers.rst import roles def yaderef_role_2(type,rawtext,text,lineno,inliner,options={},content=[]): return YadeXRefRole()('yref',rawtext,text,lineno,inliner,options,content) roles.register_canonical_role('yref', yaderef_role) roles.register_canonical_role('ysrc', yadesrc_role) roles.register_canonical_role('ydefault', ydefault_role) roles.register_canonical_role('yattrtype', yattrtype_role) roles.register_canonical_role('yattrflags', yattrflags_role) ## http://sphinx.pocoo.org/config.html#confval-rst_epilog rst_epilog = """ .. |yupdate| replace:: *(auto-updated)* .. |ycomp| replace:: *(auto-computed)* .. |ystatic| replace:: *(static)* """ import collections def customExclude(app, what, name, obj, skip, options): if name=='clone': if 'Serializable.clone' in str(obj): return False return True #escape crash on non iterable __doc__ in some qt object if hasattr(obj,'__doc__') and obj.__doc__ and not isinstance(obj.__doc__, collections.Iterable): return True if hasattr(obj,'__doc__') and obj.__doc__ and ('|ydeprecated|' in obj.__doc__ or '|yhidden|' in obj.__doc__): return True #if re.match(r'\b(__init__|__reduce__|__repr__|__str__)\b',name): return True if name.startswith('_'): if name=='__init__': # skip boost classes with parameterless ctor (arg1=implicit self) if obj.__doc__=="\n__init__( (object)arg1) -> None": return True # skip undocumented ctors if not obj.__doc__: return True # skip default ctor for serializable, taking dict of attrs if obj.__doc__=='\n__init__( (object)arg1) -> None\n\nobject __init__(tuple args, dict kwds)': return True #for i,l in enumerate(obj.__doc__.split('\n')): print name,i,l,'##' return False return True return False def isBoostFunc(what,obj): return what=='function' and obj.__repr__().startswith('.*$',doc1): return None,docc if doc1.endswith(':'): doc1=doc1[:-1] strippedDoc=doc.split('\n')[2:] # check if all lines are padded allLinesHave4LeadingSpaces=True for l in strippedDoc: if l.startswith(' '): continue allLinesHave4LeadingSpaces=False; break # remove the padding if so if allLinesHave4LeadingSpaces: strippedDoc=[l[4:] for l in strippedDoc] for i in range(len(strippedDoc)): # fix signatures inside docstring (one function with multiple signatures) strippedDoc[i],n=re.subn(r'([a-zA-Z_][a-zA-Z0-9_]*\() \(object\)arg1(, |)',r'\1',strippedDoc[i].replace('->','→')) # inspect dosctring after mangling if 'getViscoelasticFromSpheresInteraction' in name and False: print name print strippedDoc print '======================' for l in strippedDoc: print l print '======================' sig=doc1.split('(',1)[1] if removeSelf: # remove up to the first comma; if no comma present, then the method takes no arguments # if [ precedes the comma, add it to the result (ugly!) try: ss=sig.split(',',1) if ss[0].endswith('['): sig='['+ss[1] else: sig=ss[1] except IndexError: # grab the return value try: sig=') -> '+sig.split('->')[-1] #if 'Serializable' in name: print 1000*'#',name except IndexError: sig=')' return '('+sig,strippedDoc def fixSignature(app, what, name, obj, options, signature, return_annotation): #print what,name,obj,signature#,dir(obj) if what=='attribute': doc=unicode(obj.__doc__) ret='' m=re.match('.*:ydefault:`(.*?)`.*',doc) if m: typ='' #try: # clss='.'.join(name.split('.')[:-1]) # instance=eval(clss+'()') # typ='; '+getattr(instance,name.split('.')[-1]).__class__.__name__ # if typ=='; NoneType': typ='' #except TypeError: ##no registered converted # typ='' dfl=m.group(1) m2=re.match(r'\s*\(\s*\(\s*void\s*\)\s*\"(.*)\"\s*,\s*(.*)\s*\)\s*',dfl) if m2: dfl="%s, %s"%(m2.group(2),m2.group(1)) if dfl!='': ret+=' (='+dfl+'%s)'%typ else: ret+=' (=uninitalized%s)'%typ #m=re.match('.*\[(.{,8})\].*',doc) #m=re.match('.*:yunit:`(.?*)`.*',doc) #if m: # units=m.group(1) # print '@@@@@@@@@@@@@@@@@@@@@',name,units # ret+=' ['+units+']' return ret,None elif what=='class': ret=[] if len(obj.__bases__)>0: base=obj.__bases__[0] while base.__module__!='Boost.Python': ret+=[base.__name__] if len(base.__bases__)>0: base=base.__bases__[0] else: break if len(ret): return ' (inherits '+u' → '.join(ret)+')',None else: return None,None elif isBoostFunc(what,obj): sig=boostFuncSignature(name,obj)[0] or ' (wrapped c++ function)' return sig,None elif isBoostMethod(what,obj): sig=boostFuncSignature(name,obj,removeSelf=True)[0] return sig,None #else: print what,name,obj.__repr__() #return None,None from sphinx import addnodes def parse_ystaticattr(env,attr,attrnode): m=re.match(r'([a-zA-Z0-9_]+)\.(.*)\(=(.*)\)',attr) if not m: print 100*'@'+' Static attribute %s not matched'%attr attrnode+=addnodes.desc_name(attr,attr) klass,name,default=m.groups() #attrnode+=addnodes.desc_type('static','static') attrnode+=addnodes.desc_name(name,name) plist=addnodes.desc_parameterlist() if default=='': default='unspecified' plist+=addnodes.desc_parameter('='+default,'='+default) attrnode+=plist attrnode+=addnodes.desc_annotation(' [static]',' [static]') return klass+'.'+name ############################# ## set tab size ################### ## http://groups.google.com/group/sphinx-dev/browse_thread/thread/35b8071ffe9a8feb def setup(app): from sphinx.highlighting import lexers from pygments.lexers.compiled import CppLexer lexers['cpp'] = CppLexer(tabsize=3) lexers['c++'] = CppLexer(tabsize=3) from pygments.lexers.agile import PythonLexer lexers['python'] = PythonLexer(tabsize=3) app.connect('source-read',fixSrc) app.connect('autodoc-skip-member',customExclude) app.connect('autodoc-process-signature',fixSignature) app.connect('autodoc-process-docstring',fixDocstring) app.add_description_unit('ystaticattr',None,objname='static attribute',indextemplate='pair: %s; static method',parse_node=parse_ystaticattr) import sys, os # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. #sys.path.append(os.path.abspath('.')) # -- General configuration ----------------------------------------------------- # Add any Sphinx extension module names here, as strings. They can be extensions # coming with Sphinx (named 'sphinx.ext.*') or your custom ones. # # HACK: change ipython console regexp from ipython_console_highlighting.py import re sys.path.append(os.path.abspath('.')) import yade.config if 1: if yade.runtime.ipython_version<12: import ipython_directive as id else: if 12<=yade.runtime.ipython_version<13: import ipython_directive012 as id elif 13<=yade.runtime.ipython_version<200: import ipython_directive013 as id elif 200<=yade.runtime.ipython_version<500: import ipython_directive200 as id else: import ipython_directive500 as id #The next four lines are for compatibility with IPython 0.13.1 ipython_rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*') ipython_rgxout=re.compile(r'(?:Out| -> )\[(\d+)\]:\s?(.*)\s*') ipython_promptin ='Yade [%d]:' ipython_promptout=' -> [%d]: ' ipython_cont_spaces=' ' #For IPython <=0.12, the following lines are used id.rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*') id.rgxout=re.compile(r'(?:Out| -> )\[(\d+)\]:\s?(.*)\s*') id.rgxcont=re.compile(r'(?: +)\.\.+:\s?(.*)\s*') id.fmtin ='Yade [%d]:' id.fmtout =' -> [%d]: ' # for some reason, out and cont must have the trailing space id.fmtcont=' .\D.: ' id.rc_override=dict(prompt_in1="Yade [\#]:",prompt_in2=" .\D.:",prompt_out=r" -> [\#]: ") if yade.runtime.ipython_version<12: id.reconfig_shell() import ipython_console_highlighting as ich ich.IPythonConsoleLexer.input_prompt = re.compile("(Yade \[[0-9]+\]: )") ich.IPythonConsoleLexer.output_prompt = re.compile("(( -> |Out)|\[[0-9]+\]: )") ich.IPythonConsoleLexer.continue_prompt = re.compile("\s+\.\.\.+:") extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.autosummary', 'sphinx.ext.coverage', 'sphinx.ext.pngmath', 'sphinx.ext.graphviz', 'sphinx.ext.viewcode', 'sphinx.ext.inheritance_diagram', 'matplotlib.sphinxext.plot_directive', 'matplotlib.sphinxext.only_directives', #'matplotlib.sphinxext.mathmpl', 'ipython_console_highlighting', 'youtube', 'sphinx.ext.todo', ] if yade.runtime.ipython_version<12: extensions.append('ipython_directive') else: if 12<=yade.runtime.ipython_version<13: extensions.append('ipython_directive012') elif 13<=yade.runtime.ipython_version<200: extensions.append('ipython_directive013') elif 200<=yade.runtime.ipython_version<500: extensions.append('ipython_directive200') else: extensions.append('ipython_directive500') # the sidebar extension if False: if writer=='html': extensions+=['sphinx.ext.sidebar'] sidebar_all=True sidebar_relling=True #sidebar_abbrev=True sidebar_tocdepth=3 ## http://trac.sagemath.org/sage_trac/attachment/ticket/7549/trac_7549-doc_inheritance_underscore.patch # GraphViz includes dot, neato, twopi, circo, fdp. graphviz_dot = 'dot' inheritance_graph_attrs = { 'rankdir' : 'BT' } inheritance_node_attrs = { 'height' : 0.5, 'fontsize' : 12, 'shape' : 'oval' } inheritance_edge_attrs = {} my_latex_preamble=r''' \usepackage{euler} % must be loaded before fontspec for the whole doc (below); this must be kept for pngmath, however \usepackage{hyperref} \usepackage{amsmath} \usepackage{amsbsy} %\usepackage{mathabx} \usepackage{underscore} \usepackage[all]{xy} % Metadata of the pdf output \hypersetup{pdftitle={Reference Manual}} \hypersetup{pdfauthor={Vaclav Smilauer; Emanuele Catalano; Bruno Chareyre; Sergei Dorofeenko; Jerome Duriez; Nolan Dyck; Burak Er; Jan Elias; Alexander Eulitz; Anton Gladky; Christian Jakob; Francois Kneib; Janek Kozicki; Donia Marzougui; Raphael Maurin; Chiara Modenese; Luc Scholtes; Luc Sibille; Jan Stransky; Thomas Sweijen; Klaus Thoeni; Chao Yuan}} \hypersetup{pdfkeywords={Discrete element method; dem; yade; documentation; manual; python; c++; git}} % symbols \let\mat\boldsymbol % matrix \let\vec\boldsymbol % vector \let\tens\boldsymbol % tensor \def\normalized#1{\widehat{#1}} \def\locframe#1{\widetilde{#1}} % timestep \def\Dt{\Delta t} \def\Dtcr{\Dt_{\rm cr}} % algorithm complexity \def\bigO#1{\ensuremath{\mathcal{O}(#1)}} % variants for greek symbols \let\epsilon\varepsilon \let\theta\vartheta \let\phi\varphi % shorthands \let\sig\sigma \let\eps\epsilon % variables at different points of time \def\prev#1{#1^-} \def\pprev#1{#1^\ominus} \def\curr#1{#1^{\circ}} \def\nnext#1{#1^\oplus} \def\next#1{#1^+} % shorthands for geometry \def\currn{\curr{\vec{n}}} \def\currC{\curr{\vec{C}}} \def\uT{\vec{u}_T} \def\curruT{\curr{\vec{u}}_T} \def\prevuT{\prev{\vec{u}}_T} \def\currn{\curr{\vec{n}}} \def\prevn{\prev{\vec{n}}} % motion \def\pprevvel{\pprev{\dot{\vec{u}}}} \def\nnextvel{\nnext{\dot{\vec{u}}}} \def\curraccel{\curr{\ddot{\vec{u}}}} \def\prevpos{\prev{\vec{u}}} \def\currpos{\curr{\vec{u}}} \def\nextpos{\next{\vec{u}}} \def\curraaccel{\curr{\dot{\vec{\omega}}}} \def\pprevangvel{\pprev{\vec{\omega}}} \def\nnextangvel{\nnext{\vec{\omega}}} \def\loccurr#1{\curr{\locframe{#1}}} \def\numCPU{n_{\rm cpu}} \DeclareMathOperator{\Align}{Align} \DeclareMathOperator{\sign}{sgn} % sorting algorithms \def\isleq#1{\currelem{#1}\ar@/^/[ll]^{\leq}} \def\isnleq#1{\currelem{#1}\ar@/^/[ll]^{\not\leq}} \def\currelem#1{\fbox{$#1$}} \def\sortSep{||} \def\sortInv{\hbox{\phantom{||}}} \def\sortlines#1{\xymatrix@=3pt{#1}} \def\crossBound{||\mkern-18mu<} ''' pngmath_latex_preamble=r'\usepackage[active]{preview}'+my_latex_preamble pngmath_use_preview=True # Add any paths that contain templates here, relative to this directory. templates_path = ['templates'] # The suffix of source filenames. source_suffix = '.rst' # The encoding of source files. #source_encoding = 'utf-8' # The master toctree document. master_doc = 'index-toctree-reference' # General information about the project. project = u'Yade' copyright = u'2009, Václav Šmilauer' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. version = 'Yade documentation 2nd ed.' # The full version, including alpha/beta/rc tags. release = 'Yade documentation 2nd ed.' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. #language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: #today = '' # Else, today_fmt is used as the format for a strftime call. #today_fmt = '%B %d, %Y' # List of documents that shouldn't be included in the build. #unused_docs = [] # List of directories, relative to source directory, that shouldn't be searched # for source files. exclude_trees = ['_build','../_build'] # The reST default role (used for this markup: `text`) to use for all documents. #default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. #add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). #add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. #show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. modindex_common_prefix = ['yade.'] # -- Options for HTML output --------------------------------------------------- # The theme to use for HTML and HTML Help pages. Major themes that come with # Sphinx are currently 'default' and 'sphinxdoc'. html_theme = 'default' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. html_theme_options = {'stickysidebar':'true','collapsiblesidebar':'true','rightsidebar':'false'} # Add any paths that contain custom themes here, relative to this directory. #html_theme_path = [] # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". #html_title = None # A shorter title for the navigation bar. Default is the same as html_title. #html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. html_logo = '../fig/yade-logo.png' # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. html_favicon = '../fig/yade-favicon.ico' # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['static-html'] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. #html_last_updated_fmt = '%b %d, %Y' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. html_use_smartypants = True # Custom sidebar templates, maps document names to template names. #html_sidebars = {} html_index='index.html' # Additional templates that should be rendered to pages, maps page names to # template names. html_additional_pages = { 'index':'index.html'} # If false, no module index is generated. #html_use_modindex = True # If false, no index is generated. #html_use_index = True # If true, the index is split into individual pages for each letter. #html_split_index = False # If true, links to the reST sources are added to the pages. #html_show_sourcelink = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. #html_use_opensearch = '' # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml"). #html_file_suffix = '' # Output file base name for HTML help builder. htmlhelp_basename = 'Yadedoc' # -- Options for LaTeX output -------------------------------------------------- my_maketitle=r''' \begin{titlepage} \begin{flushright} \hrule{} % Upper part of the page \begin{flushright} \includegraphics[width=0.15\textwidth]{yade-logo.png}\par \end{flushright} \vspace{20 mm} \text{\sffamily\bfseries\Huge Reference Manual}\\ \vspace{20 mm} %\vspace{70 mm} \begin{sffamily}\bfseries\Large V\'{a}clav \v{S}milauer, Emanuele Catalano, Bruno Chareyre, Sergei Dorofeenko, J\'er\^ome Duriez, Nolan Dyck, Jan Eliáš, Burak Er, Alexander Eulitz, Anton Gladky, Christian Jakob, Fran\c{c}ois Kneib, Janek Kozicki, Donia Marzougui, Rapha\"el Maurin, Chiara Modenese, Luc Scholt\`{e}s, Luc Sibille, Jan Str\'{a}nsk\'{y}, Thomas Sweijen, Klaus Thoeni, Chao Yuan \end{sffamily} \vspace{20 mm} \hrule{} \vfill \textit{\large Yade Documentation 2nd edition, 2015}\\ \textit{based on Yade 1.14.0}\\ \end{flushright} \end{titlepage} \text{\sffamily\bfseries\large Citing this document:}\\ \v{S}milauer V. et al. (2015). Reference Manual. In:\textit{Yade Documentation 2nd ed.} doi:10.5281/zenodo.34045. http://yade-dem.org\\ See also http://yade-dem/doc/citing.html. ''' latex_elements=dict( papersize='a4paper', fontpkg=r''' \usepackage{euler} \usepackage{fontspec,xunicode,xltxtra} %\setmainfont[BoldFont={LMRoman10 Bold}]{CMU Concrete} %% CMU Concrete must be installed by hand as otf ''', utf8extra='', fncychap='', preamble=my_latex_preamble, footer='', inputenc='', fontenc='', maketitle=my_maketitle, ) # The paper size ('letter' or 'a4'). #latex_paper_size = 'letter' # The font size ('10pt', '11pt' or '12pt'). #latex_font_size = '10pt' # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ ('index-toctree-reference', 'YadeReference.tex', u'Reference Manual', u'Václav Šmilauer et al.', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. latex_logo = '../fig/yade-logo.png' # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. latex_use_parts = False # Additional stuff for the LaTeX preamble. #latex_preamble = '' # Documents to append as an appendix to all manuals. #latex_appendices = [] # If false, no module index is generated. #latex_use_modindex = True trunk-2017.01a/doc/sphinx/book/confTheory.py000066400000000000000000000627371304022710500207030ustar00rootroot00000000000000# -*- coding: utf-8 -*- # # Yade documentation build configuration file, created by # sphinx-quickstart on Mon Nov 16 21:49:34 2009. # # This file is execfile()d with the current directory set to its containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # relevant posts to sphinx ML # http://groups.google.com/group/sphinx-dev/browse_thread/thread/b4fbc8d31d230fc4 # http://groups.google.com/group/sphinx-dev/browse_thread/thread/118598245d5f479b ##################### ## custom yade roles ##################### ## ## http://docutils.sourceforge.net/docs/howto/rst-roles.html import sys, os, re from docutils import nodes from sphinx import addnodes from sphinx.roles import XRefRole import docutils # # needed for creating hyperlink targets. # it should be cleand up and unified for both LaTeX and HTML via # the pending_xref node which gets resolved to real link target # by sphinx automatically once all docs have been processed. # # xrefs: http://groups.google.com/group/sphinx-dev/browse_thread/thread/d719d19307654548 # # import __builtin__ if 'latex' in sys.argv: __builtin__.writer='latex' elif 'html' in sys.argv: __builtin__.writer='html' elif 'epub' in sys.argv: __builtin__.writer='epub' else: raise RuntimeError("Must have either 'latex' or 'html' on the command line (hack for reference styles)") sys.path.append(os.path.abspath('./..')) def yaderef_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :yref:`` role, by making hyperlink to yade.wrapper.*. It supports :yref:`Link text` syntax, like usual hyperlinking roles." id=rawtext.split(':',2)[2][1:-1] txt=id; explicitText=False m=re.match('(.*)\s*<(.*)>\s*',id) if m: explicitText=True txt,id=m.group(1),m.group(2) id=id.replace('::','.') #node=nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='http://beta.arcig.cz/~eudoxos/yade/doxygen/?search=%s'%id,**options) #node=nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='yade.wrapper.html#yade.wrapper.%s'%id,**options) return [mkYrefNode(id,txt,rawtext,role,explicitText,lineno,options)],[] def yadesrc_role(role,rawtext,lineno,inliner,options={},content=[]): "Handle the :ysrc:`` role, making hyperlink to git repository webpage with that path. Supports :ysrc:`Link text` syntax, like usual hyperlinking roles. If target ends with ``/``, it is assumed to be a directory." id=rawtext.split(':',2)[2][1:-1] txt=id m=re.match('(.*)\s*<(.*)>\s*',id) if m: txt,id=m.group(1),m.group(2) return [nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='https://github.com/yade/trunk/blob/master/%s'%id)],[] ### **options should be passed to nodes.reference as well # map modules to their html (rst) filenames. Used for sub-modules, where e.g. SpherePack is yade._packSphere.SpherePack, but is documented from yade.pack.rst moduleMap={ 'yade._packPredicates':'yade.pack', 'yade._packSpheres':'yade.pack', 'yade._packObb':'yade.pack' } class YadeXRefRole(XRefRole): #def process_link def process_link(self, env, refnode, has_explicit_title, title, target): print 'TARGET:','yade.wrapper.'+target return '[['+title+']]','yade.wrapper.'+target def mkYrefNode(target,text,rawtext,role,explicitText,lineno,options={}): """Create hyperlink to yade target. Targets starting with literal 'yade.' are absolute, but the leading 'yade.' will be stripped from the link text. Absolute tergets are supposed to live in page named yade.[module].html, anchored at #yade.[module2].[rest of target], where [module2] is identical to [module], unless mapped over by moduleMap. Other targets are supposed to live in yade.wrapper (such as c++ classes).""" writer=__builtin__.writer # to make sure not shadowed by a local var import string if target.startswith('yade.'): module='.'.join(target.split('.')[0:2]) module2=(module if module not in moduleMap.keys() else moduleMap[module]) if target==module: target='' # to reference the module itself uri=('%%%s#%s'%(module2,target) if writer=='latex' else '%s.html#%s'%(module2,target)) if not explicitText and module!=module2: text=module2+'.'+'.'.join(target.split('.')[2:]) text=string.replace(text,'yade.','',1) elif target.startswith('external:'): exttarget=target.split(':',1)[1] if not explicitText: text=exttarget target=exttarget if '.' in exttarget else 'module-'+exttarget uri=(('%%external#%s'%target) if writer=='latex' else 'external.html#%s'%target) else: uri=(('%%yade.wrapper#yade.wrapper.%s'%target) if writer=='latex' else 'yade.wrapper.html#yade.wrapper.%s'%target) #print writer,uri return nodes.reference(rawtext,docutils.utils.unescape(text),refuri=uri,**options) #return [refnode],[] def ydefault_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :ydefault:`something` role. fixSignature handles it now in the member signature itself, this merely expands to nothing." return [],[] def yattrtype_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :yattrtype:`something` role. fixSignature handles it now in the member signature itself, this merely expands to nothing." return [],[] # FIXME: should return readable representation of bits of the number (yade.wrapper.AttrFlags enum) def yattrflags_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :yattrflags:`something` role. fixSignature handles it now in the member signature itself." return [],[] from docutils.parsers.rst import roles def yaderef_role_2(type,rawtext,text,lineno,inliner,options={},content=[]): return YadeXRefRole()('yref',rawtext,text,lineno,inliner,options,content) roles.register_canonical_role('yref', yaderef_role) roles.register_canonical_role('ysrc', yadesrc_role) roles.register_canonical_role('ydefault', ydefault_role) roles.register_canonical_role('yattrtype', yattrtype_role) roles.register_canonical_role('yattrflags', yattrflags_role) ## http://sphinx.pocoo.org/config.html#confval-rst_epilog rst_epilog = """ .. |yupdate| replace:: *(auto-updated)* .. |ycomp| replace:: *(auto-computed)* .. |ystatic| replace:: *(static)* """ import collections def customExclude(app, what, name, obj, skip, options): if name=='clone': if 'Serializable.clone' in str(obj): return False return True #escape crash on non iterable __doc__ in some qt object if hasattr(obj,'__doc__') and obj.__doc__ and not isinstance(obj.__doc__, collections.Iterable): return True if hasattr(obj,'__doc__') and obj.__doc__ and ('|ydeprecated|' in obj.__doc__ or '|yhidden|' in obj.__doc__): return True #if re.match(r'\b(__init__|__reduce__|__repr__|__str__)\b',name): return True if name.startswith('_'): if name=='__init__': # skip boost classes with parameterless ctor (arg1=implicit self) if obj.__doc__=="\n__init__( (object)arg1) -> None": return True # skip undocumented ctors if not obj.__doc__: return True # skip default ctor for serializable, taking dict of attrs if obj.__doc__=='\n__init__( (object)arg1) -> None\n\nobject __init__(tuple args, dict kwds)': return True #for i,l in enumerate(obj.__doc__.split('\n')): print name,i,l,'##' return False return True return False def isBoostFunc(what,obj): return what=='function' and obj.__repr__().startswith('.*$',doc1): return None,docc if doc1.endswith(':'): doc1=doc1[:-1] strippedDoc=doc.split('\n')[2:] # check if all lines are padded allLinesHave4LeadingSpaces=True for l in strippedDoc: if l.startswith(' '): continue allLinesHave4LeadingSpaces=False; break # remove the padding if so if allLinesHave4LeadingSpaces: strippedDoc=[l[4:] for l in strippedDoc] for i in range(len(strippedDoc)): # fix signatures inside docstring (one function with multiple signatures) strippedDoc[i],n=re.subn(r'([a-zA-Z_][a-zA-Z0-9_]*\() \(object\)arg1(, |)',r'\1',strippedDoc[i].replace('->','→')) # inspect dosctring after mangling if 'getViscoelasticFromSpheresInteraction' in name and False: print name print strippedDoc print '======================' for l in strippedDoc: print l print '======================' sig=doc1.split('(',1)[1] if removeSelf: # remove up to the first comma; if no comma present, then the method takes no arguments # if [ precedes the comma, add it to the result (ugly!) try: ss=sig.split(',',1) if ss[0].endswith('['): sig='['+ss[1] else: sig=ss[1] except IndexError: # grab the return value try: sig=') -> '+sig.split('->')[-1] #if 'Serializable' in name: print 1000*'#',name except IndexError: sig=')' return '('+sig,strippedDoc def fixSignature(app, what, name, obj, options, signature, return_annotation): #print what,name,obj,signature#,dir(obj) if what=='attribute': doc=unicode(obj.__doc__) ret='' m=re.match('.*:ydefault:`(.*?)`.*',doc) if m: typ='' #try: # clss='.'.join(name.split('.')[:-1]) # instance=eval(clss+'()') # typ='; '+getattr(instance,name.split('.')[-1]).__class__.__name__ # if typ=='; NoneType': typ='' #except TypeError: ##no registered converted # typ='' dfl=m.group(1) m2=re.match(r'\s*\(\s*\(\s*void\s*\)\s*\"(.*)\"\s*,\s*(.*)\s*\)\s*',dfl) if m2: dfl="%s, %s"%(m2.group(2),m2.group(1)) if dfl!='': ret+=' (='+dfl+'%s)'%typ else: ret+=' (=uninitalized%s)'%typ #m=re.match('.*\[(.{,8})\].*',doc) #m=re.match('.*:yunit:`(.?*)`.*',doc) #if m: # units=m.group(1) # print '@@@@@@@@@@@@@@@@@@@@@',name,units # ret+=' ['+units+']' return ret,None elif what=='class': ret=[] if len(obj.__bases__)>0: base=obj.__bases__[0] while base.__module__!='Boost.Python': ret+=[base.__name__] if len(base.__bases__)>0: base=base.__bases__[0] else: break if len(ret): return ' (inherits '+u' → '.join(ret)+')',None else: return None,None elif isBoostFunc(what,obj): sig=boostFuncSignature(name,obj)[0] or ' (wrapped c++ function)' return sig,None elif isBoostMethod(what,obj): sig=boostFuncSignature(name,obj,removeSelf=True)[0] return sig,None #else: print what,name,obj.__repr__() #return None,None from sphinx import addnodes def parse_ystaticattr(env,attr,attrnode): m=re.match(r'([a-zA-Z0-9_]+)\.(.*)\(=(.*)\)',attr) if not m: print 100*'@'+' Static attribute %s not matched'%attr attrnode+=addnodes.desc_name(attr,attr) klass,name,default=m.groups() #attrnode+=addnodes.desc_type('static','static') attrnode+=addnodes.desc_name(name,name) plist=addnodes.desc_parameterlist() if default=='': default='unspecified' plist+=addnodes.desc_parameter('='+default,'='+default) attrnode+=plist attrnode+=addnodes.desc_annotation(' [static]',' [static]') return klass+'.'+name ############################# ## set tab size ################### ## http://groups.google.com/group/sphinx-dev/browse_thread/thread/35b8071ffe9a8feb def setup(app): from sphinx.highlighting import lexers from pygments.lexers.compiled import CppLexer lexers['cpp'] = CppLexer(tabsize=3) lexers['c++'] = CppLexer(tabsize=3) from pygments.lexers.agile import PythonLexer lexers['python'] = PythonLexer(tabsize=3) app.connect('source-read',fixSrc) app.connect('autodoc-skip-member',customExclude) app.connect('autodoc-process-signature',fixSignature) app.connect('autodoc-process-docstring',fixDocstring) app.add_description_unit('ystaticattr',None,objname='static attribute',indextemplate='pair: %s; static method',parse_node=parse_ystaticattr) import sys, os # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. #sys.path.append(os.path.abspath('.')) # -- General configuration ----------------------------------------------------- # Add any Sphinx extension module names here, as strings. They can be extensions # coming with Sphinx (named 'sphinx.ext.*') or your custom ones. # # HACK: change ipython console regexp from ipython_console_highlighting.py import re sys.path.append(os.path.abspath('.')) import yade.config if 1: if yade.runtime.ipython_version<12: import ipython_directive as id else: if 12<=yade.runtime.ipython_version<13: import ipython_directive012 as id elif 13<=yade.runtime.ipython_version<200: import ipython_directive013 as id elif 200<=yade.runtime.ipython_version<500: import ipython_directive200 as id else: import ipython_directive500 as id #The next four lines are for compatibility with IPython 0.13.1 ipython_rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*') ipython_rgxout=re.compile(r'(?:Out| -> )\[(\d+)\]:\s?(.*)\s*') ipython_promptin ='Yade [%d]:' ipython_promptout=' -> [%d]: ' ipython_cont_spaces=' ' #For IPython <=0.12, the following lines are used id.rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*') id.rgxout=re.compile(r'(?:Out| -> )\[(\d+)\]:\s?(.*)\s*') id.rgxcont=re.compile(r'(?: +)\.\.+:\s?(.*)\s*') id.fmtin ='Yade [%d]:' id.fmtout =' -> [%d]: ' # for some reason, out and cont must have the trailing space id.fmtcont=' .\D.: ' id.rc_override=dict(prompt_in1="Yade [\#]:",prompt_in2=" .\D.:",prompt_out=r" -> [\#]: ") if yade.runtime.ipython_version<12: id.reconfig_shell() import ipython_console_highlighting as ich ich.IPythonConsoleLexer.input_prompt = re.compile("(Yade \[[0-9]+\]: )") ich.IPythonConsoleLexer.output_prompt = re.compile("(( -> |Out)|\[[0-9]+\]: )") ich.IPythonConsoleLexer.continue_prompt = re.compile("\s+\.\.\.+:") extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.autosummary', 'sphinx.ext.coverage', 'sphinx.ext.pngmath', 'sphinx.ext.graphviz', 'sphinx.ext.viewcode', 'sphinx.ext.inheritance_diagram', 'matplotlib.sphinxext.plot_directive', 'matplotlib.sphinxext.only_directives', #'matplotlib.sphinxext.mathmpl', 'ipython_console_highlighting', 'youtube', 'sphinx.ext.todo', ] if yade.runtime.ipython_version<12: extensions.append('ipython_directive') else: if 12<=yade.runtime.ipython_version<13: extensions.append('ipython_directive012') elif 13<=yade.runtime.ipython_version<200: extensions.append('ipython_directive013') elif 200<=yade.runtime.ipython_version<500: extensions.append('ipython_directive200') else: extensions.append('ipython_directive500') # the sidebar extension if False: if writer=='html': extensions+=['sphinx.ext.sidebar'] sidebar_all=True sidebar_relling=True #sidebar_abbrev=True sidebar_tocdepth=3 ## http://trac.sagemath.org/sage_trac/attachment/ticket/7549/trac_7549-doc_inheritance_underscore.patch # GraphViz includes dot, neato, twopi, circo, fdp. graphviz_dot = 'dot' inheritance_graph_attrs = { 'rankdir' : 'BT' } inheritance_node_attrs = { 'height' : 0.5, 'fontsize' : 12, 'shape' : 'oval' } inheritance_edge_attrs = {} my_latex_preamble=r''' \usepackage{euler} % must be loaded before fontspec for the whole doc (below); this must be kept for pngmath, however \usepackage{hyperref} \usepackage{amsmath} \usepackage{amsbsy} %\usepackage{mathabx} \usepackage{underscore} \usepackage[all]{xy} % Metadata of the pdf output \hypersetup{pdftitle={DEM formulation}} \hypersetup{pdfauthor={Vaclav Smilauer; Bruno Chareyre}} \hypersetup{pdfkeywords={Discrete element method; micromechanics; granular materials; contact law; hydromechanical coupling; yade; documentation}} % symbols \let\mat\boldsymbol % matrix \let\vec\boldsymbol % vector \let\tens\boldsymbol % tensor \def\normalized#1{\widehat{#1}} \def\locframe#1{\widetilde{#1}} % timestep \def\Dt{\Delta t} \def\Dtcr{\Dt_{\rm cr}} % algorithm complexity \def\bigO#1{\ensuremath{\mathcal{O}(#1)}} % variants for greek symbols \let\epsilon\varepsilon \let\theta\vartheta \let\phi\varphi % shorthands \let\sig\sigma \let\eps\epsilon % variables at different points of time \def\prev#1{#1^-} \def\pprev#1{#1^\ominus} \def\curr#1{#1^{\circ}} \def\nnext#1{#1^\oplus} \def\next#1{#1^+} % shorthands for geometry \def\currn{\curr{\vec{n}}} \def\currC{\curr{\vec{C}}} \def\uT{\vec{u}_T} \def\curruT{\curr{\vec{u}}_T} \def\prevuT{\prev{\vec{u}}_T} \def\currn{\curr{\vec{n}}} \def\prevn{\prev{\vec{n}}} % motion \def\pprevvel{\pprev{\dot{\vec{u}}}} \def\nnextvel{\nnext{\dot{\vec{u}}}} \def\curraccel{\curr{\ddot{\vec{u}}}} \def\prevpos{\prev{\vec{u}}} \def\currpos{\curr{\vec{u}}} \def\nextpos{\next{\vec{u}}} \def\curraaccel{\curr{\dot{\vec{\omega}}}} \def\pprevangvel{\pprev{\vec{\omega}}} \def\nnextangvel{\nnext{\vec{\omega}}} \def\loccurr#1{\curr{\locframe{#1}}} \def\numCPU{n_{\rm cpu}} \DeclareMathOperator{\Align}{Align} \DeclareMathOperator{\sign}{sgn} % sorting algorithms \def\isleq#1{\currelem{#1}\ar@/^/[ll]^{\leq}} \def\isnleq#1{\currelem{#1}\ar@/^/[ll]^{\not\leq}} \def\currelem#1{\fbox{$#1$}} \def\sortSep{||} \def\sortInv{\hbox{\phantom{||}}} \def\sortlines#1{\xymatrix@=3pt{#1}} \def\crossBound{||\mkern-18mu<} ''' pngmath_latex_preamble=r'\usepackage[active]{preview}'+my_latex_preamble pngmath_use_preview=True # Add any paths that contain templates here, relative to this directory. templates_path = ['templates'] # The suffix of source filenames. source_suffix = '.rst' # The encoding of source files. #source_encoding = 'utf-8' # The master toctree document. master_doc = 'index-toctree-theory' # General information about the project. project = u'Yade' copyright = u'2009, Václav Šmilauer' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. version = 'Yade documentation 2nd ed.' # The full version, including alpha/beta/rc tags. release = 'Yade documentation 2nd ed.' # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. #language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: #today = '' # Else, today_fmt is used as the format for a strftime call. #today_fmt = '%B %d, %Y' # List of documents that shouldn't be included in the build. #unused_docs = [] # List of directories, relative to source directory, that shouldn't be searched # for source files. exclude_trees = ['_build','../_build'] # The reST default role (used for this markup: `text`) to use for all documents. #default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. #add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). #add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. #show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. modindex_common_prefix = ['yade.'] # -- Options for HTML output --------------------------------------------------- # The theme to use for HTML and HTML Help pages. Major themes that come with # Sphinx are currently 'default' and 'sphinxdoc'. html_theme = 'default' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. html_theme_options = {'stickysidebar':'true','collapsiblesidebar':'true','rightsidebar':'false'} # Add any paths that contain custom themes here, relative to this directory. #html_theme_path = [] # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". #html_title = None # A shorter title for the navigation bar. Default is the same as html_title. #html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. html_logo = '../fig/yade-logo.png' # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. html_favicon = '../fig/yade-favicon.ico' # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['static-html'] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. #html_last_updated_fmt = '%b %d, %Y' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. html_use_smartypants = True # Custom sidebar templates, maps document names to template names. #html_sidebars = {} html_index='index.html' # Additional templates that should be rendered to pages, maps page names to # template names. html_additional_pages = { 'index':'index.html'} # If false, no module index is generated. #html_use_modindex = True # If false, no index is generated. #html_use_index = True # If true, the index is split into individual pages for each letter. #html_split_index = False # If true, links to the reST sources are added to the pages. #html_show_sourcelink = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. #html_use_opensearch = '' # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml"). #html_file_suffix = '' # Output file base name for HTML help builder. htmlhelp_basename = 'Yadedoc' # -- Options for LaTeX output -------------------------------------------------- my_maketitle=r''' \begin{titlepage} \begin{flushright} \hrule{} % Upper part of the page \begin{flushright} \includegraphics[width=0.15\textwidth]{yade-logo.png}\par \end{flushright} \vspace{20 mm} \text{\sffamily\bfseries\Huge DEM Formulation}\\ \vspace{20 mm} %\vspace{70 mm} \begin{sffamily}\bfseries\Large V\'{a}clav \v{S}milauer, Bruno Chareyre \end{sffamily} \vspace{20 mm} \hrule{} \vfill \textit{\large Yade Documentation 2nd edition, 2015}\\ \textit{based on Yade 1.14.0}\\ \end{flushright} \end{titlepage} \text{\sffamily\bfseries\large Citing this document:}\\ \v{S}milauer V. and Chareyre B. (2015). DEM Formulation. In:\textit{Yade Documentation 2nd ed.} doi:10.5281/zenodo.34044. http://yade-dem.org\\ See also http://yade-dem/doc/citing.html. ''' latex_elements=dict( papersize='a4paper', fontpkg=r''' \usepackage{euler} \usepackage{fontspec,xunicode,xltxtra} %\setmainfont[BoldFont={LMRoman10 Bold}]{CMU Concrete} %% CMU Concrete must be installed by hand as otf ''', utf8extra='', fncychap='', preamble=my_latex_preamble, footer='', inputenc='', fontenc='', maketitle=my_maketitle, ) # The paper size ('letter' or 'a4'). #latex_paper_size = 'letter' # The font size ('10pt', '11pt' or '12pt'). #latex_font_size = '10pt' # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ ('index-toctree-theory', 'YadeTheory.tex', u'DEM Formulation', u'Václav Šmilauer', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. latex_logo = '../fig/yade-logo.png' # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. latex_use_parts = False # Additional stuff for the LaTeX preamble. #latex_preamble = '' # Documents to append as an appendix to all manuals. #latex_appendices = [] # If false, no module index is generated. #latex_use_modindex = True trunk-2017.01a/doc/sphinx/book/fullBibliography.rst.in000066400000000000000000000004221304022710500226250ustar00rootroot00000000000000.. This complete list of references is used for tex build, in which sectionning of the bibliography fails (see ) @bib2rst.bib2rst('../yade-docref.bib')@ @bib2rst.bib2rst('../yade-articles.bib')@ @bib2rst.bib2rst('../yade-theses.bib')@ @bib2rst.bib2rst('../references.bib')@trunk-2017.01a/doc/sphinx/citing.rst000066400000000000000000000063241304022710500172540ustar00rootroot00000000000000.. _citing: ################## Acknowledging Yade ################## In order to let users cite Yade consistently in publications, we provide a list of bibliographic references for the different parts of the documentation, as in the citation model pushed by `CGAL `_. This way of acknowledging Yade is also a way to make developments and documentation of Yade more attractive for researchers, who are evaluated on the basis of citations of their work by others. We therefore kindly ask users to cite Yade as accurately as possible in their papers. A more detailed discussion of the citation model and its application to Yade can be found `here `_. If new developments are presented and explained in self-contained papers (at the end of a PhD, typically), we will be glad to include them in the documentation and to reference them in the list below. Any other substantial improvement is welcome and can be discussed in the `yade-dev `_ mailing list. Citing the Yade Project as a whole (the lazy citation method) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ If it is not possible to choose the right chapter (but please try), you may cite the documentation [yade:doc]_ as a whole: V. Šmilauer et al. (2015), Yade Documentation 2nd ed. The Yade Project. DOI 10.5281/zenodo.34073 (http://yade-dem.org/doc/) Citing chapters of Yade Documentation ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The second edition of Yade documentation is seen as a collection with the three volumes (or "chapters") listed below, and edited by V. Šmilauer, B. Chareyre, and A. Gladky. Please cite the chapter that is the most relevant in your case. For instance, a paper using one of the documented contact laws will cite the reference documentation [yade:reference2]_; if programing concepts are discussed, Yade's manual [yade:manual2]_ will be cited; the theoretical background [yade:background2]_ can be used as the refence for contact detection, time-step determination, or periodic boundary conditions. * The reference documentation includes details on equations and algorithms found at the highest levels of Yade (contact laws, boundary conditions controllers, pre- and post-processing modules,...) `(pdf version) `__: V. Šmilauer et al. (2015), Reference manual. In Yade Documentation 2nd ed. The Yade Project , DOI 10.5281/zenodo.34045 (http://yade-dem.org/doc/) * Software design, user's and programmer's manuals are in `(pdf version) `__: V. Šmilauer et al. (2015), Using and programming. In Yade Documentation 2nd ed. The Yade Project , DOI 10.5281/zenodo.34043 (http://yade-dem.org/doc/) * Fundamentals of the DEM as implemented in Yade are explained in `(pdf version) `__: V. Šmilauer et al. (2015), Dem formulation. In Yade Documentation 2nd ed. The Yade Project , DOI 10.5281/zenodo.34044 (http://yade-dem.org/doc/) Plain bibtex items can be `found here `_. trunk-2017.01a/doc/sphinx/conf.py000066400000000000000000000711331304022710500165440ustar00rootroot00000000000000# -*- coding: utf-8 -*- # # Yade documentation build configuration file, created by # sphinx-quickstart on Mon Nov 16 21:49:34 2009. # # This file is execfile()d with the current directory set to its containing dir. # # Note that not all possible configuration values are present in this # autogenerated file. # # All configuration values have a default; values that are commented out # serve to show the default. # relevant posts to sphinx ML # http://groups.google.com/group/sphinx-dev/browse_thread/thread/b4fbc8d31d230fc4 # http://groups.google.com/group/sphinx-dev/browse_thread/thread/118598245d5f479b ##################### ## custom yade roles ##################### ## ## http://docutils.sourceforge.net/docs/howto/rst-roles.html import sys, os, re from docutils import nodes from sphinx import addnodes from sphinx.roles import XRefRole import docutils # # needed for creating hyperlink targets. # it should be cleand up and unified for both LaTeX and HTML via # the pending_xref node which gets resolved to real link target # by sphinx automatically once all docs have been processed. # # xrefs: http://groups.google.com/group/sphinx-dev/browse_thread/thread/d719d19307654548 # # import __builtin__ if 'latex' in sys.argv: __builtin__.writer='latex' elif 'html' in sys.argv: __builtin__.writer='html' elif 'epub' in sys.argv: __builtin__.writer='epub' else: raise RuntimeError("Must have either 'latex' or 'html' on the command line (hack for reference styles)") def yaderef_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :yref:`` role, by making hyperlink to yade.wrapper.*. It supports :yref:`Link text` syntax, like usual hyperlinking roles." id=rawtext.split(':',2)[2][1:-1] txt=id; explicitText=False m=re.match('(.*)\s*<(.*)>\s*',id) if m: explicitText=True txt,id=m.group(1),m.group(2) id=id.replace('::','.') #node=nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='http://beta.arcig.cz/~eudoxos/yade/doxygen/?search=%s'%id,**options) #node=nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='yade.wrapper.html#yade.wrapper.%s'%id,**options) return [mkYrefNode(id,txt,rawtext,role,explicitText,lineno,options)],[] def yadesrc_role(role,rawtext,lineno,inliner,options={},content=[]): "Handle the :ysrc:`` role, making hyperlink to git repository webpage with that path. Supports :ysrc:`Link text` syntax, like usual hyperlinking roles. If target ends with ``/``, it is assumed to be a directory." id=rawtext.split(':',2)[2][1:-1] txt=id m=re.match('(.*)\s*<(.*)>\s*',id) if m: txt,id=m.group(1),m.group(2) return [nodes.reference(rawtext,docutils.utils.unescape(txt),refuri='https://github.com/yade/trunk/blob/master/%s'%id)],[] ### **options should be passed to nodes.reference as well # map modules to their html (rst) filenames. Used for sub-modules, where e.g. SpherePack is yade._packSphere.SpherePack, but is documented from yade.pack.rst moduleMap={ 'yade._packPredicates':'yade.pack', 'yade._packSpheres':'yade.pack', 'yade._packObb':'yade.pack' } class YadeXRefRole(XRefRole): #def process_link def process_link(self, env, refnode, has_explicit_title, title, target): print 'TARGET:','yade.wrapper.'+target return '[['+title+']]','yade.wrapper.'+target def mkYrefNode(target,text,rawtext,role,explicitText,lineno,options={}): """Create hyperlink to yade target. Targets starting with literal 'yade.' are absolute, but the leading 'yade.' will be stripped from the link text. Absolute tergets are supposed to live in page named yade.[module].html, anchored at #yade.[module2].[rest of target], where [module2] is identical to [module], unless mapped over by moduleMap. Other targets are supposed to live in yade.wrapper (such as c++ classes).""" writer=__builtin__.writer # to make sure not shadowed by a local var import string if target.startswith('yade.'): module='.'.join(target.split('.')[0:2]) module2=(module if module not in moduleMap.keys() else moduleMap[module]) if target==module: target='' # to reference the module itself uri=('%%%s#%s'%(module2,target) if writer=='latex' else '%s.html#%s'%(module2,target)) if not explicitText and module!=module2: text=module2+'.'+'.'.join(target.split('.')[2:]) text=string.replace(text,'yade.','',1) elif target.startswith('external:'): exttarget=target.split(':',1)[1] if not explicitText: text=exttarget target=exttarget if '.' in exttarget else 'module-'+exttarget uri=(('%%external#%s'%target) if writer=='latex' else 'external.html#%s'%target) else: uri=(('%%yade.wrapper#yade.wrapper.%s'%target) if writer=='latex' else 'yade.wrapper.html#yade.wrapper.%s'%target) #print writer,uri return nodes.reference(rawtext,docutils.utils.unescape(text),refuri=uri,**options) #return [refnode],[] def ydefault_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :ydefault:`something` role. fixSignature handles it now in the member signature itself, this merely expands to nothing." return [],[] def yattrtype_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :yattrtype:`something` role. fixSignature handles it now in the member signature itself, this merely expands to nothing." return [],[] # FIXME: should return readable representation of bits of the number (yade.wrapper.AttrFlags enum) def yattrflags_role(role,rawtext,text,lineno,inliner,options={},content=[]): "Handle the :yattrflags:`something` role. fixSignature handles it now in the member signature itself." return [],[] from docutils.parsers.rst import roles def yaderef_role_2(type,rawtext,text,lineno,inliner,options={},content=[]): return YadeXRefRole()('yref',rawtext,text,lineno,inliner,options,content) roles.register_canonical_role('yref', yaderef_role) roles.register_canonical_role('ysrc', yadesrc_role) roles.register_canonical_role('ydefault', ydefault_role) roles.register_canonical_role('yattrtype', yattrtype_role) roles.register_canonical_role('yattrflags', yattrflags_role) ## http://sphinx.pocoo.org/config.html#confval-rst_epilog rst_epilog = """ .. |yupdate| replace:: *(auto-updated)* .. |ycomp| replace:: *(auto-computed)* .. |ystatic| replace:: *(static)* """ import collections def customExclude(app, what, name, obj, skip, options): if name=='clone': if 'Serializable.clone' in str(obj): return False return True #escape crash on non iterable __doc__ in some qt object if hasattr(obj,'__doc__') and obj.__doc__ and not isinstance(obj.__doc__, collections.Iterable): return True if hasattr(obj,'__doc__') and obj.__doc__ and ('|ydeprecated|' in obj.__doc__ or '|yhidden|' in obj.__doc__): return True #if re.match(r'\b(__init__|__reduce__|__repr__|__str__)\b',name): return True if name.startswith('_'): if name=='__init__': # skip boost classes with parameterless ctor (arg1=implicit self) if obj.__doc__=="\n__init__( (object)arg1) -> None": return True # skip undocumented ctors if not obj.__doc__: return True # skip default ctor for serializable, taking dict of attrs if obj.__doc__=='\n__init__( (object)arg1) -> None\n\nobject __init__(tuple args, dict kwds)': return True #for i,l in enumerate(obj.__doc__.split('\n')): print name,i,l,'##' return False return True return False def isBoostFunc(what,obj): return what=='function' and obj.__repr__().startswith('.*$',doc1): return None,docc if doc1.endswith(':'): doc1=doc1[:-1] strippedDoc=doc.split('\n')[2:] # check if all lines are padded allLinesHave4LeadingSpaces=True for l in strippedDoc: if l.startswith(' '): continue allLinesHave4LeadingSpaces=False; break # remove the padding if so if allLinesHave4LeadingSpaces: strippedDoc=[l[4:] for l in strippedDoc] for i in range(len(strippedDoc)): # fix signatures inside docstring (one function with multiple signatures) strippedDoc[i],n=re.subn(r'([a-zA-Z_][a-zA-Z0-9_]*\() \(object\)arg1(, |)',r'\1',strippedDoc[i].replace('->','→')) # inspect dosctring after mangling if 'getViscoelasticFromSpheresInteraction' in name and False: print name print strippedDoc print '======================' for l in strippedDoc: print l print '======================' sig=doc1.split('(',1)[1] if removeSelf: # remove up to the first comma; if no comma present, then the method takes no arguments # if [ precedes the comma, add it to the result (ugly!) try: ss=sig.split(',',1) if ss[0].endswith('['): sig='['+ss[1] else: sig=ss[1] except IndexError: # grab the return value try: sig=') -> '+sig.split('->')[-1] #if 'Serializable' in name: print 1000*'#',name except IndexError: sig=')' return '('+sig,strippedDoc def fixSignature(app, what, name, obj, options, signature, return_annotation): #print what,name,obj,signature#,dir(obj) if what=='attribute': doc=unicode(obj.__doc__) ret='' m=re.match('.*:ydefault:`(.*?)`.*',doc) if m: typ='' #try: # clss='.'.join(name.split('.')[:-1]) # instance=eval(clss+'()') # typ='; '+getattr(instance,name.split('.')[-1]).__class__.__name__ # if typ=='; NoneType': typ='' #except TypeError: ##no registered converted # typ='' dfl=m.group(1) m2=re.match(r'\s*\(\s*\(\s*void\s*\)\s*\"(.*)\"\s*,\s*(.*)\s*\)\s*',dfl) if m2: dfl="%s, %s"%(m2.group(2),m2.group(1)) if dfl!='': ret+=' (='+dfl+'%s)'%typ else: ret+=' (=uninitalized%s)'%typ #m=re.match('.*\[(.{,8})\].*',doc) #m=re.match('.*:yunit:`(.?*)`.*',doc) #if m: # units=m.group(1) # print '@@@@@@@@@@@@@@@@@@@@@',name,units # ret+=' ['+units+']' return ret,None elif what=='class': ret=[] if len(obj.__bases__)>0: base=obj.__bases__[0] while base.__module__!='Boost.Python': ret+=[base.__name__] if len(base.__bases__)>0: base=base.__bases__[0] else: break if len(ret): return ' (inherits '+u' → '.join(ret)+')',None else: return None,None elif isBoostFunc(what,obj): sig=boostFuncSignature(name,obj)[0] or ' (wrapped c++ function)' return sig,None elif isBoostMethod(what,obj): sig=boostFuncSignature(name,obj,removeSelf=True)[0] return sig,None #else: print what,name,obj.__repr__() #return None,None from sphinx import addnodes def parse_ystaticattr(env,attr,attrnode): m=re.match(r'([a-zA-Z0-9_]+)\.(.*)\(=(.*)\)',attr) if not m: print 100*'@'+' Static attribute %s not matched'%attr attrnode+=addnodes.desc_name(attr,attr) klass,name,default=m.groups() #attrnode+=addnodes.desc_type('static','static') attrnode+=addnodes.desc_name(name,name) plist=addnodes.desc_parameterlist() if default=='': default='unspecified' plist+=addnodes.desc_parameter('='+default,'='+default) attrnode+=plist attrnode+=addnodes.desc_annotation(' [static]',' [static]') return klass+'.'+name ############################# ## set tab size ################### ## http://groups.google.com/group/sphinx-dev/browse_thread/thread/35b8071ffe9a8feb def setup(app): from sphinx.highlighting import lexers from pygments.lexers.compiled import CppLexer lexers['cpp'] = CppLexer(tabsize=3) lexers['c++'] = CppLexer(tabsize=3) from pygments.lexers.agile import PythonLexer lexers['python'] = PythonLexer(tabsize=3) app.connect('source-read',fixSrc) app.connect('autodoc-skip-member',customExclude) app.connect('autodoc-process-signature',fixSignature) app.connect('autodoc-process-docstring',fixDocstring) app.add_description_unit('ystaticattr',None,objname='static attribute',indextemplate='pair: %s; static method',parse_node=parse_ystaticattr) import sys, os # If extensions (or modules to document with autodoc) are in another directory, # add these directories to sys.path here. If the directory is relative to the # documentation root, use os.path.abspath to make it absolute, like shown here. #sys.path.append(os.path.abspath('.')) # -- General configuration ----------------------------------------------------- # Add any Sphinx extension module names here, as strings. They can be extensions # coming with Sphinx (named 'sphinx.ext.*') or your custom ones. # # HACK: change ipython console regexp from ipython_console_highlighting.py import re sys.path.append(os.path.abspath('.')) import yade.config if 1: if yade.runtime.ipython_version<12: import ipython_directive as id else: if 12<=yade.runtime.ipython_version<13: import ipython_directive012 as id elif 13<=yade.runtime.ipython_version<200: import ipython_directive013 as id elif 200<=yade.runtime.ipython_version<500: import ipython_directive200 as id else: import ipython_directive500 as id #The next four lines are for compatibility with IPython 0.13.1 ipython_rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*') ipython_rgxout=re.compile(r'(?:Out| -> )\[(\d+)\]:\s?(.*)\s*') ipython_promptin ='Yade [%d]:' ipython_promptout=' -> [%d]: ' ipython_cont_spaces=' ' #For IPython <=0.12, the following lines are used id.rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*') id.rgxout=re.compile(r'(?:Out| -> )\[(\d+)\]:\s?(.*)\s*') id.rgxcont=re.compile(r'(?: +)\.\.+:\s?(.*)\s*') id.fmtin ='Yade [%d]:' id.fmtout =' -> [%d]: ' # for some reason, out and cont must have the trailing space id.fmtcont=' .\D.: ' id.rc_override=dict(prompt_in1="Yade [\#]:",prompt_in2=" .\D.:",prompt_out=r" -> [\#]: ") if yade.runtime.ipython_version<12: id.reconfig_shell() import ipython_console_highlighting as ich ich.IPythonConsoleLexer.input_prompt = re.compile("(Yade \[[0-9]+\]: )") ich.IPythonConsoleLexer.output_prompt = re.compile("(( -> |Out)|\[[0-9]+\]: )") ich.IPythonConsoleLexer.continue_prompt = re.compile("\s+\.\.\.+:") extensions = [ 'sphinx.ext.autodoc', 'sphinx.ext.autosummary', 'sphinx.ext.coverage', 'sphinx.ext.pngmath', 'sphinx.ext.graphviz', 'sphinx.ext.viewcode', 'sphinx.ext.inheritance_diagram', 'matplotlib.sphinxext.plot_directive', 'matplotlib.sphinxext.only_directives', #'matplotlib.sphinxext.mathmpl', 'ipython_console_highlighting', 'youtube', 'sphinx.ext.todo', ] if yade.runtime.ipython_version<12: extensions.append('ipython_directive') else: if 12<=yade.runtime.ipython_version<13: extensions.append('ipython_directive012') elif 13<=yade.runtime.ipython_version<200: extensions.append('ipython_directive013') elif 200<=yade.runtime.ipython_version<500: extensions.append('ipython_directive200') else: extensions.append('ipython_directive500') # the sidebar extension if False: if writer=='html': extensions+=['sphinx.ext.sidebar'] sidebar_all=True sidebar_relling=True #sidebar_abbrev=True sidebar_tocdepth=3 ## http://trac.sagemath.org/sage_trac/attachment/ticket/7549/trac_7549-doc_inheritance_underscore.patch # GraphViz includes dot, neato, twopi, circo, fdp. graphviz_dot = 'dot' inheritance_graph_attrs = { 'rankdir' : 'BT' } inheritance_node_attrs = { 'height' : 0.5, 'fontsize' : 12, 'shape' : 'oval' } inheritance_edge_attrs = {} my_latex_preamble=r''' \usepackage{euler} % must be loaded before fontspec for the whole doc (below); this must be kept for pngmath, however \usepackage{hyperref} \usepackage{amsmath} \usepackage{amsbsy} %\usepackage{mathabx} \usepackage{underscore} \usepackage[all]{xy} % Metadata of the pdf output \hypersetup{pdftitle={Yade Documentation}} \hypersetup{pdfauthor={Smilauer, V., et al.}} \hypersetup{pdfkeywords={Discrete element method, granular materials, contact law, hydromechanical coupling}} % symbols \let\mat\boldsymbol % matrix \let\vec\boldsymbol % vector \let\tens\boldsymbol % tensor \def\normalized#1{\widehat{#1}} \def\locframe#1{\widetilde{#1}} % timestep \def\Dt{\Delta t} \def\Dtcr{\Dt_{\rm cr}} % algorithm complexity \def\bigO#1{\ensuremath{\mathcal{O}(#1)}} % variants for greek symbols \let\epsilon\varepsilon \let\theta\vartheta \let\phi\varphi % shorthands \let\sig\sigma \let\eps\epsilon % variables at different points of time \def\prev#1{#1^-} \def\pprev#1{#1^\ominus} \def\curr#1{#1^{\circ}} \def\nnext#1{#1^\oplus} \def\next#1{#1^+} % shorthands for geometry \def\currn{\curr{\vec{n}}} \def\currC{\curr{\vec{C}}} \def\uT{\vec{u}_T} \def\curruT{\curr{\vec{u}}_T} \def\prevuT{\prev{\vec{u}}_T} \def\currn{\curr{\vec{n}}} \def\prevn{\prev{\vec{n}}} % motion \def\pprevvel{\pprev{\dot{\vec{u}}}} \def\nnextvel{\nnext{\dot{\vec{u}}}} \def\curraccel{\curr{\ddot{\vec{u}}}} \def\prevpos{\prev{\vec{u}}} \def\currpos{\curr{\vec{u}}} \def\nextpos{\next{\vec{u}}} \def\curraaccel{\curr{\dot{\vec{\omega}}}} \def\pprevangvel{\pprev{\vec{\omega}}} \def\nnextangvel{\nnext{\vec{\omega}}} \def\loccurr#1{\curr{\locframe{#1}}} \def\numCPU{n_{\rm cpu}} \DeclareMathOperator{\Align}{Align} \DeclareMathOperator{\sign}{sgn} % sorting algorithms \def\isleq#1{\currelem{#1}\ar@/^/[ll]^{\leq}} \def\isnleq#1{\currelem{#1}\ar@/^/[ll]^{\not\leq}} \def\currelem#1{\fbox{$#1$}} \def\sortSep{||} \def\sortInv{\hbox{\phantom{||}}} \def\sortlines#1{\xymatrix@=3pt{#1}} \def\crossBound{||\mkern-18mu<} ''' pngmath_latex_preamble=r'\usepackage[active]{preview}'+my_latex_preamble pngmath_use_preview=True # Add any paths that contain templates here, relative to this directory. templates_path = ['templates'] # The suffix of source filenames. source_suffix = '.rst' # The encoding of source files. #source_encoding = 'utf-8' # The master toctree document. master_doc = 'index-toctree' # General information about the project. project = u'Yade' copyright = u'2009, Václav Šmilauer' # The version info for the project you're documenting, acts as replacement for # |version| and |release|, also used in various other places throughout the # built documents. # # The short X.Y version. version = yade.config.version # The full version, including alpha/beta/rc tags. release = yade.config.revision # The language for content autogenerated by Sphinx. Refer to documentation # for a list of supported languages. #language = None # There are two options for replacing |today|: either, you set today to some # non-false value, then it is used: #today = '' # Else, today_fmt is used as the format for a strftime call. #today_fmt = '%B %d, %Y' # List of documents that shouldn't be included in the build. #unused_docs = [] # List of directories, relative to source directory, that shouldn't be searched # for source files. exclude_trees = ['_build'] # The reST default role (used for this markup: `text`) to use for all documents. #default_role = None # If true, '()' will be appended to :func: etc. cross-reference text. #add_function_parentheses = True # If true, the current module name will be prepended to all description # unit titles (such as .. function::). #add_module_names = True # If true, sectionauthor and moduleauthor directives will be shown in the # output. They are ignored by default. #show_authors = False # The name of the Pygments (syntax highlighting) style to use. pygments_style = 'sphinx' # A list of ignored prefixes for module index sorting. modindex_common_prefix = ['yade.'] # -- Options for HTML output --------------------------------------------------- # The theme to use for HTML and HTML Help pages. Major themes that come with # Sphinx are currently 'default' and 'sphinxdoc'. html_theme = 'default' # Theme options are theme-specific and customize the look and feel of a theme # further. For a list of options available for each theme, see the # documentation. html_theme_options = {'stickysidebar':'true','collapsiblesidebar':'true','rightsidebar':'false'} # Add any paths that contain custom themes here, relative to this directory. #html_theme_path = [] # The name for this set of Sphinx documents. If None, it defaults to # " v documentation". #html_title = None # A shorter title for the navigation bar. Default is the same as html_title. #html_short_title = None # The name of an image file (relative to this directory) to place at the top # of the sidebar. html_logo = 'fig/yade-logo.png' # The name of an image file (within the static path) to use as favicon of the # docs. This file should be a Windows icon file (.ico) being 16x16 or 32x32 # pixels large. html_favicon = 'fig/yade-favicon.ico' # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['static-html'] # If not '', a 'Last updated on:' timestamp is inserted at every page bottom, # using the given strftime format. #html_last_updated_fmt = '%b %d, %Y' # If true, SmartyPants will be used to convert quotes and dashes to # typographically correct entities. html_use_smartypants = True # Custom sidebar templates, maps document names to template names. #html_sidebars = {} html_index='index.html' # Additional templates that should be rendered to pages, maps page names to # template names. html_additional_pages = { 'index':'index.html'} # If false, no module index is generated. #html_use_modindex = True # If false, no index is generated. #html_use_index = True # If true, the index is split into individual pages for each letter. #html_split_index = False # If true, links to the reST sources are added to the pages. #html_show_sourcelink = True # If true, an OpenSearch description file will be output, and all pages will # contain a tag referring to it. The value of this option must be the # base URL from which the finished HTML is served. #html_use_opensearch = '' # If nonempty, this is the file name suffix for HTML files (e.g. ".xhtml"). #html_file_suffix = '' # Output file base name for HTML help builder. htmlhelp_basename = 'Yadedoc' # -- Options for LaTeX output -------------------------------------------------- my_maketitle=r''' \begin{titlepage} \begin{flushright} \hrule{} % Upper part of the page \begin{flushright} \includegraphics[width=0.15\textwidth]{yade-logo.png}\par \end{flushright} \vspace{20 mm} \text{\sffamily\bfseries\Huge Yade Documentation}\\ \vspace{5 mm} \vspace{70 mm} \begin{sffamily}\bfseries\Large V\'{a}clav \v{S}milauer, Emanuele Catalano, Bruno Chareyre, Sergei Dorofeenko, J\'er\^ome Duriez, Nolan Dyck, Jan Eli\'{a}\v{s}, Burak Er, Alexander Eulitz, Anton Gladky, Ning Guo, Christian Jakob, Fran\c{c}ois Kneib, Janek Kozicki, Donia Marzougui, Rapha\"el Maurin, Chiara Modenese, Luc Scholt\`{e}s, Luc Sibille, Jan Str\'{a}nsk\'{y}, Thomas Sweijen, Klaus Thoeni, Chao Yuan \end{sffamily} \vspace{20 mm} \hrule{} \vfill % Bottom of the page \textit{\Large 2nd Edition, after Release '''\ +yade.config.revision\ +r''', \today} \end{flushright} \end{titlepage} \text{\sffamily\bfseries\large Authors} %\begin{multicols}{2} %%Compile error \begin{itemize} \item \text{\sffamily\bfseries\normalsize V\'{a}clav \v{S}milauer} \text{\sffamily\small Freelance consultant (http://woodem.eu)} \item \text{\sffamily\bfseries\normalsize Emanuele Catalano} \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR} \item \text{\sffamily\bfseries\normalsize Bruno Chareyre} \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR} \item \text{\sffamily\bfseries\normalsize Sergei Dorofeenko} \text{\sffamily\small IPCP RAS, Chernogolovka} \item \text{\sffamily\bfseries\normalsize J\'er\^ome Duriez} \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR} \item \text{\sffamily\bfseries\normalsize Nolan Dyck} \text{\sffamily\small Univ. of Western Ontario} \item \text{\sffamily\bfseries\normalsize Jan Eliáš} \text{\sffamily\small Brno University of Technology} \item \text{\sffamily\bfseries\normalsize Burak Er} \text{\sffamily\small Bursa Technical University} \item \text{\sffamily\bfseries\normalsize Alexander Eulitz} \text{\sffamily\small TU Berlin / Institute for Machine Tools}\\ \text{\sffamily\small and Factory Management} \item \text{\sffamily\bfseries\normalsize Anton Gladky} \text{\sffamily\small TU Bergakademie Freiberg} \item \text{\sffamily\bfseries\normalsize Ning Guo} \text{\sffamily\small Hong Kong Univ. of Science and Tech.} \item \text{\sffamily\bfseries\normalsize Christian Jakob} \text{\sffamily\small TU Bergakademie Freiberg} \item \text{\sffamily\bfseries\normalsize François Kneib} \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR / Irstea Grenoble} \item \text{\sffamily\bfseries\normalsize Janek Kozicki} \text{\sffamily\small Gdansk University of Technology} \item \text{\sffamily\bfseries\normalsize Donia Marzougui} \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR} \item \text{\sffamily\bfseries\normalsize Raphaël Maurin} \text{\sffamily\small Irstea Grenoble} \item \text{\sffamily\bfseries\normalsize Chiara Modenese} \text{\sffamily\small University of Oxford} \item \text{\sffamily\bfseries\normalsize Luc Scholt\`{e}s} \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR} \item \text{\sffamily\bfseries\normalsize Luc Sibille} \text{\sffamily\small University of Nantes, lab. GeM} \item \text{\sffamily\bfseries\normalsize Jan Str\'{a}nsk\'{y}} \text{\sffamily\small CVUT Prague} \item \text{\sffamily\bfseries\normalsize Thomas Sweijen} \text{\sffamily\small Utrecht University} \item \text{\sffamily\bfseries\normalsize Klaus Thoeni} \text{\sffamily\small The University of Newcastle (Australia)} \item \text{\sffamily\bfseries\normalsize Chao Yuan} \text{\sffamily\small Grenoble INP, UJF, CNRS, lab. 3SR} \end{itemize} %\end{multicols} \text{\sffamily\bfseries\large Citing this document}\\ In order to let users cite Yade consistently in publications, we provide a list of bibliographic references for the different parts of the documentation. We therefore kindly ask users to cite Yade as accurately as possible in their papers, as explained at http://yade-dem/doc/citing.html. ''' latex_elements=dict( papersize='a4paper', fontpkg=r''' \usepackage{euler} \usepackage{fontspec,xunicode,xltxtra} %\setmainfont[BoldFont={LMRoman10 Bold}]{CMU Concrete} %% CMU Concrete must be installed by hand as otf ''', utf8extra='', fncychap='', preamble=my_latex_preamble, footer='', inputenc='', fontenc='', maketitle=my_maketitle, ) # The paper size ('letter' or 'a4'). #latex_paper_size = 'letter' # The font size ('10pt', '11pt' or '12pt'). #latex_font_size = '10pt' # Grouping the document tree into LaTeX files. List of tuples # (source start file, target name, title, author, documentclass [howto/manual]). latex_documents = [ ('index-toctree', 'Yade.tex', u'Yade Documentation', u'Václav Šmilauer', 'manual'), ('index-toctree_manuals', 'YadeManuals.tex', u'Yade Tutorial and Manuals', u'Václav Šmilauer', 'manual'), ] # The name of an image file (relative to this directory) to place at the top of # the title page. latex_logo = 'fig/yade-logo.png' # For "manual" documents, if this is true, then toplevel headings are parts, # not chapters. #latex_use_parts = False # Additional stuff for the LaTeX preamble. #latex_preamble = '' # Documents to append as an appendix to all manuals. #latex_appendices = [] # If false, no module index is generated. #latex_use_modindex = True trunk-2017.01a/doc/sphinx/consulting.rst000066400000000000000000000010431304022710500201550ustar00rootroot00000000000000.. _consulting: ######################## Support and consulting ######################## We can provide technical support and training sessions on DEM modeling for researchers and engineers, as well as consulting services for specific problems. Feel free to contact us by email at consult|A|yade-dem.org for any inquiry on such aspects. Please use this contact for discussing paid support and/or consulting, exclusively. 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They are given roughly in the order as they appear in simulation; first, two particles might establish a new interaction, which consists in #. detecting collision between particles; #. creating new interaction and determining its properties (such as stiffness); they are either precomputed or derived from properties of both particles; Then, for already existing interactions, the following is performed: #. strain evaluation; #. stress computation based on strains; #. force application to particles in interaction. This simplified description serves only to give meaning to the ordering of sections within this chapter. A more detailed description of this *simulation loop* is given later. In this chapter we refer to kinematic variables of the contacts as \`\`strains``, although at this scale it is also common to speak of \`\`displacements``. Which semantic is more appropriate depends on the conceptual model one is starting from, and therefore it cannot be decided independently of specific problems. The reader familiar with displacements can mentaly replace normal strain and shear strain by normal displacement and shear displacement, respectively, without altering the meaning of what follows. Collision detection ===================== Generalities ------------- Exact computation of collision configuration between two particles can be relatively expensive (for instance between :yref:`Sphere` and :yref:`Facet`). Taking a general pair of bodies $i$ and $j$ and their \`\`exact`` (In the sense of precision admissible by numerical implementation.) spatial predicates (called :yref:`Shape` in Yade) represented by point sets $P_i$, $P_j$ the detection generally proceeds in 2 passes: #. fast collision detection using approximate predicate $\tilde P_i$ and $\tilde P_j$; they are pre-constructed in such a way as to abstract away individual features of $P_i$ and $P_j$ and satisfy the condition .. math:: \forall {\bf x}\in R^3: x\in P_i\Rightarrow x\in \tilde P_i :label: eq-bounding-predicate (likewise for $P_j$). The approximate predicate is called \`\`bounding volume'' (:yref:`Bound` in Yade) since it bounds any particle's volume from outside (by virtue of the implication). It follows that $(P_i \cap P_j)\neq\emptyset \Rightarrow (\tilde P_i \cap \tilde P_j)\neq\emptyset$ and, by applying *modus tollens*, .. math:: \bigl(\tilde P_i \cap \tilde P_j\bigr)=\emptyset\Rightarrow\bigl( P_i \cap P_j \bigr)=\emptyset :label: eq-collide-exclude which is a candidate exclusion rule in the proper sense. #. By filtering away impossible collisions in :eq:`eq-collide-exclude`, a more expensive, exact collision detection algorithms can be run on possible interactions, filtering out remaining spurious couples $(\tilde P_i \cap \tilde P_j)\neq\emptyset \wedge \bigl(P_i \cap P_j\bigr)=\emptyset$. These algorithms operate on $P_i$ and $P_j$ and have to be able to handle all possible combinations of shape types. It is only the first step we are concerned with here. Algorithms ----------- Collision evaluation algorithms have been the subject of extensive research in fields such as robotics, computer graphics and simulations. They can be roughly divided in two groups: Hierarchical algorithms which recursively subdivide space and restrict the number of approximate checks in the first pass, knowing that lower-level bounding volumes can intersect only if they are part of the same higher-level bounding volume. Hierarchy elements are bounding volumes of different kinds: octrees [Jung1997]_, bounding spheres [Hubbard1996]_, k-DOP's [Klosowski1998]_. Flat algorithms work directly with bounding volumes without grouping them in hierarchies first; let us only mention two kinds commonly used in particle simulations: Sweep and prune algorithm operates on axis-aligned bounding boxes, which overlap if and only if they overlap along all axes. These algorithms have roughly $\bigO{n\log n}$ complexity, where $n$ is number of particles as long as they exploit :ref:`temporal coherence ` of the simulation. Grid algorithms represent continuous $R^3$ space by a finite set of regularly spaced points, leading to very fast neighbor search; they can reach the $\bigO{n}$ complexity [Munjiza1998]_ and recent research suggests ways to overcome one of the major drawbacks of this method, which is the necessity to adjust grid cell size to the largest particle in the simulation ([Munjiza2006]_, the \`\`multistep'' extension). .. _sect-temp-coherence: Temporal coherence expresses the fact that motion of particles in simulation is not arbitrary but governed by physical laws. This knowledge can be exploited to optimize performance. Numerical stability of integrating motion equations dictates an upper limit on $\Delta t$ (sect. :ref:`sect-formulation-dt`) and, by consequence, on displacement of particles during one step. This consideration is taken into account in [Munjiza2006]_, implying that any particle may not move further than to a neighboring grid cell during one step allowing the $\bigO{n}$ complexity; it is also explored in the periodic variant of the sweep and prune algorithm described below. On a finer level, it is common to enlarge $\tilde P_i$ predicates in such a way that they satisfy the :eq:`eq-bounding-predicate` condition during *several* timesteps; the first collision detection pass might then be run with stride, speeding up the simulation considerably. The original publication of this optimization by Verlet [Verlet1967]_ used enlarged list of neighbors, giving this technique the name *Verlet list*. In general cases, however, where neighbor lists are not necessarily used, the term *Verlet distance* is employed. .. _sect-sweep-and-prune: Sweep and prune ---------------- Let us describe in detail the sweep and prune algorithm used for collision detection in Yade (class :yref:`InsertionSortCollider`). Axis-aligned bounding boxes (:yref:`Aabb`) are used as $\tilde P_i$; each :yref:`Aabb` is given by lower and upper corner $\in R^3$ (in the following, $\tilde P_i^{x0}$, $\tilde P_i^{x1}$ are minimum/maximum coordinates of $\tilde P_i$ along the $x$-axis and so on). Construction of :yref:`Aabb` from various particle :yref:`Shape`'s (such as :yref:`Sphere`, :yref:`Facet`, :yref:`Wall`) is straightforward, handled by appropriate classes deriving form :yref:`BoundFunctor` (:yref:`Bo1_Sphere_Aabb`, :yref:`Bo1_Facet_Aabb`, …). Presence of overlap of two :yref:`Aabb`'s can be determined from conjunction of separate overlaps of intervals along each axis (`fig-sweep-and-prune`_): .. math:: \left(\tilde P_i \cap \tilde P_j\right)\neq\emptyset \Leftrightarrow \bigwedge_{w\in\{x,y,z\}}\left[\left(\left(\tilde P_i^{w0},\tilde P_i^{w1}\right) \cap \left(\tilde P_j^{w0},\tilde P_j^{w1}\right)\right)\neq\emptyset\right] where $(a,b)$ denotes interval in $R$. .. _fig-sweep-and-prune: .. figure:: fig/sweep-and-prune.* Sweep and prune algorithm (shown in 2D), where :yref:`Aabb` of each sphere is represented by minimum and maximum value along each axis. Spatial overlap of :yref:`Aabb`'s is present if they overlap along all axes. In this case, $\tilde P_1\cap\tilde P_2\neq\emptyset$ (but note that $P_1\cap P_2=\emptyset$) and $\tilde P_2 \cap\tilde P_3\neq\emptyset$.} The collider keeps 3 separate lists (arrays) $L_w$ for each axis $w\in\{x,y,z\}$ .. math:: L_w=\bigcup_{i} \left\{\tilde P_i^{w0}, \tilde P_i^{w1} \right\} where $i$ traverses all particles. $L_w$ arrays (sorted sets) contain respective coordinates of minimum and maximum corners for each :yref:`Aabb` (we call these coordinates *bound* in the following); besides bound, each of list elements further carries ``id`` referring to particle it belongs to, and a flag whether it is lower or upper bound. In the initial step, all lists are sorted (using quicksort, average $\bigO{n\log n}$) and one axis is used to create initial interactions: the range between lower and upper bound for each body is traversed, while bounds in-between indicate potential :yref:`Aabb` overlaps which must be checked on the remaining axes as well. At each successive step, lists are already pre-sorted. Inversions occur where a particle's coordinate has just crossed another particle's coordinate; this number is limited by numerical stability of simulation and its physical meaning (giving spatio-temporal coherence to the algorithm). The insertion sort algorithm swaps neighboring elements if they are inverted, and has complexity between \bigO{n} and \bigO{n^2}, for pre-sorted and unsorted lists respectively. For our purposes, we need only to handle inversions, which by nature of the sort algorithm are detected inside the sort loop. An inversion might signify: * overlap along the current axis, if an upper bound inverts (swaps) with a lower bound (i.e. that the upper bound with a higher coordinate was out of order in coming before the lower bound with a lower coordinate). Overlap along the other 2 axes is checked and if there is overlap along all axes, a new potential interaction is created. * End of overlap along the current axis, if lower bound inverts (swaps) with an upper bound. If there is only potential interaction between the two particles in question, it is deleted. * Nothing if both bounds are upper or both lower. Aperiodic insertion sort ^^^^^^^^^^^^^^^^^^^^^^^^^^ Let us show the sort algorithm on a sample sequence of numbers: .. math:: \sortlines{\sortSep& 3 &\sortInv& 7 &\sortInv& 2 &\sortInv& 4 &\sortSep} Elements are traversed from left to right; each of them keeps inverting (swapping) with neighbors to the left, moving left itself, until any of the following conditions is satisfied: .. FIXME table =================== ======================================================== ($\leq$) the sorting order with the left neighbor is correct, or ($||$) the element is at the beginning of the sequence. =================== ======================================================== We start at the leftmost element (the current element is marked $\currelem{i}$) .. math:: \sortlines{\sortSep& \currelem{3} &\sortInv& 7 &\sortInv& 2 &\sortInv& 4 &\sortSep.} It obviously immediately satisfies ($||$), and we move to the next element: .. math:: \sortlines{\sortSep& 3 &\sortInv& \isleq{7} &\sortInv& 2 &\sortInv& 4 &\sortSep.} Condition ($\leq$) holds, therefore we move to the right. The $\currelem{2}$ is not in order (violating ($\leq$)) and two inversions take place; after that, ($||$) holds: .. math:: \sortlines{ \sortSep& 3 &\sortInv& 7 &\sortInv& \isnleq{2} &\sortInv& 4 &\sortSep, \\ \sortSep& 3 &\sortInv& \isnleq{2} &\sortInv& 7 &\sortInv& 4 &\sortSep, \\ \sortSep& \currelem{2} &\sortInv& 3 &\sortInv& 7 &\sortInv& 4 &\sortSep. } The last element $\currelem{4}$ first violates ($\leq$), but satisfies it after one inversion .. math:: \sortlines{ \sortSep& 2 &\sortInv& 3 &\sortInv& 7 &\sortInv& \isnleq{4} &\sortSep, \\ \sortSep& 2 &\sortInv& 3 &\sortInv& \isleq{4} &\sortInv& 7 &\sortSep. } All elements having been traversed, the sequence is now sorted. It is obvious that if the initial sequence were sorted, elements only would have to be traversed without any inversion to handle (that happens in $\mathcal{O}(n)$ time). For each inversion during the sort in simulation, the function that investigates change in :yref:`Aabb` overlap is invoked, creating or deleting interactions. The periodic variant of the sort algorithm is described in :ref:`sect-periodic-insertion-sort`, along with other periodic-boundary related topics. Optimization with Verlet distances ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ As noted above, [Verlet1967]_ explored the possibility of running the collision detection only sparsely by enlarging predicates $\tilde P_i$. In Yade, this is achieved by enlarging :yref:`Aabb` of particles by fixed relative length (or Verlet's distance) in all dimensions $\Delta L$ (:yref:`InsertionSortCollider.sweepLength`). Suppose the collider run last time at step $m$ and the current step is $n$. :yref:`NewtonIntegrator` tracks the cummulated distance traversed by each particle between $m$ and $n$ by comparing the current position with the reference position from time $n$ (:yref:`Bound::refPos`), .. math:: L_{\rm mn}&=|X^n - X^m| :label: eq-verlet-l0 triggering the collider re-run as soon as one particle gives: .. math:: L_{\rm mn}&>\Delta L. :label: eq-verlet-trigger :yref:`InsertionSortCollider.targetInterv` is used to adjust $\Delta L$ independently for each particle. Larger $\Delta L$ will be assigned to the fastest ones, so that all particles would ideally reach the edge of their bounds after this "target" number of iterations. Results of using Verlet distance depend highly on the nature of simulation and choice of :yref:`InsertionSortCollider.targetInterv`. Adjusting the sizes independently for each particle is especially efficient if some parts of a problem have high-speed particles will others are not moving. If it is not the case, no significant gain should be expected as compared to targetInterv=0 (assigning the same $\Delta L$ to all particles). The number of particles and the number of available threads is also to be considered for choosing an appropriate Verlet's distance. A larger distance will result in less time spent in the collider (which runs single-threaded) and more time in computing interactions (multi-threaded). Typically, large $\Delta L$ will be used for large simulations with more than $10^5$ particles on multi-core computers. On the other hand simulations with less than $10^4$ particles on single processor will probably benefit from smaller $\Delta L$. Users benchmarks may be found on Yade's wiki (see e.g. ``_). Creating interaction between particles ================================================ Collision detection described above is only approximate. Exact collision detection depends on the geometry of individual particles and is handled separately. In Yade terminology, the :yref:`Collider` creates only *potential* interactions; potential interactions are evaluated exactly using specialized algorithms for collision of two spheres or other combinations. Exact collision detection must be run at every timestep since it is at every step that particles can change their mutual position (the collider is only run sometimes if the Verlet distance optimization is in use). Some exact collision detection algorithms are described in :ref:`sect-strain-evaluation`; in Yade, they are implemented in classes deriving from :yref:`IGeomFunctor` (prefixed with ``Ig2``). Besides detection of geometrical overlap (which corresponds to :yref:`IGeom` in Yade), there are also non-geometrical properties of the interaction to be determined (:yref:`IPhys`). In Yade, they are computed for every new interaction by calling a functor deriving from :yref:`IPhysFunctor` (prefixed with ``Ip2``) which accepts the given combination of :yref:`Material` types of both particles. Stiffnesses ----------- Basic DEM interaction defines two stiffnesses: normal stiffness $K_N$ and shear (tangent) stiffness $K_T$. It is desirable that $K_N$ be related to fictitious Young's modulus of the particles' material, while $K_T$ is typically determined as a given fraction of computed $K_N$. The $K_T/K_N$ ratio determines macroscopic Poisson's ratio of the arrangement, which can be shown by dimensional analysis: elastic continuum has two parameters ($E$ and $\nu$) and basic DEM model also has 2 parameters with the same dimensions $K_N$ and $K_T/K_N$; macroscopic Poisson's ratio is therefore determined solely by $K_T/K_N$ and macroscopic Young's modulus is then proportional to $K_N$ and affected by $K_T/K_N$. Naturally, such analysis is highly simplifying and does not account for particle radius distribution, packing configuration and other possible parameters such as the interaction radius introduced later. Normal stiffness ^^^^^^^^^^^^^^^^ The algorithm commonly used in Yade computes normal interaction stiffness as stiffness of two springs in serial configuration with lengths equal to the sphere radii (`fig-spheres-contact-stiffness`_). .. _fig-spheres-contact-stiffness: .. figure:: fig/spheres-contact-stiffness.* Series of 2 springs representing normal stiffness of contact between 2 spheres. Let us define distance $l=l_1+l_2$, where $l_i$ are distances between contact point and sphere centers, which are initially (roughly speaking) equal to sphere radii. Change of distance between the sphere centers $\Delta l$ is distributed onto deformations of both spheres $\Delta l=\Delta l_1+\Delta l_2$ proportionally to their compliances. Displacement change $\Delta l_i$ generates force $F_i=K_i \Delta l_i$, where $K_i$ assures proportionality and has physical meaning and dimension of stiffness; $K_i$ is related to the sphere material modulus $E_i$ and some length $\tilde l_i$ proportional to $r_i$. .. math:: :nowrap: \begin{align*} \Delta l&=\Delta l_1+\Delta l_2\\ K_i&=E_i \tilde l_i\\ K_N\Delta l&=F=F_1=F_2\\ K_N\left(\Delta l_1+\Delta l_2\right)&=F\\ K_N\left(\frac{F}{K_1}+\frac{F}{K_2}\right)&=F\\ K_1^{-1}+K_2^{-1}&=K_N^{-1} \\ K_N&=\frac{K_1 K_2}{K_1 + K_2} \\ K_N&=\frac{E_1 \tilde l_1 E_2 \tilde l_2}{E_1\tilde l_1+E_2\tilde l_2} \end{align*} The most used class computing interaction properties :yref:`Ip2_FrictMat_FrictMat_FrictPhys` uses $\tilde l_i=2r_i$. Some formulations define an equivalent cross-section $A_{\rm eq}$, which in that case appears in the $\tilde l_i$ term as $K_i=E_i\tilde l_i=E_i\frac{A_{\rm eq}}{l_i}$. Such is the case for the concrete model (:yref:`Ip2_CpmMat_CpmMat_CpmPhys`), where $A_{\rm eq}=\min(r_1,r_2)$. For reasons given above, no pretense about equality of particle-level $E_i$ and macroscopic modulus $E$ should be made. Some formulations, such as [Hentz2003]_, introduce parameters to match them numerically. This is not appropriate, in our opinion, since it binds those values to particular features of the sphere arrangement that was used for calibration. Other parameters ---------------- Non-elastic parameters differ for various material models. Usually, though, they are averaged from the particles' material properties, if it makes sense. For instance, :yref:`Ip2_CpmMat_CpmMat_CpmPhys` averages most quantities, while :yref:`Ip2_FrictMat_FrictMat_FrictPhys` computes internal friction angle as $\phi=\min(\phi_1,\phi_2)$ to avoid friction with bodies that are frictionless. .. _sect-strain-evaluation: Strain evaluation ================= In the general case, mutual configuration of two particles has 6 degrees of freedom (DoFs) just like a beam in 3D space: both particles have 6 DoFs each, but the interaction itself is free to move and rotate in space (with both spheres) having 6 DoFs itself; then $12-6=6$. They are shown at `fig-spheres-dofs`_. .. _fig-spheres-dofs: .. figure:: fig/spheres-dofs.* Degrees of freedom of configuration of two spheres. Normal strain appears if there is a difference of linear velocity along the interaction axis ($n$); shearing originates from the difference of linear velocities perpendicular to $n$ *and* from the part of $\vec{\omega}_1+\vec{\omega}_2$ perpendicular to $n$; twisting is caused by the part of $\vec{\omega}_1-\vec{\omega}_2$ parallel with $n$; bending comes from the part of $\vec{\omega}_1-\vec{\omega}_2$ perpendicular to $n$. We will only describe normal and shear components of strain in the following, leaving torsion and bending aside. The reason is that most constitutive laws for contacts do not use the latter two. Normal strain ------------- .. _sect-normal-strain-constants: Constants ^^^^^^^^^^ Let us consider two spheres with *initial* centers $\bar{\vec{C}_1}$, $\bar{\vec{C}}_2$ and radii $r_1$, $r_2$ that enter into contact. The order of spheres within the contact is arbitrary and has no influence on the behavior. Then we define lengths .. math:: :nowrap: \begin{align*} d_0&=|\bar{\vec{C}}_2-\bar{\vec{C}}_1| \\ d_1&=r_1+\frac{d_0-r_1-r_2}{2}, & d_2&=d_0-d_1. \end{align*} These quantities are *constant* throughout the life of the interaction and are computed only once when the interaction is established. The distance $d_0$ is the *reference distance* and is used for the conversion of absolute displacements to dimensionless strain, for instance. It is also the distance where (for usual contact laws) there is neither repulsive nor attractive force between the spheres, whence the name *equilibrium distance*. .. _fig-sphere-sphere: .. figure:: fig/sphere-sphere.* Geometry of the initial contact of 2 spheres; this case pictures spheres which already overlap when the contact is created (which can be the case at the beginning of a simulation) for the sake of generality. The initial contact point $\bar{\vec{C}}$ is in the middle of the overlap zone. Distances $d_1$ and $d_2$ define reduced (or expanded) radii of spheres; geometrical radii $r_1$ and $r_2$ are used only for collision detection and may not be the same as $d_1$ and $d_2$, as shown in fig. `fig-sphere-sphere`_. This difference is exploited in cases where the average number of contacts between spheres should be increased, e.g. to influence the response in compression or to stabilize the packing. In such case, interactions will be created also for spheres that do not geometrically overlap based on the *interaction radius* $R_I$, a dimensionless parameter determining „non-locality“ of contact detection. For $R_I=1$, only spheres that touch are considered in contact; the general condition reads .. math:: d_0&\leq R_I(r_1+r_2). :label: eq-strain-interaction-radius The value of $R_I$ directly influences the average number of interactions per sphere (percolation), which for some models is necessary in order to achieve realistic results. In such cases, :yref:`Aabb` (or $\tilde P_i$ predicates in general) must be enlarged accordingly (:yref:`Bo1_Sphere_Aabb.aabbEnlargeFactor`). Contact cross-section """"""""""""""""""""" Some constitutive laws are formulated with strains and stresses (:yref:`Law2_ScGeom_CpmPhys_Cpm`, the concrete model described later, for instance); in that case, equivalent cross-section of the contact must be introduced for the sake of dimensionality. The exact definition is rather arbitrary; the CPM model (:yref:`Ip2_CpmMat_CpmMat_CpmPhys`) uses the relation .. math:: A_{\rm eq}=\pi\min(r_1,r_2)^2 :label: eq-strain-crosssection which will be used to convert stresses to forces, if the constitutive law used is formulated in terms of stresses and strains. Note that other values than $\pi$ can be used; it will merely scale macroscopic packing stiffness; it is only for the intuitive notion of a truss-like element between the particle centers that we choose $A_{\rm eq}$ representing the circle area. Besides that, another function than $\min(r_1,r_2)$ can be used, although the result should depend linearly on $r_1$ and $r_2$ so that the equation gives consistent results if the particle dimensions are scaled. Variables ^^^^^^^^^^^ The following state variables are updated as spheres undergo motion during the simulation (as $\currC_1$ and $\currC_2$ change): .. math:: :label: eq-contact-normal \currn=\frac{\currC_2-\currC_1}{|\currC_2-\currC_1|}\equiv \normalized{\currC_2-\currC_1} and .. math:: :label: eq-contact-point \currC=\currC_1+\left(d_1-\frac{d_0-|\currC_2-\currC_1|}{2}\right)\vec{n}. The contact point $\currC$ is always in the middle of the spheres' overlap zone (even if the overlap is negative, when it is in the middle of the empty space between the spheres). The *contact plane* is always perpendicular to the contact plane normal $\currn$ and passes through $\currC$. Normal displacement and strain can be defined as .. math:: :nowrap: \begin{align*} u_N&=|\currC_2-\currC_1|-d_0, \\ \eps_N&=\frac{u_N}{d_0}=\frac{|\currC_2-\currC_1|}{d_0}-1. \end{align*} Since $u_N$ is always aligned with $\vec{n}$, it can be stored as a scalar value multiplied by $\vec{n}$ if necessary. For massively compressive simulations, it might be beneficial to use the logarithmic strain, such that the strain tends to $-\infty$ (rather than $-1$) as centers of both spheres approach. Otherwise, repulsive force would remain finite and the spheres could penetrate through each other. Therefore, we can adjust the definition of normal strain as follows: .. math:: \eps_N = \begin{cases} \log \left(\frac{|\currC_2-\currC_1|}{d_0}\right)& \hbox{if } |\currC_2-\currC_1|` associated with both particles. In the simple case of frictional material :yref:`FrictMat`, :yref:`Ip2_FrictMat_FrictMat_FrictPhys` creates a new :yref:`FrictPhys` instance, which defines normal stiffness $K_N$, shear stiffness $K_T$ and friction angle $\phi$. At each step, given normal and shear displacements $u_N$, $\uT$, normal and shear forces are computed (if $u_N>0$, the contact is deleted without generating any forces): .. math:: :nowrap: \begin{align*} \vec{F}_N&=K_N u_N \vec{n},\\ \vec{F}_T^t&=K_T \vec{u}_T \end{align*} where $\vec{F}_N$ is normal force and $\vec{F}_T$ is trial shear force. A simple non-associated stress return algorithm is applied to compute final shear force .. math:: :nowrap: \begin{align*} \vec{F}_T=\begin{cases} \vec{F}_T^t\frac{|\vec{F}_N|\tan\phi}{\vec{F}_T^t} & \hbox{if } |\vec{F}_T|>|\vec{F}_N|\tan\phi, \\ \vec{F}_T^t & \hbox{otherwise.} \end{cases} \end{align*} Summary force $\vec{F}=\vec{F}_N+\vec{F}_T$ is then applied to both particles -- each particle accumulates forces and torques acting on it in the course of each step. Because the force computed acts at contact point $\vec{C}$, which is difference from spheres' centers, torque generated by $\vec{F}$ must also be considered. .. math:: :nowrap: \begin{align*} \vec{F}_1&+=\vec{F} & \vec{F}_2&+=-\vec{F} \\ \vec{T}_1&+=d_1(-\vec{n})\times \vec{F} & \vec{T}_2&+=d_2 \vec{n} \times \vec{F}. \end{align*} Motion integration ================== Each particle accumulates generalized forces (forces and torques) from the contacts in which it participates. These generalized forces are then used to integrate motion equations for each particle separately; therefore, we omit $i$ indices denoting the $i$-th particle in this section. The customary leapfrog scheme (also known as the Verlet scheme) is used, with some adjustments for rotation of non-spherical particles, as explained below. The "leapfrog" name comes from the fact that even derivatives of position/orientation are known at on-step points, whereas odd derivatives are known at mid-step points. Let us recall that we use $\prev{a}$, $\curr{a}$, $\next{a}$ for on-step values of $a$ at $t-\Dt$, $t$ and $t+\Dt$ respectively; and $\pprev{a}$, $\nnext{a}$ for mid-step values of $a$ at $t-\Dt/2$, $t+\Dt/2$. Described integration algorithms are implemented in the :yref:`NewtonIntegrator` class in Yade. Position ---------- Integrating motion consists in using current acceleration $\curraccel$ on a particle to update its position from the current value $\currpos$ to its value at the next timestep $\nextpos$. Computation of acceleration, knowing current forces $\vec{F}$ acting on the particle in question and its mass $m$, is simply .. math:: \curraccel&=\vec{F}/m. Using the 2nd order finite difference with step $\Dt$, we obtain .. math:: \curraccel&\cong\frac{\prevpos-2\currpos+\nextpos}{\Dt^2} from which we express .. math:: \nextpos&=2\currpos-\prevpos+\curraccel\Dt^2 =\\ &=\currpos+\Dt\underbrace{\left(\frac{\currpos-\prevpos}{\Dt}+\curraccel\Dt\right)}_{(\dagger)}. Typically, $\prevpos$ is already not known (only $\currpos$ is); we notice, however, that .. math:: \pprevvel&\simeq\frac{\currpos-\prevpos}{\Dt}, i.e. the mean velocity during the previous step, which is known. Plugging this approximate into the $(\dagger)$ term, we also notice that mean velocity during the current step can be approximated as .. math:: \nnextvel&\simeq\pprevvel+\curraccel\Dt, which is $(\dagger)$; we arrive finally at .. math:: \nextpos&=\currpos+\Dt\left(\pprevvel+\curraccel\Dt\right). The algorithm can then be written down by first computing current mean velocity $\nnextvel$ which we need to store for the next step (just as we use its old value $\pprevvel$ now), then computing the position for the next time step $\nextpos$: .. math:: :label: eq-leapfrog-nextvel :nowrap: \begin{align*} \nnextvel&=\pprevvel+\curraccel\Dt \\ \nextpos&=\currpos+\nnextvel\Dt. \end{align*} Positions are known at times $i\Delta t$ (if $\Delta t$ is constant) while velocities are known at $i\Delta t+\frac{\Delta t}{2}$. The facet that they interleave (jump over each other) in such way gave rise to the colloquial name "leapfrog" scheme. Orientation (spherical) ------------------------ Updating particle orientation $\curr{q}$ proceeds in an analogous way to position update. First, we compute current angular acceleration $\curraaccel$ from known current torque $\vec{T}$. For spherical particles where the inertia tensor is diagonal in any orientation (therefore also in current global orientation), satisfying $\vec{I}_{11}=\vec{I}_{22}=\vec{I}_{33}$, we can write .. math:: \curraaccel_i&=\vec{T}_i/\vec{I}_{11}, We use the same approximation scheme, obtaining an equation analogous to :eq:`eq-leapfrog-nnextvel` .. math:: \nnextangvel&=\pprevangvel+\Dt\curraaccel. The quaternion $\Delta q$ representing rotation vector $\nnextangvel\Dt$ is constructed, i.e. such that .. math:: :nowrap: \begin{align*} (\Delta q)_{\theta}&=|\nnextangvel|, \\ (\Delta q)_{\vec{u}}&=\normalized{\nnextangvel} \end{align*} Finally, we compute the next orientation $\next{q}$ by rotation composition .. math:: \next{q}&=\Delta q\curr{q}. Orientation (aspherical) ------------------------ Integrating rotation of aspherical particles is considerably more complicated than their position, as their local reference frame is not inertial. Rotation of rigid body in the local frame, where inertia matrix $\mat{I}$ is diagonal, is described in the continuous form by Euler's equations ($i\in\{1,2,3\}$ and $i$, $j$, $k$ are subsequent indices): .. math:: \vec{T}_i=\mat{I}_{ii}\dot{\vec{\omega}}_i+(\mat{I}_{kk}-\mat{I}_{jj})\vec{\omega}_j\vec{\omega}_k. Due to the presence of the current values of both $\vec{\omega}$ and $\dot{\vec{\omega}}$, they cannot be solved using the standard leapfrog algorithm (that was the case for translational motion and also for the spherical bodies' rotation where this equation reduced to $\vec{T}=\mat{I}\dot{\vec{\omega}}$). The algorithm presented here is described by [Allen1989]_ (pg. 84--89) and was designed by Fincham for molecular dynamics problems; it is based on extending the leapfrog algorithm by mid-step/on-step estimators of quantities known at on-step/mid-step points in the basic formulation. Although it has received criticism and more precise algorithms are known ([Omelyan1999]_, [Neto2006]_, [Johnson2008]_), this one is currently implemented in Yade for its relative simplicity. .. Finchman: Leapfrog Rotational Algorithms: http://www.informaworld.com/smpp/content~content=a756872469&db=all Schvanberg: Leapfrog Rotational Algorithms: http://www.informaworld.com/smpp/content~content=a914299295&db=all Each body has its local coordinate system based on the principal axes of inertia for that body. We use $\locframe{\bullet}$ to denote vectors in local coordinates. The orientation of the local system is given by the current particle's orientation $\curr{q}$ as a quaternion; this quaternion can be expressed as the (current) rotation matrix $\mat{A}$. Therefore, every vector $\vec{a}$ is transformed as $\locframe{\vec{a}}=q\vec{a}q^{*}=\mat{A}\vec{a}$. Since $\mat{A}$ is a rotation (orthogonal) matrix, the inverse rotation $\mat{A}^{-1}=\mat{A}^{T}$. For given particle in question, we know * $\loccurr{\mat{I}}$ (constant) inertia matrix; diagonal, since in local, principal coordinates, * $\curr{\vec{T}}$ external torque, * $\curr{q}$ current orientation (and its equivalent rotation matrix $\mat{A}$), * $\pprev{\vec{\omega}}$ mid-step angular velocity, * $\pprev{\vec{L}}$ mid-step angular momentum; this is an auxiliary variable that must be tracked in addition for use in this algorithm. It will be zero in the initial step. Our goal is to compute new values of the latter three, that is $\nnext{\vec{L}}$, $\next{q}$, $\nnext{\vec{\omega}}$. We first estimate current angular momentum and compute current local angular velocity: .. math:: :nowrap: \begin{align*} \curr{\vec{L}}&=\pprev{\vec{L}}+\curr{\vec{T}}\frac{\Dt}{2}, &\loccurr{\vec{L}}&=\mat{A}\curr{\vec{L}}, \\ \nnext{\vec{L}}&=\pprev{\vec{L}}+\curr{\vec{T}}\Dt, &\nnext{\locframe{\vec{L}}}&=\mat{A}\nnext{\vec{L}}, \\ \loccurr{\vec{\omega}}&=\curr{\locframe{\mat{I}}}{}^{-1}\loccurr{\vec{L}}, \\ \nnext{\locframe{\vec{\omega}}}&=\curr{\locframe{\mat{I}}}{}^{-1}\nnext{\locframe{\vec{L}}}. \\ \end{align*} Then we compute $\curr{\dot{q}}$, using $\curr{q}$ and $\loccurr{\vec{\omega}}$: .. math:: :label: eq-quaternion-derivative :nowrap: \begin{align*} \begin{pmatrix}\curr{\dot{q}}_w \\ \curr{\dot{q}}_x \\ \curr{\dot{q}}_y \\ \curr{\dot{q}}_z\end{pmatrix}&= \def\cq{\curr{q}} \frac{1}{2}\begin{pmatrix} \cq_w & -\cq_x & -\cq_y & -\cq_z \\ \cq_x & \cq_w & -\cq_z & \cq_y \\ \cq_y & \cq_z & \cq_w & -\cq_x \\ \cq_z & -\cq_y & \cq_x & \cq_w \end{pmatrix} \begin{pmatrix} 0 \\ \loccurr{\vec{\omega}}_x \\ \loccurr{\vec{\omega}}_y \\ \loccurr{\vec{\omega}}_z \end{pmatrix}, \\ \nnext{q}&=\curr{q}+\curr{\dot{q}}\frac{\Dt}{2}.\\ \end{align*} We evaluate $\nnext{\dot{q}}$ from $\nnext{q}$ and $\nnext{\locframe{\vec{\omega}}}$ in the same way as in :eq:`eq-quaternion-derivative` but shifted by $\Dt/2$ ahead. Then we can finally compute the desired values .. math:: :nowrap: \begin{align*} \next{q}&=\curr{q}+\nnext{\dot{q}}\Dt, \\ \nnext{\vec{\omega}}&=\mat{A}^{-1}\nnext{\locframe{\vec{\omega}}} \end{align*} Clumps (rigid aggregates) ------------------------- DEM simulations frequently make use of rigid aggregates of particles to model complex shapes [Price2007]_ called *clumps*, typically composed of many spheres. Dynamic properties of clumps are computed from the properties of its members: * For non-overlapping clump members the clump's mass $m_c$ is summed over members, the inertia tensor $\mathbf{I}_c$ is computed using the parallel axes theorem: $\mathbf{I}_c = \sum_i( m_i*d_i^2 + I_i)$, where $m_i$ is the mass of clump member $i$, $d_i$ is the distance from center of clump member $i$ to clump's centroid and $I_i$ is the inertia tensor of the clump member $i$. * For overlapping clump members the clump's mass $m_c$ is summed over cells using a regular grid spacing inside axis-aligned bounding box (:yref:`Aabb`) of the clump, the inertia tensor is computed using the parallel axes theorem: $\mathbf{I}_c = \sum_j( m_j*d_j^2 + I_j)$, where $m_j$ is the mass of cell $j$, $d_j$ is the distance from cell center to clump's centroid and $I_j$ is the inertia tensor of the cell $j$. Local axes are oriented such that they are principal and inertia tensor is diagonal and clump's orientation is changed to compensate rotation of the local system, as to not change the clump members' positions in global space. Initial positions and orientations of all clump members in local coordinate system are stored. In Yade (class :yref:`Clump`), clump members behave as stand-alone particles during simulation for purposes of collision detection and contact resolution, except that they have no contacts created among themselves within one clump. It is at the stage of motion integration that they are treated specially. Instead of integrating each of them separately, forces/torques on those particles $\vec{F}_i$, $\vec{T}_i$ are converted to forces/torques on the clump itself. Let us denote $r_i$ relative position of each particle with regards to clump's centroid, in global orientation. Then summary force and torque on the clump are .. math:: :nowrap: \begin{align*} \vec{F}_c&=\sum F_i, \\ \vec{T}_c&=\sum r_i\times F_i + T_i. \end{align*} Motion of the clump is then integrated, using aspherical rotation integration. Afterwards, clump members are displaced in global space, to keep their initial positions and orientations in the clump's local coordinate system. In such a way, relative positions of clump members are always the same, resulting in the behavior of a rigid aggregate. Numerical damping ----------------- In simulations of quasi-static phenomena, it it desirable to dissipate kinetic energy of particles. Since most constitutive laws (including :yref:`Law_ScGeom_FrictPhys_Basic` shown above, :ref:`sect-formulation-stress-cundall`) do not include velocity-based damping (such as one in [Addetta2001]_), it is possible to use artificial numerical damping. The formulation is described in [Pfc3dManual30]_, although our version is slightly adapted. The basic idea is to decrease forces which increase the particle velocities and vice versa by $(\Delta F)_d$, comparing the current acceleration sense and particle velocity sense. This is done by component, which makes the damping scheme clearly non-physical, as it is not invariant with respect to coordinate system rotation; on the other hand, it is very easy to compute. Cundall proposed the form (we omit particle indices $i$ since it applies to all of them separately): .. math:: \frac{(\Delta \vec{F})_{dw}}{\vec{F}_w}=-\lambda_d\sign(\vec{F}_w\pprev{\dot{\vec{u}}}_{w}),\quad w\in\{x,y,z\} where $\lambda_d$ is the damping coefficient. This formulation has several advantages [Hentz2003]_: * it acts on forces (accelerations), not constraining uniform motion; * it is independent of eigenfrequencies of particles, they will be all damped equally; * it needs only the dimensionless parameter $\lambda_d$ which does not have to be scaled. In Yade, we use the adapted form .. math:: :label: eq-damping-yade \frac{(\Delta\vec{F})_{dw}}{\vec{F}_w}=-\lambda_d\sign\vec{F}_w\underbrace{\left(\pprev{\dot{u}}_w+\frac{\curr{\ddot{\vec{u}}}_w\Dt}{2}\right)}_{\simeq\curr{\dot{u}}_w}, where we replaced the previous mid-step velocity $\pprev{\dot{u}}$ by its on-step estimate in parentheses. This is to avoid locked-in forces that appear if the velocity changes its sign due to force application at each step, i.e. when the particle in question oscillates around the position of equilibrium with $2\Dt$ period. In Yade, damping :eq:`eq-damping-yade` is implemented in the :yref:`NewtonIntegrator` engine; the damping coefficient $\lambda_d$ is :yref:`NewtonIntegrator.damping`. .. _sect-formulation-dt: Stability considerations ------------------------------------------------------ .. \def\Dtcr{\Dt_{\rm cr}} % http://en.wikipedia.org/wiki/Harmonic_oscillator % eigenfrequency is (1/2π)√(k/m) for simple harmonic oscillator % Bruno gives √(m/k) % http://imechanica.org/node/7670#comment-13672: Δt_crit=2/ω_max The leapfrog integration scheme is conditionally stable, i.e. not magnifying errors, provided $\Dt<\Dtcr$ where $\Dtcr$ is the *critical timestep*, above which the integration is unstable. Usually, $\Dt$ is taken as a fraction of $\Dtcr$; this fraction is called the *timestep safety factor*, with meaningful values $\in\langle 0,1)$. Critical timestep ^^^^^^^^^^^^^^^^^ In order to ensure stability for the explicit integration sceheme, an upper limit is imposed on $\Dt$: .. math:: :label: eq-dt-angular \Dtcr=\frac{2}{\omega_{\rm max}} where $\omega_{\rm max}$ is the highest eigenfrequency within the system. Single mass-spring system """""""""""""""""""""""""" Single 1D mass-spring system with mass $m$ and stiffness $K$ is governed by the equation .. math:: m\ddot{x}=-Kx where $x$ is displacement from the mean (equilibrium) position. The solution of harmonic oscillation is $x(t)=A\cos(\omega t+\phi)$ where phase $\phi$ and amplitude $A$ are determined by initial conditions. The angular frequency .. math:: :label: eq-dt-omega \omega^{(1)}=\sqrt{\frac{K}{m}} does not depend on initial conditions. Since there is one single mass, $\omega_{\rm max}^{(1)}=\omega^{(1)}$. Plugging :eq:`eq-dt-omega` into :eq:`eq-dt-angular`, we obtain .. math:: \Dtcr^{(1)}=2/\omega_{\rm max}^{(1)}=2\sqrt{m/K} for a single oscillator. General mass-spring system """""""""""""""""""""""""" In a general mass-spring system, the highest frequency occurs if two connected masses $m_i$, $m_j$ are in opposite motion; let us suppose they have equal velocities (which is conservative) and they are connected by a spring with stiffness $K_{i}$: displacement $\Delta x_i$ of $m_i$ will be accompained by $\Delta x_j=-\Delta x_i$ of $m_j$, giving $\Delta F_i=-K_{i}(\Delta x_i-(-\Delta x_i))=-2K_{i}\Delta x_i$. That results in apparent stiffness $K_{i}^{(2)}=2K_{i}$, giving maximum eigenfrequency of the whole system .. math:: \omega_{\rm max}=\max_i\sqrt{K_i^{(2)}/m_i}. The overall critical timestep is then .. math:: :label: eq-dtcr-global \Dtcr=\frac{2}{\omega_{\rm max}}=\min_i\, 2\sqrt{\frac{m_i}{K_i^{(2)}}}=\min_i\, 2\sqrt{\frac{m_i}{2K_i}}=\min_i \sqrt{2}\sqrt{\frac{m_i}{K_i}}. This equation can be used for all 6 degrees of freedom (DOF) in translation and rotation, by considering generalized mass and stiffness matrices $M$ and $K$, and replacing fractions $\frac{m_i}{K_i}$ by eigen values of $M.K^{-1}$. The critical timestep is then associated to the eigen mode with highest frequency : .. math:: :label: eq-dtcr-axes \Dtcr=\min {\Dtcr}_k,\quad k\in\{1,...,6\}. DEM simulations """""""""""""""" In DEM simulations, per-particle stiffness $\vec{K}_{ij}$ is determined from the stiffnesses of contacts in which it participates [Chareyre2005]_. Suppose each contact has normal stiffness $K_{Nk}$, shear stiffness $K_{Tk}=\xi K_{Nk}$ and is oriented by normal $\vec{n}_{k}$. A translational stiffness matrix $\vec{K}_{ij}$ can be defined as the sum of contributions of all contacts in which it participates (indices $k$), as .. math:: :label: eq-dtcr-particle-stiffness \vec{K}_{ij}=\sum_k (K_{Nk}-K_{Tk})\vec{n}_{i}\vec{n}_{j}+K_{Tk}=\sum_j K_{Nk}\left((1-\xi)\vec{n}_{i}\vec{n}_{j}+\xi\right) with $i$ and $j\in\{x,y,z\}$. Equations :eq:`eq-dtcr-axes` and :eq:`eq-dtcr-particle-stiffness` determine $\Dtcr$ in a simulation. A similar approach generalized to all 6 DOFs is implemented by the :yref:`GlobalStiffnessTimeStepper` engine in Yade. The derivation of generalized stiffness including rotational terms is very similar but not developped here, for simplicity. For full reference, see "PFC3D - Theoretical Background". Note that for computation efficiency reasons, eigenvalues of the stiffness matrices are not computed. They are only approximated assuming than DOF's are uncoupled, and using diagonal terms of $K.M^{-1}$. They give good approximates in typical mechanical systems. There is one important condition that $\omega_{\rm max}>0$: if there are no contacts between particles and $\omega_{\rm max}=0$, we would obtain value $\Dtcr=\infty$. While formally correct, this value is numerically erroneous: we were silently supposing that stiffness remains constant during each timestep, which is not true if contacts are created as particles collide. In case of no contact, therefore, stiffness must be pre-estimated based on future interactions, as shown in the next section. .. _sect-dt-pwave: Estimation of $\Dtcr$ by wave propagation speed ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Estimating timestep in absence of interactions is based on the connection between interaction stiffnesses and the particle's properties. Note that in this section, symbols $E$ and $\rho$ refer exceptionally to Young's modulus and density of *particles*, not of macroscopic arrangement. In Yade, particles have associated :yref:`Material` which defines density $\rho$ (:yref:`Material.density`), and also may define (in :yref:`ElastMat` and derived classes) particle's "Young's modulus" $E$ (:yref:`ElastMat.young`). $\rho$ is used when particle's mass $m$ is initially computed from its $\rho$, while $E$ is taken in account when creating new interaction between particles, affecting stiffness $K_N$. Knowing $m$ and $K_N$, we can estimate :eq:`eq-dtcr-particle-stiffness` for each particle; we obviously neglect * number of interactions per particle $N_i$; for a "reasonable" radius distribution, however, there is a geometrically imposed upper limit (6 for a 2D-packing of spheres with equal radii, for instance); * the exact relationship the between particles' rigidities $E_i$, $E_j$, supposing only that $K_N$ is somehow proportional to them. By defining $E$ and $\rho$, particles have continuum-like quantities. Explicit integration schemes for continuum equations impose a critical timestep based on sonic speed $\sqrt{E/\rho}$; the elastic wave must not propagate farther than the minimum distance of integration points $l_{\rm min}$ during one step. Since $E$, $\rho$ are parameters of the elastic continuum and $l_{\rm min}$ is fixed beforehand, we obtain .. math:: \Dtcr^{(c)}=l_{\rm min}\sqrt{\frac{\rho}{E}}. For our purposes, we define $E$ and $\rho$ for each particle separately; $l_{\rm min}$ can be replaced by the sphere's radius $R_i$; technically, $l_{\rm min}=2R_i$ could be used, but because of possible interactions of spheres and facets (which have zero thickness), we consider $l_{\rm min}=R_i$ instead. Then .. FIXME Why not by sphere's diameter instead? We could say it is because :yref:`Sphere`-:yref:`Facet` interaction which has half length? .. math:: \Dtcr^{(p)}=\min_i R_i \sqrt{\frac{\rho_i}{E_i}}. This algorithm is implemented in the :yref:`yade.utils.PWaveTimeStep` function. Let us compare this result to :eq:`eq-dtcr-global`; this necessitates making several simplifying hypotheses: * all particles are spherical and have the same radius $R$; * the sphere's material has the same $E$ and $\rho$; * the average number of contacts per sphere is $N$; * the contacts have sufficiently uniform spatial distribution around each particle; * the $\xi=K_N/K_T$ ratio is constant for all interactions; * contact stiffness $K_N$ is computed from $E$ using a formula of the form .. math:: :label: eq-dt-kn K_N=E\pi'R', where $\pi'$ is some constant depending on the algorithm in use\footnote{For example, $\pi'=\pi/2$ in the concrete particle model (:yref:`Ip2_CpmMat_CpmMat_CpmPhys`), while $\pi'=2$ in the classical DEM model (:yref:`Ip2_FrictMat_FrictMat_FrictPhys`) as implemented in Yade.} and $R'$ is half-distance between spheres in contact, equal to $R$ for the case of interaction radius $R_I=1$. If $R_I=1$ (and $R'\equiv R$ by consequence), all interactions will have the same stiffness $K_N$. In other cases, we will consider $K_N$ as the average stiffness computed from average $R'$ (see below). As all particles have the same parameters, we drop the $i$ index in the following formulas. We try to express the average per-particle stiffness from :eq:`eq-dtcr-particle-stiffness`. It is a sum over all interactions where $K_{N}$ and $\xi$ are scalars that will not rotate with interaction, while $\vec{n}_w$ is $w$-th component of unit interaction normal $\vec{n}$. Since we supposed uniform spatial distribution, we can replace $\vec{n}_w^2$ by its average value $\overline{\vec{n}}_w^2$. Recognizing components of $\vec{n}$ as direction cosines, the average values of $\vec{n}_w^2$ is $1/3$. %we find the average value by integrating over all possible orientations, which are uniformly distributed in space: Moreover, since all directions are equal, we can write the per-body stiffness as $K=\vec{K}_w$ for all $w\in\{x,y,z\}$. We obtain .. math:: K=\sum K_N\left((1-\xi)\frac{1}{3}+\xi\right)=\sum K_N\frac{1-2\xi}{3} and can put constant terms (everything) in front of the summation. $\sum 1$ equals the number of contacts per sphere, i.e. $N$. Arriving at .. math:: K=N K_N \frac{1-2\xi}{3}, we substitute $K$ into :eq:`eq-dtcr-global` using :eq:`eq-dt-kn`: .. math:: \Dtcr=\sqrt{2}\sqrt{\frac{m}{K}}=\sqrt{2}\sqrt{\frac{\frac{4}{3}\pi R^3\rho}{N E\pi'R\frac{1-2\xi}{3}}}=\underbrace{R\sqrt{\frac{\rho}{E}}}_{\Dtcr^{(p)}}2\sqrt{\frac{\pi/\pi'}{N(1-2\xi)}}. The ratio of timestep $\Dtcr^{(p)}$ predicted by the p-wave velocity and numerically stable timestep $\Dtcr$ is the inverse value of the last (dimensionless) term: .. math:: \frac{\Dtcr^{(p)}}{\Dtcr}=2\sqrt{\frac{N(1+\xi)}{\pi/\pi'}}. Actual values of this ratio depend on characteristics of packing $N$, $K_N/K_T=\xi$ ratio and the way of computing contact stiffness from particle rigidity. Let us show it for two models in Yade: Concrete particle model computes contact stiffness from the equivalent area $A_{\rm eq}$ first :eq:`eq-strain-crosssection`, .. math:: :nowrap: \begin{align*} A_{\rm eq}&=\pi R^2 K_N&=\frac{A_{\rm eq}E}{d_0}. \end{align*} $d_0$ is the initial contact length, which will be, for interaction radius :eq:`eq-strain-interaction-radius` $R_I>1$, in average larger than $2R$. For $R_I=1.5$ ,we can roughly estimate $\overline{d}_0=1.25\cdot2R=\frac{5}{2}R$, getting .. math:: K_N=E\left(\frac{2}{5}\pi\right)R where $\frac{2}{5}\pi=\pi'$ by comparison with :eq:`eq-dt-kn`. Interaction radius $R_I=1.5$ leads to average $N\approx12$ interactions per sphere for dense packing of spheres with the same radius $R$. $\xi=0.2$ is calibrated to match the desired macroscopic Poisson's ratio $\nu=0.2$. Finally, we obtain the ratio .. math:: \frac{\Dtcr^{(p)}}{\Dtcr}=2\sqrt{\frac{12(1-2\cdot0.2)}{\frac{\pi}{(2/5)\pi}}}=3.39, showing significant overestimation by the p-wave algorithm. Non-cohesive dry friction model is the basic model proposed by Cundall explained in :ref:`sect-formulation-stress-cundall`. Supposing almost-constant sphere radius $R$ and rather dense packing, each sphere will have $N=6$ interactions on average (that corresponds to maximally dense packing of spheres with a constant radius). If we use the :yref:`Ip2_FrictMat_FrictMat_FrictPhys` class, we have $\pi'=2$, as $K_N=E2R$; we again use $\xi=0.2$ (for lack of a more significant value). In this case, we obtain the result .. math:: \frac{\Dtcr^{(p)}}{\Dtcr}=2\sqrt{\frac{6(1-2\cdot0.2)}{\pi/2}}=3.02 which again overestimates the numerical critical timestep. To conclude, p-wave timestep gives estimate proportional to the real $\Dtcr$, but in the cases shown, the value of about $\Dt=0.3\Dtcr^{(p)}$ should be used to guarantee stable simulation. Non-elastic $\Dt$ constraints ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Let us note at this place that not only $\Dtcr$ assuring numerical stability of motion integration is a constraint. In systems where particles move at relatively high velocities, position change during one timestep can lead to non-elastic irreversible effects such as damage. The $\Dt$ needed for reasonable result can be lower $\Dtcr$. We have no rigorously derived rules for such cases. .. http://books.google.cz/books?id=_KTsjCZtt_EC&lpg=PP1&ots=nK0B4wui2F&dq=stability%20analysis&pg=PR5#v=onepage&q&f=false .. The leap-frog integration scheme assumes constant $\Dt$. Although this is typically the case, and even dynamic time-stepping techniques such as :yref:`GlobalStiffnessTimeStepper` change $\Dt$ infrequently, big changes in timestep could destabilize the integration [Skeel1993]_. Periodic boundary conditions ============================ While most DEM simulations happen in $R^3$ space, it is frequently useful to avoid boundary effects by using periodic space instead. In order to satisfy periodicity conditions, periodic space is created by repetition of parallelepiped-shaped cell. In Yade, periodic space is implemented in the :yref:`Cell` class. The geometry of the cell in the reference coordinates system is defined by three edges of the parallepiped. The corresponding base vectors are stored in the columns of matrix $\mat{H}$ (:yref:`Cell.hSize`). The initial $\mat{H}$ can be explicitly defined as a 3x3 matrix at the beginning of the simulation. There are no restricitions on the possible shapes: any parallelepiped is accepted as the initial cell. If the base vectors are axis-aligned, defining only their sizes can be more convenient than defining the full $\mat{H}$ matrix; in that case it is enough to define the norms of columns in $\mat{H}$ (see :yref:`Cell.size`). After the definition of the initial cell's geometry, $\mat{H}$ should generally not be modified by direct assignment. Instead, its deformation rate will be defined via the velocity gradient :yref:`Cell.velGrad` described below. It is the only variable that let the period deformation be correctly accounted for in constitutive laws and Newton integrator (:yref:`NewtonIntegrator`). Deformations handling --------------------- The deformation of the cell over time is defined via a matrix representing the gradient of an homogeneous velocity field $\nabla \vec{v}$ (:yref:`Cell.velGrad`). This gradient represents arbitrary combinations of rotations and stretches. It can be imposed externaly or updated by :yref:`boundary controllers ` (see :yref:`PeriTriaxController` or :yref:`Peri3dController`) in order to reach target strain values or to maintain some prescribed stress. The velocity gradient is integrated automatically over time, and the cumulated transformation is reflected in the transformation matrix $\mat{F}$ (:yref:`Cell.trsf`) and the current shape of the cell $\mat{H}$. The per-step transformation update reads (it is similar for $\mat{H}$), with $I$ the identity matrix: .. math:: \next{\mat{F}}=(I+\nabla \vec{v} \Dt)\curr{\mat{F}}. $\mat{F}$ can be set back to identity at any point in simulations, in order to define the current state as reference for strains definition in boundary controllers. It will have no effect on $\mat{H}$. Along with the automatic integration of cell transformation, there is an option to homothetically displace all particles so that $\nabla \vec{v}$ is applied over the whole simulation (enabled via :yref:`Cell.homoDeform`). This avoids all boundary effects coming from change of the velocity gradient. Collision detection in periodic cell ------------------------------------ In usual implementations, particle positions are forced to be inside the cell by wrapping their positions if they get over the boundary (so that they appear on the other side). As we wanted to avoid abrupt changes of position (it would make particle's velocity inconsistent with step displacement change), a different method was chosen. .. _sect-cell-approx-collision: Approximate collision detection ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Pass 1 collision detection (based on sweep and prune algorithm, sect. :ref:`sect-sweep-and-prune`) operates on axis-aligned bounding boxes (:yref:`Aabb`) of particles. During the collision detection phase, bounds of all :yref:`Aabb's` are wrapped inside the cell in the first step. At subsequent runs, every bound remembers by how many cells it was initially shifted from coordinate given by the :yref:`Aabb` and uses this offset repeatedly as it is being updated from :yref:`Aabb` during particle's motion. Bounds are sorted using the periodic insertion sort algorithm (sect. :ref:`sect-periodic-insertion-sort`), which tracks periodic cell boundary $||$. Upon inversion of two :yref:`Aabb`'s, their collision along all three axes is checked, wrapping real coordinates inside the cell for that purpose. This algorithm detects collisions as if all particles were inside the cell but without the need of constructing "ghost particles" (to represent periodic image of a particle which enters the cell from the other side) or changing the particle's positions. It is required by the implementation (and partly by the algorithm itself) that particles do not span more than half of the current cell size along any axis; the reason is that otherwise two (or more) contacts between both particles could appear, on each side. Since Yade identifies contacts by :yref:`Body.id` of both bodies, they would not be distinguishable. In presence of shear, the sweep-and-prune collider could not sort bounds independently along three axes: collision along $x$ axis depends on the mutual position of particles on the $y$ axis. Therefore, bounding boxes *are expressed in transformed coordinates* which are perpendicular in the sense of collision detection. This requires some extra computation: :yref:`Aabb` of sphere in transformed coordinates will no longer be cube, but cuboid, as the sphere itself will appear as ellipsoid after transformation. Inversely, the sphere in simulation space will have a parallelepiped bounding "box", which is cuboid around the ellipsoid in transformed axes (the :yref:`Aabb` has axes aligned with transformed cell basis). This is shown in fig. `fig-cell-shear-aabb`_. The restriction of a single particle not spanning more than half of the transformed axis becomes stringent as :yref:`Aabb` is enlarged due to shear. Considering :yref:`Aabb` of a sphere with radius $r$ in the cell where $x'\equiv x$, $z'\equiv z$, but $\angle(y,y')=\phi$, the $x$-span of the :yref:`Aabb` will be multiplied by $1/\cos\phi$. For the infinite shear $\phi\to\pi/2$, which can be desirable to simulate, we have $1/\cos\phi \to \infty$. Fortunately, this limitation can be easily circumvented by realizing the quasi-identity of all periodic cells which, if repeated in space, create the same grid with their corners: the periodic cell can be flipped, keeping all particle interactions intact, as shown in fig. `fig-cell-flip`_. It only necessitates adjusting the :yref:`Interaction.cellDist` of interactions and re-initialization of the collider (``Collider::invalidatePersistentData``). Cell flipping is implemented in the :yref:`yade.utils.flipCell` function. .. _fig-cell-flip: .. figure:: fig/cell-flip.* Flipping cell (:yref:`yade.utils.flipCell`) to avoid infinite stretch of the bounding boxes' spans with growing $\phi$. Cell flip does not affect interactions from the point of view of the simulation. The periodic arrangement on the left is the same as the one on the right, only the cell is situated differently between identical grid points of repetition; at the same time $|\phi_2|<|\phi_1|$ and sphere bounding box's $x$-span stretched by $1/\cos\phi$ becomes smaller. Flipping can be repeated, making effective infinite shear possible. This algorithm is implemented in :yref:`InsertionSortCollider` and is used whenever simulation is periodic (:yref:`Omega.isPeriodic`); individual :yref:`BoundFunctor's` are responsible for computing sheared :yref:`Aabb's`; currently it is implemented for spheres and facets (in :yref:`Bo1_Sphere_Aabb` and :yref:`Bo1_Facet_Aabb` respectively). .. _fig-cell-shear-aabb: .. figure:: fig/cell-shear-aabb.pdf Constructing axis-aligned bounding box (:yref:`Aabb`) of a sphere in simulation space coordinates (without periodic cell -- left) and transformed cell coordinates (right), where collision detection axes $x'$, $y'$ are not identical with simulation space axes $x$, $y$. Bounds' projection to axes is shown by orange lines. Exact collision detection ^^^^^^^^^^^^^^^^^^^^^^^^^ When the collider detects approximate contact (on the :yref:`Aabb` level) and the contact does not yet exist, it creates *potential* contact, which is subsequently checked by exact collision algorithms (depending on the combination of :yref:`Shapes`). Since particles can interact over many periodic cells (recall we never change their positions in simulation space), the collider embeds the relative cell coordinate of particles in the interaction itself (:yref:`Interaction.cellDist`) as an *integer* vector $c$. Multiplying current cell size $\mat{T}\vec{s}$ by $c$ component-wise, we obtain particle offset $\Delta \vec{x}$ in aperiodic $R^3$; this value is passed (from :yref:`InteractionLoop`) to the functor computing exact collision (:yref:`IGeomFunctor`), which adds it to the position of the particle :yref:`Interaction.id2`. By storing the integral offset $c$, $\Delta\vec{x}$ automatically updates as cell parameters change. .. _sect-periodic-insertion-sort: Periodic insertion sort algorithm ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The extension of sweep and prune algorithm (described in :ref:`sect-sweep-and-prune`) to periodic boundary conditions is non-trivial. Its cornerstone is a periodic variant of the insertion sort algorithm, which involves keeping track of the "period" of each boundary; e.g. taking period $\langle 0,10)$, then $8_1\equiv-2_2<2_2$ (subscript indicating period). Doing so efficiently (without shuffling data in memory around as bound wraps from one period to another) requires moving period boundary rather than bounds themselves and making the comparison work transparently at the edge of the container. This algorithm was also extended to handle non-orthogonal periodic :yref:`Cell` boundaries by working in transformed rather than Cartesian coordinates; this modifies computation of :yref:`Aabb` from Cartesian coordinates in which bodies are positioned (treated in detail in :ref:`sect-cell-approx-collision`). The sort algorithm is tracking :yref:`Aabb` extrema along all axes. At the collider's initialization, each value is assigned an integral period, i.e. its distance from the cell's interior expressed in the cell's dimension along its respective axis, and is wrapped to a value inside the cell. We put the period number in subscript. Let us give an example of coordinate sequence along $x$ axis (in a real case, the number of elements would be even, as there is maximum and minimum value couple for each particle; this demonstration only shows the sorting algorithm, however.) .. math:: \sortlines{& 4_1 &\sortInv& 12_2 &\sortSep& -1_2 &\sortInv& -2_4 &\sortInv& 5_0 &} with cell $x$-size $s_x=10$. The $4_1$ value then means that the real coordinate $x_i$ of this extremum is $x_i+1\cdot10=4$, i.e. $x_i=-4$. The $||$ symbol denotes the periodic cell boundary. Sorting starts from the first element in the cell, i.e. right of $||$, and inverts elements as in the aperiodic variant. The rules are, however, more complicated due to the presence of the boundary $||$: ========================== ============================================================== ($\leq$) stop inverting if neighbors are ordered; ($||\bullet$) current element left of $||$ is below 0 (lower period boundary); in this case, decrement element's period, decrease its coordinate by $s_x$ and move $||$ right; ($\bullet||$) current element right of $||$ is above $s_x$ (upper period boundary); increment element's period, increase its coordinate by $s_x$ and move $||$ left; ($\crossBound$) inversion across $||$ must subtract $s_x$ from the left coordinate during comparison. If the elements are not in order, they are swapped, but they must have their periods changed as they traverse $||$. Apply ($||\circ$) if necessary; ($||\circ$) if after ($\crossBound$) the element that is now right of $||$ has $x_i5_0$, we must do $(12_2-s_x)=2_3\leq5$; we adjust periods when swapping over $||$ and apply ($||\circ$), turning $12_2$ into $2_3$; then we keep inverting, until ($\leq$): .. math:: \sortlines{ & 4_1 &\sortInv& 8_3 &\sortInv& 9_1 &\sortInv& 12_2 &\sortSep& \isnleq{5_0}, & \\ & 4_1 &\sortInv& 8_3 &\sortInv& 9_1 &\sortInv& \isnleq{5_{-1}} &\sortSep& 2_3, & \\ & 4_1 &\sortInv& 8_3 &\sortInv& \isnleq{5_{-1}} &\sortInv& 9_1 &\sortSep& 2_3, & \\ & 4_1 &\sortInv& \isleq{5_{-1}} &\sortInv& 8_3 &\sortInv& 9_1 &\sortSep& 2_3. & \\ } We move (wrapping around) to $\currelem{4_1}$, which is ordered: .. math:: \sortlines{ & \currelem{4_1}\ar@(dr,dl)[rrrrrrrr]|{\geq} &\sortInv& 5_{-1} &\sortInv& 8_3 &\sortInv& 9_1 &\sortSep& 2_3 & } and so is the last element .. math:: \sortlines{ & 4_1 &\sortInv& \isleq{5_{-1}} &\sortInv& 8_3 &\sortInv& 9_1 &\sortSep& 2_3. & } Computational aspects ===================== Cost ---- The DEM computation using an explicit integration scheme demands a relatively high number of steps during simulation, compared to implicit scehemes. The total computation time $Z$ of simulation spanning $T$ seconds (of simulated time), containing $N$ particles in volume $V$ depends on: * linearly, the number of steps $i=T/(s_t \Dtcr)$, where $s_t$ is timestep safety factor; $\Dtcr$ can be estimated by p-wave velocity using $E$ and $\rho$ (sect. :ref:`sect-dt-pwave`) as $\Dtcr^{(p)}=r\sqrt{\frac{\rho}{E}}$. Therefore .. math:: i=\frac{T}{s_t r}\sqrt{\frac{E}{\rho}}. * the number of particles $N$; for fixed value of simulated domain volume $V$ and particle radius $r$ .. math:: N=p\frac{V}{\frac{4}{3}\pi r^3}, where $p$ is packing porosity, roughly $\frac{1}{2}$ for dense irregular packings of spheres of similar radius. The dependency is not strictly linear (which would be the best case), as some algorithms do not scale linearly; a case in point is the sweep and prune collision detection algorithm introduced in sect. :ref:`sect-sweep-and-prune`, with scaling roughly $\bigO{N \log N}$. The number of interactions scales with $N$, as long as packing characteristics are the same. * the number of computational cores $\numCPU$; in the ideal case, the dependency would be inverse-linear were all algorithms parallelized (in Yade, collision detection is not). Let us suppose linear scaling. Additionally, let us suppose that the material to be simulated ($E$, $\rho$) and the simulation setup ($V$, $T$) are given in advance. Finally, dimensionless constants $s_t$, $p$ and $\numCPU$ will have a fixed value. This leaves us with one last degree of freedom, $r$. We may write .. math:: Z\propto iN\frac{1}{\numCPU}=\frac{T}{s_t r}\sqrt{\frac{E}{\rho}} p\frac{V}{\frac{4}{3}\pi r^3} \frac{1}{\numCPU}\propto \frac{1}{r}\frac{1}{r^3}=\frac{1}{r^4}. This (rather trivial) result is essential to realize DEM scaling; if we want to have finer results, refining the "mesh" by halving $r$, the computation time will grow $2^4=16$ times. For very crude estimates, one can use a known simulation to obtain a machine "constant" .. math:: \mu=\frac{Z}{Ni} with the meaning of time per particle and per timestep (in the order of $10^{-6}\,{\rm s}$ for current machines). $\mu$ will be only useful if simulation characteristics are similar and non-linearities in scaling do not have major influence, i.e. $N$ should be in the same order of magnitude as in the reference case. Result indeterminism -------------------- It is naturally expected that running the same simulation several times will give exactly the same results: although the computation is done with finite precision, round-off errors would be deterministically the same at every run. While this is true for *single-threaded* computation where exact order of all operations is given by the simulation itself, it is not true anymore in *multi-threaded* computation which is described in detail in later sections. The straight-forward manner of parallel processing in explicit DEM is given by the possibility of treating interactions in arbitrary order. Strain and stress is evaluated for each interaction independently, but forces from interactions have to be summed up. If summation order is also arbitrary (in Yade, forces are accumulated for each thread in the order interactions are processed, then summed together), then the results can be slightly different. For instance :: (1/10.)+(1/13.)+(1/17.)=0.23574660633484162 (1/17.)+(1/13.)+(1/10.)=0.23574660633484165 As forces generated by interactions are assigned to bodies in quasi-random order, summary force $F_i$ on the body can be different between single-threaded and multi-threaded computations, but also between different runs of multi-threaded computation with exactly the same parameters. Exact thread scheduling by the kernel is not predictable since it depends on asynchronous events (hardware interrupts) and other unrelated tasks running on the system; and it is thread scheduling that ultimately determines summation order of force contributions from interactions. Numerical damping influence ^^^^^^^^^^^^^^^^^^^^^^^^^^^ The effect of summation order can be significantly amplified by the usage of a *discontinuous* damping function in :yref:`NewtonIntegrator` given in :eq:`eq-damping-yade` as .. math:: \frac{(\Delta\vec{F})_{dw}}{\vec{F}_w}=-\lambda_d\sign\vec{F}_w\left(\pprev{\dot{u}}_w+\frac{\curr{\ddot{\vec{u}}}_w\Dt}{2}\right). If the $\sign$ argument is close to zero then the least significant finite precision artifact can determine whether the equation (relative increment of $\vec{F}_w$) is $+\lambda_d$ or $-\lambda_d$. Given commonly used values of $\lambda_d=0.4$, it means that such artifact propagates from least significant place to the most significant one at once. trunk-2017.01a/doc/sphinx/github.rst000066400000000000000000000161071304022710500172610ustar00rootroot00000000000000.. _yade-github-label: ############## Yade on GitHub ############## ************************************************ Fast checkout without GitHub account (read-only) ************************************************ Getting the source code without registering on GitHub can be done via a single command. It will not allow interactions with the remote repository, which you access the read-only way:: git clone https://github.com/yade/trunk.git *************************************************************************** Using branches on GitHub (for frequent commits see git/trunk section below) *************************************************************************** Most usefull commands are below. For more details, see for instance http://gitref.org/index.html and https://help.github.com/articles/set-up-git Setup ===== 1. Register on github.com 2. Add your `SSH key `_ to GitHub: On the GitHub site Click “Account Settings” (top right) > Click “SSH keys” > Click “Add SSH key” 3. Set your username and email through terminal: :: git config --global user.name "Firstname Lastname" git config --global user.email "your_email@youremail.com" You can check these settings with ``git config --list``. 4. `Fork a repo `_: Click the “Fork” button on the https://github.com/yade/trunk 5. Set Up Your Local Repo through terminal: :: git clone git@github.com:username/trunk.git This creates a new folder, named trunk, that contains the whole code. 6. Configure remotes :: cd to/newly/created/folder git remote add upstream git@github.com:yade/trunk.git git fetch upstream Now, your "trunk" folder is linked with the code hosted on github.com. Through appropriate commands explained below, you will be able to update your code to include changes commited by others, or to commit yourself changes that others can get. Retrieving older Commits ======================== In case you want to work with, or compile, an older version of Yade which is not tagged, you can create your own (local) branch of the corresponding daily build. Look `here `_ for details. Committing and updating ======================== For those used to other version control systems, note that the commit mechanisms in Git significantly differs from that of `Bazaar `_ or `SVN `_. Therefore, don't expect to find a one-to-one command replacement. In some cases, however, the equivalent bazaar command is indicated below to ease the transition. Inspecting changes ------------------ You may start by inspecting your changes with a few commands. For the "diff" command, it is convenient to copy from the output of "status" instead of typing the path to modified files. :: git status git diff path/to/modified/file.cpp Committing changes ------------------ Then you proceed to commit through terminal:: git add path/to/new/file.cpp #Version a newly created file: equivalent of "bzr add" git commit path/to/new_or_modified/file.cpp -m'Commit message'`` #Validate a change. It can be done several times after every sufficient change. No equivalent in bzr, it's like commiting to your own local repository git push #Push your changes into GitHub. Equivalent of "bzr commit", except that your are commiting to your own remote branch Changes will be pushed to your personal "fork", If you have tested your changes and you are ready to push them into the main trunk, just do a "pull request" [5] or create a patch from your commit via:: git format-patch origin #create patch file in current folder) and send to the developers mailing list (yade-dev@lists.launchpad.net) as attachment. In either way, after reviewing your changes they will be added to the main trunk. When the pull request has been reviewed and accepted, your changes are integrated in the main trunk. Everyone will get them via ``git fetch``. Updating -------- You may want to get changes done by others:: git fetch upstream #Pull new updates from the upstream to your branch. Eq. of "bzr update", updating the remote branch from the upstream yade/trunk git merge upstream/master #Merge upstream changes into your master-branch (eq. of "bzr update", updating your local repository from the remote branch) Alternatively, this will do fetch+merge all at once (discouraged if you have uncommited changes):: git pull **************************************************************** Working directly on git/trunk (recommended for frequent commits) **************************************************************** This direct access to trunk will sound more familiar to `bzr `_ or `svn `_ users. It is only possible for members of the git team "developpers". Send an email at yade-dev@lists.launchpad.net to join this team (don't forget to tell your git account name). * Get trunk: :: git clone git@github.com:yade/trunk.git This creates a new folder, named trunk, that contains the whole code. * Update :: git pull * Commit to local repository :: git commit filename1 filename2 ... * Push changes to remote trunk :: git push Now, the changes you made are included in the on-line code, and can be get back by every user. To avoid confusing logs after each commit/pull/push cycle, it is better to setup automatic rebase:: git config --global branch.autosetuprebase always Now your file ~/.gitconfig should include: [branch] autosetuprebase = always Check also .git/config file in your local trunk folder (rebase = true): [branch "master"] remote = origin merge = refs/heads/master rebase = true Auto-rebase may have unpleasant side effects by blocking "pull" if you have uncommited changes. In this case you can use "git stash":: git pull lib/SConscript: needs update refusing to pull with rebase: your working tree is not up-to-date git stash #hide the uncommited changes away git pull #now it's ok git push #push the commited changes git stash pop #get uncommited changes back ******************************************** General guidelines for pushing to yade/trunk ******************************************** 1. Set autorebase once on the computer! (see above) 2. Inspect the diff to make sure you will not commit junk code (typically some "cout<<" left here and there), using in terminal: :: git diff file1 Or using your preferred difftool, such as kdiff3: :: git difftool -t kdiff3 file1 Or, alternatively, any GUI for git: gitg, git-cola... 3. Commit selectively: :: git commit file1 file2 file3 -m "message" # is good git commit -a -m "message" # is bad. It is the best way to commit things that should not be commited 4. Be sure to work with an up-to-date version launching: :: git pull 5. Make sure it compiles and that regression tests pass: try ``yade --test`` and ``yade --check``. 6. You can finally let all Yade-users enjoy your work: :: git push **Thanks a lot for your cooperation to Yade!** trunk-2017.01a/doc/sphinx/index-toctree-book.rst000066400000000000000000000005671304022710500215040ustar00rootroot00000000000000.. Yade documentation master file, created by sphinx-quickstart on Mon Nov 16 21:49:34 2009. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. Yade Documentation ^^^^^^^^^^^^^^^^^^^^ .. toctree:: :maxdepth: 2 index-toctree-manuals.rst index-toctree-theory.rst index-toctree-reference.rst trunk-2017.01a/doc/sphinx/index-toctree-manuals.rst000066400000000000000000000003631304022710500222040ustar00rootroot00000000000000 Using and Programming ======================== .. toctree:: :maxdepth: 2 installation.rst introduction.rst tutorial.rst user.rst FEMxDEM.rst prog.rst github.rst citing.rst fullPublications.rst trunk-2017.01a/doc/sphinx/index-toctree-reference.rst000066400000000000000000000001751304022710500225030ustar00rootroot00000000000000 Reference Manual =================== .. toctree:: :maxdepth: 2 yade.wrapper.rst modules.rst fullPublications.rst trunk-2017.01a/doc/sphinx/index-toctree-theory.rst000066400000000000000000000001721304022710500220540ustar00rootroot00000000000000 Theoretical background ======================== .. toctree:: :maxdepth: 2 formulation.rst fullPublications.rst trunk-2017.01a/doc/sphinx/index-toctree.rst000066400000000000000000000011521304022710500205430ustar00rootroot00000000000000.. Yade documentation master file, created by sphinx-quickstart on Mon Nov 16 21:49:34 2009. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. Welcome to Yade's documentation! ================================ .. toctree:: :maxdepth: 2 introduction.rst tutorial.rst user.rst prog.rst installation.rst github.rst formulation.rst yade.wrapper.rst modules.rst FEMxDEM.rst citing.rst publications.rst references.rst Indices and tables ================== * :ref:`genindex` * :ref:`modindex` * :ref:`search` trunk-2017.01a/doc/sphinx/index-toctree_manuals.rst000066400000000000000000000006441304022710500222700ustar00rootroot00000000000000.. Yade documentation master file, created by sphinx-quickstart on Mon Nov 16 21:49:34 2009. You can adapt this file completely to your liking, but it should at least contain the root `toctree` directive. Welcome to Yade's documentation! ================================ .. toctree:: :maxdepth: 2 introduction.rst tutorial.rst user.rst prog.rst installation.rst github.rst citing.rst trunk-2017.01a/doc/sphinx/installation.rst000066400000000000000000000404111304022710500204730ustar00rootroot00000000000000############### Installation ############### Yade can be installed from packages (pre-compiled binaries) or source code. The choice depends on what you need: if you don't plan to modify Yade itself, package installation is easier. In the contrary case, you must download and install the source code. Packages ---------- Pre-built packages are provided for all currently supported Debian and Ubuntu versions and available on `yade-dem.org/packages `_ . These are "daily" versions of the packages which are being updated regularly and, hence, include all the newly added features. To install the daily-version you need to add the repository to your /etc/apt/sources.list, add the PGP-key AA915EEB as trusted and install ``yadedaily``:: sudo bash -c 'echo "deb http://www.yade-dem.org/packages/ xenial/" >> /etc/apt/sources.list' wget -O - http://www.yade-dem.org/packages/yadedev_pub.gpg | sudo apt-key add - sudo apt-get update sudo apt-get install yadedaily If you have another distribution, not Ubuntu Trusty (Version 14.04 LTS), be sure to use the correct name in the first line (for instance, xenial, stretch or jessie). For the list of currently supported distributions, please visit `yade-dem.org/packages `_. After that you can normally start Yade using the command ``yadedaily`` or ``yadedaily-batch``. ``yadedaily`` on older distributions can have some disabled features due to older library versions, shipped with particular distribution. The Git-repository for packaging stuff is available on `GitHub `_. Each branch corresponds to one distribution, e.g., xenial, stretch etc. The scripts for building all of this stuff are `here `__. It uses "pbuilder" to build packages, so all packages are built in a clean environment. If you do not need ``yadedaily``-package any more, just remove the corresponding line in /etc/apt/sources.list and the package itself:: sudo apt-get remove yadedaily To remove our key from keyring, execute the following command:: sudo apt-key remove AA915EEB Since 2011, all Ubuntu (starting from 11.10, Oneiric) and Debian (starting from Wheezy) versions have Yade in their main repositories. There are only stable releases in place. To install Yade, run the following:: sudo apt-get install yade After that you can normally start Yade using the command ``yade`` or ``yade-batch``. To check, what version of Yade is included in your specific distribution, visit `Ubuntu `_ or `Debian `_. The `Debian-Backports `_ repository is updated regularly to bring the newest Yade version to the users of stable Debians. Daily and stable Yade versions can coexist without any conflicts, i.e., you can use `yade`` and ``yadedaily`` at the same time. Source code ------------ Installation from source code is reasonable, when you want to add or modify constitutive laws, engines, functions etc. Installing the latest trunk version allows one to use newly added features, which are not yet available in packaged versions. Download ^^^^^^^^^^ If you want to install from source, you can install either a release (numbered version, which is frozen) or the current development version (updated by the developers frequently). You should download the development version (called ``trunk``) if you want to modify the source code, as you might encounter problems that will be fixed by the developers. Release versions will not be updated (except for updates due to critical and easy-to-fix bugs), but generally they are more stable than the trunk. #. Releases can be downloaded from the `download page `_, as compressed archive. Uncompressing the archive gives you a directory with the sources. #. The development version (``trunk``) can be obtained from the `code repository `_ at GitHub. We use `GIT `_ (the ``git`` command) for code management (install the ``git`` package on your system and create a `GitHub account `__):: git clone git@github.com:yade/trunk.git will download the whole code repository of the ``trunk``. Check out :ref:`yade-github-label` for more details on how to collaborate using ``git``. Alternatively, a read-only checkout is possible via https without a GitHub account (easier if you don't want to modify the trunk version):: git clone https://github.com/yade/trunk.git For those behind a firewall, you can download the sources from our `GitHub `__ repository as compressed archive. Release and trunk sources are compiled in exactly the same way. In order to get notifications about changes to the truck (i.e., ``commits``), use `watch option on GitHub `_. Prerequisites ^^^^^^^^^^^^^ Yade relies on a number of external software to run; they are checked before the compilation starts. Some of them are only optional. The last ones are only relevant for using the fluid coupling module (:yref:`FlowEngine`). * `cmake `_ build system * `gcc `_ compiler (g++); other compilers will not work; you need g++>=4.2 for openMP support * `boost `_ 1.47 or later * `Qt `_ library * `freeglut3 `_ * `libQGLViewer `_ * `python `_, `numpy `_, `ipython `_ * `matplotlib `_ * `eigen `_ algebra library (minimal required version 3.2.1) * `gdb `_ debugger * `sqlite3 `_ database engine * `Loki `_ library * `VTK `_ library (optional but recommended) * `CGAL `_ library (optional) * `SuiteSparse `_ sparse algebra library (fluid coupling, optional, requires eigen>=3.1) * `OpenBLAS `_ optimized and parallelized alternative to the standard blas+lapack (fluid coupling, optional) * `Metis `_ matrix preconditioning (fluid coupling, optional) Most of the list above is very likely already packaged for your distribution. In case you are confronted with some errors concerning not available packages (e.g., package libmetis-dev is not available) it may be necessary to add yade external ppa from https://launchpad.net/~yade-users/+archive/external (see below) as well as http://www.yade-dem.org/packages (see the top of this page):: sudo add-apt-repository ppa:yade-users/external sudo apt-get update The following commands have to be executed in the command line of your corresponding distribution. Just copy&paste to the terminal. Note, to execute these commands you need root privileges. * **Ubuntu**, **Debian** and their derivatives:: sudo apt-get install cmake git freeglut3-dev libloki-dev \ libboost-all-dev fakeroot dpkg-dev build-essential g++ \ python-dev ipython python-matplotlib libsqlite3-dev python-numpy python-tk gnuplot \ libgts-dev python-pygraphviz libvtk6-dev python-numpy libeigen3-dev \ python-xlib python-pyqt5 pyqt5-dev-tools python-pyqt5.qtwebkit gtk2-engines-pixbuf python-argparse \ libqglviewer-dev python-imaging libjs-jquery python-sphinx python-git python-bibtex \ libxmu-dev libxi-dev libcgal-dev help2man libbz2-dev zlib1g-dev python-minieigen Some of the packages (for example, cmake, eigen3) are mandatory, some of them are optional. Watch for notes and warnings/errors, which are shown by ``cmake`` during the configuration step. If the missing package is optional, some of Yade features will be disabled (see the messages at the end of the configuration). Additional packages, which can become mandatory later:: sudo apt-get install python-gts For effective usage of direct solvers in the PFV-type fluid coupling, the following libraries are recommended, together with eigen>=3.1: blas, lapack, suitesparse, and metis. All four of them are available in many different versions. Different combinations are possible and not all of them will work. The following was found to be effective on recent deb-based systems. On ubuntu 12.04, better compile openblas with USE_OPENMP=1, else yade will run on a single core:: sudo apt-get install libopenblas-dev libsuitesparse-metis-dev Some packages listed here are relatively new and they can be absent in your distribution (for example, libmetis-dev or python-gts). They can be installed from `yade-dem.org/packages `_ or from our `external PPA `_. If not installed the related features will be disabled automatically. If you are using other distributions than Debian or its derivatives you should install the software packages listed above. Their names in other distributions can differ from the names of the Debian-packages. .. warning:: If you have Ubuntu 14.04 Trusty, you need to add -DCMAKE_CXX_FLAGS=-frounding-math during the configuration step of compilation (see below) or to install libcgal-dev from our `external PPA `_. Otherwise the following error occurs on AMD64 architectures:: terminate called after throwing an instance of 'CGAL::Assertion_exception' what(): CGAL ERROR: assertion violation! Expr: -CGAL_IA_MUL(-1.1, 10.1) != CGAL_IA_MUL(1.1, 10.1) File: /usr/include/CGAL/Interval_nt.h Line: 209 Explanation: Wrong rounding: did you forget the -frounding-math option if you use GCC (or -fp-model strict for Intel)? Aborted Compilation ^^^^^^^^^^^ You should create a separate build-place-folder, where Yade will be configured and where the source code will be compiled. Here is an example for a folder structure:: myYade/ ## base directory trunk/ ## folder for source code in which you use github build/ ## folder in which the sources will be compiled; build-directory; use cmake here install/ ## install folder; contains the executables Then, inside this build-directory you should call ``cmake`` to configure the compilation process:: cmake -DCMAKE_INSTALL_PREFIX=/path/to/installfolder /path/to/sources For the folder structure given above call the following command in the folder "build":: cmake -DCMAKE_INSTALL_PREFIX=../install ../trunk Additional options can be configured in the same line with the following syntax:: cmake -DOPTION1=VALUE1 -DOPTION2=VALUE2 The following options are available: * CMAKE_INSTALL_PREFIX: path where Yade should be installed (/usr/local by default) * LIBRARY_OUTPUT_PATH: path to install libraries (lib by default) * DEBUG: compile in debug-mode (OFF by default) * CMAKE_VERBOSE_MAKEFILE: output additional information during compiling (OFF by default) * SUFFIX: suffix, added after binary-names (version number by default) * NOSUFFIX: do not add a suffix after binary-name (OFF by default) * YADE_VERSION: explicitly set version number (is defined from git-directory by default) * ENABLE_GUI: enable GUI option (ON by default) * ENABLE_CGAL: enable CGAL option (ON by default) * ENABLE_VTK: enable VTK-export option (ON by default) * ENABLE_OPENMP: enable OpenMP-parallelizing option (ON by default) * ENABLE_GTS: enable GTS-option (ON by default) * ENABLE_GL2PS: enable GL2PS-option (ON by default) * ENABLE_LINSOLV: enable LINSOLV-option (ON by default) * ENABLE_PFVFLOW: enable PFVFLOW-option, FlowEngine (ON by default) * ENABLE_LBMFLOW: enable LBMFLOW-option, LBM_ENGINE (ON by default) * ENABLE_SPH: enable SPH-option, Smoothed Particle Hydrodynamics (OFF by default) * ENABLE_LIQMIGRATION: enable LIQMIGRATION-option, see [Mani2013]_ for details (OFF by default) * ENABLE_MASK_ARBITRARY: enable MASK_ARBITRARY option (OFF by default) * ENABLE_PROFILING: enable profiling, e.g., shows some more metrics, which can define bottlenecks of the code (OFF by default) * runtimePREFIX: used for packaging, when install directory is not the same as runtime directory (/usr/local by default) * CHUNKSIZE: specifiy the chunk size if you want several sources to be compiled at once. Increases compilation speed but RAM-consumption during compilation as well (1 by default) * VECTORIZE: enables vectorization and alignment in Eigen3 library, experimental (OFF by default) * USE_QT5: use QT5 for GUI, experimental (ON by default) For using more extended parameters of cmake, please follow the corresponding documentation on `https://cmake.org/documentation `_. If cmake finishes without errors, you will see all enabled and disabled options at the end. Then start the actual compilation process with:: make The compilation process can take a considerable amount of time, be patient. If you are using a multi-core systems you can use the parameter ``-j`` to speed-up the compilation and split the compilation onto many cores. For example, on 4-core machines it would be reasonable to set the parameter ``-j4``. Note, Yade requires approximately 3GB RAM per core for compilation, otherwise the swap-file will be used and compilation time dramatically increases. The installation is performed with the following command:: make install The ``install`` command will in fact also recompile if source files have been modified. Hence there is no absolute need to type the two commands separately. You may receive make errors if you don't have permission to write into the target folder. These errors are not critical but without writing permissions Yade won't be installed in /usr/local/bin/. After the compilation finished successfully, the new built can be started by navigating to /path/to/installfolder/bin and calling yade via (based on version yade-2014-02-20.git-a7048f4):: cd /path/to/installfolder/bin ./yade-2014-02-20.git-a7048f4 For building the documentation you should at first execute the command ``make install`` and then ``make doc`` to build it. The generated files will be stored in your current install directory /path/to/installfolder/share/doc/yade-your-version. Once again writing permissions are necessary for installing into /usr/local/share/doc/. To open your local documentation go into the folder html and open the file index.html with a browser. ``make manpage`` command generates and moves manpages in a standard place. ``make check`` command executes standard test to check the functionality of the compiled program. Yade can be compiled not only by GCC-compiler, but also by `CLANG `_ front-end for the LLVM compiler. For that you set the environment variables CC and CXX upon detecting the C and C++ compiler to use:: export CC=/usr/bin/clang export CXX=/usr/bin/clang++ cmake -DOPTION1=VALUE1 -DOPTION2=VALUE2 Clang does not support OpenMP-parallelizing for the moment, that is why the feature will be disabled. Speed-up compilation ^^^^^^^^^^^^^^^^^^^^^ When spliting the compilation on many cores (``make -jN``), ``N`` is limited by the available cores and memory. It is possible to use more cores if remote computers are available, ditributing the compilation with `ditscc `_ (see distcc documentation for configuring slaves and master):: export CC=distcc gcc export CXX=distcc g++ cmake [options as usual] make -jN In addition, and independently of distcc, caching previous compilations with `ccache `_ can speed up re-compilation:: export CC=ccache gcc export CXX=ccache g++ cmake [options as usual] The two tools can be combined very simply, adding to the above exports:: export CCACHE_PREFIX="distcc" Yubuntu ------------ If you are not running Ubuntu nor Debian, there is a way to create a Yubuntu `live-usb `_ on any usb mass-storage device (minimum recommended size is 5GB). It is a way to make a bootable usb-key with a preinstalled minimalist operating system (Xubuntu), including Yadedaily and Paraview. More informations about this alternative are available `here `_ (see the README file first). trunk-2017.01a/doc/sphinx/introduction.rst000066400000000000000000000615611304022710500205240ustar00rootroot00000000000000############### Introduction ############### Getting started =============== .. ipython:: :suppress: In [1]: from yade import * In [7]: O.reset() Before you start moving around in Yade, you should have some prior knowledge. * Basics of command line in your Linux system are necessary for running yade. Look on the web for tutorials. * Python language; we recommend the official `Python tutorial `_. Reading further documents on the topis, such as `Dive into Python `_ will certainly not hurt either. You are advised to try all commands described yourself. Don't be afraid to experiment. Starting yade ------------- Yade is being run primarily from terminal; the name of command is ``yade``. [#f1]_ (In case you did not install from package, you might need to give specific path to the command [#fcmd]_ ):: \$ yade Welcome to Yade TCP python prompt on localhost:9001, auth cookie `sdksuy' TCP info provider on localhost:21000 [[ ^L clears screen, ^U kills line. F12 controller, F11 3d view, F10 both, F9 generator, F8 plot. ]] Yade [1]: These initial lines give you some information about * some information for :ref:`remoteaccess`, which you are unlikely to need now; * basic help for the command-line that just appeared (``Yade [1]:``). Type ``quit()``, ``exit()`` or simply press ``^D`` to quit Yade. The command-line is `ipython `_, python shell with enhanced interactive capabilities; it features persistent history (remembers commands from your last sessions), searching and so on. See ipython's documentation for more details. Typically, you will not type Yade commands by hand, but use *scripts*, python programs describing and running your simulations. Let us take the most simple script that will just print "Hello world!":: print "Hello world!" Saving such script as ``hello.py``, it can be given as argument to yade:: \$ yade hello.py Welcome to Yade TCP python prompt on localhost:9001, auth cookie `askcsu' TCP info provider on localhost:21000 Running script hello.py ## the script is being run Hello world! ## output from the script [[ ^L clears screen, ^U kills line. F12 controller, F11 3d view, F10 both, F9 generator, F8 plot. ]] Yade [1]: Yade will run the script and then drop to the command-line again. [#f2]_ If you want Yade to quit immediately after running the script, use the ``-x`` switch:: \$ yade -x script.py There is more command-line options than just ``-x``, run ``yade -h`` to see all of them. Options: --version show program's version number and exit -h, --help show this help message and exit -j THREADS, --threads=THREADS Number of OpenMP threads to run; defaults to 1. Equivalent to setting OMP_NUM_THREADS environment variable. --cores=CORES Set number of OpenMP threads (as \-\-threads) and in addition set affinity of threads to the cores given. --update Update deprecated class names in given script(s) using text search & replace. Changed files will be backed up with ~ suffix. Exit when done without running any simulation. --nice=NICE Increase nice level (i.e. decrease priority) by given number. -x Exit when the script finishes -n Run without graphical interface (equivalent to unsetting the DISPLAY environment variable) --test Run regression test suite and exit; the exists status is 0 if all tests pass, 1 if a test fails and 2 for an unspecified exception. --check Run a series of user-defined check tests as described in /build/buildd/yade- daily-1+3021+27~lucid1/scripts/test/checks/README --performance Starts a test to measure the productivity --no-gdb Do not show backtrace when yade crashes (only effective with \-\-debug). .. rubric:: Footnotes .. [#f1] The executable name can carry a suffix, such as version number (``yade-0.20``), depending on compilation options. Packaged versions on Debian systems always provide the plain ``yade`` alias, by default pointing to latest stable version (or latest snapshot, if no stable version is installed). You can use ``update-alternatives`` to change this. .. [#fcmd] In general, Unix *shell* (command line) has environment variable ``PATH`` defined, which determines directories searched for executable files if you give name of the file without path. Typically, \$PATH contains ``/usr/bin/``, ``/usr/local/bin``, ``/bin`` and others; you can inspect your ``PATH`` by typing ``echo \$PATH`` in the shell (directories are separated by ``:``). If Yade executable is not in directory contained in ``PATH``, you have to specify it by hand, i.e. by typing the path in front of the filename, such as in ``/home/user/bin/yade`` and similar. You can also navigate to the directory itself (``cd ~/bin/yade``, where ``~`` is replaced by your home directory automatically) and type ``./yade`` then (the ``.`` is the current directory, so ``./`` specifies that the file is to be found in the current directory). To save typing, you can add the directory where Yade is installed to your ``PATH``, typically by editing ``~/.profile`` (in normal cases automatically executed when shell starts up) file adding line like ``export PATH=/home/user/bin:\$PATH``. You can also define an *alias* by saying ``alias yade="/home/users/bin/yade"`` in that file. Details depend on what shell you use (bash, zsh, tcsh, …) and you will find more information in introductory material on Linux/Unix. .. [#f2] Plain Python interpreter exits once it finishes running the script. The reason why Yade does the contrary is that most of the time script only sets up simulation and lets it run; since computation typically runs in background thread, the script is technically finished, but the computation is running. Creating simulation -------------------- To create simulation, one can either use a specialized class of type :yref:`FileGenerator` to create full scene, possibly receiving some parameters. Generators are written in c++ and their role is limited to well-defined scenarios. For instance, to create triaxial test scene: .. ipython:: In [1]: TriaxialTest(numberOfGrains=200).load() In [2]: len(O.bodies) 1006 Generators are regular yade objects that support attribute access. It is also possible to construct the scene by a python script; this gives much more flexibility and speed of development and is the recommended way to create simulation. Yade provides modules for streamlined body construction, import of geometries from files and reuse of common code. Since this topic is more involved, it is explained in the *User's manual*. .. ipython:: :suppress: In [7]: O.reset() Running simulation ------------------ As explained below, the loop consists in running defined sequence of engines. Step number can be queried by ``O.iter`` and advancing by one step is done by ``O.step()``. Every step advances *virtual time* by current timestep, ``O.dt``: .. ipython:: In [1]: O.iter In [1]: O.time In [1]: O.dt=1e-4 In [1]: O.step() In [1]: O.iter 1 In [1]: O.time 1e-4 Normal simulations, however, are run continuously. Starting/stopping the loop is done by ``O.run()`` and ``O.pause()``; note that ``O.run()`` returns control to Python and the simulation runs in background; if you want to wait for it finish, use ``O.wait()``. Fixed number of steps can be run with ``O.run(1000)``, ``O.run(1000,True)`` will run and wait. To stop at absolute step number, ``O.stopAtIter`` can be set and ``O.run()`` called normally. .. ipython:: In [1]: O.run() In [1]: O.pause() In [1]: O.iter 104587 In [1]: O.run(100000,True) In [1]: O.iter 204587 In [1]: O.stopAtIter=500000 In [1]: O.wait() In [1]: O.iter 500000 Saving and loading ------------------ Simulation can be saved at any point to a binary file (optionaly compressed if the filename has extensions such as ".gz" or ".bz2"). Saving to a XML file is also possible though resulting in larger files and slower save/load, it is used when the filename contains "xml". With some limitations, it is generally possible to load the scene later and resume the simulation as if it were not interrupted. Note that since the saved scene is a dump of Yade's internal objects, it might not (probably will not) open with different Yade version. .. ipython:: In [1]: O.save('/tmp/a.yade.bz2') In [2]: O.reload() @suppress In [4]: O.save('/tmp/another.yade.bz2') In [3]: O.load('/tmp/another.yade.bz2') The principal use of saving the simulation to XML is to use it as temporary in-memory storage for checkpoints in simulation, e.g. for reloading the initial state and running again with different parameters (think tension/compression test, where each begins from the same virgin state). The functions ``O.saveTmp()`` and ``O.loadTmp()`` can be optionally given a slot name, under which they will be found in memory: .. ipython:: In [1]: O.saveTmp() In [1]: O.loadTmp() In [1]: O.saveTmp('init') ## named memory slot In [1]: O.loadTmp('init') Simulation can be reset to empty state by ``O.reset()``. It can be sometimes useful to run different simulation, while the original one is temporarily suspended, e.g. when dynamically creating packing. ``O.switchWorld()`` toggles between the primary and secondary simulation. Graphical interface -------------------- Yade can be optionally compiled with qt4-based graphical interface. It can be started by pressing ``F12`` in the command-line, and also is started automatically when running a script. .. image:: fig/qt-gui.png The windows with buttons is called ``Controller`` (can be invoked by ``yade.qt.Controller()`` from python): #. The *Simulation* tab is mostly self-explanatory, and permits basic simulation control. #. The *Display* tab has various rendering-related options, which apply to all opened views (they can be zero or more, new one is opened by the *New 3D* button). #. The *Python* tab has only a simple text entry area; it can be useful to enter python commands while the command-line is blocked by running script, for instance. 3d views can be controlled using mouse and keyboard shortcuts; help is displayed if you press the ``h`` key while in the 3d view. Note that having the 3d view open can slow down running simulation significantly, it is meant only for quickly checking whether the simulation runs smoothly. Advanced post-processing is described in dedicated section. Architecture overview ====================== .. ipython:: :suppress: In [12]: from yade import * In [1]: from yade import utils In [7]: O.reset() In the following, a high-level overview of Yade architecture will be given. As many of the features are directly represented in simulation scripts, which are written in Python, being familiar with this language will help you follow the examples. For the rest, this knowledge is not strictly necessary and you can ignore code examples. Data and functions ------------------- To assure flexibility of software design, yade makes clear distinction of 2 families of classes: *data* components and *functional* components. The former only store data without providing functionality, while the latter define functions operating on the data. In programming, this is known as *visitor* pattern (as functional components "visit" the data, without being bound to them explicitly). Entire simulation, i.e. both data and functions, are stored in a single ``Scene`` object. It is accessible through the :yref:`Omega` class in python (a singleton), which is by default stored in the ``O`` global variable: .. ipython:: Yade [1]: O.bodies # some data components Yade [2]: len(O.bodies) # there are no bodies as of yet Yade [3]: O.engines # functional components, empty at the moment Data components ^^^^^^^^^^^^^^^ Bodies """"""" Yade simulation (class ``Scene``, but hidden inside :yref:`Omega` in Python) is represented by :yref:`Bodies`, their :yref:`Interactions` and resultant generalized :yref:`forces` (all stored internally in special containers). Each :yref:`Body` comprises the following: :yref:`Shape` represents particle's geometry (neutral with regards to its spatial orientation), such as :yref:`Sphere`, :yref:`Facet` or inifinite :yref:`Wall`; it usually does not change during simulation. :yref:`Material` stores characteristics pertaining to mechanical behavior, such as Young's modulus or density, which are independent on particle's shape and dimensions; usually constant, might be shared amongst multiple bodies. :yref:`State` contains state variable variables, in particular spatial :yref:`position` and :yref:`orientation`, :yref:`linear` and :yref:`angular` velocity, :yref:`linear` and :yref:`angular` accelerator; it is updated by the :yref:`integrator` at every step. Derived classes can hold additional data, e.g. :yref:`averaged damage`. :yref:`Bound` is used for approximate ("pass 1") contact detection; updated as necessary following body's motion. Currently, :yref:`Aabb` is used most often as :yref:`Bound`. Some bodies may have no :yref:`Bound`, in which case they are exempt from contact detection. (In addition to these 4 components, bodies have several more minor data associated, such as :yref:`Body::id` or :yref:`Body::mask`.) All these four properties can be of different types, derived from their respective base types. Yade frequently makes decisions about computation based on those types: :yref:`Sphere` + :yref:`Sphere` collision has to be treated differently than :yref:`Facet` + :yref:`Sphere` collision. Objects making those decisions are called :yref:`Dispatcher`'s and are essential to understand Yade's functioning; they are discussed below. Explicitly assigning all 4 properties to each particle by hand would be not practical; there are utility functions defined to create them with all necessary ingredients. For example, we can create sphere particle using :yref:`yade.utils.sphere`: .. ipython:: In [3]: s=utils.sphere(center=[0,0,0],radius=1) In [5]: s.shape, s.state, s.mat, s.bound In [6]: s.state.pos In [7]: s.shape.radius We see that a sphere with material of type :yref:`FrictMat` (default, unless you provide another :yref:`Material`) and bounding volume of type :yref:`Aabb` (axis-aligned bounding box) was created. Its position is at origin and its radius is 1.0. Finally, this object can be inserted into the simulation; and we can insert yet one sphere as well. .. ipython:: In [1]: O.bodies.append(s) 0 In [2]: O.bodies.append(utils.sphere([0,0,2],.5)) 1 In each case, return value is :yref:`Body.id` of the body inserted. Since till now the simulation was empty, its id is 0 for the first sphere and 1 for the second one. Saving the id value is not necessary, unless you want access this particular body later; it is remembered internally in :yref:`Body` itself. You can address bodies by their id: .. ipython:: In [1]: O.bodies[1].state.pos In [2]: O.bodies[100] IndexError: Body id out of range. Adding the same body twice is, for reasons of the id uniqueness, not allowed: .. ipython:: In [1]: O.bodies.append(s) Bodies can be iterated over using standard python iteration syntax: .. ipython:: In [1]: for b in O.bodies: ...: print b.id,b.shape.radius ...: 0 1.0 1 0.5 Interactions """"""""""""""" :yref:`Interactions` are always between pair of bodies; usually, they are created by the collider based on spatial proximity; they can, however, be created explicitly and exist independently of distance. Each interaction has 2 components: :yref:`IGeom` holding geometrical configuration of the two particles in collision; it is updated automatically as the particles in question move and can be queried for various geometrical characteristics, such as penetration distance or shear strain. Based on combination of types of :yref:`Shapes` of the particles, there might be different storage requirements; for that reason, a number of derived classes exists, e.g. for representing geometry of contact between :yref:`Sphere+Sphere`, :yref:`Cylinder+Sphere` etc. Note, however, that it is possible to represent many type of contacts with the basic sphere-sphere geometry (for instance in :yref:`Ig2_Wall_Sphere_ScGeom`). :yref:`IPhys` representing non-geometrical features of the interaction; some are computed from :yref:`Materials` of the particles in contact using some averaging algorithm (such as contact stiffness from Young's moduli of particles), others might be internal variables like damage. Suppose now interactions have been already created. We can access them by the id pair: .. ipython:: :suppress: In [1]: O.engines=[InteractionLoop([Ig2_Sphere_Sphere_ScGeom()],[Ip2_FrictMat_FrictMat_FrictPhys()],[])] In [2]: utils.createInteraction(0,1); .. ipython:: In [1]: O.interactions[0,1] In [2]: O.interactions[1,0] # order of ids is not important In [2]: i=O.interactions[0,1] In [3]: i.id1,i.id2 (0, 1) In [4]: i.geom In [5]: i.phys In [6]: O.interactions[100,10111] ValueError: No such interaction Generalized forces """""""""""""""""""" Generalized forces include force, torque and forced displacement and rotation; they are stored only temporarliy, during one computation step, and reset to zero afterwards. For reasons of parallel computation, they work as accumulators, i.e. only can be added to, read and reset. .. ipython:: Yade [1]: O.forces.f(0) Yade [2]: O.forces.addF(0,Vector3(1,2,3)) Yade [3]: O.forces.f(0) @suppress In [7]: O.reset() You will only rarely modify forces from Python; it is usually done in c++ code and relevant documentation can be found in the Programmer's manual. .. _function-components: Function components ^^^^^^^^^^^^^^^^^^^^ In a typical DEM simulation, the following sequence is run repeatedly: * reset forces on bodies from previous step * approximate collision detection (pass 1) * detect exact collisions of bodies, update interactions as necessary * solve interactions, applying forces on bodies * apply other external conditions (gravity, for instance). * change position of bodies based on forces, by integrating motion equations. .. _img-yade-iter-loop: .. figure:: fig/yade-iter-loop.* Typical simulation loop; each step begins at body-centered bit at 11 o'clock, continues with interaction bit, force application bit, miscillanea and ends with time update. Each of these actions is represented by an :yref:`Engine`, functional element of simulation. The sequence of engines is called *simulation loop*. .. _sect-simulation-loop: Engines """"""""" Simulation loop, shown at img. img-yade-iter-loop_, can be described as follows in Python (details will be explained later); each of the ``O.engine`` items is instance of a type deriving from :yref:`Engine`: .. code-block:: python O.engines=[ # reset forces ForceResetter(), # approximate collision detection, create interactions InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), # handle interactions InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), # apply other conditions GravityEngine(gravity=(0,0,-9.81)), # update positions using Newton's equations NewtonIntegrator() ] There are 3 fundamental types of Engines: :yref:`GlobalEngines` operating on the whole simulation (e.g. :yref:`GravityEngine` looping over all bodies and applying force based on their mass) :yref:`PartialEngine` operating only on some pre-selected bodies (e.g. :yref:`ForceEngine` applying constant force to some bodies) :yref:`Dispatchers` do not perform any computation themselves; they merely call other functions, represented by function objects, :yref:`Functors`. Each functor is specialized, able to handle certain object types, and will be dispatched if such obejct is treated by the dispatcher. .. _dispatchers-and-functors: Dispatchers and functors """"""""""""""""""""""""" For approximate collision detection (pass 1), we want to compute :yref:`bounds` for all :yref:`bodies` in the simulation; suppose we want bound of type :yref:`axis-aligned bounding box`. Since the exact algorithm is different depending on particular :yref:`shape`, we need to provide functors for handling all specific cases. The line:: InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]) creates :yref:`InsertionSortCollider` (it internally uses :yref:`BoundDispatcher`, but that is a detail). It traverses all bodies and will, based on :yref:`shape` type of each :yref:`body`, dispatch one of the functors to create/update :yref:`bound` for that particular body. In the case shown, it has 2 functors, one handling :yref:`spheres`, another :yref:`facets`. The name is composed from several parts: ``Bo`` (functor creating :yref:`Bound`), which accepts ``1`` type :yref:`Sphere` and creates an :yref:`Aabb` (axis-aligned bounding box; it is derived from :yref:`Bound`). The :yref:`Aabb` objects are used by :yref:`InsertionSortCollider` itself. All ``Bo1`` functors derive from :yref:`BoundFunctor`. The next part, reading .. code-block:: python InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), hides 3 internal dispatchers within the :yref:`InteractionLoop` engine; they all operate on interactions and are, for performance reasons, put together: :yref:`IGeomDispatcher` uses the first set of functors (``Ig2``), which are dispatched based on combination of ``2`` :yref:`Shapes` objects. Dispatched functor resolves exact collision configuration and creates :yref:`IGeom` (whence ``Ig`` in the name) associated with the interaction, if there is collision. The functor might as well fail on approximate interactions, indicating there is no real contact between the bodies, even if they did overlap in the approximate collision detection. #. The first functor, :yref:`Ig2_Sphere_Sphere_ScGeom`, is called on interaction of 2 :yref:`Spheres` and creates :yref:`ScGeom` instance, if appropriate. #. The second functor, :yref:`Ig2_Facet_Sphere_ScGeom`, is called for interaction of :yref:`Facet` with :yref:`Sphere` and might create (again) a :yref:`ScGeom` instance. All ``Ig2`` functors derive from :yref:`IGeomFunctor` (they are documented at the same place). :yref:`IPhysDispatcher` dispatches to the second set of functors based on combination of ``2`` :yref:`Materials`; these functors return return :yref:`IPhys` instance (the ``Ip`` prefix). In our case, there is only 1 functor used, :yref:`Ip2_FrictMat_FrictMat_FrictPhys`, which create :yref:`FrictPhys` from 2 :yref:`FrictMat's`. ``Ip2`` functors are derived from :yref:`IPhysFunctor`. :yref:`LawDispatcher` dispatches to the third set of functors, based on combinations of :yref:`IGeom` and :yref:`IPhys` (wherefore ``2`` in their name again) of each particular interaction, created by preceding functors. The ``Law2`` functors represent "constitutive law"; they resolve the interaction by computing forces on the interacting bodies (repulsion, attraction, shear forces, …) or otherwise update interaction state variables. ``Law2`` functors all inherit from :yref:`LawFunctor`. There is chain of types produced by earlier functors and accepted by later ones; the user is responsible to satisfy type requirement (see img. img-dispatch-loop_). An exception (with explanation) is raised in the contrary case. .. _img-dispatch-loop: .. figure:: fig/dispatch-loop.* :width: 13cm Chain of functors producing and accepting certain types. In the case shown, the ``Ig2`` functors produce :yref:`ScfGeom` instances from all handled :yref:`Shape` combinations; the ``Ig2`` functor produces :yref:`FrictMat`. The constitutive law functor ``Law2`` accepts the combination of types produced. Note that the types are stated in the functor's class names. .. note:: When Yade starts, O.engines is filled with a reasonable default list, so that it is not strictly necessary to redefine it when trying simple things. The default scene will handle spheres, boxes, and facets with :yref:`frictional` properties correctly, and adjusts the timestep dynamically. You can find an example in simple-scene-default-engines.py. trunk-2017.01a/doc/sphinx/ipython_console_highlighting.py000066400000000000000000000101271304022710500235540ustar00rootroot00000000000000"""reST directive for syntax-highlighting ipython interactive sessions. XXX - See what improvements can be made based on the new (as of Sept 2009) 'pycon' lexer for the python console. At the very least it will give better highlighted tracebacks. """ #----------------------------------------------------------------------------- # Needed modules # Standard library import re # Third party from pygments.lexer import Lexer, do_insertions from pygments.lexers.agile import (PythonConsoleLexer, PythonLexer, PythonTracebackLexer) from pygments.token import Comment, Generic from sphinx import highlighting #----------------------------------------------------------------------------- # Global constants line_re = re.compile('.*?\n') #----------------------------------------------------------------------------- # Code begins - classes and functions class IPythonConsoleLexer(Lexer): """ For IPython console output or doctests, such as: .. sourcecode:: ipython In [1]: a = 'foo' In [2]: a Out[2]: 'foo' In [3]: print a foo In [4]: 1 / 0 Notes: - Tracebacks are not currently supported. - It assumes the default IPython prompts, not customized ones. """ name = 'IPython console session' aliases = ['ipython'] mimetypes = ['text/x-ipython-console'] input_prompt = re.compile("(In \[[0-9]+\]: )|( \.\.\.+:)") output_prompt = re.compile("(Out\[[0-9]+\]: )|( \.\.\.+:)") continue_prompt = re.compile(" \.\.\.+:") tb_start = re.compile("\-+") def get_tokens_unprocessed(self, text): pylexer = PythonLexer(**self.options) tblexer = PythonTracebackLexer(**self.options) curcode = '' insertions = [] for match in line_re.finditer(text): line = match.group() input_prompt = self.input_prompt.match(line) continue_prompt = self.continue_prompt.match(line.rstrip()) output_prompt = self.output_prompt.match(line) if line.startswith("#"): insertions.append((len(curcode), [(0, Comment, line)])) elif input_prompt is not None: insertions.append((len(curcode), [(0, Generic.Prompt, input_prompt.group())])) curcode += line[input_prompt.end():] elif continue_prompt is not None: insertions.append((len(curcode), [(0, Generic.Prompt, continue_prompt.group())])) curcode += line[continue_prompt.end():] elif output_prompt is not None: # Use the 'error' token for output. We should probably make # our own token, but error is typicaly in a bright color like # red, so it works fine for our output prompts. insertions.append((len(curcode), [(0, Generic.Error, output_prompt.group())])) curcode += line[output_prompt.end():] else: if curcode: for item in do_insertions(insertions, pylexer.get_tokens_unprocessed(curcode)): yield item curcode = '' insertions = [] yield match.start(), Generic.Output, line if curcode: for item in do_insertions(insertions, pylexer.get_tokens_unprocessed(curcode)): yield item def setup(app): """Setup as a sphinx extension.""" # This is only a lexer, so adding it below to pygments appears sufficient. # But if somebody knows that the right API usage should be to do that via # sphinx, by all means fix it here. At least having this setup.py # suppresses the sphinx warning we'd get without it. pass #----------------------------------------------------------------------------- # Register the extension as a valid pygments lexer highlighting.lexers['ipython'] = IPythonConsoleLexer() trunk-2017.01a/doc/sphinx/ipython_directive.py000066400000000000000000000442231304022710500213470ustar00rootroot00000000000000# -*- coding: utf-8 -*- """Sphinx directive to support embedded IPython code. This directive allows pasting of entire interactive IPython sessions, prompts and all, and their code will actually get re-executed at doc build time, with all prompts renumbered sequentially. To enable this directive, simply list it in your Sphinx ``conf.py`` file (making sure the directory where you placed it is visible to sphinx, as is needed for all Sphinx directives). By default this directive assumes that your prompts are unchanged IPython ones, but this can be customized. For example, the following code in your Sphinx config file will configure this directive for the following input/output prompts ``Yade [1]:`` and ``-> [1]:``:: import ipython_directive as id id.rgxin =re.compile(r'(?:In |Yade )\[(\d+)\]:\s?(.*)\s*') id.rgxout=re.compile(r'(?:Out| -> )\[(\d+)\]:\s?(.*)\s*') id.fmtin ='Yade [%d]:' id.fmtout=' -> [%d]:' id.rc_override=dict( prompt_in1="Yade [\#]:", prompt_in2=" .\D..", prompt_out=" -> [\#]:" ) id.reconfig_shell() import ipython_console_highlighting as ich ich.IPythonConsoleLexer.input_prompt= re.compile("(Yade \[[0-9]+\]: )|( \.\.\.+:)") ich.IPythonConsoleLexer.output_prompt= re.compile("(( -> )|(Out)\[[0-9]+\]: )|( \.\.\.+:)") ich.IPythonConsoleLexer.continue_prompt=re.compile(" \.\.\.+:") ToDo ---- - Turn the ad-hoc test() function into a real test suite. - Break up ipython-specific functionality from matplotlib stuff into better separated code. - Make sure %bookmarks used internally are removed on exit. Authors ------- - John D Hunter: orignal author. - Fernando Perez: refactoring, documentation, cleanups. - VáclavŠmilauer : Prompt generatlizations. """ #----------------------------------------------------------------------------- # Imports #----------------------------------------------------------------------------- # Stdlib import cStringIO import imp import os import re import shutil import sys import warnings # To keep compatibility with various python versions try: from hashlib import md5 except ImportError: from md5 import md5 # Third-party import matplotlib import sphinx from docutils.parsers.rst import directives matplotlib.use('Agg') # Our own import IPython from IPython.Shell import MatplotlibShell #----------------------------------------------------------------------------- # Globals #----------------------------------------------------------------------------- sphinx_version = sphinx.__version__.split(".") # The split is necessary for sphinx beta versions where the string is # '6b1' sphinx_version = tuple([int(re.split('[a-z]', x)[0]) for x in sphinx_version[:2]]) COMMENT, INPUT, OUTPUT = range(3) rc_override = {} rgxin = re.compile('In \[(\d+)\]:\s?(.*)\s*') rgxcont = re.compile(' \.+:\s?(.*)\s*') rgxout = re.compile('Out\[(\d+)\]:\s?(.*)\s*') fmtin = 'In [%d]:' fmtout = 'Out[%d]:' fmtcont = ' .\D.:' #----------------------------------------------------------------------------- # Functions and class declarations #----------------------------------------------------------------------------- def block_parser(part): """ part is a string of ipython text, comprised of at most one input, one ouput, comments, and blank lines. The block parser parses the text into a list of:: blocks = [ (TOKEN0, data0), (TOKEN1, data1), ...] where TOKEN is one of [COMMENT | INPUT | OUTPUT ] and data is, depending on the type of token:: COMMENT : the comment string INPUT: the (DECORATOR, INPUT_LINE, REST) where DECORATOR: the input decorator (or None) INPUT_LINE: the input as string (possibly multi-line) REST : any stdout generated by the input line (not OUTPUT) OUTPUT: the output string, possibly multi-line """ block = [] lines = part.split('\n') N = len(lines) i = 0 decorator = None while 1: if i==N: # nothing left to parse -- the last line break line = lines[i] i += 1 line_stripped = line.strip() if line_stripped.startswith('#'): block.append((COMMENT, line)) continue if line_stripped.startswith('@'): # we're assuming at most one decorator -- may need to # rethink decorator = line_stripped continue # does this look like an input line? matchin = rgxin.match(line) if matchin: lineno, inputline = int(matchin.group(1)), matchin.group(2) # the ....: continuation string #continuation = ' %s:'%''.join(['.']*(len(str(lineno))+2)) #Nc = len(continuation) # input lines can continue on for more than one line, if # we have a '\' line continuation char or a function call # echo line 'print'. The input line can only be # terminated by the end of the block or an output line, so # we parse out the rest of the input line if it is # multiline as well as any echo text rest = [] while i2: if debug: print '\n'.join(lines) else: #print 'INSERTING %d lines'%len(lines) state_machine.insert_input( lines, state_machine.input_lines.source(0)) return [] ipython_directive.DEBUG = False # Enable as a proper Sphinx directive def setup(app): setup.app = app options = {'suppress': directives.flag, 'doctest': directives.flag, 'verbatim': directives.flag, } app.add_directive('ipython', ipython_directive, True, (0, 2, 0), **options) # Simple smoke test, needs to be converted to a proper automatic test. def test(): examples = [ r""" In [9]: pwd Out[9]: '/home/jdhunter/py4science/book' In [10]: cd bookdata/ /home/jdhunter/py4science/book/bookdata In [2]: from pylab import * In [2]: ion() In [3]: im = imread('stinkbug.png') @savefig mystinkbug.png width=4in In [4]: imshow(im) Out[4]: """, r""" In [1]: x = 'hello world' # string methods can be # used to alter the string @doctest In [2]: x.upper() Out[2]: 'HELLO WORLD' @verbatim In [3]: x.st x.startswith x.strip """, r""" In [130]: url = 'http://ichart.finance.yahoo.com/table.csv?s=CROX\ .....: &d=9&e=22&f=2009&g=d&a=1&br=8&c=2006&ignore=.csv' In [131]: print url.split('&') ['http://ichart.finance.yahoo.com/table.csv?s=CROX', 'd=9', 'e=22', 'f=2009', 'g=d', 'a=1', 'b=8', 'c=2006', 'ignore=.csv'] In [60]: import urllib """, r"""\ In [133]: import numpy.random @suppress In [134]: numpy.random.seed(2358) @doctest In [135]: np.random.rand(10,2) Out[135]: array([[ 0.64524308, 0.59943846], [ 0.47102322, 0.8715456 ], [ 0.29370834, 0.74776844], [ 0.99539577, 0.1313423 ], [ 0.16250302, 0.21103583], [ 0.81626524, 0.1312433 ], [ 0.67338089, 0.72302393], [ 0.7566368 , 0.07033696], [ 0.22591016, 0.77731835], [ 0.0072729 , 0.34273127]]) """, r""" In [106]: print x jdh In [109]: for i in range(10): .....: print i .....: .....: 0 1 2 3 4 5 6 7 8 9 """, r""" In [144]: from pylab import * In [145]: ion() # use a semicolon to suppress the output @savefig test_hist.png width=4in In [151]: hist(np.random.randn(10000), 100); @savefig test_plot.png width=4in In [151]: plot(np.random.randn(10000), 'o'); """, r""" # use a semicolon to suppress the output In [151]: plt.clf() @savefig plot_simple.png width=4in In [151]: plot([1,2,3]) @savefig hist_simple.png width=4in In [151]: hist(np.random.randn(10000), 100); """, r""" # update the current fig In [151]: ylabel('number') In [152]: title('normal distribution') @savefig hist_with_text.png In [153]: grid(True) """, ] ipython_directive.DEBUG = True #options = dict(suppress=True) options = dict() for example in examples: content = example.split('\n') ipython_directive('debug', arguments=None, options=options, content=content, lineno=0, content_offset=None, block_text=None, state=None, state_machine=None, ) # Run test suite as a script if __name__=='__main__': test() trunk-2017.01a/doc/sphinx/ipython_directive012.py000066400000000000000000000650671304022710500216030ustar00rootroot00000000000000# -*- coding: utf-8 -*- """Sphinx directive to support embedded IPython code. This directive allows pasting of entire interactive IPython sessions, prompts and all, and their code will actually get re-executed at doc build time, with all prompts renumbered sequentially. It also allows you to input code as a pure python input by giving the argument python to the directive. The output looks like an interactive ipython section. To enable this directive, simply list it in your Sphinx ``conf.py`` file (making sure the directory where you placed it is visible to sphinx, as is needed for all Sphinx directives). By default this directive assumes that your prompts are unchanged IPython ones, but this can be customized. The configurable options that can be placed in conf.py are ipython_savefig_dir: The directory in which to save the figures. This is relative to the Sphinx source directory. The default is `html_static_path`. ipython_rgxin: The compiled regular expression to denote the start of IPython input lines. The default is re.compile('In \[(\d+)\]:\s?(.*)\s*'). You shouldn't need to change this. ipython_rgxout: The compiled regular expression to denote the start of IPython output lines. The default is re.compile('Out\[(\d+)\]:\s?(.*)\s*'). You shouldn't need to change this. ipython_promptin: The string to represent the IPython input prompt in the generated ReST. The default is 'In [%d]:'. This expects that the line numbers are used in the prompt. ipython_promptout: The string to represent the IPython prompt in the generated ReST. The default is 'Out [%d]:'. This expects that the line numbers are used in the prompt. ToDo ---- - Turn the ad-hoc test() function into a real test suite. - Break up ipython-specific functionality from matplotlib stuff into better separated code. Authors ------- - John D Hunter: orignal author. - Fernando Perez: refactoring, documentation, cleanups, port to 0.11. - VáclavŠmilauer : Prompt generalizations. - Skipper Seabold, refactoring, cleanups, pure python addition """ #----------------------------------------------------------------------------- # Imports #----------------------------------------------------------------------------- # Stdlib import cStringIO import os import re import sys import tempfile import ast # To keep compatibility with various python versions try: from hashlib import md5 except ImportError: from md5 import md5 # Third-party import matplotlib import sphinx from docutils.parsers.rst import directives from docutils import nodes from sphinx.util.compat import Directive matplotlib.use('Agg') # Our own from IPython import Config, InteractiveShell from IPython.core.profiledir import ProfileDir from IPython.utils import io #----------------------------------------------------------------------------- # Globals #----------------------------------------------------------------------------- # for tokenizing blocks COMMENT, INPUT, OUTPUT = range(3) #----------------------------------------------------------------------------- # Functions and class declarations #----------------------------------------------------------------------------- def block_parser(part, rgxin, rgxout, fmtin, fmtout): """ part is a string of ipython text, comprised of at most one input, one ouput, comments, and blank lines. The block parser parses the text into a list of:: blocks = [ (TOKEN0, data0), (TOKEN1, data1), ...] where TOKEN is one of [COMMENT | INPUT | OUTPUT ] and data is, depending on the type of token:: COMMENT : the comment string INPUT: the (DECORATOR, INPUT_LINE, REST) where DECORATOR: the input decorator (or None) INPUT_LINE: the input as string (possibly multi-line) REST : any stdout generated by the input line (not OUTPUT) OUTPUT: the output string, possibly multi-line """ block = [] lines = part.split('\n') N = len(lines) i = 0 decorator = None while 1: if i==N: # nothing left to parse -- the last line break line = lines[i] i += 1 line_stripped = line.strip() if line_stripped.startswith('#'): block.append((COMMENT, line)) continue if line_stripped.startswith('@'): # we're assuming at most one decorator -- may need to # rethink decorator = line_stripped continue # does this look like an input line? matchin = rgxin.match(line) if matchin: lineno, inputline = int(matchin.group(1)), matchin.group(2) # the ....: continuation string continuation = ' %s:'%''.join(['.']*(len(str(lineno))+2)) Nc = len(continuation) # input lines can continue on for more than one line, if # we have a '\' line continuation char or a function call # echo line 'print'. The input line can only be # terminated by the end of the block or an output line, so # we parse out the rest of the input line if it is # multiline as well as any echo text rest = [] while i 1: if input_lines[-1] != "": input_lines.append('') # make sure there's a blank line # so splitter buffer gets reset continuation = ' %s:'%''.join(['.']*(len(str(lineno))+2)) Nc = len(continuation) if is_savefig: image_file, image_directive = self.process_image(decorator) ret = [] is_semicolon = False for i, line in enumerate(input_lines): if line.endswith(';'): is_semicolon = True if i==0: # process the first input line if is_verbatim: self.process_input_line('') self.IP.execution_count += 1 # increment it anyway else: # only submit the line in non-verbatim mode self.process_input_line(line, store_history=True) formatted_line = '%s %s'%(input_prompt, line) else: # process a continuation line if not is_verbatim: self.process_input_line(line, store_history=True) formatted_line = '%s %s'%(continuation, line) if not is_suppress: ret.append(formatted_line) if not is_suppress and len(rest.strip()) and is_verbatim: # the "rest" is the standard output of the # input, which needs to be added in # verbatim mode ret.append(rest) self.cout.seek(0) output = self.cout.read() if not is_suppress and not is_semicolon: ret.append(output) elif is_semicolon: # get spacing right ret.append('') self.cout.truncate(0) return (ret, input_lines, output, is_doctest, image_file, image_directive) #print 'OUTPUT', output # dbg def process_output(self, data, output_prompt, input_lines, output, is_doctest, image_file): """Process data block for OUTPUT token.""" if is_doctest: submitted = data.strip() found = output if found is not None: found = found.strip() # XXX - fperez: in 0.11, 'output' never comes with the prompt # in it, just the actual output text. So I think all this code # can be nuked... # the above comment does not appear to be accurate... (minrk) ind = found.find(output_prompt) if ind<0: e='output prompt="%s" does not match out line=%s' % \ (output_prompt, found) raise RuntimeError(e) found = found[len(output_prompt):].strip() if found!=submitted: e = ('doctest failure for input_lines="%s" with ' 'found_output="%s" and submitted output="%s"' % (input_lines, found, submitted) ) raise RuntimeError(e) #print 'doctest PASSED for input_lines="%s" with found_output="%s" and submitted output="%s"'%(input_lines, found, submitted) def process_comment(self, data): """Process data fPblock for COMMENT token.""" if not self.is_suppress: return [data] def save_image(self, image_file): """ Saves the image file to disk. """ self.ensure_pyplot() command = 'plt.gcf().savefig("%s")'%image_file #print 'SAVEFIG', command # dbg self.process_input_line('bookmark ipy_thisdir', store_history=False) self.process_input_line('cd -b ipy_savedir', store_history=False) self.process_input_line(command, store_history=False) self.process_input_line('cd -b ipy_thisdir', store_history=False) self.process_input_line('bookmark -d ipy_thisdir', store_history=False) self.clear_cout() def process_block(self, block): """ process block from the block_parser and return a list of processed lines """ ret = [] output = None input_lines = None lineno = self.IP.execution_count input_prompt = self.promptin%lineno output_prompt = self.promptout%lineno image_file = None image_directive = None for token, data in block: if token==COMMENT: out_data = self.process_comment(data) elif token==INPUT: (out_data, input_lines, output, is_doctest, image_file, image_directive) = \ self.process_input(data, input_prompt, lineno) elif token==OUTPUT: out_data = \ self.process_output(data, output_prompt, input_lines, output, is_doctest, image_file) if out_data: ret.extend(out_data) # save the image files if image_file is not None: self.save_image(image_file) return ret, image_directive def ensure_pyplot(self): if self._pyplot_imported: return self.process_input_line('import matplotlib.pyplot as plt', store_history=False) def process_pure_python(self, content): """ content is a list of strings. it is unedited directive conent This runs it line by line in the InteractiveShell, prepends prompts as needed capturing stderr and stdout, then returns the content as a list as if it were ipython code """ output = [] savefig = False # keep up with this to clear figure multiline = False # to handle line continuation multiline_start = None fmtin = self.promptin ct = 0 for lineno, line in enumerate(content): line_stripped = line.strip() if not len(line): output.append(line) continue # handle decorators if line_stripped.startswith('@'): output.extend([line]) if 'savefig' in line: savefig = True # and need to clear figure continue # handle comments if line_stripped.startswith('#'): output.extend([line]) continue # deal with lines checking for multiline continuation = u' %s:'% ''.join(['.']*(len(str(ct))+2)) if not multiline: modified = u"%s %s" % (fmtin % ct, line_stripped) output.append(modified) ct += 1 try: ast.parse(line_stripped) output.append(u'') except Exception: # on a multiline multiline = True multiline_start = lineno else: # still on a multiline modified = u'%s %s' % (continuation, line) output.append(modified) try: mod = ast.parse( '\n'.join(content[multiline_start:lineno+1])) if isinstance(mod.body[0], ast.FunctionDef): # check to see if we have the whole function for element in mod.body[0].body: if isinstance(element, ast.Return): multiline = False else: output.append(u'') multiline = False except Exception: pass if savefig: # clear figure if plotted self.ensure_pyplot() self.process_input_line('plt.clf()', store_history=False) self.clear_cout() savefig = False return output class IpythonDirective(Directive): has_content = True required_arguments = 0 optional_arguments = 4 # python, suppress, verbatim, doctest final_argumuent_whitespace = True option_spec = { 'python': directives.unchanged, 'suppress' : directives.flag, 'verbatim' : directives.flag, 'doctest' : directives.flag, } shell = EmbeddedSphinxShell() def get_config_options(self): # contains sphinx configuration variables config = self.state.document.settings.env.config # get config variables to set figure output directory confdir = self.state.document.settings.env.app.confdir savefig_dir = config.ipython_savefig_dir source_dir = os.path.dirname(self.state.document.current_source) if savefig_dir is None: savefig_dir = config.html_static_path if isinstance(savefig_dir, list): savefig_dir = savefig_dir[0] # safe to assume only one path? savefig_dir = os.path.join(confdir, savefig_dir) # get regex and prompt stuff rgxin = config.ipython_rgxin rgxout = config.ipython_rgxout promptin = config.ipython_promptin promptout = config.ipython_promptout return savefig_dir, source_dir, rgxin, rgxout, promptin, promptout def setup(self): # reset the execution count if we haven't processed this doc #NOTE: this may be borked if there are multiple seen_doc tmp files #check time stamp? seen_docs = [i for i in os.listdir(tempfile.tempdir) if i.startswith('seen_doc')] if seen_docs: fname = os.path.join(tempfile.tempdir, seen_docs[0]) docs = open(fname).read().split('\n') if not self.state.document.current_source in docs: self.shell.IP.history_manager.reset() self.shell.IP.execution_count = 1 else: # haven't processed any docs yet docs = [] # get config values (savefig_dir, source_dir, rgxin, rgxout, promptin, promptout) = self.get_config_options() # and attach to shell so we don't have to pass them around self.shell.rgxin = rgxin self.shell.rgxout = rgxout self.shell.promptin = promptin self.shell.promptout = promptout self.shell.savefig_dir = savefig_dir self.shell.source_dir = source_dir # setup bookmark for saving figures directory self.shell.process_input_line('bookmark ipy_savedir %s'%savefig_dir, store_history=False) self.shell.clear_cout() # write the filename to a tempfile because it's been "seen" now if not self.state.document.current_source in docs: fd, fname = tempfile.mkstemp(prefix="seen_doc", text=True) fout = open(fname, 'a') fout.write(self.state.document.current_source+'\n') fout.close() return rgxin, rgxout, promptin, promptout def teardown(self): # delete last bookmark self.shell.process_input_line('bookmark -d ipy_savedir', store_history=False) self.shell.clear_cout() def run(self): debug = False #TODO, any reason block_parser can't be a method of embeddable shell # then we wouldn't have to carry these around rgxin, rgxout, promptin, promptout = self.setup() options = self.options self.shell.is_suppress = 'suppress' in options self.shell.is_doctest = 'doctest' in options self.shell.is_verbatim = 'verbatim' in options # handle pure python code if 'python' in self.arguments: content = self.content self.content = self.shell.process_pure_python(content) parts = '\n'.join(self.content).split('\n\n') lines = ['.. code-block:: ipython',''] figures = [] for part in parts: block = block_parser(part, rgxin, rgxout, promptin, promptout) if len(block): rows, figure = self.shell.process_block(block) for row in rows: lines.extend([' %s'%line for line in row.split('\n')]) if figure is not None: figures.append(figure) #text = '\n'.join(lines) #figs = '\n'.join(figures) for figure in figures: lines.append('') lines.extend(figure.split('\n')) lines.append('') #print lines if len(lines)>2: if debug: print '\n'.join(lines) else: #NOTE: this raises some errors, what's it for? #print 'INSERTING %d lines'%len(lines) self.state_machine.insert_input( lines, self.state_machine.input_lines.source(0)) text = '\n'.join(lines) txtnode = nodes.literal_block(text, text) txtnode['language'] = 'ipython' #imgnode = nodes.image(figs) # cleanup self.teardown() return []#, imgnode] # Enable as a proper Sphinx directive def setup(app): setup.app = app app.add_directive('ipython', IpythonDirective) app.add_config_value('ipython_savefig_dir', None, True) app.add_config_value('ipython_rgxin', re.compile('In \[(\d+)\]:\s?(.*)\s*'), True) app.add_config_value('ipython_rgxout', re.compile('Out\[(\d+)\]:\s?(.*)\s*'), True) app.add_config_value('ipython_promptin', 'In [%d]:', True) app.add_config_value('ipython_promptout', 'Out[%d]:', True) # Simple smoke test, needs to be converted to a proper automatic test. def test(): examples = [ r""" In [9]: pwd Out[9]: '/home/jdhunter/py4science/book' In [10]: cd bookdata/ /home/jdhunter/py4science/book/bookdata In [2]: from pylab import * In [2]: ion() In [3]: im = imread('stinkbug.png') @savefig mystinkbug.png width=4in In [4]: imshow(im) Out[4]: """, r""" In [1]: x = 'hello world' # string methods can be # used to alter the string @doctest In [2]: x.upper() Out[2]: 'HELLO WORLD' @verbatim In [3]: x.st x.startswith x.strip """, r""" In [130]: url = 'http://ichart.finance.yahoo.com/table.csv?s=CROX\ .....: &d=9&e=22&f=2009&g=d&a=1&br=8&c=2006&ignore=.csv' In [131]: print url.split('&') ['http://ichart.finance.yahoo.com/table.csv?s=CROX', 'd=9', 'e=22', 'f=2009', 'g=d', 'a=1', 'b=8', 'c=2006', 'ignore=.csv'] In [60]: import urllib """, r"""\ In [133]: import numpy.random @suppress In [134]: numpy.random.seed(2358) @doctest In [135]: numpy.random.rand(10,2) Out[135]: array([[ 0.64524308, 0.59943846], [ 0.47102322, 0.8715456 ], [ 0.29370834, 0.74776844], [ 0.99539577, 0.1313423 ], [ 0.16250302, 0.21103583], [ 0.81626524, 0.1312433 ], [ 0.67338089, 0.72302393], [ 0.7566368 , 0.07033696], [ 0.22591016, 0.77731835], [ 0.0072729 , 0.34273127]]) """, r""" In [106]: print x jdh In [109]: for i in range(10): .....: print i .....: .....: 0 1 2 3 4 5 6 7 8 9 """, r""" In [144]: from pylab import * In [145]: ion() # use a semicolon to suppress the output @savefig test_hist.png width=4in In [151]: hist(np.random.randn(10000), 100); @savefig test_plot.png width=4in In [151]: plot(np.random.randn(10000), 'o'); """, r""" # use a semicolon to suppress the output In [151]: plt.clf() @savefig plot_simple.png width=4in In [151]: plot([1,2,3]) @savefig hist_simple.png width=4in In [151]: hist(np.random.randn(10000), 100); """, r""" # update the current fig In [151]: ylabel('number') In [152]: title('normal distribution') @savefig hist_with_text.png In [153]: grid(True) """, ] # skip local-file depending first example: examples = examples[1:] #ipython_directive.DEBUG = True # dbg #options = dict(suppress=True) # dbg options = dict() for example in examples: content = example.split('\n') ipython_directive('debug', arguments=None, options=options, content=content, lineno=0, content_offset=None, block_text=None, state=None, state_machine=None, ) # Run test suite as a script if __name__=='__main__': if not os.path.isdir('_static'): os.mkdir('_static') test() print 'All OK? Check figures in _static/' trunk-2017.01a/doc/sphinx/ipython_directive013.py000066400000000000000000000652201304022710500215730ustar00rootroot00000000000000# -*- coding: utf-8 -*- """Sphinx directive to support embedded IPython code. From: https://github.com/ipython/ipython/blob/master/docs/sphinxext/ipython_directive.py This directive allows pasting of entire interactive IPython sessions, prompts and all, and their code will actually get re-executed at doc build time, with all prompts renumbered sequentially. It also allows you to input code as a pure python input by giving the argument python to the directive. The output looks like an interactive ipython section. To enable this directive, simply list it in your Sphinx ``conf.py`` file (making sure the directory where you placed it is visible to sphinx, as is needed for all Sphinx directives). By default this directive assumes that your prompts are unchanged IPython ones, but this can be customized. The configurable options that can be placed in conf.py are ipython_savefig_dir: The directory in which to save the figures. This is relative to the Sphinx source directory. The default is `html_static_path`. ipython_rgxin: The compiled regular expression to denote the start of IPython input lines. The default is re.compile('In \[(\d+)\]:\s?(.*)\s*'). You shouldn't need to change this. ipython_rgxout: The compiled regular expression to denote the start of IPython output lines. The default is re.compile('Out\[(\d+)\]:\s?(.*)\s*'). You shouldn't need to change this. ipython_promptin: The string to represent the IPython input prompt in the generated ReST. The default is 'In [%d]:'. This expects that the line numbers are used in the prompt. ipython_promptout: The string to represent the IPython prompt in the generated ReST. The default is 'Out [%d]:'. This expects that the line numbers are used in the prompt. ToDo ---- - Turn the ad-hoc test() function into a real test suite. - Break up ipython-specific functionality from matplotlib stuff into better separated code. Authors ------- - John D Hunter: orignal author. - Fernando Perez: refactoring, documentation, cleanups, port to 0.11. - VáclavŠmilauer : Prompt generalizations. - Skipper Seabold, refactoring, cleanups, pure python addition """ #----------------------------------------------------------------------------- # Imports #----------------------------------------------------------------------------- # Stdlib import cStringIO import os import re import sys import tempfile import ast # To keep compatibility with various python versions try: from hashlib import md5 except ImportError: from md5 import md5 # Third-party import matplotlib import sphinx from docutils.parsers.rst import directives from docutils import nodes from sphinx.util.compat import Directive matplotlib.use('Agg') # Our own from IPython import Config, InteractiveShell from IPython.core.profiledir import ProfileDir from IPython.utils import io #----------------------------------------------------------------------------- # Globals #----------------------------------------------------------------------------- # for tokenizing blocks COMMENT, INPUT, OUTPUT = range(3) #----------------------------------------------------------------------------- # Functions and class declarations #----------------------------------------------------------------------------- def block_parser(part, rgxin, rgxout, fmtin, fmtout): """ part is a string of ipython text, comprised of at most one input, one ouput, comments, and blank lines. The block parser parses the text into a list of:: blocks = [ (TOKEN0, data0), (TOKEN1, data1), ...] where TOKEN is one of [COMMENT | INPUT | OUTPUT ] and data is, depending on the type of token:: COMMENT : the comment string INPUT: the (DECORATOR, INPUT_LINE, REST) where DECORATOR: the input decorator (or None) INPUT_LINE: the input as string (possibly multi-line) REST : any stdout generated by the input line (not OUTPUT) OUTPUT: the output string, possibly multi-line """ block = [] lines = part.split('\n') N = len(lines) i = 0 decorator = None while 1: if i==N: # nothing left to parse -- the last line break line = lines[i] i += 1 line_stripped = line.strip() if line_stripped.startswith('#'): block.append((COMMENT, line)) continue if line_stripped.startswith('@'): # we're assuming at most one decorator -- may need to # rethink decorator = line_stripped continue # does this look like an input line? matchin = rgxin.match(line) if matchin: lineno, inputline = int(matchin.group(1)), matchin.group(2) # the ....: continuation string continuation = ' %s:'%''.join(['.']*(len(str(lineno))+2)) Nc = len(continuation) # input lines can continue on for more than one line, if # we have a '\' line continuation char or a function call # echo line 'print'. The input line can only be # terminated by the end of the block or an output line, so # we parse out the rest of the input line if it is # multiline as well as any echo text rest = [] while i 1: if input_lines[-1] != "": input_lines.append('') # make sure there's a blank line # so splitter buffer gets reset continuation = ' %s:'%''.join(['.']*(len(str(lineno))+2)) Nc = len(continuation) if is_savefig: image_file, image_directive = self.process_image(decorator) ret = [] is_semicolon = False for i, line in enumerate(input_lines): if line.endswith(';'): is_semicolon = True if i==0: # process the first input line if is_verbatim: self.process_input_line('') self.IP.execution_count += 1 # increment it anyway else: # only submit the line in non-verbatim mode self.process_input_line(line, store_history=True) formatted_line = '%s %s'%(input_prompt, line) else: # process a continuation line if not is_verbatim: self.process_input_line(line, store_history=True) formatted_line = '%s %s'%(continuation, line) if not is_suppress: ret.append(formatted_line) if not is_suppress and len(rest.strip()) and is_verbatim: # the "rest" is the standard output of the # input, which needs to be added in # verbatim mode ret.append(rest) self.cout.seek(0) output = self.cout.read() if not is_suppress and not is_semicolon: ret.append(output) elif is_semicolon: # get spacing right ret.append('') self.cout.truncate(0) return (ret, input_lines, output, is_doctest, image_file, image_directive) #print 'OUTPUT', output # dbg def process_output(self, data, output_prompt, input_lines, output, is_doctest, image_file): """Process data block for OUTPUT token.""" if is_doctest: submitted = data.strip() found = output if found is not None: found = found.strip() # XXX - fperez: in 0.11, 'output' never comes with the prompt # in it, just the actual output text. So I think all this code # can be nuked... # the above comment does not appear to be accurate... (minrk) ind = found.find(output_prompt) if ind<0: e='output prompt="%s" does not match out line=%s' % \ (output_prompt, found) raise RuntimeError(e) found = found[len(output_prompt):].strip() if found!=submitted: e = ('doctest failure for input_lines="%s" with ' 'found_output="%s" and submitted output="%s"' % (input_lines, found, submitted) ) raise RuntimeError(e) #print 'doctest PASSED for input_lines="%s" with found_output="%s" and submitted output="%s"'%(input_lines, found, submitted) def process_comment(self, data): """Process data fPblock for COMMENT token.""" if not self.is_suppress: return [data] def save_image(self, image_file): """ Saves the image file to disk. """ self.ensure_pyplot() command = 'plt.gcf().savefig("%s")'%image_file #print 'SAVEFIG', command # dbg self.process_input_line('bookmark ipy_thisdir', store_history=False) self.process_input_line('cd -b ipy_savedir', store_history=False) self.process_input_line(command, store_history=False) self.process_input_line('cd -b ipy_thisdir', store_history=False) self.process_input_line('bookmark -d ipy_thisdir', store_history=False) self.clear_cout() def process_block(self, block): """ process block from the block_parser and return a list of processed lines """ ret = [] output = None input_lines = None lineno = self.IP.execution_count input_prompt = self.promptin%lineno output_prompt = self.promptout%lineno image_file = None image_directive = None for token, data in block: if token==COMMENT: out_data = self.process_comment(data) elif token==INPUT: (out_data, input_lines, output, is_doctest, image_file, image_directive) = \ self.process_input(data, input_prompt, lineno) elif token==OUTPUT: out_data = \ self.process_output(data, output_prompt, input_lines, output, is_doctest, image_file) if out_data: ret.extend(out_data) # save the image files if image_file is not None: self.save_image(image_file) return ret, image_directive def ensure_pyplot(self): if self._pyplot_imported: return self.process_input_line('import matplotlib.pyplot as plt', store_history=False) def process_pure_python(self, content): """ content is a list of strings. it is unedited directive conent This runs it line by line in the InteractiveShell, prepends prompts as needed capturing stderr and stdout, then returns the content as a list as if it were ipython code """ output = [] savefig = False # keep up with this to clear figure multiline = False # to handle line continuation multiline_start = None fmtin = self.promptin ct = 0 for lineno, line in enumerate(content): line_stripped = line.strip() if not len(line): output.append(line) continue # handle decorators if line_stripped.startswith('@'): output.extend([line]) if 'savefig' in line: savefig = True # and need to clear figure continue # handle comments if line_stripped.startswith('#'): output.extend([line]) continue # deal with lines checking for multiline continuation = u' %s:'% ''.join(['.']*(len(str(ct))+2)) if not multiline: modified = u"%s %s" % (fmtin % ct, line_stripped) output.append(modified) ct += 1 try: ast.parse(line_stripped) output.append(u'') except Exception: # on a multiline multiline = True multiline_start = lineno else: # still on a multiline modified = u'%s %s' % (continuation, line) output.append(modified) try: mod = ast.parse( '\n'.join(content[multiline_start:lineno+1])) if isinstance(mod.body[0], ast.FunctionDef): # check to see if we have the whole function for element in mod.body[0].body: if isinstance(element, ast.Return): multiline = False else: output.append(u'') multiline = False except Exception: pass if savefig: # clear figure if plotted self.ensure_pyplot() self.process_input_line('plt.clf()', store_history=False) self.clear_cout() savefig = False return output class IpythonDirective(Directive): has_content = True required_arguments = 0 optional_arguments = 4 # python, suppress, verbatim, doctest final_argumuent_whitespace = True option_spec = { 'python': directives.unchanged, 'suppress' : directives.flag, 'verbatim' : directives.flag, 'doctest' : directives.flag, } shell = EmbeddedSphinxShell() def get_config_options(self): # contains sphinx configuration variables config = self.state.document.settings.env.config # get config variables to set figure output directory confdir = self.state.document.settings.env.app.confdir savefig_dir = config.ipython_savefig_dir source_dir = os.path.dirname(self.state.document.current_source) if savefig_dir is None: savefig_dir = config.html_static_path if isinstance(savefig_dir, list): savefig_dir = savefig_dir[0] # safe to assume only one path? savefig_dir = os.path.join(confdir, savefig_dir) # get regex and prompt stuff rgxin = config.ipython_rgxin rgxout = config.ipython_rgxout promptin = config.ipython_promptin promptout = config.ipython_promptout return savefig_dir, source_dir, rgxin, rgxout, promptin, promptout def setup(self): # reset the execution count if we haven't processed this doc #NOTE: this may be borked if there are multiple seen_doc tmp files #check time stamp? seen_docs = [i for i in os.listdir(tempfile.tempdir) if i.startswith('seen_doc')] if seen_docs: fname = os.path.join(tempfile.tempdir, seen_docs[0]) docs = open(fname).read().split('\n') if not self.state.document.current_source in docs: self.shell.IP.history_manager.reset() self.shell.IP.execution_count = 1 else: # haven't processed any docs yet docs = [] # get config values (savefig_dir, source_dir, rgxin, rgxout, promptin, promptout) = self.get_config_options() # and attach to shell so we don't have to pass them around self.shell.rgxin = rgxin self.shell.rgxout = rgxout self.shell.promptin = promptin self.shell.promptout = promptout self.shell.savefig_dir = savefig_dir self.shell.source_dir = source_dir # setup bookmark for saving figures directory self.shell.process_input_line('bookmark ipy_savedir %s'%savefig_dir, store_history=False) self.shell.clear_cout() # write the filename to a tempfile because it's been "seen" now if not self.state.document.current_source in docs: fd, fname = tempfile.mkstemp(prefix="seen_doc", text=True) fout = open(fname, 'a') fout.write(self.state.document.current_source+'\n') fout.close() return rgxin, rgxout, promptin, promptout def teardown(self): # delete last bookmark self.shell.process_input_line('bookmark -d ipy_savedir', store_history=False) self.shell.clear_cout() def run(self): debug = False #TODO, any reason block_parser can't be a method of embeddable shell # then we wouldn't have to carry these around rgxin, rgxout, promptin, promptout = self.setup() options = self.options self.shell.is_suppress = 'suppress' in options self.shell.is_doctest = 'doctest' in options self.shell.is_verbatim = 'verbatim' in options # handle pure python code if 'python' in self.arguments: content = self.content self.content = self.shell.process_pure_python(content) parts = '\n'.join(self.content).split('\n\n') lines = ['.. code-block:: ipython',''] figures = [] for part in parts: block = block_parser(part, rgxin, rgxout, promptin, promptout) if len(block): rows, figure = self.shell.process_block(block) for row in rows: lines.extend([' %s'%line for line in row.split('\n')]) if figure is not None: figures.append(figure) #text = '\n'.join(lines) #figs = '\n'.join(figures) for figure in figures: lines.append('') lines.extend(figure.split('\n')) lines.append('') #print lines if len(lines)>2: if debug: print '\n'.join(lines) else: #NOTE: this raises some errors, what's it for? #print 'INSERTING %d lines'%len(lines) self.state_machine.insert_input( lines, self.state_machine.input_lines.source(0)) text = '\n'.join(lines) txtnode = nodes.literal_block(text, text) txtnode['language'] = 'ipython' #imgnode = nodes.image(figs) # cleanup self.teardown() return []#, imgnode] # Enable as a proper Sphinx directive def setup(app): setup.app = app app.add_directive('ipython', IpythonDirective) app.add_config_value('ipython_savefig_dir', None, True) app.add_config_value('ipython_rgxin', re.compile('In \[(\d+)\]:\s?(.*)\s*'), True) app.add_config_value('ipython_rgxout', re.compile('Out\[(\d+)\]:\s?(.*)\s*'), True) app.add_config_value('ipython_promptin', 'In [%d]:', True) app.add_config_value('ipython_promptout', 'Out[%d]:', True) # Simple smoke test, needs to be converted to a proper automatic test. def test(): examples = [ r""" In [9]: pwd Out[9]: '/home/jdhunter/py4science/book' In [10]: cd bookdata/ /home/jdhunter/py4science/book/bookdata In [2]: from pylab import * In [2]: ion() In [3]: im = imread('stinkbug.png') @savefig mystinkbug.png width=4in In [4]: imshow(im) Out[4]: """, r""" In [1]: x = 'hello world' # string methods can be # used to alter the string @doctest In [2]: x.upper() Out[2]: 'HELLO WORLD' @verbatim In [3]: x.st x.startswith x.strip """, r""" In [130]: url = 'http://ichart.finance.yahoo.com/table.csv?s=CROX\ .....: &d=9&e=22&f=2009&g=d&a=1&br=8&c=2006&ignore=.csv' In [131]: print url.split('&') ['http://ichart.finance.yahoo.com/table.csv?s=CROX', 'd=9', 'e=22', 'f=2009', 'g=d', 'a=1', 'b=8', 'c=2006', 'ignore=.csv'] In [60]: import urllib """, r"""\ In [133]: import numpy.random @suppress In [134]: numpy.random.seed(2358) @doctest In [135]: numpy.random.rand(10,2) Out[135]: array([[ 0.64524308, 0.59943846], [ 0.47102322, 0.8715456 ], [ 0.29370834, 0.74776844], [ 0.99539577, 0.1313423 ], [ 0.16250302, 0.21103583], [ 0.81626524, 0.1312433 ], [ 0.67338089, 0.72302393], [ 0.7566368 , 0.07033696], [ 0.22591016, 0.77731835], [ 0.0072729 , 0.34273127]]) """, r""" In [106]: print x jdh In [109]: for i in range(10): .....: print i .....: .....: 0 1 2 3 4 5 6 7 8 9 """, r""" In [144]: from pylab import * In [145]: ion() # use a semicolon to suppress the output @savefig test_hist.png width=4in In [151]: hist(np.random.randn(10000), 100); @savefig test_plot.png width=4in In [151]: plot(np.random.randn(10000), 'o'); """, r""" # use a semicolon to suppress the output In [151]: plt.clf() @savefig plot_simple.png width=4in In [151]: plot([1,2,3]) @savefig hist_simple.png width=4in In [151]: hist(np.random.randn(10000), 100); """, r""" # update the current fig In [151]: ylabel('number') In [152]: title('normal distribution') @savefig hist_with_text.png In [153]: grid(True) """, ] # skip local-file depending first example: examples = examples[1:] #ipython_directive.DEBUG = True # dbg #options = dict(suppress=True) # dbg options = dict() for example in examples: content = example.split('\n') ipython_directive('debug', arguments=None, options=options, content=content, lineno=0, content_offset=None, block_text=None, state=None, state_machine=None, ) # Run test suite as a script if __name__=='__main__': if not os.path.isdir('_static'): os.mkdir('_static') test() print 'All OK? Check figures in _static/' trunk-2017.01a/doc/sphinx/ipython_directive200.py000066400000000000000000001204231304022710500215660ustar00rootroot00000000000000# -*- coding: utf-8 -*- """ Sphinx directive to support embedded IPython code. This directive allows pasting of entire interactive IPython sessions, prompts and all, and their code will actually get re-executed at doc build time, with all prompts renumbered sequentially. It also allows you to input code as a pure python input by giving the argument python to the directive. The output looks like an interactive ipython section. To enable this directive, simply list it in your Sphinx ``conf.py`` file (making sure the directory where you placed it is visible to sphinx, as is needed for all Sphinx directives). For example, to enable syntax highlighting and the IPython directive:: extensions = ['IPython.sphinxext.ipython_console_highlighting', 'IPython.sphinxext.ipython_directive'] The IPython directive outputs code-blocks with the language 'ipython'. So if you do not have the syntax highlighting extension enabled as well, then all rendered code-blocks will be uncolored. By default this directive assumes that your prompts are unchanged IPython ones, but this can be customized. The configurable options that can be placed in conf.py are: ipython_savefig_dir: The directory in which to save the figures. This is relative to the Sphinx source directory. The default is `html_static_path`. ipython_rgxin: The compiled regular expression to denote the start of IPython input lines. The default is re.compile('In \[(\d+)\]:\s?(.*)\s*'). You shouldn't need to change this. ipython_rgxout: The compiled regular expression to denote the start of IPython output lines. The default is re.compile('Out\[(\d+)\]:\s?(.*)\s*'). You shouldn't need to change this. ipython_promptin: The string to represent the IPython input prompt in the generated ReST. The default is 'In [%d]:'. This expects that the line numbers are used in the prompt. ipython_promptout: The string to represent the IPython prompt in the generated ReST. The default is 'Out [%d]:'. This expects that the line numbers are used in the prompt. ipython_mplbackend: The string which specifies if the embedded Sphinx shell should import Matplotlib and set the backend. The value specifies a backend that is passed to `matplotlib.use()` before any lines in `ipython_execlines` are executed. If not specified in conf.py, then the default value of 'agg' is used. To use the IPython directive without matplotlib as a dependency, set the value to `None`. It may end up that matplotlib is still imported if the user specifies so in `ipython_execlines` or makes use of the @savefig pseudo decorator. ipython_execlines: A list of strings to be exec'd in the embedded Sphinx shell. Typical usage is to make certain packages always available. Set this to an empty list if you wish to have no imports always available. If specified in conf.py as `None`, then it has the effect of making no imports available. If omitted from conf.py altogether, then the default value of ['import numpy as np', 'import matplotlib.pyplot as plt'] is used. ipython_holdcount When the @suppress pseudo-decorator is used, the execution count can be incremented or not. The default behavior is to hold the execution count, corresponding to a value of `True`. Set this to `False` to increment the execution count after each suppressed command. As an example, to use the IPython directive when `matplotlib` is not available, one sets the backend to `None`:: ipython_mplbackend = None An example usage of the directive is: .. code-block:: rst .. ipython:: In [1]: x = 1 In [2]: y = x**2 In [3]: print(y) See http://matplotlib.org/sampledoc/ipython_directive.html for additional documentation. Pseudo-Decorators ================= Note: Only one decorator is supported per input. If more than one decorator is specified, then only the last one is used. In addition to the Pseudo-Decorators/options described at the above link, several enhancements have been made. The directive will emit a message to the console at build-time if code-execution resulted in an exception or warning. You can suppress these on a per-block basis by specifying the :okexcept: or :okwarning: options: .. code-block:: rst .. ipython:: :okexcept: :okwarning: In [1]: 1/0 In [2]: # raise warning. ToDo ---- - Turn the ad-hoc test() function into a real test suite. - Break up ipython-specific functionality from matplotlib stuff into better separated code. Authors ------- - John D Hunter: orignal author. - Fernando Perez: refactoring, documentation, cleanups, port to 0.11. - VáclavŠmilauer : Prompt generalizations. - Skipper Seabold, refactoring, cleanups, pure python addition """ from __future__ import print_function #----------------------------------------------------------------------------- # Imports #----------------------------------------------------------------------------- # Stdlib import os import re import sys import tempfile import ast import warnings # To keep compatibility with various python versions try: from hashlib import md5 except ImportError: from md5 import md5 # Third-party import sphinx from docutils.parsers.rst import directives from docutils import nodes from sphinx.util.compat import Directive # Our own from IPython import Config, InteractiveShell from IPython.core.profiledir import ProfileDir from IPython.utils import io from IPython.utils.py3compat import PY3 if PY3: from io import StringIO else: from StringIO import StringIO #----------------------------------------------------------------------------- # Globals #----------------------------------------------------------------------------- # for tokenizing blocks COMMENT, INPUT, OUTPUT = range(3) #----------------------------------------------------------------------------- # Functions and class declarations #----------------------------------------------------------------------------- def block_parser(part, rgxin, rgxout, fmtin, fmtout): """ part is a string of ipython text, comprised of at most one input, one ouput, comments, and blank lines. The block parser parses the text into a list of:: blocks = [ (TOKEN0, data0), (TOKEN1, data1), ...] where TOKEN is one of [COMMENT | INPUT | OUTPUT ] and data is, depending on the type of token:: COMMENT : the comment string INPUT: the (DECORATOR, INPUT_LINE, REST) where DECORATOR: the input decorator (or None) INPUT_LINE: the input as string (possibly multi-line) REST : any stdout generated by the input line (not OUTPUT) OUTPUT: the output string, possibly multi-line """ block = [] lines = part.split('\n') N = len(lines) i = 0 decorator = None while 1: if i==N: # nothing left to parse -- the last line break line = lines[i] i += 1 line_stripped = line.strip() if line_stripped.startswith('#'): block.append((COMMENT, line)) continue if line_stripped.startswith('@'): # Here is where we assume there is, at most, one decorator. # Might need to rethink this. decorator = line_stripped continue # does this look like an input line? matchin = rgxin.match(line) if matchin: lineno, inputline = int(matchin.group(1)), matchin.group(2) # the ....: continuation string continuation = ' %s:'%''.join(['.']*(len(str(lineno))+2)) Nc = len(continuation) # input lines can continue on for more than one line, if # we have a '\' line continuation char or a function call # echo line 'print'. The input line can only be # terminated by the end of the block or an output line, so # we parse out the rest of the input line if it is # multiline as well as any echo text rest = [] while i 1: if input_lines[-1] != "": input_lines.append('') # make sure there's a blank line # so splitter buffer gets reset continuation = ' %s:'%''.join(['.']*(len(str(lineno))+2)) if is_savefig: image_file, image_directive = self.process_image(decorator) ret = [] is_semicolon = False # Hold the execution count, if requested to do so. if is_suppress and self.hold_count: store_history = False else: store_history = True # Note: catch_warnings is not thread safe with warnings.catch_warnings(record=True) as ws: for i, line in enumerate(input_lines): if line.endswith(';'): is_semicolon = True if i == 0: # process the first input line if is_verbatim: self.process_input_line('') self.IP.execution_count += 1 # increment it anyway else: # only submit the line in non-verbatim mode self.process_input_line(line, store_history=store_history) formatted_line = '%s %s'%(input_prompt, line) else: # process a continuation line if not is_verbatim: self.process_input_line(line, store_history=store_history) formatted_line = '%s %s'%(continuation, line) if not is_suppress: ret.append(formatted_line) if not is_suppress and len(rest.strip()) and is_verbatim: # The "rest" is the standard output of the input. This needs to be # added when in verbatim mode. If there is no "rest", then we don't # add it, as the new line will be added by the processed output. ret.append(rest) # Fetch the processed output. (This is not the submitted output.) self.cout.seek(0) processed_output = self.cout.read() if not is_suppress and not is_semicolon: # # In IPythonDirective.run, the elements of `ret` are eventually # combined such that '' entries correspond to newlines. So if # `processed_output` is equal to '', then the adding it to `ret` # ensures that there is a blank line between consecutive inputs # that have no outputs, as in: # # In [1]: x = 4 # # In [2]: x = 5 # # When there is processed output, it has a '\n' at the tail end. So # adding the output to `ret` will provide the necessary spacing # between consecutive input/output blocks, as in: # # In [1]: x # Out[1]: 5 # # In [2]: x # Out[2]: 5 # # When there is stdout from the input, it also has a '\n' at the # tail end, and so this ensures proper spacing as well. E.g.: # # In [1]: print x # 5 # # In [2]: x = 5 # # When in verbatim mode, `processed_output` is empty (because # nothing was passed to IP. Sometimes the submitted code block has # an Out[] portion and sometimes it does not. When it does not, we # need to ensure proper spacing, so we have to add '' to `ret`. # However, if there is an Out[] in the submitted code, then we do # not want to add a newline as `process_output` has stuff to add. # The difficulty is that `process_input` doesn't know if # `process_output` will be called---so it doesn't know if there is # Out[] in the code block. The requires that we include a hack in # `process_block`. See the comments there. # ret.append(processed_output) elif is_semicolon: # Make sure there is a newline after the semicolon. ret.append('') # context information filename = "Unknown" lineno = 0 if self.directive.state: filename = self.directive.state.document.current_source lineno = self.directive.state.document.current_line # output any exceptions raised during execution to stdout # unless :okexcept: has been specified. if not is_okexcept and "Traceback" in processed_output: s = "\nException in %s at block ending on line %s\n" % (filename, lineno) s += "Specify :okexcept: as an option in the ipython:: block to suppress this message\n" sys.stdout.write('\n\n>>>' + ('-' * 73)) sys.stdout.write(s) sys.stdout.write(processed_output) sys.stdout.write('<<<' + ('-' * 73) + '\n\n') # output any warning raised during execution to stdout # unless :okwarning: has been specified. if not is_okwarning: for w in ws: s = "\nWarning in %s at block ending on line %s\n" % (filename, lineno) s += "Specify :okwarning: as an option in the ipython:: block to suppress this message\n" sys.stdout.write('\n\n>>>' + ('-' * 73)) sys.stdout.write(s) sys.stdout.write(('-' * 76) + '\n') s=warnings.formatwarning(w.message, w.category, w.filename, w.lineno, w.line) sys.stdout.write(s) sys.stdout.write('<<<' + ('-' * 73) + '\n') self.cout.truncate(0) return (ret, input_lines, processed_output, is_doctest, decorator, image_file, image_directive) def process_output(self, data, output_prompt, input_lines, output, is_doctest, decorator, image_file): """ Process data block for OUTPUT token. """ # Recall: `data` is the submitted output, and `output` is the processed # output from `input_lines`. TAB = ' ' * 4 if is_doctest and output is not None: found = output # This is the processed output found = found.strip() submitted = data.strip() if self.directive is None: source = 'Unavailable' content = 'Unavailable' else: source = self.directive.state.document.current_source content = self.directive.content # Add tabs and join into a single string. content = '\n'.join([TAB + line for line in content]) # Make sure the output contains the output prompt. ind = found.find(output_prompt) if ind < 0: e = ('output does not contain output prompt\n\n' 'Document source: {0}\n\n' 'Raw content: \n{1}\n\n' 'Input line(s):\n{TAB}{2}\n\n' 'Output line(s):\n{TAB}{3}\n\n') e = e.format(source, content, '\n'.join(input_lines), repr(found), TAB=TAB) raise RuntimeError(e) found = found[len(output_prompt):].strip() # Handle the actual doctest comparison. if decorator.strip() == '@doctest': # Standard doctest if found != submitted: e = ('doctest failure\n\n' 'Document source: {0}\n\n' 'Raw content: \n{1}\n\n' 'On input line(s):\n{TAB}{2}\n\n' 'we found output:\n{TAB}{3}\n\n' 'instead of the expected:\n{TAB}{4}\n\n') e = e.format(source, content, '\n'.join(input_lines), repr(found), repr(submitted), TAB=TAB) raise RuntimeError(e) else: self.custom_doctest(decorator, input_lines, found, submitted) # When in verbatim mode, this holds additional submitted output # to be written in the final Sphinx output. # https://github.com/ipython/ipython/issues/5776 out_data = [] is_verbatim = decorator=='@verbatim' or self.is_verbatim if is_verbatim and data.strip(): # Note that `ret` in `process_block` has '' as its last element if # the code block was in verbatim mode. So if there is no submitted # output, then we will have proper spacing only if we do not add # an additional '' to `out_data`. This is why we condition on # `and data.strip()`. # The submitted output has no output prompt. If we want the # prompt and the code to appear, we need to join them now # instead of adding them separately---as this would create an # undesired newline. How we do this ultimately depends on the # format of the output regex. I'll do what works for the default # prompt for now, and we might have to adjust if it doesn't work # in other cases. Finally, the submitted output does not have # a trailing newline, so we must add it manually. out_data.append("{0} {1}\n".format(output_prompt, data)) return out_data def process_comment(self, data): """Process data fPblock for COMMENT token.""" if not self.is_suppress: return [data] def save_image(self, image_file): """ Saves the image file to disk. """ self.ensure_pyplot() command = 'plt.gcf().savefig("%s")'%image_file #print 'SAVEFIG', command # dbg self.process_input_line('bookmark ipy_thisdir', store_history=False) self.process_input_line('cd -b ipy_savedir', store_history=False) self.process_input_line(command, store_history=False) self.process_input_line('cd -b ipy_thisdir', store_history=False) self.process_input_line('bookmark -d ipy_thisdir', store_history=False) self.clear_cout() def process_block(self, block): """ process block from the block_parser and return a list of processed lines """ ret = [] output = None input_lines = None lineno = self.IP.execution_count input_prompt = self.promptin % lineno output_prompt = self.promptout % lineno image_file = None image_directive = None for token, data in block: if token == COMMENT: out_data = self.process_comment(data) elif token == INPUT: (out_data, input_lines, output, is_doctest, decorator, image_file, image_directive) = \ self.process_input(data, input_prompt, lineno) elif token == OUTPUT: out_data = \ self.process_output(data, output_prompt, input_lines, output, is_doctest, decorator, image_file) if out_data: # Then there was user submitted output in verbatim mode. # We need to remove the last element of `ret` that was # added in `process_input`, as it is '' and would introduce # an undesirable newline. assert(ret[-1] == '') del ret[-1] if out_data: ret.extend(out_data) # save the image files if image_file is not None: self.save_image(image_file) return ret, image_directive def ensure_pyplot(self): """ Ensures that pyplot has been imported into the embedded IPython shell. Also, makes sure to set the backend appropriately if not set already. """ # We are here if the @figure pseudo decorator was used. Thus, it's # possible that we could be here even if python_mplbackend were set to # `None`. That's also strange and perhaps worthy of raising an # exception, but for now, we just set the backend to 'agg'. if not self._pyplot_imported: if 'matplotlib.backends' not in sys.modules: # Then ipython_matplotlib was set to None but there was a # call to the @figure decorator (and ipython_execlines did # not set a backend). #raise Exception("No backend was set, but @figure was used!") import matplotlib matplotlib.use('agg') # Always import pyplot into embedded shell. self.process_input_line('import matplotlib.pyplot as plt', store_history=False) self._pyplot_imported = True def process_pure_python(self, content): """ content is a list of strings. it is unedited directive content This runs it line by line in the InteractiveShell, prepends prompts as needed capturing stderr and stdout, then returns the content as a list as if it were ipython code """ output = [] savefig = False # keep up with this to clear figure multiline = False # to handle line continuation multiline_start = None fmtin = self.promptin ct = 0 for lineno, line in enumerate(content): line_stripped = line.strip() if not len(line): output.append(line) continue # handle decorators if line_stripped.startswith('@'): output.extend([line]) if 'savefig' in line: savefig = True # and need to clear figure continue # handle comments if line_stripped.startswith('#'): output.extend([line]) continue # deal with lines checking for multiline continuation = u' %s:'% ''.join(['.']*(len(str(ct))+2)) if not multiline: modified = u"%s %s" % (fmtin % ct, line_stripped) output.append(modified) ct += 1 try: ast.parse(line_stripped) output.append(u'') except Exception: # on a multiline multiline = True multiline_start = lineno else: # still on a multiline modified = u'%s %s' % (continuation, line) output.append(modified) # if the next line is indented, it should be part of multiline if len(content) > lineno + 1: nextline = content[lineno + 1] if len(nextline) - len(nextline.lstrip()) > 3: continue try: mod = ast.parse( '\n'.join(content[multiline_start:lineno+1])) if isinstance(mod.body[0], ast.FunctionDef): # check to see if we have the whole function for element in mod.body[0].body: if isinstance(element, ast.Return): multiline = False else: output.append(u'') multiline = False except Exception: pass if savefig: # clear figure if plotted self.ensure_pyplot() self.process_input_line('plt.clf()', store_history=False) self.clear_cout() savefig = False return output def custom_doctest(self, decorator, input_lines, found, submitted): """ Perform a specialized doctest. """ from .custom_doctests import doctests args = decorator.split() doctest_type = args[1] if doctest_type in doctests: doctests[doctest_type](self, args, input_lines, found, submitted) else: e = "Invalid option to @doctest: {0}".format(doctest_type) raise Exception(e) class IPythonDirective(Directive): has_content = True required_arguments = 0 optional_arguments = 4 # python, suppress, verbatim, doctest final_argumuent_whitespace = True option_spec = { 'python': directives.unchanged, 'suppress' : directives.flag, 'verbatim' : directives.flag, 'doctest' : directives.flag, 'okexcept': directives.flag, 'okwarning': directives.flag } shell = None seen_docs = set() def get_config_options(self): # contains sphinx configuration variables config = self.state.document.settings.env.config # get config variables to set figure output directory confdir = self.state.document.settings.env.app.confdir savefig_dir = config.ipython_savefig_dir source_dir = os.path.dirname(self.state.document.current_source) if savefig_dir is None: savefig_dir = config.html_static_path if isinstance(savefig_dir, list): savefig_dir = savefig_dir[0] # safe to assume only one path? savefig_dir = os.path.join(confdir, savefig_dir) # get regex and prompt stuff rgxin = config.ipython_rgxin rgxout = config.ipython_rgxout promptin = config.ipython_promptin promptout = config.ipython_promptout mplbackend = config.ipython_mplbackend exec_lines = config.ipython_execlines hold_count = config.ipython_holdcount return (savefig_dir, source_dir, rgxin, rgxout, promptin, promptout, mplbackend, exec_lines, hold_count) def setup(self): # Get configuration values. (savefig_dir, source_dir, rgxin, rgxout, promptin, promptout, mplbackend, exec_lines, hold_count) = self.get_config_options() if self.shell is None: # We will be here many times. However, when the # EmbeddedSphinxShell is created, its interactive shell member # is the same for each instance. if mplbackend: import matplotlib # Repeated calls to use() will not hurt us since `mplbackend` # is the same each time. matplotlib.use(mplbackend) # Must be called after (potentially) importing matplotlib and # setting its backend since exec_lines might import pylab. self.shell = EmbeddedSphinxShell(exec_lines) # Store IPython directive to enable better error messages self.shell.directive = self # reset the execution count if we haven't processed this doc #NOTE: this may be borked if there are multiple seen_doc tmp files #check time stamp? if not self.state.document.current_source in self.seen_docs: self.shell.IP.history_manager.reset() self.shell.IP.execution_count = 1 self.shell.IP.prompt_manager.width = 0 self.seen_docs.add(self.state.document.current_source) # and attach to shell so we don't have to pass them around self.shell.rgxin = rgxin self.shell.rgxout = rgxout self.shell.promptin = promptin self.shell.promptout = promptout self.shell.savefig_dir = savefig_dir self.shell.source_dir = source_dir self.shell.hold_count = hold_count # setup bookmark for saving figures directory self.shell.process_input_line('bookmark ipy_savedir %s'%savefig_dir, store_history=False) self.shell.clear_cout() return rgxin, rgxout, promptin, promptout def teardown(self): # delete last bookmark self.shell.process_input_line('bookmark -d ipy_savedir', store_history=False) self.shell.clear_cout() def run(self): debug = False #TODO, any reason block_parser can't be a method of embeddable shell # then we wouldn't have to carry these around rgxin, rgxout, promptin, promptout = self.setup() options = self.options self.shell.is_suppress = 'suppress' in options self.shell.is_doctest = 'doctest' in options self.shell.is_verbatim = 'verbatim' in options self.shell.is_okexcept = 'okexcept' in options self.shell.is_okwarning = 'okwarning' in options # handle pure python code if 'python' in self.arguments: content = self.content self.content = self.shell.process_pure_python(content) parts = '\n'.join(self.content).split('\n\n') lines = ['.. code-block:: ipython', ''] figures = [] for part in parts: block = block_parser(part, rgxin, rgxout, promptin, promptout) if len(block): rows, figure = self.shell.process_block(block) for row in rows: lines.extend([' {0}'.format(line) for line in row.split('\n')]) if figure is not None: figures.append(figure) for figure in figures: lines.append('') lines.extend(figure.split('\n')) lines.append('') if len(lines) > 2: if debug: print('\n'.join(lines)) else: # This has to do with input, not output. But if we comment # these lines out, then no IPython code will appear in the # final output. self.state_machine.insert_input( lines, self.state_machine.input_lines.source(0)) # cleanup self.teardown() return [] # Enable as a proper Sphinx directive def setup(app): setup.app = app app.add_directive('ipython', IPythonDirective) app.add_config_value('ipython_savefig_dir', None, 'env') app.add_config_value('ipython_rgxin', re.compile('In \[(\d+)\]:\s?(.*)\s*'), 'env') app.add_config_value('ipython_rgxout', re.compile('Out\[(\d+)\]:\s?(.*)\s*'), 'env') app.add_config_value('ipython_promptin', 'In [%d]:', 'env') app.add_config_value('ipython_promptout', 'Out[%d]:', 'env') # We could just let matplotlib pick whatever is specified as the default # backend in the matplotlibrc file, but this would cause issues if the # backend didn't work in headless environments. For this reason, 'agg' # is a good default backend choice. app.add_config_value('ipython_mplbackend', 'agg', 'env') # If the user sets this config value to `None`, then EmbeddedSphinxShell's # __init__ method will treat it as []. execlines = ['import numpy as np', 'import matplotlib.pyplot as plt'] app.add_config_value('ipython_execlines', execlines, 'env') app.add_config_value('ipython_holdcount', True, 'env') # Simple smoke test, needs to be converted to a proper automatic test. def test(): examples = [ r""" In [9]: pwd Out[9]: '/home/jdhunter/py4science/book' In [10]: cd bookdata/ /home/jdhunter/py4science/book/bookdata In [2]: from pylab import * In [2]: ion() In [3]: im = imread('stinkbug.png') @savefig mystinkbug.png width=4in In [4]: imshow(im) Out[4]: """, r""" In [1]: x = 'hello world' # string methods can be # used to alter the string @doctest In [2]: x.upper() Out[2]: 'HELLO WORLD' @verbatim In [3]: x.st x.startswith x.strip """, r""" In [130]: url = 'http://ichart.finance.yahoo.com/table.csv?s=CROX\ .....: &d=9&e=22&f=2009&g=d&a=1&br=8&c=2006&ignore=.csv' In [131]: print url.split('&') ['http://ichart.finance.yahoo.com/table.csv?s=CROX', 'd=9', 'e=22', 'f=2009', 'g=d', 'a=1', 'b=8', 'c=2006', 'ignore=.csv'] In [60]: import urllib """, r"""\ In [133]: import numpy.random @suppress In [134]: numpy.random.seed(2358) @doctest In [135]: numpy.random.rand(10,2) Out[135]: array([[ 0.64524308, 0.59943846], [ 0.47102322, 0.8715456 ], [ 0.29370834, 0.74776844], [ 0.99539577, 0.1313423 ], [ 0.16250302, 0.21103583], [ 0.81626524, 0.1312433 ], [ 0.67338089, 0.72302393], [ 0.7566368 , 0.07033696], [ 0.22591016, 0.77731835], [ 0.0072729 , 0.34273127]]) """, r""" In [106]: print x jdh In [109]: for i in range(10): .....: print i .....: .....: 0 1 2 3 4 5 6 7 8 9 """, r""" In [144]: from pylab import * In [145]: ion() # use a semicolon to suppress the output @savefig test_hist.png width=4in In [151]: hist(np.random.randn(10000), 100); @savefig test_plot.png width=4in In [151]: plot(np.random.randn(10000), 'o'); """, r""" # use a semicolon to suppress the output In [151]: plt.clf() @savefig plot_simple.png width=4in In [151]: plot([1,2,3]) @savefig hist_simple.png width=4in In [151]: hist(np.random.randn(10000), 100); """, r""" # update the current fig In [151]: ylabel('number') In [152]: title('normal distribution') @savefig hist_with_text.png In [153]: grid(True) @doctest float In [154]: 0.1 + 0.2 Out[154]: 0.3 @doctest float In [155]: np.arange(16).reshape(4,4) Out[155]: array([[ 0, 1, 2, 3], [ 4, 5, 6, 7], [ 8, 9, 10, 11], [12, 13, 14, 15]]) In [1]: x = np.arange(16, dtype=float).reshape(4,4) In [2]: x[0,0] = np.inf In [3]: x[0,1] = np.nan @doctest float In [4]: x Out[4]: array([[ inf, nan, 2., 3.], [ 4., 5., 6., 7.], [ 8., 9., 10., 11.], [ 12., 13., 14., 15.]]) """, ] # skip local-file depending first example: examples = examples[1:] #ipython_directive.DEBUG = True # dbg #options = dict(suppress=True) # dbg options = dict() for example in examples: content = example.split('\n') IPythonDirective('debug', arguments=None, options=options, content=content, lineno=0, content_offset=None, block_text=None, state=None, state_machine=None, ) # Run test suite as a script if __name__=='__main__': if not os.path.isdir('_static'): os.mkdir('_static') test() print('All OK? Check figures in _static/') trunk-2017.01a/doc/sphinx/ipython_directive500.py000066400000000000000000001232251304022710500215740ustar00rootroot00000000000000# -*- coding: utf-8 -*- """ Sphinx directive to support embedded IPython code. This directive allows pasting of entire interactive IPython sessions, prompts and all, and their code will actually get re-executed at doc build time, with all prompts renumbered sequentially. It also allows you to input code as a pure python input by giving the argument python to the directive. The output looks like an interactive ipython section. To enable this directive, simply list it in your Sphinx ``conf.py`` file (making sure the directory where you placed it is visible to sphinx, as is needed for all Sphinx directives). For example, to enable syntax highlighting and the IPython directive:: extensions = ['IPython.sphinxext.ipython_console_highlighting', 'IPython.sphinxext.ipython_directive'] The IPython directive outputs code-blocks with the language 'ipython'. So if you do not have the syntax highlighting extension enabled as well, then all rendered code-blocks will be uncolored. By default this directive assumes that your prompts are unchanged IPython ones, but this can be customized. The configurable options that can be placed in conf.py are: ipython_savefig_dir: The directory in which to save the figures. This is relative to the Sphinx source directory. The default is `html_static_path`. ipython_rgxin: The compiled regular expression to denote the start of IPython input lines. The default is re.compile('In \[(\d+)\]:\s?(.*)\s*'). You shouldn't need to change this. ipython_rgxout: The compiled regular expression to denote the start of IPython output lines. The default is re.compile('Out\[(\d+)\]:\s?(.*)\s*'). You shouldn't need to change this. ipython_promptin: The string to represent the IPython input prompt in the generated ReST. The default is 'In [%d]:'. This expects that the line numbers are used in the prompt. ipython_promptout: The string to represent the IPython prompt in the generated ReST. The default is 'Out [%d]:'. This expects that the line numbers are used in the prompt. ipython_mplbackend: The string which specifies if the embedded Sphinx shell should import Matplotlib and set the backend. The value specifies a backend that is passed to `matplotlib.use()` before any lines in `ipython_execlines` are executed. If not specified in conf.py, then the default value of 'agg' is used. To use the IPython directive without matplotlib as a dependency, set the value to `None`. It may end up that matplotlib is still imported if the user specifies so in `ipython_execlines` or makes use of the @savefig pseudo decorator. ipython_execlines: A list of strings to be exec'd in the embedded Sphinx shell. Typical usage is to make certain packages always available. Set this to an empty list if you wish to have no imports always available. If specified in conf.py as `None`, then it has the effect of making no imports available. If omitted from conf.py altogether, then the default value of ['import numpy as np', 'import matplotlib.pyplot as plt'] is used. ipython_holdcount When the @suppress pseudo-decorator is used, the execution count can be incremented or not. The default behavior is to hold the execution count, corresponding to a value of `True`. Set this to `False` to increment the execution count after each suppressed command. As an example, to use the IPython directive when `matplotlib` is not available, one sets the backend to `None`:: ipython_mplbackend = None An example usage of the directive is: .. code-block:: rst .. ipython:: In [1]: x = 1 In [2]: y = x**2 In [3]: print(y) See http://matplotlib.org/sampledoc/ipython_directive.html for additional documentation. Pseudo-Decorators ================= Note: Only one decorator is supported per input. If more than one decorator is specified, then only the last one is used. In addition to the Pseudo-Decorators/options described at the above link, several enhancements have been made. The directive will emit a message to the console at build-time if code-execution resulted in an exception or warning. You can suppress these on a per-block basis by specifying the :okexcept: or :okwarning: options: .. code-block:: rst .. ipython:: :okexcept: :okwarning: In [1]: 1/0 In [2]: # raise warning. ToDo ---- - Turn the ad-hoc test() function into a real test suite. - Break up ipython-specific functionality from matplotlib stuff into better separated code. Authors ------- - John D Hunter: orignal author. - Fernando Perez: refactoring, documentation, cleanups, port to 0.11. - VáclavŠmilauer : Prompt generalizations. - Skipper Seabold, refactoring, cleanups, pure python addition """ from __future__ import print_function #----------------------------------------------------------------------------- # Imports #----------------------------------------------------------------------------- # Stdlib import atexit import os import re import sys import tempfile import ast import warnings import shutil # Third-party from docutils.parsers.rst import directives from sphinx.util.compat import Directive # Our own from traitlets.config import Config from IPython import InteractiveShell from IPython.core.profiledir import ProfileDir from IPython.utils import io from IPython.utils.py3compat import PY3 if PY3: from io import StringIO else: from StringIO import StringIO #----------------------------------------------------------------------------- # Globals #----------------------------------------------------------------------------- # for tokenizing blocks COMMENT, INPUT, OUTPUT = range(3) #----------------------------------------------------------------------------- # Functions and class declarations #----------------------------------------------------------------------------- def block_parser(part, rgxin, rgxout, fmtin, fmtout): """ part is a string of ipython text, comprised of at most one input, one output, comments, and blank lines. The block parser parses the text into a list of:: blocks = [ (TOKEN0, data0), (TOKEN1, data1), ...] where TOKEN is one of [COMMENT | INPUT | OUTPUT ] and data is, depending on the type of token:: COMMENT : the comment string INPUT: the (DECORATOR, INPUT_LINE, REST) where DECORATOR: the input decorator (or None) INPUT_LINE: the input as string (possibly multi-line) REST : any stdout generated by the input line (not OUTPUT) OUTPUT: the output string, possibly multi-line """ block = [] lines = part.split('\n') N = len(lines) i = 0 decorator = None while 1: if i==N: # nothing left to parse -- the last line break line = lines[i] i += 1 line_stripped = line.strip() if line_stripped.startswith('#'): block.append((COMMENT, line)) continue if line_stripped.startswith('@'): # Here is where we assume there is, at most, one decorator. # Might need to rethink this. decorator = line_stripped continue # does this look like an input line? matchin = rgxin.match(line) if matchin: lineno, inputline = int(matchin.group(1)), matchin.group(2) # the ....: continuation string continuation = ' %s:'%''.join(['.']*(len(str(lineno))+2)) Nc = len(continuation) # input lines can continue on for more than one line, if # we have a '\' line continuation char or a function call # echo line 'print'. The input line can only be # terminated by the end of the block or an output line, so # we parse out the rest of the input line if it is # multiline as well as any echo text rest = [] while i 1: if input_lines[-1] != "": input_lines.append('') # make sure there's a blank line # so splitter buffer gets reset continuation = ' %s:'%''.join(['.']*(len(str(lineno))+2)) if is_savefig: image_file, image_directive = self.process_image(decorator) ret = [] is_semicolon = False # Hold the execution count, if requested to do so. if is_suppress and self.hold_count: store_history = False else: store_history = True # Note: catch_warnings is not thread safe with warnings.catch_warnings(record=True) as ws: for i, line in enumerate(input_lines): if line.endswith(';'): is_semicolon = True if i == 0: # process the first input line if is_verbatim: self.process_input_line('') self.IP.execution_count += 1 # increment it anyway else: # only submit the line in non-verbatim mode self.process_input_line(line, store_history=store_history) formatted_line = '%s %s'%(input_prompt, line) else: # process a continuation line if not is_verbatim: self.process_input_line(line, store_history=store_history) formatted_line = '%s %s'%(continuation, line) if not is_suppress: ret.append(formatted_line) if not is_suppress and len(rest.strip()) and is_verbatim: # The "rest" is the standard output of the input. This needs to be # added when in verbatim mode. If there is no "rest", then we don't # add it, as the new line will be added by the processed output. ret.append(rest) # Fetch the processed output. (This is not the submitted output.) self.cout.seek(0) processed_output = self.cout.read() if not is_suppress and not is_semicolon: # # In IPythonDirective.run, the elements of `ret` are eventually # combined such that '' entries correspond to newlines. So if # `processed_output` is equal to '', then the adding it to `ret` # ensures that there is a blank line between consecutive inputs # that have no outputs, as in: # # In [1]: x = 4 # # In [2]: x = 5 # # When there is processed output, it has a '\n' at the tail end. So # adding the output to `ret` will provide the necessary spacing # between consecutive input/output blocks, as in: # # In [1]: x # Out[1]: 5 # # In [2]: x # Out[2]: 5 # # When there is stdout from the input, it also has a '\n' at the # tail end, and so this ensures proper spacing as well. E.g.: # # In [1]: print x # 5 # # In [2]: x = 5 # # When in verbatim mode, `processed_output` is empty (because # nothing was passed to IP. Sometimes the submitted code block has # an Out[] portion and sometimes it does not. When it does not, we # need to ensure proper spacing, so we have to add '' to `ret`. # However, if there is an Out[] in the submitted code, then we do # not want to add a newline as `process_output` has stuff to add. # The difficulty is that `process_input` doesn't know if # `process_output` will be called---so it doesn't know if there is # Out[] in the code block. The requires that we include a hack in # `process_block`. See the comments there. # ret.append(processed_output) elif is_semicolon: # Make sure there is a newline after the semicolon. ret.append('') # context information filename = "Unknown" lineno = 0 if self.directive.state: filename = self.directive.state.document.current_source lineno = self.directive.state.document.current_line # output any exceptions raised during execution to stdout # unless :okexcept: has been specified. if not is_okexcept and "Traceback" in processed_output: s = "\nException in %s at block ending on line %s\n" % (filename, lineno) s += "Specify :okexcept: as an option in the ipython:: block to suppress this message\n" sys.stdout.write('\n\n>>>' + ('-' * 73)) sys.stdout.write(s) sys.stdout.write(processed_output) sys.stdout.write('<<<' + ('-' * 73) + '\n\n') # output any warning raised during execution to stdout # unless :okwarning: has been specified. if not is_okwarning: for w in ws: s = "\nWarning in %s at block ending on line %s\n" % (filename, lineno) s += "Specify :okwarning: as an option in the ipython:: block to suppress this message\n" sys.stdout.write('\n\n>>>' + ('-' * 73)) sys.stdout.write(s) sys.stdout.write(('-' * 76) + '\n') s=warnings.formatwarning(w.message, w.category, w.filename, w.lineno, w.line) sys.stdout.write(s) sys.stdout.write('<<<' + ('-' * 73) + '\n') self.cout.truncate(0) return (ret, input_lines, processed_output, is_doctest, decorator, image_file, image_directive) def process_output(self, data, output_prompt, input_lines, output, is_doctest, decorator, image_file): """ Process data block for OUTPUT token. """ # Recall: `data` is the submitted output, and `output` is the processed # output from `input_lines`. TAB = ' ' * 4 if is_doctest and output is not None: found = output # This is the processed output found = found.strip() submitted = data.strip() if self.directive is None: source = 'Unavailable' content = 'Unavailable' else: source = self.directive.state.document.current_source content = self.directive.content # Add tabs and join into a single string. content = '\n'.join([TAB + line for line in content]) # Make sure the output contains the output prompt. ind = found.find(output_prompt) if ind < 0: e = ('output does not contain output prompt\n\n' 'Document source: {0}\n\n' 'Raw content: \n{1}\n\n' 'Input line(s):\n{TAB}{2}\n\n' 'Output line(s):\n{TAB}{3}\n\n') e = e.format(source, content, '\n'.join(input_lines), repr(found), TAB=TAB) raise RuntimeError(e) found = found[len(output_prompt):].strip() # Handle the actual doctest comparison. if decorator.strip() == '@doctest': # Standard doctest if found != submitted: e = ('doctest failure\n\n' 'Document source: {0}\n\n' 'Raw content: \n{1}\n\n' 'On input line(s):\n{TAB}{2}\n\n' 'we found output:\n{TAB}{3}\n\n' 'instead of the expected:\n{TAB}{4}\n\n') e = e.format(source, content, '\n'.join(input_lines), repr(found), repr(submitted), TAB=TAB) raise RuntimeError(e) else: self.custom_doctest(decorator, input_lines, found, submitted) # When in verbatim mode, this holds additional submitted output # to be written in the final Sphinx output. # https://github.com/ipython/ipython/issues/5776 out_data = [] is_verbatim = decorator=='@verbatim' or self.is_verbatim if is_verbatim and data.strip(): # Note that `ret` in `process_block` has '' as its last element if # the code block was in verbatim mode. So if there is no submitted # output, then we will have proper spacing only if we do not add # an additional '' to `out_data`. This is why we condition on # `and data.strip()`. # The submitted output has no output prompt. If we want the # prompt and the code to appear, we need to join them now # instead of adding them separately---as this would create an # undesired newline. How we do this ultimately depends on the # format of the output regex. I'll do what works for the default # prompt for now, and we might have to adjust if it doesn't work # in other cases. Finally, the submitted output does not have # a trailing newline, so we must add it manually. out_data.append("{0} {1}\n".format(output_prompt, data)) return out_data def process_comment(self, data): """Process data fPblock for COMMENT token.""" if not self.is_suppress: return [data] def save_image(self, image_file): """ Saves the image file to disk. """ self.ensure_pyplot() command = 'plt.gcf().savefig("%s")'%image_file #print 'SAVEFIG', command # dbg self.process_input_line('bookmark ipy_thisdir', store_history=False) self.process_input_line('cd -b ipy_savedir', store_history=False) self.process_input_line(command, store_history=False) self.process_input_line('cd -b ipy_thisdir', store_history=False) self.process_input_line('bookmark -d ipy_thisdir', store_history=False) self.clear_cout() def process_block(self, block): """ process block from the block_parser and return a list of processed lines """ ret = [] output = None input_lines = None lineno = self.IP.execution_count input_prompt = self.promptin % lineno output_prompt = self.promptout % lineno image_file = None image_directive = None found_input = False for token, data in block: if token == COMMENT: out_data = self.process_comment(data) elif token == INPUT: found_input = True (out_data, input_lines, output, is_doctest, decorator, image_file, image_directive) = \ self.process_input(data, input_prompt, lineno) elif token == OUTPUT: if not found_input: TAB = ' ' * 4 linenumber = 0 source = 'Unavailable' content = 'Unavailable' if self.directive: linenumber = self.directive.state.document.current_line source = self.directive.state.document.current_source content = self.directive.content # Add tabs and join into a single string. content = '\n'.join([TAB + line for line in content]) e = ('\n\nInvalid block: Block contains an output prompt ' 'without an input prompt.\n\n' 'Document source: {0}\n\n' 'Content begins at line {1}: \n\n{2}\n\n' 'Problematic block within content: \n\n{TAB}{3}\n\n') e = e.format(source, linenumber, content, block, TAB=TAB) # Write, rather than include in exception, since Sphinx # will truncate tracebacks. sys.stdout.write(e) raise RuntimeError('An invalid block was detected.') out_data = \ self.process_output(data, output_prompt, input_lines, output, is_doctest, decorator, image_file) if out_data: # Then there was user submitted output in verbatim mode. # We need to remove the last element of `ret` that was # added in `process_input`, as it is '' and would introduce # an undesirable newline. assert(ret[-1] == '') del ret[-1] if out_data: ret.extend(out_data) # save the image files if image_file is not None: self.save_image(image_file) return ret, image_directive def ensure_pyplot(self): """ Ensures that pyplot has been imported into the embedded IPython shell. Also, makes sure to set the backend appropriately if not set already. """ # We are here if the @figure pseudo decorator was used. Thus, it's # possible that we could be here even if python_mplbackend were set to # `None`. That's also strange and perhaps worthy of raising an # exception, but for now, we just set the backend to 'agg'. if not self._pyplot_imported: if 'matplotlib.backends' not in sys.modules: # Then ipython_matplotlib was set to None but there was a # call to the @figure decorator (and ipython_execlines did # not set a backend). #raise Exception("No backend was set, but @figure was used!") import matplotlib matplotlib.use('agg') # Always import pyplot into embedded shell. self.process_input_line('import matplotlib.pyplot as plt', store_history=False) self._pyplot_imported = True def process_pure_python(self, content): """ content is a list of strings. it is unedited directive content This runs it line by line in the InteractiveShell, prepends prompts as needed capturing stderr and stdout, then returns the content as a list as if it were ipython code """ output = [] savefig = False # keep up with this to clear figure multiline = False # to handle line continuation multiline_start = None fmtin = self.promptin ct = 0 for lineno, line in enumerate(content): line_stripped = line.strip() if not len(line): output.append(line) continue # handle decorators if line_stripped.startswith('@'): output.extend([line]) if 'savefig' in line: savefig = True # and need to clear figure continue # handle comments if line_stripped.startswith('#'): output.extend([line]) continue # deal with lines checking for multiline continuation = u' %s:'% ''.join(['.']*(len(str(ct))+2)) if not multiline: modified = u"%s %s" % (fmtin % ct, line_stripped) output.append(modified) ct += 1 try: ast.parse(line_stripped) output.append(u'') except Exception: # on a multiline multiline = True multiline_start = lineno else: # still on a multiline modified = u'%s %s' % (continuation, line) output.append(modified) # if the next line is indented, it should be part of multiline if len(content) > lineno + 1: nextline = content[lineno + 1] if len(nextline) - len(nextline.lstrip()) > 3: continue try: mod = ast.parse( '\n'.join(content[multiline_start:lineno+1])) if isinstance(mod.body[0], ast.FunctionDef): # check to see if we have the whole function for element in mod.body[0].body: if isinstance(element, ast.Return): multiline = False else: output.append(u'') multiline = False except Exception: pass if savefig: # clear figure if plotted self.ensure_pyplot() self.process_input_line('plt.clf()', store_history=False) self.clear_cout() savefig = False return output def custom_doctest(self, decorator, input_lines, found, submitted): """ Perform a specialized doctest. """ from .custom_doctests import doctests args = decorator.split() doctest_type = args[1] if doctest_type in doctests: doctests[doctest_type](self, args, input_lines, found, submitted) else: e = "Invalid option to @doctest: {0}".format(doctest_type) raise Exception(e) class IPythonDirective(Directive): has_content = True required_arguments = 0 optional_arguments = 4 # python, suppress, verbatim, doctest final_argumuent_whitespace = True option_spec = { 'python': directives.unchanged, 'suppress' : directives.flag, 'verbatim' : directives.flag, 'doctest' : directives.flag, 'okexcept': directives.flag, 'okwarning': directives.flag } shell = None seen_docs = set() def get_config_options(self): # contains sphinx configuration variables config = self.state.document.settings.env.config # get config variables to set figure output directory outdir = self.state.document.settings.env.app.outdir savefig_dir = config.ipython_savefig_dir source_dir = os.path.dirname(self.state.document.current_source) if savefig_dir is None: savefig_dir = config.html_static_path or '_static' if isinstance(savefig_dir, list): savefig_dir = os.path.join(*savefig_dir) savefig_dir = os.path.join(outdir, savefig_dir) # get regex and prompt stuff rgxin = config.ipython_rgxin rgxout = config.ipython_rgxout promptin = config.ipython_promptin promptout = config.ipython_promptout mplbackend = config.ipython_mplbackend exec_lines = config.ipython_execlines hold_count = config.ipython_holdcount return (savefig_dir, source_dir, rgxin, rgxout, promptin, promptout, mplbackend, exec_lines, hold_count) def setup(self): # Get configuration values. (savefig_dir, source_dir, rgxin, rgxout, promptin, promptout, mplbackend, exec_lines, hold_count) = self.get_config_options() if self.shell is None: # We will be here many times. However, when the # EmbeddedSphinxShell is created, its interactive shell member # is the same for each instance. if mplbackend and 'matplotlib.backends' not in sys.modules: import matplotlib matplotlib.use(mplbackend) # Must be called after (potentially) importing matplotlib and # setting its backend since exec_lines might import pylab. self.shell = EmbeddedSphinxShell(exec_lines) # Store IPython directive to enable better error messages self.shell.directive = self # reset the execution count if we haven't processed this doc #NOTE: this may be borked if there are multiple seen_doc tmp files #check time stamp? if not self.state.document.current_source in self.seen_docs: self.shell.IP.history_manager.reset() self.shell.IP.execution_count = 1 self.seen_docs.add(self.state.document.current_source) # and attach to shell so we don't have to pass them around self.shell.rgxin = rgxin self.shell.rgxout = rgxout self.shell.promptin = promptin self.shell.promptout = promptout self.shell.savefig_dir = savefig_dir self.shell.source_dir = source_dir self.shell.hold_count = hold_count # setup bookmark for saving figures directory self.shell.process_input_line('bookmark ipy_savedir %s'%savefig_dir, store_history=False) self.shell.clear_cout() return rgxin, rgxout, promptin, promptout def teardown(self): # delete last bookmark self.shell.process_input_line('bookmark -d ipy_savedir', store_history=False) self.shell.clear_cout() def run(self): debug = False #TODO, any reason block_parser can't be a method of embeddable shell # then we wouldn't have to carry these around rgxin, rgxout, promptin, promptout = self.setup() options = self.options self.shell.is_suppress = 'suppress' in options self.shell.is_doctest = 'doctest' in options self.shell.is_verbatim = 'verbatim' in options self.shell.is_okexcept = 'okexcept' in options self.shell.is_okwarning = 'okwarning' in options # handle pure python code if 'python' in self.arguments: content = self.content self.content = self.shell.process_pure_python(content) # parts consists of all text within the ipython-block. # Each part is an input/output block. parts = '\n'.join(self.content).split('\n\n') lines = ['.. code-block:: ipython', ''] figures = [] for part in parts: block = block_parser(part, rgxin, rgxout, promptin, promptout) if len(block): rows, figure = self.shell.process_block(block) for row in rows: lines.extend([' {0}'.format(line) for line in row.split('\n')]) if figure is not None: figures.append(figure) for figure in figures: lines.append('') lines.extend(figure.split('\n')) lines.append('') if len(lines) > 2: if debug: print('\n'.join(lines)) else: # This has to do with input, not output. But if we comment # these lines out, then no IPython code will appear in the # final output. self.state_machine.insert_input( lines, self.state_machine.input_lines.source(0)) # cleanup self.teardown() return [] # Enable as a proper Sphinx directive def setup(app): setup.app = app app.add_directive('ipython', IPythonDirective) app.add_config_value('ipython_savefig_dir', None, 'env') app.add_config_value('ipython_rgxin', re.compile('In \[(\d+)\]:\s?(.*)\s*'), 'env') app.add_config_value('ipython_rgxout', re.compile('Out\[(\d+)\]:\s?(.*)\s*'), 'env') app.add_config_value('ipython_promptin', 'In [%d]:', 'env') app.add_config_value('ipython_promptout', 'Out[%d]:', 'env') # We could just let matplotlib pick whatever is specified as the default # backend in the matplotlibrc file, but this would cause issues if the # backend didn't work in headless environments. For this reason, 'agg' # is a good default backend choice. app.add_config_value('ipython_mplbackend', 'agg', 'env') # If the user sets this config value to `None`, then EmbeddedSphinxShell's # __init__ method will treat it as []. execlines = ['import numpy as np', 'import matplotlib.pyplot as plt'] app.add_config_value('ipython_execlines', execlines, 'env') app.add_config_value('ipython_holdcount', True, 'env') metadata = {'parallel_read_safe': True, 'parallel_write_safe': True} return metadata # Simple smoke test, needs to be converted to a proper automatic test. def test(): examples = [ r""" In [9]: pwd Out[9]: '/home/jdhunter/py4science/book' In [10]: cd bookdata/ /home/jdhunter/py4science/book/bookdata In [2]: from pylab import * In [2]: ion() In [3]: im = imread('stinkbug.png') @savefig mystinkbug.png width=4in In [4]: imshow(im) Out[4]: """, r""" In [1]: x = 'hello world' # string methods can be # used to alter the string @doctest In [2]: x.upper() Out[2]: 'HELLO WORLD' @verbatim In [3]: x.st x.startswith x.strip """, r""" In [130]: url = 'http://ichart.finance.yahoo.com/table.csv?s=CROX\ .....: &d=9&e=22&f=2009&g=d&a=1&br=8&c=2006&ignore=.csv' In [131]: print url.split('&') ['http://ichart.finance.yahoo.com/table.csv?s=CROX', 'd=9', 'e=22', 'f=2009', 'g=d', 'a=1', 'b=8', 'c=2006', 'ignore=.csv'] In [60]: import urllib """, r"""\ In [133]: import numpy.random @suppress In [134]: numpy.random.seed(2358) @doctest In [135]: numpy.random.rand(10,2) Out[135]: array([[ 0.64524308, 0.59943846], [ 0.47102322, 0.8715456 ], [ 0.29370834, 0.74776844], [ 0.99539577, 0.1313423 ], [ 0.16250302, 0.21103583], [ 0.81626524, 0.1312433 ], [ 0.67338089, 0.72302393], [ 0.7566368 , 0.07033696], [ 0.22591016, 0.77731835], [ 0.0072729 , 0.34273127]]) """, r""" In [106]: print x jdh In [109]: for i in range(10): .....: print i .....: .....: 0 1 2 3 4 5 6 7 8 9 """, r""" In [144]: from pylab import * In [145]: ion() # use a semicolon to suppress the output @savefig test_hist.png width=4in In [151]: hist(np.random.randn(10000), 100); @savefig test_plot.png width=4in In [151]: plot(np.random.randn(10000), 'o'); """, r""" # use a semicolon to suppress the output In [151]: plt.clf() @savefig plot_simple.png width=4in In [151]: plot([1,2,3]) @savefig hist_simple.png width=4in In [151]: hist(np.random.randn(10000), 100); """, r""" # update the current fig In [151]: ylabel('number') In [152]: title('normal distribution') @savefig hist_with_text.png In [153]: grid(True) @doctest float In [154]: 0.1 + 0.2 Out[154]: 0.3 @doctest float In [155]: np.arange(16).reshape(4,4) Out[155]: array([[ 0, 1, 2, 3], [ 4, 5, 6, 7], [ 8, 9, 10, 11], [12, 13, 14, 15]]) In [1]: x = np.arange(16, dtype=float).reshape(4,4) In [2]: x[0,0] = np.inf In [3]: x[0,1] = np.nan @doctest float In [4]: x Out[4]: array([[ inf, nan, 2., 3.], [ 4., 5., 6., 7.], [ 8., 9., 10., 11.], [ 12., 13., 14., 15.]]) """, ] # skip local-file depending first example: examples = examples[1:] #ipython_directive.DEBUG = True # dbg #options = dict(suppress=True) # dbg options = dict() for example in examples: content = example.split('\n') IPythonDirective('debug', arguments=None, options=options, content=content, lineno=0, content_offset=None, block_text=None, state=None, state_machine=None, ) # Run test suite as a script if __name__=='__main__': if not os.path.isdir('_static'): os.mkdir('_static') test() print('All OK? Check figures in _static/') trunk-2017.01a/doc/sphinx/prog.rst000066400000000000000000003151611304022710500167500ustar00rootroot00000000000000********************** Programmer's manual ********************** Build system ============= Yade uses `cmake `__ the cross-platform, open-source build system for managing the build process. It takes care of configuration, compilation and installation. CMake is used to control the software compilation process using simple platform and compiler independent configuration files. CMake generates native makefiles and workspaces that can be used in the compiler environment of your choice. Building ------------- Yade source tree has the following structure (omiting, ``doc``, ``examples`` and ``scripts`` which don't participate in the build process); we shall call each top-level component *module*:: core/ ## core simulation building blocks extra/ ## miscillanea gui/ ## user interfaces qt4/ ## graphical user interface based on qt3 and OpenGL py/ ## python console interface (phased out) lib/ ## support libraries, not specific to simulations pkg/ ## simulation-specific files common/ ## generally useful classes dem/ ## classes for Discrete Element Method py/ ## python modules Header installation ^^^^^^^^^^^^^^^^^^^^ To allow flexibility in source layout, CMAKE will copy (symlink) all headers into flattened structure within the build directory. First 2 components of the original directory are joind by dash, deeper levels are discarded (in case of ``core`` and ``extra``, only 1 level is used). The following table makes gives a few examples: ============================================================= ========================= Original header location Included as ============================================================= ========================= ``core/Scene.hpp`` ```` ``lib/base/Logging.hpp`` ```` ``lib/serialization/Serializable.hpp`` ```` ``pkg/dem/DataClass/SpherePack.hpp`` ```` ``gui/qt3/QtGUI.hpp`` ```` ============================================================= ========================= It is advised to use ``#include`` style of inclusion rather than ``#include"Class.hpp`` even if you are in the same directory. Automatic compilation """""""""""""""""""""" In the ``pkg/`` directory, situation is different. In order to maximally ease addition of modules to yade, all ``*.cpp`` files are *automatically scanned* by CMAKE and considered for compilation. Each file may contain multiple lines that declare features that are necessary for this file to be compiled:: YADE_REQUIRE_FEATURE(vtk); YADE_REQUIRE_FEATURE(gts); This file will be compiled only if *both* ``VTK`` and ``GTS`` features are enabled. Depending on current feature set, only selection of plugins will be compiled. It is possible to disable compilation of a file by requiring any non-existent feature, such as:: YADE_REQUIRE_FEATURE(temporarily disabled 345uiysdijkn); The ``YADE_REQUIRE_FEATURE`` macro expands to nothing during actual compilation. .. _linking: Linking ^^^^^^^^ The order in which modules might depend on each other is given as follows: =========== ================================== ============================================== module resulting shared library dependencies =========== ================================== ============================================== lib ``libyade-support.so`` can depend on external libraries, may **not** depend on any other part of Yade. core ``libcore.so`` ``yade-support``; *may* depend on external libraries. pkg ``libplugins.so`` ``core``, ``yade-support`` gui ``libQtGUI.so``, ``lib``, ``core``, ``pkg`` ``libPythonUI.so`` py (many files) ``lib``, ``core``, ``pkg``, external =========== ================================== ============================================== Development tools ================= Integrated Development Environment and other tools --------------------------------------------------- A frequently used IDE is Kdevelop. We recommend using this software for navigating in the sources, compiling and debugging. Other useful tools for debugging and profiling are Valgrind and KCachegrind. A series of wiki pages is dedicated to these tools in the `development section `__ of the wiki. Hosting and versioning ---------------------- The Yade project is kindly hosted at `launchpad `__, which is used for source code, bug tracking, planning, package downloads and more. The versioning software used is `GIT `__, for which a short tutorial can be found in :ref:`yade-github-label`. GIT is a distributed revision control system. It is available packaged for all major linux distributions. The source code is hosted on `GitHub `__ , which is periodically imported to Launchpad for building PPA-packages. The repository `can be http-browsed `__. Build robot ----------- A build robot hosted at `3SR lab. `__ is tracking souce code changes. Each time a change in the source code is commited to the main development branch via GIT, the "buildbot" downloads and compiles the new version, and start a series of tests. If a compilation error has been introduced, it will be notified to the yade-dev mailing list and to the commiter, thus helping to fix problems quickly. If the compilation is successfull, the buildbot starts unit regression tests and "check tests" (see below) and report the results. If all tests are passed, a new version of the documentation is generated and uploaded to the website in `html `__ and `pdf `__ formats. As a consequence, those two links always point to the documentation (the one you are reading now) of the last successfull build, and the delay between commits and documentation updates are very short (minutes). The buildbot activity and logs can be `browsed online `__. Regression tests ---------------- Yade contains two types of regression tests, some are unit tests while others are testing more complex simulations. Altough both types can be considered regression tests, the usage is that we name the first simply "regression tests", while the latest are called "check tests". Both series of tests can be ran at yade startup by passing the options "test" or "check" :: yade --test yade --check Unit regression tests ^^^^^^^^^^^^^^^^^^^^^ Unit regression tests are testing the output of individual functors and engines in well defined conditions. They are defined in the folder :ysrc:`py/tests/`. The purpose of unit testing is to make sure that the behaviour of the most important classes remains correct during code development. Since they test classes one by one, unit tests can't detect problems coming from the interaction between different engines in a typical simulation. That is why check tests have been introduced. Check tests ^^^^^^^^^^^ Check tests perform comparisons of simulation results between different versions of yade, as discussed `here `__. They differ with regression tests in the sense that they simulate more complex situations and combinations of different engines, and usually don't have a mathematical proof (though there is no restriction on the latest). They compare the values obtained in version N with values obtained in a previous version or any other "expected" results. The reference values must be hardcoded in the script itself or in data files provided with the script. Check tests are based on regular yade scripts, so that users can easily commit their own scripts to trunk in order to get some automatized testing after commits from other developers. Since the check tests history will be mostly based on standard output generated by "yade ---check", a meaningfull checkTest should include some "print" command telling if something went wrong. If the script itself fails for some reason and can't generate an output, the log will contain "scriptName failure". If the script defines differences on obtained and awaited data, it should print some useful information about the problem and increase the value of global variable resultStatus. After this occurs, the automatic test will stop the execution with error message. An example check test can be found in checkTestTriax.py. It shows results comparison, output, and how to define the path to data files using "checksPath". Users are encouraged to add their own scripts into the scripts/test/checks/ folder. Discussion of some specific checktests design in users question is welcome. Note that re-compiling is required before that added scripts can be launched by "yade ---check" (or direct changes have to be performed in "lib" subfolders). A check test should never need more than a few seconds to run. If your typical script needs more, try and reduce the number of element or the number of steps. Conventions ============ The following rules that should be respected; documentation is treated separately. * general * C++ source files have ``.hpp`` and ``.cpp`` extensions (for headers and implementation, respectively). * All header files should have the ``#pragma once`` multiple-inclusion guard. * Try to avoid ``using namespace …`` in header files. * Use tabs for indentation. While this is merely visual in ``c++``, it has semantic meaning in python; inadverently mixing tabs and spaces can result in syntax errors. * capitalization style * Types should be always capitalized. Use CamelCase for composed names (``GlobalEngine``). Underscores should be used only in special cases, such as functor names. * Class data members and methods must not be capitalized, composed names should use use lowercased camelCase (``glutSlices``). The same applies for functions in python modules. * Preprocessor macros are uppercase, separated by underscores; those that are used outside the core take (with exceptions) the form ``YADE_*``, such as :ref:`YADE_CLASS_BASE_DOC`. * programming style * Be defensive, if it has no significant performance impact. Use assertions abundantly: they don't affect performance (in the optimized build) and make spotting error conditions much easier. * Use ``YADE_CAST`` and ``YADE_PTR_CAST`` where you want type-check during debug builds, but fast casting in optimized build. * Initialize all class variables in the default constructor. This avoids bugs that may manifest randomly and are difficult to fix. Initializing with NaN's will help you find otherwise unitialized variable. (This is taken care of by :ref:`YADE_CLASS_BASE_DOC` macros for user classes) Class naming ------------- Although for historial reasons the naming scheme is not completely consistent, these rules should be obeyed especially when adding a new class. GlobalEngines and PartialEngines GlobalEngines should be named in a way suggesting that it is a performer of certain action (like :yref:`ForceResetter`, :yref:`InsertionSortCollider`, :yref:`Recorder`); if this is not appropriate, append the ``Engine`` to the characteristics (:yref:`GravityEngine`). :yref:`PartialEngines` have no special naming convention different from :yref:`GlobalEngines`. Dispatchers Names of all dispatchers end in ``Dispatcher``. The name is composed of type it creates or, in case it doesn't create any objects, its main characteristics. Currently, the following dispatchers [#opengldispatchers]_ are defined: .. _dispatcher-names: ========================== ================ ====================== ============== ===================== =============== dispatcher arity dispatch types created type functor type functor prefix ========================== ================ ====================== ============== ===================== =============== :yref:`BoundDispatcher` 1 :yref:`Shape` :yref:`Bound` :yref:`BoundFunctor` ``Bo1`` :yref:`IGeomDispatcher` 2 (symetric) 2 × :yref:`Shape` :yref:`IGeom` :yref:`IGeomFunctor` ``Ig2`` :yref:`IPhysDispatcher` 2 (symetric) 2 × :yref:`Material` :yref:`IPhys` :yref:`IPhysFunctor` ``Ip2`` :yref:`LawDispatcher` 2 (asymetric) :yref:`IGeom` *(none)* :yref:`LawFunctor` ``Law2`` :yref:`IPhys` ========================== ================ ====================== ============== ===================== =============== Respective abstract functors for each dispatchers are :yref:`BoundFunctor`, :yref:`IGeomFunctor`, :yref:`IPhysFunctor` and :yref:`LawFunctor`. Functors Functor name is composed of 3 parts, separated by underscore. #. prefix, composed of abbreviated functor type and arity (see table above) #. Types entering the dispatcher logic (1 for unary and 2 for binary functors) #. Return type for functors that create instances, simple characteristics for functors that don't create instances. To give a few examples: * :yref:`Bo1_Sphere_Aabb` is a :yref:`BoundFunctor` which is called for :yref:`Sphere`, creating an instance of :yref:`Aabb`. * :yref:`Ig2_Facet_Sphere_ScGeom` is binary functor called for :yref:`Facet` and :yref:`Sphere`, creating and instace of :yref:`ScGeom`. * :yref:`Law2_ScGeom_CpmPhys_Cpm` is binary functor (:yref:`LawFunctor`) called for types :yref:`ScGeom (Geom)` and :yref:`CpmPhys`. .. [#opengldispatchers] Not considering OpenGL dispatchers, which might be replaced by regular virtual functions in the future. Documentation --------------- **Documenting code properly is one of the most important aspects of sustained development.** Read it again. Most code in research software like Yade is not only used, but also read, by developers or even by regular users. Therefore, when adding new class, always mention the following in the documentation: * purpose * details of the functionality, unless obvious (algorithms, internal logic) * limitations (by design, by implementation), bugs * bibliographical reference, if using non-trivial published algorithms (see below) * references to other related classes * hyperlinks to bugs, blueprints, wiki or mailing list about this particular feature. As much as it is meaningful, you should also * update any other documentation affected * provide a simple python script demonstrating the new functionality in ``scripts/test``. .. _sphinxdocumentation: Sphinx documentation ^^^^^^^^^^^^^^^^^^^^^ Most c++ classes are wrapped in Python, which provides good introspection and interactive documentation (try writing ``Material?`` in the ipython prompt; or ``help(CpmState)``). Syntax of documentation is `ReST `__ (reStructuredText, see `reStructuredText Primer `__). It is the same for c++ and python code. * Documentation of c++ classes exposed to python is given as 3rd argument to :ref:`YADE_CLASS_BASE_DOC` introduced below. * Python classes/functions are documented using regular python docstrings. Besides explaining functionality, meaning and types of all arguments should also be documented. Short pieces of code might be very helpful. See the :yref:`yade.utils` module for an example. In addition to standard ReST syntax, yade provides several shorthand macros: ``:yref:`` creates hyperlink to referenced term, for instance:: :yref:`CpmMat` becomes :yref:`CpmMat`; link name and target can be different:: :yref:`Material used in the CPM model` yielding :yref:`Material used in the CPM model`. ``:ysrc:`` creates hyperlink to file within the source tree (to its latest version in the repository), for instance :ysrc:`core/Cell.hpp`. Just like with `:yref:`, alternate text can be used with :: :ysrc:`Link text` like :ysrc:`this`. ``|ycomp|`` is used in attribute description for those that should not be provided by the used, but are auto-computed instead; ``|ycomp|`` expands to |ycomp|. ``|yupdate|`` marks attributes that are periodically update, being subset of the previous. ``|yupdate|`` expands to |yupdate|. ``\$...\$`` delimits inline math expressions; they will be replaced by:: :math:`...` and rendered via LaTeX. To write a single dollar sign, escape it with backslash ``\\$``. Displayed mathematics (standalone equations) can be inserted as explained in `Math support in Sphinx `_. Bibliographical references ^^^^^^^^^^^^^^^^^^^^^^^^^^^ As in any scientific documentation, references to publications are very important. To cite an article, add it to BibTeX file in :ysrc:`doc/references.bib`, using the BibTeX format. Please adhere to the following conventions: #. Keep entries in the form ``Author2008`` (``Author`` is the first author), ``Author2008b`` etc if multiple articles from one author; #. Try to fill `mandatory fields `_ for given type of citation; #. Do not use ``\'{i}`` funny escapes for accents, since they will not work with the HTML output; put everything in straight utf-8. In your docstring, the ``Author2008`` article can be cited by ``[Author2008]_``; for example:: According to [Allen1989]_, the integration scheme … will be rendered as According to [Allen1989]_, the integration scheme … Separate class/function documentation ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Some c++ might have long or content-rich documentation, which is rather inconvenient to type in the c++ source itself as string literals. Yade provides a way to write documentation separately in :ysrc:`py/_extraDocs.py` file: it is executed after loading c++ plugins and can set ``__doc__`` attribute of any object directly, overwriting docstring from c++. In such (exceptional) cases: #. Provide at least a brief description of the class in the c++ code nevertheless, for people only reading the code. #. Add notice saying "This class is documented in detail in the :ysrc:`py/_extraDocs.py` file". #. Add documentation to :ysrc:`py/_etraDocs.py` in this way:: module.YourClass.__doc__=''' This is the docstring for YourClass. Class, methods and functions can be documented this way. .. note:: It can use any syntax features you like. ''' .. note:: Boost::python embeds function signatures in the docstring (before the one provided by the user). Therefore, before creating separate documentation of your function, have a look at its ``__doc__`` attribute and copy the first line (and the blank lie afterwards) in the separate docstring. The first line is then used to create the function signature (arguments and return value). Internal c++ documentation ^^^^^^^^^^^^^^^^^^^^^^^^^^ `doxygen `__ was used for automatic generation of c++ code. Since user-visible classes are defined with sphinx now, it is not meaningful to use doxygen to generate overall documentation. However, take care to document well internal parts of code using regular comments, including public and private data members. Support framework ======================= Besides the framework provided by the c++ standard library (including STL), boost and other dependencies, yade provides its own specific services. Pointers --------- Shared pointers ^^^^^^^^^^^^^^^^^ Yade makes extensive use of shared pointers ``shared_ptr``. [#sharedptr]_ Although it probably has some performance impacts, it greatly simplifies memory management, ownership management of c++ objects in python and so forth. To obtain raw pointer from a ``shared_ptr``, use its ``get()`` method; raw pointers should be used in case the object will be used only for short time (during a function call, for instance) and not stored anywhere. .. [#sharedptr] Either ``boost::shared_ptr`` or ``tr1::shared_ptr`` is used, but it is always imported with the ``using`` statement so that unqualified ``shared_ptr`` can be used. Python defines thin wrappers for most c++ Yade classes (for all those registered with :ref:`YADE_CLASS_BASE_DOC` and several others), which can be constructed from ``shared_ptr``; in this way, Python reference counting blends with the ``shared_ptr`` reference counting model, preventing crashes due to python objects pointing to c++ objects that were destructed in the meantime. Typecasting ^^^^^^^^^^^^ Frequently, pointers have to be typecast; there is choice between static and dynamic casting. * ``dynamic_cast`` (``dynamic_pointer_cast`` for a ``shared_ptr``) assures cast admissibility by checking runtime type of its argument and returns NULL if the cast is invalid; such check obviously costs time. Invalid cast is easily caught by checking whether the pointer is NULL or not; even if such check (e.g. ``assert``) is absent, dereferencing NULL pointer is easily spotted from the stacktrace (debugger output) after crash. Moreover, ``shared_ptr`` checks that the pointer is non-NULL before dereferencing in debug build and aborts with "Assertion \`px!=0' failed." if the check fails. * ``static_cast`` is fast but potentially dangerous (``static_pointer_cast`` for ``shared_ptr``). Static cast will return non-NULL pointer even if types don't allow the cast (such as casting from ``State*`` to ``Material*``); the consequence of such cast is interpreting garbage data as instance of the class cast to, leading very likely to invalid memory access (segmentation fault, "crash" for short). To have both speed and safety, Yade provides 2 macros: ``YADE_CAST`` expands to ``static_cast`` in optimized builds and to ``dynamic_cast`` in debug builds. ``YADE_PTR_CAST`` expands to ``static_pointer_cast`` in optimized builds and to ``dynamic_pointer_cast`` in debug builds. Basic numerics --------------- The floating point type to use in Yade ``Real``, which is by default typedef for ``double``. [#real]_ Yade uses the `Eigen `_ library for computations. It provides classes for 2d and 3d vectors, quaternions and 3x3 matrices templated by number type; their specialization for the ``Real`` type are typedef'ed with the "r" suffix, and occasionally useful integer types with the "i" suffix: * ``Vector2r``, ``Vector2i`` * ``Vector3r``, ``Vector3i`` * ``Quaternionr`` * ``Matrix3r`` Yade additionally defines a class named :yref:`Se3r`, which contains spatial position (``Vector3r Se3r::position``) and orientation (``Quaternionr Se3r::orientation``), since they are frequently used one with another, and it is convenient to pass them as single parameter to functions. .. [#real] Historically, it was thought that Yade could be also run with single precision based on build-time parameter; it turned out however that the impact on numerical stability was such disastrous that this option is not available now. There is, however, ``QUAD_PRECISION`` parameter to scons, which will make ``Real`` a typedef for ``long double`` (extended precision; quad precision in the proper sense on IA64 processors); this option is experimental and is unlikely to be used in near future, though. Eigen provides full rich linear algebra functionality. Some code firther uses the [cgal]_ library for computational geometry. In Python, basic numeric types are wrapped and imported from the ``minieigen`` module; the types drop the ``r`` type qualifier at the end, the syntax is otherwise similar. ``Se3r`` is not wrapped at all, only converted automatically, rarely as it is needed, from/to a ``(Vector3,Quaternion)`` tuple/list. .. ipython:: @suppress Yade [0]: from math import pi # cross product Yade [1]: Vector3(1,2,3).cross(Vector3(0,0,1)) # construct quaternion from axis and angle Yade [2]: Quaternion(Vector3(0,0,1),pi/2) .. note:: Quaternions are internally stored as 4 numbers. Their usual human-readable representation is, however, (normalized) axis and angle of rotation around that axis, and it is also how they are input/output in Python. Raw internal values can be accessed using the ``[0]`` … ``[3]`` element access (or ``.W()``, ``.X()``, ``.Y()`` and ``.Z()`` methods), in both c++ and Python. .. _rtti: Run-time type identification (RTTI) ----------------------------------- Since serialization and dispatchers need extended type and inheritance information, which is not sufficiently provided by standard RTTI. Each yade class is therefore derived from ``Factorable`` and it must use macro to override its virtual functions providing this extended RTTI: ``YADE_CLASS_BASE_DOC(Foo,Bar Baz,"Docstring)`` creates the following virtual methods (mediated via the ``REGISTER_CLASS_AND_BASE`` macro, which is not user-visible and should not be used directly): * ``std::string getClassName()`` returning class name (``Foo``) as string. (There is the ``typeid(instanceOrType).name()`` standard c++ construct, but the name returned is compiler-dependent.) * ``unsigned getBaseClassNumber()`` returning number of base classes (in this case, 2). * ``std::string getBaseClassName(unsigned i=0)`` returning name of *i*-th base class (here, ``Bar`` for i=0 and ``Baz`` for i=1). .. warning:: RTTI relies on virtual functions; in order for virtual functions to work, at least one virtual method must be present in the implementation (``.cpp``) file. Otherwise, virtual method table (vtable) will not be generated for this class by the compiler, preventing virtual methods from functioning properly. Some RTTI information can be accessed from python: .. ipython:: @suppress Yade [1]: import yade.system Yade [2]: yade.system.childClasses('Shape') Yade [3]: Sphere().name ## getClassName() Serialization -------------- Serialization serves to save simulation to file and restore it later. This process has several necessary conditions: * classes know which attributes (data members) they have and what are their names (as strings); * creating class instances based solely on its name; * knowing what classes are defined inside a particular shared library (plugin). This functionality is provided by 3 macros and 4 optional methods; details are provided below. ``Serializable::preLoad``, ``Serializable::preSave``, ``Serializable::postLoad``, ``Serializable::postSave`` Prepare attributes before serialization (saving) or deserialization (loading) or process them after serialization or deserialization. See :ref:`attributeregistration`. ``YADE_CLASS_BASE_DOC_*`` Inside the class declaration (i.e. in the ``.hpp`` file within the ``class Foo { /* … */};`` block). See :ref:`attributeregistration`. Enumerate class attributes that should be saved and loaded; associate each attribute with its literal name, which can be used to retrieve it. See :ref:`YADE_CLASS_BASE_DOC`. Additionally documents the class in python, adds methods for attribute access from python, and documents each attribute. ``REGISTER_SERIALIZABLE`` In header file, but *after* the class declaration block. See :ref:`classfactory`. Associate literal name of the class with functions that will create its new instance (``ClassFactory``). ``YADE_PLUGIN`` In the implementation ``.cpp`` file. See :ref:`plugins`. Declare what classes are declared inside a particular plugin at time the plugin is being loaded (yade startup). .. _attributeregistration: Attribute registration ^^^^^^^^^^^^^^^^^^^^^^ All (serializable) types in Yade are one of the following: * Type deriving from :yref:`Serializable`, which provide information on how to serialize themselves via overriding the ``Serializable::registerAttributes`` method; it declares data members that should be serialzed along with their literal names, by which they are identified. This method then invokes ``registerAttributes`` of its base class (until ``Serializable`` itself is reached); in this way, derived classes properly serialize data of their base classes. This funcionality is hidden behind the macro :ref:`YADE_CLASS_BASE_DOC` used in class declaration body (header file), which takes base class and list of attributes:: YADE_CLASS_BASE_DOC_ATTRS(ThisClass,BaseClass,"class documentation",((type1,attribute1,initValue1,,"Documentation for attribute 1"))((type2,attribute2,initValue2,,"Documentation for attribute 2")); Note that attributes are encodes in double parentheses, not separated by commas. Empty attribute list can be given simply by ``YADE_CLASS_BASE_DOC_ATTRS(ThisClass,BaseClass,"documentation",)`` (the last comma is mandatory), or by omiting ``ATTRS`` from macro name and last parameter altogether. * Fundamental type: strings, various number types, booleans, ``Vector3r`` and others. Their "handlers" (serializers and deserializers) are defined in ``lib/serialization``. * Standard container of any serializable objects. * Shared pointer to serializable object. Yade uses the excellent `boost::serialization `_ library internally for serialization of data. .. note:: ``YADE_CLASS_BASE_DOC_ATTRS`` also generates code for attribute access from python; this will be discussed later. Since this macro serves both purposes, the consequence is that attributes that are serialized can always be accessed from python. Yade also provides callback for before/after (de) serialization, virtual functions :yref:`Serializable::preProcessAttributes` and :yref:`Serializable::postProcessAttributes`, which receive one ``bool deserializing`` argument (``true`` when deserializing, ``false`` when serializing). Their default implementation in :yref:`Serializable` doesn't do anything, but their typical use is: * converting some non-serializable internal data structure of the class (such as multi-dimensional array, hash table, array of pointers) into a serializable one (pre-processing) and fill this non-serializable structure back after deserialization (post-processing); for instance, InteractionContainer uses these hooks to ask its concrete implementation to store its contents to a unified storage (``vector >``) before serialization and to restore from it after deserialization. * precomputing non-serialized attributes from the serialized values; e.g. :yref:`Facet` computes its (local) edge normals and edge lengths from vertices' coordinates. .. _classfactory: Class factory ^^^^^^^^^^^^^^ Each serializable class must use ``REGISTER_SERIALIZABLE``, which defines function to create that class by ``ClassFactory``. ``ClassFactory`` is able to instantiate a class given its name (as string), which is necessary for deserialization. Although mostly used internally by the serialization framework, programmer can ask for a class instantiation using ``shared_ptr f=ClassFactory::instance().createShared("ClassName");``, casting the returned ``shared_ptr`` to desired type afterwards. :yref:`Serializable` itself derives from ``Factorable``, i.e. all serializable types are also factorable (It is possible that different mechanism will be in place if boost::serialization is used, though.) .. _plugins: Plugin registration ^^^^^^^^^^^^^^^^^^^ Yade loads dynamic libraries containing all its functionality at startup. ClassFactory must be taught about classes each particular file provides. ``YADE_PLUGIN`` serves this purpose and, contrary to :ref:`YADE_CLASS_BASE_DOC`, must be place in the implementation (.cpp) file. It simple enumerates classes that are provided by this file:: YADE_PLUGIN((ClassFoo)(ClassBar)); .. note:: You must use parentheses around the class name even if there is only one (preprocessor limitation): ``YADE_PLUGIN((classFoo));``. If there is no class in this file, do not use this macro at all. Internally, this macro creates function ``registerThisPluginClasses_`` declared specially as ``__attribute__((constructor))`` (see `GCC Function Attributes `_); this attributes makes the function being executed when the plugin is loaded via ``dlopen`` from ``ClassFactory::load(...)``. It registers all factorable classes from that file in the :ref:`classfactory`. .. note:: Classes that do not derive from ``Factorable``, such as ``Shop`` or ``SpherePack``, are not declared with ``YADE_PLUGIN``. --------------- This is an example of a serializable class header: .. code-block:: c++ /*! Homogeneous gravity field; applies gravity×mass force on all bodies. */ class GravityEngine: public GlobalEngine{ public: virtual void action(); // registering class and its base for the RTTI system YADE_CLASS_BASE_DOC_ATTRS(GravityEngine,GlobalEngine, // documentation visible from python and generated reference documentation "Homogeneous gravity field; applies gravity×mass force on all bodies.", // enumerating attributes here, include documentation ((Vector3r,gravity,Vector3r::ZERO,"acceleration, zero by default [kgms⁻²]")) ); }; // registration function for ClassFactory REGISTER_SERIALIZABLE(GravityEngine); and this is the implementation: .. code-block:: c++ #include #include // registering the plugin YADE_PLUGIN((GravityEngine)); void GravityEngine::action(){ /* do the work here */ } We can create a mini-simulation (with only one GravityEngine): .. ipython:: Yade [1]: O.engines=[GravityEngine(gravity=Vector3(0,0,-9.81))] Yade [2]: O.save('abc.xml') and the XML looks like this: .. literalinclude:: abc.xml :language: xml .. warning:: Since XML files closely reflect implementation details of Yade, they will not be compatible between different versions. Use them only for short-term saving of scenes. Python is *the* high-level description Yade uses. .. _pythonattributeaccess: Python attribute access ^^^^^^^^^^^^^^^^^^^^^^^^ The macro :ref:`YADE_CLASS_BASE_DOC` introduced above is (behind the scenes) also used to create functions for accessing attributes from Python. As already noted, set of serialized attributes and set of attributes accessible from Python are identical. Besides attribute access, these wrapper classes imitate also some functionality of regular python dictionaries: .. ipython:: Yade [1]: s=Sphere() Yade [2]: s.radius ## read-access Yade [3]: s.radius=4. ## write access Yade [4]: s.dict().keys() ## show all available keys Yade [5]: for k in s.dict().keys(): print s.dict()[k] ## iterate over keys, print their values ...: Yade [5]: s.dict()['radius'] ## same as: 'radius' in s.keys() Yade [6]: s.dict() ## show dictionary of both attributes and values .. _YADE_CLASS_BASE_DOC: YADE_CLASS_BASE_DOC_* macro family ----------------------------------- There is several macros that hide behind them the functionality of :ref:`sphinxdocumentation`, :ref:`rtti`, :ref:`attributeregistration`, :ref:`pythonattributeaccess`, plus automatic attribute initialization and documentation. They are all defined as shorthands for base macro ``YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY`` with some arguments left out. They must be placed in class declaration's body (``.hpp`` file): .. code-block:: c++ #define YADE_CLASS_BASE_DOC(klass,base,doc) \ YADE_CLASS_BASE_DOC_ATTRS(klass,base,doc,) #define YADE_CLASS_BASE_DOC_ATTRS(klass,base,doc,attrs) \ YADE_CLASS_BASE_DOC_ATTRS_CTOR(klass,base,doc,attrs,) #define YADE_CLASS_BASE_DOC_ATTRS_CTOR(klass,base,doc,attrs,ctor) \ YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(klass,base,doc,attrs,ctor,) #define YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(klass,base,doc,attrs,ctor,py) \ YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(klass,base,doc,attrs,,ctor,py) #define YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(klass,base,doc,attrs,init,ctor,py) \ YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(klass,base,doc,attrs,inits,ctor,py) Expected parameters are indicated by macro name components separated with underscores. Their meaning is as follows: ``klass`` (unquoted) name of this class (used for RTTI and python) ``base`` (unquoted) name of the base class (used for RTTI and python) ``doc`` docstring of this class, written in the ReST syntax. This docstring will appear in generated documentation (such as :yref:`CpmMat`). It can be as long as necessary, but sequences interpreted by c++ compiler must be properly escaped (therefore some backslashes must be doubled, like in :math:`\sigma=\epsilon E`:: ":math:`\\sigma=\\epsilon E" Use ``\n`` and ``\t`` for indentation inside the docstring. Hyperlink the documentation abundantly with ``yref`` (all references to other classes should be hyperlinks). See :ref:`sphinxdocumentation` for syntax details. ``attrs`` Attribute must be written in the form of parethesized list: .. code-block:: c++ ((type1,attr1,initValue1,attrFlags,"Attribute 1 documentation")) ((type2,attr2,,,"Attribute 2 documentation")) // initValue and attrFlags unspecified This will expand to #. data members declaration in c++ (note that all attributes are *public*): .. code-block:: c++ public: type1 attr1; type2 attr2; #. Initializers of the default (argument-less) constructor, for attributes that have non-empty ``initValue``: .. code-block:: c++ Klass(): attr1(initValue1), attr2() { /* constructor body */ } No initial value will be assigned for attribute of which initial value is left empty (as is for attr2 in the above example). Note that you still have to write the commas. #. Registration of the attribute in the serialization system (unless disabled by attrFlags -- see below) #. Registration of the attribute in python (unless disabled by attrFlags), so that it can be accessed as ``klass().name1``. The attribute is read-write by default, see attrFlags to change that. This attribute will carry the docstring provided, along with knowledge of the initial value. You can add text description to the default value using the comma operator of c++ and casting the char* to (void): .. code-block:: c++ ((Real,dmgTau,((void)"deactivated if negative",-1),,"Characteristic time for normal viscosity. [s]")) leading to :yref:`CpmMat::dmgTau`. The attribute is registered via ``boost::python::add_property`` specifying ``return_by_value`` policy rather than ``return_internal_reference``, which is the default when using ``def_readwrite``. The reason is that we need to honor custom converters for those values; see note in :ref:`customconverters` for details. .. admonition:: Attribute flags By default, an attribute will be serialized and will be read-write from python. There is a number of flags that can be passed as the 4th argument (empty by default) to change that: * ``Attr::noSave`` avoids serialization of the attribute (while still keeping its accessibility from Python) * ``Attr::readonly`` makes the attribute read-only from Python * ``Attr::triggerPostLoad`` will trigger call to ``postLoad`` function to handle attribute change after its value is set from Python; this is to ensure consistency of other precomputed data which depend on this value (such as ``Cell.trsf`` and such) * ``Attr::hidden`` will not expose the attribute to Python at all * ``Attr::noResize`` will not permit changing size of the array from Python [not yet used] Flags can be combined as usual using bitwise disjunction ``|`` (such as ``Attr::noSave | Attr::readonly``), though in such case the value should be parenthesized to avoid a warning with some compilers (g++ specifically), i.e. ``(Attr::noSave | Attr::readonly)``. Currently, the flags logic handled at runtime; that means that even for attributes with ``Attr::noSave``, their serialization template must be defined (although it will never be used). In the future, the implementation might be template-based, avoiding this necessity. ``deprec`` List of deprecated attribute names. The syntax is :: ((oldName1,newName1,"Explanation why renamed etc.")) ((oldName2,newName2,"! Explanation why removed and what to do instaed.")) This will make accessing ``oldName1`` attribute *from Python* return value of ``newName``, but displaying warning message about the attribute name change, displaying provided explanation. This happens whether the access is read or write. If the explanation's first character is ``!`` (*bang*), the message will be displayed upon attribute access, but exception will be thrown immediately. Use this in cases where attribute is no longer meaningful or was not straightforwardsly replaced by another, but more complex adaptation of user's script is needed. You still have to give ``newName2``, although its value will never be used -- you can use any variable you like, but something must be given for syntax reasons). .. warning:: Due to compiler limitations, this feature only works if Yade is compiled with gcc >= 4.4. In the contrary case, deprecated attribute functionality is disabled, even if such attributes are declared. ``init`` Parethesized list of the form: .. code-block:: c++ ((attr3,value3)) ((attr4,value4)) which will be expanded to initializers in the default ctor: .. code-block:: c++ Klass(): /* attributes declared with the attrs argument */ attr4(value4), attr5(value5) { /* constructor body */ } The purpose of this argument is to make it possible to initialize constants and references (which are not declared as attributes using this macro themselves, but separately), as that cannot be done in constructor body. This argument is rarely used, though. ``ctor`` will be put directly into the generated constructor's body. Mostly used for calling createIndex(); in the constructor. .. note:: The code must not contain commas ouside parentheses (since preprocessor uses commas to separate macro arguments). If you need complex things at construction time, create a separate init() function and call it from the constructor instead. ``py`` will be appeneded directly after generated python code that registers the class and all its attributes. You can use it to access class methods from python, for instance, to override an existing attribute with the same name etc: .. code-block:: c++ .def_readonly("omega",&CpmPhys::omega,"Damage internal variable") .def_readonly("Fn",&CpmPhys::Fn,"Magnitude of normal force.") ``def_readonly`` will not work for custom types (such as std::vector), as it bypasses conversion registry; see :ref:`customconverters` for details. Special python constructors ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ The Python wrapper automatically create constructor that takes keyword (named) arguments corresponding to instance attributes; those attributes are set to values provided in the constructor. In some cases, more flexibility is desired (such as :yref:`InteractionLoop`, which takes 3 lists of functors). For such cases, you can override the function ``Serializable::pyHandleCustomCtorArgs``, which can arbitrarily modify the new (already existing) instance. It should modify in-place arguments given to it, as they will be passed further down to the routine which sets attribute values. In such cases, you should document the constructor:: .. admonition:: Special constructor Constructs from lists of … which then appears in the documentation similar to :yref:`InteractionLoop`. Static attributes ^^^^^^^^^^^^^^^^^^^ Some classes (such as OpenGL functors) are instantiated automatically; since we want their attributes to be persistent throughout the session, they are static. To expose class with static attributes, use the ``YADE_CLASS_BASE_DOC_STATICATTRS`` macro. Attribute syntax is the same as for ``YADE_CLASS_BASE_DOC_ATTRS``: .. code-block:: c++ class SomeClass: public BaseClass{ YADE_CLASS_BASE_DOC_STATICATTRS(SomeClass,BaseClass,"Documentation of SomeClass", ((Type1,attr1,default1,"doc for attr1")) ((Type2,attr2,default2,"doc for attr2")) ); }; additionally, you *have* to allocate memory for static data members in the ``.cpp`` file (otherwise, error about undefined symbol will appear when the plugin is loaded): .. code-block: c++ /* in the .cpp file */ #include /* allocate memory for static attrs; no need to assign initial value, that is done from (hidden) initialization function at class registration time using default values given to macro in the .hpp file. */ Type1 SomeClass::attr1; Type2 SomeClass::attr2; There is no way to expose class that has both static and non-static attributes using ``YADE_CLASS_BASE_*`` macros. You have to expose non-static attributes normally and wrap static attributes separately in the ``py`` parameter. .. _valuereference: Returning attribute by value or by reference ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ When attribute is passed from c++ to python, it can be passed either as * value: new python object representing the original c++ object is constructed, but not bound to it; changing the python object doesn't modify the c++ object, unless explicitly assigned back to it, where inverse conversion takes place and the c++ object is replaced. * reference: only reference to the underlying c++ object is given back to python; modifying python object will make the c++ object modified automatically. The way of passing attributes given to ``YADE_CLASS_BASE_DOC_ATTRS`` in the ``attrs`` parameter is determined automatically in the following manner: * ``Vector3``, ``Vector3i``, ``Vector2``, ``Vector2i``, ``Matrix3`` and ``Quaternion`` objects are passed by *reference*. For instance:: O.bodies[0].state.pos[0]=1.33 will assign correct value to ``x`` component of position, without changing the other ones. * Yade classes (all that use ``shared_ptr`` when declared in python: all classes deriving from :yref:`Serializable` declared with ``YADE_CLASS_BASE_DOC_*``, and some others) are passed as *references* (technically speaking, they are passed by value of the ``shared_ptr``, but by virtue of its sharedness, they appear as references). For instance:: O.engines[4].damping=.3 will change :yref:`damping` parameter on the original engine object, not on its copy. * All other types are passed by *value*. This includes, most importantly, sequence types declared in :ref:`customconverters`, such as ``std::vector >``. For this reason, :: O.engines[4]=NewtonIntegrator() will *not* work as expected; it will replace 5th element of a *copy* of the sequence, and this change will not propagate back to c++. .. _multiple-dispatch: Multiple dispatch ------------------ Multiple dispatch is generalization of virtual methods: a :yref:`Dispatcher` decides based on type(s) of its argument(s) which of its :yref:`Functors` to call. Numer of arguments (currently 1 or 2) determines *arity* of the dispatcher (and of the functor): unary or binary. For example: .. code-block:: python InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]) creates :yref:`InsertionSortCollider`, which internally contains :yref:`Collider.boundDispatcher`, a :yref:`BoundDispatcher` (a :yref:`Dispatcher`), with 2 functors; they receive ``Sphere`` or ``Facet`` instances and create ``Aabb``. This code would look like this in c++: .. code-block:: c++ shared_ptr collider=(new InsertionSortCollider); collider->boundDispatcher->add(new Bo1_Sphere_Aabb()); collider->boundDispatcher->add(new Bo1_Facet_Aabb()); There are currenly 4 predefined dispatchers (see `dispatcher-names`_) and corresponding functor types. They are inherit from template instantiations of ``Dispatcher1D`` or ``Dispatcher2D`` (for functors, ``Functor1D`` or ``Functor2D``). These templates themselves derive from ``DynlibDispatcher`` (for dispatchers) and ``FunctorWrapper`` (for functors). Example: IGeomDispatcher ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Let's take (the most complicated perhaps) :yref:`IGeomDispatcher`. :yref:`IGeomFunctor`, which is dispatched based on types of 2 :yref:`Shape` instances (a :yref:`Functor`), takes a number of arguments and returns bool. The functor "call" is always provided by its overridden ``Functor::go`` method; it always receives the dispatched instances as first argument(s) (2 × ``const shared_ptr&``) and a number of other arguments it needs: .. code-block:: c++ class IGeomFunctor: public Functor2D< bool, //return type TYPELIST_7(const shared_ptr&, // 1st class for dispatch const shared_ptr&, // 2nd class for dispatch const State&, // other arguments passed to ::go const State&, // … const Vector3r&, // … const bool&, // … const shared_ptr& // … ) > The dispatcher is declared as follows: .. code-block:: c++ class IGeomDispatcher: public Dispatcher2D< Shape, // 1st class for dispatch Shape, // 2nd class for dispatch IGeomFunctor, // functor type bool, // return type of the functor // follow argument types for functor call // they must be exactly the same as types // given to the IGeomFunctor above. TYPELIST_7(const shared_ptr&, const shared_ptr&, const State&, const State&, const Vector3r&, const bool &, const shared_ptr& ), // handle symetry automatically // (if the dispatcher receives Sphere+Facet, // the dispatcher might call functor for Facet+Sphere, // reversing the arguments) false > { /* … */ } Functor derived from IGeomFunctor must then * override the ::go method with appropriate arguments (they must match exactly types given to ``TYPELIST_*`` macro); * declare what types they should be dispatched for, and in what order if they are not the same. .. code-block:: c++ class Ig2_Facet_Sphere_ScGeom: public IGeomFunctor{ public: // override the IGeomFunctor::go // (it is really inherited from FunctorWrapper template, // therefore not declare explicitly in the // IGeomFunctor declaration as such) // since dispatcher dispatches only for declared types // (or types derived from them), we can do // static_cast(shape1) and static_cast(shape2) // in the ::go body, without worrying about types being wrong. virtual bool go( // objects for dispatch const shared_ptr& shape1, const shared_ptr& shape2, // other arguments const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c ); /* … */ // this declares the type we want to be dispatched for, matching // first 2 arguments to ::go and first 2 classes in TYPELIST_7 above // shape1 is a Facet and shape2 is a Sphere // (or vice versa, see lines below) FUNCTOR2D(Facet,Sphere); // declare how to swap the arguments // so that we can receive those as well DEFINE_FUNCTOR_ORDER_2D(Facet,Sphere); /* … */ }; Dispatch resolution ^^^^^^^^^^^^^^^^^^^ The dispatcher doesn't always have functors that exactly match the actual types it receives. In the same way as virtual methods, it tries to find the closest match in such way that: #. the actual instances are derived types of those the functor accepts, or exactly the accepted types; #. sum of distances from actual to accepted types is sharp-minimized (each step up in the class hierarchy counts as 1) If no functor is able to accept given types (first condition violated) or multiple functors have the same distance (in condition 2), an exception is thrown. This resolution mechanism makes it possible, for instance, to have a hierarchy of :yref:`ScGeom` classes (for different combination of shapes), but only provide a :yref:`LawFunctor` accepting ``ScGeom``, rather than having different laws for each shape combination. .. note:: Performance implications of dispatch resolution are relatively low. The dispatcher lookup is only done once, and uses fast lookup matrix (1D or 2D); then, the functor found for this type(s) is cached within the ``Interaction`` (or ``Body``) instance. Thus, regular functor call costs the same as dereferencing pointer and calling virtual method. There is `blueprint `__ to avoid virtual function call as well. .. note:: At the beginning, the dispatch matrix contains just entries exactly matching given functors. Only when necessary (by passing other types), appropriate entries are filled in as well. Indexing dispatch types ^^^^^^^^^^^^^^^^^^^^^^^^ Classes entering the dispatch mechanism must provide for fast identification of themselves and of their parent class. [#rttiindex]_ This is called class indexing and all such classes derive from :yref:`Indexable`. There are ``top-level`` Indexables (types that the dispatchers accept) and each derived class registers its index related to this top-level Indexable. Currently, there are: ==================== =========================== Top-level Indexable used by ==================== =========================== :yref:`Shape` :yref:`BoundFunctor`, :yref:`IGeomDispatcher` :yref:`Material` :yref:`IPhysDispatcher` :yref:`IPhys` :yref:`LawDispatcher` :yref:`IGeom` :yref:`LawDispatcher` ==================== =========================== The top-level Indexable must use the ``REGISTER_INDEX_COUNTER`` macro, which sets up the machinery for identifying types of derived classes; they must then use the ``REGISTER_CLASS_INDEX`` macro *and* call ``createIndex()`` in their constructor. For instance, taking the :yref:`Shape` class (which is a top-level Indexable): .. code-block:: c++ // derive from Indexable class Shape: public Serializable, public Indexable { // never call createIndex() in the top-level Indexable ctor! /* … */ // allow index registration for classes deriving from ``Shape`` REGISTER_INDEX_COUNTER(Shape); }; Now, all derived classes (such as :yref:`Sphere` or :yref:`Facet`) use this: .. code-block:: c++ class Sphere: public Shape{ /* … */ YADE_CLASS_BASE_DOC_ATTRS_CTOR(Sphere,Shape,"docstring", ((Type1,attr1,default1,"docstring1")) /* … */, // this is the CTOR argument // important; assigns index to the class at runtime createIndex(); ); // register index for this class, and give name of the immediate parent class // (i.e. if there were a class deriving from Sphere, it would use // REGISTER_CLASS_INDEX(SpecialSphere,Sphere), // not REGISTER_CLASS_INDEX(SpecialSphere,Shape)!) REGISTER_CLASS_INDEX(Sphere,Shape); }; At runtime, each class within the top-level Indexable hierarchy has its own unique numerical index. These indices serve to build the dispatch matrix for each dispatcher. .. [#rttiindex] The functionality described in :ref:`rtti` serves a different purpose (serialization) and would hurt the performance here. For this reason, classes provide numbers (indices) in addition to strings. Inspecting dispatch in python ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ If there is a need to debug/study multiple dispatch, python provides convenient interface for this low-level functionality. We can inspect indices with the ``dispIndex`` property (note that the top-level indexable ``Shape`` has negative (invalid) class index; we purposively didn't call ``createIndex`` in its constructor): .. ipython:: Yade [5]: Sphere().dispIndex, Facet().dispIndex, Wall().dispIndex Yade [6]: Shape().dispIndex # top-level indexable Dispatch hierarchy for a particular class can be shown with the ``dispHierarchy()`` function, returning list of class names: 0th element is the instance itself, last element is the top-level indexable (again, with invalid index); for instance: .. ipython:: Yade [7]: ScGeom().dispHierarchy() # parent class of all other ScGeom_ classes Yade [8]: ScGridCoGeom().dispHierarchy(), ScGeom6D().dispHierarchy(), CylScGeom().dispHierarchy() Yade [8]: CylScGeom().dispHierarchy(names=False) # show numeric indices instead Dispatchers can also be inspected, using the .dispMatrix() method: .. ipython:: Yade [3]: ig=IGeomDispatcher([ ...: Ig2_Sphere_Sphere_ScGeom(), ...: Ig2_Facet_Sphere_ScGeom(), ...: Ig2_Wall_Sphere_ScGeom() ...: ]) Yade [4]: ig.dispMatrix() Yade [5]: ig.dispMatrix(False) # don't convert to class names We can see that functors make use of symmetry (i.e. that Sphere+Wall are dispatched to the same functor as Wall+Sphere). Finally, dispatcher can be asked to return functor suitable for given argument(s): .. ipython:: Yade [6]: ld=LawDispatcher([Law2_ScGeom_CpmPhys_Cpm()]) Yade [7]: ld.dispMatrix() # see how the entry for ScGridCoGeom will be filled after this request Yade [8]: ld.dispFunctor(ScGridCoGeom(),CpmPhys()) Yade [9]: ld.dispMatrix() OpenGL functors ^^^^^^^^^^^^^^^ OpenGL rendering is being done also by 1D functors (dispatched for the type to be rendered). Since it is sufficient to have exactly one class for each rendered type, the functors are found automatically. Their base functor types are ``GlShapeFunctor``, ``GlBoundFunctor``, ``GlIGeomFunctor`` and so on. These classes register the type they render using the ``RENDERS`` macro: .. code-block:: c++ class Gl1_Sphere: public GlShapeFunctor { public : virtual void go(const shared_ptr&, const shared_ptr&, bool wire, const GLViewInfo& ); RENDERS(Sphere); YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_Sphere,GlShapeFunctor,"docstring", ((Type1,staticAttr1,informativeDefault,"docstring")) /* … */ ); }; REGISTER_SERIALIZABLE(Gl1_Sphere); You can list available functors of a particular type by querying child classes of the base functor: .. ipython:: @suppress Yade [1]: import yade.system Yade [2]: yade.system.childClasses('GlShapeFunctor') .. note:: OpenGL functors may disappear in the future, being replaced by virtual functions of each class that can be rendered. Parallel execution ------------------ Yade was originally not designed with parallel computation in mind, but rather with maximum flexibility (for good or for bad). Parallel execution was added later; in order to not have to rewrite whole Yade from scratch, relatively non-instrusive way of parallelizing was used: `OpenMP `__. OpenMP is standartized shared-memory parallel execution environment, where parallel sections are marked by special ``#pragma`` in the code (which means that they can compile with compiler that doesn't support OpenMP) and a few functions to query/manipulate OpenMP runtime if necessary. There is parallelism at 3 levels: * Computation, interaction (python, GUI) and rendering threads are separate. This is done via regular threads (boost::threads) and is not related to OpenMP. * :yref:`ParallelEngine` can run multiple engine groups (which are themselves run serially) in parallel; it rarely finds use in regular simulations, but it could be used for example when coupling with an independent expensive computation: .. code-block:: python ParallelEngine([ [Engine1(),Engine2()], # Engine1 will run before Engine2 [Engine3()] # Engine3() will run in parallel with the group [Engine1(),Engine2()] # arbitrary number of groups can be used ]) ``Engine2`` will be run after ``Engine1``, but in parallel with ``Engine3``. .. warning:: It is your reponsibility to avoid concurrent access to data when using ParallelEngine. Make sure you understand *very well* what the engines run in parallel do. * Parallelism inside Engines. Some loops over bodies or interactions are parallelized (notably :yref:`InteractionLoop` and :yref:`NewtonIntegrator`, which are treated in detail later (FIXME: link)): .. code-block:: c++ #pragma omp parallel for for(long id=0; id& b(scene->bodies[id]); /* … */ } .. note :: OpenMP requires loops over contiguous range of integers (OpenMP 3 also accepts containers with random-access iterators). If you consider running parallelized loop in your engine, always evalue its benefits. OpenMP has some overhead fo creating threads and distributing workload, which is proportionally more expensive if the loop body execution is fast. The results are highly hardware-dependent (CPU caches, RAM controller). Maximum number of OpenMP threads is determined by the ``OMP_NUM_THREADS`` environment variable and is constant throughout the program run. Yade main program also sets this variable (before loading OpenMP libraries) if you use the ``-j``/``--threads`` option. It can be queried at runtime with the ``omp_get_max_threads`` function. At places which are susceptible of being accessed concurrently from multiple threads, Yade provides some mutual exclusion mechanisms, discussed elsewhere (FIXME): * simultaneously writeable container for :ref:`ForceContainer`, * mutex for :yref:`Body::state`. .. _timing: Timing ------- Yade provides 2 services for measuring time spent in different pars of the code. One has the granularity of engine and can be enabled at runtime. The other one is finer, but requires adjusting and recompiling the code being measured. Per-engine timing ^^^^^^^^^^^^^^^^^^ The coarser timing works by merely accumulating numebr of invocations and time (with the precision of the ``clock_gettime`` function) spent in each engine, which can be then post-processed by associated Python module ``yade.timing``. There is a static bool variable controlling whether such measurements take place (disabled by default), which you can change .. code-block:: c++ TimingInfo::enabled=True; // in c++ .. code-block:: python O.timingEnabled=True ## in python After running the simulation, ``yade.timing.stats()`` function will show table with the results and percentages: .. ipython:: Yade [1]: TriaxialTest(numberOfGrains=100).load() Yade [2]: O.engines[0].label='firstEngine' ## labeled engines will show by labels in the stats table Yade [2]: import yade.timing; Yade [2]: O.timingEnabled=True Yade [1]: yade.timing.reset() ## not necessary if used for the first time Yade [3]: O.run(50); O.wait() Yade [5]: yade.timing.stats() Exec count and time can be accessed and manipulated through ``Engine::timingInfo`` from c++ or ``Engine().execCount`` and ``Engine().execTime`` properties in Python. In-engine and in-functor timing ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Timing within engines (and functors) is based on :yref:`TimingDeltas` class. It is made for timing loops (functors' loop is in their respective dispatcher) and stores cummulatively time differences between *checkpoints*. .. note:: Fine timing with ``TimingDeltas`` will only work if timing is enabled globally (see previous section). The code would still run, but giving zero times and exec counts. #. Engine::timingDeltas must point to an instance of :yref:`TimingDeltas` (prefferably instantiate :yref:`TimingDeltas` in the constructor): .. code-block:: c++ // header file class Law2_ScGeom_CpmPhys_Cpm: public LawFunctor { /* … */ YADE_CLASS_BASE_DOC_ATTRS_CTOR(Law2_ScGeom_CpmPhys_Cpm,LawFunctor,"docstring", /* attrs */, /* constructor */ timingDeltas=shared_ptr(new TimingDeltas); // timingDeltas object is automatically initialized when using -DENABLE_PROFILING=1 cmake option ); // ... }; #. Inside the loop, start the timing by calling ``timingDeltas->start();`` #. At places of interest, call ``timingDeltas->checkpoint("label")``. The label is used only for post-processing, data are stored based on the checkpoint position, not the label. .. warning:: Checkpoints must be always reached in the same order, otherwise the timing data will be garbage. Your code can still branch, but you have to put checkpoints to places which are in common. .. code-block:: c++ void Law2_ScGeom_CpmPhys_Cpm::go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I, Scene* scene) { timingDeltas->start(); // the point at which the first timing starts // prepare some variables etc here timingDeltas->checkpoint("setup"); // find geometrical data (deformations) here timingDeltas->checkpoint("geom"); // compute forces here timingDeltas->checkpoint("material"); // apply forces, cleanup here timingDeltas->checkpoint("rest"); } #. Alternatively, you can compile Yade using -DENABLE_PROFILING=1 cmake option and use predefined macros TIMING_DELTAS_START and TIMING_DELTAS_CHECKPOINT. Without -DENABLE_PROFILING options, those macros are empty and do nothing. .. code-block:: c++ void Law2_ScGeom_CpmPhys_Cpm::go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I, Scene* scene) { TIMING_DELTAS_START(); // prepare some variables etc here TIMING_DELTAS_CHECKPOINT("setup") // find geometrical data (deformations) here TIMING_DELTAS_CHECKPOINT("geom") // compute forces here TIMING_DELTAS_CHECKPOINT("material") // apply forces, cleanup here TIMING_DELTAS_CHECKPOINT("rest") } The output might look like this (note that functors are nested inside dispatchers and ``TimingDeltas`` inside their engine/functor):: Name Count Time Rel. time ------------------------------------------------------------------------------------- ForceReseter 400 9449μs 0.01% BoundDispatcher 400 1171770μs 1.15% InsertionSortCollider 400 9433093μs 9.24% IGeomDispatcher 400 15177607μs 14.87% IPhysDispatcher 400 9518738μs 9.33% LawDispatcher 400 64810867μs 63.49% Law2_ScGeom_CpmPhys_Cpm setup 4926145 7649131μs 15.25% geom 4926145 23216292μs 46.28% material 4926145 8595686μs 17.14% rest 4926145 10700007μs 21.33% TOTAL 50161117μs 100.00% NewtonIntegrator 400 1866816μs 1.83% "strainer" 400 21589μs 0.02% "plotDataCollector" 160 64284μs 0.06% "damageChecker" 9 3272μs 0.00% TOTAL 102077490μs 100.00% .. warning:: Do not use :yref:`TimingDeltas` in parallel sections, results might not be meaningful. In particular, avoid timing functors inside :yref:`InteractionLoop` when running with multiple OpenMP threads. ``TimingDeltas`` data are accessible from Python as list of (*label*,*time*,*count*) tuples, one tuple representing each checkpoint: .. code-block:: python deltas=someEngineOrFunctor.timingDeltas.data() deltas[0][0] # 0th checkpoint label deltas[0][1] # 0th checkpoint time in nanoseconds deltas[0][2] # 0th checkpoint execution count deltas[1][0] # 1st checkpoint label # … deltas.reset() Timing overhead ^^^^^^^^^^^^^^^ The overhead of the coarser, per-engine timing, is very small. For simulations with at least several hundreds of elements, they are below the usual time variance (a few percent). .. TriaxialTest(numberOfGrains=800).load(); O.saveTmp(); import time; O.timingEnabled=True; t0=time.time(); O.run(2000,True); print(time.time()-t0); O.loadTmp(); O.timingEnabled=False; t0=time.time(); O.run(2000,True); print (time.time()-t0) The finer :yref:`TimingDeltas` timing can have major performance impact and should be only used during debugging and performance-tuning phase. The parts that are file-timed will take disproportionally longer time that the rest of engine; in the output presented above, :yref:`LawDispatcher` takes almost ⅔ of total simulation time in average, but the number would be twice of thrice lower typically (note that each checkpoint was timed almost 5 million times in this particular case). OpenGL Rendering ----------------- Yade provides 3d rendering based on `QGLViewer `__. It is not meant to be full-featured rendering and post-processing, but rather a way to quickly check that scene is as intended or that simulation behaves sanely. .. note:: Although 3d rendering runs in a separate thread, it has performance impact on the computation itself, since interaction container requires mutual exclusion for interaction creation/deletion. The ``InteractionContainer::drawloopmutex`` is either held by the renderer (:yref:`OpenGLRenderingEngine`) or by the insertion/deletion routine. .. warning:: There are 2 possible causes of crash, which are not prevented because of serious performance penalty that would result: #. access to :yref:`BodyContainer`, in particular deleting bodies from simulation; this is a rare operation, though. #. deleting Interaction::phys or Interaction::geom. Renderable entities (:yref:`Shape`, :yref:`State`, :yref:`Bound`, :yref:`IGeom`, :yref:`IPhys`) have their associated `OpenGL functors`_. An entity is rendered if #. Rendering such entities is enabled by appropriate attribute in :yref:`OpenGLRenderingEngine` #. Functor for that particular entity type is found via the :ref:`dispatch mechanism`. ``Gl1_*`` functors operating on Body's attributes (:yref:`Shape`, :yref:`State`, :yref:`Bound`) are called with the OpenGL context translated and rotated according to :yref:`State::pos` and :yref:`State::ori`. Interaction functors work in global coordinates. Simulation framework ====================== Besides the support framework mentioned in the previous section, some functionality pertaining to simulation itself is also provided. There are special containers for storing bodies, interactions and (generalized) forces. Their internal functioning is normally opaque to the programmer, but should be understood as it can influence performance. Scene ------ ``Scene`` is the object containing the whole simulation. Although multiple scenes can be present in the memory, only one of them is active. Saving and loading (serializing and deserializing) the ``Scene`` object should make the simulation run from the point where it left off. .. note:: All :yref:`Engines` and functors have interally a ``Scene* scene`` pointer which is updated regularly by engine/functor callers; this ensures that the current scene can be accessed from within user code. For outside functions (such as those called from python, or static functions in ``Shop``), you can use ``Omega::instance().getScene()`` to retrieve a ``shared_ptr`` of the current scene. Body container --------------- Body container is linear storage of bodies. Each body in the simulation has its unique :yref:`id`, under which it must be found in the :yref:`BodyContainer`. Body that is not yet part of the simulation typically has id equal to invalid value ``Body::ID_NONE``, and will have its ``id`` assigned upon insertion into the container. The requirements on :yref:`BodyContainer` are * O(1) access to elements, * linear-addressability (0…n indexability), * store ``shared_ptr``, not objects themselves, * *no* mutual exclusion for insertion/removal (this must be assured by the called, if desired), * intelligent allocation of ``id`` for new bodies (tracking removed bodies), * easy iteration over all bodies. .. note:: Currently, there is "abstract" class ``BodyContainer``, from which derive concrete implementations; the initial idea was the ability to select at runtime which implementation to use (to find one that performs the best for given simulation). This incurs the penalty of many virtual function calls, and will probably change in the future. All implementations of BodyContainer were removed in the meantime, except ``BodyVector`` (internally a ``vector >`` plus a few methods around), which is the fastest. Insertion/deletion ^^^^^^^^^^^^^^^^^^ Body insertion is typically used in :yref:`FileGenerator`'s: .. code-block:: c++ shared_ptr body(new Body); // … (body setup) scene->bodies->insert(body); // assigns the id Bodies are deleted only rarely: .. code-block:: c++ scene->bodies->erase(id); .. warning:: Since mutual exclusion is not assured, never insert/erase bodies from parallel sections, unless you explicitly assure there will be no concurrent access. Iteration ^^^^^^^^^^ The container can be iterated over using ``FOREACH`` macro (shorthand for ``BOOST_FOREACH``): .. code-block:: c++ FOREACH(const shared_ptr& b, *scene->bodies){ if(!b) continue; // skip deleted bodies /* do something here */ } Note a few important things: #. Always use ``const shared_ptr&`` (const reference); that avoids incrementing and decrementing the reference count on each ``shared_ptr``. #. Take care to skip NULL bodies (``if(!b) continue``): deleted bodies are deallocated from the container, but since body id's must be persistent, their place is simply held by an empty ``shared_ptr()`` object, which is implicitly convertible to ``false``. In python, the BodyContainer wrapper also has iteration capabilities; for convenience (which is different from the c++ iterator), NULL bodies as silently skipped: .. ipython:: @suppress Yade [0]: O.reset() Yade [1]: O.bodies.append([Body(),Body(),Body()]) Yade [2]: O.bodies.erase(1) Yade [3]: [b.id for b in O.bodies] In loops parallelized using OpenMP, the loop must traverse integer interval (rather than using iterators): .. code-block:: c++ const long size=(long)bodies.size(); // store this value, since it doesn't change during the loop #pragma omp parallel for for(long _id=0; _id& b(bodies[_id]); if(!b) continue; /* … */ } InteractionContainer --------------------- Interactions are stored in special container, and each interaction must be uniquely identified by pair of ids (id1,id2). * O(1) access to elements, * linear-addressability (0…n indexability), * store ``shared_ptr``, not objects themselves, * mutual exclusion for insertion/removal, * easy iteration over all interactions, * addressing symmetry, i.e. interaction(id1,id2)≡interaction(id2,id1) .. note:: As with BodyContainer, there is "abstract" class InteractionContainer, and then its concrete implementations. Currently, only InteractionVecMap implementation is used and all the other were removed. Therefore, the abstract InteractionContainer class may disappear in the future, to avoid unnecessary virtual calls. Further, there is a `blueprint `__ for storing interactions inside bodies, as that would give extra advantage of quickly getting all interactions of one particular body (currently, this necessitates loop over all interactions); in that case, InteractionContainer would disappear. Insert/erase ^^^^^^^^^^^^ Creating new interactions and deleting them is delicate topic, since many eleents of simulation must be synchronized; the exact workflow is described in :ref:`interaction-flow`. You will almost certainly never need to insert/delete an interaction manually from the container; if you do, consider designing your code differently. .. code-block:: c++ // both insertion and erase are internally protected by a mutex, // and can be done from parallel sections safely scene->interactions->insert(shared_ptr(new Interactions(id1,id2))); scene->interactions->erase(id1,id2); Iteration ^^^^^^^^^ As with BodyContainer, iteration over interactions should use the ``FOREACH`` macro: .. code-block:: c++ FOREACH(const shared_ptr& i, *scene->interactions){ if(!i->isReal()) continue; /* … */ } Again, note the usage const reference for ``i``. The check ``if(!i->isReal())`` filters away interactions that exist only *potentially*, i.e. there is only :yref:`Bound` overlap of the two bodies, but not (yet) overlap of bodies themselves. The ``i->isReal()`` function is equivalent to ``i->geom && i->phys``. Details are again explained in :ref:`interaction-flow`. In some cases, such as OpenMP-loops requiring integral index (OpenMP >= 3.0 allows parallelization using random-access iterator as well), you need to iterate over interaction indices instead: .. code-block:: c++ inr nIntr=(int)scene->interactions->size(); // hoist container size #pragma omp parallel for for(int j=0; j& i(scene->interactions[j]); if(!->isReal()) continue; /* … */ } .. _ForceContainer: ForceContainer -------------- :yref:`ForceContainer` holds "generalized forces", i.e. forces, torques, (explicit) dispalcements and rotations for each body. During each computation step, there are typically 3 phases pertaining to forces: #. Resetting forces to zero (usually done by the :yref:`ForceResetter` engine) #. Incrementing forces from parallel sections (solving interactions -- from :yref:`LawFunctor`) #. Reading absolute force values sequentially for each body: forces applied from different interactions are summed together to give overall force applied on that body (:yref:`NewtonIntegrator`, but also various other engine that read forces) This scenario leads to special design, which allows fast parallel write access: * each thread has its own storage (zeroed upon request), and only writes to its own storage; this avoids concurrency issues. Each thread identifies itself by the omp_get_thread_num() function provided by the OpenMP runtime. * before reading absolute values, the container must be synchronized, i.e. values from all threads are summed up and stored separately. This is a relatively slow operation and we provide ForceContainer::syncCount that you might check to find cummulative number of synchronizations and compare it against number of steps. Ideally, ForceContainer is only synchronized once at each step. * the container is resized whenever an element outside the current range is read/written to (the read returns zero in that case); this avoids the necessity of tracking number of bodies, but also is potential danger (such as ``scene->forces.getForce(1000000000)``, which will probably exhaust your RAM). Unlike c++, Python does check given id against number of bodies. .. code-block:: c++ // resetting forces (inside ForceResetter) scene->forces.reset() // in a parallel section scene->forces.addForce(id,force); // add force // container is not synced after we wrote to it, sync before reading scene->forces.sync(); const Vector3r& f=scene->forces.getForce(id); Synchronization is handled automatically if values are read from python: .. ipython:: Yade [0]: O.bodies.append(Body()) Yade [0]: O.forces.addF(0,Vector3(1,2,3)) Yade [0]: O.forces.f(0) Yade [0]: O.forces.f(100) .. _interaction-flow: Handling interactions ---------------------- Creating and removing interactions is a rather delicate topic and number of components must cooperate so that the whole behaves as expected. Terminologically, we distinguish potential interactions, having neither :yref:`geometry` nor :yref:`physics`. :yref:`Interaction.isReal` can be used to query the status (``Interaction::isReal()`` in c++). real interactions, having both :yref:`geometry` and :yref:`physics`. Below, we shall discuss the possibility of interactions that only have geometry but no physics. During each step in the simulation, the following operations are performed on interactions in a typical simulation: #. Collider creates potential interactions based on spatial proximity. Not all pairs of bodies are susceptible of entering interaction; the decision is done in Collider::mayCollide: * clumps may not enter interactions (only their members can) * clump members may not interact if they belong to the same clump * bitwise AND on both bodies' :yref:`masks` must be non-zero (i.e. there must be at least one bit set in common) #. Collider erases interactions that were requested for being erased (see below). #. :yref:`InteractionLoop` (via :yref:`IGeomDispatcher`) calls appropriate :yref:`IGeomFunctor` based on :yref:`Shape` combination of both bodies, if such functor exists. For real interactions, the functor updates associated :yref:`IGeom`. For potential interactions, the functor returns ``false`` if there is no geometrical overlap, and the interaction will stillremain potential-only ``true`` if there is geometrical overlap; the functor will have created an :yref:`IGeom` in such case. .. note :: For *real* interactions, the functor *must* return ``true``, even if there is no more spatial overlap between bodies. If you wish to delete an interaction without geometrical overlap, you have to do this in the :yref:`LawFunctor`. This behavior is deliberate, since different :yref:`laws` have different requirements, though ideally using relatively small number of generally useful :yref:`geometry functors`. .. note:: If there is no functor suitable to handle given combination of :yref:`shapes`, the interaction will be left in potential state, without raising any error. #. For real interactions (already existing or just created in last step), :yref:`InteractionLoop` (via :yref:`IPhysDispatcher`) calls appropriate :yref:`IPhysFunctor` based on :yref:`Material` combination of both bodies. The functor *must* update (or create, if it doesn't exist yet) associated :yref:`IPhys` instance. It is an error if no suitable functor is found, and an exception will be thrown. #. For real interactions, :yref:`InteractionLoop` (via :yref:`LawDispatcher`) calls appropriate :yref:`LawFunctor` based on combination of :yref:`IGeom` and :yref:`IPhys` of the interaction. Again, it is an error if no functor capable of handling it is found. #. :yref:`LawDispatcher` takes care of erasing those interactions that are no longer active (such as if bodies get too far apart for non-cohesive laws; or in case of complete damage for damage models). This is triggered by the :yref:`LawFunctor` returning false. For this reason it is of upmost importance for the :yref:`LawFunctor` to return consistently. Such interaction will not be deleted immediately, but will be reset to potential state. At the next execution of the collider ``InteractionContainer::conditionalyEraseNonReal`` will be called, which will completely erase interactions only if the bounding boxes ceased to overlap; the rest will be kept in potential state. Creating interactions explicitly ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Interactions may still be created explicitly with :yref:`yade.utils.createInteraction`, without any spatial requirements. This function searches current engines for dispatchers and uses them. :yref:`IGeomFunctor` is called with the ``force`` parameter, obliging it to return ``true`` even if there is no spatial overlap. Associating Material and State types ------------------------------------ Some models keep extra :yref:`state` information in the :yref:`Body.state` object, therefore requiring strict association of a :yref:`Material` with a certain :yref:`State` (for instance, :yref:`CpmMat` is associated to :yref:`CpmState` and this combination is supposed by engines such as :yref:`CpmStateUpdater`). If a :yref:`Material` has such a requirement, it must override 2 virtual methods: #. :yref:`Material.newAssocState`, which returns a new :yref:`State` object of the corresponding type. The default implementation returns :yref:`State` itself. #. :yref:`Material.stateTypeOk`, which checks whether a given :yref:`State` object is of the corresponding type (this check is run at the beginning of the simulation for all particles). In c++, the code looks like this (for :yref:`CpmMat`): .. code-block:: c++ class CpmMat: public FrictMat { public: virtual shared_ptr newAssocState() const { return shared_ptr(new CpmState); } virtual bool stateTypeOk(State* s) const { return (bool)dynamic_cast(s); } /* ... */ }; This allows one to construct :yref:`Body` objects from functions such as :yref:`yade.utils.sphere` only by knowing the requires :yref:`Material` type, enforcing the expectation of the model implementor. Runtime structure ================== Startup sequence ----------------- Yade's main program is python script in :ysrc:`core/main/main.py.in`; the build system replaces a few ``\${variables}`` in that file before copying it to its install location. It does the following: #. Process command-line options, set environment variables based on those options. #. Import main yade module (``import yade``), residing in :ysrc:`py/__init__.py.in`. This module locates plugins (recursive search for files ``lib*.so`` in the ``lib`` installation directory). :ysrc:`yade.boot` module is used to setup temporary directory, … and, most importantly, loads plugins. #. Manage further actions, such as running scripts given at command line, opening :yref:`yade.qt.Controller` (if desired), launching the ``ipython`` prompt. Singletons ----------- There are several "global variables" that are always accessible from c++ code; properly speaking, they are `Singletons `_, classes of which exactly one instance always exists. The interest is to have some general functionality acessible from anywhere in the code, without the necessity of passing pointers to such objects everywhere. The instance is created at startup and can be always retrieved (as non-const reference) using the ``instance()`` static method (e.g. ``Omega::instance().getScene()``). There are 3 singletons: ``SerializableSingleton`` Handles serialization/deserialization; it is not used anywhere except for the serialization code proper. ``ClassFactory`` Registers classes from plugins and able to factor instance of a class given its name as string (the class must derive from ``Factorable``). Not exposed to python. ``Omega`` Access to simulation(s); deserves separate section due to its importance. Omega ^^^^^^ The :yref:`Omega` class handles all simulation-related functionality: loading/saving, running, pausing. In python, the wrapper class to the singleton is instantiated [#oinst]_ as global variable ``O``. For convenience, :yref:`Omega` is used as proxy for scene's attribute: although multiple ``Scene`` objects may be instantiated in c++, it is always the current scene that :yref:`Omega` represents. The correspondence of data is literal: :yref:`Omega.materials` corresponds to ``Scene::materials`` of the current scene; likewise for :yref:`materials`, :yref:`bodies`, :yref:`interactions`, :yref:`tags`, :yref:`cell`, :yref:`engines`, :yref:`initializers`, :yref:`miscParams`. To give an overview of (some) variables: ======================== =================================== Python c++ ======================== =================================== :yref:`Omega.iter` ``Scene::iter`` :yref:`Omega.dt` ``Scene::dt`` :yref:`Omega.time` ``Scene::time`` :yref:`Omega.realtime` ``Omega::getRealTime()`` :yref:`Omega.stopAtIter` ``Scene::stopAtIter`` ======================== =================================== ``Omega`` in c++ contains pointer to the current scene (``Omega::scene``, retrieved by ``Omega::instance().getScene()``). Using :yref:`Omega.switchScene`, it is possible to swap this pointer with ``Omega::sceneAnother``, a completely independent simulation. This can be useful for example (and this motivated this functionality) if while constructing simulation, another simulation has to be run to dynamically generate (i.e. by running simulation) packing of spheres. .. rubric:: Footnotes .. [#oinst] It is understood that instantiating ``Omega()`` in python only instantiates the wrapper class, not the singleton itself. Engine loop ------------ Running simulation consists in looping over :yref:`Engines` and calling them in sequence. This loop is defined in ``Scene::moveToNextTimeStep`` function in :ysrc:`core/Scene.cpp`. Before the loop starts, :yref:`O.initializers` are called; they are only run once. The engine loop does the following in each iteration over :yref:`O.engines`: #. set ``Engine::scene`` pointer to point to the current ``Scene``. #. Call ``Engine::isActivated()``; if it returns ``false``, the engine is skipped. #. Call ``Engine::action()`` #. If :yref:`O.timingEnabled`, increment :yref:`Engine::execTime` by the difference from the last time reading (either after the previous engine was run, or immediately before the loop started, if this engine comes first). Increment :yref:`Engine::execCount` by 1. After engines are processed, :yref:`virtual time` is incremented by :yref:`timestep` and :yref:`iteration number` is incremented by 1. Background execution ^^^^^^^^^^^^^^^^^^^^^ The engine loop is (normally) executed in background thread (handled by :ysrc:`SimulationFlow` class), leaving foreground thread free to manage user interaction or running python script. The background thread is managed by :yref:`O.run()` and :yref:`O.pause()` commands. Foreground thread can be blocked until the loop finishes using :yref:`O.wait()`. Single iteration can be run without spawning additional thread using :yref:`O.step()`. Python framework ================= Wrapping c++ classes --------------------- Each class deriving from :yref:`Serializable` is automatically exposed to python, with access to its (registered) attributes. This is achieved via :ref:`YADE_CLASS_BASE_DOC`. All classes registered in class factory are default-constructed in ``Omega::buildDynlibDatabase``. Then, each serializable class calls ``Serializable::pyRegisterClass`` virtual method, which injects the class wrapper into (initially empty) ``yade.wrapper`` module. ``pyRegisterClass`` is defined by ``YADE_CLASS_BASE_DOC`` and knows about class, base class, docstring, attributes, which subsequently all appear in boost::python class definition. Wrapped classes define special constructor taking keyword arguments corresponding to class attributes; therefore, it is the same to write: .. ipython:: Yade [1]: f1=ForceEngine() Yade [2]: f1.ids=[0,4,5] Yade [2]: f1.force=Vector3(0,-1,-2) and .. ipython:: Yade [1]: f2=ForceEngine(ids=[0,4,5],force=Vector3(0,-1,-2)) Yade [2]: print f1.dict() Yade [3]: print f2.dict() Wrapped classes also inherit from :yref:`Serializable` several special virtual methods: :yref:`dict()` returning all registered class attributes as dictionary (shown above), :yref:`clone()` returning copy of instance (by copying attribute values), :yref:`updateAttrs()` and :yref:`updateExistingAttrs()` assigning attributes from given dictionary (the former thrown for unknown attribute, the latter doesn't). Read-only property ``name`` wraps c++ method ``getClassName()`` returning class name as string. (Since c++ class and the wrapper class always have the same name, getting python type using ``__class__`` and its property ``__name__`` will give the same value). .. ipython:: Yade [1]: s=Sphere() Yade [2]: s.__class__.__name__ Subclassing c++ types in python -------------------------------- In some (rare) cases, it can be useful to derive new class from wrapped c++ type in pure python. This is done in the :ref:`yade.pack` module: :yref:`Predicate` is c++ base class; from this class, several c++ classes are derived (such as :yref:`inGtsSurface`), but also python classes (such as the trivial :yref:`inSpace` predicate). ``inSpace`` derives from python class ``Predicate``; it is, however, not direct wrapper of the c++ ``Predicate`` class, since virtual methods would not work. ``boost::python`` provides special ``boost::python::wrapper`` template for such cases, where each overridable virtual method has to be declared explicitly, requesting python override of that method, if present. See `Overridable virtual functions `_ for more details. Reference counting ------------------ Python internally uses `reference counting `_ on all its objects, which is not visible to casual user. It has to be handled explicitly if using pure `Python/C API `_ with ``Py_INCREF`` and similar functions. ``boost::python`` used in Yade fortunately handles reference counting internally. Additionally, it `automatically integrates `_ reference counting for ``shared_ptr`` and python objects, if class ``A`` is wrapped as ``boost::python::class_>``. Since *all* Yade classes wrapped using :ref:`YADE_CLASS_BASE_DOC` are wrapped in this way, returning ``shared_ptr<…>`` objects from is the preferred way of passing objects from c++ to python. Returning ``shared_ptr`` is much more efficient, since only one pointer is returned and reference count internally incremented. Modifying the object from python will modify the (same) object in c++ and vice versa. It also makes sure that the c++ object will not be deleted as long as it is used somewhere in python, preventing (important) source of crashes. .. _customconverters: Custom converters ----------------- When an object is passed from c++ to python or vice versa, then either #. the type is basic type which is transparently passed between c++ and python (int, bool, std::string etc) #. the type is wrapped by boost::python (such as Yade classes, ``Vector3`` and so on), in which case wrapped object is returned; [#wrap]_ Other classes, including template containers such as ``std::vector`` must have their custom converters written separately. Some of them are provided in :ysrc:`py/wrapper/customConverters.cpp`, notably converters between python (homogeneous, i.e. with all elements of the same type) sequences and c++ ``std::vector`` of corresponding type; look in that source file to add your own converter or for inspiration. When an object is crossing c++/python boundary, boost::python's global "converters registry" is searched for class that can perform conversion between corresponding c++ and python types. The "converters registry" is common for the whole program instance: there is no need to register converters in each script (by importing ``_customConverters``, for instance), as that is done by yade at startup already. .. note:: Custom converters only work for value that are passed by value to python (not "by reference"): some attributes defined using :ref:`YADE_CLASS_BASE_DOC` are passed by value, but if you define your own, make sure that you read and understand `Why is my automatic to-python conversion not being found? `_. In short, the default for ``def_readwrite`` and ``def_readonly`` is to return references to underlying c++ objects, which avoids performing conversion on them. For that reason, return value policy must be set to ``return_by_value`` explicitly, using slighly more complicated ``add_property`` syntax, as explained at the page referenced. .. [#wrap] Wrapped classes are automatically registered when the class wrapper is created. If wrapped class derives from another wrapped class (and if this dependency is declared with the ``boost::python::bases`` template, which Yade's classes do automatically), parent class must be registered before derived class, however. (This is handled via loop in ``Omega::buildDynlibDatabase``, which reiterates over classes, skipping failures, until they all successfully register) Math classes (Vector3, Matrix3, Quaternion) are wrapped in minieigen, which is available as a separate package. Use your package manager to install it. Maintaining compatibility ========================== In Yade development, we identified compatibility to be very strong desire of users. Compatibility concerns python scripts, *not* simulations saved in XML or old c++ code. Renaming class --------------- Script :ysrc:`scripts/rename-class.py` should be used to rename class in ``c++`` code. It takes 2 parameters (old name and new name) and must be run from top-level source directory:: \$ scripts/rename-class.py OldClassName NewClassName Replaced 4 occurences, moved 0 files and 0 directories Update python scripts (if wanted) by running: perl -pi -e 's/\bOldClassName\b/NewClassName/g' `ls **/*.py |grep -v py/system.py` This has the following effects: #. If file or directory has basename ``OldClassName`` (plus extension), it will be renamed using ``bzr``. #. All occurences of whole word ``OldClassName`` will be replaced by ``NewClassName`` in c++ sources. #. An extry is added to :ysrc:`py/system.py`, which contains map of deprecated class names. At yade startup, proxy class with ``OldClassName`` will be created, which issues a ``DeprecationWarning`` when being instantiated, informing you of the new name you should use; it creates an instance of ``NewClassName``, hence not disruting your script's functioning:: Yade [3]: SimpleViscoelasticMat() /usr/local/lib/yade-trunk/py/yade/__init__.py:1: DeprecationWarning: Class `SimpleViscoelasticMat' was renamed to (or replaced by) `ViscElMat', update your code! (you can run 'yade --update script.py' to do that automatically) -> [3]: As you have just been informed, you can run ``yade --update`` to all old names with their new names in scripts you provide:: \$ yade-trunk --update script1.py some/where/script2.py This gives you enough freedom to make your class name descriptive and intuitive. Renaming class attribute ------------------------ Renaming class attribute is handled from c++ code. You have the choice of merely warning at accessing old attribute (giving the new name), or of throwing exception in addition, both with provided explanation. See ``deprec`` parameter to :ref:`YADE_CLASS_BASE_DOC` for details. Debian packaging instructions ============================== In order to make parallel installation of several Yade version possible, we adopted similar strategy as e.g. ``gcc`` packagers in Debian did: #. Real Yade packages are named ``yade-0.30`` (for stable versions) or ``yade-bzr2341`` (for snapshots). #. They provide ``yade`` or ``yade-snapshot`` virtual packages respectively. #. Each source package creates several installable packages (using ``bzr2341`` as example version): #. ``yade-bzr2341`` with the optimized binaries; the executable binary is ``yade-bzr2341`` (``yade-bzr2341-multi``, …) #. ``yade-bzr2341-dbg`` with debug binaries (debugging symbols, non-optimized, and with crash handlers); the executable binary is ``yade-bzr2341-dbg`` #. ``yade-bzr2341-doc`` with sample scripts and some documentation (see `bug #398176 `_ however) #. (future?) ``yade-bzr2341-reference`` with reference documentation (see `bug #401004 `_) #. Using `Debian alternatives `_, the highest installed package provides additionally commands without the version specification like ``yade``, ``yade-multi``, … as aliases to that version's binaries. (``yade-dbg``, … for the debuggin packages). The exact rule is: #. Stable releases have always higher priority than snapshots #. Higher versions/revisions have higher pripority than lower versions/revisions. Prepare source package ---------------------- Debian packaging files are located in :ysrc:`debian/` directory. They contain build recipe :ysrc:`debian/rules`, dependecy and package declarations :ysrc:`debian/control` and maintainer scripts. Some of those files are only provided as templates, where some variables (such as version number) are replaced by special script. The script :ysrc:`scripts/debian-prep` processes templates in :ysrc:`debian/` and creates files which can be used by debian packaging system. Before running this script: #. If you are releasing stable version, make sure there is file named ``RELEASE`` containing single line with version number (such as ``0.30``). This will make :ysrc:`scripts/debian-prep` create release packages. In absence of this file, snapshots packaging will be created instead. Release or revision number (as detected by running ``bzr revno`` in the source tree) is stored in ``VERSION`` file, where it is picked up during package build and embedded in the binary. #. Find out for which debian/ubuntu series your package will be built. This is the name that will appear on the top of (newly created) ``debian/changelog`` file. This name will be usually ``unstable``, ``testing`` or ``stable`` for debian and ``karmic``, ``lucid`` etc for ubuntu. WHen package is uploaded to Launchpad's build service, the package will be built for this specified release. Then run the script from the top-level directory, giving series name as its first (only) argument:: \$ scripts/debian-prep lucid After this, signed debian source package can be created:: \$ debuild -S -sa -k62A21250 -I -Iattic (``-k`` gives GPG key identifier, ``-I`` skips ``.bzr`` and similar directories, ``-Iattic`` will skip the useless ``attic`` directory). Create binary package --------------------- Local in-tree build Once files in ``debian/`` are prepared, packages can be build by issuing:: \$ fakeroot debian/rules binary Clean system build Using ``pbuilder`` system, package can be built in a chroot containing clean debian/ubuntu system, as if freshly installed. Package dependencies are automatically installed and package build attempted. This is a good way of testing packaging before having the package built remotely at Launchpad. Details are provided at `wiki page `_. Launchpad build service Launchpad provides service to compile package for different ubuntu releases (series), for all supported architectures, and host archive of those packages for download via APT. Having appropriate permissions at Launchpad (verified GPG key), source package can be uploaded to yade's archive by:: \$ dput ppa:yade-users/ppa ../yade-bzr2341_1_source.changes After several hours (depending on load of Launchpad build farm), new binary packages will be published at https://launchpad.net/~yade-users/+archive/ppa. This process is well documented at https://help.launchpad.net/Packaging/PPA. trunk-2017.01a/doc/sphinx/publications.rst.in000066400000000000000000000026731304022710500211030ustar00rootroot00000000000000Publications on Yade ===================== This page should be a relatively complete list of publications on Yade itself or done with Yade. If you publish something, do not hesitate to add it on the list. If you don't have direct access to the source code, please send the reference (as a bibtex item) to the `editorial board `_. If PDF is freely available, add url for direct fulltext downlad. If not, consider uploading fulltext in PDF, either to `Yade wiki `_ or to other website, if legally permitted. The first section gives the references that we kindly ask you to use for citing Yade in publications, as explained in the `"Acknowledging Yade" `_ section. .. note:: This file is generated from :ysrc:`doc/yade-articles.bib`, :ysrc:`doc/yade-conferences.bib`, :ysrc:`doc/yade-theses.bib` and :ysrc:`doc/yade-docref.bib`. Citing Yade --------------------- Corresponding bibtex entries `here `_. Pdf versions are available for each of them. See also `"Acknowledging Yade" `_. @bib2rst.bib2rst('../yade-docref.bib')@ Journal articles ----------------- @bib2rst.bib2rst('../yade-articles.bib')@ Conference materials and book chapters -------------------------------------- @bib2rst.bib2rst('../yade-conferences.bib')@ Master and PhD theses ----------------------- @bib2rst.bib2rst('../yade-theses.bib')@ trunk-2017.01a/doc/sphinx/references.rst.in000066400000000000000000000002751304022710500205240ustar00rootroot00000000000000 References ============ All external articles referenced in Yade documentation. .. note:: This file is generated from :ysrc:`doc/references.bib`. @bib2rst.bib2rst('../references.bib')@ trunk-2017.01a/doc/sphinx/sitecustomize.py000066400000000000000000000001501304022710500205150ustar00rootroot00000000000000# necessary for our docstrings containing unicode characters import sys sys.setdefaultencoding('utf-8') trunk-2017.01a/doc/sphinx/static-html/000077500000000000000000000000001304022710500174715ustar00rootroot00000000000000trunk-2017.01a/doc/sphinx/static-html/README000066400000000000000000000005641304022710500203560ustar00rootroot00000000000000This directory is currently empty, but might contain static files for the HTML output. From conf.py: # Add any paths that contain custom static files (such as style sheets) here, # relative to this directory. They are copied after the builtin static files, # so a file named "default.css" will overwrite the builtin "default.css". html_static_path = ['static-html'] trunk-2017.01a/doc/sphinx/templates/000077500000000000000000000000001304022710500172365ustar00rootroot00000000000000trunk-2017.01a/doc/sphinx/templates/index.html000066400000000000000000000172741304022710500212460ustar00rootroot00000000000000{% extends "layout.html" %} {% set title = 'Overview' %} {% block body %}

    Welcome to Yade - Open Source Discrete Element Method

    Yade is an extensible open-source framework for discrete numerical models, focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, allowing independent implementation of new alogrithms and interfaces. Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging.

    Since March 2012 Yade is using GIT as VCS and placing the source code on github. The Launchpad is importing source code several times per day.

    Please make sure you read the "Acknowledging Yade" section if you plan to cite Yade in publications.

    This documentation decribes Yade version {{ release }} / {{ version }}.

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    {% endblock %} trunk-2017.01a/doc/sphinx/templates/layout.html000066400000000000000000000017101304022710500214400ustar00rootroot00000000000000{% extends "!layout.html" %} {% block extrahead %} {{ super() }} {%- if not embedded %} {%- endif %} {% endblock %} {% block footer %} {{ super() }} {% endblock %} {% block rootrellink %}
  1. Yade | 
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    3. {% endblock %} trunk-2017.01a/doc/sphinx/tutorial-advanced.rst000066400000000000000000000007101304022710500213760ustar00rootroot00000000000000Advanced & more =============== Particle size distribution -------------------------- See :ref:`periodic-triaxial-test` Clumps ------ :yref:`Clump`; see :ref:`periodic-triaxial-test` Testing laws ------------ :yref:`LawTester`, :ysrc:`scripts/test/law-test.py` New law ------- Visualization ------------- See the example :ref:`3d-postprocessing` * :yref:`VTKRecorder` & `Paraview `__ * :yref:`yade.qt.SnapshotEngine` trunk-2017.01a/doc/sphinx/tutorial-data-mining.rst000066400000000000000000000214341304022710500220270ustar00rootroot00000000000000Data mining ============= Read ----- Local data ^^^^^^^^^^^ All data of the simulation are accessible from python; when you open the *Inspector*, blue labels of various data can be clicked -- left button for getting to the documentation, middle click to copy the name of the object (use ``Ctrl-V`` or middle-click to paste elsewhere). The interesting objects are among others (see :yref:`Omega` for a full list): #. :yref:`O.engines` Engines are accessed by their index (position) in the simulation loop:: O.engines[0] # first engine O.engines[-1] # last engine .. note:: The index can change if :yref:`O.engines` is modified. *Labeling* introduced below is a better solution for reliable access to a particular engine. #. :yref:`O.bodies` Bodies are identified by their :yref:`id`, which is guaranteed to not change during the whole simulation:: O.bodies[0] # first body [b.shape.radius in O.bodies if isinstance(b.shape,Sphere)] # list of radii of all spherical bodies sum([b.state.mass for b in O.bodies]) # sum of masses of all bodies .. note:: Uniqueness of :yref:`Body.id` is not guaranteed, since newly created bodies might recycle :yref:`ids` of :yref:`deleted` ones. #. :yref:`O.force` Generalized forces (forces, torques) acting on each particle. They are (usually) reset at the beginning of each step with :yref:`ForceResetter`, subsequently forces from individual interactions are accumulated in :yref:`InteractionLoop`. To access the data, use:: O.forces.f(0) # force on #0 O.forces.t(1) # torque on #1 #. :yref:`O.interactions` Interactions are identified by :yref:`ids` of the respective interacting particles (they are created and deleted automatically during the simulation):: O.interactions[0,1] # interactions of #0 with #1 O.interactions[1,0] # the same object O.bodies[0].intrs # all interactions of body #0 Labels """"""" :yref:`Engines` and :yref:`functors` can be *labeled*, which means that python variable of that name is automatically created. .. ipython:: @suppress Yade [1]: from yade import * Yade [1]: O.engines=[ ...: NewtonIntegrator(damping=.2,label='newton') ...: ] ...: Yade [1]: newton.damping=.4 Yade [1]: O.engines[0].damping # O.engines[0] and newton are the same objects .. rubric:: Exercises #. Find meaning of this expression:: max([b.state.vel.norm() for b in O.bodies]) #. Run the gravity deposition script, pause after a few seconds of simulation. Write expressions that compute #. kinetic energy $\sum \frac{1}{2} m_i |v_i| ^2$ #. average mass (hint: use `numpy.average `__) #. maximum $z$-coordinate of all particles #. number of interactions of body #1 Global data ^^^^^^^^^^^ Useful measures of what happens in the simulation globally: unbalanced force ratio of maximum contact force and maximum per-body force; measure of staticity, computed with :yref:`yade.utils.unbalancedForce`. porosity ratio of void volume and total volume; computed with :yref:`yade.utils.porosity`. coordination number average number of interactions per particle, :yref:`yade.utils.avgNumInteractions` stress tensor (periodic boundary conditions) averaged force in interactions, computed with :yref:`yade.utils.normalShearStressTensor` and :yref:`yade.utils.stressTensorOfPeriodicCell` fabric tensor distribution of contacts in space (not yet implemented); can be visualized with :yref:`yade.utils.plotDirections` Energies """""""" Evaluating energy data for all components in the simulation (such as gravity work, kinetic energy, plastic dissipation, damping dissipation) can be enabled with :: O.trackEnergy=True Subsequently, energy values are accessible in the :yref:`O.energy`; it is a dictionary where its entries can be retrived with ``keys()`` and their values with ``O.energy[key]``. Save ---- PyRunner ^^^^^^^^^ To save data that we just learned to access, we need to call Python from within the *simulation loop*. :yref:`PyRunner` is created just for that; it inherits periodicy control from :yref:`PeriodicEngine` and takes the code to run as text (must be quoted, i.e. inside ``'...'``) attributed called *command*. For instance, adding this to :yref:`O.engines` will print the current step number every second:: O.engines=O.engines+[ PyRunner(command='print O.iter',realPeriod=1) ] Writing complicated code inside *command* is awkward; in such case, we define a function that will be called:: def myFunction(): '''Print step number, and pause the simulation is unbalanced force is smaller than 0.05.''' print O.iter if utils.unbalancedForce()<0.05: print 'Unbalanced force is smaller than 0.05, pausing.' O.pause() O.engines=[ # ... PyRunner(command='myFunction()',iterPeriod=100) # call myFunction every 100 steps ] .. rubric:: Exercises #. Run the gravity deposition simulation, but change it such that: #. :yref:`yade.utils.unbalancedForce` is printed every 2 seconds. #. check every 1000 steps the value of unbalanced force * if smaller than 0.2, set :yref:`damping` to 0.8 (hint: use labels) * if smaller than 0.1, pause the simulation Keeping history ^^^^^^^^^^^^^^^^^ Yade provides the :yref:`yade.plot` module used for storing and plotting variables (plotting itself will be discussed later). Periodic storing of data is done with :yref:`PyRunner` and the :yref:`yade.plot.addData` function, for instance:: from yade import plot O.engines=[ # ..., PyRunner(command='addPlotData()',realPeriod=2) # call the addPlotData function every 2 seconds of human time ] def addPlotData(): # this function adds current values to the history of data, under the names specified plot.addData(i=O.iter,t=O.time,Ek=utils.kineticEnergy(),coordNum=utils.avgNumInteractions(),unForce=utils.unbalancedForce()) History is stored in :yref:`yade.plot.data`, and can be accessed using the variable name, e.g. ``plot.data['Ek']``, and saved to text file (for post-processing outside yade) with :yref:`yade.plot.saveTxt`. Plot ----- :yref:`yade.plot` provides facilities for plotting history saved with :yref:`yade.plot.addData` as 2d plots. Data to be plotted are specified using dictionary :yref:`yade.plot.plots` :: plot.plots={'t':('coordNum','unForce',None,'Ek')} History of all values is given as the name used for :yref:`yade.plot.addData`; keys of the dictionary are $x$-axis values, and values are sequence of data on the $y$ axis; the ``None`` separates data on the left and right axes (they are scaled independently). The plot itself is created with :: plot.plot() # on the command line, F8 can be used as shorthand While the plot is open, it will be updated periodically, so that simulation evolution can be seen in real-time. Energy plots ^^^^^^^^^^^^^ Plotting all energy contributions would be difficult, since names of all energies might not be known in advance. Fortunately, there is a way to handle that in Yade. It consists in two parts: #. :yref:`yade.plot.addData` is given all the energies that are currently defined:: plot.addData(i=O.iter,total=O.energy.total(),**O.energy) The :yref:`O.energy.total` functions, which sums all energies together. The ``**O.energy`` is special python syntax for converting dictionary (remember that :yref:`O.energy` is a dictionary) to named functions arguments, so that the following two commands are identical:: function(a=3,b=34) # give arguments as arguments function(**{'a':3,'b':34}) # create arguments from dictionary #. Data to plot are specified using a *function* that gives names of data to plot, rather than providing the data names directly:: plot.plots={'i':['total',O.energy.keys()]} where ``total`` is the name we gave to ``O.energy.total()`` above, while ``O.energy.keys()`` will always return list of currently defined energies. .. rubric:: Exercises #. Run the gravity deposition script, plotting unbalanced force and kinetic energy. #. While the script is running, try changing the :yref:`NewtonIntegrator.damping` parameter (do it from both *Inspector* and from the command-line). What influence does it have on the evolution of unbalanced force and kinetic energy? #. Think about and write down all energy sources (input); write down also all energy sinks (dissipation). #. Simulate gravity deposition and plot all energies as they evolve during the simulation. .. seealso:: Most :ref:`examples` use plotting facilities of Yade, some of them also track energy of the simulation. trunk-2017.01a/doc/sphinx/tutorial-examples.rst000066400000000000000000000017051304022710500214540ustar00rootroot00000000000000.. _examples: Examples ========= .. _bouncing-sphere: Bouncing sphere --------------- .. youtube:: CMfL8PGq-xQ .. literalinclude:: tutorial/01-bouncing-sphere.py .. _gravity-deposition: Gravity deposition ------------------ .. youtube:: YUlUSI9YADM .. literalinclude:: tutorial/02-gravity-deposition.py .. _oedometric-test: Oedometric test ---------------- .. youtube:: RjH1v-Fth34 .. literalinclude:: tutorial/03-oedometric-test.py Batch table ^^^^^^^^^^^^ .. literalinclude:: tutorial/03-oedometric-test.table .. _periodic-simple-shear: Periodic simple shear --------------------- .. youtube:: ZKHrILQCyZs .. literalinclude:: tutorial/04-periodic-simple-shear.py .. _3d-postprocessing: 3d postprocessing ----------------- .. literalinclude:: tutorial/05-3d-postprocessing.py .. _periodic-triaxial-test: Periodic triaxial test ---------------------- .. youtube:: utTDLZz0y_w .. literalinclude:: tutorial/06-periodic-triaxial-test.py trunk-2017.01a/doc/sphinx/tutorial-geo.rst000066400000000000000000000145101304022710500204060ustar00rootroot00000000000000Towards geomechanics ===================== .. seealso:: Examples :ref:`gravity-deposition`, :ref:`oedometric-test`, :ref:`periodic-simple-shear`, :ref:`periodic-triaxial-test` deal with topics discussed here. Parametric studies ------------------- Input parameters of the simulation (such as size distribution, damping, various contact parameters, …) influence the results, but frequently an analytical relationship is not known. To study such influence, similar simulations differing only in a few parameters can be run and results compared. Yade can be run in *batch mode*, where one simulation script is used in conjunction with *parameter table*, which specifies parameter values for each run of the script. Batch simulation are run non-interactively, i.e. without user intervention; the user must therefore start and stop the simulation explicitly. Suppose we want to study the influence of :yref:`damping` on the evolution of kinetic energy. The script has to be adapted at several places: #. We have to make sure the script reads relevant parameters from the *parameter table*. This is done using :yref:`yade.utils.readParamsFromTable`; the parameters which are read are created as variables in the ``yade.params.table`` module:: utils.readParamsFromTable(damping=.2) # yade.params.table.damping variable will be created from yade.params import table # typing table.damping is easier than yade.params.table.damping Note that :yref:`yade.utils.readParamsFromTable` takes default values of its parameters, which are used if the script is not run in non-batch mode. #. Parameters from the table are used at appropriate places:: NewtonIntegrator(damping=table.damping), #. The simulation is run non-interactively; we must therefore specify at which point it should stop:: O.engines+=[PyRunner(iterPeriod=1000,command='checkUnbalancedForce()')] # call our function defined below periodically def checkUnbalancedForce(): if utils.unbalancedForce<0.05: # exit Yade if unbalanced force drops below 0.05 utils.saveDataTxt(O.tags['d.id']+'.data.bz2') # save all data into a unique file before exiting import sys sys.exit(0) # exit the program #. Finally, we must start the simulation at the very end of the script:: O.run() # run forever, until stopped by checkUnbalancedForce() utils.waitIfBatch() # do not finish the script until the simulation ends; does nothing in non-batch mode The *parameter table* is a simple text-file, where each line specifies a simulation to run:: # comments start with # as in python damping # first non-comment line is variable name .2 .4 .6 Finally, the simulation is run using the special batch command:: user@machine:~\$ yade-batch parameters.table simulation.py .. todo:: Parametric studies need to be described better. Perhaps the behavior should be changed so that in batch mode, :yref:`O.run` and :yref:`yade.utils.waitIfBatch` are run from the main yade script by default. That would however make it only possible to exit the batch via ``sys.exit(0)``, or by a new function like ``utils.exitBatch()`` (which would call ``sys.exit(0)`` for now anyway) .. rubric:: Exercises #. Run the gravity deposition script in batch mode, varying :yref:`damping` to take values of ``.2``, ``.4``, ``.6``. See the http://localhost:9080 overview page while the batch is running. Boundary --------- Particles moving in infinite space usually need some constraints to make the simulation meaningful. Supports ^^^^^^^^^ So far, supports (unmovable particles) were providing necessary boundary: in the gravity deposition script, :yref:`yade.utils.facetBox` is by internally composed of :yref:`facets ` (triangulation elements), which is ``fixed`` in space; facets are also used for arbitrary triangulated surfaces (see relevant sections of the *User's manual*). Another frequently used boundary is :yref:`yade.utils.wall` (infinite axis-aligned plane). Periodic ^^^^^^^^^ Periodic boundary is a "boundary" created by using periodic (rather than infinite) space. Such boundary is activated by :yref:`O.periodic=True `, and the space configuration is decribed by :yref:`O.cell `. It is well suited for studying bulk material behavior, as boundary effects are avoided, leading to smaller number of particles. On the other hand, it might not be suitable for studying localization, as any cell-level effects (such as shear bands) have to satisfy periodicity as well. The periodic cell is described by its :yref:`reference size ` of box aligned with global axes, and :yref:`current transformation`, which can capture stretch, shear and rotation. Deformation is prescribed via :yref:`velocity gradient`, which updates the :yref:`transformation` before the next step. :yref:`Homothetic deformation` can smear :yref:`velocity gradient` accross the cell, making the boundary dissolve in the whole cell. Stress and strains can be controlled with :yref:`PeriTriaxController`; it is possible to prescribe mixed strain/stress :yref:`goal` state using :yref:`PeriTriaxController.stressMask`. The following creates periodic cloud of spheres and compresses to achieve $\sigma_x$=-10 kPa, $\sigma_y$=-10kPa and $\eps_z$=-0.1. Since stress is specified for $y$ and $z$, :yref:`stressMask` is ``0b011`` (x→1, y→2, z→4, in decimal 1+2=3). .. ipython:: @suppress Yade [1]: from yade import pack Yade [1]: sp=pack.SpherePack() Yade [1]: sp.makeCloud((1,1,1),(2,2,2),rMean=.2,periodic=True) Yade [1]: sp.toSimulation() # implicitly sets O.periodic=True, and O.cell.refSize to the packing period size Yade [1]: O.engines+=[PeriTriaxController(goal=(-1e4,-1e4,-.1),stressMask=0b011,maxUnbalanced=.2,doneHook='functionToRunWhenFinished()')] When the simulation :yref:`runs`, :yref:`PeriTriaxController` takes over the control and calls :yref:`doneHook` when :yref:`goal` is reached. A full simulation with PeriTriaxController might look like the following: .. literalinclude:: tutorial/peri-triax.py trunk-2017.01a/doc/sphinx/tutorial-hands-on.rst000066400000000000000000000462401304022710500213500ustar00rootroot00000000000000.. _hands-on: Hands-on ======== Shell basics ------------- Directory tree ^^^^^^^^^^^^^^^ Directory tree is hierarchical way to organize files in operating systems. A typical (reduced) tree looks like this:: / Root ├──boot System startup ├──bin Low-level programs ├──lib Low-level libraries ├──dev Hardware access ├──sbin Administration programs ├──proc System information ├──var Files modified by system services ├──root Root (administrator) home directory ├──etc Configuration files ├──media External drives ├──tmp Temporary files ├──usr Everything for normal operation (usr = UNIX system resources) │ ├──bin User programs │ ├──sbin Administration programs │ ├──include Header files for c/c++ │ ├──lib Libraries │ ├──local Locally installed software │ └──doc Documentation └──home Contains the user's home directories ├──user Home directory for user └──user1 Home directory for user1 Note that there is a single root ``/``; all other disks (such as USB sticks) attach to some point in the tree (e.g. in ``/media``). Shell navigation ^^^^^^^^^^^^^^^^^ Shell is the UNIX command-line, interface for conversation with the machine. Don't be afraid. Moving around """"""""""""""" The shell is always operated by some ``user``, at some concrete ``machine``; these two are constant. We can move in the directory structure, and the current place where we are is *current directory*. By default, it is the *home directory* which contains all files belonging to the respective user:: user@machine:~\$ # user operating at machine, in the directory ~ (= user's home directory) user@machine:~\$ ls . # list contents of the current directory user@machine:~\$ ls foo # list contents of directory foo, relative to the dcurrent directory ~ (= ls ~/foo = ls /home/user/foo) user@machine:~\$ ls /tmp # list contents of /tmp user@machine:~\$ cd foo # change directory to foo user@machine:~/foo\$ ls ~ # list home directory (= ls /home/user) user@machine:~/foo\$ cd bar # change to bar (= cd ~/foo/bar) user@machine:~/foo/bar\$ cd ../../foo2 # go to the parent directory twice, then to foo2 (cd ~/foo/bar/../../foo2 = cd ~/foo2 = cd /home/user/foo2) user@machine:~/foo2\$ cd # go to the home directory (= ls ~ = ls /home/user) user@machine:~\$ Users typically have only permissions to write (i.e. modify files) only in their home directory (abbreviated ``~``, usually is ``/home/user``) and ``/tmp``, and permissions to read files in most other parts of the system:: user@machine:~\$ ls /root # see what files the administrator has ls: cannot open directory /root: Permission denied Keys """"" Useful keys on the command-line are: ============= ========================= show possible completions of what is being typed (use abundantly!) ^C (=Ctrl+C) delete current line ^D exit the shell ↑↓ move up and down in the command history ^C interrupt currently running program ^\\ kill currently running program Shift-PgUp scroll the screen up (show part output) Shift-PgDown scroll the screen down (show future output; works only on quantum computers) ============= ========================= .. Multiple files can be selected using *patterns*. user@machine:~/foo2\$ ls *.py # * replaces any characters (except /) params.py remote.py timing.py user@machine:~/foo2\$ ls ../foo2/*.py params.py remote.py timing.py Running programs """"""""""""""""" When a program is being run (without giving its full path), several directories are searched for program of that name; those directories are given by ``\$PATH``:: user@machine:~\$ echo \$PATH # show the value of $PATH /usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin:/usr/games user@machine:~\$ which ls # say what is the real path of ls The first part of the command-line is the program to be run (``which``), the remaining parts are *arguments* (``ls`` in this case). It is upt to the program which arguments it understands. Many programs can take special arguments called *options* starting with ``-`` (followed by a single letter) or ``--`` (followed by words); one of the common options is ``-h`` or ``--help``, which displays how to use the program (try ``ls --help``). Full documentation for each program usually exists as *manual page* (or *man page*), which can be shown using e.g. ``man ls`` (``q`` to exit) Starting yade ^^^^^^^^^^^^^^ If yade is installed on the machine, it can be (roughly speaking) run as any other program; without any arguments, it runs in the "dialog mode", where a command-line is presented: :: user@machine:~\$ yade Welcome to Yade bzr2616 TCP python prompt on localhost:9002, auth cookie `adcusk' XMLRPC info provider on http://localhost:21002 [[ ^L clears screen, ^U kills line. F12 controller, F11 3d view, F10 both, F9 generator, F8 plot. ]] Yade [1]: #### hit ^D to exit Do you really want to exit ([y]/n)? Yade: normal exit. The command-line is in fact ``python``, enriched with some yade-specific features. (Pure python interpreter can be run with ``python`` or ``ipython`` commands). Instead of typing commands on-by-one on the command line, they can be be written in a file (with the .py extension) and given as argument to Yade:: user@machine:~\$ yade simulation.py For a complete help, see ``man yade`` .. rubric:: Exercises #. Open the terminal, navigate to your home directory #. Create a new empty file and save it in ``~/first.py`` #. Change directory to ``/tmp``; delete the file ``~/first.py`` #. Run program ``xeyes`` #. Look at the help of Yade. #. Look at the *manual page* of Yade #. Run Yade, exit and run it again. Python basics -------------- We assume the reader is familar with `Python tutorial `__ and only briefly review some of the basic capabilities. The following will run in pure-python interpreter (``python`` or ``ipython``), but also inside Yade, which is a super-set of Python. Numerical operations and modules: .. ipython:: Yade [1]: (1+3*4)**2 # usual rules for operator precedence, ** is exponentiation Yade [2]: import math # gain access to "module" of functions Yade [3]: math.sqrt(2) # use a function from that module Yade [4]: import math as m # use the module under a different name Yade [5]: m.cos(m.pi) Yade [6]: from math import * # import everything so that it can be used without module name Yade [7]: cos(pi) Variables: .. ipython:: Yade [1]: a=1; b,c=2,3 # multiple commands separated with ;, multiple assignment Yade [2]: a+b+c Sequences ^^^^^^^^^ Lists """""" Lists are variable-length sequences, which can be modified; they are written with braces ``[...]``, and their elements are accessed with numerical indices: .. ipython:: Yade [3]: a=[1,2,3] # list of numbers Yade [4]: a[0] # first element has index 0 Yade [5]: a[-1] # negative counts from the end Yade [7]: a[3] # error Yade [5]: len(a) # number of elements Yade [6]: a[1:] # from second element to the end Yade [7]: a+=[4,5] # extend the list Yade [8]: a+=[6]; a.append(7) # extend with single value, both have the same effect Yade [9]: 9 in a # test presence of an element Lists can be created in various ways: .. ipython:: Yade [9]: range(10) Yade [1]: range(10)[-1] List of squares of even number smaller than 20, i.e. $\left\{a^2\;\forall a\in \{0,\cdots,19\} \;\middle|\; 2 \| a\right\}$ (note the similarity): .. ipython:: Yade [1]: [a**2 for a in range(20) if a%2==0] Tuples """"""" Tuples are constant sequences: .. ipython:: Yade [1]: b=(1,2,3) Yade [2]: b[0] Yade [3]: b[0]=4 # error Dictionaries """"""""""""" Mapping from keys to values: .. ipython:: Yade [1]: czde={'jedna':'ein','dva':'zwei','tri':'drei'} Yade [1]: de={1:'ein',2:'zwei',3:'drei'}; cz={1:'jedna',2:'dva',3:'tri'} Yade [1]: czde['jedna'] ## access values Yade [2]: de[1], cz[2] Functions, conditionals ^^^^^^^^^^^^^^^^^^^^^^^^ .. ipython:: Yade [1]: 4==5 Yade [2]: a=3.1 Yade [3]: if a to see defined attributes Particles ^^^^^^^^^ Particles are the "data" component of simulation; they are the objects that will undergo some processes, though do not define those processes yet. Singles """"""""" There is a number of pre-defined functions to create particles of certain type; in order to create a sphere, one has to (see the source of :yref:`yade.utils.sphere` for instance): #. Create :yref:`Body` #. Set :yref:`Body.shape` to be an instance of :yref:`Sphere` with some given radius #. Set :yref:`Body.material` (last-defined material is used, otherwise a default material is created) #. Set position and orientation in :yref:`Body.state`, compute mass and moment of inertia based on :yref:`Material` and :yref:`Shape` In order to avoid such tasks, shorthand functions are defined in the :yref:`yade.utils` module; to mention a few of them, they are :yref:`yade.utils.sphere`, :yref:`yade.utils.facet`, :yref:`yade.utils.wall`. .. ipython:: @suppress Yade [1]: from yade import utils Yade [1]: s=utils.sphere((0,0,0),radius=1) # create sphere particle centered at (0,0,0) with radius=1 Yade [1]: s.shape # s.shape describes the geometry of the particle Yade [1]: s.shape.radius # we already know the Sphere class Yade [1]: s.state.mass, s.state.inertia # inertia is computed from density and geometry Yade [1]: s.state.pos # position is the one we prescribed Yade [1]: s2=utils.sphere((-2,0,0),radius=1,fixed=True) # explanation below In the last example, the particle was fixed in space by the ``fixed=True`` parameter to :yref:`yade.utils.sphere`; such a particle will not move, creating a primitive boundary condition. A particle object is not yet part of the simulation; in order to do so, a special function is called: .. ipython:: Yade [1]: O.bodies.append(s) # adds particle s to the simulation; returns id of the particle(s) added Packs """"" There are functions to generate a specific arrangement of particles in the :yref:`yade.pack` module; for instance, cloud (random loose packing) of spheres can be generated with the :yref:`yade._packSpheres.SpherePack` class: .. ipython:: Yade [1]: from yade import pack Yade [1]: sp=pack.SpherePack() # create an empty cloud; SpherePack contains only geometrical information Yade [1]: sp.makeCloud((1,1,1),(2,2,2),rMean=.2) # put spheres with defined radius inside box given by corners (1,1,1) and (2,2,2) Yade [1]: for c,r in sp: print c,r # print center and radius of all particles (SpherePack is a sequence which can be iterated over) ...: Yade [1]: sp.toSimulation() # create particles and add them to the simulation Boundaries """""""""" :yref:`yade.utils.facet` (triangle :yref:`Facet`) and :yref:`yade.utils.wall` (infinite axes-aligned plane :yref:`Wall`) geometries are typically used to define boundaries. For instance, a "floor" for the simulation can be created like this: .. ipython:: Yade [1]: O.bodies.append(utils.wall(-1,axis=2)) There are other conveinence functions (like :yref:`yade.utils.facetBox` for creating closed or open rectangular box, or family of :yref:`yade.ymport` functions) Look inside ^^^^^^^^^^^^ The simulation can be inspected in several ways. All data can be accessed from python directly: .. ipython:: Yade [1]: len(O.bodies) Yade [1]: O.bodies[1].shape.radius # radius of body #1 (will give error if not sphere, since only spheres have radius defined) Yade [1]: O.bodies[2].state.pos # position of body #2 Besides that, Yade says this at startup (the line preceding the command-line):: [[ ^L clears screen, ^U kills line. F12 controller, F11 3d view, F10 both, F9 generator, F8 plot. ]] :guilabel:`Controller` Pressing ``F12`` brings up a window for controlling the simulation. Although typically no human intervention is done in large simulations (which run "headless", without any graphical interaction), it can be handy in small examples. There are basic information on the simulation (will be used later). :guilabel:`3d view` The 3d view can be opened with F11 (or by clicking on button in the *Controller* -- see below). There is a number of keyboard shortcuts to manipulate it (press ``h`` to get basic help), and it can be moved, rotated and zoomed using mouse. Display-related settings can be set in the "Display" tab of the controller (such as whether particles are drawn). :guilabel:`Inspector` *Inspector* is opened by clicking on the appropriate button in the *Controller*. It shows (and updated) internal data of the current simulation. In particular, one can have a look at engines, particles (*Bodies*) and interactions (*Interactions*). Clicking at each of the attribute names links to the appropriate section in the documentation. .. rubric:: Exercises #. What is this code going to do? .. ipython:: Yade [1]: O.bodies.append([utils.sphere((2*i,0,0),1) for i in range(1,20)]) #. Create a simple simulation with cloud of spheres enclosed in the box ``(0,0,0)`` and ``(1,1,1)`` with mean radius .1. (hint: :yref:`yade._packSpheres.SpherePack.makeCloud`) #. Enclose the cloud created above in box with corners ``(0,0,0)`` and ``(1,1,1)``; keep the top of the box open. (hint: :yref:`yade.utils.facetBox`; type ``utils.facetBox?`` or ``utils.facetBox??`` to get help on the command line) #. Open the 3D view, try zooming in/out; position axes so that $z$ is upwards, $y$ goes to the right and $x$ towards you. Engines ^^^^^^^ Engines define processes undertaken by particles. As we know from the theoretical introduction, the sequence of engines is called *simulation loop*. Let us define a simple interaction loop: .. ipython:: @suppress Yade [1]: O.reset() Yade [1]: O.engines=[ # newlines and indentations are not important until the brace is closed ...: ForceResetter(), ...: InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Wall_Aabb()]), ...: InteractionLoop( # dtto for the parenthesis here ...: [Ig2_Sphere_Sphere_L3Geom(),Ig2_Wall_Sphere_L3Geom()], ...: [Ip2_FrictMat_FrictMat_FrictPhys()], ...: [Law2_L3Geom_FrictPhys_ElPerfPl()] ...: ), ...: NewtonIntegrator(damping=.2,label='newton') # define a name under which we can access this engine easily ...: ] ...: Yade [1]: O.engines Yade [1]: O.engines[-1]==newton # is it the same object? Yade [1]: newton.damping Instead of typing everything into the command-line, one can describe simulation in a file (*script*) and then run yade with that file as an argument. We will therefore no longer show the command-line unless necessary; instead, only the script part will be shown. Like this:: O.engines=[ # newlines and indentations are not important until the brace is closed ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Wall_Aabb()]), InteractionLoop( # dtto for the parenthesis here [Ig2_Sphere_Sphere_L3Geom_Inc(),Ig2_Wall_Sphere_L3Geom_Inc()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_L3Geom_FrictPhys_ElPerfPl()] ), GravityEngine(gravity=(0,0,-9.81)), # 9.81 is the gravity acceleration, and we say that NewtonIntegrator(damping=.2,label='newton') # define a name under which we can access this engine easily ] Besides engines being run, it is likewise important to define how often they will run. Some engines can run only sometimes (we will see this later), while most of them will run always; the time between two successive runs of engines is *timestep* ($\Dt$). There is a mathematical limit on the timestep value, called *critical timestep*, which is computed from properties of particles. Since there is a function for that, we can just set timestep using :yref:`yade.utils.PWaveTimeStep`:: O.dt=utils.PWaveTimeStep() Each time when the simulation loop finishes, time ``O.time`` is advanced by the timestep ``O.dt``: .. ipython:: Yade [1]: O.dt=0.01 Yade [1]: O.time Yade [1]: O.step() Yade [1]: O.time For experimenting with a single simulations, it is handy to save it to memory; this can be achieved, once everything is defined, with:: O.saveTmp() .. rubric:: Exercises #. Define *engines* as in the above example, run the *Inspector* and click through the engines to see their sequence. #. Write a simple script which will #. define particles as in the previous exercise (cloud of spheres inside a box open from the top) #. define a simple simulation loop, as the one given above #. set $\Dt$ equal to the critical P-Wave $\Dt$ #. save the initial simulation state to memory #. Run the previously-defined simulation multiple times, while changing the value of timestep (use the :guilabel:`⟳` button to reload the initial configuration). #. See what happens as you increase $\Dt$ above the P-Wave value. #. Try changing the :yref:`gravity` parameter, before running the simulation. #. Try changing :yref:`damping` #. Reload the simulation, open the 3d view, open the *Inspector*, select a particle in the 3d view (shift-click). Then run the simulation and watch how forces on that particle change; pause the simulation somewhere in the middle, look at interactions of this particle. #. At which point can we say that the deposition is done, so that the simulation can be stopped? .. seealso:: The :ref:`bouncing-sphere` example shows a basic simulation. trunk-2017.01a/doc/sphinx/tutorial-introduction.rst000066400000000000000000000006301304022710500223530ustar00rootroot00000000000000 Introduction ============= Slides `Yade: past, present and future `__ (updated version) .. todo:: Put link to the `Yade: past, present and future `__, or adapt it to give more general intro to particle models. .. todo:: Think about what is the scope of the introduction. trunk-2017.01a/doc/sphinx/tutorial.rst000066400000000000000000000022471304022710500176420ustar00rootroot00000000000000 Tutorial ============= This tutorial originated as handout for a course held at `Technische Universität Dresden `_ / `Fakultät Bauingenieurwesen `_ / `Institut für Geotechnik `_ in Jaunary 2011. The focus was to give quick and rather practical introduction to people without prior modeling experience, but with knowledge of mechanics. Some computer literacy was assumed, though basics are reviewed in the :doc:`Hands-on section `. The course did not in reality follow this document, but was based on interactive writing and commenting simple :doc:`Examples `, which were mostly suggested by participants; many thanks to them for their ideas and suggestions. A few minor bugs were discovered during the course. They were all fixed in rev. 2640 of Yade which is therefore the minimum recommended version to run the examples (notably, 0.60 will not work). .. toctree:: :maxdepth: 2 tutorial-introduction.rst tutorial-hands-on.rst tutorial-data-mining.rst tutorial-geo.rst tutorial-advanced.rst tutorial-examples.rst trunk-2017.01a/doc/sphinx/tutorial/000077500000000000000000000000001304022710500171035ustar00rootroot00000000000000trunk-2017.01a/doc/sphinx/tutorial/01-bouncing-sphere.py000066400000000000000000000022571304022710500227710ustar00rootroot00000000000000# basic simulation showing sphere falling ball gravity, # bouncing against another sphere representing the support # DATA COMPONENTS # add 2 particles to the simulation # they the default material (utils.defaultMat) O.bodies.append([ # fixed: particle's position in space will not change (support) sphere(center=(0,0,0),radius=.5,fixed=True), # this particles is free, subject to dynamics sphere((0,0,2),.5) ]) # FUNCTIONAL COMPONENTS # simulation loop -- see presentation for the explanation O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], # collision geometry [Ip2_FrictMat_FrictMat_FrictPhys()], # collision "physics" [Law2_ScGeom_FrictPhys_CundallStrack()] # contact law -- apply forces ), # Apply gravity force to particles. damping: numerical dissipation of energy. NewtonIntegrator(gravity=(0,0,-9.81),damping=0.1) ] # set timestep to a fraction of the critical timestep # the fraction is very small, so that the simulation is not too fast # and the motion can be observed O.dt=.5e-4*PWaveTimeStep() # save the simulation, so that it can be reloaded later, for experimentation O.saveTmp() trunk-2017.01a/doc/sphinx/tutorial/02-gravity-deposition.py000066400000000000000000000046171304022710500235440ustar00rootroot00000000000000# gravity deposition in box, showing how to plot and save history of data, # and how to control the simulation while it is running by calling # python functions from within the simulation loop # import yade modules that we will use below from yade import pack, plot # create rectangular box from facets O.bodies.append(geom.facetBox((.5,.5,.5),(.5,.5,.5),wallMask=31)) # create empty sphere packing # sphere packing is not equivalent to particles in simulation, it contains only the pure geometry sp=pack.SpherePack() # generate randomly spheres with uniform radius distribution sp.makeCloud((0,0,0),(1,1,1),rMean=.05,rRelFuzz=.5) # add the sphere pack to the simulation sp.toSimulation() O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( # handle sphere+sphere and facet+sphere collisions [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), NewtonIntegrator(gravity=(0,0,-9.81),damping=0.4), # call the checkUnbalanced function (defined below) every 2 seconds PyRunner(command='checkUnbalanced()',realPeriod=2), # call the addPlotData function every 200 steps PyRunner(command='addPlotData()',iterPeriod=100) ] O.dt=.5*PWaveTimeStep() # enable energy tracking; any simulation parts supporting it # can create and update arbitrary energy types, which can be # accessed as O.energy['energyName'] subsequently O.trackEnergy=True # if the unbalanced forces goes below .05, the packing # is considered stabilized, therefore we stop collected # data history and stop def checkUnbalanced(): if unbalancedForce()<.05: O.pause() plot.saveDataTxt('bbb.txt.bz2') # plot.saveGnuplot('bbb') is also possible # collect history of data which will be plotted def addPlotData(): # each item is given a names, by which it can be the unsed in plot.plots # the **O.energy converts dictionary-like O.energy to plot.addData arguments plot.addData(i=O.iter,unbalanced=unbalancedForce(),**O.energy) # define how to plot data: 'i' (step number) on the x-axis, unbalanced force # on the left y-axis, all energies on the right y-axis # (O.energy.keys is function which will be called to get all defined energies) # None separates left and right y-axis plot.plots={'i':('unbalanced',None,O.energy.keys)} # show the plot on the screen, and update while the simulation runs plot.plot() O.saveTmp() trunk-2017.01a/doc/sphinx/tutorial/03-oedometric-test.py000066400000000000000000000107211304022710500230050ustar00rootroot00000000000000# gravity deposition, continuing with oedometric test after stabilization # shows also how to run parametric studies with yade-batch # The components of the batch are: # 1. table with parameters, one set of parameters per line (ccc.table) # 2. readParamsFromTable which reads respective line from the parameter file # 3. the simulation muse be run using yade-batch, not yade # # $ yade-batch --job-threads=1 03-oedometric-test.table 03-oedometric-test.py # # load parameters from file if run in batch # default values are used if not run from batch readParamsFromTable(rMean=.05,rRelFuzz=.3,maxLoad=1e6,minLoad=1e4) # make rMean, rRelFuzz, maxLoad accessible directly as variables later from yade.params.table import * # create box with free top, and ceate loose packing inside the box from yade import pack, plot O.bodies.append(geom.facetBox((.5,.5,.5),(.5,.5,.5),wallMask=31)) sp=pack.SpherePack() sp.makeCloud((0,0,0),(1,1,1),rMean=rMean,rRelFuzz=rRelFuzz) sp.toSimulation() O.engines=[ ForceResetter(), # sphere, facet, wall InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb(),Bo1_Wall_Aabb()]), InteractionLoop( # the loading plate is a wall, we need to handle sphere+sphere, sphere+facet, sphere+wall [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom(),Ig2_Wall_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), NewtonIntegrator(gravity=(0,0,-9.81),damping=0.5), # the label creates an automatic variable referring to this engine # we use it below to change its attributes from the functions called PyRunner(command='checkUnbalanced()',realPeriod=2,label='checker'), ] O.dt=.5*PWaveTimeStep() # the following checkUnbalanced, unloadPlate and stopUnloading functions are all called by the 'checker' # (the last engine) one after another; this sequence defines progression of different stages of the # simulation, as each of the functions, when the condition is satisfied, updates 'checker' to call # the next function when it is run from within the simulation next time # check whether the gravity deposition has already finished # if so, add wall on the top of the packing and start the oedometric test def checkUnbalanced(): # at the very start, unbalanced force can be low as there is only few contacts, but it does not mean the packing is stable if O.iter<5000: return # the rest will be run only if unbalanced is < .1 (stabilized packing) if unbalancedForce()>.1: return # add plate at the position on the top of the packing # the maximum finds the z-coordinate of the top of the topmost particle O.bodies.append(wall(max([b.state.pos[2]+b.shape.radius for b in O.bodies if isinstance(b.shape,Sphere)]),axis=2,sense=-1)) global plate # without this line, the plate variable would only exist inside this function plate=O.bodies[-1] # the last particles is the plate # Wall objects are "fixed" by default, i.e. not subject to forces # prescribing a velocity will therefore make it move at constant velocity (downwards) plate.state.vel=(0,0,-.1) # start plotting the data now, it was not interesting before O.engines=O.engines+[PyRunner(command='addPlotData()',iterPeriod=200)] # next time, do not call this function anymore, but the next one (unloadPlate) instead checker.command='unloadPlate()' def unloadPlate(): # if the force on plate exceeds maximum load, start unloading if abs(O.forces.f(plate.id)[2])>maxLoad: plate.state.vel*=-1 # next time, do not call this function anymore, but the next one (stopUnloading) instead checker.command='stopUnloading()' def stopUnloading(): if abs(O.forces.f(plate.id)[2]).3, exit; otherwise do nothing if abs(O.cell.trsf[0,2])>.5: # save data from addData(...) before exiting into file # use O.tags['id'] to distinguish individual runs of the same simulation plot.saveDataTxt(O.tags['id']+'.txt') # exit the program #import sys #sys.exit(0) # no error (0) O.pause() # called periodically to store data history def addData(): # get the stress tensor (as 3x3 matrix) stress=sum(normalShearStressTensors(),Matrix3.Zero) # give names to values we are interested in and save them plot.addData(exz=O.cell.trsf[0,2],szz=stress[2,2],sxz=stress[0,2],tanPhi=stress[0,2]/stress[2,2],i=O.iter) # color particles based on rotation amount for b in O.bodies: # rot() gives rotation vector between reference and current position b.shape.color=scalarOnColorScale(b.state.rot().norm(),0,pi/2.) # define what to plot (3 plots in total) ## exz(i), [left y axis, separate by None:] szz(i), sxz(i) ## szz(exz), sxz(exz) ## tanPhi(i) # note the space in 'i ' so that it does not overwrite the 'i' entry plot.plots={'i':('exz',None,'szz','sxz'),'exz':('szz','sxz'),'i ':('tanPhi',)} # better show rotation of particles Gl1_Sphere.stripes=True # open the plot on the screen plot.plot() O.saveTmp() trunk-2017.01a/doc/sphinx/tutorial/05-3d-postprocessing.py000066400000000000000000000033301304022710500232640ustar00rootroot00000000000000# demonstrate 3d postprocessing with yade # # 1. qt.SnapshotEngine saves images of the 3d view as it appears on the screen periodically # makeVideo is then used to make real movie from those images # 2. VTKRecorder saves data in files which can be opened with Paraview # see the User's manual for an intro to Paraview # generate loose packing from yade import pack, qt sp=pack.SpherePack() sp.makeCloud((0,0,0),(2,2,2),rMean=.1,rRelFuzz=.6,periodic=True) # add to scene, make it periodic sp.toSimulation() O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), NewtonIntegrator(damping=.4), # save data for Paraview VTKRecorder(fileName='3d-vtk-',recorders=['all'],iterPeriod=1000), # save data from Yade's own 3d view qt.SnapshotEngine(fileBase='3d-',iterPeriod=200,label='snapshot'), # this engine will be called after 20000 steps, only once PyRunner(command='finish()',iterPeriod=20000) ] O.dt=.5*PWaveTimeStep() # prescribe constant-strain deformation of the cell O.cell.velGrad=Matrix3(-.1,0,0, 0,-.1,0, 0,0,-.1) # we must open the view explicitly (limitation of the qt.SnapshotEngine) qt.View() # this function is called when the simulation is finished def finish(): # snapshot is label of qt.SnapshotEngine # the 'snapshots' attribute contains list of all saved files makeVideo(snapshot.snapshots,'3d.mpeg',fps=10,bps=10000) O.pause() # set parameters of the renderer, to show network chains rather than particles # these settings are accessible from the Controller window, on the second tab ("Display") as well rr=yade.qt.Renderer() rr.shape=False rr.intrPhys=True trunk-2017.01a/doc/sphinx/tutorial/06-periodic-triaxial-test.py000066400000000000000000000063751304022710500243010ustar00rootroot00000000000000# encoding: utf-8 # periodic triaxial test simulation # # The initial packing is either # # 1. random cloud with uniform distribution, or # 2. cloud with specified granulometry (radii and percentages), or # 3. cloud of clumps, i.e. rigid aggregates of several particles # # The triaxial consists of 2 stages: # # 1. isotropic compaction, until sigmaIso is reached in all directions; # this stage is ended by calling compactionFinished() # 2. constant-strain deformation along the z-axis, while maintaining # constant stress (sigmaIso) laterally; this stage is ended by calling # triaxFinished() # # Controlling of strain and stresses is performed via PeriTriaxController, # of which parameters determine type of control and also stability # condition (maxUnbalanced) so that the packing is considered stabilized # and the stage is done. # sigmaIso=-1e5 #import matplotlib #matplotlib.use('Agg') # generate loose packing from yade import pack, qt, plot O.periodic=True sp=pack.SpherePack() if 0: ## uniform distribution sp.makeCloud((0,0,0),(2,2,2),rMean=.1,rRelFuzz=.3,periodic=True) else: ## create packing from clumps # configuration of one clump c1=pack.SpherePack([((0,0,0),.03333),((.03,0,0),.017),((0,.03,0),.017)]) # make cloud using the configuration c1 (there could c2, c3, ...; selection between them would be random) sp.makeClumpCloud((0,0,0),(2,2,2),[c1],periodic=True,num=500) # setup periodic boundary, insert the packing sp.toSimulation() O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), PeriTriaxController(label='triax', # specify target values and whether they are strains or stresses goal=(sigmaIso,sigmaIso,sigmaIso),stressMask=7, # type of servo-control dynCell=True,maxStrainRate=(10,10,10), # wait until the unbalanced force goes below this value maxUnbalanced=.1,relStressTol=1e-3, # call this function when goal is reached and the packing is stable doneHook='compactionFinished()' ), NewtonIntegrator(damping=.2), PyRunner(command='addPlotData()',iterPeriod=100), ] O.dt=.5*PWaveTimeStep() def addPlotData(): plot.addData(unbalanced=unbalancedForce(),i=O.iter, sxx=triax.stress[0],syy=triax.stress[1],szz=triax.stress[2], exx=triax.strain[0],eyy=triax.strain[1],ezz=triax.strain[2], # save all available energy data Etot=O.energy.total(),**O.energy ) # enable energy tracking in the code O.trackEnergy=True # define what to plot plot.plots={'i':('unbalanced',),'i ':('sxx','syy','szz'),' i':('exx','eyy','ezz'), # energy plot ' i ':(O.energy.keys,None,'Etot'), } # show the plot plot.plot() def compactionFinished(): # set the current cell configuration to be the reference one O.cell.trsf=Matrix3.Identity # change control type: keep constant confinement in x,y, 20% compression in z triax.goal=(sigmaIso,sigmaIso,-.2) triax.stressMask=3 # allow faster deformation along x,y to better maintain stresses triax.maxStrainRate=(1.,1.,.1) # next time, call triaxFinished instead of compactionFinished triax.doneHook='triaxFinished()' # do not wait for stabilization before calling triaxFinished triax.maxUnbalanced=10 def triaxFinished(): print 'Finished' O.pause() trunk-2017.01a/doc/sphinx/tutorial/make-simulation-video.py000066400000000000000000000024511304022710500236620ustar00rootroot00000000000000# encoding: utf-8 # use another simulation script, create 3d output and graphs # # the simulation must not run by itself (no O.run() at the end of the script) # when run, must stop by itself (without exiting) # # plotting should be set up as usual import matplotlib matplotlib.use('Agg') # headless backend, makes rendering plots after the simulation _much_ faster (and more reliable) from yade import qt,plot simulations=[ ('01-bouncing-sphere.py',u'Bouncing sphere',100000), ('02-gravity-deposition.py',u'Gravity deposition',100), ('03-oedometric-test.py',u'Oedometric test',500), ('04-periodic-simple-shear.py',u'Simple shear\nwith\nperiodic boundary',100), ('06-periodic-triaxial-test.py',u'Periodic triaxal test\nwith clumps',200) ] #for script,title in simulations: def do(n): global script,title script,title,freq=simulations[n] O.reset(); plot.reset() execfile(script,globals()) # add output engines O.engines=O.engines+[qt.SnapshotEngine(fileBase=O.tmpFilename(),iterPeriod=freq,plot='snapshot')] # add the snapshot subplot plot.plots.update({'snapshot':None}) # open the view so that it can be set up qt.View() def done(): utils.makeVideo(plot.savePlotSequence(O.tmpFilename(),title=title+u'\n\n\nVáclav Šmilauer\neu@doxos.eu\nhttp://www.yade-dem.org'),script+'.mpeg',fps=10,kbps=5000) trunk-2017.01a/doc/sphinx/tutorial/peri-triax.py000066400000000000000000000022241304022710500215410ustar00rootroot00000000000000from yade import pack,plot sp=pack.SpherePack() rMean=.05 sp.makeCloud((0,0,0),(1,1,1),rMean=rMean,periodic=True) sp.toSimulation() O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()],verletDist=.05*rMean), InteractionLoop([Ig2_Sphere_Sphere_L3Geom()],[Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_L3Geom_FrictPhys_ElPerfPl()]), NewtonIntegrator(damping=.6), PeriTriaxController(goal=(-1e6,-1e6,-.1),stressMask=0b011,maxUnbalanced=.2,doneHook='goalReached()',label='triax',maxStrainRate=(.1,.1,.1),dynCell=True), PyRunner(iterPeriod=100,command='addPlotData()') ] O.dt=.5*utils.PWaveTimeStep() O.trackEnergy=True def goalReached(): print 'Goal reached, strain',triax.strain,' stress',triax.stress O.pause() def addPlotData(): plot.addData(sx=triax.stress[0],sy=triax.stress[1],sz=triax.stress[2],ex=triax.strain[0],ey=triax.strain[1],ez=triax.strain[2], i=O.iter,unbalanced=utils.unbalancedForce(), totalEnergy=O.energy.total(),**O.energy # plot all energies ) plot.plots={'i':(('unbalanced','go'),None,'kinetic'),' i':('ex','ey','ez',None,'sx','sy','sz'),'i ':(O.energy.keys,None,('totalEnergy','bo'))} plot.plot() O.saveTmp() O.run() trunk-2017.01a/doc/sphinx/upload000077500000000000000000000001011304022710500164420ustar00rootroot00000000000000#!/bin/sh rsync -rv _build/html/ ggamma:www/NoBackup/yade-sphinx trunk-2017.01a/doc/sphinx/user.rst000066400000000000000000002650171304022710500167630ustar00rootroot00000000000000################### User's manual ################### .. The imports below are done at startup normaly, but it seems ineffective in the context of sphinx build, let us import silently .. ipython:: @suppress Yade [0]: from yade.utils import * @suppress Yade [0]: from math import * ******************* Scene construction ******************* Adding particles ================ The :yref:`BodyContainer` holds :yref:`Body` objects in the simulation; it is accessible as ``O.bodies``. Creating Body objects ---------------------- :yref:`Body` objects are only rarely constructed by hand by their components (:yref:`Shape`, :yref:`Bound`, :yref:`State`, :yref:`Material`); instead, convenience functions :yref:`sphere`, :yref:`facet` and :yref:`wall` are used to create them. Using these functions also ensures better future compatibility, if internals of :yref:`Body` change in some way. These functions receive geometry of the particle and several other characteristics. See their documentation for details. If the same :yref:`Material` is used for several (or many) bodies, it can be shared by adding it in ``O.materials``, as explained below. Defining materials ------------------ The ``O.materials`` object (instance of :yref:`Omega.materials`) holds defined shared materials for bodies. It only supports addition, and will typically hold only a few instance (though there is no limit). ``label`` given to each material is optional, but can be passed to :yref:`sphere` and other functions for constructing body. The value returned by ``O.materials.append`` is an ``id`` of the material, which can be also passed to :yref:`sphere` -- it is a little bit faster than using label, though not noticeable for small number of particles and perhaps less convenient. If no :yref:`Material` is specified when calling :yref:`sphere`, the *last* defined material is used; that is a convenient default. If no material is defined yet (hence there is no last material), a default material will be created: FrictMat(density=2e3,young=30e9,poisson=.3,frictionAngle=.5236). This should not happen for serious simulations, but is handy in simple scripts, where exact material properties are more or less irrelevant. .. ipython:: @suppress Yade [0]: O.reset() Yade [1]: len(O.materials) Yade [2]: idConcrete=O.materials.append(FrictMat(young=30e9,poisson=.2,frictionAngle=.6,label="concrete")) Yade [3]: O.materials[idConcrete] # uses the last defined material Yade [3]: O.bodies.append(sphere(center=(0,0,0),radius=1)) # material given by id Yade [4]: O.bodies.append(sphere((0,0,2),1,material=idConcrete)) # material given by label Yade [5]: O.bodies.append(sphere((0,2,0),1,material="concrete")) Yade [3]: idSteel=O.materials.append(FrictMat(young=210e9,poisson=.25,frictionAngle=.8,label="steel")) Yade [7]: len(O.materials) # implicitly uses "steel" material, as it is the last one now Yade [6]: O.bodies.append(facet([(1,0,0),(0,1,0),(-1,-1,0)])) Adding multiple particles ------------------------- As shown above, bodies are added one by one or several at the same time using the ``append`` method: .. ipython:: @suppress Yade [0]: O.reset() Yade [1]: O.bodies.append(sphere((0,10,0),1)) Yade [2]: O.bodies.append(sphere((0,0,2),1)) # this is the same, but in one function call Yade [3]: O.bodies.append([ ...: sphere((0,0,0),1), ...: sphere((0,0,2),1) ...: ]) Many functions introduced in next sections return list of bodies which can be readily added to the simulation, including * packing generators, such as :yref:`yade.pack.randomDensePack`, :yref:`yade.pack.regularHexa` * surface function :yref:`yade.pack.gtsSurface2Facets` * import functions :yref:`yade.ymport.gmsh`, :yref:`yade.ymport.stl`, … As those functions use :yref:`sphere` and :yref:`facet` internally, they accept additional argument passed to those function. In particular, material for each body is selected following the rules above (last one if not specified, by label, by index, etc.). Clumping particles together ---------------------------- In some cases, you might want to create rigid aggregate of individual particles (i.e. particles will retain their mutual position during simulation). This we call a :yref:`clump`. A clump is internally represented by a special :yref:`body`, referenced by :yref:`clumpId` of its members (see also :yref:`isClump`, :yref:`isClumpMember` and :yref:`isStandalone`). Like every body a clump has a :yref:`position`, which is the (mass) balance point between all members. A clump body itself has no :yref:`interactions` with other bodies. Interactions between clumps is represented by interactions between clump members. There are no interactions between clump members of the same clump. YADE supports different ways of creating clumps: * Create clumps and spheres (clump members) directly with one command: The function :yref:`appendClumped()` is designed for this task. For instance, we might add 2 spheres tied together: .. ipython:: @suppress Yade [0]: O.reset() Yade [1]: O.bodies.appendClumped([ ...: sphere([0,0,0],1), ...: sphere([0,0,2],1) ...: ]) Yade [2]: len(O.bodies) Yade [3]: O.bodies[1].isClumpMember, O.bodies[2].clumpId Yade [2]: O.bodies[2].isClump, O.bodies[2].clumpId -> :yref:`appendClumped()` returns a tuple of ids ``(clumpId,[memberId1,memberId2,...])`` * Use existing spheres and clump them together: For this case the function :yref:`clump()` can be used. One way to do this is to create a list of bodies, that should be clumped before using the :yref:`clump()` command: .. ipython:: @suppress Yade [0]: O.reset() Yade [1]: bodyList = [] Yade [2]: for ii in range(0,5): ...: bodyList.append(O.bodies.append(sphere([ii,0,1],.5)))#create a "chain" of 5 spheres ...: Yade [3]: print bodyList Yade [4]: idClump=O.bodies.clump(bodyList) -> :yref:`clump()` returns ``clumpId`` * Another option is to replace :yref:`standalone` spheres from a given packing (see :yref:`SpherePack` and :yref:`makeCloud`) by clumps using clump templates. This is done by a function called :yref:`replaceByClumps()`. This function takes a list of :yref:`clumpTemplates()` and a list of amounts and replaces spheres by clumps. The volume of a new clump will be the same as the volume of the sphere, that was replaced (clump volume/mass/inertia is accounting for overlaps assuming that there are only pair overlaps). -> :yref:`replaceByClumps()` returns a list of tuples: ``[(clumpId1,[memberId1,memberId2,...]),(clumpId2,[memberId1,memberId2,...]),...]`` It is also possible to :yref:`add` bodies to a clump and :yref:`release` bodies from a clump. Also you can :yref:`erase` the clump (clump members will get standalone spheres). Additionally YADE supports to achieve the :yref:`roundness` of a clump or roundness coefficient of a packing. Parts of the packing can be excluded from roundness measurement via exclude list. .. ipython:: @suppress Yade [0]: O.reset() Yade [1]: bodyList = [] Yade [2]: for ii in range(1,5): ...: bodyList.append(O.bodies.append(sphere([ii,ii,ii],.5))) ...: Yade [4]: O.bodies.clump(bodyList) Yade [5]: RC=O.bodies.getRoundness() Yade [3]: print RC -> :yref:`getRoundness()` returns roundness coefficient RC of a packing or a part of the packing .. note:: Have a look at :ysrc:`examples/clumps/` folder. There you will find some examples, that show usage of different functions for clumps. Sphere packings =============== Representing a solid of an arbitrary shape by arrangement of spheres presents the problem of sphere packing, i.e. spatial arrangement of sphere such that given solid is approximately filled with them. For the purposes of DEM simulation, there can be several requirements. #. Distribution of spheres' radii. Arbitrary volume can be filled completely with spheres provided there are no restrictions on their radius; in such case, number of spheres can be infinite and their radii approach zero. Since both number of particles and minimum sphere radius (via critical timestep) determine computation cost, radius distribution has to be given mandatorily. The most typical distribution is uniform: mean±dispersion; if dispersion is zero, all spheres will have the same radius. #. Smooth boundary. Some algorithms treat boundaries in such way that spheres are aligned on them, making them smoother as surface. #. Packing density, or the ratio of spheres volume and solid size. It is closely related to radius distribution. #. Coordination number, (average) number of contacts per sphere. #. Isotropy (related to regularity/irregularity); packings with preferred directions are usually not desirable, unless the modeled solid also has such preference. #. Permissible Spheres' overlap; some algorithms might create packing where spheres slightly overlap; since overlap usually causes forces in DEM, overlap-free packings are sometimes called “stress-free‟. Volume representation ---------------------- There are 2 methods for representing exact volume of the solid in question in Yade: boundary representation and constructive solid geometry. Despite their fundamental differences, they are abstracted in Yade in the :yref:`Predicate` class. Predicate provides the following functionality: #. defines axis-aligned bounding box for the associated solid (optionally defines oriented bounding box); #. can decide whether given point is inside or outside the solid; most predicates can also (exactly or approximately) tell whether the point is inside *and* satisfies some given padding distance from the represented solid boundary (so that sphere of that volume doesn't stick out of the solid). Constructive Solid Geometry (CSG) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ CSG approach describes volume by geometric *primitives* or primitive solids (sphere, cylinder, box, cone, …) and boolean operations on them. Primitives defined in Yade include :yref:`inCylinder`, :yref:`inSphere`, :yref:`inEllipsoid`, :yref:`inHyperboloid`, :yref:`notInNotch`. For instance, :yref:`hyperboloid` (dogbone) specimen for tension-compression test can be constructed in this way (shown at img. img-hyperboloid_):: from yade import pack ## construct the predicate first pred=pack.inHyperboloid(centerBottom=(0,0,-.1),centerTop=(0,0,.1),radius=.05,skirt=.03) ## alternatively: pack.inHyperboloid((0,0,-.1),(0,0,.1),.05,.03) ## pack the predicate with spheres (will be explained later) spheres=pack.randomDensePack(pred,spheresInCell=2000,radius=3.5e-3) ## add spheres to simulation O.bodies.append(spheres) .. _img-hyperboloid: .. figure:: fig/hyperboloid.png :width: 7cm Specimen constructed with the :yref:`yade._packPredicates.inHyperboloid` predicate, packed with :yref:`yade.pack.randomDensePack`. Boundary representation (BREP) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Representing a solid by its boundary is much more flexible than CSG volumes, but is mostly only approximate. Yade interfaces to `GNU Triangulated Surface Library `_ (GTS) to import surfaces readable by GTS, but also to construct them explicitly from within simulation scripts. This makes possible parametric construction of rather complicated shapes; there are functions to create set of 3d polylines from 2d polyline (:yref:`yade.pack.revolutionSurfaceMeridians`), to triangulate surface between such set of 3d polylines (:yref:`yade.pack.sweptPolylines2gtsSurface`). For example, we can construct a simple funnel (:ysrc:`examples/funnel.py`, shown at img-funnel_):: from numpy import linspace from yade import pack # angles for points on circles thetas=linspace(0,2*pi,num=16,endpoint=True) # creates list of polylines in 3d from list of 2d projections # turned from 0 to π meridians=pack.revolutionSurfaceMeridians( [[(3+rad*sin(th),10*rad+rad*cos(th)) for th in thetas] for rad in linspace(1,2,num=10)], linspace(0,pi,num=10) ) # create surface surf=pack.sweptPolylines2gtsSurface( meridians+ +[[Vector3(5*sin(-th),-10+5*cos(-th),30) for th in thetas]] # add funnel top ) # add to simulation O.bodies.append(pack.gtsSurface2Facets(surf)) .. _img-funnel: .. figure:: fig/funnel.* :height: 6cm Triangulated funnel, constructed with the :ysrc:`examples/funnel.py` script. GTS surface objects can be used for 2 things: #. :yref:`yade.pack.gtsSurface2Facets` function can create the triangulated surface (from :yref:`Facet` particles) in the simulation itself, as shown in the funnel example. (Triangulated surface can also be imported directly from a STL file using :yref:`yade.ymport.stl`.) #. :yref:`yade._packPredicates.inGtsSurface` predicate can be created, using the surface as boundary representation of the enclosed volume. The :ysrc:`examples/gts-horse/gts-horse.py` (img. img-horse_) shows both possibilities; first, a GTS surface is imported:: import gts surf=gts.read(open('horse.coarse.gts')) That surface object is used as predicate for packing:: pred=pack.inGtsSurface(surf) O.bodies.append(pack.regularHexa(pred,radius=radius,gap=radius/4.)) and then, after being translated, as base for triangulated surface in the simulation itself:: surf.translate(0,0,-(aabb[1][2]-aabb[0][2])) O.bodies.append(pack.gtsSurface2Facets(surf,wire=True)) .. _img-horse: .. figure:: fig/horse.png :width: 8cm Imported GTS surface (horse) used as packing predicate (top) and surface constructed from :yref:`facets` (bottom). See http://www.youtube.com/watch?v=PZVruIlUX1A for movie of this simulation. Boolean operations on predicates ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Boolean operations on pair of predicates (noted ``A`` and ``B``) are defined: * :yref:`intersection` ``A & B`` (conjunction): point must be in both predicates involved. * :yref:`union` ``A | B`` (disjunction): point must be in the first or in the second predicate. * :yref:`difference` ``A - B`` (conjunction with second predicate negated): the point must be in the first predicate and not in the second one. * :yref:`symmetric difference` ``A ^ B`` (exclusive disjunction): point must be in exactly one of the two predicates. Composed predicates also properly define their bounding box. For example, we can take box and remove cylinder from inside, using the ``A - B`` operation (img. img-predicate-difference_):: pred=pack.inAlignedBox((-2,-2,-2),(2,2,2))-pack.inCylinder((0,-2,0),(0,2,0),1) spheres=pack.randomDensePack(pred,spheresInCell=2000,radius=.1,rRelFuzz=.4) .. _img-predicate-difference: .. figure:: fig/predicate-difference.png :width: 8cm Box with cylinder removed from inside, using difference of these two predicates. Packing algorithms ------------------- Algorithms presented below operate on geometric spheres, defined by their center and radius. With a few exception documented below, the procedure is as follows: #. Sphere positions and radii are computed (some functions use volume predicate for this, some do not) #. :yref:`sphere` is called for each position and radius computed; it receives extra `keyword arguments `_ of the packing function (i.e. arguments that the packing function doesn't specify in its definition; they are noted ``**kw``). Each :yref:`sphere` call creates actual :yref:`Body` objects with :yref:`Sphere` :yref:`shape`. List of :yref:`Body` objects is returned. #. List returned from the packing function can be added to simulation using ``O.bodies.append``. Taking the example of pierced box:: pred=pack.inAlignedBox((-2,-2,-2),(2,2,2))-pack.inCylinder((0,-2,0),(0,2,0),1) spheres=pack.randomDensePack(pred,spheresInCell=2000,radius=.1,rRelFuzz=.4,wire=True,color=(0,0,1),material=1) Keyword arguments ``wire``, ``color`` and ``material`` are not declared in :yref:`yade.pack.randomDensePack`, therefore will be passed to :yref:`sphere`, where they are also documented. ``spheres`` is now list of :yref:`Body` objects, which we add to the simulation:: O.bodies.append(spheres) Packing algorithms described below produce dense packings. If one needs loose packing, :yref:`yade._packSpheres.SpherePack` class provides functions for generating loose packing, via its :yref:`yade._packSpheres.SpherePack.makeCloud` method. It is used internally for generating initial configuration in dynamic algorithms. For instance:: from yade import pack sp=pack.SpherePack() sp.makeCloud(minCorner=(0,0,0),maxCorner=(3,3,3),rMean=.2,rRelFuzz=.5) will fill given box with spheres, until no more spheres can be placed. The object can be used to add spheres to simulation:: for c,r in sp: O.bodies.append(sphere(c,r)) or, in a more pythonic way, with one single ``O.bodies.append`` call:: O.bodies.append([sphere(c,r) for c,r in sp]) Geometric ^^^^^^^^^ Geometric algorithms compute packing without performing dynamic simulation; among their advantages are * speed; * spheres touch exactly, there are no overlaps (what some people call "stress-free" packing); their chief disadvantage is that radius distribution cannot be prescribed exactly, save in specific cases (regular packings); sphere radii are given by the algorithm, which already makes the system determined. If exact radius distribution is important for your problem, consider dynamic algorithms instead. Regular """"""""" Yade defines packing generators for spheres with constant radii, which can be used with volume predicates as described above. They are dense orthogonal packing (:yref:`yade.pack.regularOrtho`) and dense hexagonal packing (:yref:`yade.pack.regularHexa`). The latter creates so-called "hexagonal close packing", which achieves maximum density (http://en.wikipedia.org/wiki/Close-packing_of_spheres). Clear disadvantage of regular packings is that they have very strong directional preferences, which might not be an issue in some cases. Irregular """""""""" Random geometric algorithms do not integrate at all with volume predicates described above; rather, they take their own boundary/volume definition, which is used during sphere positioning. On the other hand, this makes it possible for them to respect boundary in the sense of making spheres touch it at appropriate places, rather than leaving empty space in-between. GenGeo is library (python module) for packing generation developed with `ESyS-Particle `_. It creates packing by random insertion of spheres with given radius range. Inserted spheres touch each other exactly and, more importantly, they also touch the boundary, if in its neighbourhood. Boundary is represented as special object of the GenGeo library (Sphere, cylinder, box, convex polyhedron, …). Therefore, GenGeo cannot be used with volume represented by yade predicates as explained above. Packings generated by this module can be imported directly via :yref:`yade.ymport.gengeo`, or from saved file via :yref:`yade.ymport.gengeoFile`. There is an example script :ysrc:`examples/test/genCylLSM.py`. Full documentation for GenGeo can be found at `ESyS documentation website `_. To our knowledge, the GenGeo library is not currently packaged. It can be downloaded from current subversion repository :: svn checkout https://svn.esscc.uq.edu.au/svn/esys3/lsm/contrib/LSMGenGeo then following instruction in the ``INSTALL`` file. Dynamic ^^^^^^^ The most versatile algorithm for random dense packing is provided by :yref:`yade.pack.randomDensePack`. Initial loose packing of non-overlapping spheres is generated by randomly placing them in cuboid volume, with radii given by requested (currently only uniform) radius distribution. When no more spheres can be inserted, the packing is compressed and then uncompressed (see :ysrc:`py/pack/pack.py` for exact values of these "stresses") by running a DEM simulation; :yref:`Omega.switchScene` is used to not affect existing simulation). Finally, resulting packing is clipped using provided predicate, as explained above. By its nature, this method might take relatively long; and there are 2 provisions to make the computation time shorter: * If number of spheres using the ``spheresInCell`` parameter is specified, only smaller specimen with *periodic* boundary is created and then repeated as to fill the predicate. This can provide high-quality packing with low regularity, depending on the ``spheresInCell`` parameter (value of several thousands is recommended). * Providing ``memoizeDb`` parameter will make :yref:`yade.pack.randomDensePack` first look into provided file (SQLite database) for packings with similar parameters. On success, the packing is simply read from database and returned. If there is no similar pre-existent packing, normal procedure is run, and the result is saved in the database before being returned, so that subsequent calls with same parameters will return quickly. If you need to obtain full periodic packing (rather than packing clipped by predicate), you can use :yref:`yade.pack.randomPeriPack`. In case of specific needs, you can create packing yourself, "by hand". For instance, packing boundary can be constructed from :yref:`facets`, letting randomly positioned spheres in space fall down under gravity. Triangulated surfaces ===================== Yade integrates with the the `GNU Triangulated Surface library `_, exposed in python via GTS module. GTS provides variety of functions for surface manipulation (coarsening, tesselation, simplification, import), to be found in its documentation. GTS surfaces are geometrical objects, which can be inserted into simulation as set of particles whose :yref:`Body.shape` is of type :yref:`Facet` -- single triangulation elements. :yref:`yade.pack.gtsSurface2Facets` can be used to convert GTS surface triangulation into list of :yref:`bodies` ready to be inserted into simulation via ``O.bodies.append``. Facet particles are created by default as non-:yref:`Body.dynamic` (they have zero inertial mass). That means that they are fixed in space and will not move if subject to forces. You can however * prescribe arbitrary movement to facets using a :yref:`PartialEngine` (such as :yref:`TranslationEngine` or :yref:`RotationEngine`); * assign explicitly :yref:`mass` and :yref:`inertia` to that particle; * make that particle part of a clump and assign :yref:`mass` and :yref:`inertia` of the clump itself (described below). .. note:: Facets can only (currently) interact with :yref:`spheres`, not with other facets, even if they are *dynamic*. Collision of 2 :yref:`facets` will not create interaction, therefore no forces on facets. Import ------- Yade currently offers 3 formats for importing triangulated surfaces from external files, in the :yref:`yade.ymport` module: :yref:`yade.ymport.gts` text file in native GTS format. :yref:`yade.ymport.stl` STereoLitography format, in either text or binary form; exported from `Blender `_, but from many CAD systems as well. :yref:`yade.ymport.gmsh`. text file in native format for `GMSH `_, popular open-source meshing program. If you need to manipulate surfaces before creating list of facets, you can study the :ysrc:`py/ymport.py` file where the import functions are defined. They are rather simple in most cases. Parametric construction ------------------------ The GTS module provides convenient way of creating surface by vertices, edges and triangles. Frequently, though, the surface can be conveniently described as surface between polylines in space. For instance, cylinder is surface between two polygons (closed polylines). The :yref:`yade.pack.sweptPolylines2gtsSurface` offers the functionality of connecting several polylines with triangulation. .. note:: The implementation of :yref:`yade.pack.sweptPolylines2gtsSurface` is rather simplistic: all polylines must be of the same length, and they are connected with triangles between points following their indices within each polyline (not by distance). On the other hand, points can be co-incident, if the ``threshold`` parameter is positive: degenerate triangles with vertices closer that ``threshold`` are automatically eliminated. Manipulating lists efficiently (in terms of code length) requires being familiar with `list comprehensions `_ in python. .. FIXME some example here Another examples can be found in :ysrc:`examples/mill.py` (fully parametrized) or :ysrc:`examples/funnel.py` (with hardcoded numbers). .. _creating-interactions: Creating interactions ====================== In typical cases, interactions are created during simulations as particles collide. This is done by a :yref:`Collider` detecting approximate contact between particles and then an :yref:`IGeomFunctor` detecting exact collision. Some material models (such as the :yref:`concrete model`) rely on initial interaction network which is denser than geometrical contact of spheres: sphere's radii as "enlarged" by a dimensionless factor called *interaction radius* (or *interaction ratio*) to create this initial network. This is done typically in this way (see :ysrc:`examples/concrete/uniax.py` for an example): #. Approximate collision detection is adjusted so that approximate contacts are detected also between particles within the interaction radius. This consists in setting value of :yref:`Bo1_Sphere_Aabb.aabbEnlargeFactor` to the interaction radius value. #. The geometry functor (``Ig2``) would normally say that "there is no contact" if given 2 spheres that are not in contact. Therefore, the same value as for :yref:`Bo1_Sphere_Aabb.aabbEnlargeFactor` must be given to it (:yref:`Ig2_Sphere_Sphere_ScGeom.interactionDetectionFactor` ). Note that only :yref:`Sphere` + :yref:`Sphere` interactions are supported; there is no parameter analogous to :yref:`distFactor` in :yref:`Ig2_Facet_Sphere_ScGeom`. This is on purpose, since the interaction radius is meaningful in bulk material represented by sphere packing, whereas facets usually represent boundary conditions which should be exempt from this dense interaction network. #. Run one single step of the simulation so that the initial network is created. #. Reset interaction radius in both ``Bo1`` and ``Ig2`` functors to their default value again. #. Continue the simulation; interactions that are already established will not be deleted (the ``Law2`` functor in usepermitting). In code, such scenario might look similar to this one (labeling is explained in :ref:`labelingthings`):: intRadius=1.5 O.engines=[ ForceResetter(), InsertionSortCollider([ # enlarge here Bo1_Sphere_Aabb(aabbEnlargeFactor=intRadius,label='bo1s'), Bo1_Facet_Aabb(), ]), InteractionLoop( [ # enlarge here Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=intRadius,label='ig2ss'), Ig2_Facet_Sphere_ScGeom(), ], [Ip2_CpmMat_CpmMat_CpmPhys()], [Law2_ScGeom_CpmPhys_Cpm(epsSoft=0)], # deactivated ), NewtonIntegrator(damping=damping,label='damper'), ] # run one single step O.step() # reset interaction radius to the default value bo1s.aabbEnlargeFactor=1.0 ig2ss.interactionDetectionFactor=1.0 # now continue simulation O.run() Individual interactions on demand ---------------------------------- It is possible to create an interaction between a pair of particles independently of collision detection using :yref:`createInteraction`. This function looks for and uses matching ``Ig2`` and ``Ip2`` functors. Interaction will be created regardless of distance between given particles (by passing a special parameter to the ``Ig2`` functor to force creation of the interaction even without any geometrical contact). Appropriate constitutive law should be used to avoid deletion of the interaction at the next simulation step. .. ipython:: @suppress Yade [1]: O.reset() Yade [1]: O.materials.append(FrictMat(young=3e10,poisson=.2,density=1000)) Yade [1]: O.bodies.append([ ...: sphere([0,0,0],1), ...: sphere([0,0,1000],1) ...: ]) # only add InteractionLoop, no other engines are needed now Yade [1]: O.engines=[ ...: InteractionLoop( ...: [Ig2_Sphere_Sphere_ScGeom(),], ...: [Ip2_FrictMat_FrictMat_FrictPhys()], ...: [] # not needed now ...: ) ...: ] Yade [1]: i=createInteraction(0,1) # created by functors in InteractionLoop Yade [2]: i.geom, i.phys This method will be rather slow if many interaction are to be created (the functor lookup will be repeated for each of them). In such case, ask on yade-dev@lists.launchpad.net to have the :yref:`createInteraction` function accept list of pairs id's as well. Base engines ============= A typical DEM simulation in Yade does at least the following at each step (see :ref:`function-components` for details): #. Reset forces from previous step #. Detect new collisions #. Handle interactions #. Apply forces and update positions of particles Each of these points corresponds to one or several engines:: O.engines=[ ForceResetter(), # reset forces InsertionSortCollider([...]), # approximate collision detection InteractionLoop([...],[...],[...]) # handle interactions NewtonIntegrator() # apply forces and update positions ] The order of engines is important. In majority of cases, you will put any additional engine after :yref:`InteractionLoop`: * if it apply force, it should come before :yref:`NewtonIntegrator`, otherwise the force will never be effective. * if it makes use of bodies' positions, it should also come before :yref:`NewtonIntegrator`, otherwise, positions at the next step will be used (this might not be critical in many cases, such as output for visualization with :yref:`VTKRecorder`). The :yref:`O.engines` sequence must be always assigned at once (the reason is in the fact that although engines themselves are passed by reference, the sequence is *copied* from c++ to Python or from Python to c++). This includes modifying an existing ``O.engines``; therefore :: O.engines.append(SomeEngine()) # wrong will not work; :: O.engines=O.engines+[SomeEngine()] # ok must be used instead. For inserting an engine after position #2 (for example), use python slice notation:: O.engines=O.engines[:2]+[SomeEngine()]+O.engines[2:] .. note:: When Yade starts, O.engines is filled with a reasonable default list, so that it is not strictly necessary to redefine it when trying simple things. The default scene will handle spheres, boxes, and facets with :yref:`frictional` properties correctly, and adjusts the timestep dynamically. You can find an example in simple-scene-default-engines.py. Functors choice ---------------- In the above example, we omited functors, only writing ellipses ``...`` instead. As explained in :ref:`dispatchers-and-functors`, there are 4 kinds of functors and associated dispatchers. User can choose which ones to use, though the choice must be consistent. Bo1 functors ^^^^^^^^^^^^ ``Bo1`` functors must be chosen depending on the collider in use; they are given directly to the collider (which internally uses :yref:`BoundDispatcher`). At this moment (September 2010), the most common choice is :yref:`InsertionSortCollider`, which uses :yref:`Aabb`; functors creating :yref:`Aabb` must be used in that case. Depending on particle :yref:`shapes` in your simulation, choose appropriate functors:: O.engines=[..., InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), ... ] Using more functors than necessary (such as :yref:`Bo1_Facet_Aabb` if there are no :yref:`facets` in the simulation) has no performance penalty. On the other hand, missing functors for existing :yref:`shapes` will cause those bodies to not collider with other bodies (they will freely interpenetrate). There are other colliders as well, though their usage is only experimental: * :yref:`SpatialQuickSortCollider` is correctness-reference collider operating on :yref:`Aabb`; it is significantly slower than :yref:`InsertionSortCollider`. * :yref:`PersistentTriangulationCollider` only works on spheres; it does not use a :yref:`BoundDispatcher`, as it operates on spheres directly. * :yref:`FlatGridCollider` is proof-of-concept grid-based collider, which computes grid positions internally (no :yref:`BoundDispatcher` either) Ig2 functors ^^^^^^^^^^^^^ ``Ig2`` functor choice (all of the derive from :yref:`IGeomFunctor`) depends on #. shape combinations that should collide; for instance:: InteractionLoop([Ig2_Sphere_Sphere_ScGeom()],[],[]) will handle collisions for :yref:`Sphere` + :yref:`Sphere`, but not for :yref:`Facet` + :yref:`Sphere` -- if that is desired, an additional functor must be used:: InteractionLoop([ Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom() ],[],[]) Again, missing combination will cause given shape combinations to freely interpenetrate one another. #. :yref:`IGeom` type accepted by the ``Law2`` functor (below); it is the first part of functor's name after ``Law2`` (for instance, :yref:`Law2_ScGeom_CpmPhys_Cpm` accepts :yref:`ScGeom`). Ip2 functors ^^^^^^^^^^^^ ``Ip2`` functors (deriving from :yref:`IPhysFunctor`) must be chosen depending on #. :yref:`Material` combinations within the simulation. In most cases, ``Ip2`` functors handle 2 instances of the same :yref:`Material` class (such as :yref:`Ip2_FrictMat_FrictMat_FrictPhys` for 2 bodies with :yref:`FrictMat`) #. :yref:`IPhys` accepted by the constitutive law (``Law2`` functor), which is the second part of the ``Law2`` functor's name (e.g. :yref:`Law2_ScGeom_FrictPhys_CundallStrack` accepts :yref:`FrictPhys`) .. note:: Unlike with ``Bo1`` and ``Ig2`` functors, unhandled combination of :yref:`Materials` is an error condition signaled by an exception. Law2 functor(s) ^^^^^^^^^^^^^^^^ ``Law2`` functor was the ultimate criterion for the choice of ``Ig2`` and ``Ip2`` functors; there are no restrictions on its choice in itself, as it only applies forces without creating new objects. In most simulations, only one ``Law2`` functor will be in use; it is possible, though, to have several of them, dispatched based on combination of :yref:`IGeom` and :yref:`IPhys` produced previously by ``Ig2`` and ``Ip2`` functors respectively (in turn based on combination of :yref:`Shapes` and :yref:`Materials`). .. note:: As in the case of ``Ip2`` functors, receiving a combination of :yref:`IGeom` and :yref:`IPhys` which is not handled by any ``Law2`` functor is an error. .. warning:: Many ``Law2`` exist in Yade, and new ones can appear at any time. In some cases different functors are only different implementations of the same contact law (e.g. :yref:`Law2_ScGeom_FrictPhys_CundallStrack` and :yref:`Law2_L3Geom_FrictPhys_ElPerfPl`). Also, sometimes, the peculiarity of one functor may be reproduced as a special case of a more general one. Therefore, for a given constitutive behavior, the user may have the choice between different functors. It is strongly recommended to favor the most used and most validated implementation when facing such choice. A list of available functors classified from mature to unmaintained is updated `here `_ to guide this choice. Examples ^^^^^^^^ Let us give several example of the chain of created and accepted types. Basic DEM model ^^^^^^^^^^^^^^^^ Suppose we want to use the :yref:`Law2_ScGeom_FrictPhys_CundallStrack` constitutive law. We see that #. the ``Ig2`` functors must create :yref:`ScGeom`. If we have for instance :yref:`spheres` and :yref:`boxes` in the simulation, we will need functors accepting :yref:`Sphere` + :yref:`Sphere` and :yref:`Box` + :yref:`Sphere` combinations. We don't want interactions between boxes themselves (as a matter of fact, there is no such functor anyway). That gives us :yref:`Ig2_Sphere_Sphere_ScGeom` and :yref:`Ig2_Box_Sphere_ScGeom`. #. the ``Ip2`` functors should create :yref:`FrictPhys`. Looking at :yref:`InteractionPhysicsFunctors`, there is only :yref:`Ip2_FrictMat_FrictMat_FrictPhys`. That obliges us to use :yref:`FrictMat` for particles. The result will be therefore:: InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ) Concrete model ^^^^^^^^^^^^^^^ In this case, our goal is to use the :yref:`Law2_ScGeom_CpmPhys_Cpm` constitutive law. * We use :yref:`spheres` and :yref:`facets` in the simulation, which selects ``Ig2`` functors accepting those types and producing :yref:`ScGeom`: :yref:`Ig2_Sphere_Sphere_ScGeom` and :yref:`Ig2_Facet_Sphere_ScGeom`. * We have to use :yref:`Material` which can be used for creating :yref:`CpmPhys`. We find that :yref:`CpmPhys` is only created by :yref:`Ip2_CpmMat_CpmMat_CpmPhys`, which determines the choice of :yref:`CpmMat` for all particles. Therefore, we will use:: InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_CpmMat_CpmMat_CpmPhys()], [Law2_ScGeom_CpmPhys_Cpm()] ) Imposing conditions ==================== In most simulations, it is not desired that all particles float freely in space. There are several ways of imposing boundary conditions that block movement of all or some particles with regard to global space. Motion constraints ------------------ * :yref:`Body.dynamic` determines whether a body will be accelerated by :yref:`NewtonIntegrator`; it is mandatory to make it false for bodies with zero mass, where applying non-zero force would result in infinite displacement. :yref:`Facets` are case in the point: :yref:`facet` makes them non-dynamic by default, as they have zero volume and zero mass (this can be changed, by passing ``dynamic=True`` to :yref:`facet` or setting :yref:`Body.dynamic`; setting :yref:`State.mass` to a non-zero value must be done as well). The same is true for :yref:`wall`. Making sphere non-dynamic is achieved simply by:: b = sphere([x,y,z],radius,dynamic=False) b.dynamic=True #revert the previous * :yref:`State.blockedDOFs` permits selective blocking of any of 6 degrees of freedom in global space. For instance, a sphere can be made to move only in the xy plane by saying: .. ipython:: @suppress Yade [1]: O.reset() Yade [1]: O.bodies.append(sphere((0,0,0),1)) Yade [1]: O.bodies[0].state.blockedDOFs='zXY' In contrast to :yref:`Body.dynamic`, :yref:`blockedDOFs` will only block forces (and acceleration) in selected directions. Actually, ``b.dynamic=False`` is nearly only a shorthand for ``b.state.blockedDOFs=='xyzXYZ'`` . A subtle difference is that the former does reset the velocity components automaticaly, while the latest does not. If you prescribed linear or angular velocity, they will be applied regardless of :yref:`blockedDOFs`. It also implies that if the velocity is not zero when degrees of freedom are blocked via blockedDOFs assignements, the body will keep moving at the velocity it has at the time of blocking. The differences are shown below: .. ipython:: @suppress Yade [1]: O.reset() Yade [1]: b1 = sphere([0,0,0],1,dynamic=True) Yade [1]: b1.state.blockedDOFs Yade [1]: b1.state.vel = Vector3(1,0,0) #we want it to move... Yade [1]: b1.dynamic = False #... at a constant velocity Yade [1]: print b1.state.blockedDOFs, b1.state.vel Yade [1]: # oops, velocity has been reset when setting dynamic=False Yade [1]: b1.state.vel = (1,0,0) # we can still assign it now Yade [1]: print b1.state.blockedDOFs, b1.state.vel Yade [1]: b2 = sphere([0,0,0],1,dynamic=True) #another try Yade [1]: b2.state.vel = (1,0,0) Yade [1]: b2.state.blockedDOFs = "xyzXYZ" #this time we assign blockedDOFs directly, velocity is unchanged Yade [1]: print b2.state.blockedDOFs, b2.state.vel It might be desirable to constrain motion of some particles constructed from a generated sphere packing, following some condition, such as being at the bottom of a specimen; this can be done by looping over all bodies with a conditional:: for b in O.bodies: # block all particles with z coord below .5: if b.state.pos[2]<.5: b.dynamic=False Arbitrary spatial predicates introduced above can be expoited here as well:: from yade import pack pred=pack.inAlignedBox(lowerCorner,upperCorner) for b in O.bodies: if b.shape.name!=Sphere: continue # skip non-spheres # ask the predicate if we are inside if pred(b.state.pos,b.shape.radius): b.dynamic=False .. _imposing_motion_force: Imposing motion and forces -------------------------- Imposed velocity ^^^^^^^^^^^^^^^^ If a degree of freedom is blocked and a velocity is assigned along that direction (translational or rotational velocity), then the body will move at constant velocity. This is the simpler and recommended method to impose the motion of a body. This, for instance, will result in a constant velocity along $x$ (it can still be freely accelerated along $y$ and $z$):: O.bodies.append(sphere((0,0,0),1)) O.bodies[0].state.blockedDOFs='x' O.bodies[0].state.vel=(10,0,0) Conversely, modifying the position directly is likely to break Yade's algorithms, especially those related to collision detection and contact laws, as they are based on bodies velocities. Therefore, unless you really know what you are doing, don't do that for imposing a motion:: O.bodies.append(sphere((0,0,0),1)) O.bodies[0].state.blockedDOFs='x' O.bodies[0].state.pos=10*O.dt #REALLY BAD! Don't assign position Imposed force ^^^^^^^^^^^^^ Applying a force or a torque on a body is done via functions of the :yref:`ForceContainer`. It is as simple as this:: O.forces.addF(0,(1,0,0)) #applies for one step This way, the force applies for one time step only, and is resetted at the beginning of each step. For this reason, imposing a force at the begining of one step will have no effect at all, since it will be immediatly resetted. The only way is to place a :yref:`PyRunner` inside the simulation loop. Applying the force permanently is possible with another function (in this case it does not matter if the command comes at the begining of the time step):: O.forces.setPermF(0,(1,0,0)) #applies permanently The force will persist across iterations, until it is overwritten by another call to ``O.forces.setPermF(id,f)`` or erased by ``O.forces.reset(resetAll=True)``. The permanent force on a body can be checked with ``O.forces.permF(id)``. Boundary controllers -------------------- Engines deriving from :yref:`BoundaryController` impose boundary conditions during simulation, either directly, or by influencing several bodies. You are referred to their individual documentation for details, though you might find interesting in particular * :yref:`UniaxialStrainer` for applying strain along one axis at constant rate; useful for plotting strain-stress diagrams for uniaxial loading case. See :ysrc:`examples/concrete/uniax.py` for an example. * :yref:`TriaxialStressController` which applies prescribed stress/strain along 3 perpendicular axes on cuboid-shaped packing using 6 walls (:yref:`Box` objects) (:yref:`ThreeDTriaxialEngine` is generalized such that it allows independent value of stress along each axis) * :yref:`PeriTriaxController` for applying stress/strain along 3 axes independently, for simulations using periodic boundary conditions (:yref:`Cell`) Field appliers --------------- Engines deriving from :yref:`FieldApplier` acting on all particles. The one most used is :yref:`GravityEngine` applying uniform acceleration field (:yref:`GravityEngine` is deprecated, use :yref:`NewtonIntegrator.gravity` instead!). Partial engines --------------- Engines deriving from :yref:`PartialEngine` define the :yref:`ids` attribute determining bodies which will be affected. Several of them warrant explicit mention here: * :yref:`TranslationEngine` and :yref:`RotationEngine` for applying constant speed linear and rotational motion on subscribers. * :yref:`ForceEngine` and :yref:`TorqueEngine` applying given values of force/torque on subscribed bodies at every step. * :yref:`StepDisplacer` for applying generalized displacement delta at every timestep; designed for precise control of motion when testing constitutive laws on 2 particles. The real value of partial engines is if you need to prescribe complex types of force or displacement fields. For moving a body at constant velocity or for imposing a single force, the methods explained in `Imposing motion and forces`_ are much simpler. There are several interpolating engines (:yref:`InterpolatingDirectedForceEngine` for applying force with varying magnitude, :yref:`InterpolatingHelixEngine` for applying spiral displacement with varying angular velocity and possibly others); writing a new interpolating engine is rather simple using examples of those that already exist. Convenience features ========================= .. _labelingthings: Labeling things ---------------- Engines and functors can define that ``label`` attribute. Whenever the ``O.engines`` sequence is modified, python variables of those names are created/update; since it happens in the ``__builtins__`` namespaces, these names are immediately accessible from anywhere. This was used in :ref:`creating-interactions` to change interaction radius in multiple functors at once. .. warning:: Make sure you do not use label that will overwrite (or shadow) an object that you already use under that variable name. Take care not to use syntactically wrong names, such as "er*452" or "my engine"; only variable names permissible in Python can be used. Simulation tags ---------------- :yref:`Omega.tags` is a dictionary (it behaves like a dictionary, although the implementation in c++ is different) mapping keys to labels. Contrary to regular python dictionaries that you could create, * ``O.tags`` is *saved and loaded with simulation*; * ``O.tags`` has some values pre-initialized. After Yade startup, ``O.tags`` contains the following: .. ipython:: @suppress Yade [1]: O.reset() Yade [1]: dict(O.tags) # convert to real dictionary author Real name, username and machine as obtained from your system at simulation creation id Unique identifier of this Yade instance (or of the instance which created a loaded simulation). It is composed of date, time and process number. Useful if you run simulations in parallel and want to avoid overwriting each other's outputs; embed ``O.tags['id']`` in output filenames (either as directory name, or as part of the file's name itself) to avoid it. This is explained in :ref:`batch-output-separate` in detail. isoTime Time when simulation was created (with second resolution). d.id, id.d Simulation description and id joined by period (and vice-versa). Description is used in batch jobs; in non-batch jobs, these tags are identical to id. You can add your own tags by simply assigning value, with the restriction that the left-hand side object must be a string and must not contain ``=``. .. ipython:: Yade [2]: O.tags['anythingThat I lik3']='whatever' Yade [2]: O.tags['anythingThat I lik3'] Saving python variables ------------------------ Python variable lifetime is limited; in particular, if you save simulation, variables will be lost after reloading. Yade provides limited support for data persistence for this reason (internally, it uses special values of ``O.tags``). The functions in question are :yref:`saveVars` and :yref:`loadVars`. :yref:`saveVars` takes dictionary (variable names and their values) and a *mark* (identification string for the variable set); it saves the dictionary inside the simulation. These variables can be re-created (after the simulation was loaded from a XML file, for instance) in the ``yade.params.``\ *mark* namespace by calling :yref:`loadVars` with the same identification *mark*: .. ipython:: Yade [3]: a=45; b=pi/3 Yade [3]: saveVars('ab',a=a,b=b) # save simulation (we could save to disk just as well) Yade [3]: O.saveTmp() Yade [4]: O.loadTmp() Yade [4]: loadVars('ab') Yade [5]: yade.params.ab.a # import like this Yade [5]: from yade.params import ab Yade [6]: ab.a, ab.b # also possible Yade [5]: from yade.params import * Yade [6]: ab.a, ab.b Enumeration of variables can be tedious if they are many; creating local scope (which is a function definition in Python, for instance) can help:: def setGeomVars(): radius=a*4 thickness=22 p_t=4/3*pi dim=Vector3(1.23,2.2,3) # # define as much as you want here # it all appears in locals() (and nothing else does) # saveVars('geom',loadNow=True,**locals()) setGeomVars() from yade.params.geom import * # use the variables now .. note:: Only types that can be `pickled `_ can be passed to :yref:`saveVars`. ************************* Controlling simulation ************************* Tracking variables =================== Running python code ------------------- A special engine :yref:`PyRunner` can be used to periodically call python code, specified via the ``command`` parameter. Periodicity can be controlled by specifying computation time (``realPeriod``), virutal time (``virtPeriod``) or iteration number (``iterPeriod``). For instance, to print kinetic energy (using :yref:`kineticEnergy`) every 5 seconds, the following engine will be put to ``O.engines``:: PyRunner(command="print 'kinetic energy',kineticEnergy()",realPeriod=5) For running more complex commands, it is convenient to define an external function and only call it from within the engine. Since the ``command`` is run in the script's namespace, functions defined within scripts can be called. Let us print information on interaction between bodies 0 and 1 periodically:: def intrInfo(id1,id2): try: i=O.interactions[id1,id2] # assuming it is a CpmPhys instance print id1,id2,i.phys.sigmaN except: # in case the interaction doesn't exist (yet?) print "No interaction between",id1,id2 O.engines=[..., PyRunner(command="intrInfo(0,1)",realPeriod=5) ] More useful examples will be given below. The :yref:`yade.plot` module provides simple interface and storage for tracking various data. Although originally conceived for plotting only, it is widely used for tracking variables in general. The data are in :yref:`yade.plot.data` dictionary, which maps variable names to list of their values; the :yref:`yade.plot.addData` function is used to add them. .. ipython:: @suppress Yade [1]: O.reset() Yade [1]: from yade import plot Yade [1]: plot.data Yade [1]: plot.addData(sigma=12,eps=1e-4) # not adding sigma will add a NaN automatically # this assures all variables have the same number of records Yade [2]: plot.addData(eps=1e-3) # adds NaNs to already existing sigma and eps columns Yade [3]: plot.addData(force=1e3) Yade [4]: plot.data # retrieve only one column Yade [5]: plot.data['eps'] # get maximum eps Yade [5]: max(plot.data['eps']) New record is added to all columns at every time :yref:`yade.plot.addData` is called; this assures that lines in different columns always match. The special value ``nan`` or ``NaN`` (`Not a Number `_) is inserted to mark the record invalid. .. note:: It is not possible to have two columns with the same name, since data are stored as a dictionary. To record data periodically, use :yref:`PyRunner`. This will record the *z* coordinate and velocity of body #1, iteration number and simulation time (every 20 iterations):: O.engines=O.engines+[PyRunner(command='myAddData()', iterPeriod=20)] from yade import plot def myAddData(): b=O.bodies[1] plot.addData(z1=b.state.pos[2], v1=b.state.vel.norm(), i=O.iter, t=O.time) .. note:: Arbitrary string can be used as column label for :yref:`yade.plot.data`. If it cannot be used as keyword name for :yref:`yade.plot.addData` (since it is a python keyword (``for``), or has spaces inside (``my funny column``), you can pass dictionary to :yref:`yade.plot.addData` instead:: plot.addData(z=b.state.pos[2],**{'my funny column':b.state.vel.norm()}) An exception are columns having leading of trailing whitespaces. They are handled specially in :yref:`yade.plot.plots` and should not be used (see below). Labels can be conveniently used to access engines in the ``myAddData`` function:: O.engines=[..., UniaxialStrainer(...,label='strainer') ] def myAddData(): plot.addData(sigma=strainer.avgStress,eps=strainer.strain) In that case, naturally, the labeled object must define attributes which are used (:yref:`UniaxialStrainer.strain` and :yref:`UniaxialStrainer.avgStress` in this case). Plotting variables ------------------- Above, we explained how to track variables by storing them using :yref:`yade.plot.addData`. These data can be readily used for plotting. Yade provides a simple, quick to use, plotting in the :yref:`yade.plot` module. Naturally, since direct access to underlying data is possible via :yref:`yade.plot.data`, these data can be processed in any way. The :yref:`yade.plot.plots` dictionary is a simple specification of plots. Keys are x-axis variable, and values are tuple of y-axis variables, given as strings that were used for :yref:`yade.plot.addData`; each entry in the dictionary represents a separate figure:: plot.plots={ 'i':('t',), # plot t(i) 't':('z1','v1') # z1(t) and v1(t) } Actual plot using data in :yref:`yade.plot.data` and plot specification of :yref:`yade.plot.plots` can be triggered by invoking the :yref:`yade.plot.plot` function. Live updates of plots ^^^^^^^^^^^^^^^^^^^^^ Yade features live-updates of figures during calculations. It is controlled by following settings: * :yref:`yade.plot.live` - By setting ``yade.plot.live=True`` you can watch the plot being updated while the calculations run. Set to ``False`` otherwise. * :yref:`yade.plot.liveInterval` - This is the interval in seconds between the plot updates. * :yref:`yade.plot.autozoom` - When set to ``True`` the plot will be automatically rezoomed. Controlling line properties ^^^^^^^^^^^^^^^^^^^^^^^^^^^ In this subsection let us use a *basic complete script* like :ysrc:`examples/simple-scene/simple-scene-plot.py`, which we will later modify to make the plots prettier. Line of interest from that file is, and generates a picture presented below:: plot.plots={'i':('t'),'t':('z_sph',None,('v_sph','go-'),'z_sph_half')} .. figure:: fig/simple-scene-plot-1.* Figure generated by :ysrc:`examples/simple-scene/simple-scene-plot.py`. The line plots take an optional second string argument composed of a line color (eg. ``'r'``, ``'g'`` or ``'b'``), a line style (eg. ``'-'``, ``'–-'`` or ``':'``) and a line marker (``'o'``, ``'s'`` or ``'d'``). A red dotted line with circle markers is created with 'ro:' argument. For a listing of all options please have a look at http://matplotlib.sourceforge.net/api/pyplot_api.html#matplotlib.pyplot.plot For example using following plot.plots() command, will produce a following graph:: plot.plots={'i':(('t','xr:'),),'t':(('z_sph','r:'),None,('v_sph','g--'),('z_sph_half','b-.'))} .. figure:: fig/simple-scene-plot-2.* Figure generated by changing parameters to plot.plots as above. And this one will produce a following graph:: plot.plots={'i':(('t','xr:'),),'t':(('z_sph','Hr:'),None,('v_sph','+g--'),('z_sph_half','*b-.'))} .. figure:: fig/simple-scene-plot-3.* Figure generated by changing parameters to plot.plots as above. .. note:: You can learn more in matplotlib tutorial http://matplotlib.sourceforge.net/users/pyplot_tutorial.html and documentation http://matplotlib.sourceforge.net/users/pyplot_tutorial.html#controlling-line-properties .. note:: Please note that there is an extra ``,`` in ``'i':(('t','xr:'),)``, otherwise the ``'xr:'`` wouldn't be recognized as a line style parameter, but would be treated as an extra data to plot. Controlling text labels ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ It is possible to use TeX syntax in plot labels. For example using following two lines in :ysrc:`examples/simple-scene/simple-scene-plot.py`, will produce a following picture:: plot.plots={'i':(('t','xr:'),),'t':(('z_sph','r:'),None,('v_sph','g--'),('z_sph_half','b-.'))} plot.labels={'z_sph':'\$z_{sph}\$' , 'v_sph':'\$v_{sph}\$' , 'z_sph_half':'\$z_{sph}/2\$'} .. figure:: fig/simple-scene-plot-4.* Figure generated by :ysrc:`examples/simple-scene/simple-scene-plot.py`, with TeX labels. Greek letters are simply a ``'\$\alpha$'``, ``'\$\beta\$'`` etc. in those labels. To change the font style a following command could be used:: yade.plot.matplotlib.rc('mathtext', fontset='stixsans') But this is not part of yade, but a part of matplotlib, and if you want something more complex you really should have a look at matplotlib users manual http://matplotlib.sourceforge.net/users/index.html Multiple figures ^^^^^^^^^^^^^^^^^ Since :yref:`yade.plot.plots` is a dictionary, multiple entries with the same key (x-axis variable) would not be possible, since they overwrite each other: .. ipython:: Yade [1]: plot.plots={ ...: 'i':('t',), ...: 'i':('z1','v1') ...: } Yade [2]: plot.plots You can, however, distinguish them by prepending/appending space to the x-axis variable, which will be removed automatically when looking for the variable in :yref:`yade.plot.data` -- both $x$-axes will use the ``i`` column: .. ipython:: Yade [1]: plot.plots={ ...: 'i':('t',), ...: 'i ':('z1','v1') # note the space in 'i ' ...: } Yade [2]: plot.plots Split y1 y2 axes ^^^^^^^^^^^^^^^^^ To avoid big range differences on the $y$ axis, it is possible to have left and right $y$ axes separate (like ``axes x1y2`` in gnuplot). This is achieved by inserting ``None`` to the plot specifier; variables coming before will be plot normally (on the left *y*-axis), while those after will appear on the right:: plot.plots={'i':('z1',None,'v1')} Exporting ^^^^^^^^^ Plots can be exported to external files for later post-processing via that :yref:`yade.plot.saveGnuplot` function. Note that all data you added via plot.addData is saved - even data that you don't plot live during simulation. By editing the generated .gnuplot file you can plot any of the added Data afterwards. * Data file is saved (compressed using bzip2) separately from the gnuplot file, so any other programs can be used to process them. In particular, the ``numpy.genfromtxt`` (`documented here `_) can be useful to import those data back to python; the decompression happens automatically. * The gnuplot file can be run through gnuplot to produce the figure; see :yref:`yade.plot.saveGnuplot` documentation for details. Stop conditions ================ For simulations with pre-determined number of steps, number of steps can be prescribed: # absolute iteration number O.stopAtIter=35466 O.run() O.wait() or :: # number of iterations to run from now O.run(35466,True) # wait=True causes the simulation to run 35466 iterations, then stopping. Frequently, decisions have to be made based on evolution of the simulation itself, which is not yet known. In such case, a function checking some specific condition is called periodically; if the condition is satisfied, ``O.pause`` or other functions can be called to stop the stimulation. See documentation for :yref:`Omega.run`, :yref:`Omega.pause`, :yref:`Omega.step`, :yref:`Omega.stopAtIter` for details. For simulations that seek static equilibrium, the :yref:`unbalancedForce` can provide a useful metrics (see its documentation for details); for a desired value of ``1e-2`` or less, for instance, we can use:: def checkUnbalanced(): if unbalancedForce<1e-2: O.pause() O.engines=O.engines+[PyRunner(command="checkUnbalanced()",iterPeriod=100)] # this would work as well, without the function defined apart: # PyRunner(command="if unablancedForce<1e-2: O.pause()",iterPeriod=100) O.run(); O.wait() # will continue after O.pause() will have been called Arbitrary functions can be periodically checked, and they can also use history of variables tracked via :yref:`yade.plot.addData`. For example, this is a simplified version of damage control in :ysrc:`examples/concrete/uniax.py`; it stops when current stress is lower than half of the peak stress:: O.engines=[..., UniaxialStrainer=(...,label='strainer'), PyRunner(command='myAddData()',iterPeriod=100), PyRunner(command='stopIfDamaged()',iterPeriod=100) ] def myAddData(): plot.addData(t=O.time,eps=strainer.strain,sigma=strainer.stress) def stopIfDamaged(): currSig=plot.data['sigma'][-1] # last sigma value maxSig=max(plot.data['sigma']) # maximum sigma value # print something in any case, so that we know what is happening print plot.data['eps'][-1],currSig if currSig<.5*maxSig: print "Damaged, stopping" print 'gnuplot',plot.saveGnuplot(O.tags['id']) import sys sys.exit(0) O.run(); O.wait() # this place is never reached, since we call sys.exit(0) directly .. _checkpointing: Checkpoints ------------ Occasionally, it is useful to revert to simulation at some past point and continue from it with different parameters. For instance, tension/compression test will use the same initial state but load it in 2 different directions. Two functions, :yref:`Omega.saveTmp` and :yref:`Omega.loadTmp` are provided for this purpose; *memory* is used as storage medium, which means that saving is faster, and also that the simulation will disappear when Yade finishes. :: O.saveTmp() # do something O.saveTmp('foo') O.loadTmp() # loads the first state O.loadTmp('foo') # loads the second state .. warning:: ``O.loadTmp`` cannot be called from inside an engine, since *before* loading a simulation, the old one must finish the current iteration; it would lead to deadlock, since ``O.loadTmp`` would wait for the current iteration to finish, while the current iteration would be blocked on ``O.loadTmp``. A special trick must be used: a separate function to be run after the current iteration is defined and is invoked from an independent thread launched only for that purpose:: O.engines=[...,PyRunner('myFunc()',iterPeriod=345)] def myFunc(): if someCondition: import thread # the () are arguments passed to the function thread.start_new_thread(afterIterFunc,()) def afterIterFunc(): O.pause(); O.wait() # wait till the iteration really finishes O.loadTmp() O.saveTmp() O.run() .. _remoteaccess: Remote control =============== Yade can be controlled remotely over network. At yade startup, the following lines appear, among other messages:: TCP python prompt on localhost:9000, auth cookie `dcekyu' TCP info provider on localhost:21000 They inform about 2 ports on which connection of 2 different kind is accepted. Python prompt -------------- ``TCP python prompt`` is telnet server with authenticated connection, providing full python command-line. It listens on port 9000, or higher if already occupied (by another yade instance, for example). Using the authentication cookie, connection can be made using telnet:: \$ telnet localhost 9000 Trying 127.0.0.1... Connected to localhost. Escape character is '^]'. Enter auth cookie: dcekyu __ __ ____ __ _____ ____ ____ \ \ / /_ _| _ \ ___ ___ / / |_ _/ ___| _ \ \ V / _` | | | |/ _ \ / _ \ / / | || | | |_) | | | (_| | |_| | __/ | (_) / / | || |___| __/ |_|\__,_|____/ \___| \___/_/ |_| \____|_| (connected from 127.0.0.1:40372) >>> The python pseudo-prompt ``>>>`` lets you write commands to manipulate simulation in variety of ways as usual. Two things to notice: #. The new python interpreter (``>>>``) lives in a namespace separate from ``Yade [1]:`` command-line. For your convenience, ``from yade import *`` is run in the new python instance first, but local and global variables are not accessible (only builtins are). #. The (fake) ``>>>`` interpreter does not have rich interactive feature of IPython, which handles the usual command-line ``Yade [1]:``; therefore, you will have no command history, ``?`` help and so on. .. note:: By giving access to python interpreter, full control of the system (including reading user's files) is possible. For this reason, **connection are only allowed from localhost**, not over network remotely. Of course you can log into the system via SSH over network to get remote access. .. warning:: Authentication cookie is trivial to crack via bruteforce attack. Although the listener stalls for 5 seconds after every failed login attempt (and disconnects), the cookie could be guessed by trial-and-error during very long simulations on a shared computer. Info provider ------------- ``TCP Info provider`` listens at port 21000 (or higher) and returns some basic information about current simulation upon connection; the connection terminates immediately afterwards. The information is python dictionary represented as string (serialized) using standard `pickle `_ module. This functionality is used by the batch system (described below) to be informed about individual simulation progress and estimated times. If you want to access this information yourself, you can study :ysrc:`core/main/yade-batch.in` for details. Batch queuing and execution (yade-batch) ======================================== Yade features light-weight system for running one simulation with different parameters; it handles assignment of parameter values to python variables in simulation script, scheduling jobs based on number of available and required cores and more. The whole batch consists of 2 files: simulation script regular Yade script, which calls :yref:`readParamsFromTable` to obtain parameters from parameter table. In order to make the script runnable outside the batch, :yref:`readParamsFromTable` takes default values of parameters, which might be overridden from the parameter table. :yref:`readParamsFromTable` knows which parameter file and which line to read by inspecting the ``PARAM_TABLE`` environment variable, set by the batch system. parameter table simple text file, each line representing one parameter set. This file is read by :yref:`readParamsFromTable` (using :yref:`TableParamReader` class), called from simulation script, as explained above. For better reading of the text file you can make use of tabulators, these will be ignored by :yref:`readParamsFromTable`. Parameters are not restricted to numerical values. You can also make use of strings by "quoting" them (' ' may also be used instead of " "). This can be useful for nominal parameters. The batch can be run as :: yade-batch parameters.table simulation.py and it will intelligently run one simulation for each parameter table line. A minimal example is found in :ysrc:`examples/test/batch/params.table` and :ysrc:`examples/test/batch/sim.py`, another example follows. Example -------- Suppose we want to study influence of parameters *density* and *initialVelocity* on position of a sphere falling on fixed box. We create parameter table like this:: description density initialVelocity # first non-empty line are column headings reference 2400 10 hi_v = 20 # = to use value from previous line lo_v = 5 # comments are allowed hi_rho 5000 10 # blank lines as well: hi_rho_v = 20 hi_rh0_lo_v = 5 Each line give one combination of these 2 parameters and assigns (which is optional) a *description* of this simulation. In the simulation file, we read parameters from table, at the beginning of the script; each parameter has default value, which is used if not specified in the parameters file: .. code-block:: python readParamsFromTable( gravity=-9.81, density=2400, initialVelocity=20, noTableOk=True # use default values if not run in batch ) from yade.params.table import * print gravity, density, initialVelocity after the call to :yref:`readParamsFromTable`, corresponding python variables are created in the ``yade.params.table`` module and can be readily used in the script, e.g. .. code-block:: python GravityEngine(gravity=(0,0,gravity)) Let us see what happens when running the batch:: \$ yade-batch batch.table batch.py Will run `/usr/local/bin/yade-trunk' on `batch.py' with nice value 10, output redirected to `batch.@.log', 4 jobs at a time. Will use table `batch.table', with available lines 2, 3, 4, 5, 6, 7. Will use lines 2 (reference), 3 (hi_v), 4 (lo_v), 5 (hi_rho), 6 (hi_rho_v), 7 (hi_rh0_lo_v). Master process pid 7030 These lines inform us about general batch information: `nice `_ level, log file names, how many cores will be used (4); table name, and line numbers that contain parameters; finally, which lines will be used; master `PID `_ is useful for killing (stopping) the whole batch with the ``kill`` command. :: Job summary: #0 (reference/4): PARAM_TABLE=batch.table:2 DISPLAY= /usr/local/bin/yade-trunk --threads=4 --nice=10 -x batch.py > batch.reference.log 2>&1 #1 (hi_v/4): PARAM_TABLE=batch.table:3 DISPLAY= /usr/local/bin/yade-trunk --threads=4 --nice=10 -x batch.py > batch.hi_v.log 2>&1 #2 (lo_v/4): PARAM_TABLE=batch.table:4 DISPLAY= /usr/local/bin/yade-trunk --threads=4 --nice=10 -x batch.py > batch.lo_v.log 2>&1 #3 (hi_rho/4): PARAM_TABLE=batch.table:5 DISPLAY= /usr/local/bin/yade-trunk --threads=4 --nice=10 -x batch.py > batch.hi_rho.log 2>&1 #4 (hi_rho_v/4): PARAM_TABLE=batch.table:6 DISPLAY= /usr/local/bin/yade-trunk --threads=4 --nice=10 -x batch.py > batch.hi_rho_v.log 2>&1 #5 (hi_rh0_lo_v/4): PARAM_TABLE=batch.table:7 DISPLAY= /usr/local/bin/yade-trunk --threads=4 --nice=10 -x batch.py > batch.hi_rh0_lo_v.log 2>&1 displays all jobs with command-lines that will be run for each of them. At this moment, the batch starts to be run. :: #0 (reference/4) started on Tue Apr 13 13:59:32 2010 #0 (reference/4) done (exit status 0), duration 00:00:01, log batch.reference.log #1 (hi_v/4) started on Tue Apr 13 13:59:34 2010 #1 (hi_v/4) done (exit status 0), duration 00:00:01, log batch.hi_v.log #2 (lo_v/4) started on Tue Apr 13 13:59:35 2010 #2 (lo_v/4) done (exit status 0), duration 00:00:01, log batch.lo_v.log #3 (hi_rho/4) started on Tue Apr 13 13:59:37 2010 #3 (hi_rho/4) done (exit status 0), duration 00:00:01, log batch.hi_rho.log #4 (hi_rho_v/4) started on Tue Apr 13 13:59:38 2010 #4 (hi_rho_v/4) done (exit status 0), duration 00:00:01, log batch.hi_rho_v.log #5 (hi_rh0_lo_v/4) started on Tue Apr 13 13:59:40 2010 #5 (hi_rh0_lo_v/4) done (exit status 0), duration 00:00:01, log batch.hi_rh0_lo_v.log information about job status changes is being printed, until:: All jobs finished, total time 00:00:08 Log files: batch.reference.log batch.hi_v.log batch.lo_v.log batch.hi_rho.log batch.hi_rho_v.log batch.hi_rh0_lo_v.log Bye. .. _batch-output-separate: Separating output files from jobs ---------------------------------- As one might output data to external files during simulation (using classes such as :yref:`VTKRecorder`), it is important to name files in such way that they are not overwritten by next (or concurrent) job in the same batch. A special tag ``O.tags['id']`` is provided for such purposes: it is comprised of date, time and PID, which makes it always unique (e.g. ``20100413T144723p7625``); additional advantage is that alphabetical order of the ``id`` tag is also chronological. To add the used parameter set or the description of the job, if set, you could add O.tags['params'] to the filename. For smaller simulations, prepending all output file names with ``O.tags['id']`` can be sufficient: .. code-block:: python saveGnuplot(O.tags['id']) For larger simulations, it is advisable to create separate directory of that name first, putting all files inside afterwards: .. code-block:: python os.mkdir(O.tags['id']) O.engines=[ # … VTKRecorder(fileName=O.tags['id']+'/'+'vtk'), # … ] # … O.saveGnuplot(O.tags['id']+'/'+'graph1') Controlling parallel computation -------------------------------- Default total number of available cores is determined from ``/proc/cpuinfo`` (provided by Linux kernel); in addition, if ``OMP_NUM_THREADS`` environment variable is set, minimum of these two is taken. The ``-j``/``--jobs`` option can be used to override this number. By default, each job uses all available cores for itself, which causes jobs to be effectively run in parallel. Number of cores per job can be globally changed via the ``--job-threads`` option. Table column named ``!OMP_NUM_THREADS`` (``!`` prepended to column generally means to assign *environment variable*, rather than python variable) controls number of threads for each job separately, if it exists. If number of cores for a job exceeds total number of cores, warning is issued and only the total number of cores is used instead. Merging gnuplot from individual jobs ------------------------------------ Frequently, it is desirable to obtain single figure for all jobs in the batch, for comparison purposes. Somewhat heiristic way for this functionality is provided by the batch system. ``yade-batch`` must be run with the ``--gnuplot`` option, specifying some file name that will be used for the merged figure:: yade-trunk --gnuplot merged.gnuplot batch.table batch.py Data are collected in usual way during the simulation (using :yref:`yade.plot.addData`) and saved to gnuplot file via :yref:`yade.plot.saveGnuplot` (it creates 2 files: gnuplot command file and compressed data file). The batch system *scans*, once the job is finished, log file for line of the form ``gnuplot [something]``. Therefore, in order to print this *magic line* we put:: print 'gnuplot',plot.saveGnuplot(O.tags['id']) and the end of the script (even after waitIfBatch()) , which prints:: gnuplot 20100413T144723p7625.gnuplot to the output (redirected to log file). This file itself contains single graph: .. _img-yade-multi-gnuplot-single: .. figure:: fig/yade-multi-gnuplot-single.* Figure from single job in the batch. At the end, the batch system knows about all gnuplot files and tries to merge them together, by assembling the ``merged.gnuplot`` file. .. _img-yade-multi-gnuplot-merged: .. figure:: fig/yade-multi-gnuplot-merged.* Merged figure from all jobs in the batch. Note that labels are prepended by job description to make lines distinguishable. HTTP overview -------------- While job is running, the batch system presents progress via simple HTTP server running at port 9080, which can be acessed from regular web browser by requesting the ``http://localhost:9080`` URL. This page can be accessed remotely over network as well. .. _img-yade-multi-summary: .. figure:: fig/yade-multi-summary.* Summary page available at port 9080 as batch is processed (updates every 5 seconds automatically). Possible job statuses are pending, running, done, failed. *************** Postprocessing *************** 3d rendering & videos ====================== There are multiple ways to produce a video of simulation: #. Capture screen output (the 3d rendering window) during the simulation − there are tools available for that (such as `Istanbul `_ or `RecordMyDesktop `_, which are also packaged for most Linux distributions). The output is "what you see is what you get", with all the advantages and disadvantages. #. Periodic frame snapshot using :yref:`SnapshotEngine` (see :ysrc:`examples/bulldozer/bulldozer.py` for a full example):: O.engines=[ #... SnapshotEngine(iterPeriod=100,fileBase='/tmp/bulldozer-',viewNo=0,label='snapshooter') ] which will save numbered files like ``/tmp/bulldozer-0000.png``. These files can be processed externally (with `mencoder `_ and similar tools) or directly with the :yref:`makeVideo`:: makeVideo(frameSpec,out,renameNotOverwrite=True,fps=24,kbps=6000,bps=None) The video is encoded using the default mencoder codec (mpeg4). #. Specialized post-processing tools, notably `Paraview `_. This is described in more detail in the following section. Paraview --------- Saving data during the simulation ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ Paraview is based on the `Visualization Toolkit `_, which defines formats for saving various types of data. One of them (with the ``.vtu`` extension) can be written by a special engine :yref:`VTKRecorder`. It is added to the simulation loop:: O.engines=[ # ... VTKRecorder(iterPeriod=100,recorders=['spheres','facets','colors'],fileName='/tmp/p1-') ] * :yref:`iterPeriod` determines how often to save simulation data (besides :yref:`iterPeriod`, you can also use :yref:`virtPeriod` or :yref:`realPeriod`). If the period is too high (and data are saved only few times), the video will have few frames. * :yref:`fileName` is the prefix for files being saved. In this case, output files will be named ``/tmp/p1-spheres.0.vtu`` and ``/tmp/p1-facets.0.vtu``, where the number is the number of iteration; many files are created, putting them in a separate directory is advisable. * :yref:`recorders` determines what data to save :yref:`yade.exporter.VTKExporter` plays a similar role, with the difference that it is more flexible. It will save any user defined variable associated to the bodies. Loading data into Paraview ^^^^^^^^^^^^^^^^^^^^^^^^^^ All sets of files (``spheres``, ``facets``, …) must be opened one-by-one in Paraview. The open dialogue automatically collapses numbered files in one, making it easy to select all of them: .. _img-paraview-open-files: .. figure:: fig/paraview-open-files.png Click on the "Apply" button in the "Object inspector" sub-window to make loaded objects visible. You can see tree of displayed objects in the "Pipeline browser": .. _img-paraview-rendering-apply: .. figure:: fig/paraview-rendering-apply.png Rendering spherical particles. Glyphs """"""""""""""""""""""""""""""""""""""""""" .. |paraview-glyph-icon| image:: fig/paraview-glyph-icon.png Spheres will only appear as points. To make them look as spheres, you have to add "glyph" to the ``p1-spheres.*`` item in the pipeline using the |paraview-glyph-icon| icon. Then set (in the Object inspector) * "Glyph type" to *Sphere* * "Radius" to *1* * "Scale mode" to *Scalar* (*Scalar* is set above to be the *radii* value saved in the file, therefore spheres with radius *1* will be scaled by their true radius) * "Set scale factor" to *1* * optionally uncheck "Mask points" and "Random mode" (they make some particles not to be rendered for performance reasons, controlled by the "Maximum Number of Points") After clicking "Apply", spheres will appear. They will be rendered over the original white points, which you can disable by clicking on the eye icon next to ``p1-spheres.*`` in the Pipeline browser. Rendering spherical particles. PointSprite """"""""""""""""""""""""""""""""""""""""""" Another opportunity to display spheres is an using *PointSprite* plugin. This technique requires much less RAM in comparison to Glyphs. * "Tools -> Manage Plugins" * "PointSprite_Plugin -> Load selected -> Close" * Load VTU-files * "Representation -> Point Sprite" * "Point Sprite -> Scale By -> radii" * "Edit Radius Transfer Function -> Proportional -> Multiplier = 1.0 -> Close" Rendering interactions as force chain """"""""""""""""""""""""""""""""""""""""""" Data saved by ``VTKRecorder`` (the steps below generates cones rahter than tubes) or ``export.VTKExporter(...).exportInteractions(what=[('forceN','i.phys.normalForce().norm()')])`` (the steps below generates per interaction tubes with constant radius): * Load interactions VTP or VTK files * Filters -> Cell Data To Point Data * Filters -> Tube * Set color by "forceN" * Set "Vary Radius" to "By Scalar" * Set "Radius" and "Radius Factor" such that the result looks OK (in 3D postprocessing tutorial script, Radius=0.0005 and Radius Factor=100 looks reasonably) Facet transparency """"""""""""""""""" If you want to make facet objects transparent, select ``p1-facets.*`` in the Pipeline browser, then go to the Object inspector on the Display tab. Under "Style", you can set the "Opacity" value to something smaller than 1. Animation """""""""" You can move between frames (snapshots that were saved) via the "Animation" menu. After setting the view angle, zoom etc to your satisfaction, the animation can be saved with *File/Save animation*. Micro-stress and micro-strain ============================= It is sometimes useful to visualize a DEM simulation through equivalent strain fields or stress fields. This is possible with :yref:`TesselationWrapper`. This class handles the triangulation of spheres in a scene, build tesselation on request, and give access to computed quantities: volume, porosity and local deformation for each sphere. The definition of microstrain and microstress is at the scale of particle-centered subdomains shown below, as explained in [Catalano2014a]_ . .. figure:: fig/micro-domains.* Micro-strain ------------ Below is an output of the :yref:`defToVtk` function visualized with paraview (in this case Yade's TesselationWrapper was used to process experimental data obtained on sand by Edward Ando at Grenoble University, 3SR lab.). The output is visualized with paraview, as explained in the previous section. Similar results can be generated from simulations: .. code-block:: python tt=TriaxialTest() tt.generate("test.yade") O.load("test.yade") O.run(100,True) TW=TesselationWrapper() TW.triangulate() #compute regular Delaunay triangulation, don’t construct tesselation TW.computeVolumes() #will silently tesselate the packing, then compute volume of each Voronoi cell TW.volume(10) #get volume associated to sphere of id 10 TW.setState(0) #store current positions internaly for later use as the "0" state O.run(100,True) #make particles move a little (let's hope they will!) TW.setState(1) #store current positions internaly in the "1" (deformed) state #Now we can define strain by comparing states 0 and 1, and average them at the particles scale TW.defToVtk("strain.vtk") .. figure:: fig/localstrain.* Micro-stress ------------ Stress fields can be generated by combining the volume returned by TesselationWrapper to per-particle stress given by :yref:`bodyStressTensors`. Since the stress $\sigma$ from bodyStressTensor implies a division by the volume $V_b$ of the solid particle, one has to re-normalize it in order to obtain the micro-stress as defined in [Catalano2014a]_ (equation 39 therein), i.e. $\overline{\sigma}^k = \sigma^k \times V_b^k / V_{\sigma}^k$ where $V_{\sigma}^k$ is the volume assigned to particle $k$ in the tesselation. For instance: .. code-block:: python #"b" being a body TW=TesselationWrapper() TW.computeVolumes() s=bodyStressTensors() stress = s[b.id]**4.*pi/3.*b.shape.radius**3/TW.volume(b.id) As any other value, the stress can be exported to a vtk file for display in Paraview using :yref:`yade.export.VTKExporter`. ****************************** Python specialties and tricks ****************************** Importing Yade in other Python applications =========================================== Yade can be imported in other Python applications. To do so, you need somehow to make yade executable .py extended. The easiest way is to create a symbolic link, i.e. (suppose your Yade executable file is called "yade-trunk" and you want make it "yadeimport.py"): .. code-block:: console \$ cd /path/where/you/want/yadeimport \$ ln -s /path/to/yade/executable/yade-trunk yadeimport.py Then you need to make your yadeimport.py findable by Python. You can export PYTHONPATH environment variable, or simply use sys.path directly in Python script: .. code-block:: python import sys sys.path.append('/path/where/you/want/yadeimport') from yadeimport import * print Matrix3(1,2,3, 4,5,6, 7,8,9) print O.bodies # any other Yade code .. perhaps turn this section into a list of FAQs on python as gathered from the yade-users list? ************** Extending Yade ************** * new particle shape * new constitutive law **************** Troubleshooting **************** Crashes ======= It is possible that you encounter crash of Yade, i.e. Yade terminates with error message such as :: Segmentation fault (core dumped) without further explanation. Frequent causes of such conditions are * program error in Yade itself; * fatal condition in your particular simulation (such as impossible dispatch); * problem with graphics card driver. Try to reproduce the error (run the same script) with debug-enabled version of Yade. Debugger will be automatically launched at crash, showing backtrace of the code (in this case, we triggered crash by hand):: Yade [1]: import os,signal Yade [2]: os.kill(os.getpid(),signal.SIGSEGV) SIGSEGV/SIGABRT handler called; gdb batch file is `/tmp/yade-YwtfRY/tmp-0' GNU gdb (GDB) 7.1-ubuntu Copyright (C) 2010 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Type "show copying" and "show warranty" for details. This GDB was configured as "x86_64-linux-gnu". For bug reporting instructions, please see: . [Thread debugging using libthread_db enabled] [New Thread 0x7f0fb1268710 (LWP 16471)] [New Thread 0x7f0fb29f2710 (LWP 16470)] [New Thread 0x7f0fb31f3710 (LWP 16469)] … What looks as cryptic message is valuable information for developers to locate source of the bug. In particular, there is (usually) line ````; lines below it are source of the bug (at least very likely so):: Thread 1 (Thread 0x7f0fcee53700 (LWP 16465)): #0 0x00007f0fcd8f4f7d in __libc_waitpid (pid=16497, stat_loc=, options=0) at ../sysdeps/unix/sysv/linux/waitpid.c:41 #1 0x00007f0fcd88c7e9 in do_system (line=) at ../sysdeps/posix/system.c:149 #2 0x00007f0fcd88cb20 in __libc_system (line=) at ../sysdeps/posix/system.c:190 #3 0x00007f0fcd0b4b23 in crashHandler (sig=11) at core/main/pyboot.cpp:45 #4 #5 0x00007f0fcd87ed57 in kill () at ../sysdeps/unix/syscall-template.S:82 #6 0x000000000051336d in posix_kill (self=, args=) at ../Modules/posixmodule.c:4046 #7 0x00000000004a7c5e in call_function (f=Frame 0x1c54620, for file , line 1, in (), throwflag=) at ../Python/ceval.c:3750 #8 PyEval_EvalFrameEx (f=Frame 0x1c54620, for file , line 1, in (), throwflag=) at ../Python/ceval.c:2412 If you think this might be error in Yade, file a bug report as explained below. Do not forget to attach *full* yade output from terminal, including startup messages and debugger output -- select with right mouse button, with middle button paste the bugreport to a file and attach it. Attach your simulation script as well. Reporting bugs ============== Bugs are general name for defects (functionality shortcomings, misdocumentation, crashes) or feature requests. They are tracked at http://bugs.launchpad.net/yade. When reporting a new bug, be as specific as possible; state version of yade you use, system version and so on, as explained in the above section on crashes. Getting help ============= Questions and answers --------------------- Please use Launchpad interface at https://answers.launchpad.net/yade/ for asking questions about Yade. In case you're not familiar with computer oriented discussion lists, please read `this wiki page `_ (a Yade-oriented and shortened version of `How To Ask Questions The Smart Way `_) before posting, in order to increase your chances getting help. Do not forget to state what *version* of Yade you use (shown when you start Yade), whether you installed it from source code or a package, what operating system (such as Ubuntu 10.04), and if you have done any local modifications to source code in case of compiled version. Mailing lists -------------- In addition to the Q&A Launchpad interface, Yade has two mailing-lists. Both are hosted at http://www.launchpad.net and before posting, you must register to Launchpad and subscribe to the list by adding yourself to "team" of the same name running the list. yade-users@lists.launchpad.net is a general discussion list for all Yade users. Add yourself to `yade-users team `_ so that you can post messages. `List archive `_ is available. yade-dev@lists.launchpad.net is for discussions about Yade development; you must be member of `yade-dev team `_ to post. This list is `archived `_ as well. Wiki ----- http://www.yade-dem.org/wiki/ Private and/or paid support ---------------------------- You might contact developers by their private mail (rather than by mailing list) if you do not want to disclose details on the mailing list. This is also a suitable method for proposing financial reward for implementation of a substantial feature that is not yet in Yade -- typically, though, we will request this feature to be part of the public codebase once completed, so that the rest of the community can benefit from it as well. trunk-2017.01a/doc/sphinx/yade.bodiesHandling.rst000066400000000000000000000002671304022710500216320ustar00rootroot00000000000000.. _yade.bodiesHandling: yade.bodiesHandling module ========================================== .. automodule:: yade.bodiesHandling :members: :undoc-members: :inherited-members: trunk-2017.01a/doc/sphinx/yade.geom.rst000066400000000000000000000002311304022710500176360ustar00rootroot00000000000000.. _yade.geom: yade.geom module ========================================== .. automodule:: yade.geom :members: :undoc-members: :inherited-members: trunk-2017.01a/doc/sphinx/yadeBookSphinx.py000066400000000000000000000222701304022710500205440ustar00rootroot00000000000000#!/usr/bin/python # encoding: utf-8 # # module documentation # import sys,os,os.path outDir=sys.argv[2] if len(sys.argv)>2 else 'book/_build/' for d in (outDir,outDir+'/latex',outDir+'/html',outDir+'/html/_static'): if not os.path.exists(d): os.mkdir(d) #We assume that modules have been documented by a previous run of yadeSphinx #def moduleDoc(module,submodules=[]): #f=open('yade.'+module+'.rst','w') #modFmt=""".. automodule:: yade.%s #:members: #:undoc-members: #:inherited-members: #""" #f.write(""".. _yade.%s: #yade.%s module #========================================== #"""%(module,module)) ##f.write(".. module:: yade.%s\n\n"%module+modFmt%module) #f.write(modFmt%module) #for sub in submodules: ##f.write(".. submodule:: yade.%s\n\n"%sub+modFmt%sub) #f.write(".. currentmodule:: yade.%s\n\n%s\n\n"%(module,modFmt%sub)) #f.close() ## ## put all yade modules here, as {module:[submodules]} ## ## don't forget to put the module in index.rst as well! ## #mods={'export':[],'post2d':[],'pack':['_packSpheres','_packPredicates','_packObb'],'plot':[],'timing':[],'utils':['_utils'],'polyhedra_utils':['_polyhedra_utils'],'ymport':[],'geom':[],'bodiesHandling':[],'qt':['qt._GLViewer'],'linterpolation':[]} ## ## generate documentation, in alphabetical order #mm=mods.keys(); mm.sort() #for m in mm: moduleDoc(m,mods[m]) #with open('modules.rst','w') as f: #f.write("Yade modules\n=============\n\n.. toctree::\n\t:maxdepth: 2\n\n") #for m in mm: f.write('\tyade.%s.rst\n\n'%m) #import sys #sys.exit(0) # # wrapper documentation # # classes already documented docClasses=set() def autodocClass(klass): global docClasses docClasses.add(klass) return ".. autoclass:: %s\n\t:members:\n\t:undoc-members:\n\t:inherited-members:\n\n"%(klass) # \t:inherited-members:\n # \n\t:show-inheritance: def autodocDerived(klass,doSections=True): global docClasses ret='' if doSections: ret+='%s\n'%klass+'^'*100+'\n\n' #ret+='.. inheritance-diagram:: %s\n\n'%klass ret+=inheritanceDiagram(klass) ret+=autodocClass(klass) childs=list(yade.system.childClasses(klass)); childs.sort(); for k in childs: if not k in docClasses: ret+=autodocClass(k) return ret def inheritanceDiagram(klass): """Generate simple inheritance graph for given classname *klass* using dot (http://www.graphviz.org) syntax. Classes in the docClasses set (already documented) are framed differently and the inheritance tree stops there. """ global docClasses def mkUrl(c): global writer # useless, doesn't work in LaTeX anyway... return ('#yade.wrapper.%s'%c if writer=='html' else '%%yade.wrapper#yade.wrapper.%s'%c) # HTML/LaTeX def mkNode(c,style='solid',fillcolor=None): return '\t\t"%s" [shape="box",fontsize=8,style="setlinewidth(0.5),%s",%sheight=0.2,URL="yade.wrapper.html#yade.wrapper.%s"];\n'%(c,style,'fillcolor=%s,'%fillcolor if fillcolor else '',c) ret=".. graphviz::\n\n\tdigraph %s {\n\t\trankdir=RL;\n\t\tmargin=.2;\n"%klass+mkNode(klass) childs=yade.system.childClasses(klass) if len(childs)==0: return '' for c in childs: try: base=eval(c).__bases__[0].__name__ if base!=klass and base in docClasses: continue # skip classes deriving from classes that are already documented if c not in docClasses: ret+=mkNode(c) else: # classes of which childs are documented elsewhere are marked specially ret+=mkNode(c,style='filled,dashed',fillcolor='grey') ret+='\t\t"%s" -> "%s" [arrowsize=0.5,style="setlinewidth(0.5)"];\n'%(c,base) except NameError: pass #print 'WARN: unable to find class object for',c return ret+'\t}\n\n' def sect(title,text,tops,reverse=False): subsects=[autodocDerived(top,doSections=(len(tops)>1)) for top in tops] if reverse: subsects.reverse() return title+'\n'+100*'-'+'\n\n'+text+'\n\n'+'\n\n'.join(subsects)+'\n' def genWrapperRst(): global docClasses docClasses=set() # reset globals wrapper=file('yade.wrapper.rst','w') wrapper.write(""".. _yade.wrapper:: Class reference (yade.wrapper module) ======================================= .. toctree:: :maxdepth: 2 .. currentmodule:: yade.wrapper .. autosummary:: """+ sect('Bodies','',['Body','Shape','State','Material','Bound'])+ sect('Interactions','',['Interaction','IGeom','IPhys'])+ sect('Global engines','',['FieldApplier','Collider','BoundaryController','GlobalEngine'],reverse=True)+ sect('Partial engines','',['PartialEngine'])+ sect('Bounding volume creation','',['BoundFunctor','BoundDispatcher'])+ sect('Interaction Geometry creation','',['IGeomFunctor','IGeomDispatcher'])+ sect('Interaction Physics creation','',['IPhysFunctor','IPhysDispatcher'])+ sect('Constitutive laws','',['LawFunctor','LawDispatcher'])+ sect('Callbacks','',[#'BodyCallback', 'IntrCallback'])+ sect('Preprocessors','',['FileGenerator'])+ sect('Rendering','',['OpenGLRenderer','GlShapeFunctor','GlStateFunctor','GlBoundFunctor','GlIGeomFunctor','GlIPhysFunctor'])+ # ,'GlShapeDispatcher','GlStateDispatcher','GlBoundDispatcher','GlIGeomDispatcher','GlIPhysDispatcher'])+ sect('Simulation data','',['Omega','BodyContainer','InteractionContainer','ForceContainer','MaterialContainer','Scene','Cell']) +""" Other classes --------------- """ +''.join([autodocClass(k) for k in (yade.system.childClasses('Serializable')-docClasses)|set(['Serializable','TimingDeltas','Cell'])]) ) wrapper.close() def makeBaseClassesClickable(f,writer): out=[] import re,shutil changed=False for l in open(f): if writer=='html': if not '(inherits ' in l: out.append(l) continue m=re.match(r'(^.*\(inherits )([a-zA-Z0-9_ →]*)(\).*$)',l) if not m: out.append(l) continue #raise RuntimeError("Line %s unmatched?"%l) bases=m.group(2) bb=bases.split(' → ') #print bases,'@',bb bbb=' → '.join(['%s'%(b,b) for b in bb]) out.append(m.group(1)+bbb+m.group(3)) elif writer=='latex': if not (r'\pysiglinewithargsret{\strong{class }\code{yade.wrapper.}\bfcode{' in l and r'\emph{inherits' in l): out.append(l) continue #print l m=re.match(r'(^.*}}{\\emph{inherits )([a-zA-Z0-9_\\() -]*)(}}.*$)',l) if not m: #print 'WARN: Line %s unmatched?'%l continue bases=m.group(2) bb=bases.split(r' \(\rightarrow\) ') bbb=r' \(\rightarrow\) '.join([r'\hyperref[yade.wrapper:yade.wrapper.%s]{%s}'%(b.replace(r'\_',r'_'),b) for b in bb]) out.append(m.group(1)+bbb+m.group(3)+'\n') changed=True if changed: shutil.move(f,f+'_') ff=open(f,'w') for l in out: ff.write(l) ff.close() def processTemplate(f1,f2): "Copy file f1 to f2, evaluating all occurences of @...@ with eval(); they should expand to a string and can contain arbitrary python expressions." import re def doEval(match): import bib2rst return str(eval(match.group(1))) ff2=open(f2,'w') for l in open(f1): ff2.write(re.sub(r'@([^@]*)@',doEval,l)) def genReferences(): import sys processTemplate('book/fullBibliography.rst.in','fullPublications.rst') import sphinx,sys,shutil sys.path.append('.') # for bib2rst genReferences() for bib in ('references','yade-articles','yade-theses','yade-conferences','yade-docref'): shutil.copyfile('../%s.bib'%bib,outDir+'/latex/%s.bib'%bib) global writer writer=None #writers=['html','latex','epub'] writers=['latex'] volumes=['Book','Reference','Manual','Theory'] #would work if yade was exiting correctly (it seems) for vol in volumes: # no way to use custom file name for conf.py, instead we replace it by the variants shutil.copy('book/conf'+vol+'.py','book/conf.py') for writer in writers: #genWrapperRst() # HACK: must rewrite sys.argv, since reference generator in conf.py determines if we output latex/html by inspecting it sys.argv=['sphinx-build','-a','-c','book','-E','-b','%s'%writer,'-d',outDir+'/doctrees','.',outDir+'/%s'%writer] try: sphinx.main(sys.argv) except SystemExit: pass import glob texDocs=glob.glob(outDir+'latex/*.tex') if writer=='html': makeBaseClassesClickable((outDir+'/html/yade.wrapper.html'),writer) elif writer=='latex': for texdoc in texDocs: makeBaseClassesClickable(texdoc,writer) if (os.path.exists('/usr/share/javascript/jquery/jquery.js')): #Check, whether jquery.js installed in system if os.path.isfile(outDir+'/html/_static/jquery.js'): os.system('rm '+ outDir+'/html/_static/jquery.js') os.system('ln -s /usr/share/javascript/jquery/jquery.js '+ outDir+'/html/_static/jquery.js') # HACK!!!!========================================================================== # New sphinx-python versions (hopefully) are producing empty "verbatim"-environments. # That is why xelatex crashes. # The following "script" removes all empty environments. Needs to be fixed in python-sphinx. if (writer=='latex'): for texdoc in texDocs: infile = open(texdoc,"r") lines = infile.readlines() infile.close() out=[] for i in range(0,len(lines)): if (i<>len(lines) and lines[i].strip()=="\\begin{Verbatim}[commandchars=\\\\\{\\}]" and lines[i+1].strip()=="\\end{Verbatim}"): lines[i]=''; lines[i+1]='' else: out.append(lines[i]) file(texdoc,'w').write('') for i in out: file(texdoc,'a').write(i) # HACK!!!!========================================================================== sys.exit() trunk-2017.01a/doc/sphinx/yadeSphinx.py000066400000000000000000000212621304022710500177310ustar00rootroot00000000000000#!/usr/bin/python # encoding: utf-8 # # module documentation # import sys,os,os.path outDir=sys.argv[2] if len(sys.argv)>2 else '_build' for d in (outDir,outDir+'/latex',outDir+'/html'): if not os.path.exists(d): os.mkdir(d) def moduleDoc(module,submodules=[]): f=open('yade.'+module+'.rst','w') modFmt=""".. automodule:: yade.%s :members: :undoc-members: :inherited-members: """ f.write(""".. _yade.%s: yade.%s module ========================================== """%(module,module)) #f.write(".. module:: yade.%s\n\n"%module+modFmt%module) f.write(modFmt%module) for sub in submodules: #f.write(".. submodule:: yade.%s\n\n"%sub+modFmt%sub) f.write(".. currentmodule:: yade.%s\n\n%s\n\n"%(module,modFmt%sub)) f.close() # # put all yade modules here, as {module:[submodules]} # # don't forget to put the module in index.rst as well! # mods={'export':[],'post2d':[],'pack':['_packSpheres','_packPredicates','_packObb'],'plot':[],'timing':[],'utils':['_utils'],'polyhedra_utils':['_polyhedra_utils'],'ymport':[],'geom':[],'bodiesHandling':[],'qt':['qt._GLViewer'],'linterpolation':[],'gridpfacet':[]} # # generate documentation, in alphabetical order mm=mods.keys(); mm.sort() for m in mm: moduleDoc(m,mods[m]) with open('modules.rst','w') as f: f.write("Yade modules\n=============\n\n.. toctree::\n\t:maxdepth: 2\n\n") for m in mm: f.write('\tyade.%s.rst\n\n'%m) #import sys #sys.exit(0) # # wrapper documentation # # classes already documented docClasses=set() def autodocClass(klass): global docClasses docClasses.add(klass) return ".. autoclass:: %s\n\t:members:\n\t:undoc-members:\n\t:inherited-members:\n\n"%(klass) # \t:inherited-members:\n # \n\t:show-inheritance: def autodocDerived(klass,doSections=True): global docClasses ret='' if doSections: ret+='%s\n'%klass+'^'*100+'\n\n' #ret+='.. inheritance-diagram:: %s\n\n'%klass ret+=inheritanceDiagram(klass) ret+=autodocClass(klass) childs=list(yade.system.childClasses(klass)); childs.sort(); for k in childs: if not k in docClasses: ret+=autodocClass(k) return ret def inheritanceDiagram(klass): """Generate simple inheritance graph for given classname *klass* using dot (http://www.graphviz.org) syntax. Classes in the docClasses set (already documented) are framed differently and the inheritance tree stops there. """ global docClasses def mkUrl(c): global writer # useless, doesn't work in LaTeX anyway... return ('#yade.wrapper.%s'%c if writer=='html' else '%%yade.wrapper#yade.wrapper.%s'%c) # HTML/LaTeX def mkNode(c,style='solid',fillcolor=None): return '\t\t"%s" [shape="box",fontsize=8,style="setlinewidth(0.5),%s",%sheight=0.2,URL="yade.wrapper.html#yade.wrapper.%s"];\n'%(c,style,'fillcolor=%s,'%fillcolor if fillcolor else '',c) ret=".. graphviz::\n\n\tdigraph %s {\n\t\trankdir=RL;\n\t\tmargin=.2;\n"%klass+mkNode(klass) childs=yade.system.childClasses(klass) if len(childs)==0: return '' for c in childs: try: base=eval(c).__bases__[0].__name__ if base!=klass and base in docClasses: continue # skip classes deriving from classes that are already documented if c not in docClasses: ret+=mkNode(c) else: # classes of which childs are documented elsewhere are marked specially ret+=mkNode(c,style='filled,dashed',fillcolor='grey') ret+='\t\t"%s" -> "%s" [arrowsize=0.5,style="setlinewidth(0.5)"];\n'%(c,base) except NameError: pass #print 'WARN: unable to find class object for',c return ret+'\t}\n\n' def sect(title,text,tops,reverse=False): subsects=[autodocDerived(top,doSections=(len(tops)>1)) for top in tops] if reverse: subsects.reverse() return title+'\n'+100*'-'+'\n\n'+text+'\n\n'+'\n\n'.join(subsects)+'\n' def genWrapperRst(): global docClasses docClasses=set() # reset globals wrapper=file('yade.wrapper.rst','w') wrapper.write(""".. _yade.wrapper:: Class reference (yade.wrapper module) ======================================= .. toctree:: :maxdepth: 2 .. currentmodule:: yade.wrapper .. autosummary:: """+ sect('Bodies','',['Body','Shape','State','Material','Bound'])+ sect('Interactions','',['Interaction','IGeom','IPhys'])+ sect('Global engines','',['FieldApplier','Collider','BoundaryController','GlobalEngine'],reverse=True)+ sect('Partial engines','',['PartialEngine'])+ sect('Bounding volume creation','',['BoundFunctor','BoundDispatcher'])+ sect('Interaction Geometry creation','',['IGeomFunctor','IGeomDispatcher'])+ sect('Interaction Physics creation','',['IPhysFunctor','IPhysDispatcher'])+ sect('Constitutive laws','',['LawFunctor','LawDispatcher'])+ sect('Callbacks','',[#'BodyCallback', 'IntrCallback'])+ sect('Preprocessors','',['FileGenerator'])+ sect('Rendering','',['OpenGLRenderer','GlShapeFunctor','GlStateFunctor','GlBoundFunctor','GlIGeomFunctor','GlIPhysFunctor'])+ # ,'GlShapeDispatcher','GlStateDispatcher','GlBoundDispatcher','GlIGeomDispatcher','GlIPhysDispatcher'])+ sect('Simulation data','',['Omega','BodyContainer','InteractionContainer','ForceContainer','MaterialContainer','Scene','Cell']) +""" Other classes --------------- """ +''.join([autodocClass(k) for k in (yade.system.childClasses('Serializable')-docClasses)|set(['Serializable','TimingDeltas','Cell'])]) ) wrapper.close() def makeBaseClassesClickable(f,writer): out=[] import re,shutil changed=False for l in open(f): if writer=='html': if not '(inherits ' in l: out.append(l) continue m=re.match(r'(^.*\(inherits )([a-zA-Z0-9_ →]*)(\).*$)',l) if not m: out.append(l) continue #raise RuntimeError("Line %s unmatched?"%l) bases=m.group(2) bb=bases.split(' → ') #print bases,'@',bb bbb=' → '.join(['%s'%(b,b) for b in bb]) out.append(m.group(1)+bbb+m.group(3)) elif writer=='latex': if not (r'\pysiglinewithargsret{\strong{class }\code{yade.wrapper.}\bfcode{' in l and r'\emph{inherits' in l): out.append(l) continue #print l m=re.match(r'(^.*}}{\\emph{inherits )([a-zA-Z0-9_\\() -]*)(}}.*$)',l) if not m: #print 'WARN: Line %s unmatched?'%l continue bases=m.group(2) bb=bases.split(r' \(\rightarrow\) ') bbb=r' \(\rightarrow\) '.join([r'\hyperref[yade.wrapper:yade.wrapper.%s]{%s}'%(b.replace(r'\_',r'_'),b) for b in bb]) out.append(m.group(1)+bbb+m.group(3)+'\n') changed=True if changed: shutil.move(f,f+'_') ff=open(f,'w') for l in out: ff.write(l) ff.close() def processTemplate(f1,f2): "Copy file f1 to f2, evaluating all occurences of @...@ with eval(); they should expand to a string and can contain arbitrary python expressions." import re def doEval(match): import bib2rst return str(eval(match.group(1))) ff2=open(f2,'w') for l in open(f1): ff2.write(re.sub(r'@([^@]*)@',doEval,l)) def genReferences(): import sys processTemplate('references.rst.in','references.rst') processTemplate('publications.rst.in','publications.rst') import sphinx,sys,shutil sys.path.append('.') # for bib2rst genReferences() for bib in ('references','yade-articles','yade-theses','yade-conferences','yade-docref'): shutil.copyfile('../%s.bib'%bib,outDir+'/latex/%s.bib'%bib) global writer writer=None for writer in ['html','latex','epub']: genWrapperRst() # HACK: must rewrite sys.argv, since reference generator in conf.py determines if we output latex/html by inspecting it sys.argv=['sphinx-build','-a','-E','-b','%s'%writer,'-d',outDir+'/doctrees','.',outDir+'/%s'%writer] try: sphinx.main(sys.argv) except SystemExit: pass if writer=='html': makeBaseClassesClickable((outDir+'/html/yade.wrapper.html'),writer) elif writer=='latex': makeBaseClassesClickable((outDir+'/latex/Yade.tex'),writer) if (os.path.exists('/usr/share/javascript/jquery/jquery.js')): #Check, whether jquery.js installed in system os.system('rm '+ outDir+'/html/_static/jquery.js') os.system('ln -s /usr/share/javascript/jquery/jquery.js '+ outDir+'/html/_static/jquery.js') # HACK!!!!========================================================================== # New sphinx-python versions (hopefully) are producing empty "verbatim"-environments. # That is why xelatex crashes. # The following "script" removes all empty environments. Needs to be fixed in python-sphinx. if (writer=='latex'): infile = open(outDir+'/latex/Yade.tex',"r") lines = infile.readlines() infile.close() out=[] for i in range(0,len(lines)): if (i<>len(lines) and lines[i].strip()=="\\begin{Verbatim}[commandchars=\\\\\{\\}]" and lines[i+1].strip()=="\\end{Verbatim}"): lines[i]=''; lines[i+1]='' else: out.append(lines[i]) file(outDir+'/latex/Yade.tex','w').write('') for i in out: file(outDir+'/latex/Yade.tex','a').write(i) # HACK!!!!========================================================================== sys.exit() trunk-2017.01a/doc/sphinx/youtube.py000066400000000000000000000027471304022710500173200ustar00rootroot00000000000000from docutils import nodes from docutils.parsers.rst import directives CODE = """\ %(extra)s """ PARAM = """\n """ def youtube(name, args, options, content, lineno, contentOffset, blockText, state, stateMachine): """ Restructured text extension for inserting youtube embedded videos """ if len(content) == 0: return string_vars = { 'yid': content[0], 'width': 640, 'height': 480, 'extra': '' } extra_args = content[1:] # Because content[0] is ID extra_args = [ea.strip().split("=") for ea in extra_args] # key=value extra_args = [ea for ea in extra_args if len(ea) == 2] # drop bad lines extra_args = dict(extra_args) if 'width' in extra_args: string_vars['width'] = extra_args.pop('width') if 'height' in extra_args: string_vars['height'] = extra_args.pop('height') if extra_args: params = [PARAM % (key, extra_args[key]) for key in extra_args] string_vars['extra'] = "".join(params) return [nodes.raw('', CODE % (string_vars), format='html')] youtube.content = True directives.register_directive('youtube', youtube) trunk-2017.01a/doc/yade-articles.bib000066400000000000000000000772621304022710500171510ustar00rootroot00000000000000@article{Bance2014, title={Micromagnetics of shape anisotropy based permanent magnets}, author={Bance, S. and Fischbacher, J. and Schrefl, T. and Zins, I. and Rieger, G. and Cassignol, C.}, journal={Journal of Magnetism and Magnetic Materials}, volume={363}, pages={121--124}, year={2014}, publisher={Elsevier} } @article{Bonilla2015, year={2015}, journal={Acta Geotechnica}, doi={10.1007/s11440-015-0374-z}, title={Rock slope stability analysis using photogrammetric data and DFN–DEM modelling}, url={http://dx.doi.org/10.1007/s11440-015-0374-z}, publisher={Springer Berlin Heidelberg}, author={Bonilla-Sierra, V. and Scholtès, L. and Donzé, F.V. and Elmouttie, M.K.}, pages={1-15} } @article{Boon2012a, title = {A new algorithm for contact detection between convex polygonal and polyhedral particles in the discrete element method}, journal = {Computers and Geotechnics}, volume = {44}, number = {0}, pages = {73 - 82}, year = {2012}, doi = {10.1016/j.compgeo.2012.03.012}, url = {http://www.sciencedirect.com/science/article/pii/S0266352X12000535}, author = {Boon,C.W. and Houlsby, G.T. and Utili, S.} } @article{Boon2012b, title = {A new contact detection algorithm for three-dimensional non-spherical particles}, journal = {Powder Technology}, year = {2013}, doi = {10.1016/j.powtec.2012.12.040}, url = {http://www.sciencedirect.com/science/article/pii/S003259101200839X}, author = {Boon,C.W. and Houlsby, G.T. and Utili, S.} } @article{Boon2014, title={New insights into the 1963 Vajont slide using 2D and 3D distinct-element method analyses}, journal={Géotechnique}, author={Boon, C.W. and Houlsby, G.T. and Utili, S.}, year={2014}, volume={64}, number={10}, pages={800--816}, publisher={Thomas Telford} } @article{Boon2015, title={A new rock slicing method based on linear programming}, author={Boon, C.W. and Houlsby, G.T. and Utili, S.}, journal={Computers and Geotechnics}, volume={65}, pages={12--29}, year={2015}, publisher={Elsevier} } @article{Bourrier2015, title={A reliability-based approach for the design of rockfall protection fences}, author={Bourrier, F. and Lambert, S. and Baroth, J.}, journal={Rock Mechanics and Rock Engineering}, volume={48}, number={1}, pages={247--259}, year={2015}, publisher={Springer} } @article{Bourrier2013, title = {Discrete modeling of granular soils reinforcement by plant roots}, journal = {Ecological Engineering}, author={Bourrier, F. and Kneib, F. and Chareyre, B. and Fourcaud, T.}, year = {2013}, doi = {10.1016/j.ecoleng.2013.05.002}, url = {http://dx.doi.org/10.1016/j.ecoleng.2013.05.002} } @Article{Catalano2014a, title = {Pore-scale modeling of fluid-particles interaction and emerging poromechanical effects}, author = {Catalano, E. and Chareyre, B. and Barthélémy, E.}, journal = {International Journal for Numerical and Analytical Methods in Geomechanics}, year = {2014}, volume = {38}, number = {1}, pages = {51--71}, doi = {10.1002/nag.2198}, note = {http://arxiv.org/pdf/1304.4895.pdf}, url = {http://dx.doi.org/10.1002/nag.2198} } @article{Chareyre2012a, author = {Chareyre, B. and Cortis, A. and Catalano, E. and Barthélemy, E.}, title = {Pore-Scale Modeling of Viscous Flow and Induced Forces in Dense Sphere Packings}, journal = {Transport in Porous Media}, publisher = {Springer Netherlands}, volume={92}, number={2}, year={2012}, pages = {473-493}, url = {http://dx.doi.org/10.1007/s11242-011-9915-6}, doi = {10.1007/s11242-011-9915-6} } @article{Chen2007, title = {Prediction/Verification of Particle Motion in One Dimension with the Discrete-Element Method}, author = {Chen, F. and Drumm, E. 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Owen}, month = {Nov}, year = {2011}, booktitle = {II International Conference on Particle-based Methods - Fundamentals and Applications}, address = {Barcelona, Spain}, pages = {1--11}, url={http://people.3sr-grenoble.fr/users/bchareyre/pubs/SariChareyreCatalanoPhilippeVincens_Particles2011.pdf} } @InProceedings{Favier2009b, author = {L. Favier and D. Daudon and F. Donzé and J. Mazars}, title = {Validation of a DEM granular flow model aimed at forecasting snow avalanche pressure}, year = {2009}, journal = {AIP Conference Proceedings}, volume = {1145}, number = {1}, pages = {617-620}, url = {http://link.aip.org/link/?APC/1145/617/1}, doi = {10.1063/1.3180002} } @InProceedings{ Thoeni2011, title = {Discrete Modelling of a Rockfall Protective System}, booktitle = {Particles 2011: Fundamentals and Applications}, series = {II International Conference on Particle-based Methods}, author = {K. Thoeni and C. Lambert and A. Giacomini and S.W. Sloan}, editor = {E. Onate and D.R.J. 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Owen}, location = {Barcelona, Spain}, year = {2011}, isbn = {978-84-89925-69-4}, url = {https://yade-dem.org/w/images/3/32/ScholtesDonzeParticles2011.pdf} } @InProceedings{ Kozicki2011, title = {Numerical simulation of sand behaviour using DEM with two different descriptions of grain roughness}, booktitle = {II International Conference on Particle-based Methods - Fundamentals and Applications}, author = {J. Kozicki and J. Tejchman}, editor = {E. Onate and D.R.J. Owen}, location = {Barcelona, Spain}, year = {2011}, isbn = {978-84-89925-69-4}, url = {https://yade-dem.org/w/images/9/96/KozickyTejchmanParticles2011.pdf} } @InProceedings{ Stransky2011, title = {Calibration of particle-based models using cells with periodic boundary conditions}, booktitle = {II International Conference on Particle-based Methods - Fundamentals and Applications}, author = {J. Stransky and M. Jirasek}, editor = {E. Onate and D.R.J. 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Owen}, address = {Barcelone, Spain}, year = {2009}, pages = {167-170}, } @InProceedings{Hicher2011, title = {Multiscale Modeling of Particle Removal Impact on Granular Material Behavior}, booktitle = {Engineering Mechanics Institute, EMI 2011}, author = {Hicher, P.Y and Scholtès, L. and Sibille, L.}, address = {Boston, USA}, year = {2011}, } @InProceedings{Nicot2010, title = {Multiscale modeling of instability in granular materials}, booktitle = {Engineering Mechanics Institute, EMI 2010}, author = {Nicot, F. and Sibille, L. and Daouadji, A. and Hicher, P.Y. and Darve, F.}, address = {Los Angeles, USA}, year = {2010}, } @InProceedings{Lomine2010b, title = {Modelling of fluid-solid interaction in granular media with coupled LB/DE methods: application to solid particle detachment under hydraulic loading}, booktitle = {19th Discrete Simulation of Fluid Dynamics, DSFD 2010}, author = {Lominé, F. and Poullain, P. and Sibille, L.}, address = {Roma, Italy}, year = {2010}, } @InProceedings{Modenese2012, author = "C. Modenese and S. Utili and G.T. Houlsby", title = "DEM Modelling of Elastic Adhesive Particles with Application to Lunar Soil", booktitle = "Earth and Space 2012: Engineering, Science, Construction, and Operations in Challenging Environments ¬© 2012 ASCE", year = "2012", url={http://ascelibrary.org/doi/abs/10.1061/9780784412190.006}, doi={10.1061/9780784412190.006} } @incollection{Modenese2012a, author = {Modenese, C and Utili, S and Houlsby, G T}, editor = {Wu, Chuan-Yu}, title = {{A study of the influence of surface energy on the mechanical properties of lunar soil using DEM}}, booktitle = {{Discrete Element Modelling of Particulate Media}}, publisher = {Royal Society of Chemistry}, year = {2012}, series = {Special Publication}, doi = {10.1039/9781849735032-00069}, url = {http://pubs.rsc.org/en/content/chapter/bk9781849733601-00069/978-1-84973-503-2} } @incollection{Modenese2012b, author = {Modenese, C and Utili, S and Houlsby, G T}, editor = {Wu, Chuan-Yu}, title = {{A numerical investigation of quasi-static conditions for granular media}}, booktitle = {{Discrete Element Modelling of Particulate Media}}, publisher = {Royal Society of Chemistry}, year = {2012}, series = {Special Publication}, doi = {10.1039/9781849735032-00187}, url = {http://pubs.rsc.org/en/content/chapter/bk9781849733601-00187/978-1-84973-503-2} } @incollection{Chareyre2012b, title = {The properties of some stress tensors investigated by DEM simulations}, author = {B. Chareyre and L. Scholtès and F. Darve}, month = {Aug}, year = {2012}, booktitle = {Euromech Colloquium 539; Mechanics of Unsaturated Porous Media: Effective Stress principle; from micromechanics to thermodynamics}, address = {Utrecht, Netherlands}, url = {http://www.geo.uu.nl/hydrogeology/Colloquium2012/Bruno%20Chareyre_Euromech.pdf} } @incollection{Chareyre2012c, title = {Micro-poromechanics: recent advances in numerical models and perspectives}, author = {B. Chareyre}, booktitle = {ICACM symposium 2012, The role of structure on emerging material properties}, year = {2012}, month = {June}, address = {New York, USA} } @incollection{Michallet2012, title = {Physical and numerical modelling of sand liquefaction in waves interacting with a vertical wall}, author = {H. Michallet and E. Catalano and C. Berni and V. Rameliarison and E. Barthélémy}, month = {Aug}, year = {2012}, booktitle = {ICSE6 - 6th International conference on Scour and Erosion}, address = {Paris, France} } @incollection{Hasan2010b, title = {Microtomography-based Discrete Element Modeling to Simulate Snow Microstructure Deformation}, author = {A. Hasan and B. Chareyre and J. Kozicki and F. Flin and F. Darve and J. Meyssonnier}, booktitle = {AGU Fall Meeting Abstracts}, volume = {1}, pages = {0566}, year = {2010} } @incollection{Tran2012b, title={Coupling of Random Field Theory and the Discrete Element Method in the Reliability Analysis of Geotechnical Problems}, author={Tran, V.D.H and Meguid, M.A and Chouinard, L.E}, booktitle={Canadian Society for Civil Engineering (CSCE) Annual Conference 2012, Edmonton}, year={2012}, month={May} } @incollection{Tran2012b, title={A Discrete Element Study of the Earth Pressure Distribution on Cylindrical Shafts}, author={Tran, V.D.H and Meguid, M.A and Chouinard, L.E}, booktitle={Tunnelling Association of Canada (TAC) Conference 2012, Montreal}, year={2012}, month={October} } @InProceedings{ Harthong2013, title = {Directional plastic flow and fabric dependencies in granular materials}, author = {Barthélémy Harthong and Richard G Wan}, Booktitle = {{Powders and Grains 2013: Proceedings of the 6th International Conference on Micromechanics of Granular Media. AIP Conference Proceedings}}, volume = {1542}, year = {2009}, number = {1}, month = {July}, doi = {http://dx.doi.org/10.1063/1.4811900}, pages = {193–197}, address = {Sydney, Australia}, url = {https://www.yade-dem.org/publi/APC000193.pdf} } @InProceedings{ Hilton2013b, author = {J. E. Hilton and P. W. Cleary and A. Tordesillas}, title = {Unitary stick-slip motion in granular beds}, publisher = {AIP}, year = {2013}, Booktitle = {{Powders and Grains 2013: Proceedings of the 6th International Conference on Micromechanics of Granular Media. AIP Conference Proceedings}}, volume = {1542}, number = {1}, pages = {843–846}, address = {Sydney, Australia}, url = {http://scitation.aip.org/getpdf/servlet/GetPDFServlet?filetype=pdf&id=APCPCS001542000001000843000001&idtype=cvips&doi=10.1063/1.4812063&prog=normal}, doi = {10.1063/1.4812063} } @InProceedings{ Catalano2013b, author = {Catalano E. and Chareyre B. and Barthélémy E.}, title = {DEM-PFV analysis of solid-fluid transition in granular sediments under the action of waves}, publisher = {AIP}, year = {2013}, Booktitle = {{Powders and Grains 2013: Proceedings of the 6th International Conference on Micromechanics of Granular Media. AIP Conference Proceedings}}, volume = {1542}, number = {1}, pages = {1063–1066}, address = {Sydney, Australia}, url = {http://link.aip.org/link/?APC/1542/1063/1}, doi = {10.1063/1.4812118} } @InProceedings{ Guo2013, author = {Ning Guo and Jidong Zhao}, title = {A hierarchical model for cross-scale simulation of granular media}, publisher = {AIP}, year = {2013}, Booktitle = {{Powders and Grains 2013: Proceedings of the 6th International Conference on Micromechanics of Granular Media. AIP Conference Proceedings}}, volume = {1542}, number = {1}, pages = {1222–1225}, address = {Sydney, Australia}, url = {https://www.yade-dem.org/publi/APC001222.pdf}, doi = {10.1063/1.4812158} } @InProceedings{ Hadda2013b, author = {Nejib Hadda and François Nicot and Luc Sibille and Farhang Radjai and Antoinette Tordesillas and Félix Darve}, title = {A multiscale description of failure in granular materials}, publisher = {AIP}, year = {2013}, Booktitle = {{Powders and Grains 2013: Proceedings of the 6th International Conference on Micromechanics of Granular Media. AIP Conference Proceedings}}, volume = {1542}, number = {1}, pages = {585–588}, address = {Sydney, Australia}, url = {https://www.yade-dem.org/publi/APC000585.pdf}, doi = {10.1063/1.4811999} } @InProceedings{ Kozicki2013, author = {Jan Kozicki and Jacek Tejchman and Danuta Lesniewska}, title = {Study of some micro-structural phenomena in granular shear zones}, publisher = {AIP}, year = {2013}, Booktitle = {{Powders and Grains 2013: Proceedings of the 6th International Conference on Micromechanics of Granular Media. AIP Conference Proceedings}}, volume = {1542}, number = {1}, pages = {495–498}, address = {Sydney, Australia}, url = {https://www.yade-dem.org/publi/APC000495.pdf}, doi = {10.1063/1.4811976} } @InProceedings{Maurin2013, title={Discrete element modelling of bedload transport}, author={R. Maurin and B. Chareyre and J. Chauchat and P. Frey}, booktitle={Proceedings of THESIS 2013, Two-pHase modElling for Sediment dynamIcS in Geophysical Flows}, adress = {Chatou, France}, pages={6p}, url = {https://www.yade-dem.org/publi/Maurin_et_al_THESIS_meta.pdf}, year={2013} } @Inproceedings{Maurin2014a, title={DEM-CFD coupling applied to bedload transport}, author={R. Maurin and J. Chauchat and B. Chareyre and P. Frey}, booktitle={Modelling Granular Media Across Scales, Montpellier}, year={2014}, month={July} } @Inproceedings{Maurin2014b, title={DEM-CFD coupling applied to bedload transport}, author={R. Maurin and J. Chauchat and B. Chareyre and P. Frey}, booktitle={Condensed Matter in Paris}, year={2014}, month={August} } @Inproceedings{Maurin2014c, title={DEM-fluid coupling applied to bedload transport}, author={R. Maurin and J. Chauchat and B. Chareyre and P. Frey}, booktitle={Yade workshop, Grenoble}, year={2014}, month={July} } @InProceedings{Elias2013, author={Eliáš, J.}, title={Dem simulation of railway ballast using polyhedral elemental shapes}, journal={Particle-Based Methods III: Fundamentals and Applications - Proceedings of the 3rd International Conference on Particle-based MethodsFundamentals and Applications, Particles 2013}, year={2013}, pages={247-256}, url={https://www.vutbr.cz/www_base/gigadisk.php?i=95194aa9a}, document_type={Conference Paper}, source={Scopus}, } @InProceedings{Yuan2014, author={Chao Yuan and Bruno Chareyre and Félix Darve}, title={Pore-Scale Simulations of Drainage for Two-phase Flow in Dense Sphere Packings}, journal={XX . International Conference on Computational Methods in Water Resources}, year={2014}, pages={232}, url={http://cmwr14.de/images/bookofabstracts/CMWR14BookofAbstracts.pdf} } @InProceedings{Sweijen2014, author={Thomas Sweijen and Majid Hassanizadeh and Bruno Chareyre}, title={Pore-Scale modeling of swelling porous media; application to super absorbent polymers}, journal={XX . International Conference on Computational Methods in Water Resources}, year={2014}, pages={227}, url={http://cmwr14.de/images/bookofabstracts/CMWR14BookofAbstracts.pdf} } @InProceedings{Effeindzourou2015, author = {A. Effeindzourou and K. Thoeni and A. Giacomini and S.W. Sloan}, booktitle = {{Computer Methods and Recent Advances in Geomechanics}}, editor = {{F. Oka and A. Murakami and R. Uzuoka and and S. Kimoto}}, pages = {1083--1088}, publisher = {Taylor and Francis}, series = {{14th International Conference of the IACMAG}}, title = {{A discrete model for rock impacts on muckpiles}}, url = {http://dx.doi.org/10.1201/b17435-189}, year = {2015} } @inproceedings{Effeindzourou2015a, author = {Effeindzourou, A. and Thoeni, K. and Chareyre, B. and Giacomini, A.}, booktitle = {{Particle-Based Methods IV: Fundamentals and Applications}}, location = {Barcelona, Spain}, pages = {744--754}, series = {{4th International Conference on Particle-based Methods}}, title = {{A general method for modelling deformable structures in DEM}}, year = {2015} } @InCollection{Thoeni2015, author = {K. Thoeni and A. Giacomini and C. Lambert and S.W. Sloan}, booktitle = {{Engineering Geology for Society and Territory - Volume 2}}, doi = {10.1007/978-3-319-09057-3_356}, editor = {G. Lollino and D. Giordan and G.B. Crosta and J. Corominas and R. Azzam and J. Wasowski and N. Sciarra}, isbn = {978-3-319-09056-6}, pages = {2007--2011}, publisher = {Springer}, title = {{Rockfall Trajectory Analysis with Drapery Systems}}, url = {http://dx.doi.org/10.1007/978-3-319-09057-3_356}, year = {2015} } @Proceedings{1stYadeWorkshop, pages = {565}, series = {{1st Yade Workshop - Grenoble}}, title = {{Booklet of presentations of the 1st Yade Workshop}}, url = {https://yade-dem.org/publi/1stWorkshop/booklet.pdf}, year = {2014} } @InProceedings{Kozicki2005a, title = {Discrete lattice model used to describe the fracture process of concrete}, author = {Kozicki, J.}, journal = {Discrete Element Group for Risk Mitigation Annual Report 1, Grenoble University of Joseph Fourier, France}, pages = {95--101}, year = {2005}, url={https://yade-dem.org/w/images/f/f0/Discrete_lattice_model_DEM_risk_mitigation_kozicki.pdf} } @article{Tejchman2011, title={Comparative Modelling of Shear Zone Patterns in Granular Bodies with Finite and Discrete Element Model}, author={Tejchman, J.}, journal={Advances in Bifurcation and Degradation in Geomaterials}, pages={255--260}, year={2011} } @InProceedings{Nitka2015b, title={Discrete Modelling of Micro-structural Phenomena in Granular Shear Zones}, author={Nitka, Michal and Tejchman, Jacek and Kozicki, Jan}, booktitle={Bifurcation and Degradation of Geomaterials in the New Millennium}, pages={7--12}, year={2015}, publisher={Springer} } @InProceedings{Bonilla2014, title={Coupling photogrammetric data with a discrete element model for rock slope stability assessment}, author={Bonilla-Sierra, V and Donzé, FV and Scholtès, L and Elmouttie, M}, booktitle={Rock Engineering and Rock Mechanics: Structures in and on Rock Masses}, pages={433}, year={2014}, publisher={CRC Press} } @InProceedings{Skarzynski2014, title={Two-scale model for concrete beams subjected to three point bending—numerical analyses and experiments}, author={Skarzynski, M Nitka and Tejchman, J}, booktitle={Computational Modelling of Concrete Structures}, volume={1}, pages={149}, year={2014}, publisher={CRC Press} } @InProceedings{Nitka2014, title={Discrete modeling of micro-structure evolution during concrete fracture using DEM}, author={Nitka, M and Tejchman, J}, booktitle={Computational Modelling of Concrete Structures}, volume={1}, pages={345}, year={2014}, publisher={CRC Press} } @InProceedings{Sayeed2014, title={Mechanical Behavior of Granular Materials Considering Confining Pressure Dependency}, author={Sayeed, Md Abu and Sazzad, Md Mahmud and Suzuki, Kiichi}, booktitle={GeoCongress 2012}, volume={10}, pages={9780784412121--225}, year={2014} } @InProceedings{Nicot2015, title={Micromechanical Analysis of Second Order Work in Granular Media}, author={Nicot, F and Hadda, N and Bourrier, F and Sibille, L and Tordesillas, A and Darve, F}, booktitle={Bifurcation and Degradation of Geomaterials in the New Millennium}, pages={67--74}, year={2015}, publisher={Springer} } @InProceedings{Albaba2015, title={Modeling the Impact of Granular Flow against an Obstacle}, author={Albaba, Adel and Lambert, Stéphane and Nicot, François and Chareyre, Bruno}, booktitle={Recent Advances in Modeling Landslides and Debris Flows}, pages={95--105}, year={2015}, publisher={Springer} } @InProceedings{Hadda2015b, title={A microstructural cluster-based description of diffuse and localized failures}, author={Hadda, N and Bourrier, F and Sibille, L and Nicot, F and Wan, R and Darve, F}, booktitle={Geomechanics from Micro to Macro: Proceedings of the International Symposium on Geomechanics from Micro and Macro (IS-Cambridge 2014)}, pages={169-174}, year={2015}, publisher={CRC Press/Balkema} } @InProceedings{Bourrier2015b, title={How Can Reliability-Based Approaches Improve the Design of Rockfall Protection Fences?}, author={Bourrier, Franck and Baroth, Julien and Lambert, Stéphane}, booktitle={Engineering Geology for Society and Territory-Volume 2}, pages={1985--1988}, year={2015}, publisher={Springer} } @InProceedings{Wan2015b, title={Plastic Deformations in Granular Materials with Rotation of Principal Stress Axes}, author={Wan, Richard and Hadda, Nejib}, booktitle={Bifurcation and Degradation of Geomaterials in the New Millennium}, pages={305--310}, year={2015}, publisher={Springer} } @InProceedings{Li2014, title={Constrictions and filtration of fine particles in numerical granular filters: Influence of the fabric within the material}, author={Li, W and Vincens, E and Reboul, N and Chareyre, B}, booktitle={Scour and Erosion: Proceedings of the 7th International Conference on Scour and Erosion, Perth, Australia, 2-4 December 2014}, pages={241}, year={2014}, organization={CRC Press} } @InProceedings{Uhlmann2014, title={Investigation of material removal and surface topography formation in vibratory finishing}, author={Uhlmann, Eckart and Dethlefs, Arne and Eulitz, Alexander}, journal={Procedia CIRP}, volume={14}, pages={25--30}, year={2014}, publisher={Elsevier} } @InProceedings{Nitka2014b, title={Discrete modeling of micro-structure evolution during concrete fracture using DEM}, author={Nitka, M and Tejchman, J}, journal={Computational Modelling of Concrete Structures}, volume={1}, pages={345}, year={2014}, publisher={CRC Press} } @InProceedings{Nitka2014c, title={Effect of mean grain diameter on vortices, force chains and local volume changes in granular shear zones}, author={Nitka, M and Tejchman, J and Kozicki, J and Lesniewska, D}, journal={Digital Humanitarians: How Big Data Is Changing the Face of Humanitarian Response}, pages={177}, year={2014}, publisher={CRC Press} } @incollection{Guo2014b, year={2015}, booktitle={Bifurcation and Degradation of Geomaterials in the New Millennium}, editor={Chau, Kam-Tim and Zhao, Jidong}, doi={10.1007/978-3-319-13506-9_18}, title={A Multiscale Investigation of Strain Localization in Cohesionless Sand}, url={http://dx.doi.org/10.1007/978-3-319-13506-9_18}, author={Guo, Ning and Zhao, Jidong}, pages={121-126} } @incollection{Toraldo2015, year={2015}, booktitle={Annual Report 1}, editor={Grenoble Geomechanics Group}, title={Numerical modelling of the localized fluidization in a saturated granular medium using the coupled method DEM-PFV}, url={http://people.3sr-grenoble.fr/users/bchareyre/pubs/GGG-Annual_Report_1-March_2015.pdf}, author={Toraldo, Marcella and Chareyre, Bruno and Sibille, Luc}, pages={131--138} } @InProceedings{Gladky2015a, title = {DEM simulation of the dry and weakly wetted bulk flow on a pelletizing table}, booktitle = {13th U.S. National Congress on Computational Mechanics}, author = {Gladky, Anton and Lieberwirth, Holger and Schwarze, Ruediger}, address = {San Diego, USA}, month = {July}, year = {2015}, } @InProceedings{Gladky2015b, title = {DEM simulations of weakly wetted granular materials: implementation of capillary bridge models}, booktitle = {Fourth Conference on Particle-Based Methods (PARTICLES 2015)}, author = {Gladky, Anton and Roy, Sudeshna and Weinhart, Thomas and Luding, Stefan and Schwarze, Ruediger}, address = {Barcelona, Spain}, month = {September}, url = {https://yade-dem.org/w/images/5/56/Part2015_.pdf}, year = {2015}, } @InProceedings{Suhr2015, Title = {Tribological effects in granular materials and their impact on the macroscopic material behaviour}, Author = {Suhr, Bettina and Six, Klaus}, Booktitle = {Proceedings of the IV International Conference on Particle-based Methods (PARTICLES 2015)}, Year = {2015}, Editor = {E. Oñate and M. Bischoff and D.R.J. Owen and P. Wriggers and T. Zohdi}, Pages = {878 - 889}, Publisher = {International Center for Numerical Methods in Engineering (CIMNE) Barcelona, Spain}, Url = {http://congress.cimne.com/particles2015/frontal/doc/E-book_PARTICLES_2015.pdf} } @InProceedings{Duriez2015, title = {Effective stress in unsaturated granular materials: micro-mechanical insights}, author = {J. Duriez and R. Wan}, booktitle = {Coupled Problems in Science and Engineering VI}, year = {2015}, adress = {Venice}, pages = {1232--1242}, editors= {B. Schrefler, E. Onate and M. Papadrakakis}, url = {http://congress.cimne.com/coupled2015/frontal/doc/Ebook_COUPLED_15.pdf} } @InProceedings{Darve2016, title = {DEM modelling in Geomechanics: some recent breakthroughs}, author = {F. Darve, J. Duriez, R. Wan}, booktitle = {Proceedings of the 7th International Conference on Discrete Element Methods}, editor={Li, Xikui and Feng, Yuntian and Mustoe, Graham}, year = {2016}, publisher={Springer}, adress = {Dalian} } trunk-2017.01a/doc/yade-docref.bib000066400000000000000000000022441304022710500165710ustar00rootroot00000000000000 @book{yade:doc2, altnote = "\\url{http://yade-dem.org/doc/}", author = "V. Šmilauer et al.", doi = "10.5281/zenodo.34073", note = "http://yade-dem.org/doc/", title = "{{Y}ade {D}ocumentation 2nd ed}", publisher = "{The {Y}ade Project}", year = "2015" } @incollection{yade:manual2, altnote = "\\url{http://yade-dem.org/doc/}", author = "V. Šmilauer et al.", doi = "10.5281/zenodo.34043", booktitle = "{Y}ade {D}ocumentation 2nd ed", note = "http://yade-dem.org/doc/", publisher = "{The {Y}ade Project}", title = "Using and Programming", year = "2015" } @incollection{yade:background2, altnote = "\\url{http://yade-dem.org/doc/}", author = "V. Šmilauer et al.", doi = "10.5281/zenodo.34044", booktitle = "{Y}ade {D}ocumentation 2nd ed", note = "http://yade-dem.org/doc/", publisher = "{The {Y}ade Project}", title = "DEM formulation", year = "2015" } @incollection{yade:reference2, altnote = "\\url{http://yade-dem.org/doc/}", author = "V. Šmilauer et al.", doi = "10.5281/zenodo.34045", booktitle = "{Y}ade {D}ocumentation 2nd ed", note = "http://yade-dem.org/doc/", publisher = "{The {Y}ade Project}", title = "Reference Manual", year = "2015" } trunk-2017.01a/doc/yade-logo-note.png000066400000000000000000001056071304022710500172710ustar00rootroot00000000000000PNG  IHDR] pHYs  tIME  UE7tEXtCommentCreated with The GIMPd%n IDATxڬidy&.yoYY{U/@wc&H ")j %rOXqB B(&($ }+9n1=cngtTWgV=yy9E_GFeћO$ `8FQ>|yqnYK B Ѥ͆?,jh!aEq8BU0 wvwjکS:d2q]?GQ'2z4LQYJ %BB%2aC1!R4LbڦaJBe%:RIYhT*VVPF/\@)RJu孃yTl6]ǕRjhAq7Jn''Ir||)ܲ8r*P$V7p(W븛P a̼Y&,˄)(<5ZB)9J)`8e2sJR&q$ Sr9_^\nsTW޺r|t! 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P<*,#˅{\&CD[Zf/ND-k1Z3Y9\RQQ1SR,S7щhd31 rJ[ڍG?vޣs<* i2~s]ڌ?.]^[_޸xn1oe&e">bgD@lD^~8,݃m+N5$84Ʉ}dUlX{ÛkPy PN( .m}>]߀GjE)Q03!YT7]C;^M/3aI1_~W?]S~x/Uc/d~u7BAg]Ptp*U$hNsuJRُ(H0a@PZٲն `.ْd)JEꎛ1kVM:2'tE%FD)dQ'|* !"3Ż,eK93Z>F@ӓ0+H)1ډn~wi%2;`SȽmzog%7᣼le-YPD,vqXj%T٣K1sP"5 M5$]eTYxR.sy˥gjaɑ0 dg]3dxxU(BEǖŚT0޺ymcǏ$gEηz+ jAZΥWP!Zr%l`uX AmPbi7v?WDmm6/m[ߧϔoSYhr@)b Uޕ1snZ:j:i}Lr6 Y Z`X$b1ɾqk"I}< KԒDZ6ǽ˿żџ|=k;/C!z0rԢXJ4~qUCjG"-u/*t "+#y"ODnį 'Wi5$f҉A t)y)a#&D5pY鱏Ue>wlLʤ!x2ww>U$2 ,Y8 3؈SMީex諊^9w$ j A@RTǽ /j%Dnb 2;ck;5. ~ùU$Ǫ1T>Q코sv蘝gϞ8u/Vlu>jtb$FE?=dŒSȊ .9^D_c5Y ߝ# gƔuYr%ÊRd%ouݾR4q07W9ю<;p"v:[ȋwhLX:H':+޻s\:b{?0P*CTJ*xZrO4d /t jW U'Xy}5F9WfE;l³u:#猸$";<9|A1ge՜-H,Y$%I|u9C%;|ݏ ! &\sv`,E,(a43j31!,hNt:ɺbr?r3U,ood2 W8IEXŋ*h6KSPWt/.:;S!ݕYjDe =zOb*ZEf$,Ƥ1 `,Z>f"**X\.g%h_UBlQ]M>uAչߧȭM¥q 3!\fOH'5gBFb*/-Ǩ^ouYy>_ϻ>UU;wPAIENDB`trunk-2017.01a/doc/yade-theses.bib000066400000000000000000000141731304022710500166260ustar00rootroot00000000000000@phdthesis{Kozicki2007b, title={Application of Discrete Models to Describe the Fracture Process in Brittle Materials}, author={J. Kozicki}, year={2007}, school={Gdansk University of Technology}, url={http://janek.kozicki.pl/phdthesis/kozicki_2007_PhD.pdf} } @mastersthesis{Catalano2008a, title={Infiltration effects on a partially saturated slope - An application of the Discrete Element Method and its implementation in the open-source software YADE}, author={E. Catalano}, year={2008}, school={UJF-Grenoble}, url={https://yade-dem.org/w/images/a/af/SlopeStability.pdf} } @phdthesis{Chen2009a, title={Coupled Flow Discrete Element Method Application in Granular Porous Media using Open Source Codes}, author={Chen, F.}, school = {University of Tennessee, Knoxville}, journal={Doctoral Dissertations}, pages={21}, year={2009}, url={http://trace.tennessee.edu/cgi/viewcontent.cgi?article=1051&context=utk_graddiss} } @phdthesis{Duriez2009a, title={Stabilité des massifs rocheux : une approche mécanique}, author={J. Duriez}, year={2009}, school={Institut polytechnique de Grenoble}, url={http://tel.archives-ouvertes.fr/tel-00462072/fr/} } @phdthesis{Scholtes2009d, author = { Luc Scholtès }, title = { Modélisation micromécanique des milieux granulaires partiellement saturés }, year = {2009}, school = {Institut National Polytechnique de Grenoble}, url = {http://tel.archives-ouvertes.fr/tel-00363961/en/} } @phdthesis{Smilauer2010b, title={Cohesive Particle Model using the Discrete Element Method on the Yade Platform}, author={Václav Šmilauer}, year={2010}, school={Czech Technical University in Prague, Faculty of Civil Engineering \& Université Grenoble I -- Joseph Fourier, École doctorale I-MEP2}, url={http://beta.arcig.cz/\~eudoxos/smilauer2010-phd-thesis.pdf}, note={`LaTeX sources `__} } @article{Smilauer2010c, title={Doctoral thesis statement}, journal={(PhD thesis summary)}, author={Václav Šmilauer}, year={2010}, url={http://beta.arcig.cz/\~eudoxos/smilauer2010-phd-thesis-statement.pdf}, note={`LaTeX sources `__} } @phdthesis{Jerier2009b, author = {Jerier, J.F.}, title = {Modélisation de la compression haute densité des poudres métalliques ductiles par la méthode des éléments discrets (in french)}, year = {2009}, school = {Université Grenoble I – Joseph Fourier}, url = {http://tel.archives-ouvertes.fr/tel-00443670/fr/} } @phdthesis{Tran2011b, author = {Van Tieng TRAN}, title = {Structures en béton soumises à des chargements mécaniques extrêmes: modélisation de la réponse locale par la méthode des éléments discrets (in french)}, year = {2011}, school = {Université Grenoble I – Joseph Fourier}, url = {https://yade-dem.org/w/images/2/27/VanTranTiengThesis.pdf} } @mastersthesis{Marzougui2011, author = {Marzougui, D.}, title = {Hydromechanical modeling of the transport and deformation in bed load sediment with discrete elements and finite volume}, year = {2011}, school = {Ecole Nationale d'Ingénieur de Tunis}, url = {http://yade-dem.org/publi/MasterMarzougui_meta.pdf} } @phdthesis{Chen2011b, title={Discrete Element Method (DEM) Analyses for Hot-Mix Asphalt (HMA) Mixture Compaction}, author={Chen, J.}, school = {University of Tennessee, Knoxville}, year={2011}, url = {http://trace.tennessee.edu/cgi/viewcontent.cgi?article=2102&context=utk_graddiss} } @phdthesis{Favier2009c, title={Approche numérique par éléments discrets 3D de la sollicitation d'un écoulement granulaire sur un obstacle}, school = {Université Grenoble I – Joseph Fourier}, author={Favier, L.}, year={2009} } @phdthesis{Charlas2013, author = {Benoit Charlas}, school = {Université de Grenoble}, title = {Etude du comportement mécanique d'un hydrure intermétallique utilisé pour le stockage d'hydrogène}, year = {2013}, url = {https://www.yade-dem.org/w/images/8/89/These_BenoitCharlas.pdf} } @phdthesis{Catalano2012, author = {Emanuele Catalano}, school = {Université de Grenoble}, title = {A pore-scale coupled hydromechanical model for biphasic granular media}, year = {2012}, url = {https://yade-dem.org/publi/Catalano_Thesis.pdf} } @mastersthesis{GaeblerMedack2013, author = {Gäbler, Nils and Medack, Jörg}, title = {Experimental and simulative study of particle dynamics on a chute}, year = {2013}, note = {Project work}, school = {Institute of Mechanics and Fluid Dynamics, TU Bergakademie Freiberg} } @mastersthesis{GentzAverhausVilbusch2014, author = {Gentz, Julia and Averhaus, Jan and Vilbusch, Stephan}, title = {Numerical simulation of particle movement on a pelletizing disc -- set-up and validation of a DEM model}, year = {2014}, note = {Project work}, school = {Institute of Mechanics and Fluid Dynamics, TU Bergakademie Freiberg} } @phdthesis{Guo2014c, author = {N. Guo}, title = {Multiscale characterization of the shear behavior of granular media}, school = {The Hong Kong University of Science and Technology}, year = {2014}, address = {Hong Kong} } @mastersthesis{Borrmann2014, title = {DEM-CFD Simulation: Erprobung neuer Kopplungsansätze in ausgewählten Softwarepaketen (in german)}, author = {Sebastian, Borrmann}, school = {Institute of Mechanics and Fluid Dynamics, TU Bergakademie Freiberg}, year = {2014}, month = {12} } @mastersthesis{Medack2014, title = {Untersuchungen zur Beeinflussung der örtlichen Aufgabegutverteilung auf der Schurre eines Hammerbrechers (in german)}, author = {Medack, Jörg}, school = {Institute for Mineral Processing Machines, TU Bergakademie Freiberg}, year = {2014}, month = {8} } @phdthesis{Maurin2015, author = {Raphael Maurin}, school = {Université Grenoble Alpes}, title = {Investigation of granular behavior in bedload transport using an Eulerian-Lagrangian model}, year = {2015}, url = {https://yade-dem.org/publi/PhD_MAURIN_VF.pdf} } @mastersthesis{Morales2012a, title={Cave Back Estimation Through Discrete Element Method, Based on Production Information}, author={D. Morales}, year={2012}, school={Universidad de Chile}, url={https://dl.dropboxusercontent.com/u/7663386/0_tesis.pdf} } trunk-2017.01a/examples/000077500000000000000000000000001304022710500150005ustar00rootroot00000000000000trunk-2017.01a/examples/2D-Tori.py000066400000000000000000000032751304022710500165410ustar00rootroot00000000000000#!/usr/local/bin/yade-trunk -x # -*- coding: utf-8 -*- #Author : Kneib François, francois.kneib@gmail.com #This script is designed to show the "circleView" features, which allow to display circles instead of spheres for 2D simulations. #/!\ this is just a DISPLAY FEATURE, computed particles still are SPHERICAL. from yade import qt X=1 Y=1 Z=1 O.periodic=True O.cell.hSize=Matrix3( X, 0, 0, 0, Y, 0, 0, 0, Z) O.materials.append(FrictMat(density=1000,young=1e5,poisson=0.5,frictionAngle=radians(20),label='sphereMat')) #Generate the 2D packing. Y is the "flat" axis. sp=pack.SpherePack() sp.makeCloud((0.,Y/2.,0.),(X,Y/2.,Z),rMean=X/50.,rRelFuzz=0.1) sp.toSimulation(material='sphereMat') O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), NewtonIntegrator(damping=0.1, gravity=(0.,0.,-10)), ] O.dt=2e-06 #Block the "flat" axis (Y), and only allow rotations around it. for i in O.bodies: i.state.blockedDOFs="yXZ" i.shape.color=(0.,0.,1.) #Fix some spheres to make the simulation "interesting". for i in range(0,int(len(O.bodies)/10)): O.bodies[i].state.blockedDOFs="xyzXYZ" O.bodies[i].shape.color=(1.,0.,0.) #Enable 3D view. qt.View() #Activate the circle (torus) view Gl1_Sphere.circleView=1 #Thickness of the circles : Gl1_Sphere.circleRelThickness=0.3 #Tell the viewer which axis is "flat", so that it can rotate the tori around the two others to make them face to the "flat" axis. Gl1_Sphere.circleAllowedRotationAxis='y' #Make the background white R=yade.qt.Renderer() R.bgColor=(1.,1.,1.) R.intrPhys=True trunk-2017.01a/examples/FEMxDEM/000077500000000000000000000000001304022710500161255ustar00rootroot00000000000000trunk-2017.01a/examples/FEMxDEM/biaxialSmooth.py000066400000000000000000000065561304022710500213160ustar00rootroot00000000000000""" Author: Ning Guo run `mv biaxialSmooth.yade.gz 0.yade.gz` to generate initial RVE packing """ from esys.escript import * from esys.finley import Rectangle from esys.weipa import saveVTK from esys.escript.pdetools import Projector from msFEM2D import MultiScale from saveGauss import saveGauss2D import time vel = -0.0001; confining=-1.e5; lx = 0.05; ly = 0.1; # sample size, 50mm by 100mm nx = 8; ny = 16; # sample discretization, 8 by 16 quadrilateral elements mydomain = Rectangle(l0=lx,l1=ly,n0=nx,n1=ny,order=2,integrationOrder=2) dim = mydomain.getDim() k = kronecker(mydomain) numg = 4*nx*ny; # number of Gauss points, 4 GP each element (reduced integration) nump = 16; # number of processes for multiprocessing prob = MultiScale(domain=mydomain,ng=numg,np=nump,random=False,rtol=1e-2,usePert=False,pert=-2.e-5,verbose=True) disp = Vector(0.,Solution(mydomain)) t=0 stress = prob.getCurrentStress() # initial stress proj = Projector(mydomain) sig = proj(stress) # project Gauss point value to nodal value sig_bounda = interpolate(sig,FunctionOnBoundary(mydomain)) # interpolate traction = matrix_mult(sig_bounda,mydomain.getNormal()) # boundary traction x = mydomain.getX() # nodal coordinate bx = FunctionOnBoundary(mydomain).getX() topSurf = whereZero(bx[1]-sup(bx[1])) tractTop = traction*topSurf # traction at top surface forceTop = integrate(tractTop,where=FunctionOnBoundary(mydomain)) # resultant force at top lengthTop = integrate(topSurf,where=FunctionOnBoundary(mydomain)) # length of top surface fout=file('./result/biaxial_surf.dat','w') fout.write('0 '+str(forceTop[1])+' '+str(lengthTop)+'\n') # Dirichlet BC positions, smooth at bottom and top, fixed at the center of bottom Dbc = whereZero(x[1])*[0,1]+whereZero(x[1]-ly)*[0,1]+whereZero(x[1])*whereZero(x[0]-.5*lx)*[1,1] # Dirichlet BC values Vbc = whereZero(x[1])*[0,0]+whereZero(x[1]-ly)*[0,vel]+whereZero(x[1])*whereZero(x[0]-.5*lx)*[0,0] # Neumann BC, constant confining pressure Nbc = whereZero(bx[0])*[-confining,0]+whereZero(bx[0]-lx)*[confining,0] time_start = time.time() while t < 100: # apply 100 load steps prob.initialize(f=Nbc, specified_u_mask=Dbc, specified_u_val=Vbc) # initialize BC t += 1 du=prob.solve(iter_max=100) # get solution: nodal displacement disp += du stress=prob.getCurrentStress() dom = prob.getDomain() # domain is updated Lagrangian formulation proj = Projector(dom) sig = proj(stress) sig_bounda = interpolate(sig,FunctionOnBoundary(dom)) traction = matrix_mult(sig_bounda,dom.getNormal()) tractTop = traction*topSurf forceTop = integrate(tractTop,where=FunctionOnBoundary(dom)) lengthTop = integrate(topSurf,where=FunctionOnBoundary(dom)) fout.write(str(t*vel/ly)+' '+str(forceTop[1])+' '+str(lengthTop)+'\n') vR=prob.getLocalVoidRatio() fabric=prob.getLocalFabric() strain = prob.getCurrentStrain() saveGauss2D(name='./result/gauss/time_'+str(t)+'.dat',strain=strain,stress=stress,fabric=fabric) volume_strain = trace(strain) dev_strain = symmetric(strain) - volume_strain*k/dim shear = sqrt(2*inner(dev_strain,dev_strain)) saveVTK("./result/vtk/biaxialSmooth_%d.vtu"%t,disp=disp,shear=shear,e=vR) prob.getCurrentPacking(pos=(),time=t,prefix='./result/packing/') time_elapse = time.time() - time_start fout.write("#Elapsed time in hours: "+str(time_elapse/3600.)+'\n') fout.close() prob.exitSimulation() trunk-2017.01a/examples/FEMxDEM/footing.msh000066400000000000000000012424201304022710500203100ustar00rootroot00000000000000$MeshFormat 2.2 0 8 $EndMeshFormat $Nodes 5151 1 0 0 0 2 0.4 0 0 3 0.6 0 0 4 0.6 -0.3 0 5 0.6 -0.4 0 6 0.4 -0.4 0 7 0 -0.4 0 8 0 -0.3 0 9 0.4 -0.3 0 10 0.009999999999981926 0 0 11 0.01999999999996121 0 0 12 0.02999999999994401 0 0 13 0.03999999999992994 0 0 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4907 4908 4793 2562 9 2 0 3 4390 208 209 4908 248 4909 2563 9 2 0 3 4390 209 4391 4909 4910 4796 2564 9 2 0 3 4391 209 210 4910 249 4911 2565 9 2 0 3 4391 210 4392 4911 4912 4799 2566 9 2 0 3 4392 210 211 4912 250 4913 2567 9 2 0 3 4392 211 4393 4913 4914 4802 2568 9 2 0 3 4393 211 212 4914 251 4915 2569 9 2 0 3 4393 212 4394 4915 4916 4805 2570 9 2 0 3 4394 212 213 4916 252 4917 2571 9 2 0 3 4394 213 4395 4917 4918 4808 2572 9 2 0 3 4395 213 214 4918 253 4919 2573 9 2 0 3 4395 214 4396 4919 4920 4811 2574 9 2 0 3 4396 214 215 4920 254 4921 2575 9 2 0 3 4396 215 4397 4921 4922 4814 2576 9 2 0 3 4397 215 216 4922 255 4923 2577 9 2 0 3 4397 216 4398 4923 4924 4817 2578 9 2 0 3 4398 216 217 4924 256 4925 2579 9 2 0 3 4398 217 4399 4925 4926 4820 2580 9 2 0 3 4399 217 218 4926 257 4927 2581 9 2 0 3 4399 218 4400 4927 4928 4823 2582 9 2 0 3 4400 218 219 4928 258 4929 2583 9 2 0 3 4400 219 4401 4929 4930 4826 2584 9 2 0 3 4401 219 220 4930 259 4931 2585 9 2 0 3 4401 220 4402 4931 4932 4829 2586 9 2 0 3 4402 220 221 4932 260 4933 2587 9 2 0 3 4402 221 4403 4933 4934 4832 2588 9 2 0 3 4403 221 222 4934 261 4935 2589 9 2 0 3 4403 222 4404 4935 4936 4835 2590 9 2 0 3 4404 222 223 4936 262 4937 2591 9 2 0 3 4404 223 4405 4937 4938 4838 2592 9 2 0 3 4405 223 224 4938 263 4939 2593 9 2 0 3 4405 224 4406 4939 4940 4841 2594 9 2 0 3 4406 224 225 4940 264 4941 2595 9 2 0 3 4406 225 4407 4941 4942 4844 2596 9 2 0 3 4407 225 226 4942 265 4943 2597 9 2 0 3 4407 226 4408 4943 4944 4847 2598 9 2 0 3 4408 226 227 4944 266 4945 2599 9 2 0 3 4408 227 4409 4945 4946 4850 2600 9 2 0 3 4409 227 228 4946 267 4947 2601 9 2 0 3 4409 228 4410 4947 4948 4853 2602 9 2 0 3 4410 228 229 4948 268 4949 2603 9 2 0 3 4410 229 4411 4949 4950 4856 2604 9 2 0 3 4411 229 230 4950 269 4951 2605 9 2 0 3 4411 230 4412 4951 4952 4859 2606 9 2 0 3 4412 230 231 4952 270 4953 2607 9 2 0 3 4412 231 4413 4953 4954 4862 2608 9 2 0 3 4413 231 232 4954 271 4955 2609 9 2 0 3 4413 232 4414 4955 4956 4865 2610 9 2 0 3 4414 232 233 4956 272 4957 2611 9 2 0 3 4414 233 4415 4957 4958 4868 2612 9 2 0 3 4415 233 234 4958 273 4959 2613 9 2 0 3 4415 234 4416 4959 4960 4871 2614 9 2 0 3 4416 234 235 4960 274 4961 2615 9 2 0 3 4416 235 4417 4961 4962 4874 2616 9 2 0 3 4417 235 236 4962 275 4963 2617 9 2 0 3 4417 236 4418 4963 4964 4877 2618 9 2 0 3 4418 236 237 4964 276 4965 2619 9 2 0 3 4418 237 4419 4965 4966 4880 2620 9 2 0 3 4419 237 238 4966 277 4967 2621 9 2 0 3 4419 238 4420 4967 4968 4883 2622 9 2 0 3 4420 238 239 4968 278 4969 2623 9 2 0 3 4420 239 4421 4969 4970 4886 2624 9 2 0 3 4421 239 240 4970 279 4971 2625 9 2 0 3 4421 240 4422 4971 4972 4889 2626 9 2 0 3 4422 240 241 4972 280 4973 2627 9 2 0 3 4422 241 4423 4973 4974 4892 2628 9 2 0 3 4423 241 242 4974 281 4975 2629 9 2 0 3 4423 242 4424 4975 4976 4895 2630 9 2 0 3 4424 242 243 4976 282 4977 2631 9 2 0 3 4424 243 4425 4977 4978 4898 2632 9 2 0 3 4425 243 244 4978 283 4979 2633 9 2 0 3 4425 244 352 4979 4980 4901 2634 9 2 0 3 352 244 6 4980 284 356 2635 9 2 0 4 9 355 187 360 5017 196 2636 9 2 0 4 187 355 4981 5017 5018 5019 2637 9 2 0 4 187 4981 188 5019 5020 197 2638 9 2 0 4 188 4981 4982 5020 5021 5022 2639 9 2 0 4 188 4982 189 5022 5023 198 2640 9 2 0 4 189 4982 4983 5023 5024 5025 2641 9 2 0 4 189 4983 190 5025 5026 199 2642 9 2 0 4 190 4983 4984 5026 5027 5028 2643 9 2 0 4 190 4984 191 5028 5029 200 2644 9 2 0 4 191 4984 4985 5029 5030 5031 2645 9 2 0 4 191 4985 192 5031 5032 201 2646 9 2 0 4 192 4985 4986 5032 5033 5034 2647 9 2 0 4 192 4986 193 5034 5035 202 2648 9 2 0 4 193 4986 4987 5035 5036 5037 2649 9 2 0 4 193 4987 194 5037 5038 203 2650 9 2 0 4 194 4987 4988 5038 5039 5040 2651 9 2 0 4 194 4988 195 5040 5041 204 2652 9 2 0 4 195 4988 4989 5041 5042 5043 2653 9 2 0 4 195 4989 4 5043 5044 205 2654 9 2 0 4 4 4989 403 5044 5045 408 2655 9 2 0 4 355 354 4981 359 5046 5018 2656 9 2 0 4 4981 354 4990 5046 5047 5048 2657 9 2 0 4 4981 4990 4982 5048 5049 5021 2658 9 2 0 4 4982 4990 4991 5049 5050 5051 2659 9 2 0 4 4982 4991 4983 5051 5052 5024 2660 9 2 0 4 4983 4991 4992 5052 5053 5054 2661 9 2 0 4 4983 4992 4984 5054 5055 5027 2662 9 2 0 4 4984 4992 4993 5055 5056 5057 2663 9 2 0 4 4984 4993 4985 5057 5058 5030 2664 9 2 0 4 4985 4993 4994 5058 5059 5060 2665 9 2 0 4 4985 4994 4986 5060 5061 5033 2666 9 2 0 4 4986 4994 4995 5061 5062 5063 2667 9 2 0 4 4986 4995 4987 5063 5064 5036 2668 9 2 0 4 4987 4995 4996 5064 5065 5066 2669 9 2 0 4 4987 4996 4988 5066 5067 5039 2670 9 2 0 4 4988 4996 4997 5067 5068 5069 2671 9 2 0 4 4988 4997 4989 5069 5070 5042 2672 9 2 0 4 4989 4997 4998 5070 5071 5072 2673 9 2 0 4 4989 4998 403 5072 5073 5045 2674 9 2 0 4 403 4998 402 5073 5074 407 2675 9 2 0 4 354 353 4990 358 5075 5047 2676 9 2 0 4 4990 353 4999 5075 5076 5077 2677 9 2 0 4 4990 4999 4991 5077 5078 5050 2678 9 2 0 4 4991 4999 5000 5078 5079 5080 2679 9 2 0 4 4991 5000 4992 5080 5081 5053 2680 9 2 0 4 4992 5000 5001 5081 5082 5083 2681 9 2 0 4 4992 5001 4993 5083 5084 5056 2682 9 2 0 4 4993 5001 5002 5084 5085 5086 2683 9 2 0 4 4993 5002 4994 5086 5087 5059 2684 9 2 0 4 4994 5002 5003 5087 5088 5089 2685 9 2 0 4 4994 5003 4995 5089 5090 5062 2686 9 2 0 4 4995 5003 5004 5090 5091 5092 2687 9 2 0 4 4995 5004 4996 5092 5093 5065 2688 9 2 0 4 4996 5004 5005 5093 5094 5095 2689 9 2 0 4 4996 5005 4997 5095 5096 5068 2690 9 2 0 4 4997 5005 5006 5096 5097 5098 2691 9 2 0 4 4997 5006 4998 5098 5099 5071 2692 9 2 0 4 4998 5006 5007 5099 5100 5101 2693 9 2 0 4 4998 5007 402 5101 5102 5074 2694 9 2 0 4 402 5007 401 5102 5103 406 2695 9 2 0 4 353 352 4999 357 5104 5076 2696 9 2 0 4 4999 352 5008 5104 5105 5106 2697 9 2 0 4 4999 5008 5000 5106 5107 5079 2698 9 2 0 4 5000 5008 5009 5107 5108 5109 2699 9 2 0 4 5000 5009 5001 5109 5110 5082 2700 9 2 0 4 5001 5009 5010 5110 5111 5112 2701 9 2 0 4 5001 5010 5002 5112 5113 5085 2702 9 2 0 4 5002 5010 5011 5113 5114 5115 2703 9 2 0 4 5002 5011 5003 5115 5116 5088 2704 9 2 0 4 5003 5011 5012 5116 5117 5118 2705 9 2 0 4 5003 5012 5004 5118 5119 5091 2706 9 2 0 4 5004 5012 5013 5119 5120 5121 2707 9 2 0 4 5004 5013 5005 5121 5122 5094 2708 9 2 0 4 5005 5013 5014 5122 5123 5124 2709 9 2 0 4 5005 5014 5006 5124 5125 5097 2710 9 2 0 4 5006 5014 5015 5125 5126 5127 2711 9 2 0 4 5006 5015 5007 5127 5128 5100 2712 9 2 0 4 5007 5015 5016 5128 5129 5130 2713 9 2 0 4 5007 5016 401 5130 5131 5103 2714 9 2 0 4 401 5016 400 5131 5132 405 2715 9 2 0 4 352 6 5008 356 5133 5105 2716 9 2 0 4 5008 6 285 5133 294 5134 2717 9 2 0 4 5008 285 5009 5134 5135 5108 2718 9 2 0 4 5009 285 286 5135 295 5136 2719 9 2 0 4 5009 286 5010 5136 5137 5111 2720 9 2 0 4 5010 286 287 5137 296 5138 2721 9 2 0 4 5010 287 5011 5138 5139 5114 2722 9 2 0 4 5011 287 288 5139 297 5140 2723 9 2 0 4 5011 288 5012 5140 5141 5117 2724 9 2 0 4 5012 288 289 5141 298 5142 2725 9 2 0 4 5012 289 5013 5142 5143 5120 2726 9 2 0 4 5013 289 290 5143 299 5144 2727 9 2 0 4 5013 290 5014 5144 5145 5123 2728 9 2 0 4 5014 290 291 5145 300 5146 2729 9 2 0 4 5014 291 5015 5146 5147 5126 2730 9 2 0 4 5015 291 292 5147 301 5148 2731 9 2 0 4 5015 292 5016 5148 5149 5129 2732 9 2 0 4 5016 292 293 5149 302 5150 2733 9 2 0 4 5016 293 400 5150 5151 5132 2734 9 2 0 4 400 293 5 5151 303 404 $EndElements trunk-2017.01a/examples/FEMxDEM/footing.py000066400000000000000000000067411304022710500201540ustar00rootroot00000000000000""" Author: Ning Guo run `mv footing.yade.gz 0.yade.gz` to generate initial RVE packing """ from esys.escript import * from esys.finley import ReadGmsh from esys.weipa import saveVTK from esys.escript.pdetools import Projector from msFEM import MultiScale from saveGauss import saveGauss2D import time vel = -0.00025; surcharge=-20.e3; # surcharge equals to the initial vertical stress of the RVE packing dim = 2; B = 0.05; L = 0.6; H = 0.4; mydomain = ReadGmsh('footing.msh',numDim=dim,integrationOrder=2) # read Gmsh mesh with 6-node triangle element (2500 tri6); each element has 3 Gauss points k = kronecker(mydomain) numg = 3*2500; # number of Gauss points nump = 16; # number of processes in multiprocessing packNo=range(0,numg,50) prob = MultiScale(domain=mydomain,ng=numg,np=nump,random=False,rtol=1e-2,usePert=False,pert=-2.e-5,verbose=False) disp = Vector(0.,Solution(mydomain)) t=0 stress = prob.getCurrentStress() proj = Projector(mydomain) sig = proj(stress) sig_bounda = interpolate(sig,FunctionOnBoundary(mydomain)) traction = matrix_mult(sig_bounda,mydomain.getNormal()) x = mydomain.getX() bx = FunctionOnBoundary(mydomain).getX() footingBase = whereZero(bx[1]-sup(bx[1]))*whereNonPositive(bx[0]-B) tractFoot = traction*footingBase forceFoot = integrate(tractFoot,where=FunctionOnBoundary(mydomain)) lengthFoot = integrate(footingBase,where=FunctionOnBoundary(mydomain)) fout=file('./result/bearing.dat','w') fout.write('0 '+str(forceFoot[0])+' '+str(forceFoot[1])+' '+str(lengthFoot)+'\n') # Dirichlet BC, rollers at left and right, fixties at bottom, rigid and rough footing Dbc = whereZero(x[0])*[1,0]+whereZero(x[0]-sup(x[0]))*[1,0]+whereZero(x[1]-inf(x[1]))*[1,1]+whereZero(x[1]-sup(x[1]))*whereNonPositive(x[0]-B)*[1,1] Vbc = whereZero(x[0])*[0,0]+whereZero(x[0]-sup(x[0]))*[0,0]+whereZero(x[1]-inf(x[1]))*[0,0]+whereZero(x[1]-sup(x[1]))*whereNonPositive(x[0]-B)*[0,vel] # Neumann BC, surcharge at the rest area of the top surface Nbc = whereZero(bx[1]-sup(bx[1]))*wherePositive(bx[0]-B)*[0,surcharge] time_start = time.time() while t < 58: # apply 58 loading step; further loading would abort the program due to severe mesh distortion prob.initialize(f=Nbc, specified_u_mask=Dbc, specified_u_val=Vbc) t += 1 du=prob.solve(iter_max=100) disp += du stress=prob.getCurrentStress() dom = prob.getDomain() # domain updated (Lagrangian) proj = Projector(dom) sig = proj(stress) sig_bounda = interpolate(sig,FunctionOnBoundary(dom)) traction = matrix_mult(sig_bounda,dom.getNormal()) tractFoot = traction*footingBase forceFoot = integrate(tractFoot,where=FunctionOnBoundary(dom)) lengthFoot = integrate(footingBase,where=FunctionOnBoundary(dom)) fout.write(str(t*vel)+' '+str(forceFoot[0])+' '+str(forceFoot[1])+' '+str(lengthFoot)+'\n') vR=prob.getLocalVoidRatio() rotation=prob.getLocalAvgRotation() fabric=prob.getLocalFabric() strain = prob.getCurrentStrain() saveGauss2D(name='./result/gauss/time_'+str(t)+'.dat',strain=strain,stress=stress,fabric=fabric) volume_strain = trace(strain) dev_strain = symmetric(strain) - volume_strain*k/dim shear = sqrt(2*inner(dev_strain,dev_strain)) saveVTK("./result/vtk/footing_%d.vtu"%t,disp=disp,stress=stress,shear=shear,e=vR,rot=rotation) prob.getCurrentPacking(pos=packNo,time=t,prefix='./result/packing/') # output packing time_elapse = time.time() - time_start fout.write("#Elapsed time in hours: "+str(time_elapse/3600.)+'\n') fout.close() prob.exitSimulation() trunk-2017.01a/examples/FEMxDEM/prepareRVE.py000066400000000000000000000027551304022710500205230ustar00rootroot00000000000000from yade import pack O.materials.append(FrictMat(young=6.e8,poisson=.8,frictionAngle=.0)) sp = pack.SpherePack() size = .24 sp.makeCloud(minCorner=(0,0,.05),maxCorner=(size,size,.05),rMean=.005,rRelFuzz=.4,num=400,periodic=True,seed=1) sp.toSimulation() O.cell.hSize = Matrix3(size,0,0, 0,size,0, 0,0,.1) print len(O.bodies) for p in O.bodies: p.state.blockedDOFs = 'zXY' p.state.mass = 2650 * 0.1 * pi * p.shape.radius**2 # 0.1 = thickness of cylindrical particle inertia = 0.5 * p.state.mass * p.shape.radius**2 p.state.inertia = (.5*inertia,.5*inertia,inertia) O.dt = utils.PWaveTimeStep() print O.dt O.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), PeriTriaxController( dynCell=True, goal=(-1.e5,-1.e5,0), stressMask=3, relStressTol=.001, maxUnbalanced=.001, maxStrainRate=(.5,.5,.0), doneHook='term()', label='biax' ), NewtonIntegrator(damping=.1) ] def term(): O.engines = O.engines[:3]+O.engines[4:] print getStress() print O.cell.hSize setContactFriction(0.5) O.cell.trsf=Matrix3.Identity O.cell.velGrad=Matrix3.Zero for p in O.bodies: p.state.vel = Vector3.Zero p.state.angVel = Vector3.Zero p.state.refPos = p.state.pos p.state.refOri = p.state.ori O.save('0.yade.gz') O.pause() O.run();O.wait() trunk-2017.01a/examples/FEMxDEM/retainingSmooth.py000066400000000000000000000063701304022710500216570ustar00rootroot00000000000000""" Author: Ning Guo run `mv retainingSmooth.yade.gz 0.yade.gz` to generate initial RVE packing """ from esys.escript import * from esys.finley import Rectangle from esys.weipa import saveVTK from esys.escript.pdetools import Projector from msFEM2D import MultiScale from saveGauss import saveGauss2D import time vel = -0.00017; surcharge=-2.e4; # surcharge equals to the initial vertical stress of the RVE packing; vel<0 passive failure; vel>0 active failure B = 0.4; H = 0.2; wallH = 0.17; baseH = H-wallH; # setup dimensions nx = 40; ny = 20 # discretization with 40x20 quads mydomain = Rectangle(l0=B,l1=H,n0=nx,n1=ny,order=2,integrationOrder=2) dim = mydomain.getDim() k = kronecker(mydomain) numg = 4*nx*ny; nump = 16; packNo=range(0,numg,16) disp = Vector(0.,Solution(mydomain)) prob = MultiScale(domain=mydomain,ng=numg,np=nump,random=False,rtol=1e-2,usePert=False,pert=-2.e-5,verbose=True) t=0 time_start = time.time() x = mydomain.getX() bx = FunctionOnBoundary(mydomain).getX() left = whereZero(x[0]) right = whereZero(x[0]-B) bottom = whereZero(x[1]) top = whereZero(bx[1]-H) base = whereZero(x[0]-B)*whereNegative(x[1]-baseH) wall = whereZero(x[0]-B)*whereNonNegative(x[1]-baseH) wallBF = whereZero(bx[0]-B)*whereNonNegative(bx[1]-baseH) # Dirichlet BC, all fixed in space except wall (only fixed in x direction, smooth) Dbc = left*[1,1]+base*[1,1]+bottom*[1,1]+wall*[1,0] Vbc = left*[0,0]+base*[0,0]+bottom*[0,0]+wall*[vel,0] # Neumann BC, apply surcharge at the top surface Nbc = top*[0,surcharge] stress = prob.getCurrentStress() proj = Projector(mydomain) sig = proj(stress) sig_bounda = interpolate(sig,FunctionOnBoundary(mydomain)) traction = matrix_mult(sig_bounda,mydomain.getNormal()) tract = traction*wallBF # traction on wall forceWall = integrate(tract,where=FunctionOnBoundary(mydomain)) # force on wall lengthWall = integrate(wallBF,where=FunctionOnBoundary(mydomain)) fout=file('./result/pressure.dat','w') fout.write('0 '+str(forceWall[0])+' '+str(lengthWall)+'\n') while t < 100: prob.initialize(f=Nbc,specified_u_mask=Dbc,specified_u_val=Vbc) t += 1 du=prob.solve(iter_max=100) disp += du stress=prob.getCurrentStress() dom = prob.getDomain() proj = Projector(dom) sig = proj(stress) sig_bounda = interpolate(sig,FunctionOnBoundary(dom)) traction = matrix_mult(sig_bounda,dom.getNormal()) tract = traction*wallBF forceWall = integrate(tract,where=FunctionOnBoundary(dom)) lengthWall = integrate(wallBF,where=FunctionOnBoundary(dom)) fout.write(str(t*vel)+' '+str(forceWall[0])+' '+str(lengthWall)+'\n') vR=prob.getLocalVoidRatio() rotation=prob.getLocalAvgRotation() fabric=prob.getLocalFabric() strain = prob.getCurrentStrain() saveGauss2D(name='./result/gauss/time_'+str(t)+'.dat',strain=strain,stress=stress,fabric=fabric) volume_strain = trace(strain) dev_strain = symmetric(strain) - volume_strain*k/dim shear = sqrt(2*inner(dev_strain,dev_strain)) saveVTK("./result/vtk/retainingSmooth_%d.vtu"%t,disp=disp,stress=stress,shear=shear,e=vR,rot=rotation) prob.getCurrentPacking(pos=packNo,time=t,prefix='./result/packing/') time_elapse = time.time() - time_start fout.write("#Elapsed time in hours: "+str(time_elapse/3600.)+'\n') fout.close() prob.exitSimulation() trunk-2017.01a/examples/FEMxDEM/triaxialRough.py000066400000000000000000000060111304022710500213170ustar00rootroot00000000000000""" Author: Ning Guo run `mv triaxialRough.yade.gz 0.yade.gz` to generate initial RVE packing """ from esys.escript import * from esys.finley import Brick from esys.weipa import saveVTK from esys.escript.pdetools import Projector from msFEM3D import MultiScale from saveGauss import saveGauss3D import time vel = -0.0001; confining=-1.e5; lx = 0.05; ly = 0.05; lz = 0.1; # sample dimension nx = 8; ny = 8; nz = 16; # discretization mydomain = Brick(l0=lx,l1=ly,l2=lz,n0=nx,n1=ny,n2=nz,order=2,integrationOrder=2) # 20-noded,8-Gauss hexahedral element dim = 3; k = kronecker(mydomain) numg = 8*nx*ny*nz; # number of Gauss points packNo=range(0,numg,8) prob = MultiScale(domain=mydomain,ng=numg,useMPI=True,rtol=1e-2) # mpi is activated disp = Vector(0.,Solution(mydomain)) t=0 stress = prob.getCurrentStress() proj = Projector(mydomain) sig = proj(stress) sig_bounda = interpolate(sig,FunctionOnBoundary(mydomain)) traction = matrix_mult(sig_bounda,mydomain.getNormal()) # traction on boundary x = mydomain.getX() bx = FunctionOnBoundary(mydomain).getX() topSurf = whereZero(bx[2]-lz) tractTop = traction*topSurf # traction on top surface forceTop = integrate(tractTop,where=FunctionOnBoundary(mydomain)) # force on top areaTop = integrate(topSurf,where=FunctionOnBoundary(mydomain)) fout=file('./result/resultant.dat','w') fout.write('0 '+str(forceTop[2])+' '+str(areaTop)+'\n') # Dirichlet BC, rough loading ends Dbc = whereZero(x[2])*[1,1,1]+whereZero(x[2]-lz)*[1,1,1] Vbc = whereZero(x[2])*[0,0,0]+whereZero(x[2]-lz)*[0,0,vel] # Neumann BC, constant lateral confining Nbc = whereZero(bx[0])*[-confining,0,0]+whereZero(bx[0]-sup(bx[0]))*[confining,0,0]+whereZero(bx[1])*[0,-confining,0]+whereZero(bx[1]-sup(bx[1]))*[0,confining,0] time_start = time.time() while t < 100: prob.initialize(f=Nbc, specified_u_mask=Dbc, specified_u_val=Vbc) t += 1 du=prob.solve(iter_max=100) disp += du stress=prob.getCurrentStress() dom = prob.getDomain() proj = Projector(dom) sig = proj(stress) sig_bounda = interpolate(sig,FunctionOnBoundary(dom)) traction = matrix_mult(sig_bounda,dom.getNormal()) tractTop = traction*topSurf forceTop = integrate(tractTop,where=FunctionOnBoundary(dom)) areaTop = integrate(topSurf,where=FunctionOnBoundary(dom)) fout.write(str(t*vel/lz)+' '+str(forceTop[2])+' '+str(areaTop)+'\n') vR=prob.getLocalVoidRatio() rotation=prob.getLocalAvgRotation() fabric=prob.getLocalFabric() strain = prob.getCurrentStrain() saveGauss3D(name='./result/gauss/time_'+str(t)+'.dat',strain=strain,stress=stress,fabric=fabric) volume_strain = trace(strain) dev_strain = symmetric(strain) - volume_strain*k/dim shear = sqrt(2./3.*inner(dev_strain,dev_strain)) saveVTK("./result/vtk/triaxialRough_%d.vtu"%t,disp=disp,shear=shear,e=vR,rot=rotation) prob.getCurrentPacking(pos=packNo,time=t,prefix='./result/packing/') time_elapse = time.time() - time_start fout.write("#Elapsed time in hours: "+str(time_elapse/3600.)+'\n') fout.close() prob.exitSimulation() trunk-2017.01a/examples/FEMxDEM/undrain.py000066400000000000000000000074761304022710500201550ustar00rootroot00000000000000""" Author: Ning Guo run `mv undrain.yade.gz 0.yade.gz` to generate initial RVE packing """ from esys.escript import * from esys.finley import Rectangle from esys.weipa import saveVTK from esys.escript.pdetools import Projector from msFEMup import MultiScale from saveGauss import saveGauss2D import time confining = -2.e5; pore = 1.e5 # initial pore pressure perm = 0.001**2/(180.*8.9e-4); # unscaled permeability, using KC equation kf = 2.2e9 # fluid bulk modulus dt = .1; vel = -0.0001 # time step and loading speed lx = 0.05; ly = 0.1 # sample dimension nx = 8; ny = 16 # discretization mydomain = Rectangle(l0=lx,l1=ly,n0=nx,n1=ny,order=2,integrationOrder=2) k = kronecker(mydomain); dim = 2. numg = 4*nx*ny; # no. of Gauss points mpi = True # use MPI prob = MultiScale(domain=mydomain,pore0=pore,perm=perm,kf=kf,dt=dt,ng=numg,useMPI=mpi,rtol=1.e-2) disp = Vector(0.,Solution(mydomain)) t = 0 ux = mydomain.getX() # disp. node coordinate px = ReducedSolution(mydomain).getX() # press. node coordinate bx = FunctionOnBoundary(mydomain).getX() topSurf = whereZero(bx[1]-ly) uDbc = whereZero(ux[1])*[0,1]+whereZero(ux[0]-lx/2.)*whereZero(ux[1])*[1,1]+whereZero(ux[1]-ly)*[0,1] # disp. Dirichlet BC mask vDbc = whereZero(ux[1])*[0,0]+whereZero(ux[0]-lx/2.)*whereZero(ux[1])*[0,0]+whereZero(ux[1]-ly)*[0,vel*dt] # disp. Dirichlet BC value uNbc = whereZero(bx[0])*[-confining,0]+whereZero(bx[0]-lx)*[confining,0] # disp. Neumann BC stress = prob.getCurrentStress() # effective stress at GP proj = Projector(mydomain) sig = proj(stress) # effective stress at node (reduced) sig_bound = interpolate(sig,FunctionOnBoundary(mydomain)) traction = matrix_mult(sig_bound,mydomain.getNormal()) tractTop = traction*topSurf forceTop = integrate(tractTop,where=FunctionOnBoundary(mydomain)) lengthTop = integrate(topSurf,where=FunctionOnBoundary(mydomain)) fout = file('./result/resultantForce.dat','w') fout.write('0 '+str(forceTop[1])+' '+str(lengthTop)+'\n') time_start = time.time() while t < 400: prob.initialize(f=uNbc,umsk=uDbc,uvalue=vDbc) t += 1 du = prob.solve(globalIter=10,solidIter=50) disp += du pore = prob.getCurrentPore() # pore pressure at node (reduced) flux = prob.getCurrentFlux() # Darcy flux at GP stress = prob.getCurrentStress() # effective stress at GP strain = prob.getCurrentStrain() # disp. grad at GP volume_strain = trace(strain) # volumetric strain dev_strain = symmetric(strain) - volume_strain*k/dim # deviatoric strain shear = sqrt(2.*inner(dev_strain,dev_strain)) # shear strain fab = prob.getLocalFabric() # fabric tensor at GP dev_fab = 4.*(fab-trace(fab)/dim*k) anis = sqrt(.5*inner(dev_fab,dev_fab)) p = prob.getEquivalentPorosity() # porosity at GP rot = prob.getLocalAvgRotation() # average rotation at GP saveGauss2D(name='./result/gauss/time_'+str(t)+'.dat',strain=strain,fabric=fab,stress=stress) dom = prob.getDomain() # domain updated (Lagrangian) proj = Projector(dom) flux = proj(flux) # Darcy flux at node (reduced) p = proj(p) # porosity at node (reduced) shear = proj(shear) # shear strain at node (reduced) anis = proj(anis) rot = proj(rot) saveVTK("./result/vtk/undrain_%d.vtu"%t,disp=disp,pore=pore,flux=flux,shear=shear,p=p,anis=anis,rot=rot) sig = proj(stress) # effective stress at node (reduced) sig_bound = interpolate(sig,FunctionOnBoundary(dom)) traction = matrix_mult(sig_bound,dom.getNormal()) tractTop = traction*topSurf forceTop = integrate(tractTop,where=FunctionOnBoundary(dom)) lengthTop = integrate(topSurf,where=FunctionOnBoundary(dom)) fout.write(str(t*vel*dt/ly)+' '+str(forceTop[1])+' '+str(lengthTop)+'\n') prob.getCurrentPacking(time=t,prefix='./result/packing/') time_elapse = time.time() - time_start fout.write('#Elapsed time in hours: '+str(time_elapse/3600.)+'\n') fout.close() prob.exitSimulation() trunk-2017.01a/examples/FluidCouplingLBM/000077500000000000000000000000001304022710500200775ustar00rootroot00000000000000trunk-2017.01a/examples/FluidCouplingLBM/Buoyancy_Gradient.m000066400000000000000000000076121304022710500236710ustar00rootroot00000000000000%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %Authors: Luc Sibille luc.sibille@3sr-grenoble.fr % Franck Lomine franck.lomine@insa-rennes.fr % % Script to interpret the DEM-LBM buoyancy simulation performed with the script buoyancy.py % This script was written for the OZ ALERT school in Grenoble 2011 % Script updated in 2014 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% clear all close all radFactor = 0.6; rhoSolid = 3000; gravity = 0.1; %----- reading of LBM.log file logfile='LBM.log'; fid = fopen(logfile); tline = fgetl(fid); fscanf(fid,'%s %s %s',[3,1]); fscanf(fid,'%s',[1,1]); Lx0=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); Ly0=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); depth=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); thickness=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); NbBodies=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); dP=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); Nu=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); rhoFluid=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); dx=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); Nx=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); Ny=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); Nz=fscanf(fid,'%f',[1,1]); tline = fgetl(fid); tline = fgetl(fid); fscanf(fid,'%s',[1,1]); tau=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); omega=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); IterMax=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); SaveMode=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); IterSave=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); SaveGridRatio=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); IntervalLBM=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); LBMConvergenceCriterion=fscanf(fid,'%f',[1,1]); tline = fgetl(fid); tline = fgetl(fid); fscanf(fid,'%s %s',[2,1]); LBMdt=fscanf(fid,'%f',[1,1]); fclose(fid); %------------------------------- C=dx/LBMdt; Cs2=C^2/3; path1 = './lbm-nodes/' path2 = './dem-bodies/' fiVx=dir([path1 'Vx_*']); fiRho=dir([path1 'Rho_*']); fiBodies=dir([path2 'spheres_*']); nb_file =length(fiVx) for i=1:nb_file vxfile=[path1 fiVx(i).name] ux = importdata(vxfile); ux=ux'; Vdarcy(i) = mean( ux(1,:) ); rhofile=[path1 fiRho(i).name]; rho = importdata(rhofile); rho=rho'; DP(i) = Cs2*(rho(1,90)-rho(end,90)); fid2 = fopen([path2 fiBodies(i).name],'r'); [donnees2] = fscanf(fid2,'%d %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f %f',[17,inf]); id=donnees2(1,:); x=donnees2(2,:); y=donnees2(3,:); r=donnees2(5,:); fclose(fid2); clear donnees2 xmin(i)=min(x); xmax(i)=max(x); if i==1 %computation of Terzaghi critical hydraulic gradient Stotal = 0.005*(max(x+r)-min(x-r)); Ssolid = sum( pi*(r/radFactor).^2 ); Swater = Stotal-Ssolid; Wwater = rhoFluid*gravity*Swater; Wsolid = rhoSolid*gravity*Ssolid; %Wsolid = rhoSolid*gravity*sum( pi*(r/radFactor).^2 ); Wtotal = Wwater+Wsolid; HgradCrit = Wtotal/Stotal/(rhoFluid*gravity); end end L = xmax(1)-xmin(1); Hgrad = DP/(rhoFluid*gravity*L); figure(1) hold on %plot(DP,Vdarcy) plot(Hgrad,Vdarcy,'b') plot([HgradCrit HgradCrit], [0 max(Vdarcy)],'r') xlabel('Hydraulic gradient') ylabel('Darcy velocity') legend('Darcy velocity','Terzaghi critical gradient') figure(2) hold on % plot(DP,xmin,'b') % plot(DP,xmax,'r') plot(Hgrad,xmin,'b') plot(Hgrad,xmax,'g') plot([HgradCrit HgradCrit], [0 max(xmax)],'r') xlabel('Hydraulic gradient') ylabel('Max and min particle positions') legend('Top particle position','Bottom particle position','Terzaghi critical gradient') trunk-2017.01a/examples/FluidCouplingLBM/buoyancy.py000066400000000000000000000210441304022710500223030ustar00rootroot00000000000000############################################################################################################################## #Authors: Luc Sibille luc.sibille@3sr-grenoble.fr # Franck Lomine franck.lomine@insa-rennes.fr # # Script to simulate buoyancy in a granular assembly with the DEM-LBM coupling. # This script was written for a practical work in the OZ ALERT school in Grenoble 2011. # Script updated in 2014 ############################################################################################################################## from yade import pack,timing,utils rMean = 0.00035 #mean radius (m) of solid particles Gravity=-0.1 #gravity (m.s-2) that will be applied to solid particles #definition of the simulation domain (position of walls), the domain is a 3D domain but particles will be generated on a unique plane at z=0, be carefull that wall normal to z directions do not touch particles. lowerCornerW = (0.00001,0.00001,-0.002) upperCornerW = (0.00701,0.00501,0.002) #definitions of the domain for particles: positions in z direction is set to 0 to force a 2D granular assembly lowerCornerS = (0.00001,0.00001,0) upperCornerS = (0.00701,0.00501,0) nbSpheres = 70 #this not the real number of particles but number of times where we try to insert a new particle, the real number of particles can be much lower! ## Build of the engine vector O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), HydrodynamicsLawLBM( EngineIsActivated=False, WallYm_id=0, WallYp_id=1, WallXm_id=2, WallXp_id=3, WallZp_id=5, WallZm_id=4, useWallYm=1, useWallYp=1, YmBCType=2, YpBCType=2, useWallXm=0, useWallXp=0, XmBCType=1, XpBCType=1, LBMSavedData='spheres,velXY,rho,nodeBD', tau=1.1, dP=(0,0,0), IterSave=200, IterPrint=100, RadFactor=0.6, # The radius of particles seen by the LBM engine is reduced here by a factor RadFactor=0.6 to allow flow between particles in this 2D case. Nx=250, Rho=1000, Nu=1.0e-6, periodicity='', bc='', VbCutOff=0.0, applyForcesAndTorques=True, label="Elbm" ), NewtonIntegrator(damping=0.2,gravity=(Gravity,0.,0.),label="ENewton"), ] ############################################################################################################### # Creation of 6 walls at the limit of the simulation domain # defintiion of the material for walls O.materials.append(FrictMat(young=50e6,poisson=.5,frictionAngle=0.0,density=3000,label='walls')) ## create walls around the packing wallOversizeFactor=1.001 thickness=0.00001; #bottom box center= ((lowerCornerW[0]+upperCornerW[0])/2,lowerCornerW[1]-thickness/2.0,(lowerCornerW[2]+upperCornerW[2])/2) halfSize= (wallOversizeFactor*fabs(lowerCornerW[0]-upperCornerW[0])/2+thickness,thickness/2.0,wallOversizeFactor*fabs(lowerCornerW[2]-upperCornerW[2])/2+thickness) b1=utils.box(center=[center[0],center[1],center[2]],extents=[halfSize[0],halfSize[1],halfSize[2]],color=[0,1,0],fixed=True,wire=True,material='walls') O.bodies.append(b1) #-- #Top box center=((lowerCornerW[0]+upperCornerW[0])/2,upperCornerW[1]+thickness/2.0,(lowerCornerW[2]+upperCornerW[2])/2) halfSize =(wallOversizeFactor*fabs(lowerCornerW[0]-upperCornerW[0])/2+thickness,thickness/2.0,wallOversizeFactor*fabs(lowerCornerW[2]-upperCornerW[2])/2+thickness) b2=utils.box(center=[center[0],center[1],center[2]],extents=[halfSize[0],halfSize[1],halfSize[2]],color=[0,1,0],fixed=True,wire=True,material='walls') O.bodies.append(b2) #-- center=(lowerCornerW[0]-thickness/2.0,(lowerCornerW[1]+upperCornerW[1])/2,(lowerCornerW[2]+upperCornerW[2])/2) halfSize=(thickness/2.0,wallOversizeFactor*fabs(lowerCornerW[1]-upperCornerW[1])/2+thickness,wallOversizeFactor*fabs(lowerCornerW[2]-upperCornerW[2])/2+thickness) b3=utils.box(center=[center[0],center[1],center[2]],extents=[halfSize[0],halfSize[1],halfSize[2]],color=[0,1,0],fixed=True,wire=True,material='walls') O.bodies.append(b3) #-- center=(upperCornerW[0]+thickness/2.0,(lowerCornerW[1]+upperCornerW[1])/2,(lowerCornerW[2]+upperCornerW[2])/2) halfSize=(thickness/2.0,wallOversizeFactor*fabs(lowerCornerW[1]-upperCornerW[1])/2+thickness,wallOversizeFactor*fabs(lowerCornerW[2]-upperCornerW[2])/2+thickness) b4=utils.box(center=[center[0],center[1],center[2]],extents=[halfSize[0],halfSize[1],halfSize[2]],color=[0,1,0],fixed=True,wire=True,material='walls') O.bodies.append(b4) #-- center=((lowerCornerW[0]+upperCornerW[0])/2,(lowerCornerW[1]+upperCornerW[1])/2,lowerCornerW[2]-thickness/2.0) halfSize=(wallOversizeFactor*fabs(lowerCornerW[0]-upperCornerW[0])/2+thickness,wallOversizeFactor*fabs(lowerCornerW[1]-upperCornerW[1])/2+thickness,thickness/2.0) b5=utils.box(center=[center[0],center[1],center[2]],extents=[halfSize[0],halfSize[1],halfSize[2]],color=[0,1,0],fixed=True,wire=True,material='walls') O.bodies.append(b5) #-- center=((lowerCornerW[0]+upperCornerW[0])/2,(lowerCornerW[1]+upperCornerW[1])/2,upperCornerW[2]+thickness/2.0) halfSize=(wallOversizeFactor*fabs(lowerCornerW[0]-upperCornerW[0])/2+thickness,wallOversizeFactor*fabs(lowerCornerW[1]-upperCornerW[1])/2+thickness,thickness/2.0); b6=utils.box(center=[center[0],center[1],center[2]],extents=[halfSize[0],halfSize[1],halfSize[2]],color=[0,1,0],fixed=True,wire=True,material='walls') O.bodies.append(b6) ############################################################################################################### # Creation of the assembly of particles # defintiion of the material for particles O.materials.append(FrictMat(young=50e6,poisson=.5,frictionAngle=35*3.1415926535/180,density=3000,label='spheres')) ## use a SpherePack object to generate a random loose particles packing sp=pack.SpherePack() sp.makeCloud(lowerCornerS,upperCornerS,-1,0.33,nbSpheres,False, 0.5,seed=1) #"seed" make the "random" generation always the same sp.toSimulation(material='spheres') # loop over bodies to change their 3D inertia into 2D inertia (by default in YADE particles are 3D spheres, here we want to cylinder with a length=1). for s in O.bodies: if isinstance(s.shape,Box): continue r=s.shape.radius oldm=s.state.mass oldI=s.state.inertia m=oldm*3./4./r s.state.mass=m s.state.inertia[0] = 15./16./r*oldI[0] #inertia with respect to x and y axes are not used and the computation here is wrong s.state.inertia[1] = 15./16./r*oldI[1] #inertia with respect to x and y axes are not used and the computation here is wrong s.state.inertia[2] = 15./16./r*oldI[2] #only inertia with respect to z axis is usefull O.dt=0.00005 #use a fix value of time step, it is better to not use a time stepper computing a new step at each iteration since DEM time step is eventually fixed by the LBM engine. yade.qt.View() #to see what is happening print"___________________" print"PHASE 1" print "Settlement of particle under gravity only, fluid flow is not activated at the present time... please wait" print"___________________" O.run(60000,1) #settlement of particle under gravity only, no action of the fluid flow. #definition of a runnable python function to increase progressively the fluid pressure gradient. def IncrDP(): currentDP=Elbm.dP Elbm.dP=(currentDP[0]+1.0/10000.0,0,0) #O.engines[6].dP=currentDP+1.0/100.0 if not(O.iter%100): print "dP=", Elbm.dP[0] O.engines=O.engines+[PyRunner(iterPeriod=1,command='IncrDP()')] #Necessary to initiate correctly the LBM engine O.resetTime() #Activation of the LBM engine Elbm.EngineIsActivated=True #Cundall damping for solid particles removed (the fluid viscosity should be enough to damp the solid particles ... in general, not always...) ENewton.damping=0.0 # Now you just need to run the simulation as long as you want to ... note that if you wait to long the pressure gradient will become very large inducing great fluid velocities, and the fluid simulation may become crazy!! Look at the Mach number (M) printed in the console, it should not be too high... print"___________________" print"PHASE 2" print "Fluid flow has been activated now with a gradual increase of the pressure gradient." print "Run the simulation, until the pressure gradient is strong enough to compensate the gravity forces, then particles will mouve to the right." print"..." print"..." print "Velocity and pressure field of the fluid can be plotted with the matlab script yadeLBMvisu.m" print "Terzaghi critical hydraulic gradient can be compared with the one deduced from the simulation with the matlab script Buoyancy_Gradient.m" print"___________________" trunk-2017.01a/examples/FluidCouplingLBM/yadeLBMvisu.m000066400000000000000000000104141304022710500224410ustar00rootroot00000000000000%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %Authors: Luc Sibille luc.sibille@3sr-grenoble.fr % Franck Lomine franck.lomine@insa-rennes.fr % % Script to visualize the fluid flow simulated with LBM written for a practical work in the OZ ALERT school in Grenoble 2011. % Script updated in 2014 %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% clear all close all %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% %%%% The only thing you have to do is choose below the iteration number for %%%% which you want to plot the fluid flow. This iteration number should %%%% correspond to one the saving iteration appearing in the same of the %%%% files saved in ./dem-bodies or ./lbm-nodes IterNumber=600; %%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%%% vxfile=sprintf('lbm-nodes/Vx_%.10d',IterNumber); vyfile=sprintf('lbm-nodes/Vy_%.10d',IterNumber); ux = importdata(vxfile); uy = importdata(vyfile); %ux=ux'; %uy=uy'; u = sqrt(ux.*ux+uy.*uy); rhofile=sprintf('lbm-nodes/Rho_%.10d',IterNumber); rho = importdata(rhofile); nodebdfile=sprintf('lbm-nodes/NodeBoundary_%.10d',IterNumber); nodeBD = importdata(nodebdfile); nodeBD=nodeBD'; spherefile=sprintf('dem-bodies/spheres_%.10d',IterNumber); tmpMat = importdata(spherefile); Sid=tmpMat(:,1); Sx=tmpMat(:,2); Sy=tmpMat(:,3); Sz=tmpMat(:,4); Sr=tmpMat(:,5); clear tmpMat %----- reading of LBM.log file logfile='LBM.log'; fid = fopen(logfile); tline = fgetl(fid); fscanf(fid,'%s %s %s',[3,1]); fscanf(fid,'%s',[1,1]); Lx0=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); Ly0=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); depth=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); thickness=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); NbBodies=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); dP=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); Nu=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); Rho=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); dx=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); Nx=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); Ny=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); Nz=fscanf(fid,'%f',[1,1]); tline = fgetl(fid); tline = fgetl(fid); fscanf(fid,'%s',[1,1]); tau=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); omega=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); IterMax=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); SaveMode=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); IterSave=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); SaveGridRatio=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); IntervalLBM=fscanf(fid,'%f',[1,1]); fscanf(fid,'%s',[1,1]); LBMConvergenceCriterion=fscanf(fid,'%f',[1,1]); tline = fgetl(fid); tline = fgetl(fid); fscanf(fid,'%s %s',[2,1]); LBMdt=fscanf(fid,'%f',[1,1]); fclose(fid); %------------------------------- fig1=figure(1) set(gcf, 'color', 'white'); clf nodeBD=flipdim(nodeBD',1); imagesc(nodeBD); title('Obstacle Boundaries'); axis equal; axis off %--------------------------------------- % VELOCITIES (colormap) %-------------------------------------- fig2=figure(2) set(gcf, 'color', 'white'); %set(gca,'ZDir','reverse') clf; hold on imagesc(u); title('Velocity colormap'); umax_current=max(max(u)); if(umax_current==0.) umax_current=umax_current+1.e-9;end; caxis([0. umax_current]); colorbar('location','southoutside'); theta = -pi:2*pi/40:pi; for aa=1:length(Sx) fill(ceil(Sx(aa)/dx)+Sr(aa)/dx*cos(theta),ceil(Sy(aa)/dx)+Sr(aa)/dx*sin(theta),[1 1 1]); end hold off; axis equal; axis off; fig3=figure(3) rhomax_current=max(max(rho)); rhomin_current=min(min(rho)); set(gcf, 'color', 'white'); %set(gca,'ZDir','reverse') clf; hold on %rho=flipdim(rho,1) imagesc(rho); title('Rho'); if(rhomax_current==rhomin_current) rhomax_current=rhomax_current+1.e-9;end; caxis([rhomin_current rhomax_current]); colorbar; theta = -pi:2*pi/40:pi; for aa=1:length(Sx) %fill(ceil(Sx(aa)/dx)+Sr(aa)/dx*cos(theta),ceil(Sy(aa)/dx)+Sr(aa)/dx*sin(theta),[1 1 1]); fill((Sx(aa)/dx)+1+ceil(Sr(aa)/dx)*cos(theta),(Sy(aa)/dx)+1+ceil(Sr(aa)/dx)*sin(theta),[1 1 1]); end hold off; axis equal; axis off; trunk-2017.01a/examples/FluidCouplingPFV/000077500000000000000000000000001304022710500201205ustar00rootroot00000000000000trunk-2017.01a/examples/FluidCouplingPFV/oedometer.py000066400000000000000000000145161304022710500224640ustar00rootroot00000000000000# -*- coding: utf-8 -*- #************************************************************************* # Copyright (C) 2010 by Bruno Chareyre * # bruno.chareyre_at_grenoble-inp.fr * # * # This program is free software; it is licensed under the terms of the * # GNU General Public License v2 or later. See file LICENSE for details. * #*************************************************************************/ ## Example script for using the DEM-PFV coupling introduced with E. Catalano, as reported in: ## * [Chareyre2012a] Chareyre, B., Cortis, A., Catalano, E., Barthélemy, E. (2012), Pore-scale modeling of viscous flow and induced forces in dense sphere packings. Transport in Porous Media (92), pages 473-493. DOI 10.1007/s11242-011-9915-6 ## http://dx.doi.org/10.1007/s11242-011-9915-6 ## * [Catalano2014a] Catalano, E., Chareyre, B., Barthélémy, E. (2013), Pore-scale modeling of fluid-particles interaction and emerging poromechanical effects. International Journal for Numerical and Analytical Methods in Geomechanics. DOI 10.1002/nag.2198 ## http://arxiv.org/pdf/1304.4895.pdf ## Also used in: ## * Tong et al.2012 (http://dx.doi.org/10.2516/ogst/2012032) ## * Sari et al 2011 (http://people.3sr-grenoble.fr/users/bchareyre/pubs/SariChareyreCatalanoPhilippeVincens_Particles2011.pdf) ## The DEM-PFV is applied here to 1D consolidation (oedometer test). The example includes the determination of oedometer modulus Ee and permeability K. ## The 1D consolidation is simulated as a coupled problem and the analytical solution corresponding to the abovementionned Ee and K is used for comparison. ## See triax-tutorial/script-session1.py for more detailed explanations of the packing generation procedure. ## ______________ First section, similar to triax-tutorial/script-session1.py _________________ from yade import pack num_spheres=1000# number of spheres young=1e6 compFricDegree = 3 # initial contact friction during the confining phase finalFricDegree = 30 # contact friction during the deviatoric loading mn,mx=Vector3(0,0,0),Vector3(1,1,1) # corners of the initial packing O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),density=2600,label='spheres')) O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls')) walls=aabbWalls([mn,mx],thickness=0,material='walls') wallIds=O.bodies.append(walls) sp=pack.SpherePack() sp.makeCloud(mn,mx,-1,0.3333,num_spheres,False, 0.95,seed=1) #"seed" make the "random" generation always the same sp.toSimulation(material='spheres') triax=TriaxialStressController( maxMultiplier=1.+2e4/young, # spheres growing factor (fast growth) finalMaxMultiplier=1.+2e3/young, # spheres growing factor (slow growth) thickness = 0, stressMask = 7, max_vel = 0.005, internalCompaction=True, # If true the confining pressure is generated by growing particles ) newton=NewtonIntegrator(damping=0.2) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()],label="iloop" ), FlowEngine(dead=1,label="flow"),#introduced as a dead engine for the moment, see 2nd section GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8), triax, newton ] triax.goal1=triax.goal2=triax.goal3=-10000 while 1: O.run(1000, True) unb=unbalancedForce() if unb<0.001 and abs(-10000-triax.meanStress)/10000<0.001: break setContactFriction(radians(finalFricDegree)) ## ______________ Oedometer section _________________ #A. Check bulk modulus of the dry material from load/unload cycles triax.stressMask=2 triax.goal1=triax.goal3=0 triax.internalCompaction=False triax.wall_bottom_activated=False #load triax.goal2=-11000; O.run(2000,1) #unload triax.goal2=-10000; O.run(2000,1) #load triax.goal2=-11000; O.run(2000,1) e22=triax.strain[1] #unload triax.goal2=-10000; O.run(2000,1) e22=e22-triax.strain[1] modulus = 1000./abs(e22) #B. Activate flow engine and set boundary conditions in order to get permeability flow.dead=0 flow.defTolerance=0.3 flow.meshUpdateInterval=200 flow.useSolver=3 flow.permeabilityFactor=1 flow.viscosity=10 flow.bndCondIsPressure=[0,0,1,1,0,0] flow.bndCondValue=[0,0,1,0,0,0] flow.boundaryUseMaxMin=[0,0,0,0,0,0] O.dt=0.1e-3 O.dynDt=False O.run(1,1) Qin = flow.getBoundaryFlux(2) Qout = flow.getBoundaryFlux(3) permeability = abs(Qin)/1.e-4 #size is one, we compute K=V/∇H print "Qin=",Qin," Qout=",Qout," permeability=",permeability #C. now the oedometer test, drained at the top, impermeable at the bottom plate flow.bndCondIsPressure=[0,0,0,1,0,0] flow.bndCondValue=[0,0,0,0,0,0] newton.damping=0 #we want the theoretical value from Terzaghi's solution #keep in mind that we are not in an homogeneous material and the small strain #assumption is not verified => we don't expect perfect match #there can be also an overshoot of pressure in the very beginning due to dynamic effects Cv=permeability*modulus/1e4 zeroTime=O.time zeroe22 = - triax.strain[1] dryFraction=0.05 #the top layer is affected by drainage on a certain depth, we account for it here drye22 = 1000/modulus*dryFraction wetHeight=1*(1-dryFraction) def consolidation(Tv): #see your soil mechanics handbook... U=1 for k in range(50): M=pi/2*(2*k+1) U=U-2/M**2*exp(-M**2*Tv) return U triax.goal2=-11000 from yade import plot ## a function saving variables def history(): plot.addData(e22=-triax.strain[1]-zeroe22,e22_theory=drye22+(1-dryFraction)*consolidation((O.time-zeroTime)*Cv/wetHeight**2)*1000./modulus,t=O.time,p=flow.getPorePressure((0.5,0.1,0.5)),s22=-triax.stress(3)[1]-10000) #plot.addData(e22=-triax.strain[1],t=O.time,s22=-triax.stress(2)[1],p=flow.MeasurePorePressure((0.5,0.5,0.5))) O.engines=O.engines+[PyRunner(iterPeriod=200,command='history()',label='recorder')] ##make nice animations: #O.engines=O.engines+[PyRunner(iterPeriod=200,command='flow.saveVtk()')] from yade import plot plot.plots={'t':('e22','e22_theory',None,'s22','p')} plot.plot() O.saveTmp() O.timingEnabled=1 from yade import timing print "starting oedometer simulation" O.run(200,1) timing.stats() ## Make more steps to see the convergence to the stationnary solution trunk-2017.01a/examples/HydroForceEngine/000077500000000000000000000000001304022710500201725ustar00rootroot00000000000000trunk-2017.01a/examples/HydroForceEngine/buoyantParticles.py000066400000000000000000000126771304022710500241110ustar00rootroot00000000000000######################################################################################################################################################################### # Author: Raphael Maurin, raphael.maurin@imft.fr # 07/07/2016 # # Example script to use HydroForceEngine in order to apply buoyancy force to particles. # The fluid is supposed at rest (vxFluidPY is a zero vector) so that the particles are only submitted to a drag force opposing the motion of the particle. # Three spheres with density 1500, 1000 and 500kg/m3 are positionned at the middle of a fluid sample of density 1000 kg/m3, and let evolved with time # We observe clearly that one sphere sediment down to the bottom, another one is rising to the top of the water free-surface and the third one does not move # ############################################################################################################################################################################ #Import libraries from yade import pack, plot import math import random as rand import numpy as np ## ## Main parameters of the simulation ## #Particles diameterPart = 6e-3 #Diameter of the particles, in meter restitCoef = 0.5 #Restitution coefficient of the particles partFrictAngle = atan(0.4) #friction angle of the particles, in radian densPart1 = 1050 #density of the particles, in kg/m3 densPart2 = 1000 #density of the particles, in kg/m3 densPart3 = 950 #density of the particles, in kg/m3 #fluid densFluidPY = 1000. #Density of the fluid kinematicViscoFluid = 1e-6 #kinematic viscosity of the fluid fluidHeight = 20.*diameterPart #Water depth in m. ndimz = 1 groundPosition = 0.#Definition of the position of the ground, in m gravityVector = Vector3(0,0.0,-9.81) #Gravity vector #Particles contact law/material parameters normalStiffness = 1e4 youngMod = normalStiffness/diameterPart #Young modulus of the particles from the stiffness wanted. poissonRatio = 0.5 #poisson's ratio of the particles. Classical values, does not have much influence #Material of particle 1, 2, and 3, with different density densPart1, densPart2 and densPart3 defined above (1500, 1000 and 500kg/m3 by default) O.materials.append(ViscElMat(en=restitCoef, et=0., young=youngMod, poisson=poissonRatio, density=densPart1, frictionAngle=partFrictAngle, label='Mat1')) O.materials.append(ViscElMat(en=restitCoef, et=0., young=youngMod, poisson=poissonRatio, density=densPart2, frictionAngle=partFrictAngle, label='Mat2')) O.materials.append(ViscElMat(en=restitCoef, et=0., young=youngMod, poisson=poissonRatio, density=densPart3, frictionAngle=partFrictAngle, label='Mat3')) #Time of simulation endTime = 2. ######################## ## FRAMEWORK CREATION ## ######################## # Reference walls: build a wall at the ground and draw the position of the free-surface to have a reference for the eyes in the 3D view lowPlane = box(center= (0, 0,groundPosition),extents=(200,200,0),fixed=True,wire=False,color = (0.,1.,0.)) WaterSurface = box(center= (0,0,groundPosition+fluidHeight),extents=(200,200,0),fixed=True,wire=False,color = (0,0,1),mask = 0) O.bodies.append([lowPlane,WaterSurface]) #add to simulation id1 = O.bodies.append(sphere(center = (0,2*diameterPart,groundPosition + fluidHeight/2.), radius = diameterPart/2.,material = 'Mat1')) id2 = O.bodies.append(sphere(center = (0,0,groundPosition + fluidHeight/2.), radius = diameterPart/2.,material = 'Mat2')) id3 = O.bodies.append(sphere(center = (0,-2*diameterPart,groundPosition + fluidHeight/2.), radius = diameterPart/2.,material = 'Mat3')) # Collect the ids of the spheres which are dynamic to add a fluid force through HydroForceEngines idApplyForce = [id1,id2,id3] ######################### #### SIMULATION LOOP##### ######################### O.engines = [ # Reset the forces ForceResetter(), # Detect the potential contacts InsertionSortCollider([Bo1_Sphere_Aabb(), Bo1_Wall_Aabb(),Bo1_Facet_Aabb(),Bo1_Box_Aabb()],label='contactDetection',allowBiggerThanPeriod = True), # Calculate the different interactions InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(), Ig2_Box_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()] ,label = 'interactionLoop'), #Apply an hydrodynamic force to the particles HydroForceEngine(densFluid = densFluidPY,viscoDyn = kinematicViscoFluid*densFluidPY,zRef = groundPosition,gravity = gravityVector,deltaZ = fluidHeight/ndimz,expoRZ = 0.,lift = False,nCell = ndimz,vCell = 1.,vxFluid = np.zeros(ndimz),phiPart = np.zeros(ndimz),vxPart = np.zeros(ndimz),vFluctX = np.zeros(len(O.bodies)),vFluctY = np.zeros(len(O.bodies)),vFluctZ = np.zeros(len(O.bodies)),ids = idApplyForce, label = 'hydroEngine'), #To plot the wall normal position of the spheres with time PyRunner(command = 'plotPos()', virtPeriod = 0.01, label = 'plot'), # Integrate the equation and calculate the new position/velocities... NewtonIntegrator(gravity=gravityVector, label='newtonIntegr') ] #save the initial configuration to be able to recharge the simulation starting configuration easily O.saveTmp() #Time step O.dt = 5e-7 #Low no purpose, in order to observe the sedimentation #Plot the wall normal position of the spheres with time def plotPos(): plot.addData(z1 = O.bodies[2].state.pos[2]/fluidHeight,z2 = O.bodies[3].state.pos[2]/fluidHeight,z3 = O.bodies[4].state.pos[2]/fluidHeight, time = O.time) if O.time>endTime: print('\nEnd of the simulation, {0}s simulated as asked!\n'.format(endTime)) O.pause() plot.plots={'time':('z1','z2','z3')} plot.plot() trunk-2017.01a/examples/HydroForceEngine/fluidizedBed.py000066400000000000000000000233361304022710500231450ustar00rootroot00000000000000######################################################################################################################################################################### # Author: Raphael Maurin, raphael.maurin@imft.fr # 08/07/2016 # # Very simplified fluidized bed simulations in order to underline the possibility of HydroForceEngine. # Particles are deposited under gravity inside a box. Once the particles at rest, a constant fluid velocity is applied against gravity, submitting the # particles to a constant drag force. Then, a discrete random walk model is applied to mimick the effect of the turbulent fluid velocity fluctuations. # It associates to each particle a random fluid velocity fluctuations in the x, y and z directions, which are taken into account in the evaluation # of the drag applied by the fluid on the particle. The intensity of the fluctuation is based on the value of u*, which is imposed through simplifiedReynoldsStress = u*^2 # The values taken for the fluid velocity and simplifiedReynolds stress have been arbitrarily chosen to have a nice rendering # # The example allows to get familiar with HydroForceEngine and in particular with the included DRW model functions (turbulentFluctuationFluidizedBed() here) # For details on the process, it is necessary to have a look to the documentation and the C++ code in pkg/common/ForceEngine.cpp and hpp as HydroForceEngine contains # multiple parameters ############################################################################################################################################################################ # ATTENTION: to fit the formulation of HydroForceEngine, the fluid velocity can only be applied along the x axis. Therefore, the gravity is here aligned with x, and all the # configuration is defined accordingly. For the 3D visualization, two walls of the cell have been made transparent and clicking on the right xyz button after openning the # 3D view allows one to see the sample in the usual way with gravity going from top to bottom. #Import libraries from yade import pack, plot import math import random as rand import numpy as np ## ## Main parameters of the simulation ## #Particles diameterPart = 6e-3 #Diameter of the particles, in meter densPart = 2500 #density of the particles, in kg/m3 restitCoef = 0.8 #Restitution coefficient of the particles partFrictAngle = atan(0.4) #friction angle of the particles, in radian #fluid densFluidPY = 1.225 #Density of the fluid, (air) in kg/m3 kinematicViscoFluid = 1.48e-5 #kinematic viscosity of the fluid, (air) in m2/s #Configuration: inclined channel lengthCell = 100 #length cell along the gravity axis (x), in diameter widthCell = 10 #length cell along the two other axis, in diameter Nlayer = 2.5 #nb of layer of particle deposited, in diameter phiPartMax = 0.61 #Value of the dense packing solid volume fraction endTime = 10 #Time simulated (in seconds) ## ## Secondary parameters of the simulation ## expoDrag_PY = 3.1 # Richardson Zaki exponent for the hindrance function of the drag force applied to the particles ndimz = 20 #Number of cells in the height dz = widthCell*diameterPart/ndimz # Fluid discretization step in the wall-normal direction # Initialization of the main vectors vxFluidPY = np.ones(ndimz)*18.5 # Vertical fluid velocity profile: u^f = u_x^f(z) e_x, with x the streamwise direction and z the wall-normal phiPartPY = np.zeros(ndimz) # Vertical particle volume fraction profile vxPartPY = np.zeros(ndimz) # Vertical average particle velocity profile #Geometrical configuration, define useful quantities length = lengthCell*diameterPart #length of the stream, in m width = widthCell*diameterPart #width of the stream, in m groundPosition = 0. #Definition of the position of the ground, in m gravityVector = Vector3(-9.81,0.0,0.) #Gravity vector. Inclined along x to have an effect opposed to the fluid flow (which can only be along x) #Particles contact law/material parameters maxPressure = (densPart-densFluidPY)*phiPartMax*Nlayer*diameterPart*9.81#Estimated max particle pressure from the static load normalStiffness = maxPressure*diameterPart*1e4 #Evaluate the minimal normal stiffness to be in the rigid particle limit (cf Roux and Combe 2002) youngMod = normalStiffness/diameterPart #Young modulus of the particles from the stiffness wanted. poissonRatio = 0.5 #poisson's ratio of the particles. Classical values, does not have much influence O.materials.append(ViscElMat(en=restitCoef, et=0., young=youngMod, poisson=poissonRatio, density=densPart, frictionAngle=partFrictAngle, label='Mat')) ######################## ## FRAMEWORK CREATION ## ######################## # Walls to create a box lowPlane = box(center= (groundPosition, width/2.0,width/2.),extents=(0,width/2.,width/2.),fixed=True,wire=False,color = (0.,1.,0.),material = 'Mat') sidePlane1 = box(center= (length/2., width,width/2.),extents=(length/2.,0.,width/2.),fixed=True,wire=True,color = (0.,1.,0.),material = 'Mat') sidePlane2 = box(center= (length/2., 0.,width/2.),extents=(length/2.,0.,width/2.),fixed=True,wire=True,color = (0.,1.,0.),material = 'Mat') sidePlane3 = box(center= (length/2.,width/2., 0.),extents=(length/2.,width/2.,0.),fixed=True,wire=False,color = (0.,1.,0.),material = 'Mat') #Made invisible (wire = True) in order to see inside the cell sidePlane4 = box(center= (length/2.,width/2., width),extents=(length/2.,width/2.,0.),fixed=True,wire=False,color = (0.,1.,0.),material = 'Mat') #Made invisible (wire = True) in order to see inside the cell O.bodies.append([lowPlane,sidePlane1,sidePlane2,sidePlane3,sidePlane4]) #Create a loose cloud of particle inside the cell partCloud = pack.SpherePack() partVolume = pi/6.*pow(diameterPart,3) #Volume of a particle partNumber = int(Nlayer*phiPartMax*diameterPart*width*width/partVolume) #Volume of beads to obtain Nlayer layers of particles partCloud.makeCloud(minCorner=(0,0.,0),maxCorner=(length,width,width),rRelFuzz=0., rMean=diameterPart/2.0, num = partNumber) partCloud.toSimulation(material='Mat') #Send this packing to simulation with material Mat #Evaluate the deposition time considering the free-fall time of the highest particle to the ground depoTime = sqrt(length*2/9.31) # Collect the ids of the spheres which are dynamic to add a fluid force through HydroForceEngines idApplyForce = [] for b in O.bodies: if isinstance(b.shape,Sphere) and b.dynamic: idApplyForce+=[b.id] ######################### #### SIMULATION LOOP##### ######################### O.engines = [ # Reset the forces ForceResetter(), # Detect the potential contacts InsertionSortCollider([Bo1_Sphere_Aabb(), Bo1_Wall_Aabb(),Bo1_Facet_Aabb(),Bo1_Box_Aabb()],label='contactDetection',allowBiggerThanPeriod = True), # Calculate the different interactions InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(), Ig2_Box_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()] ,label = 'interactionLoop'), #Apply an hydrodynamic force to the particles HydroForceEngine(densFluid = densFluidPY,viscoDyn = kinematicViscoFluid*densFluidPY,zRef = groundPosition,gravity = gravityVector,deltaZ = dz,expoRZ = expoDrag_PY,lift = False,nCell = ndimz,vCell = length*width*dz ,vxFluid = vxFluidPY,phiPart = phiPartPY,vxPart = vxPartPY,ids = idApplyForce,vFluctX = np.zeros(len(O.bodies)),vFluctY = np.zeros(len(O.bodies)),vFluctZ = np.zeros(len(O.bodies)), label = 'hydroEngine', dead = True), #Measurement, output files PyRunner(command = 'measure()', virtPeriod = 0.1, label = 'measurement', dead = True), # Check if the packing is stabilized, if yes activate the hydro force on the grains and the slope. PyRunner(command='gravityDeposition(depoTime)',virtPeriod = 0.01,label = 'gravDepo'), #Apply fluid turbulent fluctuations from a discrete random walk model PyRunner(command='turbulentFluctuations()',virtPeriod = 0.01,label = 'turbFluct'), #GlobalStiffnessTimeStepper, determine the time step GlobalStiffnessTimeStepper(defaultDt = 1e-4, viscEl = True,timestepSafetyCoefficient = 0.7, label = 'GSTS'), # Integrate the equation and calculate the new position/velocities... NewtonIntegrator(damping=0.2, gravity=gravityVector, label='newtonIntegr') ] #save the initial configuration to be able to recharge the simulation starting configuration easily O.saveTmp() #run #O.run() ##################################################################################################################################### ##################################################### FUNCTION DEFINITION ######################################################### ##################################################################################################################################### ###### ###### ### LET THE TIME FOR THE GRAVITY DEPOSITION AND ACTIVATE THE FLUID AT THE END ### ###### ###### def gravityDeposition(lim): if O.time=endTime: print('\n End of the simulation, simulated {0}s as required !\n '.format(endTime)) O.pause() #Z scale used for the possible plot at the end global zAxis for i in range(0,ndimz): zAxis[i] = i*dz/diameterPart ## Paste the following (uncommented) code in the console at the end of the simulation to observe the shape of the granular depth profiles (solid volume fraction and velocity) #import matplotlib.pyplot as pyp #pyp.figure('solid volume fraction profile') #pyp.plot(phiPartPY,zAxis,'g') #pyp.xlabel(r'$\phi$') #pyp.ylabel(r'$z/d$') #pyp.figure('streamwise particle velocity profile') #pyp.plot(vxPartPY,zAxis,'g') #pyp.xlabel(r'$$') #pyp.ylabel(r'$z/d$') #pyp.show() #Plot the dimensionless sediment transport rate as a function of time during the simulation plot.plots={'time':('SedimentRate')} plot.plot() ################ ########################################## #Imposed fluid profile, corresponding to a Shields number 0.5 vxFluidPY = np.array([ 0. , 0.06156562, 0.08728988, 0.10283756, 0.11005262, 0.11059876, 0.1060113 , 0.0976961 , 0.08701183, 0.07527384, 0.06375715, 0.05362684, 0.04587625, 0.04124045, 0.04014932, 0.04265518, 0.04835575, 0.05637364, 0.06555057, 0.07466258, 0.0825892 , 0.08848402, 0.09180331, 0.09234952, 0.09026192, 0.08598644, 0.08023121, 0.07377648, 0.0673878 , 0.06174271, 0.05740186, 0.0547775 , 0.05407727, 0.05527346, 0.05813167, 0.0622459 , 0.06708855, 0.07204081, 0.07651257, 0.07999516, 0.08215522, 0.08283083, 0.08204372, 0.07996273, 0.07689339, 0.0732465 , 0.06949481, 0.06610862, 0.06347541, 0.06185502, 0.0613583 , 0.06194208, 0.06343303, 0.0655741 , 0.06804706, 0.07051492, 0.0726754 , 0.07429343, 0.07521449, 0.07537433, 0.07479194, 0.07357723, 0.07192908, 0.07010514, 0.06839215, 0.06704851, 0.06626627, 0.06614762, 0.06669344, 0.06779834, 0.06927958, 0.07091005, 0.07245458, 0.07369861, 0.07446029, 0.07462772, 0.07419583, 0.07325704, 0.07196604, 0.07049793, 0.06903213, 0.06774085, 0.06677561, 0.0662449 , 0.06619538, 0.06661213, 0.06742787, 0.0685343 , 0.06978656, 0.07102537, 0.07210075, 0.07289378, 0.07334036, 0.07343889, 0.07323677, 0.07280684, 0.0722337 , 0.07160383, 0.07099545, 0.07047215, 0.07007524, 0.06982274, 0.06971082, 0.06971833, 0.06980796, 0.06993805, 0.07007409, 0.07019433, 0.07028775, 0.07034303, 0.07035078, 0.07031745, 0.07026673, 0.07022685, 0.070222 , 0.07026871, 0.07037337, 0.0705376 , 0.07075427, 0.07100814, 0.07128164, 0.07155703, 0.07182318, 0.07207437, 0.07230019, 0.0724788 , 0.0725801 , 0.07257863, 0.07245956, 0.07222669, 0.07189895, 0.07150785, 0.07108934, 0.07068479, 0.07033428, 0.0700743 , 0.06993614, 0.06994256, 0.07010162, 0.07040221, 0.07081663, 0.07130815, 0.07183653, 0.07236057, 0.0728381 , 0.07323606, 0.07353095, 0.07371097, 0.0737761 , 0.07373514, 0.07360549, 0.073415 , 0.07319872, 0.07299079, 0.07282058, 0.07271034, 0.07267235, 0.07270862, 0.07281215, 0.07297214, 0.07317416, 0.07340123, 0.07363392, 0.07385621, 0.07405428, 0.07421823, 0.07434827, 0.07445663, 0.07456325, 0.07469148, 0.07486482, 0.07510363, 0.0754249 , 0.07583499, 0.0763238 , 0.07687 , 0.07744048, 0.07799326, 0.07848547, 0.07887646, 0.07913544, 0.07924846, 0.07921931, 0.07907331, 0.07885561, 0.07862464, 0.07844374, 0.07837516, 0.07847163, 0.0787705 , 0.07928899, 0.08002083, 0.0809382 , 0.08199479, 0.08313004, 0.08427904, 0.08537916, 0.08637918, 0.08724493, 0.08796148, 0.08853075, 0.08897183, 0.08931631, 0.0896013 , 0.08986449, 0.09013922, 0.09045455, 0.09083446, 0.0912941 , 0.09184645, 0.09249791, 0.09325393, 0.09411605, 0.0950802 , 0.09613639, 0.09727042, 0.09846512, 0.0997008 , 0.10095958, 0.10222823, 0.10349927, 0.10477299, 0.10605354, 0.10735303, 0.10868852, 0.11007881, 0.11154475, 0.11310325, 0.11476599, 0.11653497, 0.118402 , 0.12034988, 0.12235397, 0.12438468, 0.12641134, 0.12840556, 0.13034169, 0.13220338, 0.13398571, 0.13570116, 0.13738374, 0.13909178, 0.1409052 , 0.14291927, 0.14523157, 0.14793003, 0.1510891 , 0.15476738, 0.15900948, 0.16384828, 0.16930529, 0.17539348, 0.18211907, 0.1894816 , 0.19747537, 0.20609019, 0.2153121 , 0.22512414, 0.23550562, 0.24643343, 0.25788275, 0.26982699, 0.28223862, 0.29508925, 0.3083499 , 0.32199109, 0.33598346, 0.35029802, 0.36490592, 0.37977898, 0.39488962, 0.41021114, 0.42571807, 0.4413862 , 0.45719298, 0.47311751, 0.4891401 , 0.50524264, 0.52140786, 0.53761979, 0.55386412, 0.57012801, 0.58639949, 0.60266791, 0.61892388, 0.63515886, 0.65136517, 0.66753551, 0.68366317, 0.69974232, 0.71576767, 0.73173404, 0.74763662, 0.76347108, 0.77923328, 0.79491932, 0.81052539, 0.82604798, 0.8414839 , 0.85683046, 0.87208498, 0.88724521, 0.90230903, 0.91727463, 0.93214057, 0.94690566, 0.96156893, 0.97612958, 0.99058652, 1.00493896, 1.0191864 , 1.03332831, 1.04736448, 1.06129493, 1.07511968, 1.08883882, 1.10245244, 1.11596073, 1.1293639 , 1.14266233, 1.15585634, 1.16894621, 1.18193214, 1.19481443, 1.2075934 , 1.22026932, 1.23284246, 1.24531294, 1.257681 , 1.26994706, 1.2821116 , 1.29417505, 1.30613785, 1.31800031, 1.32976287, 1.34142608, 1.3529905 , 1.36445665, 1.37582494, 1.38709576, 1.39826949, 1.40934651, 1.42032734, 1.43121251, 1.44200244, 1.45269741, 1.46329784, 1.47380421, 1.4842169 , 1.4945363 , 1.50476284, 1.51489687, 1.52493875, 1.53488882, 1.5447474 , 1.55451477, 1.56419123, 1.57377699, 1.58327231, 1.59267751, 1.60199298, 1.61121897, 1.62035577, 1.6294036 , 1.63836267, 1.64723331, 1.65601585, 1.66471064, 1.67331804, 1.68183842, 1.69027212, 1.6986195 , 1.70688092, 1.71505672, 1.72314731, 1.73115306, 1.73907436, 1.74691168, 1.75466545, 1.76233612, 1.76992419, 1.77743015, 1.78485456, 1.79219798, 1.79946097, 1.80664408, 1.81374788, 1.82077303, 1.82772023, 1.83459016, 1.84138355, 1.84810114, 1.85474367, 1.8613119 , 1.86780655, 1.87422842, 1.88057834, 1.88685715, 1.89306574, 1.89920502, 1.90527587, 1.9112792 , 1.91721589, 1.92308686, 1.92889305, 1.9346354 , 1.94031485, 1.94593232, 1.95148872, 1.956985 , 1.96242207, 1.96780085, 1.97312225, 1.97838716, 1.9835965 , 1.98875115, 1.99385197, 1.99889988, 2.00389572, 2.00884037, 2.01373468, 2.01857948, 2.02337561, 2.02812387, 2.03282505, 2.03747992, 2.04208926, 2.04665378, 2.05117424, 2.05565134, 2.06008578, 2.06447826, 2.06882943, 2.07313998, 2.07741053, 2.08164173, 2.08583421, 2.08998857, 2.09410541, 2.09818531, 2.10222885, 2.10623657, 2.11020902, 2.11414674, 2.11805024, 2.12192005, 2.12575664, 2.12956052, 2.13333217, 2.13707204, 2.14078061, 2.14445833, 2.14810563, 2.15172294, 2.1553107 , 2.1588693 , 2.16239916, 2.16590066, 2.1693742 , 2.17282014, 2.17623887, 2.17963073, 2.18299609, 2.1863353 , 2.18964869, 2.19293659, 2.19619934, 2.19943724, 2.20265063, 2.2058398 , 2.20900506, 2.2121467 , 2.21526502, 2.21836029, 2.22143281, 2.22448284, 2.22751065, 2.23051652, 2.23350069, 2.23646343, 2.23940498, 2.2423256 , 2.24522553, 2.248105 , 2.25096425, 2.25380351, 2.256623 , 2.25942296, 2.26220359, 2.26496512, 2.26770775, 2.27043169, 2.27313715, 2.27582432, 2.2784934 , 2.2811446 , 2.28377809, 2.28639406, 2.28899271, 2.2915742 , 2.29413873, 2.29668646, 2.29921756, 2.30173222, 2.30423059, 2.30671284, 2.30917913, 2.31162963, 2.31406448, 2.31648385, 2.31888789, 2.32127674, 2.32365056, 2.32600949, 2.32835368, 2.33068326, 2.33299837, 2.33529916, 2.33758576, 2.33985829, 2.34211691, 2.34436172, 2.34659286, 2.34881046, 2.35101464, 2.35320552, 2.35538322, 2.35754787, 2.35969957, 2.36183844, 2.3639646 , 2.36607817, 2.36817924, 2.37026793, 2.37234435, 2.3744086 , 2.37646079, 2.37850103, 2.3805294 , 2.38254602, 2.38455099, 2.38654439, 2.38852634, 2.39049692, 2.39245622, 2.39440435, 2.39634139, 2.39826743, 2.40018257, 2.40208688, 2.40398047, 2.40586341, 2.40773578, 2.40959768, 2.41144918, 2.41329037, 2.41512133, 2.41694214, 2.41875287, 2.4205536 , 2.42234442, 2.42412539, 2.42589659, 2.4276581 , 2.42940998, 2.43115232, 2.43288518, 2.43460863, 2.43632274, 2.43802758, 2.43972322, 2.44140973, 2.44308716, 2.4447556 , 2.4464151 , 2.44806572, 2.44970754, 2.4513406 , 2.45296499, 2.45458074, 2.45618793, 2.45778662, 2.45937686, 2.46095872, 2.46253225, 2.4640975 , 2.46565454, 2.46720342, 2.46874419, 2.47027691, 2.47180164, 2.47331842, 2.47482732, 2.47632837, 2.47782164, 2.47930717, 2.48078502, 2.48225523, 2.48371786, 2.48517295, 2.48662055, 2.48806071, 2.48949348, 2.4909189 , 2.49233702, 2.49374788, 2.49515154, 2.49654803, 2.4979374 , 2.49931969, 2.50069495, 2.50206322, 2.50342454, 2.50477896, 2.50612651, 2.50746724, 2.50880118, 2.51012839, 2.51144889, 2.51276272, 2.51406994, 2.51537057, 2.51666465, 2.51795223, 2.51923333, 2.520508 , 2.52177627, 2.52303818, 2.52429376, 2.52554305, 2.52678609, 2.52802291, 2.52925355, 2.53047803, 2.5316964 , 2.53290869, 2.53411492, 2.53531514, 2.53650937, 2.53769765, 2.53888 , 2.54005647, 2.54122708, 2.54239187, 2.54355086, 2.54470408, 2.54585156, 2.54699334, 2.54812944, 2.5492599 , 2.55038473, 2.55150398, 2.55261766, 2.55372581, 2.55482845, 2.55592562, 2.55701733, 2.55810362, 2.55918451, 2.56026002, 2.5613302 , 2.56239505, 2.56345461, 2.5645089 , 2.56555795, 2.56660178, 2.56764042, 2.56867388, 2.56970221, 2.57072541, 2.57174351, 2.57275654, 2.57376452, 2.57476747, 2.57576542, 2.57675838, 2.57774639, 2.57872946, 2.57970761, 2.58068087, 2.58164925, 2.58261279, 2.58357149, 2.58452539, 2.5854745 , 2.58641884, 2.58735843, 2.58829329, 2.58922345, 2.59014892, 2.59106972, 2.59198587, 2.59289739, 2.5938043 , 2.59470662, 2.59560436, 2.59649755, 2.5973862 , 2.59827033, 2.59914996, 2.60002511, 2.60089579, 2.60176202, 2.60262382, 2.6034812 , 2.60433419, 2.60518279, 2.60602703, 2.60686692, 2.60770247, 2.60853371, 2.60936065, 2.6101833 , 2.61100168, 2.6118158 , 2.61262569, 2.61343135, 2.6142328 , 2.61503005, 2.61582313, 2.61661203, 2.61739678, 2.6181774 , 2.61895388, 2.61972626, 2.62049454, 2.62125873, 2.62201885, 2.62277492, 2.62352694, 2.62427492, 2.62501889, 2.62575884, 2.62649481, 2.62722678, 2.62795479, 2.62867884, 2.62939894, 2.6301151 , 2.63082734, 2.63153566, 2.63224009, 2.63294062, 2.63363727, 2.63433004, 2.63501896, 2.63570404, 2.63638527, 2.63706267, 2.63773625, 2.63840603, 2.639072 , 2.63973419, 2.64039259, 2.64104723, 2.6416981 , 2.64234522, 2.64298859, 2.64362823, 2.64426414, 2.64489633, 2.64552481, 2.64614958, 2.64677067, 2.64738806, 2.64800178, 2.64861182, 2.6492182 , 2.64982092, 2.65041999, 2.65101542, 2.6516072 , 2.65219536, 2.6527799 , 2.65336081, 2.65393812, 2.65451182, 2.65508192, 2.65564842, 2.65621134, 2.65677067, 2.65732642, 2.6578786 , 2.65842722, 2.65897226, 2.65951375, 2.66005168, 2.66058606, 2.6611169 , 2.66164419, 2.66216794, 2.66268815, 2.66320484, 2.66371799, 2.66422761, 2.66473371, 2.66523629, 2.66573534, 2.66623088, 2.66672291, 2.66721142, 2.66769641, 2.6681779 , 2.66865588, 2.66913034, 2.6696013 , 2.67006875, 2.67053269, 2.67099312, 2.67145005, 2.67190346, 2.67235337, 2.67279976, 2.67324264, 2.67368201, 2.67411786, 2.6745502 , 2.67497901, 2.6754043 , 2.67582607, 2.67624431, 2.67665901, 2.67707018, 2.6774778 , 2.67788188, 2.67828241, 2.67867939, 2.6790728 , 2.67946264, 2.67984891, 2.6802316 , 2.6806107 , 2.68098621, 2.68135811, 2.6817264 , 2.68209106, 2.6824521 , 2.68280949, 2.68316323, 2.6835133 , 2.6838597 , 2.68420241, 2.68454142, 2.68487671, 2.68520828, 2.6855361 , 2.68586015, 2.68618044, 2.68649692, 2.68680959, 2.68711843, 2.68742342, 2.68772453, 2.68802174, 2.68831504, 2.68860439, 2.68888977, 2.68917115, 2.6894485 , 2.6897218 , 2.689991 , 2.69025609, 2.69051701, 2.69077374, 2.69102624, 2.69127446, 2.69151836, 2.69175789, 2.69199301, 2.69222365, 2.69244977, 2.6926713 , 2.69288819, 2.69310035, 2.69330773, 2.69351023, 2.69370778, 2.69390028, 2.69408764, 2.69426974, 2.69444647, 2.6946177 , 2.69478329, 2.69494307, 2.69509687, 2.69524449, 2.69538571, 2.69552028, 2.69564788, 2.69576818, 2.69588076, 2.6959851 , 2.69608056, 2.6961663 , 2.69624114, 2.6963033 , 2.69634954, 2.69637016, 2.69633447, 2.69633447]) if ndimz!=len(vxFluidPY): print '\n Bug: ndimz should necessarily be equal to the length of the imposed fluid profile vxFluidPY !\n' exit() trunk-2017.01a/examples/LudingPM/000077500000000000000000000000001304022710500164575ustar00rootroot00000000000000trunk-2017.01a/examples/LudingPM/LudingPM_1.py000066400000000000000000000063051304022710500207340ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 from yade import utils, plot o = Omega() fr = 0.5;rho=2000 o.dt = 0.00002 r1 = 2.0e-1 r2 = 2.0e-1 #======================================= k1 = 105.0 kp = 5.0*k1 kc = k1 DeltaPMax = 0.031 Chi1 = 0.34 Chi2 = 0.69 Chi3 = 1.1 Chi4 = 1.39 #======================================= particleMass = 4.0/3.0*math.pi*r1*r1*r1*rho Vi1 = math.sqrt(k1/particleMass)*DeltaPMax*Chi1 Vi2 = math.sqrt(k1/particleMass)*DeltaPMax*Chi2 Vi3 = math.sqrt(k1/particleMass)*DeltaPMax*Chi3 Vi4 = math.sqrt(k1/particleMass)*DeltaPMax*Chi4 PhiF1 = DeltaPMax*(kp-k1)*(r1+r2)/(kp*2*r1*r2) PhiF2 = DeltaPMax*(kp-k1)*(r1+r2)/(kp*2*r1*r2) PhiF3 = DeltaPMax*(kp-k1)*(r1+r2)/(kp*2*r1*r2) PhiF4 = DeltaPMax*(kp-k1)*(r1+r2)/(kp*2*r1*r2) #======================================= mat1 = O.materials.append(LudingMat(frictionAngle=fr,density=rho,k1=k1, kp=kp, kc=kc, PhiF=PhiF1, G0 = 0.0)) mat2 = O.materials.append(LudingMat(frictionAngle=fr,density=rho,k1=k1, kp=kp, kc=kc, PhiF=PhiF2, G0 = 0.0)) mat3 = O.materials.append(LudingMat(frictionAngle=fr,density=rho,k1=k1, kp=kp, kc=kc, PhiF=PhiF3, G0 = 0.0)) mat4 = O.materials.append(LudingMat(frictionAngle=fr,density=rho,k1=k1, kp=kp, kc=kc, PhiF=PhiF4, G0 = 0.0)) id11 = O.bodies.append(sphere(center=[0,0,0],radius=r1,material=mat1,fixed=True)) id12 = O.bodies.append(sphere(center=[0,0,(r1 + r2)],radius=r2,material=mat1,fixed=False)) id21 = O.bodies.append(sphere(center=[0,3.0*r1,0],radius=r1,material=mat2,fixed=True)) id22 = O.bodies.append(sphere(center=[0,3.0*r1,(r1 + r2)],radius=r2,material=mat2,fixed=False)) id31 = O.bodies.append(sphere(center=[0,6.0*r1,0],radius=r1,material=mat3,fixed=True)) id32 = O.bodies.append(sphere(center=[0,6.0*r1,(r1 + r2)],radius=r2,material=mat3,fixed=False)) id41 = O.bodies.append(sphere(center=[0,9.0*r1,0],radius=r1,material=mat4,fixed=True)) id42 = O.bodies.append(sphere(center=[0,9.0*r1,(r1 + r2)],radius=r2,material=mat4,fixed=False)) o.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_LudingMat_LudingMat_LudingPhys()], [Law2_ScGeom_LudingPhys_Basic()], ), NewtonIntegrator(damping=0,gravity=[0,0,0]), PyRunner(command='addPlotData()',iterPeriod=1000), ] O.bodies[id12].state.vel=[0,0,-Vi1] O.bodies[id22].state.vel=[0,0,-Vi2] O.bodies[id32].state.vel=[0,0,-Vi3] O.bodies[id42].state.vel=[0,0,-Vi4] def addPlotData(): f1 = [0,0,0] f2 = [0,0,0] f3 = [0,0,0] f4 = [0,0,0] try: f1=O.forces.f(id12) f2=O.forces.f(id22) f3=O.forces.f(id32) f4=O.forces.f(id42) except: f1 = [0,0,0] f2 = [0,0,0] f3 = [0,0,0] f4 = [0,0,0] s1 = (O.bodies[id12].state.pos[2]-O.bodies[id11].state.pos[2])-(r1 + r2) s2 = (O.bodies[id22].state.pos[2]-O.bodies[id21].state.pos[2])-(r1 + r2) s3 = (O.bodies[id32].state.pos[2]-O.bodies[id31].state.pos[2])-(r1 + r2) s4 = (O.bodies[id42].state.pos[2]-O.bodies[id41].state.pos[2])-(r1 + r2) plot.addData(fc1=f1[2], sc1=-s1, fc2=f2[2], sc2=-s2, fc3=f3[2], sc3=-s3, fc4=f4[2], sc4=-s4) plot.plots={'sc1':('fc1'), 'sc2':('fc2'), 'sc3':('fc3'), 'sc4':('fc4')}; plot.plot() from yade import qt qt.View() O.run(320000) O.wait() plot.saveGnuplot('sim-data_LudigPM') trunk-2017.01a/examples/LudingPM/LudingPM_2.py000066400000000000000000000031351304022710500207330ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 from yade import utils, plot o = Omega() fr = 0.5;rho=2000 o.dt = 0.00002 r1 = 2.0e-1 r2 = 2.0e-1 #======================================= k1 = 105.0 kp = 5.0*k1 kc = k1 DeltaPMax = 0.031 Chi1 = 0.34 #======================================= particleMass = 4.0/3.0*math.pi*r1*r1*r1*rho Vi1 = math.sqrt(k1/particleMass)*DeltaPMax*Chi1 PhiF1 = DeltaPMax*(kp-k1)*(r1+r2)/(kp*2*r1*r2) #======================================= mat1 = O.materials.append(LudingMat(frictionAngle=fr,density=rho,k1=k1, kp=kp, kc=kc, PhiF=PhiF1, G0 = 0.0)) id11 = O.bodies.append(sphere(center=[0,0,0],radius=r1,material=mat1,fixed=True)) id12 = O.bodies.append(sphere(center=[0,0,(r1 + r2)],radius=r2,material=mat1,fixed=False)) o.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_LudingMat_LudingMat_LudingPhys()], [Law2_ScGeom_LudingPhys_Basic()], ), NewtonIntegrator(damping=0,gravity=[0,0,0]), PyRunner(command='changeVelDir()',iterPeriod=6000,label='Cvel'), PyRunner(command='addPlotData()',iterPeriod=300), ] O.bodies[id12].state.vel=[0,0,-Vi1] def changeVelDir(): O.bodies[id12].state.vel*=-1 Cvel.iterPeriod = int(Cvel.iterPeriod*1.5) def addPlotData(): f1 = [0,0,0] try: f1=O.forces.f(id12) except: f1 = [0,0,0] s1 = (O.bodies[id12].state.pos[2]-O.bodies[id11].state.pos[2])-(r1 + r2) plot.addData(fc1=f1[2], sc1=-s1) plot.plots={'sc1':('fc1')}; plot.plot() from yade import qt qt.View() O.run(150000) O.wait() plot.saveGnuplot('sim-data_LudigPM') trunk-2017.01a/examples/LudingPM/README000066400000000000000000000001231304022710500173330ustar00rootroot00000000000000Simple scripts to test LudingPM. See [Luding2008]_ ,[Singh2013]_ for more details. trunk-2017.01a/examples/PIDController.py000066400000000000000000000040051304022710500200310ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 from yade import utils, plot o = Omega() fr = 0.0;rho=2000 tc = 0.001; en = 0.3; et = 0.3; o.dt = 0.02*tc mat1 = O.materials.append(ViscElMat(frictionAngle=fr, density=rho,tc=tc,en=en,et=et)) spheresID = O.bodies.append(pack.regularHexa(pack.inCylinder((0,0,-2.0),(0,0,2.0),2.0),radius=0.2,gap=0.1,color=(0,1,0),material=mat1)) idWalls = O.bodies.append(geom.facetCylinder(center=(0.0,0.0,0.0),radius = 2.05, height = 4.0, wallMask=6, material=mat1, segmentsNumber = 20, color=(0,0,1))) idTop = O.bodies.append(geom.facetCylinder(center=(0.0,0.0,0.0),radius = 2.05, height = 4.0, wallMask=1, material=mat1, segmentsNumber = 5, color=(1,0,0), wire=False)) o.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()],verletDist=1.0,label='collider'), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0,gravity=[0,0,-9.81],label='newtonInt'), TranslationEngine(translationAxis=[0,0,1],velocity=-2.0,ids=idTop,dead=False,label='translat'), CombinedKinematicEngine(ids=idTop,label='combEngine',dead=True) + ServoPIDController(axis=[0,0,1],maxVelocity=2.0,iterPeriod=1000,ids=idTop,target=1.0e7,kP=1.0,kI=1.0,kD=1.0) + RotationEngine(rotationAxis=(0,0,1), angularVelocity=10.0, rotateAroundZero=True, zeroPoint=(0,0,0)), PyRunner(command='addPlotData()',iterPeriod=1000, label='graph'), PyRunner(command='switchTranslationEngine()',iterPeriod=45000, nDo = 2, label='switchEng'), ] O.step() from yade import qt qt.View() r=qt.Renderer() r.bgColor=1,1,1 def addPlotData(): fMove = Vector3(0,0,0) for i in idTop: fMove += O.forces.f(i) plot.addData(z=O.iter, pMove=fMove[2], pFest=fMove[2]) def switchTranslationEngine(): print "Switch from TranslationEngine engine to ServoPIDController" translat.dead = True combEngine.dead = False plot.plots={'z':('pMove','pFest')}; plot.plot() trunk-2017.01a/examples/PotentialBlocks/000077500000000000000000000000001304022710500200755ustar00rootroot00000000000000trunk-2017.01a/examples/PotentialBlocks/cubePBscaled.py000077500000000000000000000440071304022710500227730ustar00rootroot00000000000000#!/usr/local/bin/yade-trunk -x # -*- encoding=utf-8 -*- # CWBoon 2015 # Some of the parameters are defunct.. # I use this for jointed rock mass, but you can use it to generate granular particles too from yade import pack import math O.engines=[ ForceResetter(), InsertionSortCollider([PotentialBlock2AABB()],verletDist=0), InteractionLoop( [Ig2_PB_PB_ScGeom()], [Ip2_FrictMat_FrictMat_KnKsPBPhys(Knormal = 1e8, Kshear = 1e8,useFaceProperties=False,calJointLength=False,twoDimension=True,unitWidth2D=1.0,viscousDamping=0.7)], [Law2_SCG_KnKsPBPhys_KnKsPBLaw(label='law',neverErase=False)] #[Ip2_FrictMat_FrictMat_FrictPhys()], #[Law2_ScGeom_FrictPhys_CundallStrack()] ), #GravityEngine(gravity=[0,-10,0]), #GlobalStiffnessTimeStepper(), NewtonIntegrator(damping=0.0,exactAsphericalRot=False,gravity=[0,-10,0]), #PotentialBlockVTKRecorder(fileName='/home/chiab/yadeNew/mosek/8Nov/BranchA/scripts2/boon/ComputersGeotechnics/vtk/1000PP',iterPeriod=100,sampleX=50,sampleY=50,sampleZ=50) ] powderDensity = 10000 distanceToCentre= 0.5 meanSize = 1.0 wallThickness = 0.5*meanSize O.materials.append(FrictMat(young=150e6,poisson=.4,frictionAngle=radians(0.0),density=powderDensity,label='frictionless')) lengthOfBase = 9.0*meanSize heightOfBase = 14.0*meanSize sp=pack.SpherePack() mn,mx=Vector3(-0.5*(lengthOfBase-wallThickness),0.5*meanSize,-0.5*(lengthOfBase-wallThickness)),Vector3(0.5*(lengthOfBase-wallThickness),7.0*heightOfBase,0.5*(lengthOfBase-wallThickness)) sphereRad = sqrt(3.0)*0.5*meanSize sp.makeCloud(mn,mx,sphereRad,0,100,False) count= 0 rPP=0.05*meanSize for s in sp: b=Body() radius=2.2 dynamic=True wire=False color=[0,0,255.0] highlight=False b.shape=PotentialBlock(k=0.2, r=0.05*meanSize, R=1.02*sphereRad, a=[1.0,-1.0,0.0,0.0,0.0,0.0], b=[0.0,0.0,1.0,-1.0,0.0,0.0], c=[0.0,0.0,0.0,0.0,1.0,-1.0], d=[distanceToCentre-rPP,distanceToCentre-rPP,distanceToCentre-rPP,distanceToCentre-rPP,distanceToCentre-rPP,distanceToCentre-rPP],isBoundary=False,color=color,wire=wire,highlight=highlight,minAabb=Vector3(sphereRad,sphereRad,sphereRad),maxAabb=Vector3(sphereRad,sphereRad,sphereRad),maxAabbRotated=Vector3(sphereRad,sphereRad,sphereRad),minAabbRotated=Vector3(sphereRad,sphereRad,sphereRad),AabbMinMax=False) length=meanSize V= 1.0 geomInert=(2./5.)*powderDensity*V*sphereRad**2 utils._commonBodySetup(b,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=s[0], noBound=False, resetState=True, fixed=False) b.state.pos = s[0] #s[0] stores center b.state.ori = Quaternion((random.random(),random.random(),random.random()),random.random()) #s[2] O.bodies.append(b) b.dynamic = True count =count+1 #v1 = (0, 0, 0.2) (0, 0, 1) (0,0,2.498) #v2 = (-0.0943, 0.1633, -0.0667) (-0.4714, 0.8165, -0.3334) #v3 = (0.1886 0 -0.0667) (0.9428, 0, -0.3333) #edge = 0.3266 1.6333 4.08 #volume = 0.0041 0.5132 8 r=0.1*wallThickness bbb=Body() wire=False color=[0,255,0] highlight=False bbb.shape=PotentialBlock(k=0.1, r=0.1*wallThickness, R=0.2*lengthOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=count,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),maxAabb=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),maxAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),minAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(bbb,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True, fixed=True) bbb.dynamic=False bbb.state.pos = [0.0,0,0] lidID = O.bodies.append(bbb) b1=Body() wire=False color=[0,255,0] highlight=False b1.shape=PotentialBlock(k=0.1, r=0.1*wallThickness, R=0.2*lengthOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=count,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),minAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(b1,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) b1.dynamic=False b1.state.pos = [lengthOfBase/3.0,0,lengthOfBase/3.0] O.bodies.append(b1) b2=Body() wire=False color=[0,255,0] highlight=False b2.shape=PotentialBlock(k=0.1, r=0.1*wallThickness, R=0.2*lengthOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=count,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),minAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(b2,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) b2.dynamic=False b2.state.pos = [-lengthOfBase/3.0,0,lengthOfBase/3.0] O.bodies.append(b2) b3=Body() wire=False color=[0,255,0] highlight=False b3.shape=PotentialBlock(k=0.1, r=0.1*wallThickness, R=0.2*lengthOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=count,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),minAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(b3,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) b3.dynamic=False b3.state.pos = [0.0,0,lengthOfBase/3.0] O.bodies.append(b3) b4=Body() wire=False color=[0,255,0] highlight=False b4.shape=PotentialBlock(k=0.1, r=0.1*wallThickness, R=0.2*lengthOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=count,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),minAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(b4,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) b4.dynamic=False b4.state.pos = [lengthOfBase/3.0,0,-lengthOfBase/3.0] O.bodies.append(b4) b5=Body() wire=False color=[0,255,0] highlight=False b5.shape=PotentialBlock(k=0.1, r=0.1*wallThickness, R=0.2*lengthOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=count,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),minAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(b5,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) b5.dynamic=False b5.state.pos = [0.0,0,-lengthOfBase/3.0] O.bodies.append(b5) b6=Body() wire=False color=[0,255,0] highlight=False b6.shape=PotentialBlock(k=0.1, r=0.1*wallThickness, R=0.2*lengthOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=count,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),minAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(b6,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) b6.dynamic=False b6.state.pos = [-lengthOfBase/3.0,0.0,-lengthOfBase/3.0] O.bodies.append(b6) b7=Body() wire=False color=[0,255,0] highlight=False b7.shape=PotentialBlock(k=0.1, r=0.1*wallThickness, R=0.2*lengthOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=count,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),minAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(b7,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) b7.dynamic=False b7.state.pos = [-lengthOfBase/3.0,0.0,0.0] O.bodies.append(b7) b8=Body() wire=False color=[0,255,0] highlight=False b8.shape=PotentialBlock(k=0.1, r=0.1*wallThickness, R=0.2*lengthOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=count,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),minAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(b8,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) b8.dynamic=False b8.state.pos = [lengthOfBase/3.0,0.0,0.0] O.bodies.append(b8) bA=Body() wire=False color=[0,255,0] highlight=False bA.shape=PotentialBlock(k=0.1, r=0.1*wallThickness, R=0.5*heightOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[0.5*wallThickness-r,0.5*wallThickness-r,0.5*heightOfBase-r,0.5*heightOfBase-r,0.5*lengthOfBase-r,0.5*lengthOfBase-r], id=count+1,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(0.3*wallThickness,0.5*heightOfBase,0.5*lengthOfBase),maxAabb=1.02*Vector3(0.3*wallThickness,0.5*heightOfBase,0.5*lengthOfBase),maxAabbRotated=1.02*Vector3(0.5*wallThickness,0.5*heightOfBase,0.5*lengthOfBase),minAabbRotated=1.02*Vector3(0.5*wallThickness,0.5*heightOfBase,0.5*lengthOfBase)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(bA,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) bA.dynamic=False bA.state.pos = [0.5*lengthOfBase,0.5*heightOfBase,0] O.bodies.append(bA) bB=Body() wire=False color=[0,255,0] highlight=False bB.shape=PotentialBlock(k=0.1, r=0.1*wallThickness, R=0.5*heightOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[0.5*wallThickness-r,0.5*wallThickness-r,0.5*heightOfBase-r,0.5*heightOfBase-r,0.5*lengthOfBase-r,0.5*lengthOfBase-r], id=count+2,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(0.3*wallThickness,0.5*heightOfBase,0.5*lengthOfBase),maxAabb=1.02*Vector3(0.3*wallThickness,0.5*heightOfBase,0.5*lengthOfBase),maxAabbRotated=1.02*Vector3(0.5*wallThickness,0.5*heightOfBase,0.5*lengthOfBase),minAabbRotated=1.02*Vector3(0.5*wallThickness,0.5*heightOfBase,0.5*lengthOfBase)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(bB,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) bB.dynamic=False bB.state.pos = [-0.5*lengthOfBase,0.5*heightOfBase,0] O.bodies.append(bB) bC=Body() wire=False color=[0,255,0] highlight=False bC.shape=PotentialBlock(k=0.1, r=0.1*wallThickness, R=0.5*heightOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[0.5*lengthOfBase-r,0.5*lengthOfBase-r,0.5*heightOfBase-r,0.5*heightOfBase-r,0.5*wallThickness-r,0.5*wallThickness-r], id=count+3,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.3*wallThickness),maxAabb=1.02*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.3*wallThickness),maxAabbRotated=1.02*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.5*wallThickness),minAabbRotated=1.02*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.5*wallThickness)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(bC,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) bC.dynamic=False bC.state.pos = [0,0.5*heightOfBase,0.5*lengthOfBase] O.bodies.append(bC) bD=Body() wire=False color=[0,255,0] highlight=False bD.shape=PotentialBlock(k=0.1, r=0.1*wallThickness, R=0.5*heightOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[0.5*lengthOfBase-r,0.5*lengthOfBase-r,0.5*heightOfBase-r,0.5*heightOfBase-r,0.5*wallThickness-r,0.5*wallThickness-r], id=count+4,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.3*wallThickness),maxAabb=1.02*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.3*wallThickness),maxAabbRotated=1.02*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.5*wallThickness),minAabbRotated=1.02*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.5*wallThickness)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(bD,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) bD.dynamic=False bD.state.pos = [0.0,0.5*heightOfBase,-0.5*lengthOfBase] O.bodies.append(bD) escapeNo=0 def myAddPlotData(): global escapeNo global wallThickness global meanSize uf=utils.unbalancedForce() if isnan(uf): uf = 1.0 KE = utils.kineticEnergy() for b in O.bodies: if b.state.pos[1] < -5.0*meanSize and b.dynamic==True: escapeNo = escapeNo+1 O.bodies.erase(b.id) if O.iter>12000: removeLid() plot.addData(timeStep1=O.iter,timeStep2=O.iter,timeStep3=O.iter,timeStep4=O.iter,time=O.time,unbalancedForce=uf,kineticEn=KE,outsideNo=escapeNo) from yade import plot plot.plots={'timeStep1':('unbalancedForce'),'timeStep2':('kineticEn'),'time':('outsideNo')} O.engines=O.engines+[PyRunner(iterPeriod=10,command='myAddPlotData()')] def removeLid(): global lidID if (O.bodies[lidID]): O.bodies.erase(lidID) O.engines=O.engines+[PotentialBlockVTKRecorder(fileName='/home/boon/yadeRev/trunk/examples/PotentialParticles/vtk/cubeScaled',iterPeriod=1000,sampleX=50,sampleY=50,sampleZ=50)] #for b in O.bodies: # b.state.blockedDOFs=['rx','ry','rz','x','z'] #O.bodies[0].state.pos = [0,meanSize*10.0,0] #O.bodies[0].state.vel =[0,0.0,0] O.dt = 0.2*sqrt(O.bodies[0].state.mass*0.33333333/1.0e8) #from yade import qt #qt.Controller() #qt.View() #Gl1_PotentialBlock.sizeX = 30 #Gl1_PotentialBlock.sizeY = 30 #Gl1_PotentialBlock.sizeZ = 30 #from yade import qt #qt.View() import yade.timing O.timingEnabled = True yade.timing.reset() #O.engines[2].geomDispatcher.functors[0].timingDeltas.data #yade.timing.stats() trunk-2017.01a/examples/PotentialParticles/000077500000000000000000000000001304022710500206065ustar00rootroot00000000000000trunk-2017.01a/examples/PotentialParticles/basic.py000066400000000000000000000042071304022710500222440ustar00rootroot00000000000000O.engines=[ ForceResetter(), InsertionSortCollider([PotentialParticle2AABB()]), InteractionLoop( [Ig2_PP_PP_ScGeom()], [Ip2_FrictMat_FrictMat_KnKsPhys(Knormal = 1e14, Kshear = 1e8,useFaceProperties=False,calJointLength=False,twoDimension=True,unitWidth2D=1.0,viscousDamping=0.7)], [Law2_SCG_KnKsPhys_KnKsLaw(label='law',neverErase=False)] ), NewtonIntegrator(), ] radius = 1 pos = Vector3(0,0,0) sphere=Body() radius=1 dynamic=True wire=False color=[0,0,255.0] highlight=False d = 1*radius aabb = 1.0*radius sphere.shape=PotentialParticle( k=1, r=.1*radius, R=1.*radius, a=[1.0,-1.0,0.0,0.0,0.0,0.0], b=[0.0,0.0,1.0,-1.0,0.0,0.0], c=[0.0,0.0,0.0,0.0,1.0,-1.0], d=[d,d,d,d,d,d], minAabb=Vector3(aabb,aabb,aabb), maxAabb=Vector3(aabb,aabb,aabb), maxAabbRotated=Vector3(aabb,aabb,aabb), minAabbRotated=Vector3(aabb,aabb,aabb), id=0 ) volume=4/3.*pi*radius**3 geomInert=(2./5.)*volume*radius**2 utils._commonBodySetup(sphere,volume,Vector3(geomInert,geomInert,geomInert), material=-1,pos=pos, noBound=False, resetState=True, fixed=False, blockedDOFs="") sphere.state.pos = pos sphere.state.ori = Quaternion.Identity O.bodies.append(sphere) pos = Vector3(3,0,0) box=Body() radius=1 dynamic=True wire=False color=[0,0,255.0] highlight=False d = 1*radius aabb = 1.0*radius box.shape=PotentialParticle( k=.05, r=.05*radius, R=1.*radius, a=[1.0,-1.0,0.0,0.0,0.0,0.0], b=[0.0,0.0,1.0,-1.0,0.0,0.0], c=[0.0,0.0,0.0,0.0,1.0,-1.0], d=[d,d,d,d,d,d], minAabb=sqrt(3)*Vector3(aabb,aabb,aabb), maxAabb=sqrt(3)*Vector3(aabb,aabb,aabb), maxAabbRotated=sqrt(3)*Vector3(aabb,aabb,aabb), minAabbRotated=sqrt(3)*Vector3(aabb,aabb,aabb), id=1 ) volume=4/3.*pi*radius**3 geomInert=(2./5.)*volume*radius**2 utils._commonBodySetup(box,volume,Vector3(geomInert,geomInert,geomInert), material=-1,pos=pos, noBound=False, resetState=True, fixed=False, blockedDOFs="") box.state.pos = pos box.state.ori = Quaternion((1,2,3),1) O.bodies.append(box) O.step() sphere.state.vel = (10,0,0) O.dt = 1e-5 from yade import qt qt.View() s = 20 Gl1_PotentialParticle.sizeX = s Gl1_PotentialParticle.sizeY = s Gl1_PotentialParticle.sizeZ = s Gl1_PotentialParticle.aabbEnlargeFactor = 3 trunk-2017.01a/examples/PotentialParticles/cubePPscaled.py000066400000000000000000000416651304022710500235260ustar00rootroot00000000000000#!/usr/local/bin/yade-trunk -x # -*- encoding=utf-8 -*- # CWBoon 2015 from yade import pack import math O.engines=[ ForceResetter(), InsertionSortCollider([PotentialParticle2AABB()],verletDist=0), InteractionLoop( [Ig2_PP_PP_ScGeom()], [Ip2_FrictMat_FrictMat_KnKsPhys(Knormal = 1e8, Kshear = 1e8,useFaceProperties=False,calJointLength=False,twoDimension=True,unitWidth2D=1.0,viscousDamping=0.7)], [Law2_SCG_KnKsPhys_KnKsLaw(label='law',neverErase=False)] ), GravityEngine(gravity=[0,-10,0]), NewtonIntegrator(damping=0.0,exactAsphericalRot=False,gravity=[0,-10,0]), PotentialParticleVTKRecorder(fileName='/tmp/potentialParticleTest',iterPeriod=100,sampleX=50,sampleY=50,sampleZ=50) ] powderDensity = 10000 distanceToCentre= 0.5 meanSize = 1.0 wallThickness = 0.5*meanSize O.materials.append(FrictMat(young=150e6,poisson=.4,frictionAngle=radians(0.0),density=powderDensity,label='frictionless')) lengthOfBase = 9.0*meanSize heightOfBase = 14.0*meanSize sp=pack.SpherePack() mn,mx=Vector3(-0.5*(lengthOfBase-wallThickness),0.5*meanSize,-0.5*(lengthOfBase-wallThickness)),Vector3(0.5*(lengthOfBase-wallThickness),7.0*heightOfBase,0.5*(lengthOfBase-wallThickness)) sphereRad = sqrt(3.0)*0.5*meanSize sp.makeCloud(mn,mx,sphereRad,0,100,False) count= 0 rPP=0.05*meanSize for s in sp: b=Body() radius=2.2 dynamic=True wire=False color=[0,0,255.0] highlight=False b.shape=PotentialParticle(k=0.2, r=0.05*meanSize, R=1.02*sphereRad, a=[1.0,-1.0,0.0,0.0,0.0,0.0], b=[0.0,0.0,1.0,-1.0,0.0,0.0], c=[0.0,0.0,0.0,0.0,1.0,-1.0], d=[distanceToCentre-rPP,distanceToCentre-rPP,distanceToCentre-rPP,distanceToCentre-rPP,distanceToCentre-rPP,distanceToCentre-rPP],isBoundary=False,color=color,wire=wire,highlight=highlight,minAabb=Vector3(sphereRad,sphereRad,sphereRad),maxAabb=Vector3(sphereRad,sphereRad,sphereRad),maxAabbRotated=Vector3(sphereRad,sphereRad,sphereRad),minAabbRotated=Vector3(sphereRad,sphereRad,sphereRad),AabbMinMax=False, id=count) length=meanSize V= 1.0 geomInert=(2./5.)*powderDensity*V*sphereRad**2 utils._commonBodySetup(b,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=s[0], noBound=False, resetState=True, fixed=False) b.state.pos = s[0] #s[0] stores center b.state.ori = Quaternion((random.random(),random.random(),random.random()),random.random()) #s[2] O.bodies.append(b) b.dynamic = True count =count+1 r=0.1*wallThickness bbb=Body() wire=False color=[0,255,0] highlight=False bbb.shape=PotentialParticle(k=0.1, r=0.1*wallThickness, R=0.2*lengthOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=count,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),maxAabb=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),maxAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),minAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(bbb,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True, fixed=True) bbb.dynamic=False bbb.state.pos = [0.0,0,0] lidID = O.bodies.append(bbb) b1=Body() wire=False color=[0,255,0] highlight=False b1.shape=PotentialParticle(k=0.1, r=0.1*wallThickness, R=0.2*lengthOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=count,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),minAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(b1,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) b1.dynamic=False b1.state.pos = [lengthOfBase/3.0,0,lengthOfBase/3.0] O.bodies.append(b1) b2=Body() wire=False color=[0,255,0] highlight=False b2.shape=PotentialParticle(k=0.1, r=0.1*wallThickness, R=0.2*lengthOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=count,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),minAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(b2,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) b2.dynamic=False b2.state.pos = [-lengthOfBase/3.0,0,lengthOfBase/3.0] O.bodies.append(b2) b3=Body() wire=False color=[0,255,0] highlight=False b3.shape=PotentialParticle(k=0.1, r=0.1*wallThickness, R=0.2*lengthOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=count,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),minAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(b3,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) b3.dynamic=False b3.state.pos = [0.0,0,lengthOfBase/3.0] O.bodies.append(b3) b4=Body() wire=False color=[0,255,0] highlight=False b4.shape=PotentialParticle(k=0.1, r=0.1*wallThickness, R=0.2*lengthOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=count,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),minAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(b4,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) b4.dynamic=False b4.state.pos = [lengthOfBase/3.0,0,-lengthOfBase/3.0] O.bodies.append(b4) b5=Body() wire=False color=[0,255,0] highlight=False b5.shape=PotentialParticle(k=0.1, r=0.1*wallThickness, R=0.2*lengthOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=count,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),minAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(b5,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) b5.dynamic=False b5.state.pos = [0.0,0,-lengthOfBase/3.0] O.bodies.append(b5) b6=Body() wire=False color=[0,255,0] highlight=False b6.shape=PotentialParticle(k=0.1, r=0.1*wallThickness, R=0.2*lengthOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=count,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),minAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(b6,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) b6.dynamic=False b6.state.pos = [-lengthOfBase/3.0,0.0,-lengthOfBase/3.0] O.bodies.append(b6) b7=Body() wire=False color=[0,255,0] highlight=False b7.shape=PotentialParticle(k=0.1, r=0.1*wallThickness, R=0.2*lengthOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=count,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),minAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(b7,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) b7.dynamic=False b7.state.pos = [-lengthOfBase/3.0,0.0,0.0] O.bodies.append(b7) b8=Body() wire=False color=[0,255,0] highlight=False b8.shape=PotentialParticle(k=0.1, r=0.1*wallThickness, R=0.2*lengthOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[lengthOfBase/6.0-r,lengthOfBase/6.0-r,0.5*wallThickness-r,0.5*wallThickness-r,lengthOfBase/6.0-r,lengthOfBase/6.0-r], id=count,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabb=1.02*Vector3(lengthOfBase/6.0,0.4*wallThickness,lengthOfBase/6.0),maxAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0),minAabbRotated=1.02*Vector3(lengthOfBase/6.0,0.5*wallThickness,lengthOfBase/6.0)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(b8,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) b8.dynamic=False b8.state.pos = [lengthOfBase/3.0,0.0,0.0] O.bodies.append(b8) bA=Body() wire=False color=[0,255,0] highlight=False bA.shape=PotentialParticle(k=0.1, r=0.1*wallThickness, R=0.5*heightOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[0.5*wallThickness-r,0.5*wallThickness-r,0.5*heightOfBase-r,0.5*heightOfBase-r,0.5*lengthOfBase-r,0.5*lengthOfBase-r], id=count+1,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(0.3*wallThickness,0.5*heightOfBase,0.5*lengthOfBase),maxAabb=1.02*Vector3(0.3*wallThickness,0.5*heightOfBase,0.5*lengthOfBase),maxAabbRotated=1.02*Vector3(0.5*wallThickness,0.5*heightOfBase,0.5*lengthOfBase),minAabbRotated=1.02*Vector3(0.5*wallThickness,0.5*heightOfBase,0.5*lengthOfBase)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(bA,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) bA.dynamic=False bA.state.pos = [0.5*lengthOfBase,0.5*heightOfBase,0] O.bodies.append(bA) bB=Body() wire=False color=[0,255,0] highlight=False bB.shape=PotentialParticle(k=0.1, r=0.1*wallThickness, R=0.5*heightOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[0.5*wallThickness-r,0.5*wallThickness-r,0.5*heightOfBase-r,0.5*heightOfBase-r,0.5*lengthOfBase-r,0.5*lengthOfBase-r], id=count+2,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(0.3*wallThickness,0.5*heightOfBase,0.5*lengthOfBase),maxAabb=1.02*Vector3(0.3*wallThickness,0.5*heightOfBase,0.5*lengthOfBase),maxAabbRotated=1.02*Vector3(0.5*wallThickness,0.5*heightOfBase,0.5*lengthOfBase),minAabbRotated=1.02*Vector3(0.5*wallThickness,0.5*heightOfBase,0.5*lengthOfBase)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(bB,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) bB.dynamic=False bB.state.pos = [-0.5*lengthOfBase,0.5*heightOfBase,0] O.bodies.append(bB) bC=Body() wire=False color=[0,255,0] highlight=False bC.shape=PotentialParticle(k=0.1, r=0.1*wallThickness, R=0.5*heightOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[0.5*lengthOfBase-r,0.5*lengthOfBase-r,0.5*heightOfBase-r,0.5*heightOfBase-r,0.5*wallThickness-r,0.5*wallThickness-r], id=count+3,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.3*wallThickness),maxAabb=1.02*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.3*wallThickness),maxAabbRotated=1.02*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.5*wallThickness),minAabbRotated=1.02*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.5*wallThickness)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(bC,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) bC.dynamic=False bC.state.pos = [0,0.5*heightOfBase,0.5*lengthOfBase] O.bodies.append(bC) bD=Body() wire=False color=[0,255,0] highlight=False bD.shape=PotentialParticle(k=0.1, r=0.1*wallThickness, R=0.5*heightOfBase,a=[1,-1,0,0,0,0], b=[0,0,1,-1,0,0], c=[0,0,0,0,1,-1], d=[0.5*lengthOfBase-r,0.5*lengthOfBase-r,0.5*heightOfBase-r,0.5*heightOfBase-r,0.5*wallThickness-r,0.5*wallThickness-r], id=count+4,isBoundary=True,isBoundaryPlane=[True,True,True,True,True,True],color=color ,wire=wire,highlight=highlight,AabbMinMax=True, minAabb=1.02*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.3*wallThickness),maxAabb=1.02*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.3*wallThickness),maxAabbRotated=1.02*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.5*wallThickness),minAabbRotated=1.02*Vector3(0.5*lengthOfBase,0.5*heightOfBase,0.5*wallThickness)) length=lengthOfBase V=lengthOfBase*lengthOfBase*wallThickness geomInert=(1./6.)*V*length*wallThickness utils._commonBodySetup(bD,V,Vector3(geomInert,geomInert,geomInert), material='frictionless',pos=[0.0,0,0], noBound=False, resetState=True,fixed=True) bD.dynamic=False bD.state.pos = [0.0,0.5*heightOfBase,-0.5*lengthOfBase] O.bodies.append(bD) escapeNo=0 def myAddPlotData(): global escapeNo global wallThickness global meanSize uf=utils.unbalancedForce() if isnan(uf): uf = 1.0 KE = utils.kineticEnergy() for b in O.bodies: if b.state.pos[1] < -5.0*meanSize and b.dynamic==True: escapeNo = escapeNo+1 O.bodies.erase(b.id) if O.iter>12000: removeLid() plot.addData(timeStep1=O.iter,timeStep2=O.iter,timeStep3=O.iter,timeStep4=O.iter,time=O.time,unbalancedForce=uf,kineticEn=KE,outsideNo=escapeNo) from yade import plot plot.plots={'timeStep1':('unbalancedForce'),'timeStep2':('kineticEn'),'time':('outsideNo')} O.engines=O.engines+[PyRunner(iterPeriod=10,command='myAddPlotData()')] def removeLid(): global lidID if (O.bodies[lidID]): O.bodies.erase(lidID) O.dt = 0.2*sqrt(O.bodies[0].state.mass*0.33333333/1.0e8) trunk-2017.01a/examples/ResetRandomPosition.py000066400000000000000000000035231304022710500213250ustar00rootroot00000000000000# -*- coding: utf-8 from yade import pack,export,qt import gts,os def Plane(v1,v2,v3,v4): pts = [ [Vector3(v1),Vector3(v2),Vector3(v3),Vector3(v4)] ] return pack.sweptPolylines2gtsSurface(pts,capStart=True,capEnd=True) # Parameters tc=0.001# collision time en=0.3 # normal restitution coefficient es=0.3 # tangential restitution coefficient frictionAngle=radians(35)# density=2700 # facets material facetMat=O.materials.append(ViscElMat(frictionAngle=frictionAngle,tc=tc,en=en,et=es)) # default spheres material dfltSpheresMat=O.materials.append(ViscElMat(density=density,frictionAngle=frictionAngle,tc=tc,en=en,et=es)) O.dt=.2*tc # time step Rs=0.02 # mean particle radius Rf=0.01 # dispersion (Rs±Rf*Rs) nSpheres=1000# number of particles # Create geometry pln=Plane( (-.5, -.5, 0), (.5, -.5, -.05), (.5, .5, 0), (-.5, .5, -.05) ); plnIds=O.bodies.append(pack.gtsSurface2Facets(pln,material=facetMat,color=(0,1,0))) fct=Plane( (-.25, -.25, .5), (.25, -.25, .5), (.25, .25, .5), (-.25, .25, .5) ); fctIds=O.bodies.append(pack.gtsSurface2Facets(fct,material=facetMat,color=(1,0,0),noBound=True)) # Create spheres sp=pack.SpherePack(); sp.makeCloud(Vector3(-.5, -.5, 0),Vector3(.5, .5, .2), Rs, Rf, int(nSpheres), False) spheres=O.bodies.append([sphere(s[0],s[1],color=(0.929,0.412,0.412),material=dfltSpheresMat) for s in sp]) # Create engines O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0,gravity=[0,0,-9.81]), ResetRandomPosition(virtPeriod=0.01,factoryFacets=fctIds,velocity=(0,0,-2),subscribedBodies=spheres,point=(0,0,-.5),normal=(0,0,1),maxAttempts=100), ] renderer = qt.Renderer() qt.View() O.saveTmp() O.run() trunk-2017.01a/examples/ViscElMatchMaker.py000066400000000000000000000053301304022710500204750ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 # This example shows, how matchmaker can be used to # set the parameters of ViscoElastic model. from yade import utils, plot o = Omega() fr = 0.5;rho=2000 tc = 0.001; en = 0.5; et = 0.5; o.dt = 0.002*tc r1 = 0.002381 r2 = 0.002381 mat1 = O.materials.append(ViscElMat(frictionAngle=fr,tc=tc,en=en,et=et,density=rho)) mat2 = O.materials.append(ViscElMat(frictionAngle=fr,tc=tc,en=en,et=et,density=rho)) mat3 = O.materials.append(ViscElMat(frictionAngle=fr,tc=tc,en=en,et=et,density=rho)) id11 = O.bodies.append(sphere(center=[0,0,0],radius=r1,material=mat1,fixed=True,color=[0,0,1])) id12 = O.bodies.append(sphere(center=[0,0,(r1+r2)],radius=r2,material=mat2,fixed=False,color=[0,0,1])) id21 = O.bodies.append(sphere(center=[3*r1,0,0],radius=r1,material=mat1,fixed=True,color=[0,1,0])) id22 = O.bodies.append(sphere(center=[3*r1,0,(r1+r2)],radius=r2,material=mat3,fixed=False,color=[0,1,0])) id31 = O.bodies.append(sphere(center=[6*r1,0,0],radius=r1,material=mat2,fixed=True,color=[1,0,0])) id32 = O.bodies.append(sphere(center=[6*r1,0,(r1+r2)],radius=r2,material=mat3,fixed=False,color=[1,0,0])) o.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()],verletDist=(r1+r2)*5.0), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys( en=MatchMaker(matches=((mat1,mat2,.9),(mat1,mat3,.5),(mat2,mat3,.1))), # Set parameters et=MatchMaker(matches=((mat1,mat2,.9),(mat1,mat3,.5),(mat2,mat3,.1))), frictAngle=MatchMaker(matches=((mat1,mat2,.1),(mat1,mat3,.2),(mat2,mat3,.3))) )], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0,gravity=[0,0,-9.81]), PyRunner(command='addPlotData()',iterPeriod=100), ] vel=-0.50 O.bodies[id12].state.vel=[0,0,vel] O.bodies[id22].state.vel=[0,0,vel] O.bodies[id32].state.vel=[0,0,vel] def addPlotData(): s1 = (O.bodies[id12].state.pos[2]-O.bodies[id11].state.pos[2])-(r1+r2) s2 = (O.bodies[id22].state.pos[2]-O.bodies[id11].state.pos[2])-(r1+r2) s3 = (O.bodies[id32].state.pos[2]-O.bodies[id11].state.pos[2])-(r1+r2) plot.addData(mat1mat2=s1,mat1mat3=s2,mat2mat3=s3,it=O.iter) plot.plots={'it':('mat1mat2','mat1mat3','mat2mat3')}; plot.plot() O.step() from yade import qt qt.View() print "Friction coefficient for id11 and id12 is %g"%(math.atan(O.interactions[id11,id12].phys.tangensOfFrictionAngle)) print "Friction coefficient for id21 and id22 is %g"%(math.atan(O.interactions[id21,id22].phys.tangensOfFrictionAngle)) print "Friction coefficient for id31 and id32 is %g"%(math.atan(O.interactions[id31,id32].phys.tangensOfFrictionAngle)) O.run(100000, True) #plot.saveGnuplot('sim-data_') trunk-2017.01a/examples/WireMatPM/000077500000000000000000000000001304022710500166055ustar00rootroot00000000000000trunk-2017.01a/examples/WireMatPM/wirecontacttest.py000066400000000000000000000123041304022710500224010ustar00rootroot00000000000000# -*- coding: utf-8 -*- from yade import plot, qt #### define parameters for the net # wire diameter d = 2.7/1000. # particle radius radius = d*4. # define piecewise linear stress-strain curve [Pa] strainStressValues=[(0.0019230769,2.5e8),(0.0192,3.2195e8),(0.05,3.8292e8),(0.15,5.1219e8),(0.25,5.5854e8),(0.3,5.6585e8),(0.35,5.6585e8)] # elastic material properties particleVolume = 4./3.*pow(radius,3)*pi particleMass = 3.9/1000. density = particleMass/particleVolume young = strainStressValues[0][1] / strainStressValues[0][0] poisson = 0.3 #### material definition netMat = O.materials.append( WireMat( young=young,poisson=poisson,frictionAngle=radians(30),density=density,isDoubleTwist=True,diameter=d,strainStressValues=strainStressValues,lambdaEps=0.4,lambdak=0.66) ) wireMat = O.materials.append( WireMat( young=young,poisson=poisson,frictionAngle=radians(30),density=density,isDoubleTwist=False,diameter=3.4/1000,strainStressValues=strainStressValues ) ) blocMat = O.materials.append(FrictMat(young=60e3,poisson=0.15,frictionAngle=radians(30),density=44.5/((4./3.*pi*0.02**3)*1576.))) #### define parameters for the net packing # mesh geometry mos = 0.08 a = 0.04 b = 0.04 # wire diameter d = 2.7/1000. # net dimension cornerCoord=[0,0,0] Lx = 2. Ly = 2. # properties of particles kw = {'color':[0,1,0],'wire':True,'highlight':False,'fixed':False,'material':netMat} ##### create packing for net [netpack,lx,ly] = hexaNet( radius=radius, cornerCoord=cornerCoord, xLength=Lx, yLength=Ly, mos=mos, a=a, b=b, startAtCorner=True, isSymmetric=False, **kw ) O.bodies.append(netpack) #### get bodies for single wire at the boundary in y-direction and change properties bb = uniaxialTestFeatures(axis=0) negIds,posIds=bb['negIds'],bb['posIds'] for id in negIds: O.bodies[id].material = O.materials[wireMat] O.bodies[id].shape.color = [0,0,1] for id in posIds: O.bodies[id].material = O.materials[wireMat] O.bodies[id].shape.color = [0,0,1] #### define engines to create link interactionRadius=2.8 # value has to be adjusted according to the particle size of the net and the mesh opening size of the net (check always if links are created) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=interactionRadius,label='aabb')]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=interactionRadius,label='Ig2ssGeom')], [Ip2_WireMat_WireMat_WirePhys(linkThresholdIteration=1,label='wire_wire'),Ip2_FrictMat_FrictMat_FrictPhys(label='block_wire')], [Law2_ScGeom_WirePhys_WirePM(linkThresholdIteration=1,label='Law_1'),Law2_ScGeom_FrictPhys_CundallStrack(label='Law_2')] ), NewtonIntegrator(damping=0.), ] #### define additional vertical interactions at the boundary for boundary wire for i in range(24)[1::2]: # odd - start at second item and take every second item createInteraction(negIds[i],negIds[i+1]) del posIds[1] posIds.append(1) for i in range(25)[::2]: # even - start at the beginning at take every second item createInteraction(posIds[i],posIds[i+1]) #### time step definition for first time step to create links O.step() ##### delete horizontal interactions for corner particles bb = uniaxialTestFeatures(axis=1) negIds,posIds,axis,crossSectionArea=bb['negIds'],bb['posIds'],bb['axis'],bb['area'] ##### delete some interactions O.interactions.erase(0,50) O.interactions.erase(0,51) O.interactions.erase(1,1250) O.interactions.erase(1,1251) #### time step definition for deleting some links which have been created by the Ig2 functor O.step() #### initializes now the interaction detection factor aabb.aabbEnlargeFactor=-1. Ig2ssGeom.interactionDetectionFactor=-1. #### define boundary conditions fixedIds=negIds movingIds=posIds for id in fixedIds: O.bodies[id].shape.color = [1,0,0] O.bodies[id].state.blockedDOFs='xyzXYZ' for id in movingIds: O.bodies[id].shape.color = [1,0,0] O.bodies[id].state.blockedDOFs='xyzXYZ' #### import block as a sphere after net has been created bloc=O.bodies.append(sphere([1.0,1.0,0.65],radius=0.15,wire=False,highlight=False,color=[1,1,0],material=blocMat)) O.bodies[bloc].state.isDamped=False # switch damping off since free fall under gravity #### plot some results plot.plots={'t':['vz',None,('f_unbal','g--')]} #plot.liveInterval=2. plot.plot(noShow=False, subPlots=False) def addPlotData(): plot.addData(t=O.time, vz=-O.bodies[bloc].state.vel[2], f_unbal=unbalancedForce(useMaxForce=False) ) #### define engines for simulation v = qt.Controller() v = qt.View() rr = qt.Renderer() rr.intrAllWire = True O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(label='aabb')]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(label='Ig2ssGeom')], [Ip2_WireMat_WireMat_WirePhys(label='wire_wire'),Ip2_FrictMat_FrictMat_FrictPhys(label='block_wire')], [Law2_ScGeom_WirePhys_WirePM(label='Law_1'),Law2_ScGeom_FrictPhys_CundallStrack(label='Law_2')] ), NewtonIntegrator(damping=0.2,gravity=[0,0,-9.81],label='NewtonGravity'), PyRunner(initRun=True,iterPeriod=100,command='addPlotData()'), ] #### time step definition for simulation ## critical time step proposed by Bertrand kn = 16115042 # stiffness of single wire from code, has to be changed if you change the stress-strain curve for the wire O.dt = 0.2*sqrt(particleMass/(2.*kn)) O.run(200000) trunk-2017.01a/examples/WireMatPM/wirepackings.py000066400000000000000000000061171304022710500216520ustar00rootroot00000000000000# encoding: utf-8 from yade import qt #### short description of script print 'This script shows the use of the function hexaNet of module pack (interactions are not initialised)' #### define parameters for the net # mesh geometry mos = 0.08 a = 0.04 b = 0.04 # wire diameter d = 2.7/1000. # net dimension Lx = 0.2 Ly = 0.15 # properties of particles radius = d*4. #### startAtCorner=True kw = {'color':[1,1,0],'wire':True,'highlight':False,'fixed':False,'material':-1} #### packing 1 [netpack,lx,ly] = hexaNet( radius=radius, cornerCoord=[0,0,0], xLength=Lx, yLength=Ly, mos=mos, a=a, b=b, startAtCorner=True, isSymmetric=True, **kw ) O.bodies.append(netpack) print 'Packing 1:' print 'Real net length in x-direction [m]: ', lx print 'Real net length in y-direction [m]: ', ly #### packing 2 [netpack,lx,ly] = hexaNet( radius=radius, cornerCoord=[0.4,0,0], xLength=Lx, yLength=Ly, mos=mos, a=a, b=b, startAtCorner=True, isSymmetric=False, **kw ) O.bodies.append(netpack) print 'Packing 2:' print 'Real net length in x-direction [m]: ', lx print 'Real net length in y-direction [m]: ', ly #### packing 3 [netpack,lx,ly] = hexaNet( radius=radius, cornerCoord=[0,-0.4,0], xLength=Lx, yLength=Ly+0.05, mos=mos, a=a, b=b, startAtCorner=True, isSymmetric=True, **kw ) O.bodies.append(netpack) print 'Packing 3:' print 'Real net length in x-direction [m]: ', lx print 'Real net length in y-direction [m]: ', ly #### packing 4 [netpack,lx,ly] = hexaNet( radius=radius, cornerCoord=[0.4,-0.4,0], xLength=Lx, yLength=Ly+0.05, mos=mos, a=a, b=b, startAtCorner=True, isSymmetric=False, **kw ) O.bodies.append(netpack) print 'Packing 4:' print 'Real net length in x-direction [m]: ', lx print 'Real net length in y-direction [m]: ', ly #### startAtCorner=False kw = {'color':[1,0,0],'wire':True,'highlight':False,'fixed':False,'material':-1} #### packing 1 [netpack,lx,ly] = hexaNet( radius=radius, cornerCoord=[1,0,0], xLength=Lx, yLength=Ly, mos=mos, a=a, b=b, startAtCorner=False, isSymmetric=True, **kw ) O.bodies.append(netpack) print 'Packing 1:' print 'Real net length in x-direction [m]: ', lx print 'Real net length in y-direction [m]: ', ly #### packing 2 [netpack,lx,ly] = hexaNet( radius=radius, cornerCoord=[1.4,0,0], xLength=Lx, yLength=Ly, mos=mos, a=a, b=b, startAtCorner=False, isSymmetric=False, **kw ) O.bodies.append(netpack) print 'Packing 2:' print 'Real net length in x-direction [m]: ', lx print 'Real net length in y-direction [m]: ', ly #### packing 3 [netpack,lx,ly] = hexaNet( radius=radius, cornerCoord=[1,-0.4,0], xLength=Lx, yLength=Ly+0.05, mos=mos, a=a, b=b, startAtCorner=False, isSymmetric=True, **kw ) O.bodies.append(netpack) print 'Packing 3:' print 'Real net length in x-direction [m]: ', lx print 'Real net length in y-direction [m]: ', ly #### packing 4 [netpack,lx,ly] = hexaNet( radius=radius, cornerCoord=[1.4,-0.4,0], xLength=Lx, yLength=Ly+0.05, mos=mos, a=a, b=b, startAtCorner=False, isSymmetric=False, **kw ) O.bodies.append(netpack) print 'Packing 4:' print 'Real net length in x-direction [m]: ', lx print 'Real net length in y-direction [m]: ', ly ## to see it v=qt.Controller() v=qt.View() trunk-2017.01a/examples/WireMatPM/wiretensiltest.py000066400000000000000000000112021304022710500222400ustar00rootroot00000000000000# -*- coding: utf-8 -*- from yade import plot #### short description of script print 'This script shows a tensile test of a net by using the UniaxialStrainer' #### define parameters for the net # wire diameter d = 2.7/1000. # particle radius radius = d*4. # define piecewise lineare stress-strain curve strainStressValues=[(0.0019230769,2.5e8),(0.0192,3.2195e8),(0.05,3.8292e8),(0.15,5.1219e8),(0.25,5.5854e8),(0.3,5.6585e8),(0.35,5.6585e8)] # elastic material properties particleVolume = 4./3.*pow(radius,3)*pi particleMass = 3.9/1000. density = particleMass/particleVolume young = strainStressValues[0][1] / strainStressValues[0][0] poisson = 0.3 #### material definition netMat = O.materials.append( WireMat( young=young,poisson=poisson,frictionAngle=radians(30),density=density,isDoubleTwist=True,diameter=d,strainStressValues=strainStressValues,lambdaEps=0.4,lambdak=0.66) ) wireMat = O.materials.append( WireMat( young=young,poisson=poisson,frictionAngle=radians(30),density=density,isDoubleTwist=False,diameter=3.4/1000,strainStressValues=strainStressValues ) ) #### get net packing kw = {'color':[1,1,0],'wire':True,'highlight':False,'fixed':False,'material':netMat} [netpack,lx,ly] = hexaNet( radius=radius, cornerCoord=[0,0,0], xLength=1.0, yLength=0.55, mos=0.08, a=0.04, b=0.04, startAtCorner=False, isSymmetric=True, **kw ) O.bodies.append(netpack) print 'Real net length in x-direction [m]: ', lx print 'Real net length in y-direction [m]: ', ly #### get bodies for single wire at the boundary in y-direction and change properties bb = uniaxialTestFeatures(axis=0) negIds,posIds=bb['negIds'],bb['posIds'] for id in negIds: O.bodies[id].material = O.materials[wireMat] O.bodies[id].shape.color = [0,0,1] for id in posIds: O.bodies[id].material = O.materials[wireMat] O.bodies[id].shape.color = [0,0,1] #### define engines to create link interactionRadius=2.8 O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=interactionRadius,label='aabb')]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=interactionRadius,label='Ig2ssGeom')], [Ip2_WireMat_WireMat_WirePhys(linkThresholdIteration=1,label='interactionPhys')], [Law2_ScGeom_WirePhys_WirePM(linkThresholdIteration=1,label='interactionLaw')] ), NewtonIntegrator(damping=0.), ] #### define additional vertical interactions at the boundary createInteraction(negIds[0],negIds[2]) createInteraction(negIds[3],negIds[4]) createInteraction(negIds[5],negIds[6]) createInteraction(negIds[7],negIds[1]) createInteraction(posIds[0],posIds[2]) createInteraction(posIds[3],posIds[4]) createInteraction(posIds[5],posIds[6]) createInteraction(posIds[7],posIds[1]) #### time step definition for first time step to create links O.step() #### initialize values for UniaxialStrainer bb = uniaxialTestFeatures(axis=1) negIds,posIds,axis,crossSectionArea=bb['negIds'],bb['posIds'],bb['axis'],bb['area'] strainRateTension = 0.1 setSpeeds = True ##### delete horizontal interactions for corner particles bb = uniaxialTestFeatures(axis=1) negIds,posIds,axis,crossSectionArea=bb['negIds'],bb['posIds'],bb['axis'],bb['area'] ##### delete some interactions O.interactions.erase(0,4) O.interactions.erase(0,5) O.interactions.erase(1,154) O.interactions.erase(1,155) O.interactions.erase(2,26) O.interactions.erase(2,27) O.interactions.erase(3,176) O.interactions.erase(3,177) #### time step definition for deleting some links which have been created by the Ig2 functor O.step() #### initializes now the interaction detection factor aabb.aabbEnlargeFactor=-1. Ig2ssGeom.interactionDetectionFactor=-1. #### define engines for simulation with UniaxialStrainer O.engines = O.engines[:3] + [ UniaxialStrainer(strainRate=strainRateTension,axis=axis,asymmetry=1,posIds=posIds,negIds=negIds,crossSectionArea=crossSectionArea,blockDisplacements=True,blockRotations=False,setSpeeds=setSpeeds,label='strainer'), NewtonIntegrator(damping=0.5), PyRunner(initRun=True,iterPeriod=1000,command='addPlotData()'), ] #### plot some results plot.plots={'un':('Fn',)} plot.plot(noShow=False, subPlots=False) def addPlotData(): Fn = 0. for i in posIds: try: inter=O.interactions.withBody(i)[0] F = abs(inter.phys.normalForce[1]) except: F = 0 Fn += F un = O.bodies[O.bodies[posIds[0]].id].state.pos[1] - O.bodies[O.bodies[posIds[0]].id].state.refPos[1] if un > 0.10: O.pause() plot.addData( un=un*1000, Fn=Fn/1000 ) #### time step definition for simulation ## critical time step proposed by Bertrand kn = 16115042 # stiffness of single wire from code O.dt = 0.2*sqrt(particleMass/(2.*kn)) #### to see it from yade import qt v = qt.Controller() v = qt.View() rr = qt.Renderer() rr.intrAllWire = True trunk-2017.01a/examples/adaptiveintegrator/000077500000000000000000000000001304022710500206745ustar00rootroot00000000000000trunk-2017.01a/examples/adaptiveintegrator/simple-scene-plot-NewtonIntegrator.py000066400000000000000000000037531304022710500301250ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- import matplotlib matplotlib.use('TkAgg') O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), NewtonIntegrator(damping=0.0,gravity=(0,0,-9.81)), ### ### NOTE this extra engine: ### ### You want snapshot to be taken every 1 sec (realTimeLim) or every 50 iterations (iterLim), ### whichever comes soones. virtTimeLim attribute is unset, hence virtual time period is not taken into account. PyRunner(iterPeriod=20,command='myAddPlotData()') ] O.bodies.append(box(center=[0,0,0],extents=[.5,.5,.5],fixed=True,color=[1,0,0])) O.bodies.append(sphere([0,0,2],1,color=[0,1,0])) O.dt=.002*PWaveTimeStep() ############################################ ##### now the part pertaining to plots ##### ############################################ from yade import plot ## we will have 2 plots: ## 1. t as function of i (joke test function) ## 2. i as function of t on left y-axis ('|||' makes the separation) and z_sph, v_sph (as green circles connected with line) and z_sph_half again as function of t plot.plots={'i':('t'),'t':('z_sph',None,('v_sph','go-'),'z_sph_half')} ## this function is called by plotDataCollector ## it should add data with the labels that we will plot ## if a datum is not specified (but exists), it will be NaN and will not be plotted def myAddPlotData(): sph=O.bodies[1] ## store some numbers under some labels plot.addData(t=O.time,i=O.iter,z_sph=sph.state.pos[2],z_sph_half=.5*sph.state.pos[2],v_sph=sph.state.vel.norm()) print "Now calling plot.plot() to show the figures. The timestep is artificially low so that you can watch graphs being updated live." plot.liveInterval=.2 plot.plot(subPlots=False) O.run(int(5./O.dt)); #plot.saveGnuplot('/tmp/a') ## you can also access the data in plot.data['i'], plot.data['t'] etc, under the labels they were saved. trunk-2017.01a/examples/adaptiveintegrator/simple-scene-plot-RungeKuttaCashKarp54.py000066400000000000000000000047651304022710500304770ustar00rootroot00000000000000#!/usr/bin/python # Burak ER # burak.er@btu.edu.tr # github.com/burak-er # Mechanical Engineering Department # Bursa Technical University # # -*- coding: utf-8 -*- import matplotlib matplotlib.use('TkAgg') # Use an integrator engine that is derived from the interface Integrator. #RungeKuttaCashKarp54Integrator integrator performs one step of simulation for the given tolerances. Whether the time step is given, it completes it then stops. integrator=RungeKuttaCashKarp54Integrator([ ForceResetter(), GeneralIntegratorInsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), GravityEngine(gravity=Vector3(0,0,-9.81)), PyRunner(virtPeriod=1e-99,command='myAddPlotData()')#use virtPeriod on this integrator. ]); #Tolerances can be set for the optimum accuracy integrator.rel_err=1e-6; integrator.abs_err=1e-6; O.engines=[integrator, ] O.bodies.append(box(center=[0,0,0],extents=[.5,.5,.5],fixed=True,color=[1,0,0])) O.bodies.append(sphere([0,0,2],1,color=[0,1,0])) O.dt=1e-2# this signifies the endpoint. It is not much important for the accuracy of the integration where accuracy is defined by rel_err and abs_err of the integrator. ############################################ ##### now the part pertaining to plots ##### ############################################ from yade import plot ## we will have 2 plots: ## 1. t as function of i (joke test function) ## 2. i as function of t on left y-axis ('|||' makes the separation) and z_sph, v_sph (as green circles connected with line) and z_sph_half again as function of t plot.plots={'i':('t'),'t':('z_sph',None,('v_sph','go-'),'z_sph_half')} ## this function is called by plotDataCollector ## it should add data with the labels that we will plot ## if a datum is not specified (but exists), it will be NaN and will not be plotted def myAddPlotData(): sph=O.bodies[1] ## store some numbers under some labels plot.addData(t=O.time,i=O.iter,z_sph=sph.state.pos[2],z_sph_half=.5*sph.state.pos[2],v_sph=sph.state.vel.norm()) print "Now calling plot.plot() to show the figures. The timestep is artificially low so that you can watch graphs being updated live." plot.liveInterval=.2 plot.plot(subPlots=False) print "Number of threads ", os.environ['OMP_NUM_THREADS'] O.run(int(5./O.dt)); #plot.saveGnuplot('/tmp/a') ## you can also access the data in plot.data['i'], plot.data['t'] etc, under the labels they were saved. trunk-2017.01a/examples/agglomerate/000077500000000000000000000000001304022710500172675ustar00rootroot00000000000000trunk-2017.01a/examples/agglomerate/README000066400000000000000000000013631304022710500201520ustar00rootroot00000000000000A series of scripts that prepare and agglomerate packing, i.e. cohesive elastic aggregates, each composed of dense particle packing A general idea: - create a "macro" particles as large spheres using makeCloud - "mesh" these macroparticles with smaller spheres - run compression to make the loose packing denser - save the result - use the resulting packing in actual simulation Scripts in order to run: - makeCloud.py ... a script to prepare loose packing of macro particles using makeCloud - divide.py ... a script to divide the macro particles from previous step into clump of particles - compress.py ... a script to create dense packing of agglomerates - simulation.py ... use of prepared dense packing of agglomerates in a simple simulation trunk-2017.01a/examples/agglomerate/compress.py000066400000000000000000000032321304022710500214740ustar00rootroot00000000000000###################################################################### # Compress the loose packing into dense packing. Each agglomerate is # considered as clump in this stage ###################################################################### from yade import export,ymport import random random.seed(1) # add walls first dim = (15,15,15) walls = aabbWalls(((0,0,0),(dim))) wallIds = O.bodies.append(walls) # load spheres from file, including information of their agglomerates ids attrs = [] sp = ymport.textExt('/tmp/divided.txt',format='x_y_z_r_attrs',attrs=attrs) n = max(int(a[0]) for a in attrs)+1 colors = [randomColor() for _ in xrange(n)] agglomerates = [[] for _ in xrange(n)] for s,a in zip(sp,attrs): aa = int(a[0]) s.agglomerate = aa s.shape.color = colors[aa] agglomerates[aa].append(s) for a in agglomerates: O.bodies.appendClumped(a) O.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), TriaxialStressController( thickness = 0, stressMask = 7, internalCompaction = False, label = 'compressor', ), NewtonIntegrator(damping=.6), ] O.dt = PWaveTimeStep() # compress the sample compressor.goal1 = compressor.goal2 = compressor.goal3 = -1e-7 O.run(50000,True) compressor.goal1 = compressor.goal2 = compressor.goal3 = -1e-5 O.run(30000,True) # save the result, including information of agglomerates which the particle belongs to export.textExt('/tmp/compressed.txt','x_y_z_r_attrs',attrs=['b.agglomerate']) try: from yade import qt qt.View() except: pass trunk-2017.01a/examples/agglomerate/divide.py000066400000000000000000000022311304022710500211030ustar00rootroot00000000000000###################################################################### # A script for subdivision of macro perticles into a dense packing of # smaller particles # # Each aggragate is a dense packing, but macroscopically the packing # is loose ###################################################################### from yade import export,ymport import random random.seed(1) # to make colors always the same # load macroparticles sp = ymport.text('/tmp/cloud.txt') colors = [randomColor() for s in sp] # each macroparticle is filled randomDensePack for si,s in enumerate(sp): sphere = pack.inSphere(s.state.pos, s.shape.radius) sp1 = pack.randomDensePack( sphere, spheresInCell = 500, radius = .2, memoizeDb = '/tmp/agglomeratepackaux.db', returnSpherePack = True, ) ids = sp1.toSimulation(color=colors[si]) # add the result to simulation with uniform color for i in ids: O.bodies[i].agglomerate = si # tell each particle who is its agglomerate # save the result, including information of agglomerates which the particle belongs to export.textExt('/tmp/divided.txt','x_y_z_r_attrs',attrs=['b.agglomerate']) try: from yade import qt qt.View() except: pass trunk-2017.01a/examples/agglomerate/makeCloud.py000066400000000000000000000010211304022710500215370ustar00rootroot00000000000000###################################################################### # A script for prepare loose packing of macro particles ###################################################################### from yade import export dim = (15,15,15) # dimensions for makeCloud radius = 1 fuzz = 0.2 # use of makeCloud function sp = pack.SpherePack() sp.makeCloud((0,0,0), dim, rMean=radius, rRelFuzz=fuzz, seed=1) sp.toSimulation() # save the result export.text('/tmp/cloud.txt') try: from yade import qt qt.View() except: pass trunk-2017.01a/examples/agglomerate/simulation.py000066400000000000000000000033151304022710500220270ustar00rootroot00000000000000###################################################################### # Gravity deposition as a simple simulation illustrating creation of # cohesive contacts and deleting the unwanted between different # agglomerates # # Using CpmMat, but the same procedure can be used with any material ###################################################################### from yade import ymport wall = O.bodies.append(wall((0,0,3),2)) O.materials.append(CpmMat(neverDamage=True,frictionAngle=0)) # load spheres from file, including information of their agglomerates ids attrs = [] sp = ymport.textExt('/tmp/compressed.txt',format='x_y_z_r_attrs',attrs=attrs) n = max(int(a[0]) for a in attrs)+1 colors = [randomColor() for _ in xrange(n)] for s,a in zip(sp,attrs): aa = int(a[0]) s.agglomerate = aa s.shape.color = colors[aa] O.bodies.append(sp) factor=1.5 O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=factor,label='bo1aabbs'),Bo1_Wall_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=factor,label='ig2sss'),Ig2_Wall_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys(),Ip2_CpmMat_CpmMat_CpmPhys(cohesiveThresholdIter=1)], [Law2_ScGeom_FrictPhys_CundallStrack(),Law2_ScGeom_CpmPhys_Cpm()] ), NewtonIntegrator(gravity=(0,0,-30)), ] O.dt = PWaveTimeStep() # create cohesive interactions, possible also between different agglomerates O.step() ig2sss.interactionDetectionFactor = bo1aabbs.aabbEnlargeFactor = 1 # delete the inter-agglomerate interactions for i in O.interactions: b1,b2 = [O.bodies[ii] for ii in (i.id1,i.id2)] if b1.agglomerate != b2.agglomerate: O.interactions.erase(i.id1,i.id2) O.step() try: from yade import qt qt.View() except: pass trunk-2017.01a/examples/baraban/000077500000000000000000000000001304022710500163665ustar00rootroot00000000000000trunk-2017.01a/examples/baraban/BicyclePedalEngine.py000066400000000000000000000035221304022710500224100ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- import time ## PhysicalParameters Density=2400 frictionAngle=radians(35) tc = 0.001 en = 0.3 es = 0.3 ## Import wall's geometry facetMat=O.materials.append(ViscElMat(frictionAngle=frictionAngle,tc=tc,en=en,et=es)) # **params sets kn, cn, ks, cs sphereMat=O.materials.append(ViscElMat(density=Density,frictionAngle=frictionAngle,tc=tc,en=en,et=es)) from yade import ymport fctIds=O.bodies.append(ymport.stl('baraban.stl',color=(1,0,0),material=facetMat)) ## Spheres sphereRadius = 0.2 nbSpheres = (10,10,10) #nbSpheres = (50,50,50) for i in xrange(nbSpheres[0]): for j in xrange(nbSpheres[1]): for k in xrange(nbSpheres[2]): x = (i*2 - nbSpheres[0])*sphereRadius*1.1 y = (j*2 - nbSpheres[1])*sphereRadius*1.1 z = (k*2 - nbSpheres[2])*sphereRadius*1.1 s=sphere([x,y,z],sphereRadius,material=sphereMat) O.bodies.append(s) ## Timestep O.dt=.2*tc ## Engines O.engines=[ ## Resets forces and momenta the act on bodies ForceResetter(), ## Using bounding boxes find possible body collisions. InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), ## Interactions InteractionLoop( ## Create geometry information about each potential collision. [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom()], ## Create physical information about the interaction. [Ip2_ViscElMat_ViscElMat_ViscElPhys()], ## Constitutive law [Law2_ScGeom_ViscElPhys_Basic()], ), ## Apply gravity ## Cundall damping must been disabled! NewtonIntegrator(damping=0,gravity=[0,-9.81,0]), ## Saving results #VTKRecorder(virtPeriod=0.04,fileName='/tmp/stlimp-',recorders=['spheres','facets']), ## Apply kinematics to walls BicyclePedalEngine(ids=fctIds,rotationAxis=[0,0,1],radius = 1.2,angularVelocity=4.0) ] from yade import qt qt.View() #O.saveTmp() #O.run() trunk-2017.01a/examples/baraban/baraban.py000066400000000000000000000034701304022710500203320ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- import time ## PhysicalParameters Density=2400 frictionAngle=radians(35) tc = 0.001 en = 0.3 es = 0.3 ## Import wall's geometry facetMat=O.materials.append(ViscElMat(frictionAngle=frictionAngle,tc=tc,en=en,et=es)) sphereMat=O.materials.append(ViscElMat(density=Density,frictionAngle=frictionAngle,tc=tc,en=en,et=es)) from yade import ymport fctIds=O.bodies.append(ymport.stl('baraban.stl',color=(1,0,0),material=facetMat)) ## Spheres sphereRadius = 0.2 nbSpheres = (10,10,10) #nbSpheres = (50,50,50) for i in xrange(nbSpheres[0]): for j in xrange(nbSpheres[1]): for k in xrange(nbSpheres[2]): x = (i*2 - nbSpheres[0])*sphereRadius*1.1 y = (j*2 - nbSpheres[1])*sphereRadius*1.1 z = (k*2 - nbSpheres[2])*sphereRadius*1.1 s=sphere([x,y,z],sphereRadius,material=sphereMat) O.bodies.append(s) ## Timestep O.dt=.2*tc ## Engines O.engines=[ ## Resets forces and momenta the act on bodies ForceResetter(), ## Using bounding boxes find possible body collisions. InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), ## Interactions InteractionLoop( ## Create geometry information about each potential collision. [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom()], ## Create physical information about the interaction. [Ip2_ViscElMat_ViscElMat_ViscElPhys()], ## Constitutive law [Law2_ScGeom_ViscElPhys_Basic()], ), ## Apply gravity ## Cundall damping must been disabled! NewtonIntegrator(damping=0,gravity=[0,-9.81,0]), ## Saving results #VTKRecorder(virtPeriod=0.04,fileName='/tmp/stlimp-',recorders=['spheres','facets']), ## Apply kinematics to walls RotationEngine(ids=fctIds,rotationAxis=[0,0,1],rotateAroundZero=True,angularVelocity=0.5) ] from yade import qt qt.View() #O.saveTmp() #O.run() trunk-2017.01a/examples/baraban/baraban.stl000066400000000000000000000161641304022710500205100ustar00rootroot00000000000000Binary STL output from Blender: /home/sega/YADE/data/baraban.stl 7@"@^?@@@^?@?@{@ 7@"@^?@?@{@9@23@{@ O@@^ 7@"@^9@23@{@ O@@^9@23@{@cf@@{@ ?@^O@@^cf@@{@ ?@^cf@@{@`f?@y@ =>lz@^?@^`f?@y@ =>lz@^`f?@y@>@y@ ~=߾lz@^=>lz@^>@y@ ~=߾lz@^>@y@̾@y@ @^~=߾lz@^̾@y@ @^̾@y@nf@y@ O@^ @^nf@y@ O@^nf@y@kf@y@ 7"@^O@^kf@y@ 7"@^kf@y@923@y@ @?@^7"@^923@y@ @?@^923@y@@?@y@ "7@^@?@^@?@y@ "7@^@?@y@539@w@ O@^"7@^539@w@ O@^539@w@df@w@ 롚 ?^O@^df@w@ 롚 ?^df@w@bf?w@ iz=>^롚 ?^bf?w@ iz=>^bf?w@>w@ jzM=߾^iz=>^>w@ jzM=߾^>w@̾w@ ^jzM=߾^̾w@ ^̾w@lfw@ O^^lfw@ O^lfw@jfw@ "7^O^jfw@ "7^jfw@539w@ ?@^"7^539w@ ?@^539w@@@w@ 7"^?@^@@w@ 7"^@@w@943w@ O^ 7"^943w@ O^943w@ifw@ 롚^O^ifw@ 롚^ifw@jfy@ =߾jz^롚^jfy@ =߾jz^jfy@̾y@ W=>jz^=߾jz^̾y@ W=>jz^̾y@>y@ ?^W=>jz^>y@ ?^>y@df?y@ O@^?^df?y@ O@^df?y@ef@y@ 7@"^O@^ef@y@ 7@"^ef@y@9@43y@ @@?^7@"^9@43y@ @@?^9@43y@?@@y@ "@7^@@?^?@@y@ "@7^?@@y@13@9{@ @O^"@7^13@9{@ @O^13@9{@@hf{@ @,^@O^@hf{@ @,^@hf{@@hf{@ lz@>߾^@,^@hf{@ lz@>߾^@hf{@@̾{@ mz@=>^lz@>߾^@̾{@ mz@=>^@̾{@@>{@ @?^mz@=>^@>{@ @?^@>{@@ff?{@ @O@^@?^@ff?{@ @O@^@ff?{@@ff@{@ "@7@^@O@^@ff@{@ "@7@^@ff@{@13@9@{@ ?@@@^"@7@^13@9@{@ ?@@@^13@9@{@?@?@{@ ?@@@^ 7@"@^.&^ 7@"@^O@@^.&^ O@@^?@^.&^ ?@^=>lz@^.&^ =>lz@^~=߾lz@^.&^ ~=߾lz@^ @^.&^ @^O@^.&^ O@^7"@^.&^ 7"@^@?@^.&^ @?@^"7@^.&^ "7@^O@^.&^ O@^롚 ?^.&^ 롚 ?^iz=>^.&^ iz=>^jzM=߾^.&^ jzM=߾^^.&^ ^O^.&^ O^"7^.&^ "7^?@^.&^ ?@^ 7"^.&^ 7"^O^.&^ O^롚^.&^ 롚^=߾jz^.&^ =߾jz^W=>jz^.&^ W=>jz^?^.&^ ?^O@^.&^ O@^7@"^.&^ 7@"^@@?^.&^ @@?^"@7^.&^ "@7^@O^.&^ @O^@,^.&^ @,^lz@>߾^.&^ lz@>߾^mz@=>^.&^ mz@=>^@?^.&^ @?^@O@^.&^ @O@^"@7@^.&^ "@7@^?@@@^.&^ 9@23@{@?@?@{@,,4Ӵy@ cf@@{@9@23@{@,,4Ӵy@ `f?@y@cf@@{@,,4Ӵy@ >@y@`f?@y@,,4Ӵy@ ̾@y@>@y@,,4Ӵy@ nf@y@̾@y@,,4Ӵy@ kf@y@nf@y@,,4Ӵy@ 923@y@kf@y@,,4Ӵy@ @?@y@923@y@,,4Ӵy@ 539@w@@?@y@,,4Ӵy@ df@w@539@w@,,4Ӵy@ bf?w@df@w@,,4Ӵy@ >w@bf?w@,,4Ӵy@ ̾w@>w@,,4Ӵy@ lfw@̾w@,,4Ӵy@ jfw@lfw@,,4Ӵy@ 539w@jfw@,,4Ӵy@ @@w@539w@,,4Ӵy@ 943w@@@w@,,4Ӵy@ ifw@943w@,,4Ӵy@ jfy@ifw@,,4Ӵy@ ̾y@jfy@,,4Ӵy@ >y@̾y@,,4Ӵy@ df?y@>y@,,4Ӵy@ ef@y@df?y@,,4Ӵy@ 9@43y@ef@y@,,4Ӵy@ ?@@y@9@43y@,,4Ӵy@ 13@9{@?@@y@,,4Ӵy@ @hf{@13@9{@,,4Ӵy@ @hf{@@hf{@,,4Ӵy@ @̾{@@hf{@,,4Ӵy@ @>{@@̾{@,,4Ӵy@ @ff?{@@>{@,,4Ӵy@ @ff@{@@ff?{@,,4Ӵy@ 13@9@{@@ff@{@,,4Ӵy@ ?@?@{@13@9@{@,,4Ӵy@ trunk-2017.01a/examples/baraban/rotating-cylinder.py000066400000000000000000000044051304022710500224010ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- cylHt,cylRd=1,.2 nSpheres=2e4 def unitSquare(): """Return square composed of 2 facets in the xy plane, centered at zero with unit extents.""" import gts vv=[gts.Vertex(1,1,0),gts.Vertex(-1,1,0),gts.Vertex(-1,-1,0),gts.Vertex(1,-1,0)] ee=[gts.Edge(vv[0],vv[1]),gts.Edge(vv[1],vv[2]),gts.Edge(vv[2],vv[3]),gts.Edge(vv[3],vv[0]),gts.Edge(vv[0],vv[2])] surf=gts.Surface() surf.add(gts.Face(ee[0],ee[1],ee[4])); surf.add(gts.Face(ee[2],ee[3],ee[4])) return surf def unitCylinder(nDiv=24): """Returns GTS surface approximating cylinder (without caps), with of height 2 and radius 2, centered at origin, axis coincident with the z-axis. :param int nDiv: polyhedron approximating circle. """ import numpy; from yade import pack thetas=numpy.linspace(0,2*pi,nDiv,endpoint=True) ptsBase=[Vector3(cos(th),sin(th),-1) for th in thetas] ptsTop=[p+Vector3(0,0,2) for p in ptsBase] return pack.sweptPolylines2gtsSurface([ptsBase,ptsTop]) from yade import pack,timing cyl=unitCylinder(); sq=unitSquare(); sq.translate(0,0,-1); cyl.copy(sq) cyl.scale(cylRd,cylRd,.5*cylHt); cyl.rotate(1,0,0,-pi/4) # 45° anti-colckwise in the yz plane # calling gtsSurface2Facets with just "cyl" (without constructing the faces tuple) ignores 2 faces that were copy'd before; bug in pygts? cylIds=O.bodies.append(pack.gtsSurface2Facets(cyl)) sp=pack.SpherePack(); wd=cylRd*sqrt(2); rMean=(.2*wd*wd*cylHt/(nSpheres*(4/3.)*pi))**(1/3.) print 'Generating cloud…' sp.makeCloud((-wd/2,-wd/2,-.5*cylHt),(wd/2,wd/2,.5*cylHt),rMean,0,int(nSpheres),False) sp.rotate((1,0,0),-pi/4) O.bodies.append([sphere(s[0],s[1]) for s in sp]) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb(),]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), RotationEngine(rotateAroundZero=True,zeroPoint=(0,0,0),rotationAxis=(0,1,1),angularVelocity=30*(2*pi/60),ids=cylIds,label='rotor'), NewtonIntegrator(damping=.3,gravity=(0,0,-1e3)), # gravity artificially high, to make it faster going ;-) ] O.dt=PWaveTimeStep() O.stopAtIter=int(2*pi/(rotor.angularVelocity*O.dt)) O.timingEnabled=True; timing.reset() from yade import qt qt.Controller() qt.View() trunk-2017.01a/examples/billiard.py000066400000000000000000000027061304022710500171410ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # The script was implemented to check the following task # http://math.stackexchange.com/questions/658871/perfectly-centered-break-of-a-perfectly-aligned-pool-ball-rack/659318#659318 massBall = 1.0 radiusBall = 1.0 rowsN = 5 velBall = 10.0 vBall = 4.0/3.0 * math.pi * math.pow(radiusBall, 3.0) rhoBall = massBall/vBall ## PhysicalParameters Density=rhoBall frictionAngle=0.0 kn = 10e+11 ks = 10e+11 cn = 0.0 cs = 0.0 ## Import wall's geometry param = {'kn':kn*2.0, 'ks':ks*2.0, 'cn':cn*2.0, 'cs':cs*2.0} sphereMat=O.materials.append(ViscElMat(density=Density,frictionAngle=frictionAngle,**param)) ## Spheres sphereIds = [] for r in range(0,rowsN): yPos = r*pow(3.0, 1.0/2.0)*radiusBall for i in range(r+1): xPos = i*2*radiusBall - r*pow(radiusBall, 3.0/2.0) sphereIds.append(O.bodies.append(sphere([xPos,yPos,0.0],radiusBall,material=sphereMat))) ## schlagBall schlagBall = O.bodies.append(sphere([0.0,-2.0*radiusBall,0.0],radiusBall,material=sphereMat)) O.bodies[schlagBall].state.vel=Vector3(0,velBall,0) ## Timestep O.dt=.01*PWaveTimeStep() ## Engines O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0), ] from yade import qt qt.View() #O.run(int(0.3/O.dt), True) trunk-2017.01a/examples/bouncingbubble.py000066400000000000000000000013731304022710500203360ustar00rootroot00000000000000 #Simulates a 5mm Diameter bubble in water rising and colliding with another bubble of the same diameter rad = 2.5e-3 #O.materials.append(FrictMat(young=1e3,density=1000)) O.materials.append(BubbleMat(density=1000,surfaceTension=71.97e-3)) O.bodies.append([ utils.sphere(center=(0,0,0),radius=rad,fixed=True), utils.sphere((0,0,-2*rad*1.1),rad) ]) O.dt = 1e-7 O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop([Ig2_Sphere_Sphere_ScGeom()],[Ip2_BubbleMat_BubbleMat_BubblePhys()],[Law2_ScGeom_BubblePhys_Bubble()]), # InteractionLoop([Ig2_Sphere_Sphere_ScGeom()],[Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_ScGeom_FrictPhys_CundallStrack()]), NewtonIntegrator(damping=0.1,gravity=(0,0,9.81)) ] O.saveTmp() trunk-2017.01a/examples/bulldozer/000077500000000000000000000000001304022710500170025ustar00rootroot00000000000000trunk-2017.01a/examples/bulldozer/README000066400000000000000000000011371304022710500176640ustar00rootroot00000000000000bulldozer.py and bulldozerVTK.py show how simple it is possible to simulate relatively difficult things. bulldozer.py is using Law2_ScGeom_FrictPhys_CundallStrack constitutive law for interaction between elements. It stores screenshots from simulation in /tmp/bulldozer-????.png files and creates video then. bulldozerVTK.py is using Law2_ScGeom_ViscElPhys_Basic - visco-elastic model for interaction between elements. Also it saves snapshots in VTK-format in /tmp/bulldozer-*.vtu files. If you open those with paraview (or other VTK-based) program, you can create video from them, make screenshots etc. trunk-2017.01a/examples/bulldozer/bulldozer.py000066400000000000000000000053371304022710500213660ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- ### Simpificated buldozer simulation from numpy import linspace from numpy import arange import gts import itertools from yade import geom,pack ###Initial Data numKnifeParts = 10 radiusKnife=1 lengthKnife=2 buldozerHeight=1.2 radiusSph = 0.05 numBoxes = Vector3(15,5,2) gapBetweenBoxes = 0.05 sizeBox = (lengthKnife-(numBoxes[1]-1)*gapBetweenBoxes)/numBoxes[1] ### Creating the Buldozer Knife ### from facets, using GTS Knife=[] for i in linspace(pi, pi*3/2, num=numKnifeParts, endpoint=True): Knife.append(Vector3(radiusKnife*cos(i),0,radiusKnife*sin(i))) KnifeP=[Knife,[p+Vector3(0,lengthKnife,0) for p in Knife]] KnifePoly=pack.sweptPolylines2gtsSurface(KnifeP,threshold=1e-4) KnifeIDs=[] KnifeIDs=O.bodies.append(pack.gtsSurface2Facets(KnifePoly,color=(1,0,0),wire=False)) KnifeIDs+=O.bodies.append(geom.facetBox((-lengthKnife/2-radiusKnife,lengthKnife/2,-radiusKnife+buldozerHeight/2),(lengthKnife/2,lengthKnife/2,buldozerHeight/2.),wallMask=47,color=(0,1,0),wire=False)) KnifeIDs+=O.bodies.append(geom.facetBox((-lengthKnife/2-radiusKnife-lengthKnife/4.,lengthKnife/2,-radiusKnife+buldozerHeight*3./2.-buldozerHeight/4.),(lengthKnife/4.,lengthKnife/3.,buldozerHeight/4.),wallMask=47,color=(0,0,1),wire=False)) O.bodies.append(geom.facetBox((0,lengthKnife/2,radiusKnife),(lengthKnife*4,lengthKnife*4,lengthKnife),wallMask=16,color=(1,1,1),wire=False)) ### Creating the material for buldozer colorsph1=Vector3(120,234,150); colorsph2=Vector3(1,1,0); colorsph1.normalize(); colorsph2.normalize(); colorSph=colorsph1 for xyz in itertools.product(arange(0,numBoxes[0]),arange(0,numBoxes[1]),arange(0,numBoxes[2])): ids_spheres=O.bodies.appendClumped(pack.regularHexa(pack.inEllipsoid((xyz[0]*(sizeBox+gapBetweenBoxes),xyz[1]*(sizeBox+gapBetweenBoxes)+sizeBox*0.5,xyz[2]*(sizeBox+gapBetweenBoxes)-radiusKnife+sizeBox*0.6),(sizeBox/2,sizeBox/2,sizeBox/2)),radius=radiusSph,gap=0,color=colorSph)) if (colorSph==colorsph1): colorSph=colorsph2 else: colorSph=colorsph1 from yade import qt O.dt=2*PWaveTimeStep() # We do not need now a high accuracy O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb(),]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), TranslationEngine(translationAxis=[1,0,0],velocity=5,ids=KnifeIDs), # Buldozer motion NewtonIntegrator(damping=.3,gravity=(0,0,-9.8)), #qt.SnapshotEngine(iterPeriod=100,fileBase='/tmp/bulldozer-',label='snapshooter'), ] O.saveTmp() qt.Controller() qt.View() r=qt.Renderer() r.lightPos=Vector3(0,0,50) O.stopAtIter=2000 O.run() #encodeVideoFromFrames(snapshooter.savedSnapshots,out='/tmp/bulldozer.ogg',fps=2) trunk-2017.01a/examples/bulldozer/bulldozerVTK.py000066400000000000000000000060501304022710500217440ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- ### Simpificated buldozer simulation with VTK recorder ### vtk-files are saved in /tmp directory with names buldozer-*.vtk from numpy import linspace from numpy import arange import gts import itertools from yade import geom,pack ###Initial Data numKnifeParts = 10 radiusKnife=1 lengthKnife=2 buldozerHeight=1.2 radiusSph = 0.05 numBoxes = Vector3(8,5,2) gapBetweenBoxes = 0.05 sizeBox = (lengthKnife-(numBoxes[1]-1)*gapBetweenBoxes)/numBoxes[1] ## PhysicalParameters Density=2400 frictionAngle=radians(35) tc = 0.001 en = 0.3 es = 0.3 ## Materials facetMat=O.materials.append(ViscElMat(frictionAngle=frictionAngle,tc=tc,en=en,et=es)) sphereMat=O.materials.append(ViscElMat(density=Density,frictionAngle=frictionAngle,tc=tc,en=en,et=es)) ### Creating the Buldozer Knife ### from facets, using GTS Knife=[] for i in linspace(pi, pi*3/2, num=numKnifeParts, endpoint=True): Knife.append(Vector3(radiusKnife*cos(i),0,radiusKnife*sin(i))) KnifeP=[Knife,[p+Vector3(0,lengthKnife,0) for p in Knife]] KnifePoly=pack.sweptPolylines2gtsSurface(KnifeP,threshold=1e-4) KnifeIDs=O.bodies.append(pack.gtsSurface2Facets(KnifePoly,color=(1,0,0),wire=False,material=facetMat)) KnifeIDs+=O.bodies.append(geom.facetBox((-lengthKnife/2-radiusKnife,lengthKnife/2,-radiusKnife+buldozerHeight/2),(lengthKnife/2,lengthKnife/2,buldozerHeight/2.),wallMask=47,color=(0,1,0),wire=False)) KnifeIDs+=O.bodies.append(geom.facetBox((-lengthKnife/2-radiusKnife-lengthKnife/4.,lengthKnife/2,-radiusKnife+buldozerHeight*3./2.-buldozerHeight/4.),(lengthKnife/4.,lengthKnife/3.,buldozerHeight/4.),wallMask=47,color=(0,0,1),wire=False)) O.bodies.append(geom.facetBox((0,0,radiusKnife),(lengthKnife*3,lengthKnife*3,lengthKnife),wallMask=16,color=(1,1,1),wire=False,material=facetMat)) ### Creating the material for buldozer colorsph1=Vector3(120,234,150); colorsph2=Vector3(0,0,1); colorsph1.normalize(); colorsph2.normalize(); colorSph=colorsph1 for xyz in itertools.product(arange(0,numBoxes[0]),arange(0,numBoxes[1]),arange(0,numBoxes[2])): ids_spheres=O.bodies.appendClumped(pack.regularHexa(pack.inEllipsoid((xyz[0]*(sizeBox+gapBetweenBoxes),xyz[1]*(sizeBox+gapBetweenBoxes)+sizeBox*0.5,xyz[2]*(sizeBox+gapBetweenBoxes)-radiusKnife+sizeBox*0.6),(sizeBox/2,sizeBox/2,sizeBox/2)),radius=radiusSph,gap=0,color=colorSph,material=sphereMat)) if (colorSph==colorsph1): colorSph=colorsph2 else: colorSph=colorsph1 O.dt=.2*tc O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb(),]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), TranslationEngine(translationAxis=[1,0,0],velocity=2,ids=KnifeIDs), # Buldozer motion NewtonIntegrator(damping=0,gravity=[0,0,-9.8]), VTKRecorder(iterPeriod=1000,fileName='/tmp/bulldozer-',recorders=['spheres','facets']) ] O.saveTmp() from yade import qt qt.Controller() qt.View() r=qt.Renderer() r.lightPos=Vector3(0,0,50) O.run(20000) #qt.makeSimulationVideo('/tmp/buldozer.ogg',iterPeriod=1000,fps=30) trunk-2017.01a/examples/capillary/000077500000000000000000000000001304022710500167605ustar00rootroot00000000000000trunk-2017.01a/examples/capillary/capillar.py000066400000000000000000000072071304022710500211270ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 # The simulation of different capillary bridge models. # Parameters are set like in experiments of [Willett2000] from yade import utils, plot o = Omega() fr = 0.5;rho=2000 tc = 0.001; en = 0.7; et = 0.7; o.dt = 0.0002*tc r = 0.002381 Gamma = 20.6*1e-3 Theta = 0 VB = 74.2*1e-12 CapillarType1 = "Willett_numeric" CapillarType2 = "Willett_analytic" CapillarType3 = "Rabinovich" CapillarType4 = "Lambert" CapillarType5 = "Weigert" CapillarType6 = "Soulie" mat1 = O.materials.append(ViscElCapMat(frictionAngle=fr,density=rho,Vb=VB,gamma=Gamma,theta=Theta,Capillar=True,CapillarType=CapillarType1,tc=tc,en=en,et=et)) mat2 = O.materials.append(ViscElCapMat(frictionAngle=fr,density=rho,Vb=VB,gamma=Gamma,theta=Theta,Capillar=True,CapillarType=CapillarType2,tc=tc,en=en,et=et)) mat3 = O.materials.append(ViscElCapMat(frictionAngle=fr,density=rho,Vb=VB,gamma=Gamma,theta=Theta,Capillar=True,CapillarType=CapillarType3,tc=tc,en=en,et=et)) mat4 = O.materials.append(ViscElCapMat(frictionAngle=fr,density=rho,Vb=VB,gamma=Gamma,theta=Theta,Capillar=True,CapillarType=CapillarType4,tc=tc,en=en,et=et)) mat5 = O.materials.append(ViscElCapMat(frictionAngle=fr,density=rho,Vb=VB,gamma=Gamma,theta=Theta,Capillar=True,CapillarType=CapillarType5,tc=tc,en=en,et=et)) mat6 = O.materials.append(ViscElCapMat(frictionAngle=fr,density=rho,Vb=VB,gamma=Gamma,theta=Theta,Capillar=True,CapillarType=CapillarType6,tc=tc,en=en,et=et)) id1 = O.bodies.append(sphere(center=[0,0,0],radius=r,material=mat1,fixed=True)) id2 = O.bodies.append(sphere(center=[0,0,2*r],radius=r,material=mat1,fixed=True)) id3 = O.bodies.append(sphere(center=[3.0*r,0,0],radius=r,material=mat2,fixed=True)) id4 = O.bodies.append(sphere(center=[3.0*r,0,2*r],radius=r,material=mat2,fixed=True)) id5 = O.bodies.append(sphere(center=[6.0*r,0,0],radius=r,material=mat3,fixed=True)) id6 = O.bodies.append(sphere(center=[6.0*r,0,2*r],radius=r,material=mat3,fixed=True)) id7 = O.bodies.append(sphere(center=[9.0*r,0,0],radius=r,material=mat4,fixed=True)) id8 = O.bodies.append(sphere(center=[9.0*r,0,2*r],radius=r,material=mat4,fixed=True)) id9 = O.bodies.append(sphere(center=[12.0*r,0,0],radius=r,material=mat5,fixed=True)) id10= O.bodies.append(sphere(center=[12.0*r,0,2*r],radius=r,material=mat5,fixed=True)) id11= O.bodies.append(sphere(center=[15.0*r,0,0],radius=r,material=mat6,fixed=True)) id12= O.bodies.append(sphere(center=[15.0*r,0,2*r],radius=r,material=mat6,fixed=True)) o.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_ViscElCapMat_ViscElCapMat_ViscElCapPhys()], [Law2_ScGeom_ViscElCapPhys_Basic()], ), NewtonIntegrator(damping=0,gravity=[0,0,0]), PyRunner(command='addPlotData()',iterPeriod=100), ] vel = 0.01 O.bodies[id2].state.vel=[0,0,vel] O.bodies[id4].state.vel=[0,0,vel] O.bodies[id6].state.vel=[0,0,vel] O.bodies[id8].state.vel=[0,0,vel] O.bodies[id10].state.vel=[0,0,vel] O.bodies[id12].state.vel=[0,0,vel] def addPlotData(): f1=O.forces.f(id2) f2=O.forces.f(id4) f3=O.forces.f(id6) f4=O.forces.f(id8) f5=O.forces.f(id10) f6=O.forces.f(id12) s1 = (O.bodies[id2].state.pos[2]-O.bodies[id1].state.pos[2])-2*r sc=s1 plot.addData(Willett_numeric=-f1[2], Willett_analytic=-f2[2], Rabinovich=-f3[2], Lambert=-f4[2], Weigert=-f5[2], Soulie=-f6[2], sc=sc) plot.plots={'sc':('Willett_numeric','Willett_analytic','Rabinovich','Lambert','Weigert','Soulie')}; plot.plot() O.step() from yade import qt qt.View() O.run(250000, True) #plot.saveGnuplot('sim-data_'+CapillarType1) trunk-2017.01a/examples/capillary/liquidmigration/000077500000000000000000000000001304022710500221615ustar00rootroot00000000000000trunk-2017.01a/examples/capillary/liquidmigration/showcase.py000066400000000000000000000064561304022710500243620ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 # The script implements the show case in this article [Mani2013] from yade import utils, plot o = Omega() fr = 0.5;rho=2000 tc = 0.001; en = 0.7; et = 0.7; o.dt = 1.0 r1 = 1.0 r2 = 1.0 Gamma = 20.6*1e-3 Theta = 0 VB3 = 74.2*1e-12 CapillarType = "Lambert" mat1 = O.materials.append(ViscElCapMat(frictionAngle=fr,density=rho,Vb=VB3,gamma=Gamma,theta=Theta,Capillar=True,CapillarType=CapillarType,tc=tc,en=en,et=et)) d = 0.9999 id1 = O.bodies.append(sphere(center=[0,0,0], radius=r2,material=mat1,fixed=True, color=[0,1,0])) id2 = O.bodies.append(sphere(center=[0,(r1+r2)*d,0], radius=r2,material=mat1,fixed=True, color=[0,1,0])) id3 = O.bodies.append(sphere(center=[(r1+r2)*d,(r1+r2)*d,0], radius=r2,material=mat1,fixed=True, color=[0,1,0])) id4 = O.bodies.append(sphere(center=[(r1+r2)*d,(r1+r2)*d*2,0], radius=r2,material=mat1,fixed=True, color=[0,1,0])) id5 = O.bodies.append(sphere(center=[(r1+r2)*d*2,(r1+r2)*d,0], radius=r2,material=mat1,fixed=True, color=[0,1,0])) Vf = 0.0e-1 Vfmin = 0.0e-1 O.bodies[id1].state.Vf = Vf O.bodies[id1].state.Vmin = Vfmin O.bodies[id2].state.Vf = Vf O.bodies[id2].state.Vmin = Vfmin O.bodies[id3].state.Vf = Vf O.bodies[id3].state.Vmin = Vfmin O.bodies[id4].state.Vf = Vf O.bodies[id4].state.Vmin = Vfmin O.bodies[id5].state.Vf = Vf O.bodies[id5].state.Vmin = Vfmin vel = 0.0 O.bodies[id1].state.vel=[0,0,vel] O.bodies[id2].state.vel=[0,0,-vel] O.bodies[id3].state.vel=[vel,0,0] O.bodies[id4].state.vel=[-vel,0,0] o.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()],verletDist=(r1+r2)*5.0), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_ViscElCapMat_ViscElCapMat_ViscElCapPhys()], [Law2_ScGeom_ViscElCapPhys_Basic()], ), LiqControl(label='lqc'), NewtonIntegrator(damping=0,gravity=[0,0,0]), PyRunner(command='showData()',iterPeriod=1), ] def showData(): print "Step %d"%O.iter print "idB=%d, Vf=%s, Vmin=%s;"%(id1, O.bodies[id1].state.Vf, O.bodies[id1].state.Vmin) print "idB=%d, Vf=%s, Vmin=%s;"%(id2, O.bodies[id2].state.Vf, O.bodies[id2].state.Vmin) print "idB=%d, Vf=%s, Vmin=%s;"%(id3, O.bodies[id3].state.Vf, O.bodies[id3].state.Vmin) print "idB=%d, Vf=%s, Vmin=%s;"%(id4, O.bodies[id4].state.Vf, O.bodies[id4].state.Vmin) print "idB=%d, Vf=%s, Vmin=%s;"%(id5, O.bodies[id5].state.Vf, O.bodies[id5].state.Vmin) try: print "Interaction[1, 2].Vb=%s"%(O.interactions[id1,id2].phys.Vb) except: pass try: print "Interaction[2, 3].Vb=%s"%(O.interactions[id2,id3].phys.Vb) except: pass try: print "Interaction[3, 4].Vb=%s"%(O.interactions[id3,id4].phys.Vb) except: pass try: print "Interaction[3, 5].Vb=%s"%(O.interactions[id3,id5].phys.Vb) except: pass print showData() O.run(1, True) for i in range(5): O.bodies[i].state.Vf = 0 O.bodies[i].state.Vmin = 0 O.interactions[id1,id2].phys.Vmax = 5.0 lqc.addLiqInter(id1, id2, 1.0) O.interactions[id2,id3].phys.Vmax = 5.0 lqc.addLiqInter(id2, id3, 1.0) O.interactions[id3,id4].phys.Vmax = 5.0 lqc.addLiqInter(id3, id4, 1.0) O.interactions[id3,id5].phys.Vmax = 5.0 lqc.addLiqInter(id3, id5, 1.0) O.run(1, True) vel = 1.0 O.bodies[id3].state.vel=[vel,0,0] O.bodies[id4].state.vel=[vel,0,0] O.bodies[id5].state.vel=[vel,0,0] from yade import qt qt.View() trunk-2017.01a/examples/capillaryLaplaceYoung/000077500000000000000000000000001304022710500212645ustar00rootroot00000000000000trunk-2017.01a/examples/capillaryLaplaceYoung/CapillaryPhys-example.py000066400000000000000000000046741304022710500260660ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- """ To run this script you need to have all 10 text files from https://yade-dem.org/wiki/CapillaryTriaxialTest in the same folder as you run this script in console! This script shows how to use Law2_ScGeom_CapillaryPhys_Capillarity. The user can switch between hertz and linear model by setting "model_type" """ model_type = 1 #1=Hertz model with capillary forces, else linear model with capillary model #some parameters: shear_modulus = 1e5 poisson_ratio = 0.3 young_modulus = 2*shear_modulus*(1+poisson_ratio) friction = 0.5 angle = atan(friction) local_damping = 0.01 viscous_normal = 0.021 viscous_shear = 0.8*viscous_normal lowercorner = Vector3(0,0,0) uppercorner = Vector3(0.002,0.002,0.004) #creating a material (FrictMat): id_SphereMat=O.materials.append(FrictMat(young=young_modulus,poisson=poisson_ratio,density=2500,frictionAngle=angle)) SphereMat=O.materials[id_SphereMat] #generate particles: sp=pack.SpherePack() sp.makeCloud(lowercorner,uppercorner,.0002,rRelFuzz=.3) O.bodies.append([sphere(c,r,material=SphereMat) for c,r in sp]) #generate boundary: O.bodies.append(geom.facetBox(uppercorner/2,uppercorner/2,wire=True,fixed=True,material=SphereMat)) #define engines: if model_type == 1:#hertz model with capillary forces O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_MindlinCapillaryPhys(label='ContactModel')],#for hertz model only [Law2_ScGeom_MindlinPhys_Mindlin()]#for hertz model only ), Law2_ScGeom_CapillaryPhys_Capillarity(capillaryPressure=10000),#for hertz model only NewtonIntegrator(damping=local_damping,gravity=(0,0,-9.81)), ] ContactModel.betan=viscous_normal ContactModel.betas=viscous_shear ContactModel.useDamping=True else: O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_CapillaryPhys()], #for linear model only [Law2_ScGeom_FrictPhys_CundallStrack()], #for linear model only ), Law2_ScGeom_CapillaryPhys_Capillarity(capillaryPressure=10000),#for linear model only NewtonIntegrator(damping=local_damping,gravity=(0,0,-9.81)), ] #set time step and run simulation: O.dt=0.5*PWaveTimeStep() from yade import qt qt.View() print('Press PLAY button') #O.run(10000,True) trunk-2017.01a/examples/capillaryLaplaceYoung/README.txt000066400000000000000000000100741304022710500227640ustar00rootroot00000000000000This folder illustrates the use of Law2_ScGeom_CapillaryPhys_Capillarity engine to describe capillary interaction between particle pairs in YADE (see also the wiki page https://www.yade-dem.org/wiki/CapillaryTriaxialTest) I. Simulation scripts examples ------------------------------ Two examples of simulations using Law2_ScGeom_CapillaryPhys_Capillarity are herein provided: - CapillaryPhys-example.py is a (simple) packing-scale simulation considering capillary interaction and gravity - capillaryBridge.py defines and let evolve a capillary bridge between two particles only II. Capillary files scripts --------------------------- As explained on the wiki page (see above) and in Law2_ScGeom_CapillaryPhys_Capillarity doc, so-called capillary files are required in order to use Law2_ScGeom_CapillaryPhys_Capillarity engine. These capillary files include capillary bridges configurations data (for positiv capillary pressure values). A version of capillary files can be downloaded from the wiki page, they consider a zero contact (wetting) angle and some given particle radius ratio. Also, three .m files are herein provided in order to enable users to build their own capillary files for any contact angle or particle radius ratio, or to study capillary bridges as such (solveLiqBridge.m). A capillary files generation requires launching writesCapFile() (in writesCapFile.m) only, after providing a couple of parameters therein (see description of writesCapFile.m below). The two other files (solveLiqBridge.m and solveLaplace_uc.m) define functions used by writesCapFile() and do not require any user input. Specifically, the roles of the three .m files are as follows: - solveLiqBridge.m solves the Laplace-Young equation for one given bridge, defined in terms of the input attributes of the solveLiqBridge function (see therein). The solveLiqBridge function is usually called by other files (see below) during capillary files generation, however it can also be executed on its own in order to study (e.g. plot) capillary bridge profile. Code comments include references to: * Duriez2016: J. Duriez and R. Wan, Contact angle mechanical influence for wet granular soils, Acta Geotechnica, 2016, doi:10.1007/s11440-016-0500-6 * Lian1993: G. Lian and C. Thornton and M. J. Adams, A Theoretical Study of the Liquid Bridge Forces between Two Rigid Spherical Bodies, Journal of Colloid and Interface Science, 161(1), 1993 * Scholtes2008 (french): L. Scholtes, Modelisation Micro-Mecanique des Milieux Granulaires Partiellement Satures, PhD Thesis from Institut polytechnique de Grenoble, 2008 * Soulie2005 (french): F. Soulie, Cohesion par capillarite et comportement mecanique de milieux granulaires, PhD Thesis from Universite Montpellier II, 2005 * Soulie2006: F. Soulie and F. Cherblanc and M. S. El Youssoufi and C. Saix, Influence of liquid bridges on the mechanical behaviour of polydisperse granular materials, International Journal for Numerical and Analytical Methods in Geomechanics, 30(3), 2006 - solveLaplace_uc.m calls several times solveLiqBridge in order to compute all possible bridges configurations for given contact angle, capillary pressure, and particle radius ratio. It is usually called by writesCapFile (see below) during capillary files generation, however it can also be executed on its own. In particular, it may output text files including bridges data for one given capillary pressure. - writesCapFile.m, finally, is the conductor during the capillary files generation, and is the only one that actually requires the user's attention for such task. Parameters are to be defined by the user directly in the .m file (from l. 10 to 30) before launching. Generating a complete set of 10 capillary files typically requires few days in terms of computation time with MATLAB and much (~ 7*) more with Octave. The .m files makes wide use of iterative procedures and a greater performance for MATLAB is indeed expected. In case Octave is still chosen for generation, you may want to uncomment some Octave specific command ('fflush(..)') in writesCapFile.m in order for the terminal to update you on the progress. trunk-2017.01a/examples/capillaryLaplaceYoung/capillaryBridge.py000066400000000000000000000032241304022710500247340ustar00rootroot00000000000000# capillary bridge example between 2 spheres r1,r2 = 1e-4,4e-4 # better take small particles z1,z2=0,0.95*(r1+r2) O.bodies.append(sphere(center=Vector3(0,0,z1),radius=r1,dynamic=0)) O.bodies.append(sphere(center=Vector3(0,0,z2),radius=r2,dynamic=0)) O.engines=[ForceResetter() ,InsertionSortCollider([Bo1_Sphere_Aabb()]) ,InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_CapillaryPhys()], [Law2_ScGeom_FrictPhys_CundallStrack(neverErase=1)] ) ,Law2_ScGeom_CapillaryPhys_Capillarity(capillaryPressure=1e3) ,NewtonIntegrator() ,GlobalStiffnessTimeStepper() ,PyRunner(command='computeThings()',iterPeriod=1) ] from yade import plot def computeThings(): if O.interactions.has(0,1) and O.interactions[0,1].isReal: i = O.interactions[0,1] un = i.geom.penetrationDepth vM = i.phys.vMeniscus delta1,delta2 = i.phys.Delta1,i.phys.Delta2 fCap = i.phys.fCap.norm() nn11,nn33 = i.phys.nn11,i.phys.nn33 else: un,vM,delta1,delta2,fCap,nn11,nn33 = float('nan'),float('nan'),float('nan'),float('nan'),float('nan'),float('nan'),float('nan') plot.addData(delta1 = delta1, delta2 = delta2, fCap = fCap , it =O.iter, un = un ,vM = vM , nn11 = nn11, nn33 = nn33) plot.plots={'un':'fCap','un ':'vM',' un':('delta1','delta2'),' un ':('nn11','nn33')} plot.plot() # spheres get closer: O.bodies[1].state.vel=Vector3(0,0,-0.002) O.run(500,wait=1) # spheres move apart: O.bodies[1].state.vel=Vector3(0,0,0.02) O.run(4000,wait=1) trunk-2017.01a/examples/capillaryLaplaceYoung/solveLaplace_uc.m000066400000000000000000000077561304022710500245620ustar00rootroot00000000000000% J. Duriez (jerome.duriez@ucalgary.ca) function stabSol = solveLaplace_uc(theta,rRatio,uStar,delta1Cons,deltaZ,save) % Solves Laplace-Young equation for given r, uc* and theta % Making recursively use of solveLiqBridge function, the present function % identifies all possible bridges configurations for given r, uc*, and % theta % Input attributes (see also solveLiqBridge function): % theta: contact angle (deg) % rRatio: rMax / rMin for the considered particles pair % uStar: dimensionless capillary pressure % delta1Cons: vector of delta1 (see solveLiqBridge) values to consider % deltaZ: see solveLiqBridge % save: 0/1 to save text files including the capillary bridges data (if 1) % Returns a table (matrix) of capillary bridges data (see sol_u below), % possibly (in case save=1) also written in text files. % Removal of possible d1=0 since such bridge is physically impossible, and % d1 = 0 might make trouble if theta = 0 (leads to inf. initial rhoPrime): delta1Cons = delta1Cons(delta1Cons~=0); % And of d1 values such that d1 + theta > 90 delta1Cons = delta1Cons(delta1Cons + theta <= 90); %------------ All possible bridges for these r, uc*, theta: --------------- % data table initialization: sol_u = -ones(length(delta1Cons),9); % 9 col. are [dist uc(=cst) V F delta1 delta2 E nn11 nn33] minDzUsed = deltaZ; % tic for i=1:length(delta1Cons) dzUsed = deltaZ; delta1 = delta1Cons(i); [dist,vol,force,delta1,delta2,eStar,nn11,nn33,out] = solveLiqBridge(rRatio,theta,uStar,delta1,dzUsed,0,0,0); while out == 0 dzUsed = dzUsed / 2;minDzUsed = min(dzUsed,minDzUsed); % disp(['Refining deltaZ to ',num2str(dzUsed),' in solveLaplace']) [dist,vol,force,delta1,delta2,eStar,nn11,nn33,out] = solveLiqBridge(rRatio,theta,uStar,delta1,dzUsed,0,0,0); end sol_u(i,:) = [dist,uStar,vol,force,delta1,delta2,eStar,nn11,nn33]; end % toc % Get rid of unphysical solutions with negativ distances and/or volume: physSol = sol_u( sol_u(:,1)>=0 & sol_u(:,3)>=0,: ); % NB: vol>=0 is true for vol = Inf % Get rid of diverged solutions with infinite volume (should <=> infinite % profile): nonDvSol = physSol(isfinite(physSol(:,3)),:); % nNonDvSol = length(nonDvSol(:,1)); % disp(['We had to suppress ',num2str((1-nNonDvSol/nPhysSol)*100),' % of diverged "solutions"']) % Get rid of unstable physical solutions:(those with biggest volumes) % We use volume values for this purpose, see e.g. Duriez2016 distRupt = max(nonDvSol(:,1)); % eRupt = nonDvSol(nonDvSol(:,1)==distRupt,7); % does not work since eRupt can be a global maximum % (when two branches are increasing with d*) vRupt = nonDvSol(nonDvSol(:,1)==distRupt,3); stabSol = nonDvSol(nonDvSol(:,3)>=vRupt,:); % ----------- Save of data in text files ----------- if save ~=0 % three text files are generated: one, "Raw", includes all computed data; % another, "Phys", restricts to physical solutions (with positiv distance % and volume); the last one, "Stab" restricts to the stable physical % solutions if minDzUsed == deltaZ strDz = ['With deltaZ = ',num2str(deltaZ)]; else strDz = ['With deltaZ between ',num2str(deltaZ),' and ',num2str(minDzUsed)]; end nomFic = ['capDataRaw_r',num2str(rRatio),'_theta',num2str(theta),'_ucStar',num2str(uStar),'.txt']; head_wE = ['dist*\tuc*\tV*\tF*\tdelta1 (deg)\tdelta2(deg)\tE* (-)\tn11 (-)\tn33 (-)\t',strDz,'\n']; writeFile(nomFic,head_wE,sol_u) nomFic = ['capDataPhys_r',num2str(rRatio),'_theta',num2str(theta),'_ucStar',num2str(uStar),'.txt']; writeFile(nomFic,head_wE,nonDvSol) nomFic = ['capDataStab_r',num2str(rRatio),'_theta',num2str(theta),'_ucStar',num2str(uStar),'.txt']; head_woE = ['dist*\tuc*\tV*\tF*\tdelta1 (deg)\tdelta2(deg)\tn11 (-)\tn33 (-)\t',strDz,'\n']; writeFile(nomFic,head_woE,stabSol(:,[1:6,8:9])) end % --------------------------------------------------- end function writeFile(nomFic,headLine,data) fic = fopen(nomFic,'w'); fprintf(fic,headLine); fclose(fic); dlmwrite(nomFic,data,'-append','delimiter','\t') end trunk-2017.01a/examples/capillaryLaplaceYoung/solveLiqBridge.m000066400000000000000000000234341304022710500243630ustar00rootroot00000000000000% J. Duriez (jerome.duriez@ucalgary.ca) function [dist,vol,force,delta1,delta2,eStar,nn11,nn33,out] = solveLiqBridge(rRatio,theta,uStar,delta1,deltaZ,plot,speak,plot3D) %Computes one single liquid (capillary) bridge % Lian's method: iterative determination using Taylor expansion with % finite difference (FD) increment = deltaZ (a function attribute) % Attributes: rRatio = R2 / R1 >=1, theta = contact angle (deg), uStar = % dimensionless cap. pressure (uc*R2/gamma), delta1 = filling angle on % smallest particle (deg), deltaZ = increment of FD scheme (e.g. 2e-6) % Last ones = booleans to resp. plot the profile in 2D, output messages, % and plot the liq bridge in 3D % Outputs: dist = interparticle distance ; % vol = dimensionless volume (= vol% /R2^3) % force = dimensionless force = force/(2*pi*gamma*R2) % delta1/2 = filling angles on the 2 particles (degrees) % eStar = free energy/(gamma*% R2^2) % nn11 = 11-term of integral(ni nj dS) / R2^2 = 22-term % nn33 = 33-term, with 3 axis = the meniscus orientation % NB: surface / R2^2 = 2*nn11 + nn33 % out = 1 or 0 depending whether things went fine (see below): 1 if yes % close all global cstC % cstC is the dimensionless capillary force: constant all along the profile % see [9] Lian1993, (6) Duriez2016, or (2.51) Soulie2005 ~ (10) Soulie2006.. cstC = 1/rRatio * sin(radians(delta1)) * sin(radians(delta1+theta)) + 1/2 * uStar * rRatio^-2 * sin(radians(delta1))^2; % Use of cstC to get the right filling angle delta2: fun = @(delta2)cstC_delta2(delta2,theta,uStar); delta2 = fzero(fun,[0 90]); % fzero does not catch multiple roots, if it occurs % Discrete set of profile values: rho = -ones(30000,1); % preallocating 26000 or 30000 makes 90 profile computations take ~ 10.8s instead of ~ 14.5 % Discrete set of slope values: rhoPrime = -ones(30000,1); step = 1; % Boundary conditions on left contact line: see left (smallest) particle rho(1) = 1/rRatio * sin(radians(delta1)); rhoPrime(1) = - 1 / tan(radians(delta1+theta)); % Boundary condition on right contact line: see right (biggest) particle rhoRight = sin(radians(delta2)); %------------------------------------------------------------------------- % Finite diff. scheme to compute whole profile ie compute rho and rhoPrime % See Lian1993, Duriez2016, etc.. % Some remarks about next loop: % - this loop may extend the size of rho without problem % - just keep a simple and efficient test to stop computations. A more restrictive % one may lead to go beyond the right contact line and lead to divergence.. while rho(step) < 1.00001*rhoRight rho2d = rhoSecond(rho(step),rhoPrime(step),uStar); % all terms are at "i" rho(step+1) = rho(step) + deltaZ * rhoPrime(step) + 1/2 * deltaZ^2 * rho2d; rhoPrime(step+1) = drho(rho(step+1),rho(step),deltaZ,rho2d); % i+1 value of rhoPrime, function of rho_{i+1}, rho_i, and rho2d_i. Used next time in loop. step=step+1; end %------------------------------------------------------------------------- % Two following lines to suppress extra data due to preallocation. Keep % this order ! rhoPrime = rhoPrime(rho>0); rho = rho(rho>0); % --------------- Output computations from now on: ------------------------ d1 = radians(delta1); d2 = radians(delta2); % Inter particle dimensionless distance: % see (7) Duriez2016, (33) Scholtes2008, etc. (not (5) Soulie2006..) lastZ = deltaZ*(length(rho) -1); dist = lastZ - 1/rRatio * ( 1-cos(d1) ) - ( 1-cos(d2) ); % Dimensionless capillary force: force = cstC; % Dimensionless volume: % Cf (4) Soulie2006, (34) Appendix Scholtes2008, (8) Duriez2016 etc. : vol = pi*sum(rho(2:length(rho)).^2)*deltaZ; vol = vol - pi/3 * rRatio^(-3) * ( 1-cos(d1) )^2 * ( 2+cos(d1) ); vol = vol - pi/3 * ( 1-cos(d2) )^2 * ( 2+cos(d2) ); % Capillary bridge dimensionless free energy: % (12) Duriez2016 rather than [35] Lian1993 (was for cst volume stability) dArea = rho .* ( 1+rhoPrime.^2).^(1/2); % ~ infinitesimal liquid gas area eStar = 2*pi * sum(dArea(2:length(dArea))) * deltaZ + uStar * vol; %+/- uStar changes the values but not the shape eStar = eStar - 2*pi*cos(radians(theta)) * ( (1-cos(d1))/rRatio^2 + 1 - cos(d2) ); rhoRed = rho(2:length(rho)); rhoPrRed = rhoPrime(2:length(rho)); % Surface: surf = 2*pi * sum( rhoRed .* (1 + rhoPrRed.^2).^0.5 ) * deltaZ; % Surface integral of dyadic product n*n (diagonal axisymmetric matrix): nn11 = pi * sum( rhoRed ./ (1 + rhoPrRed.^2).^0.5 ) * deltaZ; % = n22 nn33 = 2*pi * sum( rhoRed .* rhoPrRed.^2 ./ (1 + rhoPrRed.^2).^0.5 ) * deltaZ; % --------------- Miscellaneous checks and plots -------------------------- % Check whether surf = tr(integral n*n) if (surf - (2*nn11 + nn33) ) / surf > 0.0025 % strict equality beyond reach disp(surf) disp(2*nn11 + nn33) startStr = ['r = ',num2str(rRatio),';theta = ',num2str(theta),';u* = ',num2str(uStar)]; error(['Liq-gas area # tr(integral over liq-gas surf. n*n) for ',startStr,';delta1 = ',num2str(delta1),';dZ = ',num2str(deltaZ)]) end if plot==1 % && dist >=0 && vol >=0 %&& isfinite(vol) plotProfile(rho,deltaZ,rRatio,delta1,delta2,theta,cstC,uStar) end if plot3D==1 plot3Dbridge(rho,deltaZ,rRatio) end % Check if the neck has been reached: (there is a risk because of divergence possibility) if uStar~= 0 % "y0" computation according to [10] Lian1993, (or (2.54) Soulie2005 - (11) Soulie2006) rhoNeck = ( -1 + sqrt(1+2*uStar*cstC) ) / uStar; else rhoNeck = cstC; end if (min(rho) - rhoNeck) / rhoNeck > 0.002 strU = num2str(uStar); strD1 = num2str(delta1); strDz = num2str(deltaZ); if speak ~= 0 disp(['Profile with u*=',strU,', delta1=',strD1,' and deltaZ=',strDz,' has not reached its neck !']) end out = 0; else out = 1; end end function angleRad = radians(angle) angleRad = angle * pi / 180; end function y = cstC_delta2(delta2,theta,uStar) % from e.g. (2.52) Soulie 2005 global cstC y = sin(radians(delta2)) * sin(radians(delta2+theta)) + 1/2 * uStar * sin(radians(delta2))^2 - cstC; end function drho = drho(rho,prevRho,deltaZ,rho2d) % returns rhoPrime at i+1, see (4) Duriez2016 %drho = sqrt( ( rho/(cstK - 1/2*uStar*rho^2) )^2 - 1 );% [11] Lian1993 always positiv, which is not true drho = (rho - prevRho) / deltaZ + 1/2*deltaZ * rho2d; % NB: the rho2d term has a real influence end function rho2d = rhoSecond(rho,rhoP,uStar) % see e.g. (5) Duriez2016 rho2d = (1+rhoP^2) / rho + uStar*(1+rhoP^2)^1.5; end function plotProfile(rho,deltaZ,rRatio,delta1,delta2,theta,cstC,uStar) if uStar~= 0 % "y0" computation, see e.g. [10] Lian1993, (2.54) Soulie2005, (11) Soulie2006.. rhoNeck = ( -1 + sqrt(1+2*uStar*cstC) ) / uStar; else rhoNeck = cstC; end lastZ = deltaZ*(length(rho) -1); vecZ = 0:deltaZ:lastZ; % Toroidal profile parameters: see [15]-[17] Lian1993, for r=1 d1Rad = radians(delta1);d2Rad = radians(delta2); thRad = radians(theta); dist = lastZ - (1-cos(d1Rad)) - (1-cos(d2Rad)); % TODO: only for r=1 rho1 = ( dist/2. + 1 - cos(d1Rad) )/cos(d2Rad+thRad); rho2 = sin(d2Rad) - (1-sin(d2Rad+thRad)) * ( dist/2 + 1-cos(d2Rad) ) / cos(d2Rad+thRad); figure(); plot(vecZ,rho,'o');hold on; plot([0;lastZ],[1/rRatio * sin(radians(delta1));1/rRatio * sin(radians(delta1))],'r') plot([0;lastZ],[rhoNeck;rhoNeck],'m') plot([0;lastZ],[sin(radians(delta2));sin(radians(delta2))],'g') plot(vecZ,rho1 + abs(rho2) - ( rho1^2 - (vecZ-lastZ/2).^2 ).^(1/2),'b'); legend('Profile','Left value','Neck value','Right value','Toroidal profile') xlabel('Interparticle axis, z') ylabel('\rho(z)') title(['\delta_1 = ',num2str(delta1)]) if rRatio ~= 1 disp('Plotted toroidal profile is obviously wrong because rRatio # 1') end % disp([num2str(delta1),' profile plotted with ',num2str(length(rho)),' rho values']) end function plot3Dbridge(rho,deltaZ,rRatio) nPtsAlongAxis = 200 ; % grid-step along "rho" and z axis (the x,y plane of the 3D figure in fact) nRhoVal =length(rho); lastZ = deltaZ*(nRhoVal -1); x = -max(rho):max(rho)/nPtsAlongAxis:max(rho); y = 0:lastZ / (nPtsAlongAxis-1):lastZ; % will then reach exactly lastZ alt = zeros(length(y),length(x)); for i = 1:length(y) indRho = floor( (i-1)*(nRhoVal-1)/(nPtsAlongAxis) ) +1; for j = 1:length(x) if rho(indRho)^2 - x(j)^2 >=0 alt(i,j) = rho(indRho) * sqrt(rho(indRho)^2 - x(j)^2) / rho(indRho); % else % alt(i,j) = NaN; % not pretty... 2d step with matAltToPlot % necessary end end end figure();set(gca,'FontSize',14); surf(x,y,matAltToPlot(alt),'LineStyle','none') % filled surface, with color according to altitude % surf(x,y,matAltToPlot(alt),'FaceColor','none') % just the mesh ylabel('Interparticle axis, z') hold on delta1 = asin(rRatio*rho(1)); yC1 = - cos(delta1)/rRatio; delta2 = asin(rho(nRhoVal)); yC2 = lastZ + cos(delta2); % Center of right sphere: x = -max(rho):max(rho)/40:max(rho); y = x + lastZ/2; altSph1 = zeros(length(x),length(x)); altSph2 = zeros(length(x),length(x)); for i=1:length(x) for j=1:length(x) alt1 = 1/rRatio^2 - x(j)^2 - (y(i)-yC1)^2; if alt1>=0 altSph1(i,j) = alt1^(1/2); end alt2 = 1 - x(j)^2 - (y(i)- yC2)^2; if alt2>=0 altSph2(i,j) = alt2^(1/2); end end end surf(x,y,matAltToPlot(altSph1),'FaceColor','none') surf(x,y,matAltToPlot(altSph2),'FaceColor','none') caxis([0,max(rho)]) grid off axis square end function retMat = matAltToPlot(matAlt) sizeY = size(matAlt,1);sizeX = size(matAlt,2); plotAlt = ones(sizeY,sizeX); for i = 2:sizeY-1 for j = 2:sizeX-1 if ~matAlt(i,j) test = matAlt(i-1,j-1) || matAlt(i-1,j) || matAlt(i-1,j+1); test = test || matAlt(i,j-1) || matAlt(i,j+1); test = test || matAlt(i+1,j-1) || matAlt(i+1,j) || matAlt(i+1,j+1); if ~test plotAlt(i,j) = 0; end end end end retMat = zeros(sizeY,sizeX); for i = 1:sizeY*sizeX if ~plotAlt(i) retMat(i) = NaN; else retMat(i) = matAlt(i); end end end trunk-2017.01a/examples/capillaryLaplaceYoung/writesCapFile.m000066400000000000000000000251561304022710500242140ustar00rootroot00000000000000% J. Duriez (jerome.duriez@ucalgary.ca) function writesCapFile() % Builds capillary files for given radius ratio and contact angle % The historical template of YADE capillary files is kept: each line of % the capillary file is a bridge configuration. Configurations are % grouped by distance values, then (for any distance value) by capillary % pressure values. % The user is expected to modify l. 10 to 27 to taylor the generation to % his needs. % ---------------- Parameters to define by the user ----------------------- % Laplace-Young resolution parameters: deltaZ = 2e-6; % use 2e-6, typically theta = 0; % contact angle, in degrees dDelta1 = 0.3; % delta1 (see solveLiqBridge.m) increment between two configurations % Capillary files construction parameters: nValUc = 350; % # (at most) of capillary pressure values to consider for % one given distance nValDist = 80; % # of distance values (linearly spaced between 0 and some % rupture distance computed in Preliminary A below) to consider % See also if needed l. 147 that defines the capillary file names % List of radius ratio to consider: rRatioVec = [1 1.1 1.25 1.5 1.75 2 3 4 5 10]; % historical rRatio values in YADE % As many capillary files as length(rRatioVec) will be generated suffixe = ''; % string to append at the end of generated files names % ---- End of parameters definitions, no further action is required ! ----- % ---------------- Some data vector initializations ----------------------- % maximum possible interparticle distances for given rRatio: maxD = -ones(length(rRatioVec),1); % Private (J. Duriez) remark: for theta=0; dz=1e-5 or 2e-6; delta1=15:0.2:90; % and rRatioVec = [1;1.1;1.25;1.5;1.75;2;3;4;5], we get here: % maxD = [0.3995;0.3808;0.3567;0.3241;0.2983;0.2772;0.2199;0.1852;0.1615]; % Compares favourably with historical (L. Scholtes') data: dRupt_rMeSch.eps % initial guess (e.g. from L. Scholtes data) of maximum uc values for given rRatio: maxUc_r = [1 1493;1.1 1567;1.25 1781;1.5 2137;1.75 2469;2 2849;3 4274;4 5644;5 6987;10 14370]; % these initial guess are not mandatory but may help save some time below % ---------- Generation of all capillary files really starts here --------- for i =1:length(rRatioVec) rRatio = rRatioVec(i); % ##### Preliminary A: find maxD values ##### % It is considered to be for zero suction (corresponds ~ to Scholtes' data) % And assumed to occur for delta1 greater than 15 deg (> 30 deg in Scholtes) fprintf(['\nFor r = ',num2str(rRatio),', starting search for maximum distance\n']) % fflush(stdout); % Octave command for flush display d1here = 15:0.5:90-theta; % I got the exact same results with 15:1:90 or 15:0.2:90 data = solveLaplace_uc(theta,rRatio,0,d1here,deltaZ,0); maxD(i) = max(data(:,1)); disp(['For r = ',num2str(rRatio),', maximum distance found: maxD = ',num2str(maxD(i))]) disp(''); % fflush(stdout); % Octave command for flush display % #### Preliminary B: computing the set of d* values to consider, valDist #### % -- Following lines are for geometric exponential sequence -- % valDist was a ~ 10-exponential sequence in L. Scholtes' data, but I % (JD) think there was too much small values % valDist = -ones(nValDist,1); % valDist(1)=0;valDist(2) = 5e-5;% 1e-4 in Scholtes maybe too high (cf e.g. F* for r=3) % cst = 1 / (nValDist-2) * log(maxD(i) / valDist(2)); % valDist(3:nValDist) = valDist(2) * exp( ((3:nValDist)'-2) * cst); % -- Anyway, I (JD) think a linear sequence is just as good, or better -- incDist = maxD(i) / (nValDist - 1); valDist = 0:incDist:maxD(i); if length(valDist) ~= nValDist error('We did not construct a consistent set of distances') end % #### Preliminary C: find the greatest admissible suction for r,theta #### % It is considered to be the suction leading, for contacting particles, to % a mean filling angle <= 1 deg (was ~ 2 deg in L. Scholtes' data). d1MaxUc = 0:dDelta1:min(45,90-theta); disp('Starting search for maximum suction');%fflush(stdout); if isempty(find(maxUc_r(:,1)==rRatio,1)) index = find(maxUc_r(:,1) < rRatio,1,'last'); ucTried = floor(maxUc_r(index,2)); else ucTried = floor(maxUc_r(maxUc_r(:,1)==rRatio,2)); end data = solveLaplace_uc(0,rRatio,ucTried,d1MaxUc,deltaZ,0); % Filling angles for contact situation are, if necessary, extrapolated: deltaC = guessDeltaContact(data); while deltaC > 1 prevMaxDelta1 = max(data(:,5)); d1MaxUc = 0:dDelta1:prevMaxDelta1; ucTried = floor(ucTried*1.2); % floor because no need to take care of digits after comma here data = solveLaplace_uc(0,rRatio,ucTried,d1MaxUc,deltaZ,0); deltaC = guessDeltaContact(data); end maxUc = ucTried ; disp(['For r = ',num2str(rRatio),', maximum suction found: final uc = ',num2str(maxUc)]) disp('');%fflush(stdout); % #### End of Preliminary C #### % #### Preliminary D: choosing list of uc* values, valUc ##### % we define valUc as a geometric sequence --with 0 as first term, though-- % so that log(uc*_{i+1}) - log(uc*_i) = cst, and reaching maxUc as the last % (i.e. nValUc-th) term valUc = -ones(nValUc,1); valUc(1)=0;valUc(2) = 0.002;% 0.002 as first positiv uc* value corresponds ~ to Scholtes cst = 1 / (nValUc-2) * log(maxUc / valUc(2))/log(10); valUc(3:nValUc) = valUc(2) * 10.^( ((3:nValUc)'-2) * cst); % #### Preliminaries completed: computing data for all uc values in valUc ! ##### bigData = -ones(nValDist*nValUc,8); % will gather all data lineInBigData = 1; disp('Starting solving for all uc values');tic % fflush(stdout); output = zeros(10);iOut = 1; % these things are just to control some message display for indUc = 1:nValUc % message display: if indUc >= iOut * nValUc / length(output) && output(iOut) == 0 disp([num2str(iOut / length(output)* 100),'% of uc values just completed']) % fflush(stdout); toc;tic; output(iOut) = 0; iOut = iOut+1; end if indUc == 1 delta1Int = 0:dDelta1:90-theta; end smallData = solveLaplace_uc(theta,rRatio,valUc(indUc),delta1Int,deltaZ,0); delta1Int = 0:dDelta1:max(smallData(:,5)); % Filling bigData: nLinesSmallData = length(smallData(:,1)); bigData(lineInBigData:lineInBigData+nLinesSmallData-1,:) = smallData(:,[1:6,8:9]); lineInBigData = lineInBigData + nLinesSmallData; end disp('All uc values computed !');toc % fflush(stdout); % Cleaning and sorting the computed data: bigData = bigData(bigData(:,1)>=0,:); % removal of possible extra data, due to preallocation bigData = sortrows(bigData); % sorts according to increasing distance nomCapFic = ['M(r=',num2str(rRatio),')',suffixe]; fic = fopen(nomCapFic,'w'); % first line of the file=rRatio value: fprintf(fic,[num2str(rRatio),'\n',num2str(nValDist),'\n']);% for direct use in YADE % alternatively, you may want to save some details about the % construction. If yes, replace with the 2 following lines % fprintf(fic,[num2str(rRatio),' ; theta = ',num2str(theta),' ; dDelta1 = ',num2str(dDelta1)]); % fprintf(fic,[' ; deltaZ less or equal than ',num2str(deltaZ),'\n',num2str(nValDist),'\n']); % in this case, you may need to manually suppress these extra % characters before using the capillary file in YADE fclose(fic); % the final data have to conform valDist data. This is achieved through % interpolation, below: for indD =1:nValDist dWanted = valDist(indD); dataCapFile = interpolate(dWanted,valUc,bigData); dlmwrite(nomCapFic,dataCapFile,'-append','delimiter','\t') end end end function deltaC = guessDeltaContact(data) data = sortrows(data); % sorts the data according to increasing distance dist1 = data(1,1);dist2 = data(2,1); % the two lowest computed distances data1 = data(1,:); data2 = data(2,:); % the data for these two distances data_contact = data1 - ( data2 - data1 ) / (dist2 - dist1) * dist1; deltaC = mean(data_contact(5:6)); % mean delta1, delta2 end function outData = interpolate(dist,valUc,bigData) % input bigData is a distance sorted bridges data table (matrix), obtained % directly from solving Laplace-Young equ. It hence shows no specific % distance values pattern. % Output outData is a data table for the given distance "dist" (and many uc % values) which is obtained distance-interpolating from bigData dataGreaterDist = bigData(bigData(:,1)>= dist,:); if isempty(dataGreaterDist) % may happen for maxD, see for instance delta1 % increment = 0.5 for maxD determination (with uc*=0), vs possibly % another value for computing bigData outData = []; out = '\nWARNING: Reaching the last distance value was not possible here. Before use in YADE, you need to'; out = [out,' modify by hand the 2d line (where nValDist appears) of this capillary file:\n']; out = [out,'Just substract 1 to the nValDist value appearing therein\n']; fprintf([out,'Sorry about that..\n\n']); return end maxUc_dist = max(dataGreaterDist(:,2)); valUcOK = valUc(valUc <= maxUc_dist); nValUcOK = length(valUcOK); data_dist = -ones(nValUcOK,8); % all data for one given distance for i = 1:nValUcOK currUc = valUcOK(i); data_uc = bigData(bigData(:,2) == currUc,:); if size(data_uc,1) == 1 % one single liq bridge data is useless nValUcOK = i-1; break end if dist < min(data_uc(:,1)) data1 = data_uc(1,:); data2 = data_uc(2,:); dist1 = data1(1) ; dist2 = data2(1); data_dist(i,:) = data1 + ( data2 - data1 ) / (dist2 - dist1) * (dist - dist1); else data_dInf = data_uc(data_uc(:,1) <= dist,:); % not empty after previous if data_dInf = data_dInf(size(data_dInf,1),:); dInf = data_dInf(1); data_dSup = data_uc(data_uc(:,1) >= dist,:); % not empty either data_dSup = data_dSup(1,:); dSup = data_dSup(1); data_dist(i,:) = data_dInf + (data_dSup-data_dInf)/(dSup-dInf) * (dist-dInf); end end data_dist = data_dist(data_dist(:,2) >= 0,:); % in case we faced the break above if size(data_dist,1) > nValUcOK error('Problem here !') end if size(data_dist,1) == 0 % may happen for dist = maxD out = '\nWARNING: Reaching the last distance value was not possible here. Before use in YADE, you need to'; out = [out,' modify by hand the 2d line (where nValDist appears) of this capillary file:\n']; out = [out,'Just substract 1 to the nValDist value appearing therein\n']; fprintf([out,'Sorry about that..\n\n']); end outData = [nValUcOK 0 0 0 0 0 0 0;data_dist]; end trunk-2017.01a/examples/chained-cylinders/000077500000000000000000000000001304022710500203655ustar00rootroot00000000000000trunk-2017.01a/examples/chained-cylinders/CohesiveCylinderSphere.py000066400000000000000000000034771304022710500253600ustar00rootroot00000000000000# encoding: utf-8 from yade import qt from yade.gridpfacet import * qt.View() O.dt=5e-07 O.materials.append(CohFrictMat(young=8e5,poisson=0.3,density=4e3,frictionAngle=radians(30),normalCohesion=1e5,shearCohesion=1e5,momentRotationLaw=True,label='cylindermat')) O.materials.append(CohFrictMat(young=8e5,poisson=0.3,density=4e3,frictionAngle=radians(30),normalCohesion=1e5,shearCohesion=1e5,momentRotationLaw=False,label='spheremat')) rCyl=0.006 cylindersBodies=[] for i in arange(0,0.3,0.3/15.): cylindersBodies.append(chainedCylinder(begin=Vector3(i,0,0),radius=rCyl,end=Vector3(i+0.3/15.,0,0),fixed=False,wire=False,material='cylindermat')) ChainedState.currentChain=ChainedState.currentChain+1 O.bodies[0].state.blockedDOFs='xyzXYZ' O.bodies[-1].state.blockedDOFs='xyzXYZ' IdSphere=O.bodies.append(sphere([0.15,0,2.*rCyl],rCyl,wire=False,fixed=False,material='spheremat')) def main(): if O.iter>50000 : O.bodies[IdSphere].dynamic=False O.bodies[IdSphere].state.vel[2]=0.1 O.engines=[ ForceResetter(), InsertionSortCollider([ Bo1_ChainedCylinder_Aabb(), Bo1_Sphere_Aabb(), ]), InteractionLoop( #Geometric interactions [Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D(), Ig2_Sphere_ChainedCylinder_CylScGeom6D(), #used for the cohesive sphere-cylinder interaction # Ig2_Sphere_Sphere_ScGeom6D() ], #Physical interactions [Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=True,label='ipf'), # Ip2_FrictMat_FrictMat_FrictPhys() ], #LContact Laws: [Law2_ScGeom6D_CohFrictPhys_CohesionMoment(), Law2_CylScGeom6D_CohFrictPhys_CohesionMoment(), #used for the cohesive sphere-cylinder interaction # Law2_ScGeom_FrictPhys_CundallStrack(), ] ), ## Motion equation NewtonIntegrator(gravity=(0,0,0),damping=0.3,label='newton'), PyRunner(command='main()',iterPeriod=1000), ] trunk-2017.01a/examples/chained-cylinders/chained-cylinder-roots.py000066400000000000000000000061251304022710500253110ustar00rootroot00000000000000#--- bruno.chareyre@hmg.inpg.fr --- #!/usr/bin/python # -*- coding: utf-8 -*- # Experiment beam-like behaviour with chained cylinders + CohFrict connexions from yade import pack from yade.gridpfacet import * young=4.0e6 poisson=3 density=1e3 frictionAngle1=radians(15) frictionAngle2=radians(15) frictionAngle3=radians(15) O.dt=5e-4 O.materials.append(FrictMat(young=4000000.0,poisson=0.5,frictionAngle=frictionAngle1,density=1600,label='spheremat')) O.materials.append(FrictMat(young=1.0e6,poisson=0.2,density=2.60e3,frictionAngle=frictionAngle2,label='walllmat')) Ns=90 sp=pack.SpherePack() #cohesive spheres crash because sphere-cylnder functor geneteragets ScGeom3D #O.materials.append(CohFrictMat(young=1.0e5,poisson=0.03,density=2.60e2,frictionAngle=frictionAngle,label='spheremat')) if os.path.exists("cloud4cylinders"+`Ns`): print "loading spheres from file" sp.load("cloud4cylinders"+`Ns`) else: print "generating spheres" Ns=sp.makeCloud(Vector3(-0.3,0.2,-1.0),Vector3(+0.3,+0.5,+1.0),-1,.2,Ns,False,0.8) sp.save("cloud4cylinders"+`Ns`) O.bodies.append([sphere(center,rad,material='spheremat') for center,rad in sp]) walls=aabbWalls((Vector3(-0.3,-0.15,-1),Vector3(+0.3,+1.0,+1)),thickness=.1,material='walllmat') wallIds=O.bodies.append(walls) O.initializers=[ BoundDispatcher([Bo1_Sphere_Aabb(),Bo1_ChainedCylinder_Aabb(),Bo1_Box_Aabb()]) ] O.engines=[ ForceResetter(), InsertionSortCollider([ Bo1_ChainedCylinder_Aabb(), Bo1_Sphere_Aabb(), Bo1_Box_Aabb() ]), InteractionLoop( [Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D(), Ig2_Sphere_ChainedCylinder_CylScGeom(), Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=False,label='ipf'),Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom6D_CohFrictPhys_CohesionMoment(label='law'),Law2_ScGeom_FrictPhys_CundallStrack(),Law2_CylScGeom_FrictPhys_CundallStrack()] ), ## Motion equation NewtonIntegrator(damping=0.05,label='newton',gravity=[1,-9.81,0]), ] #Assemble cylinders in sinusoidal shapes O.materials.append(CohFrictMat(young=young,poisson=poisson,density=3.0*density,frictionAngle=frictionAngle3,normalCohesion=1e40,shearCohesion=1e40,momentRotationLaw=True,label='cylindermat')) Ne=30 dy=0.03 dx=0.2 dz=0.2 Nc=1 #nb. of additional chains for j in range(-Nc, Nc+1): dyj = abs(float(j))*dy dxj = abs(float(j))*dx dzj = float(j)*dz for i in range(0, Ne): omega=20/float(Ne); hy=0.0; hz=0.05; hx=1.5; px=float(i)*hx/float(Ne)-0.8+dxj; py=sin(float(i)*omega)*hy+dyj; pz=cos(float(i)*omega)*hz+dzj; px2=float(i+1.)*hx/float(Ne)-0.8+dxj; py2=sin(float(i+1.)*omega)*hy+dyj; pz2=cos(float(i+1.)*omega)*hz+dzj; chainedCylinder(begin=Vector3(pz,py,px), radius=0.02,end=Vector3(pz2,py2,px2),color=Vector3(0.6,0.5,0.5),material='cylindermat') if (i == Ne-1): #close the chain with a node of size 0 print "closing chain" b=chainedCylinder(begin=Vector3(pz2,py2,px2), radius=0.02,end=Vector3(pz2,py2,px2),color=Vector3(0.6,0.5,0.5),material='cylindermat') b.state.blockedDOFs='xyzXYZ' ChainedState.currentChain=ChainedState.currentChain+1 O.saveTmp() trunk-2017.01a/examples/chained-cylinders/chained-cylinder-spring.py000066400000000000000000000035751304022710500254530ustar00rootroot00000000000000#--- bruno.chareyre@hmg.inpg.fr --- #!/usr/bin/python # -*- coding: utf-8 -*- # Experiment beam-like behaviour with chained cylinders + CohFrict connexions from yade.gridpfacet import * young=1.0e6 poisson=4 density=2.60e3 frictionAngle=radians(30) O.materials.append(CohFrictMat(young=young,poisson=poisson,density=density,frictionAngle=frictionAngle,normalCohesion=1e13,shearCohesion=1e13,momentRotationLaw=True,label='mat')) O.dt=1e-4 O.engines=[ ForceResetter(), InsertionSortCollider([ Bo1_ChainedCylinder_Aabb(), Bo1_Sphere_Aabb() ]), InteractionLoop( [Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D(),Ig2_Sphere_ChainedCylinder_CylScGeom()], [Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=True)], [Law2_ScGeom6D_CohFrictPhys_CohesionMoment(label='law')] ), ## Motion equation NewtonIntegrator(damping=0.15,gravity=[0,-9.81,0]), PyRunner(iterPeriod=500,command='history()'), #PyRunner(iterPeriod=5000,command='if O.iter<21000 : yade.qt.center()') ] #Generate a spiral Ne=200 for i in range(0, Ne): omega=60.0/float(Ne); hy=0.10; hz=0.15; px=float(i)*(omega/60.0); py=sin(float(i)*omega)*hy; pz=cos(float(i)*omega)*hz; px2=float(i+1.)*(omega/60.0); py2=sin(float(i+1.)*omega)*hy; pz2=cos(float(i+1.)*omega)*hz; chainedCylinder(begin=Vector3(pz,py,px), radius=0.005,end=Vector3(pz2,py2,px2),color=Vector3(0.6,0.5,0.5)) def outp(id=1): for i in O.interactions: if i.id1 == 1: print i.phys.shearForce print i.phys.normalForce return i O.bodies[Ne-1].state.blockedDOFs='xyzXYZ' yade.qt.View(); #plot some results from yade import plot plot.plots={'t':('pos1',None,'vel1')} def history(): plot.addData(pos1=O.bodies[0].state.pos[1], # potential elastic energy vel1=O.bodies[0].state.vel[1], t=O.time) #yade.qt.Renderer().bound=True plot.plot(subPlots=False) O.saveTmp() #O.bodies[0].state.angVel=Vector3(0.05,0,0) trunk-2017.01a/examples/clumps/000077500000000000000000000000001304022710500163035ustar00rootroot00000000000000trunk-2017.01a/examples/clumps/addToClump-example.py000066400000000000000000000042041304022710500223420ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- '''This example shows usage of addToClump() and appendClumped().''' from yade import pack,export,qt #define material for all bodies: id_Mat=O.materials.append(FrictMat(young=1e6,poisson=0.3,density=1000,frictionAngle=1)) Mat=O.materials[id_Mat] #define engines: O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), NewtonIntegrator(damping=0.7,gravity=[0,0,-10]) ] #create a box: id_box = O.bodies.append(box((0,0,0),(2,2,.1),fixed=True,material=Mat)) #### show how to use appendClumped(): #create 2 clumps: clump1=O.bodies.appendClumped([\ sphere([0,0,1], material=Mat, radius=0.5),\ sphere([0.2,0,1], material=Mat, radius=0.5)\ ]) clump2=O.bodies.appendClumped([\ sphere([3,1,2], material=Mat, radius=0.5),\ sphere([3.2,1,2], material=Mat, radius=0.5)\ ]) #get clump ids: id_clump1 = clump1[0] id_clump2 = clump2[0] #definition for getting informations from all clumps: def getClumpInfo(): for b in O.bodies: if b.isClump: print 'Clump ',b.id,' has following members:' keys = b.shape.members.keys() for ii in range(0,len(keys)): print '- Body ',keys[ii] print 'inertia:',b.state.inertia print 'mass:',b.state.mass,'\n' #### show how to use addToClump(): #create a new sphere: id_new=O.bodies.append(sphere([0,0.2,1], material=Mat, radius=0.5)) print '\nSTATE before adding sphere to clump ------------' getClumpInfo() #add a sphere to the clump: O.bodies.addToClump([id_new],id_clump1) print '\nSTATE after adding sphere to clump ------------' getClumpInfo() #add a clump to a clump: O.bodies.addToClump([id_clump2],id_clump1) print '\nSTATE after adding the second clump to clump ------------' getClumpInfo() #try to add clump member to a clump (should give error message): #O.bodies.addToClump(1,id_clump1) #try to add clump to the same clump (should give error message): #O.bodies.addToClump(id_clump1,id_clump1) O.dt=1e-6 print '\nPress Play button ... ' renderer = qt.Renderer() qt.View() trunk-2017.01a/examples/clumps/apply-buoyancy-clumps.py000066400000000000000000000122031304022710500231300ustar00rootroot00000000000000!/usr/bin/python # -*- coding: utf-8 -*- ''' The script shows how to include the effect of buoyancy in a particle assembly under condition of an increasing water-level. Water-level at start of the sim- ulation is at the lower boundary of the model. During the calculation particles get partly surrounded by water and buoyancy (=fluidDensity*volumeOfDisplacedWater) is increasing until particle is completely surrounded. When particle is sur- rounded volumeOfDisplacedWater is equal to the volume of the particle. For calculation of buoyancy of a clump the equivalent radius R = (3*clumpMass/(4*pi*particleDensity))^1/3 of a sphere with clump mass and clump volume V = (4*pi*R^3)/3 = clumpMass/particleDensity is used. This approximation can be used for well rounded clumps. Buoyancy is included with an additional force F_buo = -volumeOfDisplacedWater*fluidDensity*gravityAcceleration.''' #define material properties: shearModulus = 3.2e10 poissonRatio = 0.15 youngModulus = 2*shearModulus*(1+poissonRatio) angle = 0.5 #friction angle in radians rho_p = 2650 #density of particles rho_f = 5000 #density of the fluid rho_f > rho_p = floating particles v_iw = 1 #velocity of increasing water-level #model boundaries: boundaryMin = Vector3(-1.5,-1.5,0) boundaryMax = Vector3(1.5,1.5,2) #define colors: sphereColor = (.8,.8,0.)#dirty yellow clumpColor = (1.,.55,0.)#dark orange boxColor = (.1,.5,.1)#green waterColor = (.2,.2,.7)#blue #material: id_Mat=O.materials.append(FrictMat(young=youngModulus,poisson=poissonRatio,density=rho_p,frictionAngle=angle)) Mat=O.materials[id_Mat] #create assembly of spheres: sp=pack.SpherePack() sp.makeCloud(minCorner=boundaryMin,maxCorner=boundaryMax,rMean=.2,rRelFuzz=.5,num=100,periodic=False) O.bodies.append([sphere(c,r,material=Mat,color=sphereColor) for c,r in sp]) #create template for clumps and replace 10% of spheres by clumps: templateList = [clumpTemplate(relRadii=[1,.5],relPositions=[[0,0,0],[.7,0,0]])] O.bodies.replaceByClumps(templateList,[.1]) #color clumps: for b in O.bodies: if b.isClumpMember: b.shape.color=clumpColor #create boundary: O.bodies.append(geom.facetBox((0,0,1), (boundaryMax-boundaryMin)/2, fixed=True, material=Mat, color=boxColor)) #define engines: O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_MindlinPhys()], [Law2_ScGeom_MindlinPhys_Mindlin(neverErase=False)] ), NewtonIntegrator(gravity=(0,0,-10),damping=0.7,label='integrator') ] #definition to apply buoyancy: def applyBuoyancy(): global waterLevel waterLevel = (O.time-t0) * v_iw + boundaryMin[2] for b in O.bodies: zMin = 1e9 zMax = -1e9 if b.isStandalone and isinstance(b.shape,Sphere): rad = b.shape.radius zMin = b.state.pos[2] - rad dh = min((waterLevel - zMin),2*rad) #to get sure, that dh is not bigger than 2*radius elif b.isClump: #determine rad, zMin and zMax for clumps: for ii in b.shape.members.keys(): pos = O.bodies[ii].state.pos zMin = min(zMin,pos[2]-O.bodies[ii].shape.radius) zMax = max(zMax,pos[2]+O.bodies[ii].shape.radius) #get equivalent radius from clump mass: rad = ( 3*b.state.mass/(4*pi*O.bodies[b.shape.members.keys()[0]].mat.density) )**(1./3.) #get dh relative to equivalent sphere, but acting when waterLevel is between clumps z-dimensions zMin and zMax: dh = min((waterLevel - zMin)*2*rad/(zMax - zMin),2*rad) else: continue if dh > 0: F_buo = -1*(pi/3)*dh*dh*(3*rad - dh)*rho_f*integrator.gravity # = -V*rho*g O.forces.setPermF(b.id,F_buo) #STEP1: reduce overlaps from replaceByClumps() method: O.dt=1e-6 #small time step for preparation steps via calm() print '\nSTEP1 in progress. Please wait a minute ...\n' O.engines=O.engines+[PyRunner(iterPeriod=10000,command='calm()',label='calmRunner')] O.run(100000,True) #STEP2: let particles settle down calmRunner.dead=True O.dt=2e-5 print '\nSTEP2 in progress. Please wait a minute ...\n' O.run(50000,True) #start PyRunner engine to apply buoyancy: t0 = O.time waterLevel = boundaryMin[2] O.engines=O.engines+[PyRunner(iterPeriod=100,command='applyBuoyancy()',label='buoLabel')] #create 2 facets, that show water height: idsWaterFacets = [] idsWaterFacets.append(O.bodies.append(facet( \ [ boundaryMin, [boundaryMax[0],boundaryMin[1],boundaryMin[2]], [boundaryMax[0],boundaryMax[1],boundaryMin[2]] ], \ fixed=True,material=FrictMat(young=0),color=waterColor,wire=False)))#no interactions will appear idsWaterFacets.append(O.bodies.append(facet( \ [ [boundaryMax[0],boundaryMax[1],boundaryMin[2]], [boundaryMin[0],boundaryMax[1],boundaryMin[2]], boundaryMin ], \ fixed=True,material=FrictMat(young=0),color=waterColor,wire=False)))#no interactions will appear #set velocity of incr. water level to the facets: for ids in idsWaterFacets: O.bodies[ids].state.vel = [0,0,v_iw] #STEP3: simulate buoyancy with increasing water table condition O.dt=3e-5 from yade import qt qt.Controller() v=qt.View() v.eyePosition=(-7,0,2); v.upVector=(0,0,1); v.viewDir=(1,0,-.1); v.axes=True; v.sceneRadius=1.9 print '\nSTEP3 started ...\n' O.run(70000) trunk-2017.01a/examples/clumps/clump-hopper-test.py000066400000000000000000000051041304022710500222450ustar00rootroot00000000000000# -*- coding: utf-8 from yade import pack,export,qt,geom import itertools from numpy import * kinEnergyMax = 100000 # Parameters tc=0.001# collision time en=.3 # normal restitution coefficient es=.3 # tangential restitution coefficient frictionAngle=radians(35)# density=2700 # facets material facetMat=O.materials.append(ViscElMat(frictionAngle=frictionAngle,tc=tc,en=en,et=es)) # default spheres material dfltSpheresMat=O.materials.append(ViscElMat(density=density,frictionAngle=frictionAngle,tc=tc,en=en,et=es)) O.dt=.05*tc # time step Rs=0.05 # particle radius # Create geometry x0=0.; y0=0.; z0=0.; ab=.7; at=2.; h=1.; hl=h; al=at*3 zb=z0; x0b=x0-ab/2.; y0b=y0-ab/2.; x1b=x0+ab/2.; y1b=y0+ab/2. zt=z0+h; x0t=x0-at/2.; y0t=y0-at/2.; x1t=x0+at/2.; y1t=y0+at/2. zl=z0-hl;x0l=x0-al/2.; y0l=y0-al/2.; x1l=x0+al/2.; y1l=y0+al/2. vibrationPlate = O.bodies.append(geom.facetBunker((x0,y0,z0), dBunker=ab*4.0,dOutput=ab*1.7,hBunker=ab*3,hOutput=ab,hPipe=ab/3.0, wallMask=4,segmentsNumber=10,material=facetMat)) # Create engines O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), DomainLimiter(lo=(-4,-4,-1),hi=(4,4,4),iterPeriod=5000,label='domLim'), NewtonIntegrator(damping=0, gravity=[0,0,-9.81]), PyRunner(iterPeriod=6500,command='addBodies()',nDo=7,label='addb'), PyRunner(iterPeriod=1000,command='state()',label='state'), ] numSphereGen = 0 def addBodies(): global numSphereGen # Create clumps... clumpColor=(0.0, 0.5, 0.5) for k,l in itertools.product(arange(0,10),arange(0,10)): clpId,sphId=O.bodies.appendClumped([sphere(Vector3(x0t+Rs*(k*4+2),y0t+Rs*(l*4+2),i*Rs*2+zt+ab*3),Rs,color=clumpColor,material=dfltSpheresMat) for i in xrange(4)]) numSphereGen += len(sphId) # ... and spheres spheresColor=(0.4, 0.4, 0.4) for k,l in itertools.product(arange(0,9),arange(0,9)): sphAloneId=O.bodies.append( [sphere( Vector3(x0t+Rs*(k*4+4),y0t+Rs*(l*4+4),i*Rs*2.3+zt+ab*3),Rs,color=spheresColor,material=dfltSpheresMat) for i in xrange(4) ] ) numSphereGen += len(sphAloneId) def state(): global numSphereGen print "Iter %d: Total number of generated spheres %d, removed particles %d, current particles %d, kinEnergy %g"%(O.iter, numSphereGen, domLim.nDeleted, numSphereGen-domLim.nDeleted, utils.kineticEnergy()) if (utils.kineticEnergy() > kinEnergyMax): print "Kinetic energy is over a threshold value! Error!" addBodies() from yade import qt qt.View() O.saveTmp() #O.run(50001) trunk-2017.01a/examples/clumps/clump-hopper-viscoelastic.py000066400000000000000000000056541304022710500237700ustar00rootroot00000000000000# -*- coding: utf-8 from yade import pack,export,qt import gts,os,random,itertools from numpy import * # Parameters tc=0.001# collision time en=.3 # normal restitution coefficient es=.3 # tangential restitution coefficient frictionAngle=radians(35)# density=2700 # facets material facetMat=O.materials.append(ViscElMat(frictionAngle=frictionAngle,tc=tc,en=en,et=es)) # default spheres material dfltSpheresMat=O.materials.append(ViscElMat(density=density,frictionAngle=frictionAngle,tc=tc,en=en,et=es)) O.dt=.05*tc # time step Rs=0.05 # particle radius # Create geometry x0=0.; y0=0.; z0=0.; ab=.7; at=2.; h=1.; hl=h; al=at*3 zb=z0; x0b=x0-ab/2.; y0b=y0-ab/2.; x1b=x0+ab/2.; y1b=y0+ab/2. zt=z0+h; x0t=x0-at/2.; y0t=y0-at/2.; x1t=x0+at/2.; y1t=y0+at/2. zl=z0-hl;x0l=x0-al/2.; y0l=y0-al/2.; x1l=x0+al/2.; y1l=y0+al/2. left = pack.sweptPolylines2gtsSurface([[Vector3(x0b,y0b,zb),Vector3(x0t,y0t,zt),Vector3(x0t,y1t,zt),Vector3(x0b,y1b,zb)]],capStart=True,capEnd=True) lftIds=O.bodies.append(pack.gtsSurface2Facets(left,material=facetMat,color=(0,1,0))) right = pack.sweptPolylines2gtsSurface([[Vector3(x1b,y0b,zb),Vector3(x1t,y0t,zt),Vector3(x1t,y1t,zt),Vector3(x1b,y1b,zb)]],capStart=True,capEnd=True) rgtIds=O.bodies.append(pack.gtsSurface2Facets(right,material=facetMat,color=(0,1,0))) near = pack.sweptPolylines2gtsSurface([[Vector3(x0b,y0b,zb),Vector3(x0t,y0t,zt),Vector3(x1t,y0t,zt),Vector3(x1b,y0b,zb)]],capStart=True,capEnd=True) nearIds=O.bodies.append(pack.gtsSurface2Facets(near,material=facetMat,color=(0,1,0))) far = pack.sweptPolylines2gtsSurface([[Vector3(x0b,y1b,zb),Vector3(x0t,y1t,zt),Vector3(x1t,y1t,zt),Vector3(x1b,y1b,zb)]],capStart=True,capEnd=True) farIds=O.bodies.append(pack.gtsSurface2Facets(far,material=facetMat,color=(0,1,0))) table = pack.sweptPolylines2gtsSurface([[Vector3(x0l,y0l,zl),Vector3(x0l,y1l,zl),Vector3(x1l,y1l,zl),Vector3(x1l,y0l,zl)]],capStart=True,capEnd=True) tblIds=O.bodies.append(pack.gtsSurface2Facets(table,material=facetMat,color=(0,1,0))) # Create clumps... clumpColor=(0.0, 0.5, 0.5) for k,l in itertools.product(arange(0,10),arange(0,10)): clpId,sphId=O.bodies.appendClumped([sphere(Vector3(x0t+Rs*(k*4+2),y0t+Rs*(l*4+2),i*Rs*2+zt),Rs,color=clumpColor,material=dfltSpheresMat) for i in xrange(4)]) # ... and spheres spheresColor=(0.4, 0.4, 0.4) for k,l in itertools.product(arange(0,9),arange(0,9)): sphAloneId=O.bodies.append( [sphere( Vector3(x0t+Rs*(k*4+4),y0t+Rs*(l*4+4),i*Rs*2.3+zt),Rs,color=spheresColor,material=dfltSpheresMat) for i in xrange(4) ] ) # Create engines O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0, gravity=[0,0,-9.81]), #VTKRecorder(virtPeriod=0.01,fileName='/tmp/',recorders=['spheres','velocity','facets']) ] from yade import qt qt.View() O.saveTmp() trunk-2017.01a/examples/clumps/clump-inbox-viscoelastic.py000066400000000000000000000024771304022710500236120ustar00rootroot00000000000000# -*- coding: utf-8 from yade import pack,export,qt,geom import gts,os,random,itertools from numpy import * # Parameters tc=0.001# collision time en=.3 # normal restitution coefficient es=.3 # tangential restitution coefficient frictionAngle=radians(35)# density=2700 # facets material facetMat=O.materials.append(ViscElMat(frictionAngle=frictionAngle,tc=tc,en=en,et=es)) # default spheres material dfltSpheresMat=O.materials.append(ViscElMat(density=density,frictionAngle=frictionAngle,tc=tc,en=en,et=es)) O.dt=.05*tc # time step Rs=0.1 # particle radius # Create geometry box = O.bodies.append(geom.facetBox((0,0,0),(1,1,1),wallMask=31,material=facetMat)) # Create clumps... for j in xrange(10): clpId,sphId=O.bodies.appendClumped([sphere(Vector3(0,Rs*2*i,(j+1)*Rs*2),Rs,material=dfltSpheresMat) for i in xrange(4)]) # ... and spheres sphAloneId=O.bodies.append( [sphere( Vector3(0.5,Rs*2*i,(j+1)*Rs*2), Rs, material=dfltSpheresMat) for i in xrange(4) ] ) # Create engines O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0,gravity=[0,0,-9.81]), ] renderer = qt.Renderer() qt.View() O.saveTmp() trunk-2017.01a/examples/clumps/clump-viscoelastic.py000066400000000000000000000055701304022710500224720ustar00rootroot00000000000000# -*- coding: utf-8 from yade import pack,export,qt import gts,os,random,itertools from numpy import * # Parameters tc=0.001# collision time en=.3 # normal restitution coefficient es=.3 # tangential restitution coefficient frictionAngle=radians(35)# density=2700 # facets material facetMat=O.materials.append(ViscElMat(frictionAngle=frictionAngle,tc=tc,en=en,et=es)) # default spheres material dfltSpheresMat=O.materials.append(ViscElMat(density=density,frictionAngle=frictionAngle,tc=tc,en=en,et=es)) O.dt=.01*tc # time step Rs=0.1 # particle radius # Create geometry plnSurf = pack.sweptPolylines2gtsSurface([[Vector3(-.5,0,0),Vector3(.5,0,0),Vector3(.5, 0, -.5),Vector3(-.5, 0, -.5)]],capStart=True,capEnd=True) plnIds=O.bodies.append(pack.gtsSurface2Facets(plnSurf,material=facetMat,color=(0,1,0))) plnSurf1 = pack.sweptPolylines2gtsSurface([[Vector3(-.5,-.5,-.5),Vector3(.5,-.5,-.5),Vector3(.5, 1.5, -.5),Vector3(-.5, 1.5, -.5)]],capStart=True,capEnd=True) plnIds1=O.bodies.append(pack.gtsSurface2Facets(plnSurf1,material=facetMat,color=(0,1,0))) # Create clumps clpId,sphId=O.bodies.appendClumped([sphere(Vector3(0,Rs*2*i,Rs*2),Rs,material=dfltSpheresMat) for i in xrange(4)]) # Create engines O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0, gravity=[0,0,-9.81]), ] renderer = qt.Renderer() qt.View() O.saveTmp() clump = O.bodies[clpId] spheres = [ O.bodies[id] for id in sphId ] print '\nClump:\n======' #print '\nMaterial:' if clump.mat: print clump.mat.dict() else: print 'no material' print '\nshape:' if clump.shape: print clump.shape.dict() else: print 'no shape' print '\nState:' if clump.state: print clump.state.dict() else: print 'no state' print '\nControl:' mass = sum( [ s.state.mass for s in spheres ] ) xm_ = [ s.state.pos[0]*s.state.mass for s in spheres ] ym_ = [ s.state.pos[1]*s.state.mass for s in spheres ] zm_ = [ s.state.pos[2]*s.state.mass for s in spheres ] centroid = Vector3( sum(xm_)/mass, sum(ym_)/mass, sum(zm_)/mass ) def sphereInertiaTensor(p, m, r, c): ''' Inertia tensor sphere with position p, mass m and radus r relative point c ''' I = zeros((3,3)) rp = array(p)-array(c) I[0,0] = 2./5.*m*r*r + m*(rp[1]**2+rp[2]**2) I[1,1] = 2./5.*m*r*r + m*(rp[0]**2+rp[2]**2) I[2,2] = 2./5.*m*r*r + m*(rp[0]**2+rp[1]**2) for k,l in itertools.product(arange(0,3),arange(0,3)): if not k==l: I[k,l] = -m*rp[k]*rp[l] return I I = zeros((3,3)) for s in spheres: I += sphereInertiaTensor(s.state.pos,s.state.mass,s.shape.radius,centroid) I_eigenvalues, I_eigenvectors = linalg.eig(I) print 'mass = ', mass print 'centroid = ', centroid print 'I = \n', I print 'I_eigenvalues = ', I_eigenvalues print 'I_eigenvectors = \n', I_eigenvectors trunk-2017.01a/examples/clumps/releaseFromClump-example.py000066400000000000000000000037621304022710500235630ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- '''This example shows usage of releaseFromClump() and clump().''' #define material for all bodies: id_Mat=O.materials.append(FrictMat(young=1e6,poisson=0.3,density=1000,frictionAngle=1)) Mat=O.materials[id_Mat] #define engines: O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), NewtonIntegrator(damping=0.7,gravity=[0,0,-10]) ] #create a box: id_box = O.bodies.append(box((0,0,0),(5,5,.1),fixed=True,material=Mat)) #### show how to use clump(): #create spheres parallel to x-axis: bodyList1 = [] for ii in range(-2,2): bodyList1.append(O.bodies.append(sphere((ii,0,1),radius=.5,material=Mat))) #create spheres parallel to y-axis: bodyList2 = [] for ii in range(-3,2): bodyList2.append(O.bodies.append(sphere((-1,ii,1.5),radius=.5,material=Mat))) #create 2 clumps, and give each clump a different color idClump1=O.bodies.clump(bodyList1) idClump2=O.bodies.clump(bodyList2) for ii in bodyList1: O.bodies[ii].shape.color=(.1,.5,.1) for ii in bodyList2: O.bodies[ii].shape.color=(.2,.2,.7) #definition for getting informations from all clumps: def getClumpInfo(): for b in O.bodies: if b.isClump: print 'Clump ',b.id,' has following members:' keys = b.shape.members.keys() for ii in range(0,len(keys)): print '- Body ',keys[ii] O.dt=1e-6 #### show how to use releaseFromClump(): print '\nSTATE before releasing spheres from clump ------------' getClumpInfo() raw_input('\nPress Play button ... and look what happens.\n Then press Pause button and press ENTER on console!') for ii in bodyList2: if ii > max(bodyList2)-2: clId = O.bodies[ii].clumpId O.bodies.releaseFromClump(ii,clId) print 'Sphere ',ii,' released from clump ',clId print '\nSTATE after releasing spheres from clump ------------' getClumpInfo() print '\nPress Play button again ... ' trunk-2017.01a/examples/clumps/replaceByClumps-example.py000066400000000000000000000045521304022710500234060ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- '''This example shows usage of clumpTemplate(), replaceByClumps() and getRoundness().''' #define material for all bodies: id_Mat=O.materials.append(FrictMat(young=1e7,poisson=0.3,density=1000,frictionAngle=1)) Mat=O.materials[id_Mat] #define engines: O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), NewtonIntegrator(damping=0.7,gravity=[0,0,-10]) ] from yade import qt qt.Controller() qt.View() #create a box: id_box = O.bodies.append(box((0,0,0),(2,2,.1),fixed=True,material=Mat)) #create assembly of spheres: sp=pack.SpherePack() sp.makeCloud(minCorner=(-1.5,-1.5,.1),maxCorner=(1.5,1.5,2),rMean=.2,rRelFuzz=.5,num=100,periodic=False) O.bodies.append([sphere(c,r,material=Mat) for c,r in sp]) print len(sp),' particles generated.' print 'Roundness coefficient without clumps is: ',O.bodies.getRoundness() #### show how to use makeClumpTemplate(): #dyad: relRadList1 = [1,1] relPosList1 = [[1,0,0],[-1,0,0]] #peanut: relRadList2 = [.5,1,.5] relPosList2 = [[1,0,0],[0,0,0],[-1,0,0]] #stick: relRadList3 = [1,1,1,1,1] relPosList3 = [[0,1,0],[0,2,0],[0,3,0],[0,4,0],[0,5,0]] templates= [] templates.append(clumpTemplate(relRadii=relRadList1,relPositions=relPosList1)) templates.append(clumpTemplate(relRadii=relRadList2,relPositions=relPosList2)) templates.append(clumpTemplate(relRadii=relRadList3,relPositions=relPosList3)) #### show how to use replaceByClumps(): #replace by 50% dyads, 30% peanuts and 10% sticks: O.bodies.replaceByClumps(templates,[.5,.3,.1]) #### show how to use getRoundness(): #create a list of all standalone spheres: standaloneList = [] for b in O.bodies: if b.isStandalone: standaloneList.append(b.id) print 'Roundness coefficient for spheres and clumps is: ',O.bodies.getRoundness() print 'Roundness coefficient just for clumps is: ',O.bodies.getRoundness(standaloneList) O.dt=1e-6 #NOTE, that after replacing some overlaps may occur. #So after replacing calm() function may be helpful: if 0: print '\nPlease wait a minute ...\n' O.engines=O.engines+[PyRunner(iterPeriod=10000,command='calm()',label='calmRunner')] O.run(1000000,True) calmRunner.dead=True print '\nPress Play button ... ' trunk-2017.01a/examples/clumps/save-load-clumps.py000066400000000000000000000037121304022710500220340ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- '''This example shows usage of save and load clumps.''' from yade import pack,export,qt,ymport #define material for all bodies: id_Mat=O.materials.append(FrictMat(young=1e6,poisson=0.3,density=1000,frictionAngle=1)) Mat=O.materials[id_Mat] #define engines: O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), NewtonIntegrator(damping=0.7,gravity=[0,0,-10]) ] #create a box: id_box = O.bodies.append(box((0,0,0),(2,2,.1),fixed=True,material=Mat)) #### show how to use appendClumped(): #create 2 clumps: clump1=O.bodies.appendClumped([\ sphere([0,0,1], material=Mat, radius=0.5),\ sphere([0.2,0,1], material=Mat, radius=0.5)\ ]) clump2=O.bodies.appendClumped([\ sphere([3,1,2], material=Mat, radius=0.5),\ sphere([3.2,1,2], material=Mat, radius=0.5)\ ]) #get clump ids: id_clump1 = clump1[0] id_clump2 = clump2[0] #definition for getting informations from all clumps: def getClumpInfo(): for b in O.bodies: if b.isClump: print 'Clump ',b.id,' has following members:' keys = b.shape.members.keys() for ii in range(0,len(keys)): print '- Body ',keys[ii] print 'inertia:',b.state.inertia print 'mass:',b.state.mass,'\n' #### show how to use addToClump(): #create a new sphere: id_new=O.bodies.append(sphere([0,0.2,1], material=Mat, radius=0.5)) #add a sphere to the clump: O.bodies.addToClump([id_new],id_clump1) #add a clump to a clump: O.bodies.addToClump([id_clump2],id_clump1) print '\nSTATE after adding the second clump to clump ------------' getClumpInfo() print "Save clumps" export.textClumps("savedClumps.txt") print "Load clumps" ymport.textClumps("savedClumps.txt", shift=Vector3(0,0,1.5)) print "After saving" getClumpInfo() O.dt=1e-6 print '\nPress Play button ... ' renderer = qt.Renderer() qt.View() trunk-2017.01a/examples/clumps/triax-basic-with-clumps.py000066400000000000000000000042101304022710500233320ustar00rootroot00000000000000# encoding: utf-8 # Copyright (C) 2012 by Bruno Chareyre # An update of the original script from Janek Kozicki from yade import pack from numpy import arange import itertools import random import yade.plot ## corners of the initial packing mn,mx=Vector3(0,0,0),Vector3(10,10,10) ## create material #0, which will be used as default O.materials.append(FrictMat(young=6e6,poisson=.4,frictionAngle=radians(5),density=2600)) O.materials.append(FrictMat(young=6e6,poisson=.4,frictionAngle=0,density=2600,label='frictionless')) d=8 # clumps for xyz in itertools.product(arange(0,d),arange(0,d),arange(0,d)): ids_spheres=O.bodies.appendClumped(pack.regularHexa(pack.inEllipsoid((mn[0]+xyz[0]*(mx[0]-mn[0])/d,mn[0]+xyz[1]*(mx[1]-mn[1])/d,mn[2]+xyz[2]*(mx[2]-mn[2])/d),(0.45+random.random()*0.1,0.45+random.random()*0.1,0.45+random.random()*0.1)),radius=0.15+random.random()*0.05,gap=0,color=[random.random(),random.random(),random.random()])) ## create walls around the packing walls=aabbWalls(material='frictionless') wallIds=O.bodies.append(walls) from yade import qt qt.Controller() qt.View() ## hope that we got the ids right?! triax=TriaxialCompressionEngine( wall_bottom_id=wallIds[2], wall_top_id=wallIds[3], wall_left_id=wallIds[0], wall_right_id=wallIds[1], wall_back_id=wallIds[4], wall_front_id=wallIds[5], internalCompaction=False, sigmaIsoCompaction=-50e3, sigmaLateralConfinement=-50e3, strainRate=0.02, frictionAngleDegree=30, StabilityCriterion = 0.01, max_vel=1, ) recorder=TriaxialStateRecorder( iterPeriod=20, file="./WallStresses_clumps", truncate=1 ) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), GlobalStiffnessTimeStepper(timestepSafetyCoefficient=0.6), triax, recorder, # you can add TriaxialStateRecorder and such here… NewtonIntegrator(damping=.4) ] #yade.plot.plots={'eps':('sigma',)} #O.saveTmp('initial'); #def addPlotData(): # yade.plot.addData({'t':O.time,'i':O.iter,'eps':strainer.strain,'sigma':strainer.avgStress}) trunk-2017.01a/examples/concrete/000077500000000000000000000000001304022710500166025ustar00rootroot00000000000000trunk-2017.01a/examples/concrete/README000066400000000000000000000007551304022710500174710ustar00rootroot00000000000000uniax.py shows uniaxiax tension/compression test on concrete specimen with optional confinement. Run using yade-multi and confined.table (see comments in that file) to run simulation with different confinement values. Run plain uniax.py to get one unconfined tension/compression simulation. Type yade.plot.plot() to see strain/stress plot during the simulation. See comments at the beginning of uniax.py for more information. The periodic.py is uniax.py, but running on a periodic sample. trunk-2017.01a/examples/concrete/confined.table000066400000000000000000000010761304022710500214040ustar00rootroot00000000000000# # Use this table with yade-multi like this: # # yade-version-multi --gnuplot confined.gnuplot confined.table uniax.py # # and watch http://localhost:9080 while it runs # # OMP_NUM_THREADS: number of threads to use (bang at the beginning: passed as environment variable) # isoPrestress: confinement (bang at the end = parameter and value will appear in the job id) # doModes: run both tension&compression only in the unconfined case, otherwise just compression # !OMP_NUM_THREADS isoPrestress! doModes 2 0 3 2 -20e6 2 2 -50e6 2 2 -100e6 2 2 -200e6 2 2 -400e6 2 trunk-2017.01a/examples/concrete/interaction-histogram.py000066400000000000000000000023711304022710500234710ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # demonstration of the yade.post2d module (see its documentation for details) # import pylab # the matlab-like interface of matplotlib pylab.ioff() import numpy import os.path # run uniax.py to get this file loadFile='/tmp/uniax-tension.yade.gz' if not os.path.exists(loadFile): raise RuntimeError("Run uniax.py first so that %s is created"%loadFile) O.load(loadFile) # axis normal to the plane in which we do the histogram axis=0 # x, i.e. plot the yz plane ax1,ax2=(axis+1)%3,(axis+2)%3 ## get the other two indices, i.e. 1 and 2 in this case angles,forces=[],[] for i in O.interactions: if not i.isReal: continue norm=i.geom.normal angle=atan(norm[ax2]/norm[ax1]) force=i.phys.normalForce.norm() angles.append(angle) forces.append(force) # easier: plain histogram #pylab.hist(angles,weights=forces,bins=20) # polar histogram pylab.figure() ## prepare data values,bins=numpy.histogram(angles,weights=forces,bins=20) ## prepare polar plot pylab.subplot(111,polar=True); ## plot bar chart, with the histogram data ### bins has one edge extra, remove it: [:-1] pylab.bar(left=bins[:-1],height=values,width=.7*pi/20); # predefined function pylab.figure() plotDirections(noShow=True).savefig('/tmp/a.pdf') pylab.show() trunk-2017.01a/examples/concrete/periodic.py000066400000000000000000000162771304022710500207670ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- from __future__ import division from yade import plot,pack import time, sys, os, copy """ A fairly complex script performing uniaxial tension-compression test on hyperboloid-shaped specimen. Most parameters of the model (and of the setup) can be read from table using yade-multi. After the simulation setup, tension loading is run and stresses are periodically saved for plotting as well as checked for getting below the maximum value so far. This indicates failure (see stopIfDamaged function). After failure in tension, the original setup is loaded anew and the sense of loading reversed. After failure in compression, strain-stress curves are saved via plot.saveGnuplot and we exit, giving some useful information like peak stresses in tension/compression. Running this script for the first time can take long time, as the specimen is prepared using triaxial compression. Next time, however, an attempt is made to load previously-generated packing (from /tmp/triaxPackCache.sqlite) and this expensive procedure is avoided. The specimen length can be specified, its diameter is half of the length and skirt of the hyperboloid is 4/5 of the width. The particle size is constant and can be specified using the sphereRadius parameter. The 3d display has displacement scaling applied, so that the fracture looks more spectacular. The scale is 1000 for tension and 100 for compression. """ # default parameters or from table readParamsFromTable(noTableOk=True, # unknownOk=True, young=24e9, poisson=.2, sigmaT=3.5e6, frictionAngle=atan(0.8), epsCrackOnset=1e-4, relDuctility = 30, intRadius=1.5, dtSafety=.4, damping=0.2, strainRateTension=10, strainRateCompression=50, # 1=tension, 2=compression (ANDed; 3=both) doModes=3, biaxial=True, # isotropic confinement (should be negative) isoPrestress=0 ) from yade.params.table import * if 'description' in O.tags.keys(): O.tags['id']=O.tags['id']+O.tags['description'] packingFile='periCube.pickle' # got periodic packing? Memoization not (yet) supported, so just generate it if there is not the right file # Save and reuse next time. if not os.path.exists(packingFile): sp=pack.randomPeriPack(radius=.05e-3,rRelFuzz=0.,initSize=Vector3(1.5e-3,1.5e-3,1.5e-3)) dd=dict(cell=(sp.cellSize[0],sp.cellSize[1],sp.cellSize[2]),spheres=sp.toList()) import cPickle as pickle pickle.dump(dd,open(packingFile,'w')) # # load the packing (again); # import cPickle as pickle concreteId=O.materials.append(CpmMat(young=young, frictionAngle=frictionAngle, density=4800, sigmaT=sigmaT, relDuctility=relDuctility, epsCrackOnset=epsCrackOnset, poisson=poisson, isoPrestress=isoPrestress)) sphDict=pickle.load(open(packingFile)) from yade import pack sp=pack.SpherePack() sp.fromList(sphDict['spheres']) sp.cellSize=sphDict['cell'] import numpy avgRadius=numpy.average([r for c,r in sp]) O.bodies.append([sphere(c,r,color=randomColor()) for c,r in sp]) O.periodic=True O.cell.setBox(sp.cellSize) axis=2 ax1=(axis+1)%3 ax2=(axis+2)%3 O.dt=dtSafety*PWaveTimeStep() import yade.plot as yp O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=intRadius,label='is2aabb')],verletDist=.05*avgRadius), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=intRadius,label='ss2d3dg')], [Ip2_CpmMat_CpmMat_CpmPhys()], [Law2_ScGeom_CpmPhys_Cpm()], ), NewtonIntegrator(damping=damping,label='newton'), CpmStateUpdater(realPeriod=1,label='updater'), # #UniaxialStrainer(strainRate=strainRateTension,axis=axis,asymmetry=0,posIds=posIds,negIds=negIds,crossSectionArea=crossSectionArea,blockDisplacements=False,blockRotations=False,setSpeeds=setSpeeds,label='strainer'), # PeriTriaxController(goal=[1,1,1],stressMask=( (7^(1<0: O.wait(); O.loadTmp('initial') print "Reversing plot data"; plot.reverseData() maxStrainRate=Vector3(1,1,1); goal=Vector3(1,1,1); if not biaxial: # uniaxial maxStrainRate[axis]=abs(strainRateTension) if mode=='tension' else abs(strainRateCompression) maxStrainRate[ax1]=maxStrainRate[ax2]=1000*maxStrainRate[axis] goal[axis]=1 if mode=='tension' else -1; else: maxStrainRate[axis]=abs(strainRateTension) if mode=='tension' else abs(strainRateCompression) maxStrainRate[ax1]=maxStrainRate[axis] maxStrainRate[ax2]=1000*maxStrainRate[axis] goal[axis]=1 if mode=='tension' else -1; goal[ax1]=goal[axis] strainer.maxStrainRate=maxStrainRate strainer.goal=goal try: from yade import qt renderer=qt.Renderer() renderer.scaleDisplacements=True renderer.displacementScale=(1000,1000,1000) if mode=='tension' else (100,100,100) except ImportError: pass print "init done, will now run." O.step(); O.step(); # to create initial contacts # now reset the interaction radius and go ahead ss2d3dg.interactionDetectionFactor=-1. is2aabb.aabbEnlargeFactor=-1. O.run() def stopIfDamaged(): global mode if O.iter<2 or not plot.data.has_key('sigma'): return # do nothing at the very beginning sigma,eps=plot.data['sigma'],plot.data['eps'] extremum=max(sigma) if (strainer.maxStrainRate>0) else min(sigma) # FIXME: only temporary, should be .5 minMaxRatio=0.5 if mode=='tension' else 0.5 if extremum==0: return print O.tags['id'],mode,strainer.strain[axis],sigma[-1] #print 'strain',strainer['strain'],'stress',strainer['stress'] import sys; sys.stdout.flush() if abs(sigma[-1]/extremum)6e-3: if mode=='tension' and doModes & 2: # only if compression is enabled mode='compression' #O.save('/tmp/uniax-tension.xml.bz2') print "Damaged, switching to compression... "; O.pause() # important! initTest must be launched in a separate thread; # otherwise O.load would wait for the iteration to finish, # but it would wait for initTest to return and deadlock would result import thread; thread.start_new_thread(initTest,()) return else: print "Damaged, stopping." ft,fc=max(sigma),min(sigma) print 'Strengths fc=%g, ft=%g, |fc/ft|=%g'%(fc,ft,abs(fc/ft)) title=O.tags['description'] if 'description' in O.tags.keys() else O.tags['params'] print 'gnuplot',plot.saveGnuplot(O.tags['id'],title=title) print 'Bye.' # O.pause() sys.exit(0) def addPlotData(): yade.plot.addData(t=O.time,i=O.iter,eps=strainer.strain[axis],eps_=strainer.strain[axis],sigma=strainer.stress[axis]+isoPrestress,eps1=strainer.strain[ax1],eps2=strainer.strain[ax2],sig1=strainer.stress[ax1],sig2=strainer.stress[ax2],relResid=updater.avgRelResidual) initTest() waitIfBatch() trunk-2017.01a/examples/concrete/triax.py000066400000000000000000000160521304022710500203070ustar00rootroot00000000000000################################################################################ # # Triaxial test. Axial strain rate is prescribed and transverse prestress. # Test is possible on prism or cylinder # An independent c++ engine may be created from this script in the future. # ################################################################################ from yade import pack, plot import os # default parameters or from table readParamsFromTable(noTableOk=True, # type of test ['cyl','cube'] testType = 'cyl', # material parameters young = 20e9, poisson = .2, frictionAngle = 1.2, sigmaT = 1.5e6, epsCrackOnset = 1e-4, relDuctility = 30, # prestress preStress = -3e6, # axial strain rate strainRate = -100, # assamlby parameters rParticle = .075e-3, # width = 2e-3, height = 5e-3, bcCoeff = 5, # facets division nw = 24, nh = 15, # output specifications fileName = 'test', exportDir = '/tmp', runGnuplot = False, runInGui = True, ) from yade.params.table import * assert testType in ['cyl','cube'] # materials concMat = O.materials.append(CpmMat( young=young,frictionAngle=frictionAngle,poisson=poisson,sigmaT=sigmaT, epsCrackOnset=epsCrackOnset,relDuctility=relDuctility )) frictMat = O.materials.append(FrictMat( young=young,poisson=poisson,frictionAngle=frictionAngle )) # spheres pred = pack.inCylinder((0,0,0),(0,0,height),.5*width) if testType=='cyl' else pack.inAlignedBox((-.5*width,-.5*width,0),(.5*width,.5*width,height)) if testType=='cube' else None sp=SpherePack() sp = pack.randomDensePack(pred,spheresInCell=2000,radius=rParticle,memoizeDb='/tmp/triaxTestOnCylinder.sqlite',returnSpherePack=True) spheres=sp.toSimulation(color=(0,1,1),material=concMat) # bottom and top of specimen. Will have prescribed velocity bot = [O.bodies[s] for s in spheres if O.bodies[s].state.pos[2]height-rParticle*bcCoeff] vel = strainRate*(height-rParticle*2*bcCoeff) for s in bot: s.shape.color = (1,0,0) s.state.blockedDOFs = 'xyzXYZ' s.state.vel = (0,0,-vel) for s in top: s.shape.color = Vector3(0,1,0) s.state.blockedDOFs = 'xyzXYZ' s.state.vel = (0,0,vel) # facets facets = [] if testType == 'cyl': rCyl2 = .5*width / cos(pi/float(nw)) for r in xrange(nw): for h in xrange(nh): v1 = Vector3( rCyl2*cos(2*pi*(r+0)/float(nw)), rCyl2*sin(2*pi*(r+0)/float(nw)), height*(h+0)/float(nh) ) v2 = Vector3( rCyl2*cos(2*pi*(r+1)/float(nw)), rCyl2*sin(2*pi*(r+1)/float(nw)), height*(h+0)/float(nh) ) v3 = Vector3( rCyl2*cos(2*pi*(r+1)/float(nw)), rCyl2*sin(2*pi*(r+1)/float(nw)), height*(h+1)/float(nh) ) v4 = Vector3( rCyl2*cos(2*pi*(r+0)/float(nw)), rCyl2*sin(2*pi*(r+0)/float(nw)), height*(h+1)/float(nh) ) f1 = facet((v1,v2,v3),color=(0,0,1),material=frictMat) f2 = facet((v1,v3,v4),color=(0,0,1),material=frictMat) facets.extend((f1,f2)) elif testType == 'cube': nw2 = nw/4 for r in xrange(nw2): for h in xrange(nh): v11 = Vector3( -.5*width + (r+0)*width/nw2, -.5*width, height*(h+0)/float(nh) ) v12 = Vector3( -.5*width + (r+1)*width/nw2, -.5*width, height*(h+0)/float(nh) ) v13 = Vector3( -.5*width + (r+1)*width/nw2, -.5*width, height*(h+1)/float(nh) ) v14 = Vector3( -.5*width + (r+0)*width/nw2, -.5*width, height*(h+1)/float(nh) ) f11 = facet((v11,v12,v13),color=(0,0,1),material=frictMat) f12 = facet((v11,v13,v14),color=(0,0,1),material=frictMat) v21 = Vector3( +.5*width, -.5*width + (r+0)*width/nw2, height*(h+0)/float(nh) ) v22 = Vector3( +.5*width, -.5*width + (r+1)*width/nw2, height*(h+0)/float(nh) ) v23 = Vector3( +.5*width, -.5*width + (r+1)*width/nw2, height*(h+1)/float(nh) ) v24 = Vector3( +.5*width, -.5*width + (r+0)*width/nw2, height*(h+1)/float(nh) ) f21 = facet((v21,v22,v23),color=(0,0,1),material=frictMat) f22 = facet((v21,v23,v24),color=(0,0,1),material=frictMat) v31 = Vector3( +.5*width - (r+0)*width/nw2, +.5*width, height*(h+0)/float(nh) ) v32 = Vector3( +.5*width - (r+1)*width/nw2, +.5*width, height*(h+0)/float(nh) ) v33 = Vector3( +.5*width - (r+1)*width/nw2, +.5*width, height*(h+1)/float(nh) ) v34 = Vector3( +.5*width - (r+0)*width/nw2, +.5*width, height*(h+1)/float(nh) ) f31 = facet((v31,v32,v33),color=(0,0,1),material=frictMat) f32 = facet((v31,v33,v34),color=(0,0,1),material=frictMat) v41 = Vector3( -.5*width, +.5*width - (r+0)*width/nw2, height*(h+0)/float(nh) ) v42 = Vector3( -.5*width, +.5*width - (r+1)*width/nw2, height*(h+0)/float(nh) ) v43 = Vector3( -.5*width, +.5*width - (r+1)*width/nw2, height*(h+1)/float(nh) ) v44 = Vector3( -.5*width, +.5*width - (r+0)*width/nw2, height*(h+1)/float(nh) ) f41 = facet((v41,v42,v43),color=(0,0,1),material=frictMat) f42 = facet((v41,v43,v44),color=(0,0,1),material=frictMat) facets.extend((f11,f12,f21,f22,f31,f32,f41,f42)) O.bodies.append(facets) mass = O.bodies[0].state.mass for f in facets: f.state.mass = mass f.state.blockedDOFs = 'XYZz' # plots plot.plots = { 'e':('s',), } def plotAddData(): f1 = sum(O.forces.f(b.id)[2] for b in top) f2 = sum(O.forces.f(b.id)[2] for b in bot) f = .5*(f2-f1) s = f/(pi*.25*width*width) if testType=='cyl' else f/(width*width) if testType=='cube' else None e = (top[0].state.displ()[2] - bot[0].state.displ()[2]) / (height-rParticle*2*bcCoeff) plot.addData( i = O.iter, s = s, e = e, ) # apply prestress to facets def addForces(): for f in facets: n = f.shape.normal a = f.shape.area O.forces.addF(f.id,preStress*a*n) # stop condition and exit of the simulation def stopIfDamaged(maxEps=5e-3): extremum = max(abs(s) for s in plot.data['s']) s = abs(plot.data['s'][-1]) e = abs(plot.data['e'][-1]) if O.iter < 1000 or s > .5*extremum and e < maxEps: return f = os.path.join(exportDir,fileName) print 'gnuplot',plot.saveGnuplot(f,term='png') if runGnuplot: import subprocess os.chdir(exportDir) subprocess.Popen(['gnuplot',f+'.gnuplot']).wait() print 'Simulation finished' O.pause() #sys.exit(0) # results in some threading exception O.dt=.5*utils.PWaveTimeStep() enlargeFactor=1.5 O.engines=[ ForceResetter(), InsertionSortCollider([ Bo1_Sphere_Aabb(aabbEnlargeFactor=enlargeFactor,label='bo1s'), Bo1_Facet_Aabb() ]), InteractionLoop( [ Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=enlargeFactor,label='ss2d3dg'), Ig2_Facet_Sphere_ScGeom(), ], [ Ip2_CpmMat_CpmMat_CpmPhys(cohesiveThresholdIter=O.iter+5), Ip2_FrictMat_CpmMat_FrictPhys(), Ip2_FrictMat_FrictMat_FrictPhys(), ], [ Law2_ScGeom_CpmPhys_Cpm(), Law2_ScGeom_FrictPhys_CundallStrack(), ], ), PyRunner(iterPeriod=1,command="addForces()"), NewtonIntegrator(damping=.3), CpmStateUpdater(iterPeriod=50,label='cpmStateUpdater'), PyRunner(command='plotAddData()',iterPeriod=10), PyRunner(iterPeriod=50,command='stopIfDamaged()'), ] # run one step O.step() # reset interaction detection enlargement bo1s.aabbEnlargeFactor=ss2d3dg.interactionDetectionFactor=1.0 # initialize auto-updated plot if runInGui: plot.plot() try: from yade import qt renderer=qt.Renderer() # uncomment following line to exagerate displacement #renderer.dispScale=(100,100,100) except: pass # run O.run() trunk-2017.01a/examples/concrete/uniax-post.py000066400000000000000000000033561304022710500212720ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # # demonstration of the yade.post2d module (see its documentation for details) # from yade import post2d import pylab # the matlab-like interface of matplotlib loadFile='/tmp/uniax-tension.yade.gz' if not os.path.exists(loadFile): raise RuntimeError("Run uniax.py first so that %s is created"%loadFile) O.load(loadFile) # flattener that project to the xz plane flattener=post2d.AxisFlatten(useRef=False,axis=1) # return scalar given a Body instance extractDmg=lambda b: b.state.normDmg # will call flattener.planar implicitly # the same as: extractVelocity=lambda b: flattener.planar(b,b.state['vel']) extractVelocity=lambda b: b.state.vel # create new figure pylab.figure() # plot raw damage post2d.plot(post2d.data(extractDmg,flattener)) pylab.suptitle('damage') # plot smooth damage into new figure pylab.figure(); ax,map=post2d.plot(post2d.data(extractDmg,flattener,stDev=2e-3)) pylab.suptitle('smooth damage') # show color scale pylab.colorbar(map,orientation='horizontal') # shear stress NOT WORKING (AttributeError: 'CpmState' object has no attribute 'tau' and no 'sigma'): #pylab.figure() #post2d.plot(post2d.data(lambda b: b.state.sigma,flattener)) #pylab.suptitle('sigma') #pylab.figure() #post2d.plot(post2d.data(lambda b: b.state.tau,flattener,stDev=2e-3)) #pylab.suptitle('smooth tau (in grid)') # raw velocity (vector field) plot pylab.figure(); post2d.plot(post2d.data(extractVelocity,flattener)) pylab.suptitle('velocity') # smooth velocity plot; data are sampled at regular grid pylab.figure(); ax,map=post2d.plot(post2d.data(extractVelocity,flattener,stDev=1e-3)) pylab.suptitle('smooth velocity') # save last (current) figure to file pylab.gcf().savefig('/tmp/foo.png') # show the figures pylab.show() trunk-2017.01a/examples/concrete/uniax.py000066400000000000000000000160161304022710500203040ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- from __future__ import division from yade import plot,pack,timing import time, sys, os, copy #import matplotlib #matplotlib.rc('text',usetex=True) #matplotlib.rc('text.latex',preamble=r'\usepackage{concrete}\usepackage{euler}') """ A fairly complex script performing uniaxial tension-compression test on hyperboloid-shaped specimen. Most parameters of the model (and of the setup) can be read from table using yade-multi. After the simulation setup, tension loading is run and stresses are periodically saved for plotting as well as checked for getting below the maximum value so far. This indicates failure (see stopIfDamaged function). After failure in tension, the original setup is loaded anew and the sense of loading reversed. After failure in compression, strain-stress curves are saved via plot.saveGnuplot and we exit, giving some useful information like peak stresses in tension/compression. Running this script for the first time can take long time, as the specimen is prepared using triaxial compression. Next time, however, an attempt is made to load previously-generated packing (from /tmp/triaxPackCache.sqlite) and this expensive procedure is avoided. The specimen length can be specified, its diameter is half of the length and skirt of the hyperboloid is 4/5 of the width. The particle size is constant and can be specified using the sphereRadius parameter. The 3d display has displacement scaling applied, so that the fracture looks more spectacular. The scale is 1000 for tension and 100 for compression. """ # default parameters or from table readParamsFromTable(noTableOk=True, # unknownOk=True, young=24e9, poisson=.2, sigmaT=3.5e6, frictionAngle=atan(0.8), epsCrackOnset=1e-4, relDuctility=30, intRadius=1.5, dtSafety=.8, damping=0.4, strainRateTension=.05, strainRateCompression=.5, setSpeeds=True, # 1=tension, 2=compression (ANDed; 3=both) doModes=3, specimenLength=.15, sphereRadius=3.5e-3, # isotropic confinement (should be negative) isoPrestress=0, ) from yade.params.table import * if 'description' in O.tags.keys(): O.tags['id']=O.tags['id']+O.tags['description'] # make geom; the dimensions are hard-coded here; could be in param table if desired # z-oriented hyperboloid, length 20cm, diameter 10cm, skirt 8cm # using spheres 7mm of diameter concreteId=O.materials.append(CpmMat(young=young,frictionAngle=frictionAngle,poisson=poisson,density=4800,sigmaT=sigmaT,relDuctility=relDuctility,epsCrackOnset=epsCrackOnset,isoPrestress=isoPrestress)) sps=SpherePack() sp=pack.randomDensePack(pack.inHyperboloid((0,0,-.5*specimenLength),(0,0,.5*specimenLength),.25*specimenLength,.17*specimenLength),spheresInCell=2000,radius=sphereRadius,memoizeDb='/tmp/triaxPackCache.sqlite',returnSpherePack=True) #sp=pack.randomDensePack(pack.inAlignedBox((-.25*specimenLength,-.25*specimenLength,-.5*specimenLength),(.25*specimenLength,.25*specimenLength,.5*specimenLength)),spheresInCell=2000,radius=sphereRadius,memoizeDb='/tmp/triaxPackCache.sqlite',returnSpherePack=True) sp.toSimulation(material=concreteId) bb=uniaxialTestFeatures() negIds,posIds,axis,crossSectionArea=bb['negIds'],bb['posIds'],bb['axis'],bb['area'] O.dt=dtSafety*PWaveTimeStep() print 'Timestep',O.dt mm,mx=[pt[axis] for pt in aabbExtrema()] coord_25,coord_50,coord_75=mm+.25*(mx-mm),mm+.5*(mx-mm),mm+.75*(mx-mm) area_25,area_50,area_75=approxSectionArea(coord_25,axis),approxSectionArea(coord_50,axis),approxSectionArea(coord_75,axis) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=intRadius,label='is2aabb'),],verletDist=.05*sphereRadius), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=intRadius,label='ss2sc')], [Ip2_CpmMat_CpmMat_CpmPhys()], [Law2_ScGeom_CpmPhys_Cpm()], ), NewtonIntegrator(damping=damping,label='damper'), CpmStateUpdater(realPeriod=.5), UniaxialStrainer(strainRate=strainRateTension,axis=axis,asymmetry=0,posIds=posIds,negIds=negIds,crossSectionArea=crossSectionArea,blockDisplacements=False,blockRotations=False,setSpeeds=setSpeeds,label='strainer'), PyRunner(virtPeriod=1e-6/strainRateTension,realPeriod=1,command='addPlotData()',label='plotDataCollector',initRun=True), PyRunner(realPeriod=4,command='stopIfDamaged()',label='damageChecker'), ] #O.miscParams=[Gl1_CpmPhys(dmgLabel=False,colorStrain=False,epsNLabel=False,epsT=False,epsTAxes=False,normal=False,contactLine=True)] # plot stresses in ¼, ½ and ¾ if desired as well; too crowded in the graph that includes confinement, though plot.plots={'eps':('sigma',)} #,'sigma.50')},'t':('eps')} #'sigma.25','sigma.50','sigma.75')} O.saveTmp('initial'); O.timingEnabled=False global mode mode='tension' if doModes & 1 else 'compression' def initTest(): global mode print "init" if O.iter>0: O.wait(); O.loadTmp('initial') print "Reversing plot data"; plot.reverseData() else: plot.plot(subPlots=False) strainer.strainRate=abs(strainRateTension) if mode=='tension' else -abs(strainRateCompression) try: from yade import qt renderer=qt.Renderer() renderer.dispScale=(1000,1000,1000) if mode=='tension' else (100,100,100) except ImportError: pass print "init done, will now run." O.step(); # to create initial contacts # now reset the interaction radius and go ahead ss2sc.interactionDetectionFactor=1. is2aabb.aabbEnlargeFactor=1. O.run() def stopIfDamaged(): global mode if O.iter<2 or not plot.data.has_key('sigma'): return # do nothing at the very beginning sigma,eps=plot.data['sigma'],plot.data['eps'] extremum=max(sigma) if (strainer.strainRate>0) else min(sigma) minMaxRatio=0.5 if mode=='tension' else 0.5 if extremum==0: return import sys; sys.stdout.flush() if abs(sigma[-1]/extremum)(5e-3 if isoPrestress==0 else 5e-2): if mode=='tension' and doModes & 2: # only if compression is enabled mode='compression' O.save('/tmp/uniax-tension.yade.gz') print "Saved /tmp/uniax-tension.yade.gz (for use with interaction-histogram.py and uniax-post.py)" print "Damaged, switching to compression... "; O.pause() # important! initTest must be launched in a separate thread; # otherwise O.load would wait for the iteration to finish, # but it would wait for initTest to return and deadlock would result import thread; thread.start_new_thread(initTest,()) return else: print "Damaged, stopping." ft,fc=max(sigma),min(sigma) print 'Strengths fc=%g, ft=%g, |fc/ft|=%g'%(fc,ft,abs(fc/ft)) title=O.tags['description'] if 'description' in O.tags.keys() else O.tags['params'] print 'gnuplot',plot.saveGnuplot(O.tags['id'],title=title) print 'Bye.' O.pause() #sys.exit(0) # results in some threading exception def addPlotData(): yade.plot.addData({'t':O.time,'i':O.iter,'eps':strainer.strain,'sigma':strainer.avgStress+isoPrestress, 'sigma.25':forcesOnCoordPlane(coord_25,axis)[axis]/area_25+isoPrestress, 'sigma.50':forcesOnCoordPlane(coord_50,axis)[axis]/area_50+isoPrestress, 'sigma.75':forcesOnCoordPlane(coord_75,axis)[axis]/area_75+isoPrestress, }) plot.plot(subPlots=False) #O.run() initTest() waitIfBatch() trunk-2017.01a/examples/conveyor/000077500000000000000000000000001304022710500166445ustar00rootroot00000000000000trunk-2017.01a/examples/conveyor/conveyor.geo000066400000000000000000000010621304022710500212030ustar00rootroot00000000000000acc = 100.0; wid = 500.0; len = 1500.0; h = 300.0; Point(1) = {0, 0, -wid/5.0, acc}; Point(2) = {-wid, 0, 0, acc}; Point(3) = {wid, 0, 0, acc}; Point(4) = {wid/1.1, 0, -wid/10.0, acc}; Point(5) = {-wid/1.1, 0, -wid/10.0, acc}; Point(6) = {wid/2.0, 0, +wid/10.0, acc}; Point(7) = {-wid/2.0, 0, +wid/10.0, acc}; Point(8) = {-wid, 0, h, acc}; Point(9) = {wid, 0, h, acc}; Spline(1) = {2, 5, 7, 1, 6, 4, 3}; Line(2) = {8, 2}; Line(3) = {3, 9}; Extrude {0, len, 0} { Line{2, 1, 3}; } Line(16) = {8, 9}; Line Loop(17) = {16, -3, -1, -2}; Plane Surface(18) = {17}; trunk-2017.01a/examples/conveyor/conveyor.mesh000066400000000000000000001404401304022710500213710ustar00rootroot00000000000000 MeshVersionFormatted 2 Dimension 3 Vertices 441 0 0 -100 1 -500 0 0 2 500 0 0 3 454.54545454545 0 -50 4 -454.54545454545 0 -50 5 250 0 50 6 -250 0 50 7 -500 0 300 8 500 0 300 9 -500 1500 300 10 -500 1500 0 11 -454.54545454545 1500 -50 13 -250 1500 50 14 0 1500 -100 15 250 1500 50 16 454.54545454545 1500 -50 17 500 1500 0 18 500 1500 300 20 -439.88134513266 0 -44.523673195083 1 -362.83621367891 0 7.7663721559698 1 -279.5676899846 0 48.28686863902 1 -192.63906004976 0 24.407224564095 1 -120.43749167986 0 -34.43426658243 1 -44.683026495718 0 -88.284497185875 1 44.683026492925 0 -88.284497187232 1 120.43749167789 0 -34.434266584101 1 192.63906004808 0 24.407224562925 1 279.56768998311 0 48.286868639328 1 362.83621367809 0 7.7663721565244 1 439.88134513224 0 -44.523673194873 1 -500 0 199.99999999993 2 -500 0 100.00000000007 2 500 0 99.999999999799 3 500 0 199.99999999973 3 -500 1500 199.99999999993 4 -500 1500 100.00000000007 4 -500 99.99999999974 300 5 -500 199.99999999954 300 5 -500 299.9999999991 300 5 -500 399.99999999856 300 5 -500 499.99999999802 300 5 -500 599.99999999783 300 5 -500 699.99999999767 300 5 -500 799.99999999751 300 5 -500 899.99999999735 300 5 -500 999.99999999719 300 5 -500 1099.9999999976 300 5 -500 1199.9999999982 300 5 -500 1299.9999999988 300 5 -500 1399.9999999994 300 5 -500 99.99999999974 0 6 -500 199.99999999954 0 6 -500 299.9999999991 0 6 -500 399.99999999856 0 6 -500 499.99999999802 0 6 -500 599.99999999783 0 6 -500 699.99999999767 0 6 -500 799.99999999751 0 6 -500 899.99999999735 0 6 -500 999.99999999719 0 6 -500 1099.9999999976 0 6 -500 1199.9999999982 0 6 -500 1299.9999999988 0 6 -500 1399.9999999994 0 6 -439.88134513266 1500 -44.523673195083 8 -362.83621367891 1500 7.7663721559698 8 -279.5676899846 1500 48.28686863902 8 -192.63906004976 1500 24.407224564095 8 -120.43749167986 1500 -34.43426658243 8 -44.683026495718 1500 -88.284497185875 8 44.683026492925 1500 -88.284497187232 8 120.43749167789 1500 -34.434266584101 8 192.63906004808 1500 24.407224562925 8 279.56768998311 1500 48.286868639328 8 362.83621367809 1500 7.7663721565244 8 439.88134513224 1500 -44.523673194873 8 500 99.99999999974 0 10 500 199.99999999954 0 10 500 299.9999999991 0 10 500 399.99999999856 0 10 500 499.99999999802 0 10 500 599.99999999783 0 10 500 699.99999999767 0 10 500 799.99999999751 0 10 500 899.99999999735 0 10 500 999.99999999719 0 10 500 1099.9999999976 0 10 500 1199.9999999982 0 10 500 1299.9999999988 0 10 500 1399.9999999994 0 10 500 1500 99.999999999799 12 500 1500 199.99999999973 12 500 99.99999999974 300 14 500 199.99999999954 300 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PhysicalParameters Density=1000 frictionAngle=0.4 tc = 0.001 en = 0.3 es = 0.3 ## Import wall's geometry mat=O.materials.append(ViscElMat(density=Density,frictionAngle=frictionAngle,tc=tc,en=en,et=es)) sp=pack.SpherePack() sp.makeCloud((-0.3,0.05,0.05),(0.3,0.7,0.5),rMean=0.03, rRelFuzz=0.001) particles=O.bodies.append([sphere(c,r,mask=3) for c,r in sp]) from yade import ymport fctIds= O.bodies.append(ymport.gmsh('conveyor.mesh',scale=0.001,color=(1,0,0))) voxIds= O.bodies.append(utils.geom.facetBunker(center=[0,1.5,-0.7],dBunker=1.1, dOutput=0.2,hBunker=0.2,hOutput=0.2,hPipe=0.1, mask=5)) for i in fctIds: O.bodies[i].state.vel=Vector3(0,0.2,0) # Set conveyor velocity ## Timestep O.dt=.2*tc ## Engines O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0,gravity=[0,0,-9.81], mask=2), DomainLimiter(lo=(-0.6,0.0,-1.0),hi=(0.6,2.0,1.0),iterPeriod=200), ] from yade import qt qt.View() #O.saveTmp() #O.run() trunk-2017.01a/examples/cylinders/000077500000000000000000000000001304022710500167745ustar00rootroot00000000000000trunk-2017.01a/examples/cylinders/bendingbeams.py000066400000000000000000000044231304022710500217670ustar00rootroot00000000000000# encoding: utf-8 "An example showing various bending beams." from yade.gridpfacet import * #### Parameter #### L=10. # length of the beam n=12 # number of nodes used to generate the beam r=L/50. # radius of the beam element #### Engines #### O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_GridConnection_Aabb()]), InteractionLoop( [Ig2_GridNode_GridNode_GridNodeGeom6D()], [Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=False)], [Law2_ScGeom6D_CohFrictPhys_CohesionMoment()] ), NewtonIntegrator(gravity=(0,0,-10),damping=0.5,label='newton') ] #### Create materials and set different properties #### O.materials.append(CohFrictMat(young=1e6,poisson=0.3,density=1e1,frictionAngle=10,normalCohesion=1e7,shearCohesion=1e7,momentRotationLaw=False,label='mat1')) O.materials.append(CohFrictMat(young=1e6,poisson=0.3,density=1e1,frictionAngle=10,normalCohesion=1e7,shearCohesion=1e7,momentRotationLaw=True,label='mat2')) O.materials.append(CohFrictMat(young=3e6,poisson=0.3,density=1e1,frictionAngle=10,normalCohesion=1e7,shearCohesion=1e7,momentRotationLaw=True,label='mat3')) O.materials.append(CohFrictMat(young=1e7,poisson=0.3,density=1e1,frictionAngle=10,normalCohesion=1e7,shearCohesion=1e7,momentRotationLaw=True,label='mat4')) #### Vertices #### vertices1=[] vertices2=[] vertices3=[] vertices4=[] for i in range(0,n): vertices1.append( [i*L/n,0,0] ) vertices2.append( [i*L/n,1,0] ) vertices3.append( [i*L/n,2,0] ) vertices4.append( [i*L/n,3,0] ) #### Create cylinder connections #### nodesIds=[] cylIds=[] cylinderConnection(vertices1,r,nodesIds,cylIds,color=[1,0,0],highlight=False,intMaterial='mat1') cylinderConnection(vertices2,r,nodesIds,cylIds,color=[0,1,0],highlight=False,intMaterial='mat2') cylinderConnection(vertices3,r,nodesIds,cylIds,color=[0,0,1],highlight=False,intMaterial='mat3') cylinderConnection(vertices4,r,nodesIds,cylIds,color=[1,1,1],highlight=False,intMaterial='mat4') #### Set boundary conditions #### for i in range(0,4): O.bodies[nodesIds[i*n]].dynamic=False # O.bodies[nodesIds[i*n]].state.blockedDOFs='xyzXYZ' # O.bodies[nodesIds[i*n]].state.blockedDOFs='xyz' #### For viewing #### from yade import qt qt.View() #### Set a time step #### O.dt=1e-05 #### Allows to reload the simulation #### O.saveTmp() trunk-2017.01a/examples/cylinders/cylinder-cylinder.py000066400000000000000000000046641304022710500230000ustar00rootroot00000000000000# encoding: utf-8 "An example showing how to create two cylinders which are interacting." from yade.gridpfacet import * #### Parameter #### L=1. # length of the cylinder element r=0.1 # radius of the cylinder element phi=30. # friction angle E=1e6 # Young's modulus #### Engines #### O.engines=[ ForceResetter(), InsertionSortCollider([ Bo1_GridConnection_Aabb(), ]), InteractionLoop([ Ig2_GridNode_GridNode_GridNodeGeom6D(), Ig2_GridConnection_GridConnection_GridCoGridCoGeom(), ], [ Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=False), # internal cylinder physics Ip2_FrictMat_FrictMat_FrictPhys() # physics for external interactions, i.e., cylinder-cylinder interaction ], [ Law2_ScGeom6D_CohFrictPhys_CohesionMoment(), # contact law for "internal" cylinder forces Law2_GridCoGridCoGeom_FrictPhys_CundallStrack() # contact law for cylinder-cylinder interaction ] ), NewtonIntegrator(gravity=(-0.,0,-10),damping=0.5,label='newton'), ] #### Creat materials #### O.materials.append( CohFrictMat( young=E,poisson=0.3,density=1000,frictionAngle=radians(phi),normalCohesion=1e10,shearCohesion=1e10,momentRotationLaw=True,label='cMat' ) ) # material to create the gridConnections O.materials.append( FrictMat( young=E,poisson=0.3,density=1000,frictionAngle=radians(phi),label='fMat' ) ) # material for general interactions #### Create cylinders #### nodesIds=[] cylIds=[] cylinder((0,0,0),(L,0,0),radius=r,nodesIds=nodesIds,cylIds=cylIds, fixed=True,color=[1,0,0],intMaterial='cMat',extMaterial='fMat') cylinder((L/4,2*L/3,L),(L/4,-L/3,L),radius=r,nodesIds=nodesIds,cylIds=cylIds, fixed=False,color=[0,1,0],intMaterial='cMat',extMaterial='fMat') cylinder((0,2*L/3,L),(0,-L/3,L),radius=r,nodesIds=nodesIds,cylIds=cylIds, fixed=False,color=[0,1,0],intMaterial='cMat',extMaterial='fMat') cylinder((L/2,L/2,L),(L/2,-L/2,L),radius=r,nodesIds=nodesIds,cylIds=cylIds, fixed=False,color=[0,1,1],intMaterial='cMat',extMaterial='fMat') cylinder((3*L/4,L/3,L),(3*L/4,-2*L/3,L),radius=r,nodesIds=nodesIds,cylIds=cylIds, fixed=False,color=[0,0,1],intMaterial='cMat',extMaterial='fMat') cylinder((L,L/3,L),(L,-2*L/3,L),radius=r,nodesIds=nodesIds,cylIds=cylIds, fixed=False,color=[0,0,1],intMaterial='cMat',extMaterial='fMat') #### For viewing #### from yade import qt qt.View() Gl1_Sphere.stripes=True #### Set a time step #### O.dt=1e-06 #### Allows to reload the simulation #### O.saveTmp() trunk-2017.01a/examples/cylinders/cylinderconnection-roots.py000066400000000000000000000065731304022710500244160ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- "Beam-like behaviour with cylinderConnections for roots interaction with spheres." from yade import pack from yade.gridpfacet import * #### Parameter #### young=4.0e6 poisson=3 density=1e3 frictionAngle1=radians(15) frictionAngle2=radians(15) frictionAngle3=radians(15) #### Engines #### O.engines=[ ForceResetter(), InsertionSortCollider([ Bo1_Box_Aabb(), Bo1_Sphere_Aabb(), Bo1_GridConnection_Aabb(), ]), InteractionLoop([ Ig2_Sphere_Sphere_ScGeom(), Ig2_Box_Sphere_ScGeom(), Ig2_GridNode_GridNode_GridNodeGeom6D(), Ig2_Sphere_GridConnection_ScGridCoGeom(), Ig2_GridConnection_GridConnection_GridCoGridCoGeom() ], [ Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=False), # internal cylinder physics Ip2_FrictMat_FrictMat_FrictPhys() # physics for external interactions, i.e., cylinder-cylinder, sphere-sphere, cylinder-sphere ], [ Law2_ScGeom_FrictPhys_CundallStrack(), # contact law for sphere-sphere Law2_ScGridCoGeom_FrictPhys_CundallStrack(), # contact law for cylinder-sphere Law2_ScGeom6D_CohFrictPhys_CohesionMoment(), # contact law for "internal" cylinder forces Law2_GridCoGridCoGeom_FrictPhys_CundallStrack() # contact law for cylinder-cylinder interaction ] ), GlobalStiffnessTimeStepper(timestepSafetyCoefficient=0.1,label='ts'), NewtonIntegrator(gravity=(1,-9.81,0),damping=0.5,label='newton'), ] #### Spheres #### O.materials.append(FrictMat(young=4.0e6,poisson=0.5,frictionAngle=frictionAngle1,density=1600,label='spheremat')) Ns=90 sp=pack.SpherePack() if os.path.exists("cloud4cylinders"+`Ns`): print "loading spheres from file" sp.load("cloud4cylinders"+`Ns`) else: print "generating spheres" Ns=sp.makeCloud(Vector3(-0.3,0.2,-1.0),Vector3(+0.3,+0.5,+1.0),-1,.2,Ns,False,0.8) sp.save("cloud4cylinders"+`Ns`) O.bodies.append([sphere(center,rad,material='spheremat') for center,rad in sp]) #### Walls #### O.materials.append(FrictMat(young=1.0e6,poisson=0.2,density=2.60e3,frictionAngle=frictionAngle2,label='wallmat')) walls=aabbWalls((Vector3(-0.3,-0.15,-1),Vector3(+0.3,+1.0,+1)),thickness=.1,material='wallmat') wallIds=O.bodies.append(walls) #Assemble cylinders in sinusoidal shapes O.materials.append( CohFrictMat( young=10*young,poisson=poisson,density=density,frictionAngle=frictionAngle3,normalCohesion=1e40,shearCohesion=1e40,momentRotationLaw=True,label='cylindermat') ) # material to create the gridConnections O.materials.append( FrictMat( young=young,poisson=poisson,density=13.0*density,frictionAngle=frictionAngle3,label='fMat' ) ) # material for general interactions with cylinders Ne=30 # number of cylinders dy=0.03 dx=0.2 dz=0.2 Nc=1 # number of additional cylinderConnection nodesIds=[] cylIds=[] for j in range(-Nc, Nc+1): dyj = abs(float(j))*dy dxj = abs(float(j))*dx dzj = float(j)*dz vertices=[] for i in range(0, Ne+1): omega=20/float(Ne); hy=0.0; hz=0.05; hx=1.5; px=float(i)*hx/float(Ne)-0.8+dxj; py=sin(float(i)*omega)*hy+dyj; pz=cos(float(i)*omega)*hz+dzj; vertices.append([pz,py,px]) cylinderConnection(vertices,0.02,nodesIds,cylIds,color=[1,0,0],highlight=False,intMaterial='cylindermat',extMaterial='fMat') O.bodies[nodesIds[-1]].state.blockedDOFs='xyzXYZ' O.bodies[nodesIds[-Ne-1]].state.blockedDOFs='xyzXYZ' #### For viewing #### from yade import qt qt.View() Gl1_Sphere.stripes=True #### Allows to reload the simulation #### O.saveTmp() trunk-2017.01a/examples/cylinders/mikado.py000066400000000000000000000064141304022710500206170ustar00rootroot00000000000000# encoding: utf-8 "An example showing how two create cylinders with random length." from yade.gridpfacet import * #### Parameters #### Lmin=3. # minimum length Lmax=6. # maximum length n=10 # number of cylinders in one direction r=0.5 # radius of the cylinder element phi=30. # friction angle E=1e6 # Young's modulus #### Engines #### O.engines=[ ForceResetter(), InsertionSortCollider([ Bo1_GridConnection_Aabb(), Bo1_PFacet_Aabb(), ]), InteractionLoop([ Ig2_GridNode_GridNode_GridNodeGeom6D(), Ig2_GridConnection_GridConnection_GridCoGridCoGeom(), # cylinder-cylinder interaction Ig2_Sphere_PFacet_ScGridCoGeom(), # needed for GridNode-pFacet interaction (why is this not included in Ig2_GridConnection_PFacet_ScGeom???) Ig2_GridConnection_PFacet_ScGeom(), # Cylinder-pFcet interaction ], [ Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=False), Ip2_FrictMat_FrictMat_FrictPhys() ], [ Law2_ScGeom6D_CohFrictPhys_CohesionMoment(), # contact law for "internal" cylider forces Law2_ScGridCoGeom_FrictPhys_CundallStrack(), # contact law for Cylinder-pFacet interaction Law2_GridCoGridCoGeom_FrictPhys_CundallStrack() # contact law for cylinder-cylinder interaction ] ), GlobalStiffnessTimeStepper(timestepSafetyCoefficient=0.1,label='ts'), NewtonIntegrator(gravity=(0.,0,-10),damping=0.5,label='newton'), #NewtonIntegrator(gravity=(-1.,0,-10),damping=0.5,label='newton'), ] #### Creat materials #### O.materials.append( CohFrictMat( young=E,poisson=0.3,density=1000,frictionAngle=radians(phi),normalCohesion=1e10,shearCohesion=1e10,momentRotationLaw=True,label='cMat' ) ) # material to create the gridConnections O.materials.append( FrictMat( young=E,poisson=0.3,density=1000,frictionAngle=radians(phi),label='fMat' ) ) # material for general interactions #### Create cylinders #### nodesIds=[] cylIds=[] ext=12. dxy=ext/(n-1) dL=Lmax-Lmin random.seed( 10 ) for i in range(0,n): y=-ext/2+i*dxy for i in range(0,n): x=-ext/2+i*dxy L=Lmin+dL*random.random() color=[random.random(),random.random(),random.random()] cylinder((x,y,2*r),(x,y,L+2*r),radius=r,nodesIds=nodesIds,cylIds=cylIds, fixed=False,color=color,intMaterial='cMat',extMaterial='fMat') #### Creat ground with pFacets #### color=[255./255.,102./255.,0./255.] n0=O.bodies.append( gridNode([-10,-10,0],r,wire=False,fixed=True,material='cMat',color=color) ) n1=O.bodies.append( gridNode([10,-10,0],r,wire=False,fixed=True,material='cMat',color=color) ) n2=O.bodies.append( gridNode([10,10,0],r,wire=False,fixed=True,material='cMat',color=color) ) n3=O.bodies.append( gridNode([-10,10,0],r,wire=False,fixed=True,material='cMat',color=color) ) O.bodies.append( gridConnection(n0,n1,r,color=color,material='fMat') ) O.bodies.append( gridConnection(n1,n2,r,color=color,material='fMat') ) O.bodies.append( gridConnection(n2,n0,r,color=color,material='fMat') ) O.bodies.append( gridConnection(n2,n3,r,color=color,material='fMat') ) O.bodies.append( gridConnection(n3,n0,r,color=color,material='fMat') ) O.bodies.append( pfacet(n0,n1,n2,wire=False,material='fMat',color=color) ) O.bodies.append( pfacet(n0,n2,n3,wire=False,material='fMat',color=color) ) #### For viewing #### from yade import qt qt.View() Gl1_Sphere.stripes=True #### Allows to reload the simulation #### O.saveTmp() trunk-2017.01a/examples/deformableelem/000077500000000000000000000000001304022710500177435ustar00rootroot00000000000000trunk-2017.01a/examples/deformableelem/Minimal.py000066400000000000000000000053171304022710500217110ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # Created by Burak ER from yade.deformableelementsutils import *; O=Omega() ## Create deformable elements internal materials and interaction element material mat=LinIsoRayleighDampElastMat(label='aluminiummaterial'); intermat=LinCohesiveStiffPropDampElastMat(label='intermat') intermat.youngmodulus=70e11; mat.density=2700; mat.youngmodulus=70e9 O.materials.append(intermat) O.materials.append(mat) ## Generate deformable element mesh from GMSH2 format nodesofelement1=[[0, 0 ,0],[0, 1, 0],[1 ,0 ,0],[0, 0 ,1]] nodesofelement2=[[0, 0 ,0],[0, 1, 0],[1,0 ,0],[0, 0 ,-1]] noderadius=0.1*(0.75*tetrahedronvolume(nodesofelement1))**0.33333333; [elbody, nodebodies1]=tetrahedral_element(mat,nodesofelement1,Lin4NodeTetra,radius=noderadius) [elbody, nodebodies2]=tetrahedral_element(mat,nodesofelement2,Lin4NodeTetra,radius=noderadius) nodebodies1[3].state.pos+=Vector3(0,0,0.01); interfaceelementpairs=[]; interfaceelementpairs.append([nodebodies1[0], nodebodies2[0]]); interfaceelementpairs.append([nodebodies1[1], nodebodies2[1]]); interfaceelementpairs.append([nodebodies1[2], nodebodies2[2]]); [elbody, nodebodies]=interaction_element(intermat,interfaceelementpairs,Lin4NodeTetra_Lin4NodeTetra_InteractionElement); #mesh=tetrahedral_mesh_generator('model.msh',Lin4NodeTetra,'aluminiummaterial',Lin4NodeTetra_Lin4NodeTetra_InteractionElement,'intermat') ## Define the body boundary force # x position limits of bodies that are subject to the force force_tail_body_lowerlimit=-1.01; force_tail_body_upperlimit=-0.9999; # Angular frequency of the force amplitude=100000; period=(1e-3) omega=2*pi/period; applicationperiod=period/2; ## Define the fixed boundary # x position limits of bodies that are subject to the fixed boundary fixed_tail_body_lowerlimit=0.99; fixed_tail_body_upperlimit=1.01; # Time step determines the exiting period of the integrator since the integrator performs one step from current_time to current_time+dt; using many substeps for any value of dt; then stops. O.dt=1e-9; O.engines=[ ForceResetter(), ## Apply internal force to the deformable elements and internal force of the interaction element FEInternalForceEngine([If2_Lin4NodeTetra_LinIsoRayleighDampElast(),If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat()]), NewtonIntegrator(damping=0,gravity=[0,0,0]), #PyRunner(virtPeriod=1e-99,command='applyforcetoelements()'), # ## Plotting data: adds plots after one step of the integrator engine #PyRunner(virtPeriod=1e-99,command='addplot()') ] from yade import plot plot.plots={'t':'vel','time':'pos','tm':'force'} plot.plot(subPlots=True) try: from yade import qt qt.View() qt.Controller() except ImportError: pass trunk-2017.01a/examples/deformableelem/MinimalTensileTest.py000066400000000000000000000141211304022710500240660ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # Created by Burak ER from yade.deformableelementsutils import *; O=Omega() pressure=70e7;# N/m^2 wx=1;#m wy=1;#m wz=1;#m ## Create deformable elements internal materials and interaction element material mat=LinIsoRayleighDampElastMat(label='aluminiummaterial'); intermat=LinCohesiveStiffPropDampElastMat(label='intermat') intermat.youngmodulus=70e11; mat.density=2700; mat.beta=0.05; mat.alpha=0.05; mat.youngmodulus=70e9; O.materials.append(intermat) O.materials.append(mat) #create points of a cube with number of 8 points p0=Vector3([0, 0 ,0]); p1=Vector3([0, wy, 0]); p2=Vector3([wx ,0 ,0]); p3=Vector3([0, 0 ,wz]); p4=Vector3([0, wy, wz]); p5=Vector3([wx, wy, 0]); p6=Vector3([wx, 0 ,wz]); p7=Vector3([wx, wy ,wz]); nodesofelement1=[p0,p1,p2,p3]; nodesofelement2=[p3,p4,p1,p7]; nodesofelement3=[p2,p5,p1,p7]; nodesofelement4=[p7,p2,p3,p6]; nodesofelement5=[p1,p2,p3,p7]; noderadius=0.1*(0.75*tetrahedronvolume(nodesofelement1))**0.33333333; [elbody1, nodebodies1]=tetrahedral_element(mat,nodesofelement1,Lin4NodeTetra,radius=noderadius) [elbody2, nodebodies2]=tetrahedral_element(mat,nodesofelement2,Lin4NodeTetra,radius=noderadius) [elbody3, nodebodies3]=tetrahedral_element(mat,nodesofelement3,Lin4NodeTetra,radius=noderadius) [elbody4, nodebodies4]=tetrahedral_element(mat,nodesofelement4,Lin4NodeTetra,radius=noderadius) [elbody5, nodebodies5]=tetrahedral_element(mat,nodesofelement5,Lin4NodeTetra,radius=noderadius) interfaceelementpairs=[]; #interface of 1-5 interfaceelementpairs.append([nodebodies1[1], nodebodies5[0]]); interfaceelementpairs.append([nodebodies1[2], nodebodies5[1]]); interfaceelementpairs.append([nodebodies1[3], nodebodies5[2]]); [elbodyinter, nodebodiesinter]=interaction_element(intermat,interfaceelementpairs,Lin4NodeTetra_Lin4NodeTetra_InteractionElement); #interface of 2-5 interfaceelementpairs=[]; interfaceelementpairs.append([nodebodies2[0], nodebodies5[2]]); interfaceelementpairs.append([nodebodies2[2], nodebodies5[0]]); interfaceelementpairs.append([nodebodies2[3], nodebodies5[3]]); [elbodyinter, nodebodiesinter]=interaction_element(intermat,interfaceelementpairs,Lin4NodeTetra_Lin4NodeTetra_InteractionElement); #interface of 3-5 interfaceelementpairs=[]; interfaceelementpairs.append([nodebodies3[0], nodebodies5[1]]); interfaceelementpairs.append([nodebodies3[2], nodebodies5[0]]); interfaceelementpairs.append([nodebodies3[3], nodebodies5[3]]); [elbodyinter, nodebodiesinter]=interaction_element(intermat,interfaceelementpairs,Lin4NodeTetra_Lin4NodeTetra_InteractionElement); #interface of 3-5 interfaceelementpairs=[]; interfaceelementpairs.append([nodebodies3[0], nodebodies5[1]]); interfaceelementpairs.append([nodebodies3[2], nodebodies5[0]]); interfaceelementpairs.append([nodebodies3[3], nodebodies5[3]]); [elbodyinter, nodebodiesinter]=interaction_element(intermat,interfaceelementpairs,Lin4NodeTetra_Lin4NodeTetra_InteractionElement); #interface of 4-5 interfaceelementpairs=[]; interfaceelementpairs.append([nodebodies4[0], nodebodies5[3]]); interfaceelementpairs.append([nodebodies4[1], nodebodies5[1]]); interfaceelementpairs.append([nodebodies4[2], nodebodies5[2]]); [elbodyinter, nodebodiesinter]=interaction_element(intermat,interfaceelementpairs,Lin4NodeTetra_Lin4NodeTetra_InteractionElement); # Time step determines the exiting period of the integrator since the integrator performs one step from current_time to current_time+dt; using many substeps for any value of dt; then stops. initpos0=O.bodies[nodebodies1[0].id].state.pos; def applyforcetoelements(): pos0=O.bodies[nodebodies3[0].id].state.pos; pos1=O.bodies[nodebodies3[1].id].state.pos; pos2=O.bodies[nodebodies3[2].id].state.pos; area1=0.5*((pos1-pos0).cross(pos2-pos0)).norm(); pos0=O.bodies[nodebodies1[0].id].state.pos; pos1=O.bodies[nodebodies1[1].id].state.pos; pos2=O.bodies[nodebodies1[2].id].state.pos; area2=0.5*((pos1-pos0).cross(pos2-pos0)).norm(); Traction=area1*pressure; O.forces.addF(nodebodies3[0].id,Vector3(0,0,-(0.3*Traction))); O.forces.addF(nodebodies3[1].id,Vector3(0,0,-(0.3*Traction))); O.forces.addF(nodebodies3[2].id,Vector3(0,0,-(0.3*Traction))); Traction=area2*pressure; O.forces.addF(nodebodies1[0].id,Vector3(0,0,-(0.3*Traction))); O.forces.addF(nodebodies1[1].id,Vector3(0,0,-(0.3*Traction))); O.forces.addF(nodebodies1[2].id,Vector3(0,0,-(0.3*Traction))); def fixboundryelements(): nodebodies1[3].state.blockedDOFs='xyzXYZ' nodebodies2[0].state.blockedDOFs='xyzXYZ' nodebodies2[1].state.blockedDOFs='xyzXYZ' nodebodies2[3].state.blockedDOFs='xyzXYZ' nodebodies3[3].state.blockedDOFs='xyzXYZ' nodebodies4[0].state.blockedDOFs='xyzXYZ' nodebodies4[2].state.blockedDOFs='xyzXYZ' nodebodies4[3].state.blockedDOFs='xyzXYZ' nodebodies5[2].state.blockedDOFs='xyzXYZ' nodebodies5[3].state.blockedDOFs='xyzXYZ' fixboundryelements(); def addplot(): vecpos=(O.bodies[nodebodies1[0].id].state.pos-initpos0) plot.addData(displacement=abs(vecpos[2]),time=O.time) ##integratoreng=RungeKuttaCashKarp54Integrator([ ## ForceResetter(), ## Apply internal force to the deformable elements and internal force of the interaction element ## FEInternalForceEngine([If2_Lin4NodeTetra_LinIsoRayleighDampElast(),If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat()]), ## PyRunner(virtPeriod=1e-99,command='applyforcetoelements()'), ##]) ##O.engines=[integratoreng, ## PyRunner(iterPeriod=1,command='addplot()') ##] ##integratoreng.rel_err=1e-3; ##integratoreng.abs_err=1e-3; O.engines=[ForceResetter(), PyRunner(virtPeriod=1e-99,command='applyforcetoelements()'), ## Apply internal force to the deformable elements and internal force of the interaction element FEInternalForceEngine([If2_Lin4NodeTetra_LinIsoRayleighDampElast(),If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat()]), NewtonIntegrator(damping=0,gravity=[0,0,0]), PyRunner(virtPeriod=1e-99,command='addplot()'), ]; O.dt=1e-7; from yade import plot plot.plots={'time':'displacement'} plot.plot(subPlots=False) try: from yade import qt qt.View() qt.Controller() except ImportError: pass trunk-2017.01a/examples/deformableelem/ReadMe000066400000000000000000000001071304022710500210210ustar00rootroot00000000000000This folder includes the simulation files for the deformable elements. trunk-2017.01a/examples/deformableelem/main.py000066400000000000000000000017411304022710500212440ustar00rootroot00000000000000#!/usr/bin/env python # -*- coding: utf-8 -*- # # untitled.py # # Copyright 2014 Burak ER # # This program is free software; you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by # the Free Software Foundation; either version 2 of the License, or # (at your option) any later version. # # This program is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the # GNU General Public License for more details. # # You should have received a copy of the GNU General Public License # along with this program; if not, write to the Free Software # Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, # MA 02110-1301, USA. # # import sys from yadeimport import * def main(): execfile("testDeformableBodies_pressure.py"); return 0 if __name__ == '__main__': main() trunk-2017.01a/examples/deformableelem/model.geo000066400000000000000000000002121304022710500215320ustar00rootroot00000000000000Merge "model.msh"; Physical Volume(100002) = {100001}; Physical Volume(100003) = {100001}; Field[1] = Max; Field[1].FieldsList = {1, -3}; trunk-2017.01a/examples/deformableelem/model.msh000066400000000000000000002161741304022710500215670ustar00rootroot00000000000000$MeshFormat 2.000000 0 8 $EndMeshFormat $Nodes 391 1 1.000000 -0.000000 0.100001 2 1.000000 0.057628 0.081449 3 1.000000 0.093943 0.033143 4 1.000000 0.095747 -0.027197 5 1.000000 0.057793 -0.081311 6 1.000000 0.000213 -0.099978 7 1.000000 -0.057462 -0.081583 8 1.000000 -0.093881 -0.033347 9 1.000000 -0.095809 0.026994 10 1.000000 -0.061597 0.078191 11 -1.000000 0.019509 0.098078 12 -1.000000 -0.040630 0.091124 13 -1.000000 -0.088702 0.045164 14 -1.000000 -0.098583 -0.014392 15 -1.000000 -0.072274 -0.068806 16 -1.000000 -0.019297 -0.098100 17 -1.000000 0.040819 -0.091026 18 -1.000000 0.088058 -0.046370 19 -1.000000 0.098604 0.014177 20 -1.000000 0.072410 0.068640 21 0.938054 0.024884 0.096449 22 0.942040 0.099428 0.005807 23 0.937511 -0.039138 0.091924 24 0.938529 -0.099197 -0.008157 25 0.937866 -0.085505 0.051146 26 -0.935772 -0.009233 0.099090 27 -0.935059 -0.098116 0.019135 28 -0.936955 0.047824 0.087279 29 -0.932001 0.012945 -0.098726 30 -0.939627 0.098408 -0.016167 31 -0.941572 0.091831 0.039309 32 0.940439 0.077604 0.062311 33 0.942163 0.084067 -0.053835 34 0.942625 0.035114 -0.093344 35 0.940410 -0.025721 -0.096193 36 0.939409 -0.076290 -0.063912 37 -0.935795 -0.065696 0.074826 38 -0.933838 -0.090360 -0.042063 39 -0.933082 -0.048316 -0.087018 40 -0.931798 0.067594 -0.073269 41 -0.871443 -0.075186 -0.065258 42 -0.869209 0.044603 -0.089003 43 -0.871593 -0.099242 -0.007698 44 0.881241 0.009830 -0.099031 45 0.875387 0.093148 0.035763 46 -0.864205 0.090445 -0.041904 47 0.878132 -0.089425 -0.043812 48 0.879260 -0.048259 -0.087047 49 -0.872222 -0.084249 0.053495 50 -0.870940 -0.021108 -0.097594 51 0.872440 0.049522 0.086374 52 -0.873039 -0.032991 0.093988 53 0.872787 -0.013273 0.098693 54 0.874853 -0.067709 0.073175 55 -0.876103 0.028308 0.095409 56 -0.881567 0.078171 0.061620 57 0.877005 -0.098192 0.018359 58 -0.811006 -0.093050 -0.036088 59 -0.812500 -0.056997 0.081965 60 -0.815107 0.006523 0.099357 61 0.802304 0.015762 0.098448 62 -0.891527 0.098734 0.012860 63 0.816626 -0.068002 -0.072933 64 -0.810476 -0.094957 0.029800 65 0.818500 -0.013640 -0.098656 66 0.800850 0.074404 0.066211 67 -0.811756 0.008702 -0.099144 68 -0.822586 0.064940 0.075446 69 -0.810348 -0.050539 -0.085830 70 0.814331 -0.098360 -0.016659 71 -0.805975 0.064981 -0.075414 72 -0.834882 0.097205 0.022391 73 -0.745277 -0.099836 -0.001669 74 -0.752836 -0.022840 -0.097068 75 -0.746826 -0.077739 0.062145 76 0.755653 -0.085163 -0.051785 77 -0.787922 0.096181 -0.025768 78 0.813475 -0.089194 0.044245 79 -0.736253 0.073409 -0.067424 80 0.811367 -0.046396 0.088044 81 0.879466 0.096680 -0.024119 82 -0.750530 -0.015133 0.098509 83 -0.770244 0.093506 0.034581 84 -0.757482 0.046185 0.088156 85 -0.760407 0.031490 -0.094445 86 0.726801 0.044933 0.088826 87 -0.746685 -0.075100 -0.065363 88 0.808824 0.099272 0.007394 89 0.745199 -0.021133 0.097586 90 0.740502 0.093959 0.033089 91 0.882076 0.063560 -0.076578 92 0.822272 0.043508 -0.089586 93 0.756728 -0.035506 -0.093225 94 0.759724 0.023852 -0.096761 95 0.753758 -0.099192 0.008204 96 -0.684587 -0.092912 -0.036540 97 -0.682890 -0.092967 0.036358 98 -0.683525 -0.043358 0.089667 99 -0.690823 -0.046726 -0.087868 100 0.695500 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endsolid vcg trunk-2017.01a/examples/deformableelem/testDeformableBodies.py000066400000000000000000000102051304022710500244010ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # Created by Burak ER from yade.deformableelementsutils import *; O=Omega() ## Create deformable elements internal materials and interaction element material mat=LinIsoRayleighDampElastMat(label='aluminiummaterial'); intermat=LinCohesiveStiffPropDampElastMat(label='intermat') intermat.youngmodulus=70e11; mat.density=2700; mat.youngmodulus=70e9 O.materials.append(intermat) O.materials.append(mat) ## Generate deformable element mesh from GMSH2 format mesh=tetrahedral_mesh_generator('model.msh',Lin4NodeTetra,'aluminiummaterial',Lin4NodeTetra_Lin4NodeTetra_InteractionElement,'intermat') ## Define the body boundary force # x position limits of bodies that are subject to the force force_tail_body_lowerlimit=-1.01; force_tail_body_upperlimit=-0.9999; # Angular frequency of the force amplitude=1000; period=(1e-4) omega=2*pi/period; applicationperiod=period/2; ## Define the fixed boundary # x position limits of bodies that are subject to the fixed boundary fixed_tail_body_lowerlimit=0.99; fixed_tail_body_upperlimit=1.01; def getinitialpos(): positions=[]; for body in O.bodies: positions.append(body.state.pos) return positions def getboundarybodies(): bdy=[]; for body in O.bodies: if(body.shape.dispIndex==12): if(body.state.pos[0]fixed_tail_body_lowerlimit): bdy.append(body.id) return bdy def getforcebodies(): bdy=[]; for body in O.bodies: if(body.shape.dispIndex==12): if(body.state.pos[0]force_tail_body_lowerlimit): if(O.time it is pressure applied on the one end of the rod # x position limits of bodies that are subject to the force force_tail_body_lowerlimit=-1.01; force_tail_body_upperlimit=-0.9999; # Pressure Properties #pressure=Vector3(1.5e6,0,0); pressure=Vector3(1.5e8,0,0); period=(3e-4) omega=2*pi/period; applicationperiod=period/2; # Displacement Properties(Displacement Application) boundary_displacement_vector=Vector3(0.3,0,0); ## Define the fixed boundary # x position limits of bodies that are subject to the fixed boundary fixed_tail_body_lowerlimit=0.99; fixed_tail_body_upperlimit=1.01; def getinitialpos(): positions=[]; for body in O.bodies: positions.append(body.state.pos) return positions def getboundarybodies(mesh): bdy = []; listofbodies = dict(); listofboundarybodies = dict(); for body in mesh: if (len(body) > 1): listofbodies[body[0].id] = []; for bdyy in body[1]: if (bdyy.shape.dispIndex == 12): if (bdyy.state.pos[0] < fixed_tail_body_upperlimit): if (bdyy.state.pos[0] > fixed_tail_body_lowerlimit): listofbodies[body[0].id].append(bdyy); #add node to boundary bodies of body if (listofbodies[body[0].id].index( bdyy) == 2): #if this body has three nodes of it on the boundary then add it to the traction force list. listofboundarybodies[body[0].id] = listofbodies[body[0].id]; return listofboundarybodies; def getforcebodies(mesh): bdy = []; listofbodies = dict(); listofboundarybodies = dict(); for body in mesh: if(len(body) > 1): listofbodies[body[0].id] = []; for bdyy in body[1]: if (bdyy.shape.dispIndex == 12): if (bdyy.state.pos[0] < force_tail_body_upperlimit): if (bdyy.state.pos[0] > force_tail_body_lowerlimit): listofbodies[body[0].id].append(bdyy); #add node to boundary bodies of body if (listofbodies[body[0].id].index( bdyy) == 2): #if this body has three nodes of it on the boundary then add it to the traction force list. listofboundarybodies[body[0].id] = listofbodies[body[0].id]; return listofboundarybodies; initialpositions=getinitialpos(); forcebodies=getforcebodies(modelmesh); boundarybodies=getboundarybodies(modelmesh); def displaceelements(): for deformablebody in forcebodies: for node in forcebodies[deformablebody]: if(O.time50000: O.bodies[IdSphere].dynamic=False O.bodies[IdSphere].state.vel[2]=0.1 O.saveTmp() trunk-2017.01a/examples/grids/GridConnection_Spring.py000066400000000000000000000045431304022710500227170ustar00rootroot00000000000000#--- bruno.chareyre@hmg.inpg.fr --- #!/usr/bin/python # -*- coding: utf-8 -*- # Experiment beam-like behaviour with chained cylinders + CohFrict connexions from yade.gridpfacet import * young=1.0e10 poisson=4 density=2.60e3 frictionAngle=radians(30) O.materials.append(CohFrictMat(young=young,poisson=poisson,density=density,frictionAngle=frictionAngle,normalCohesion=1e13,shearCohesion=1e13,momentRotationLaw=True,label='mat')) O.engines=[ ForceResetter(), InsertionSortCollider([ Bo1_Sphere_Aabb(), Bo1_GridConnection_Aabb(), ]), InteractionLoop( # Geometric interactions [ Ig2_GridNode_GridNode_GridNodeGeom6D(), Ig2_Sphere_GridConnection_ScGridCoGeom(), # used for the cohesive sphere-cylinder interaction ], [ # Interaction phusics Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=True), ], # Interaction law [ Law2_ScGeom6D_CohFrictPhys_CohesionMoment(), Law2_ScGridCoGeom_CohFrictPhys_CundallStrack(), # used for the cohesive sphere-cylinder interaction ] ), GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8,label='ts'), NewtonIntegrator(gravity=(0,-9.81,0),damping=0.15,label='newton'), PyRunner(iterPeriod=500,command='history()'), ] ### Generate a spiral ### Create all nodes first nodesIds=[] rCyl=0.005 Ne=200 for i in range(0, Ne+1): omega=60.0/float(Ne); hy=0.10; hz=0.15; px=float(i)*(omega/60.0); py=sin(float(i)*omega)*hy; pz=cos(float(i)*omega)*hz; nodesIds.append( O.bodies.append( gridNode([px,py,pz],rCyl,wire=False,fixed=False,color=Vector3(0.6,0.5,0.5),material='mat') ) ) ### Now create connection between the nodes for i,j in zip( nodesIds[:-1], nodesIds[1:]): O.bodies.append( gridConnection(i,j,rCyl,color=Vector3(0.6,0.5,0.5),material='mat') ) def outp(id=1): for i in O.interactions: if i.id1 == 1: print i.phys.shearForce print i.phys.normalForce return i O.bodies[Ne-1].state.blockedDOFs='xyzXYZ' yade.qt.View(); #plot some results from yade import plot plot.plots={'t':('pos1',None,'vel1')} def history(): plot.addData(pos1=O.bodies[0].state.pos[1], # potential elastic energy vel1=O.bodies[0].state.vel[1], t=O.time) #yade.qt.Renderer().bound=True plot.plot(subPlots=False) O.saveTmp() #O.bodies[0].state.angVel=Vector3(0.05,0,0) trunk-2017.01a/examples/grids/Simple_GridConnection_Falling.py000066400000000000000000000022461304022710500243400ustar00rootroot00000000000000# encoding: utf-8 from yade import pack,geom,qt from yade.gridpfacet import * from pylab import * qt.View() O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_GridConnection_Aabb()]), InteractionLoop( [Ig2_GridNode_GridNode_GridNodeGeom6D()], [Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=False)], [Law2_ScGeom6D_CohFrictPhys_CohesionMoment()] ), NewtonIntegrator(gravity=(0,0,-10),damping=0.1,label='newton') ] O.materials.append(CohFrictMat(young=3e2,poisson=0.3,density=1e1,frictionAngle=10,normalCohesion=1e7,shearCohesion=1e7,momentRotationLaw=True,label='mat')) ### Parameters ### L=0.1 #length [m] n=10 #number of nodes for the length [#] r=L/100. #radius color=[255./255.,102./255.,0./255.] ### Create all nodes first nodeIds=[] for i in range(0,n): nodeIds.append( O.bodies.append( gridNode([i*L/n,0,0],r,wire=False,fixed=False,material='mat',color=color) ) ) ### Create connections between the nodes connectionIds=[] for i,j in zip(nodeIds[:-1],nodeIds[1:]): connectionIds.append( O.bodies.append( gridConnection(i,j,r,color=color) ) ) ### Set a fixed node O.bodies[0].dynamic=False O.dt=1e-06 O.saveTmp() trunk-2017.01a/examples/grids/Simple_Grid_Falling.py000066400000000000000000000025551304022710500223230ustar00rootroot00000000000000# encoding: utf-8 from yade import pack,geom,qt from yade.gridpfacet import * from pylab import * qt.View() O.engines=[ ForceResetter(), InsertionSortCollider([ Bo1_GridConnection_Aabb(), ]), InteractionLoop( [Ig2_GridNode_GridNode_GridNodeGeom6D()], [Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=False)], [Law2_ScGeom6D_CohFrictPhys_CohesionMoment()] ), NewtonIntegrator(gravity=(0,0,-10),damping=0.1,label='newton') ] O.materials.append(CohFrictMat(young=3e2,poisson=0.3,density=1e1,frictionAngle=10,normalCohesion=1e7,shearCohesion=1e7,momentRotationLaw=True,label='spheremat')) ### Parameters of a rectangular grid ### L=0.1 #length [m] l=0.05 #width [m] nbL=10 #number of nodes for the length [#] nbl=5 #number of nodes for the width [#] r=L/100. #radius color=[255./255.,102./255.,0./255.] nodesIds=[] #Create all nodes first : for i in range(0,nbL): for j in range(0,nbl): nodesIds.append( O.bodies.append(gridNode([i*L/nbL,j*l/nbl,0],r,wire=False,fixed=False,material='spheremat',color=color)) ) #Create connection between the nodes for i in range(0,len(nodesIds)): for j in range(i+1,len(nodesIds)): dist=(O.bodies[i].state.pos - O.bodies[j].state.pos).norm() if(dist<=L/nbL*1.01): O.bodies.append( gridConnection(i,j,r,color=color) ) #Set a fixed node O.bodies[0].dynamic=False O.dt=1e-05 O.saveTmp() trunk-2017.01a/examples/gts-horse/000077500000000000000000000000001304022710500167135ustar00rootroot00000000000000trunk-2017.01a/examples/gts-horse/gts-horse.py000066400000000000000000000040371304022710500212040ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # © 2009 Václav Šmilauer from yade import pack import gts, os.path, locale locale.setlocale(locale.LC_ALL, 'en_US.UTF-8') #gts is locale-dependend. If, for example, german locale is used, gts.read()-function does not import floats normally ''' if you get "Error: unsupported locale setting" -> type as root: "dpkg-reconfigure locales" -> choose "en_US.UTF-8" (press space to choose) ''' # coarsen the original horse if we have it # do nothing if we have the coarsened horse already if not os.path.exists('horse.coarse.gts'): if os.path.exists('horse.gts'): surf=gts.read(open('horse.gts')); surf.coarsen(1000); surf.write(open('horse.coarse.gts','w')) else: print """horse.gts not found, you need to download input data: wget http://gts.sourceforge.net/samples/horse.gts.gz gunzip horse.gts.gz """ quit() surf=gts.read(open('horse.coarse.gts')) if surf.is_closed(): pred=pack.inGtsSurface(surf) aabb=pred.aabb() dim0=aabb[1][0]-aabb[0][0]; radius=dim0/40. # get some characteristic dimension, use it for radius O.bodies.append(pack.regularHexa(pred,radius=radius,gap=radius/4.)) surf.translate(0,0,-(aabb[1][2]-aabb[0][2])) # move surface down so that facets are underneath the falling spheres O.bodies.append(pack.gtsSurface2Facets(surf,wire=True)) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()],label='collider'), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), NewtonIntegrator(damping=.1,gravity=[0,0,-5000]), PyRunner(iterPeriod=1000,command='timing.stats(); O.pause();'), PyRunner(iterPeriod=10,command='addPlotData()') ] O.dt=.7*PWaveTimeStep() O.saveTmp() O.timingEnabled=True O.trackEnergy=True from yade import plot plot.plots={'i':('total',O.energy.keys,)} def addPlotData(): plot.addData(i=O.iter,total=O.energy.total(),**O.energy) plot.plot(subPlots=False) from yade import timing from yade import qt qt.View() trunk-2017.01a/examples/gts-horse/gts-operators.py000066400000000000000000000033021304022710500220740ustar00rootroot00000000000000""" This file shows 2 ways to fill union of triangulated surfaces: You can either use union of 2 inGtsSurface predicates or create union of surfaces using GTS calls first and use a single isGtsSurface as predicate with the united surface. The disadvantage of the predicate union | is that each sphere must fit whole in one surface or another: with padding, several points on the sphere are tested. Therefore, areas near both surfaces' boundary will not be filled at all. Note that GTS only moves references to surfaces around, therefore e.g. translating surface that is part of the union will move also the part of the united surface. Therefore, we use the copy() method for deep copy here. """ from yade import pack,qt import gts, locale locale.setlocale(locale.LC_ALL, 'en_US.UTF-8') #gts is locale-dependend. If, for example, german locale is used, gts.read()-function does not import floats normally ''' if you get "Error: unsupported locale setting" -> type as root: "dpkg-reconfigure locales" -> choose "en_US.UTF-8" (press space to choose) ''' s1=gts.read(open('horse.coarse.gts')) s2=gts.Surface(); s2.copy(s1); s2.translate(0.04,0,0) O.bodies.append(pack.gtsSurface2Facets(s1,color=(0,1,0))+pack.gtsSurface2Facets(s2,color=(1,0,0))) s12=gts.Surface(); s12.copy(s1.union(s2)); s12.translate(0,0,.1) radius=0.002 O.bodies.append(pack.gtsSurface2Facets(s12,color=(0,0,1))) qt.View() from time import time t0=time() O.bodies.append(pack.regularHexa(pack.inGtsSurface(s1) | pack.inGtsSurface(s2),radius,gap=0,color=(0,1,0))) t1=time() print 'Using predicate union: %gs'%(t1-t0) O.bodies.append(pack.regularHexa(pack.inGtsSurface(s12),radius,gap=0.,color=(1,0,0))) t2=time() print 'Using surface union: %gs'%(t2-t1) trunk-2017.01a/examples/gts-horse/gts-random-pack-obb.py000066400000000000000000000031771304022710500230240ustar00rootroot00000000000000# -*- coding: utf-8 -*- """ CAUTION: Running this script can take very long! """ from numpy import arange from yade import pack import pylab # define the section shape as polygon in 2d; repeat first point at the end to close the polygon sq2=sqrt(2) poly=((3+.1,0),(3+0,.1),(3+sq2,.1+sq2),(3+.1+sq2,sq2),(3+.1,0)) #pylab.plot(*zip(*poly)); pylab.xlim(xmin=0); pylab.grid(); pylab.title('Meridian of the revolution surface\n(close to continue)'); pylab.gca().set_aspect(aspect='equal',adjustable='box'); pylab.show() thetas=arange(0,pi/8,pi/24) pts=pack.revolutionSurfaceMeridians([poly for theta in thetas],thetas,origin=Vector3(-4,0,-1),orientation=Quaternion((0,1,0),0.0)) surf=pack.sweptPolylines2gtsSurface(pts,capStart=True,capEnd=True,threshold=1e-4) O.bodies.append(pack.gtsSurface2Facets(surf,color=(1,0,1))) # fill this solid with triaxial packing; it will compute minimum-volume oriented bounding box # to minimize the number of throw-away spheres. # It does away with about 3k spheres for radius 3e-2 sp1=SpherePack() sp1=pack.randomDensePack(pack.inGtsSurface(surf),radius=3e-2,rRelFuzz=1e-1,memoizeDb='/tmp/gts-triax.sqlite',returnSpherePack=True) sp1.toSimulation() # translate the surface away and pack it again with sphere, but without the oriented bounding box (useOBB=False) # Here, we need 20k spheres (with more or less the same result) surf.translate(0,0,1); O.bodies.append(pack.gtsSurface2Facets(surf,color=(1,0,0))) sp2=SpherePack() sp2=pack.randomDensePack(pack.inGtsSurface(surf),radius=3e-2,rRelFuzz=1e-1,memoizeDb='/tmp/gts-triax-packings.sqlite',useOBB=False,returnSpherePack=True) sp2.toSimulation() from yade import qt qt.View() trunk-2017.01a/examples/gts-horse/gts-random-pack.py000066400000000000000000000063071304022710500222620ustar00rootroot00000000000000 """ CAUTION: Running this script can take very long! """ from numpy import arange from yade import pack import pylab # define the section shape as polygon in 2d; repeat first point at the end to close the polygon poly=((1e-2,5e-2),(5e-2,2e-2),(7e-2,-2e-2),(1e-2,-5e-2),(1e-2,5e-2)) # show us the meridian shape #pylab.plot(*zip(*poly)); pylab.xlim(xmin=0); pylab.grid(); pylab.title('Meridian of the revolution surface\n(close to continue)'); pylab.gca().set_aspect(aspect='equal',adjustable='box'); pylab.show() # angles at which we want this polygon to appear thetas=arange(0,pi/2,pi/24) # create 3d points from the 2d ones, turning the 2d meridian around the +y axis # for each angle, put the poly a little bit higher (+2e-3*theta); # this is just to demonstrate that you can do whatever here as long as the resulting # meridian has the same number of points # # There is origin (translation) and orientation arguments, allowing to transform all the 3d points once computed. # # without these transformation, it would look a little simpler: # pts=pack.revolutionSurfaceMeridians([[(pt[0],pt[1]+2e-3*theta) for pt in poly] for theta in thetas],thetas # pts=pack.revolutionSurfaceMeridians([[(pt[0],pt[1]+1e-2*theta) for pt in poly] for theta in thetas],thetas,origin=Vector3(0,-.05,.1),orientation=Quaternion((1,1,0),pi/4)) # connect meridians to make surfaces # caps will close it at the beginning and the end # threshold will merge points closer than 1e-4; this is important: we want it to be closed for filling surf=pack.sweptPolylines2gtsSurface(pts,capStart=True,capEnd=True,threshold=1e-4) # add the surface as facets to the simulation, to make it visible O.bodies.append(pack.gtsSurface2Facets(surf,color=(1,0,1))) # now fill the inGtsSurface predicate constructed form the same surface with sphere packing generated by TriaxialTest # with given radius and standard deviation (see documentation of pack.randomDensePack) # # The memoizeDb will save resulting packing into given file and next time, if you run with the same # parameters (or parameters that can be scaled to the same one), # it will load the packing instead of running the triaxial compaction again. # Try running for the second time to see the speed difference! memoizeDb='/tmp/gts-triax-packings.sqlite' sp=SpherePack() sp=pack.randomDensePack(pack.inGtsSurface(surf),radius=5e-3,rRelFuzz=1e-4,memoizeDb=memoizeDb,returnSpherePack=True) sp.toSimulation() # We could also fill the horse with triaxial packing, but have nice approximation, the triaxial would run terribly long, # since horse discard most volume of its bounding box # Here, we would use a very crude one, however if 1: import gts horse=gts.read(open('horse.coarse.gts')) #; horse.scale(.25,.25,.25) O.bodies.append(pack.gtsSurface2Facets(horse)) sp=pack.randomDensePack(pack.inGtsSurface(horse),radius=5e-3,memoizeDb=memoizeDb,returnSpherePack=True) sp.toSimulation() horse.translate(.07,0,0) O.bodies.append(pack.gtsSurface2Facets(horse)) # specifying spheresInCell makes the packing periodic, with the given number of spheres, proportions being equal to that of the predicate sp=pack.randomDensePack(pack.inGtsSurface(horse),radius=1e-3,spheresInCell=2000,memoizeDb=memoizeDb,returnSpherePack=True) sp.toSimulation() trunk-2017.01a/examples/gts-horse/horse.coarse.gts000066400000000000000000000723221304022710500220330ustar00rootroot00000000000000336 1002 668 GtsSurface GtsFace GtsEdge GtsVertex 0.01632376508 0.02011445965 0.03949959237 0.01658055601 0.02674922323 0.04300259797 0.01342358396 0.04386696349 0.0605453965 0.03001315348 0.01873622255 -0.04975389892 0.03116204225 0.01487261331 -0.04662516627 0.03463446561 0.01417249157 -0.06445953302 0.03853905253 -0.06858153453 -0.05929809 0.03482282022 -0.07347322551 -0.06009816584 0.03366937294 -0.06833041545 -0.06716035938 -0.00372101118 -0.05117824214 -0.005623645339 0.007895279935 -0.05575069912 -0.005892351915 -0.0051427155 -0.06231273516 -0.02069042783 -0.004407438103 0.0225899988 -0.0146861251 -0.0003199737081 0.02192630914 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477 718 603 128 738 976 949 55 838 977 968 978 332 586 959 199 571 907 979 570 568 133 11 637 939 7 980 560 618 39 551 947 839 750 981 919 971 908 890 657 763 975 268 772 141 638 977 175 318 616 52 982 284 521 143 983 675 984 950 135 485 957 985 986 705 567 926 431 799 356 987 988 161 956 353 989 928 639 953 751 990 934 903 438 555 29 988 948 753 873 209 324 936 430 226 991 818 251 836 30 905 992 538 944 739 197 976 734 676 909 266 304 58 517 993 994 733 832 859 962 855 893 677 789 913 693 159 979 704 794 418 995 938 984 42 319 204 969 973 115 870 996 315 263 821 17 963 444 994 185 769 980 762 970 561 450 997 982 901 195 111 998 935 840 210 904 817 322 812 889 474 981 653 397 888 464 475 967 506 90 869 798 826 943 314 432 456 478 301 224 899 985 991 999 668 856 987 701 303 132 811 510 292 844 489 827 310 993 665 800 257 946 50 941 1000 297 744 558 983 788 422 989 145 174 346 240 306 129 546 891 244 60 539 966 895 575 992 124 217 576 357 21 955 386 747 886 674 999 702 253 906 1000 288 1001 877 773 1002 998 51 972 845 1002 910 816 345 27 679 408 682 737 617 153 250 945 172 837 771 553 391 961 824 619 807 650 672 512 921 632 556 717 469 548 828 661 313 978 863 631 748 409 379 754 535 871 796 974 331 849 806 334 852 67 1001 764 879 997 404 990 986 644 258 480 329 579 875 996 765 995 587 932 417 960 585 424 649 917 918 880 142 trunk-2017.01a/examples/hdaps.py000066400000000000000000000011351304022710500164510ustar00rootroot00000000000000 # With Thinkpad laptops, control the sphere's motion by tilting the # laptop. O.bodies.append( geom.facetBox(center=(0,0,.1),extents=(.5,.5,.1),wallMask=31,color=(0,0,1))+ [sphere((0,0,.1),.04,color=(1,1,1))] ) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop([Ig2_Facet_Sphere_ScGeom()],[Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_ScGeom_FrictPhys_CundallStrack()]), HdapsGravityEngine(calibrate=(-495,-495),calibrated=True,zeroGravity=(0,0,-1)), NewtonIntegrator(damping=.3), ] O.dt=PWaveTimeStep() import yade.qt yade.qt.View() O.run() trunk-2017.01a/examples/hourglass/000077500000000000000000000000001304022710500170075ustar00rootroot00000000000000trunk-2017.01a/examples/hourglass/.gitignore000066400000000000000000000000041304022710500207710ustar00rootroot00000000000000cpt trunk-2017.01a/examples/hourglass/hourglass.geo000066400000000000000000000013311304022710500215100ustar00rootroot00000000000000acc = 0.003; r0 = 0.0025; r1 = 0.015; h1 = 0.020; r2 = 0.017; h2 = 0.035; Point(1) = {0.0, 0.0, 0.0, acc}; Point(2) = {r0, 0.0, 0.0, acc}; Point(3) = {r1, 0.0, h1, acc}; Point(4) = {r2, 0.0, h2, acc}; Spline(1) = {2, 3, 4}; Translate {0, 0, h2} { Duplicata { Point{1}; } } Extrude {{0, 0, 1}, {0, 0, 0}, Pi/2} { Line{1}; } Rotate {{0, 0, 1}, {0, 0, 0}, Pi/2} { Duplicata { Surface{5}; } } Rotate {{0, 0, 1}, {0, 0, 0}, Pi/2} { Duplicata { Surface{6}; } } Rotate {{0, 0, 1}, {0, 0, 0}, Pi/2} { Duplicata { Surface{11}; } } Rotate {{0, 1, 0}, {0, 0, 0}, Pi} { Duplicata { Surface{5, 16, 11, 6}; } } Line Loop(39) = {4, 8, 13, 18}; Plane Surface(40) = {39}; Line Loop(41) = {38, 33, 28, 23}; Plane Surface(42) = {41}; trunk-2017.01a/examples/hourglass/hourglass.mesh000066400000000000000000003424511304022710500217050ustar00rootroot00000000000000 MeshVersionFormatted 2 Dimension 3 Vertices 1013 0 0 0 1 0.0025 0 0 2 0.015 0 0.02 3 0.017 0 0.035 4 0 0 0.035 5 1.5308084989342E-19 0.0025 0 6 9.1848509936051E-19 0.015 0.02 7 1.0409497792753E-18 0.017 0.035 8 -0.017 2.0818995585505E-18 0.035 16 -0.015 1.836970198721E-18 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53 4 53 54 4 54 55 4 55 56 4 56 8 4 8 57 8 57 58 8 58 59 8 59 60 8 60 61 8 61 62 8 62 63 8 63 64 8 64 9 8 9 65 9 65 66 9 66 67 9 67 68 9 68 69 9 69 70 9 70 71 9 71 72 9 72 73 9 73 74 9 74 75 9 75 76 9 76 11 9 11 77 10 77 6 10 9 78 13 78 79 13 79 80 13 80 81 13 81 82 13 82 83 13 83 84 13 84 85 13 85 12 13 12 86 14 86 87 14 87 88 14 88 89 14 89 90 14 90 91 14 91 92 14 92 93 14 93 94 14 94 95 14 95 96 14 96 97 14 97 14 14 14 98 15 98 11 15 12 99 18 99 100 18 100 101 18 101 102 18 102 103 18 103 104 18 104 105 18 105 106 18 106 4 18 2 107 20 107 14 20 11 108 22 108 109 22 109 110 22 110 111 22 111 112 22 112 113 22 113 114 22 114 115 22 115 116 22 116 117 22 117 118 22 118 119 22 119 16 22 16 120 23 120 121 23 121 122 23 122 123 23 123 124 23 124 125 23 125 126 23 126 127 23 127 18 23 18 128 24 128 129 24 129 130 24 130 131 24 131 132 24 132 133 24 133 134 24 134 135 24 135 136 24 136 137 24 137 138 24 138 139 24 139 6 24 14 140 27 140 141 27 141 142 27 142 143 27 143 144 27 144 145 27 145 146 27 146 147 27 147 148 27 148 149 27 149 150 27 150 151 27 151 21 27 21 152 28 152 153 28 153 154 28 154 155 28 155 156 28 156 157 28 157 158 28 158 159 28 159 16 28 2 160 32 160 161 32 161 162 32 162 163 32 163 164 32 164 165 32 165 166 32 166 167 32 167 168 32 168 169 32 169 170 32 170 171 32 171 23 32 23 172 33 172 173 33 173 174 33 174 175 33 175 176 33 176 177 33 177 178 33 178 179 33 179 21 33 18 180 38 180 181 38 181 182 38 182 183 38 183 184 38 184 185 38 185 186 38 186 187 38 187 23 38 Triangles 2000 56 193 55 5 199 41 40 5 29 200 28 5 27 207 26 5 207 27 203 5 207 191 192 5 206 39 38 5 39 206 202 5 191 206 192 5 24 210 2 5 210 48 2 5 210 36 6 5 48 210 6 5 208 38 37 5 38 208 206 5 192 206 208 5 26 209 25 5 209 26 207 5 207 192 209 5 220 197 219 5 198 221 218 5 223 41 199 5 197 223 199 5 29 225 200 5 225 198 200 5 194 226 211 5 229 190 193 5 205 231 213 5 231 205 212 5 232 193 190 5 193 232 55 5 193 233 229 5 189 234 219 5 234 189 218 5 235 188 214 5 201 236 235 5 238 189 222 5 189 238 224 5 239 188 235 5 190 241 232 5 243 35 4 5 49 243 4 5 47 244 8 5 244 56 8 5 245 191 207 5 245 203 224 5 203 245 207 5 191 246 206 5 202 246 222 5 246 202 206 5 244 193 56 5 211 228 194 5 217 230 196 5 230 213 196 5 212 228 195 5 218 221 234 5 220 219 234 5 222 199 202 5 200 224 203 5 238 246 191 5 238 222 246 5 245 238 191 5 224 238 245 5 235 236 239 5 189 224 218 5 198 224 200 5 198 218 224 5 222 189 219 5 222 197 199 5 219 197 222 5 42 216 43 5 217 30 31 5 223 42 41 5 42 223 216 5 30 225 29 5 225 30 217 5 54 55 232 5 195 228 216 5 211 216 228 5 205 214 188 5 205 213 214 5 214 213 230 5 221 196 213 5 196 221 198 5 221 213 231 5 195 220 212 5 220 195 197 5 212 220 231 5 195 247 197 5 223 247 216 5 247 223 197 5 247 195 216 5 212 248 228 5 229 249 190 5 249 229 226 5 198 250 196 5 217 250 225 5 250 217 196 5 250 198 225 5 253 31 32 5 194 249 226 5 248 194 228 5 251 205 188 5 205 251 212 5 248 212 251 5 231 220 234 5 221 231 234 5 235 252 201 5 252 235 214 5 204 236 201 5 230 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154 155 26 155 597 607 26 607 597 582 26 613 116 618 26 117 603 118 26 613 603 117 26 154 612 153 26 154 607 612 26 616 619 603 26 578 620 592 26 620 578 589 26 561 573 611 26 589 611 573 26 589 600 611 26 150 621 593 26 561 622 563 26 622 561 611 26 622 621 563 26 593 621 622 26 151 621 150 26 622 610 593 26 617 610 600 26 611 600 610 26 611 610 622 26 572 620 569 26 620 573 569 26 592 620 572 26 620 589 573 26 616 603 613 26 613 618 604 26 604 616 613 26 624 592 572 26 624 616 604 26 592 624 604 26 625 148 149 26 625 610 617 26 626 151 21 26 626 152 563 26 152 626 21 26 626 621 151 26 563 621 626 26 623 572 596 26 623 624 572 26 623 616 624 26 148 617 147 26 617 615 147 26 625 617 148 26 118 619 119 26 619 118 603 26 618 116 115 26 614 618 115 26 618 614 566 26 157 627 596 26 627 623 596 26 616 628 619 26 628 616 623 26 158 627 157 26 158 628 627 26 623 627 628 26 141 629 140 26 629 564 140 26 630 109 108 26 564 630 108 26 119 631 16 26 631 159 16 26 629 562 564 26 562 630 564 26 631 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42 126 127 1009 42 155 156 994 42 178 179 995 42 18 180 996 42 919 974 978 42 902 978 974 42 181 1008 946 42 127 947 1009 42 920 977 976 42 901 976 977 42 908 1002 950 42 913 988 958 42 16 986 999 42 172 998 987 42 928 1004 984 42 927 1003 985 42 905 984 1004 42 904 985 1003 42 925 960 988 42 917 997 957 42 905 1004 983 42 929 983 1004 42 899 1011 963 42 898 1010 956 42 899 979 1011 42 182 964 1008 42 126 1009 966 42 912 1013 959 42 900 981 1012 42 925 1012 981 42 927 992 1003 42 928 991 1004 42 930 1003 992 42 929 1004 991 42 919 978 1006 42 920 1007 977 42 918 979 1005 42 920 987 998 42 918 999 986 42 918 1011 979 42 933 976 1013 42 End trunk-2017.01a/examples/hourglass/hourglass.py000066400000000000000000000051161304022710500213730ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 # Anton Gladky # If you want to change the number of generated particles, # change it in line 44. Do not forget yo increase the firstIterRun # in line 62 not to revolute the hourglass before particles are # settled down at the bottom. from yade import ymport import time utils.readParamsFromTable(descriptionIn = 'noDescription', frIn = 0.5, enIn=0.01, etIn=0.01, tcIn=0.0001, # Frictionangle (rad), strength-parameter rhoIn = 1500.0, # Density dumpVTKIn = 4000 # Periods of dumps in iterations ) from yade.params.table import * import shutil try: shutil.rmtree('cpt') except OSError: pass os.mkdir('cpt') folderNameBase = 'cpt/' + str(descriptionIn) folderName = folderNameBase os.mkdir(folderNameBase) o = Omega() o.dt = 0.05*tcIn rotPeriod = 0.01 rotPeriodIter = int(rotPeriod/o.dt) mat1 = O.materials.append(ViscElMat(frictionAngle=frIn, density=rhoIn,tc=tcIn, en=enIn, et=etIn,)) id_HourGl = O.bodies.append(ymport.gmsh("hourglass.mesh",scale=1.0, material=mat1,color=(0,0,1),mask=5)) o.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()],verletDist=(2.0e-3),label='collider',ompThreads=1), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0,gravity=Vector3(0,0,-90.81), label='newt'), CircularFactory(maxParticles=1500, #Number of generated particles center=(0.0e-3, 0.0e-3,20.0e-3), radius = (12.0e-3), PSDsizes = [0.5e-3], PSDcum = [1.0], vMin=0.1,vMax=0.1,vAngle=0,massFlowRate=0.01, normal=(0.0,0.0,-1.0),label='factorySpheres',mask=3,materialId=mat1, stopIfFailed=False), RotationEngine(ids=id_HourGl, angularVelocity = math.pi/rotPeriod, rotateAroundZero=True, rotationAxis=Vector3(1,0,0), zeroPoint=Vector3(0.,0.,0.), label='rotEng', dead=True), VTKRecorder(iterPeriod=dumpVTKIn,fileName=folderName+'/spheres-',mask=2, recorders=['spheres','velocity','colors','intr','ids','mask','materialId','stress'], label='VTK_box1'), VTKRecorder(iterPeriod=dumpVTKIn,fileName=folderName+'/facetB-',mask=4, recorders=['facets'],label='VTK_box2'), PyRunner(iterPeriod=rotPeriodIter,initRun=False,firstIterRun=13000,command='startStepRotation()'), ] def startStepRotation(): if (rotEng.dead): rotEng.dead = False else: rotEng.dead = True from yade import qt qt.View() r=qt.Renderer() trunk-2017.01a/examples/jointedCohesiveFrictionalPM/000077500000000000000000000000001304022710500223725ustar00rootroot00000000000000trunk-2017.01a/examples/jointedCohesiveFrictionalPM/README000066400000000000000000000041361304022710500232560ustar00rootroot00000000000000This folder illustrates the modelling of fractured/jointed rock media, as initiated by Luc Scholtes: how Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM can be used to deal with jointed media (media containing pre-existing discontinuity surfaces e.g. fractures). For details/remarks/improvements, please send emails to lscholtes63@gmail.com or use https://answers.launchpad.net/yade/+addquestion. Also, please refer to following references (from https://www.yade-dem.org/doc/publications.html) for more details and explananations: Hartong2012a, Scholtes2012, Scholtes2013, Duriez2016 This folder includes the following files: 1-packInGtsSurface.py is a simple script used to generate a packing (parallellepiped_10.spheres) from a meshed closed surface (parallellepiped.gts). Packing generation can be done with other methods. The point here is to generate a packing and to save it in a text file (parallellepiped_10.spheres). 2-identificationSpheresOnJoint.py is a script used to identify the spheres belonging to a predefined packing (parallellepiped_10.spheres) interacting along pre-existing discontinuity surfaces defined by a meshed surface (persistentPlane30Deg.stl). Executing this script produces 2 text files containing respectively spheres from packing (parallellepiped_10_persistentPlane30Deg.spheres) and spheres attributes regarding jcfPM variables (parallellepiped_10_persistentPlane30Deg_jointedPM.spheres). 3-gravityLoading.py is a simple example showing how to use Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM. It simulates the loading of a pre-fractured packing (parallellepiped_10_persistentPlane30Deg.spheres) by gravity to emphasize how the pre-existing discontinuity affects the behavior. User can play along with joint surface properties (smooth contact logic or not, joint friction angle,...) to see the effect on the simulated behavior. A more compact way of use is proposed in gravityBis.py. This script is stand-alone, and calls itself the scrit identifBis.py. This later script can be called from any script in JCFpm modelling to detect spheres that should interact according to smooth contact logic.trunk-2017.01a/examples/jointedCohesiveFrictionalPM/gravityBis.py000066400000000000000000000100121304022710500250610ustar00rootroot00000000000000# encoding: utf-8 # example of use JCFpm classes : Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM... # a cubic rock massif, containing a rock joint with ~ 31 deg. dip angle. At one time, the mechanical properties of the joint are degraded, triggering a smooth sliding # definition of a predicate for use of randomDensePack() function from yade import pack dimModele = 10.0 pred = pack.inAlignedBox((0,0,0),(dimModele,dimModele,dimModele)) # the packing of spheres : def mat(): return JCFpmMat(type=1,young=1e8,poisson=0.3,frictionAngle=radians(30),density=3000,tensileStrength=1e6,cohesion=1e6,jointNormalStiffness=1e7,jointShearStiffness=1e7,jointCohesion=1e6,jointFrictionAngle=radians(20),jointDilationAngle=0.0) nSpheres = 3000.0 poros=0.13 rMeanSpheres = dimModele * pow(3.0/4.0*(1-poros)/(pi*nSpheres),1.0/3.0) print '' print 'Creating a cubic sample of spheres (may take some time and cause warnings)' print '' sp = pack.randomDensePack(pred,radius=rMeanSpheres,rRelFuzz=0.3,memoizeDb='/tmp/gts-triax-packings.sqlite',returnSpherePack=True) sp.toSimulation(color=(0.9,0.8,0.6),wire=False,material=mat) print '' print 'Sample created !' # Definition of the facets for joint's geometry import gts # joint with ~ 31 deg. dip angle v1 = gts.Vertex(0 , 0 , 0.8*dimModele) v2 = gts.Vertex(0 , dimModele , 0.8*dimModele ) v3 = gts.Vertex(dimModele , dimModele , 0.2*dimModele) v4 = gts.Vertex(dimModele , 0 , 0.2*dimModele) e1 = gts.Edge(v1,v2) e2 = gts.Edge(v2,v4) e3 = gts.Edge(v4,v1) f1 = gts.Face(e1,e2,e3) e4 = gts.Edge(v4,v3) e5 = gts.Edge(v3,v2) f2 = gts.Face(e2,e4,e5) s1 = gts.Surface() s1.add(f1) s1.add(f2) facet = gtsSurface2Facets(s1,wire = False,material=mat) O.bodies.append(facet) yade.qt.View() yade.qt.Controller() O.saveTmp() # identification of spheres onJoint, and so on: execfile('identifBis.py') dim=utils.aabbExtrema() xsup=dim[1][0] yinf=dim[0][1] ysup=dim[1][1] zinf=dim[0][2] zsup=dim[1][2] e=2*rMeanSpheres for o in O.bodies: if isinstance(o.shape,Sphere): o.shape.color=(0.9,0.8,0.6) ## to fix boundary particles on ground if o.state.pos[2]<(zinf+2*e) : o.state.blockedDOFs+='xyz' o.shape.color=(1,1,1) ## to identify indicator on top if o.state.pos[2]>(zsup-e) and o.state.pos[0]>(xsup-e) and o.state.pos[1]>((yinf+ysup-e)/2.0) and o.state.pos[1]<((yinf+ysup+e)/2) : refPoint=o.id O.bodies[refPoint].shape.highlight=True #### Engines definition O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], # [Ip2_JCFpmMat_JCFpmMat_JCFpmPhys(cohesiveTresholdIteration=1,alpha=0.3,tensileStrength=1e6,cohesion=1e6,jointNormalStiffness=1e7,jointShearStiffness=1e7,jointCohesion=1e6,jointFrictionAngle=radians(20),jointDilationAngle=0.0)], [Ip2_JCFpmMat_JCFpmMat_JCFpmPhys(cohesiveTresholdIteration=1)], [Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM(smoothJoint=True)] ), GlobalStiffnessTimeStepper(timestepSafetyCoefficient=0.8), PyRunner(iterPeriod=1000,initRun=False,command='jointStrengthDegradation()'), PyRunner(iterPeriod=10,initRun=True,command='dataCollector()'), NewtonIntegrator(damping=0.7,gravity=(0.,0.,-10.)), ] #### dataCollector from yade import plot plot.plots={'iterations':'v','x':'z'} def dataCollector(): R=O.bodies[refPoint] plot.addData(v=R.state.vel[2],z=R.state.pos[2],x=R.state.pos[0],iterations=O.iter,t=O.realtime) #### joint strength degradation stableIter=1000 stableVel=0.001 degrade=True def jointStrengthDegradation(): global degrade if degrade and O.iter>=stableIter and abs(O.bodies[refPoint].state.vel[2])Rmax: Rmax=o.shape.radius Rmean=R/numSpheres #### Identification of the spheres on joint (some DIY here!) -> work to do on import function textExt to directly load material properties from the ascii file inFile=open(packing+'_jointedPM.spheres','r') for line in inFile: if '#' in line : continue id = int(line.split()[0]) onJ = int(line.split()[1]) nj = int(line.split()[2]) j11 = float(line.split()[3]) j12 = float(line.split()[4]) j13 = float(line.split()[5]) j21 = float(line.split()[6]) j22 = float(line.split()[7]) j23 = float(line.split()[8]) j31 = float(line.split()[9]) j32 = float(line.split()[10]) j33 = float(line.split()[11]) O.bodies[id].state.onJoint=onJ O.bodies[id].state.joint=nj O.bodies[id].state.jointNormal1=(j11,j12,j13) O.bodies[id].state.jointNormal2=(j21,j22,j23) O.bodies[id].state.jointNormal3=(j31,j32,j33) inFile.close #### Boundary conditions e=2*Rmean Xmax=0 Ymax=0 baseBodies=[] for o in O.bodies: if isinstance(o.shape,Sphere): o.shape.color=(0.9,0.8,0.6) ## to fix boundary particles on ground if o.state.pos[1]<(yinf+2*e) : o.state.blockedDOFs+='xyz' baseBodies.append(o.id) o.shape.color=(1,1,1) ## to identify indicator on top if o.state.pos[1]>(ysup-e) and o.state.pos[0]>(xsup-e) and o.state.pos[2]>(zinf+(Z-e)/2) and o.state.pos[2]<(zsup-(Z-e)/2) : refPoint=o.id p0=o.state.pos[1] baseBodies=tuple(baseBodies) O.bodies[refPoint].shape.color=(1,0,0) #### Engines definition interactionRadius=1. # to set initial contacts to larger neighbours O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=interactionRadius,label='is2aabb'),]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=interactionRadius,label='ss2d3dg')], [Ip2_JCFpmMat_JCFpmMat_JCFpmPhys(cohesiveTresholdIteration=1,label='interactionPhys')], [Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM(smoothJoint=smoothContact,label='interactionLaw')] ), GlobalStiffnessTimeStepper(timestepSafetyCoefficient=0.8), PyRunner(iterPeriod=1000,initRun=False,command='jointStrengthDegradation()'), VTKRecorder(iterPeriod=5000,initRun=True,fileName=(output+'-'),recorders=['spheres','velocity','intr']), PyRunner(iterPeriod=10,initRun=True,command='dataCollector()'), NewtonIntegrator(damping=0.7,gravity=(0.,-9.82,0.)), ] #### dataCollector plot.plots={'iterations':('p',)} def dataCollector(): R=O.bodies[refPoint] plot.addData(v=R.state.vel[1],p=R.state.pos[1]-p0,iterations=O.iter,t=O.realtime) plot.saveDataTxt(output) #### joint strength degradation stableIter=2000 stableVel=0.001 degrade=True def jointStrengthDegradation(): global degrade if degrade and O.iter>=stableIter and abs(O.bodies[refPoint].state.vel[1])P;S. 16fxkl7\u[kZ} AG+C*o懎|?v:3+qx&tBg $ bd'$"\l"K<ߜ=>#gy/ٚ1-yUR}Yy92-B/x#,/yw;{ͦ'O+(W7>gBPd Z,"-pq^]"{88GqTd;vk_!L'_1!aie l@Ujѷ3]H!!:9#&w4m 'gD}8$!CָLKdPQ5$ h5hZd"TPik+B\pgƘɒ1n-eh޽+>j?pd:ϠC~oMHh\Rb:j'yvbaV"*&DP,BxBb!}(gX2g(ZQ%x晙'A9sUm(lX1[?3fTm'W:g#ac5ֱOϴ>~Qil"pϞ7o@]w$)ΉHP0wuC b^U0.'܅ &'d[mm5Ī~0U/n=;vC*PUY-,yX"]I9.}RBQyCC&Vf<2Μ+Q\ޖ$F dl>v2N9=Dhu$+Q,PT[nԩYA 33Ia)y_՘/4#đG$ws*ȝդ9 Bi4M@ 1IXMHNʤjk+UoxqU Ƙ޳\V5ﾻxnqt$tp1;@ bG, 9330]X( c40I3"LurB i >Wb_?C{1?Lk7}TK֟pjKSZ5c/ S<'Pe_ܼo5юp4[+sD)Wm65Ԏ#>spt, ѝ |) Cn\h45q|陴$ 2/Èo{dvc$:P^Pd]V V64{ 3dعcO ljwN*<4X݃Ɋ _s*{ H)MUI\> +Y Z,2O۔BYhpXZBP(I^` O>9366޽ɣy|Lcm KƬ.?w=s1wO᧜}nP¬<_"ܷF|3gfZ KGBU/W(3,.Ci~8K5-K}V>v2,,v'TѹD_,7 Nx)cfT*}WTfăQBmEUEZ#?[yawZ*P0 JXw2}>Č8m%Pe豼~mnZ~\K?۝{w0I؝ݸ<¦/yf iJC'[-B!/^Q#I@*:m-ݽ? l4UTOV|+#V<J34E!aXK؁̣k5z 27oMqw&'jյ75F" - yŒV Y0I&,TNw 7 LYo;p姠{To.Y6fy-Kߩ;cӄ.a9V伓'gC"sOdY,OAZ4qqHȲЍ$H MPD_AosLSz3 Tʭ$`qݤzGNħ>E![Z({O(Y_qHR5,<U=8$fKx,Bn}zݧ |Ze2V0rUգaqU{v6YbCc;1OuT!$$y>~}M $ )n ,,RM -hb@f cI8`n;GZm/4}\Q6HH zjۄɃJ9V}Zmj @EY=:?M$6$.w:l}ǿ7$p <喉%mӳIWD%pc#Yuޫ)"?уG .XϏ};z>|w2qLé3Isp2<5qY7kcG>(`fc I|n/Pv PEB 0t6 Ԗz&J%CyBKUP`_?T&C -X $_Di,K^=k͊W^n$ )b8S I|v[Gurƥt9BLWݶ-8ol 1KƬ:|x ߰6ffü6Iհ07f'~B5q"/?{Ȟ})G'f )]]"1]*Cq1{$rqhw4M\Lb\>:ıxk9Txcz(: \VW a gC  8X"  >+%!!DrxĨbnΧ$\ZH">P0P.U m< 9uB݋f)-/$I|`LRqKc˅7k:2|薉p!?Lj%o,y գ+τō5tY6fy'|osղ3=tn{Յ߸ A6^ǿ~zT߫2q׮WəBdǰ0˼\J(CCdMMS:,A*{J soPR& (ܔr3B NpV-"f0o:6ӊ;k׹xm@7n햧_?_|:c෦*UU uZ WZġZ(cAIYAbC֮$%B#Fz S9;&Eju-~Ir; khw‡>4V@qL;zGL!' { Uªg;{ȏNxYB>}{%oh4T;v~3iNΡ"PūpU5-F]B vYGק6)]&dP}$Bh"8Q%"ε Đ2U'RPt- Tዄy'pAuW5MeL(MJ%}_ /}[ժ (T1HKUb۷~+5U ( i#6;ݒpݾ2SQ ˔ J`FU}N74bO̸QVq=\C1zl8'vl 9=#c{"ŘΒ1qEo[p4';L U–%H,Ϋ nDk\9ڣs|꩙B1n=_okiIbiQ%&.ld ](TOCc7l B~$) MS ; qqk BOݺv ӔVUu诔(#wVcEyD"hѷ؁:#QqIrVE|@qE$|QcE(WNԪ2:hh%p[NLW#W4#n_)/.T#1 RfJ  7xc$1nWd\ç}DŽNκ$Py=,Y6f5z7.m9Ǫcy8}^VPz/U".aĢg OlX6ʹTFSFLއZ#zKu )̼j"qTd*FGxB1fKƬF_^K|,jt=8풘hnO ^c{fG?$&$-$.i$v)$P l)a# qlԵT`uRZo."a<,WE&M^]+"|@uF\EзGvwk0v՚tw1DCtGq::V"T6D>>z*p$L|TD~軵?-p[>gӓ oO RQ!퇪fSDŽ<Tv|h6uá6A`8x}$6˙jMBI^;wXOП˗oX>(HbHp xKE'/ +w.ؐi%{6)zxձGw`:Y6f5z7VG3;6|ӳI*n>Vӧg mc^$sf6,C\2|L#IUU#͖v:h6$a $jSVKw$:m/¸jOf c*6^;]'TŰ`;2d} ! ycPlnH~IzǦGlLZ[b♆W& JEƃwb[ iBSzÇ*zw6~NxCGO1Fd^"\.7(<8H|Եa;P[W#VGfAio(C_B N D+SAOvϘض}\)PG,|X6fuA^By-X~icbɱ\}L(-DpĂSOH>1:ļu~Aw.|.8xnŸư1T];s9@a;I}'.iJ||r@=nii}>PsCJP *7q@gչ =2t'ւK UD哿M^v$T(:H*%qw~yk2;vLݱ oc,t IDATy:,y ߖѣi ijAN)wDull'?pqD"$T&:`i1rJGoФj==Ҕϫs:(=nH5+ Bo,V&*kR-^G-q UU4;uOgJ(-hhG!6$Sj$61T"zX -%A$~:RZa\ǟ_Hc; r;C9-x T/gp.Gp`xb"q #z/) 7~z2p8Xq[)7GpKqXS)KlqbTx^;'~_ӳFu4W#KƬR=Nxr;Ѓ>3LR =M㺠~$lF$9#Ϟ=Iҭ7K(I$۪j \C Hc4~LR=\$(2ݻ'Y>Hݡ[psm*u 7uuYqȴ6KqGbn_O8vAӧg҂8$N]^B1?KXr@ 8&vz'TՊmTZk33U1qdvܘBIAd\T;6A'C`&RPcS՛5*84U8O y:ilmjh@# <PNjQ$n{&m?0 0wJL)MU;"+!3:hja |*('ju>i$c8X`dvK b(E\iuDd8Y!pjwf,^" f52')iBmQ(TmqJ\ka3P٫Z5D)xYĦ pcmSU%^BuHwugzc (;=7' E\,yz]{&#ܝ$yV[!l=;=o<3+K17[\PeZSzX\Tq"MБ#N'$f&* /U3J %z\X=--IbaAE c8_ݹh<$zCG,lu$va(84U#5?(4 󜫄sgkM`W{lUXk9 4-녷_"Í僵H~{!`hy00~W0JC}nN@%rP5tO_+e:ܧ{)}2pRIHZ:,xIJ/, E#e"8Rpx5`8$!k 9nZh~> *(ؒSxˇ>ӕb"E ޳^pMr@joUx^S.ZV,9 a )`DI3 QU1)ɭW&8f IUd==+x~c͕ƒ1%Ͼ ܝ)3+O== -ǎ>;\]2ItM:jZs^H ++t ۵LӔ՗Ztag`ӎ*oԵTbM ] {8Tķk}%"RԪ5#@⠊RAj#/8R<@\ ScʅpE8)Ctl4@$yyH~M j[UCu?v".'Gh1j$6. 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normalizes normalRef normalFacetSphere=i.geom.normal # geom.normal is oriented from id1 to id2 -> normalFacetSphere from facet (i.id1) to sphere (i.id2) if O.bodies[i.id2].state.onJoint==False : ## particles has not yet been identified as belonging to a joint plane O.bodies[i.id2].state.onJoint=True O.bodies[i.id2].state.joint=1 O.bodies[i.id2].shape.color=jointcolor1 if nRef.dot(normalFacetSphere)>=0 : O.bodies[i.id2].state.jointNormal1=nRef elif nRef.dot(normalFacetSphere)<0 : O.bodies[i.id2].state.jointNormal1=-nRef elif O.bodies[i.id2].state.onJoint==True : ## particles has already been identified as belonging to, at least, 1 facet if O.bodies[i.id2].state.joint==1 and ((O.bodies[i.id2].state.jointNormal1.cross(nRef)).norm()>0.05) : ## particles has already been identified as belonging to only 1 facet O.bodies[i.id2].state.joint=2 O.bodies[i.id2].shape.color=jointcolor2 if nRef.dot(normalFacetSphere)>=0 : O.bodies[i.id2].state.jointNormal2=nRef elif nRef.dot(normalFacetSphere)<0 : O.bodies[i.id2].state.jointNormal2=-nRef elif O.bodies[i.id2].state.joint==2 and ((O.bodies[i.id2].state.jointNormal1.cross(nRef)).norm()>0.05) and ((O.bodies[i.id2].state.jointNormal2.cross(nRef)).norm()>0.05): ## particles has already been identified as belonging to more than 1 facet O.bodies[i.id2].state.joint=3 O.bodies[i.id2].shape.color=jointcolor3 if nRef.dot(normalFacetSphere)>=0 : O.bodies[i.id2].state.jointNormal3=nRef elif nRef.dot(normalFacetSphere)<0 : O.bodies[i.id2].state.jointNormal3=-nRef elif O.bodies[i.id2].state.joint==3 and ((O.bodies[i.id2].state.jointNormal1.cross(nRef)).norm()>0.05) and ((O.bodies[i.id2].state.jointNormal2.cross(nRef)).norm()>0.05) and ((O.bodies[i.id2].state.jointNormal3.cross(nRef)).norm()>0.05): O.bodies[i.id2].state.joint=4 O.bodies[i.id2].shape.color=jointcolor5 #### second step -> find spheres interacting with spheres on facet (could be executed in the same timestep as step 1?) for j in O.interactions: #if not i.isReal : continue ## Rk: facet are only stored in id1 if isinstance(O.bodies[j.id1].shape,Facet) and isinstance(O.bodies[j.id2].shape,Sphere): vertices=O.bodies[j.id1].shape.vertices normalRef=vertices[0].cross(vertices[1]) # defines the normal to the facet normalRef nRef=normalRef/(normalRef.norm()) ## normalizes normalRef if ((O.bodies[j.id2].state.jointNormal1.cross(nRef)).norm()<0.05) : jointNormalRef=O.bodies[j.id2].state.jointNormal1 elif ((O.bodies[j.id2].state.jointNormal2.cross(nRef)).norm()<0.05) : jointNormalRef=O.bodies[j.id2].state.jointNormal2 elif ((O.bodies[j.id2].state.jointNormal3.cross(nRef)).norm()<0.05) : jointNormalRef=O.bodies[j.id2].state.jointNormal3 else : continue facetCenter=O.bodies[j.id1].state.pos #### seek for each sphere interacting with the identified sphere j.id2 for n in O.interactions.withBody(j.id2) : if isinstance(O.bodies[n.id1].shape,Sphere) and isinstance(O.bodies[n.id2].shape,Sphere): if j.id2==n.id1: # the sphere that was detected on facet (that is, j.id2) is id1 of interaction n sphOnF=n.id1 othSph=n.id2 elif j.id2==n.id2: # here, this sphere that was detected on facet (that is, j.id2) is id2 of interaction n sphOnF=n.id2 othSph=n.id1 facetSphereDir=(O.bodies[othSph].state.pos-facetCenter) if O.bodies[othSph].state.onJoint==True : if O.bodies[othSph].state.joint==3 and ((O.bodies[othSph].state.jointNormal1.cross(jointNormalRef)).norm()>0.05) and ((O.bodies[othSph].state.jointNormal2.cross(jointNormalRef)).norm()>0.05) and ((O.bodies[othSph].state.jointNormal3.cross(jointNormalRef)).norm()>0.05): O.bodies[othSph].state.joint=4 O.bodies[othSph].shape.color=jointcolor5 elif O.bodies[othSph].state.joint==2 and ((O.bodies[othSph].state.jointNormal1.cross(jointNormalRef)).norm()>0.05) and ((O.bodies[othSph].state.jointNormal2.cross(jointNormalRef)).norm()>0.05): O.bodies[othSph].state.joint=3 if facetSphereDir.dot(jointNormalRef)>=0: O.bodies[othSph].state.jointNormal3=jointNormalRef elif facetSphereDir.dot(jointNormalRef)<0: O.bodies[othSph].state.jointNormal3=-jointNormalRef elif O.bodies[othSph].state.joint==1 and ((O.bodies[othSph].state.jointNormal1.cross(jointNormalRef)).norm()>0.05) : O.bodies[othSph].state.joint=2 if facetSphereDir.dot(jointNormalRef)>=0: O.bodies[othSph].state.jointNormal2=jointNormalRef elif facetSphereDir.dot(jointNormalRef)<0: O.bodies[othSph].state.jointNormal2=-jointNormalRef elif O.bodies[othSph].state.onJoint==False : O.bodies[othSph].state.onJoint=True O.bodies[othSph].state.joint=1 O.bodies[othSph].shape.color=jointcolor4 if facetSphereDir.dot(jointNormalRef)>=0: O.bodies[othSph].state.jointNormal1=jointNormalRef elif facetSphereDir.dot(jointNormalRef)<0: O.bodies[othSph].state.jointNormal1=-jointNormalRef ##### to delete facets for b in O.bodies: if isinstance(b.shape,Facet): O.bodies.erase(b.id) O.resetTime() O.interactions.clear() print '\nIdentificationSpheresOnJoint executed ! Spheres onJoint (and so on...) detected, facets deleted, simulation may go on.\n\n' trunk-2017.01a/examples/jointedCohesiveFrictionalPM/identificationSpheresOnJoint.py000066400000000000000000000225721304022710500306000ustar00rootroot00000000000000# -*- coding: utf-8 -*- from yade import pack, utils, ymport, export packing='parallellepiped_10' DFN='persistentPlane30Deg' ############################ material definition facetMat = O.materials.append(JCFpmMat(type=0,young=1,frictionAngle=radians(1),poisson=0.4,density=1)) def sphereMat(): return JCFpmMat(type=1,young=1,frictionAngle=radians(1),density=1,poisson=1,tensileStrength=1e6,cohesion=1e6,jointNormalStiffness=1,jointShearStiffness=1,jointTensileStrength=1e6,jointCohesion=1e6,jointFrictionAngle=1) ############################ Import of the sphere assembly O.bodies.append(ymport.text(packing+'.spheres',scale=1,shift=Vector3(0,0,0),material=sphereMat)) #(-3,-4,-8) #### some preprocessing (not mandatory) dim=utils.aabbExtrema() xinf=dim[0][0] xsup=dim[1][0] yinf=dim[0][1] ysup=dim[1][1] zinf=dim[0][2] zsup=dim[1][2] R=0 Rmax=0 numSpheres=0. for o in O.bodies: if isinstance(o.shape,Sphere): o.shape.color=(0,0,1) numSpheres+=1 R+=o.shape.radius if o.shape.radius>Rmax: Rmax=o.shape.radius else : o.shape.color=(0,0,0) Rmean=R/numSpheres print 'number of spheres=', numSpheres, ' | Rmean=', Rmean, ' | dim=', dim ############################ import stl file O.bodies.append(ymport.stl(DFN+'.stl',color=(0.9,0.9,0.9),wire=False,material=facetMat)) ############################ engines definition interactionRadius=1.; O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=interactionRadius,label='is2aabb'),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=interactionRadius,label='ss2d3dg'),Ig2_Facet_Sphere_ScGeom()], [Ip2_JCFpmMat_JCFpmMat_JCFpmPhys(cohesiveTresholdIteration=1,label='interactionPhys')], [Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM(smoothJoint=True,label='interactionLaw')] ), NewtonIntegrator(damping=1) ] ############################ timestep + opening yade windows O.dt=0.001*utils.PWaveTimeStep() from yade import qt v=qt.Controller() v=qt.View() ############################ Identification spheres on joint #### color set for particles on joint jointcolor1=(0,1,0) jointcolor2=(1,0,0) jointcolor3=(0,0,1) jointcolor4=(1,1,1) jointcolor5=(0,0,0) #### first step-> find spheres on facet O.step(); for i in O.interactions: ##if not i.isReal : continue if isinstance(O.bodies[i.id1].shape,Facet) and isinstance(O.bodies[i.id2].shape,Sphere): vertices=O.bodies[i.id1].shape.vertices normalRef=vertices[0].cross(vertices[1]) # defines the normal to the facet normalRef nRef=normalRef/(normalRef.norm()) ## normalizes normalRef normalFacetSphere=i.geom.normal # geom.normal is oriented from id1 to id2 -> normalFacetSphere from facet (i.id1) to sphere (i.id2) if O.bodies[i.id2].state.onJoint==False : ## particles has not yet been identified as belonging to a joint plane O.bodies[i.id2].state.onJoint=True O.bodies[i.id2].state.joint=1 O.bodies[i.id2].shape.color=jointcolor1 if nRef.dot(normalFacetSphere)>=0 : O.bodies[i.id2].state.jointNormal1=nRef elif nRef.dot(normalFacetSphere)<0 : O.bodies[i.id2].state.jointNormal1=-nRef elif O.bodies[i.id2].state.onJoint==True : ## particles has already been identified as belonging to, at least, 1 facet if O.bodies[i.id2].state.joint==1 and ((O.bodies[i.id2].state.jointNormal1.cross(nRef)).norm()>0.05) : ## particles has already been identified as belonging to only 1 facet O.bodies[i.id2].state.joint=2 O.bodies[i.id2].shape.color=jointcolor2 if nRef.dot(normalFacetSphere)>=0 : O.bodies[i.id2].state.jointNormal2=nRef elif nRef.dot(normalFacetSphere)<0 : O.bodies[i.id2].state.jointNormal2=-nRef elif O.bodies[i.id2].state.joint==2 and ((O.bodies[i.id2].state.jointNormal1.cross(nRef)).norm()>0.05) and ((O.bodies[i.id2].state.jointNormal2.cross(nRef)).norm()>0.05): ## particles has already been identified as belonging to more than 1 facet O.bodies[i.id2].state.joint=3 O.bodies[i.id2].shape.color=jointcolor3 if nRef.dot(normalFacetSphere)>=0 : O.bodies[i.id2].state.jointNormal3=nRef elif nRef.dot(normalFacetSphere)<0 : O.bodies[i.id2].state.jointNormal3=-nRef elif O.bodies[i.id2].state.joint==3 and ((O.bodies[i.id2].state.jointNormal1.cross(nRef)).norm()>0.05) and ((O.bodies[i.id2].state.jointNormal2.cross(nRef)).norm()>0.05) and ((O.bodies[i.id2].state.jointNormal3.cross(nRef)).norm()>0.05): O.bodies[i.id2].state.joint=4 O.bodies[i.id2].shape.color=jointcolor5 #### second step -> find spheres interacting with spheres on facet (could be executed in the same timestep as step 1?) for j in O.interactions: #if not i.isReal : continue if isinstance(O.bodies[j.id1].shape,Facet) and isinstance(O.bodies[j.id2].shape,Sphere): vertices=O.bodies[j.id1].shape.vertices normalRef=vertices[0].cross(vertices[1]) # defines the normal to the facet normalRef nRef=normalRef/(normalRef.norm()) ## normalizes normalRef if ((O.bodies[j.id2].state.jointNormal1.cross(nRef)).norm()<0.05) : jointNormalRef=O.bodies[j.id2].state.jointNormal1 elif ((O.bodies[j.id2].state.jointNormal2.cross(nRef)).norm()<0.05) : jointNormalRef=O.bodies[j.id2].state.jointNormal2 elif ((O.bodies[j.id2].state.jointNormal3.cross(nRef)).norm()<0.05) : jointNormalRef=O.bodies[j.id2].state.jointNormal3 else : continue facetCenter=O.bodies[j.id1].state.pos #### seek for each sphere interacting with the identified sphere j.id2 for n in O.interactions.withBody(j.id2) : if n.id1==j.id2 and isinstance(O.bodies[n.id2].shape,Sphere): facetSphereDir=(O.bodies[n.id2].state.pos-facetCenter) if O.bodies[n.id2].state.onJoint==True : if O.bodies[n.id2].state.joint==3 and ((O.bodies[n.id2].state.jointNormal1.cross(jointNormalRef)).norm()>0.05) and ((O.bodies[n.id2].state.jointNormal2.cross(jointNormalRef)).norm()>0.05) and ((O.bodies[n.id2].state.jointNormal3.cross(jointNormalRef)).norm()>0.05): O.bodies[n.id2].state.joint=4 O.bodies[n.id2].shape.color=jointcolor5 elif O.bodies[n.id2].state.joint==2 and ((O.bodies[n.id2].state.jointNormal1.cross(jointNormalRef)).norm()>0.05) and ((O.bodies[n.id2].state.jointNormal2.cross(jointNormalRef)).norm()>0.05): O.bodies[n.id2].state.joint=3 if facetSphereDir.dot(jointNormalRef)>=0: O.bodies[n.id2].state.jointNormal3=jointNormalRef elif facetSphereDir.dot(jointNormalRef)<0: O.bodies[n.id2].state.jointNormal3=-jointNormalRef elif O.bodies[n.id2].state.joint==1 and ((O.bodies[n.id2].state.jointNormal1.cross(jointNormalRef)).norm()>0.05) : O.bodies[n.id2].state.joint=2 if facetSphereDir.dot(jointNormalRef)>=0: O.bodies[n.id2].state.jointNormal2=jointNormalRef elif facetSphereDir.dot(jointNormalRef)<0: O.bodies[n.id2].state.jointNormal2=-jointNormalRef elif O.bodies[n.id2].state.onJoint==False : O.bodies[n.id2].state.onJoint=True O.bodies[n.id2].state.joint=1 O.bodies[n.id2].shape.color=jointcolor4 if facetSphereDir.dot(jointNormalRef)>=0: O.bodies[n.id2].state.jointNormal1=jointNormalRef elif facetSphereDir.dot(jointNormalRef)<0: O.bodies[n.id2].state.jointNormal1=-jointNormalRef elif n.id2==j.id2 and isinstance(O.bodies[n.id1].shape,Sphere): facetSphereDir=(O.bodies[n.id1].state.pos-facetCenter) if O.bodies[n.id1].state.onJoint==True : if O.bodies[n.id1].state.joint==3 and ((O.bodies[n.id1].state.jointNormal1.cross(jointNormalRef)).norm()>0.05) and ((O.bodies[n.id1].state.jointNormal2.cross(jointNormalRef)).norm()>0.05) and ((O.bodies[n.id1].state.jointNormal3.cross(jointNormalRef)).norm()>0.05): O.bodies[n.id1].state.joint=4 O.bodies[n.id1].shape.color=jointcolor5 elif O.bodies[n.id1].state.joint==2 and ((O.bodies[n.id1].state.jointNormal1.cross(jointNormalRef)).norm()>0.05) and ((O.bodies[n.id1].state.jointNormal2.cross(jointNormalRef)).norm()>0.05): O.bodies[n.id1].state.joint=3 if facetSphereDir.dot(jointNormalRef)>=0: O.bodies[n.id1].state.jointNormal3=jointNormalRef elif facetSphereDir.dot(jointNormalRef)<0: O.bodies[n.id1].state.jointNormal3=-jointNormalRef elif O.bodies[n.id1].state.joint==1 and ((O.bodies[n.id1].state.jointNormal1.cross(jointNormalRef)).norm()>0.05) : O.bodies[n.id1].state.joint=2 if facetSphereDir.dot(jointNormalRef)>=0: O.bodies[n.id1].state.jointNormal2=jointNormalRef elif facetSphereDir.dot(jointNormalRef)<0: O.bodies[n.id1].state.jointNormal2=-jointNormalRef elif O.bodies[n.id1].state.onJoint==False : O.bodies[n.id1].state.onJoint=True O.bodies[n.id1].state.joint=1 O.bodies[n.id1].shape.color=jointcolor4 if facetSphereDir.dot(jointNormalRef)>=0: O.bodies[n.id1].state.jointNormal1=jointNormalRef elif facetSphereDir.dot(jointNormalRef)<0: O.bodies[n.id1].state.jointNormal1=-jointNormalRef #### for visualization: #bj=0 #vert=(0.,1.,0.) #hor=(0.,1.,1.) #for o in O.bodies: #if o.state.onJoint==True : # or o.shape.name=='Facet': ##if o.shape.name=='Facet': ##o.shape.wire=True ##o.state.pos+=(0,50,0) ##bj+=1 #if o.state.jointNormal1.dot(hor)>0 : ##o.state.pos+=(0,50,0) #o.shape.color=jointcolor1 #elif o.state.jointNormal1.dot(hor)<0 : ##o.state.pos+=(0,55,0) #o.shape.color=jointcolor2 #if o.mat.type>2 : #bj+=1 #o.shape.color=jointcolor5 ##print o.state.jointNormal.dot(vert) #### Save text file with informations on each sphere export.text(packing+'_'+DFN+'.spheres') export.textExt(packing+'_'+DFN+'_jointedPM.spheres',format='jointedPM') O.wait() trunk-2017.01a/examples/jointedCohesiveFrictionalPM/jointedModel.png000066400000000000000000006613271304022710500255340ustar00rootroot00000000000000PNG  IHDR IDATxWdYrYYZazbh4R x>p 9zӣ5!Җ4Hи$P٪DZwUfĽϽU== `rYMMTfdHQD0 0 0o1~aaSކaa6 0 0aaa 0 0 c'0maa;)o0 0 LyaaN`0 0 0vSކaa6 0 0aaa 0 0 c'0maa;)o0 0 LyaaN`0 0 0vSކaa6 0 0aaa 0 0 c'0maa;)o0 0 LyaaN`0 0 0vSކaa6 0 0aaa 0 0 c'0maa;)o0 0 LyaaN`0 0 0vSކaa6 0 0aaa 0 0 c'0maa;)o0 0 LyaaN`0 0 0vSކaa6 0 0aaa 0 0 c'0maa;)o0 0 LyaaN`0 0 0vSކaa6 0 0aaa 0 0 c'0maa;)o0 0 LyaaNO0 xcNc{o32 E 07O~`RUXU4yD6p >a-LyaO?5J*K2= %Qb#<O76MaƛSކaon>h8@fw'>:-K\.e@u{OGޣwCm!F`kxkK C_+fYq^S2 ƔaƛO|tZ8'Ĥ,*i\$y!LG"(}n溦̣0ږhղ20Yš(7 [)o07%O>1+,Ks|2ЛCb'>8)K* sr :TuFH" ,,rrL,̓0gґm BzJ1O]?aw& 0djqYjAB6H}{jܝd[1F CXrtX۶PXVşᗿ4w3B+O|a0mf˂ʲWSw+sw#80c,p\`ݭթB%8ܼ)Ee"}ri{teAEu'Q!9 ׶뚊1H3?y~rp|q 0Ř6 xsQk&Ni0@f~Gc8!!"`Win=B%3Ρ~99 D"gݚN u`Щsޣ4i~ NL@wv]SUaSa,(#9&k2cp0&0:Դ*LܳM'XytD6," B@fyeUaQ`! 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G>Ͽ| :ycqyh`\)2)y XeѶuYNrc񨛈ion!q᷀p#_o2jNvNR]lDZ1y=7,l6(MSɨ[nv:6n""z6{dłLDg"3:hEW2AW55S5-V RCά$"Gg{/yCc$Dt:cAb b[=ẙ""ztxxMt.!+ qf ݂Q7=*?L ?>|:A?5??|:A?5?"}?[l??"}?[l?p!???p!??>=O?bl??>=O?bl?l?}%?5??l?}%?5?L?X ?(>?L?X ?(>ܳ]??'B=5?ܳ]??'B=5L?W ?þ?L?W ?þ?}%?5??}%?5&><O?Zl?&><O?Zl$(5??$(5?}?al?}?alo;A?5?o;A?5L ?þL ?þܳ]?͹?trunk-2017.01a/examples/jointedCohesiveFrictionalPM/testingJoint.py000066400000000000000000000103641304022710500254310ustar00rootroot00000000000000# encoding: utf-8 # Abstract : this script defines a "rock joint" sample : two rectangular blocks separated by an horizontal joint surface. Imposing relative movements of the blocks, that are clumps, allows to test directly the behaviour of the joint, described by JCFpm model. # jerome.duriez@3sr-grenoble.fr # Mechanical properties of rock matrix and rock joint : def mat(): return JCFpmMat(type=1,young=15.e9,frictionAngle=radians(35),density=3000,poisson=0.35,tensileStrength=4.5e6,cohesion=45.e6,jointNormalStiffness=5.e7,jointShearStiffness=2.5e7,jointCohesion=0.,jointTensileStrength=0.,jointFrictionAngle=radians(35.),jointDilationAngle=0.0) # --- Creating a sample of spheres # definition of a predicate from yade import pack Lx = 10 Ly = 10 Lz = 6 pred = pack.inAlignedBox((0,0,0),(Lx,Ly,Lz)) # use of randomDensePack() function nSpheres = 1500.0 poros=0.13 # apparently the value of porosity of samples generated by pack.randomDensePack rMeanSpheres = pow(Lx*Ly*Lz*3.0/4.0*(1-poros)/(pi*nSpheres),1.0/3.0) print '\nGenerating sphere sample, be patient' sp = pack.randomDensePack(pred,radius=rMeanSpheres,rRelFuzz=0.3,memoizeDb='/tmp/gts-triax-packings.sqlite',returnSpherePack=True) sp.toSimulation(color=(0.9,0.8,0.6),wire=False,material=mat) print 'Sphere sample generated !' # --- The joint surface : half of the height import gts v1 = gts.Vertex(0 , 0 , Lz/2.0) v2 = gts.Vertex(Lx, 0 , Lz/2.0) v3 = gts.Vertex(Lx, Ly, Lz/2.0) v4 = gts.Vertex(0 , Ly, Lz/2.0) e1 = gts.Edge(v1,v2) e2 = gts.Edge(v2,v4) e3 = gts.Edge(v4,v1) f1 = gts.Face(e1,e2,e3) e4 = gts.Edge(v4,v3) e5 = gts.Edge(v3,v2) f2 = gts.Face(e2,e4,e5) s1 = gts.Surface() s1.add(f1) s1.add(f2) facet = gtsSurface2Facets(s1,wire = False,material=mat) O.bodies.append(facet) # --- Identification of spheres onJoint, and so on: execfile('identifBis.py') # --- Engines definition O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_JCFpmMat_JCFpmMat_JCFpmPhys(cohesiveTresholdIteration=1)], [Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM(smoothJoint=True)]), GlobalStiffnessTimeStepper(timestepSafetyCoefficient=0.8), NewtonIntegrator(damping=0.2), PyRunner(command='afficheIt()',initRun=True,iterPeriod=1000), ] def afficheIt(): print 'It', O.iter O.step() # --- Clumping the blocks upperBlock=[] lowerBlock=[] for inte in O.interactions: if not inte.phys.isOnJoint: bod1 = O.bodies[inte.id1] bod2 = O.bodies[inte.id2] if bod1.state.pos[2]Lz/2.0: print '\n **** ERROR !!!! ******* \n\n' else: if not (bod2.id in lowerBlock): lowerBlock.append(bod2.id) bod2.shape.color=Vector3(1,0,0) else: if not (bod1.id in upperBlock): upperBlock.append(bod1.id) bod1.shape.color=Vector3(0,0,1) if bod2.state.pos[2] 0: # run simulatinon until the interaction is broken sn,st = i.phys.sigmaN, i.phys.sigmaT.norm() # store last values O.step() if O.iter > 1e6: raise RuntimeError, "TODO" # not to run forever plot.addData(sn=sn,st=st) # after the interaction is broken, save stress to plot.data and return return # run n simulations from tension to compression n = 50 for i in xrange(n): sim(i*pi/(n-1)) # plot the results plot.plots = {'sn':'st'} plot.matplotlib.pyplot.axes().set_aspect(1) plot.plot() trunk-2017.01a/examples/mortar/modelTests/shear.py000066400000000000000000000070201304022710500221020ustar00rootroot00000000000000from yade import plot ###################################################################### # Script to test brick material in shear. The material is # initially BrickMat. After failure and deletion of cohesive mortar # interaction, the simulation continues with PolyhedraMat. ###################################################################### ###################################################################### # I N P U T S ###################################################################### x,y,z = .2,.5,.7 # dimension of the bricks vDspl = -1e-3 # vertical displacement (+=tension, -=compression) hDspl = 1e-3 # horizontal displacement for shear nSteps = 1000 # each phase will take nSteps iterations ###################################################################### young = 4e9 poisson = .2 tensileStrength = .2e3 cohesion = .3e6 frictionAngle = atan(.5) compressiveStrength = 10e6 frictionAngle2 = atan(.4) # independent friction angle for PolyhedraMat for residual strength ###################################################################### O.dt = 1e-3 mortar = MortarMat(young=young,poisson=1/(2*(1+poisson)),tensileStrength=tensileStrength,cohesion=cohesion,frictionAngle=frictionAngle,compressiveStrength=compressiveStrength) polyMat = PolyhedraMat(young=young/z,poisson=1e3,frictionAngle=frictionAngle2) for mat in (mortar,polyMat): O.materials.append(mat) # two bricks with blockedDOFs, initially with MortarMat bs = b1,b2 = [polyhedron(((-x,-y,-z),(+x,-y,-z),(-x,+y,-z),(+x,+y,-z),(-x,-y,+z),(+x,-y,+z),(-x,+y,+z),(+x,+y,+z)),material=mortar) for i in (0,1)] b2.state.pos = b2.state.refPos = (0,0,2*z) for b in bs: b.state.blockedDOFs = 'xyzXYZ' O.bodies.append(bs) # function to plot the results def plotAddData(): dspl = O.bodies[1].state.displ() dn = dspl[2] ds = dspl[0] try: i = O.interactions[0,1] fn = i.phys.normalForce.norm() fs = i.phys.shearForce.norm() except (IndexError,AttributeError): fn = fs = 0. plot.addData( i = O.iter, dn = dn, ds = ds, fn = fn, fs = fs, ) # checkpoints def checkpoint(): if O.iter==nSteps: O.bodies[1].state.vel = (hDspl/(nSteps*O.dt),0,0) elif O.iter==2*nSteps: O.pause() plot.saveDataTxt('/tmp/shear.dat') # # factor to safely create interaction of just touching bricks factor=1.1 O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Polyhedra_Aabb(aabbEnlargeFactor=factor,label='bo1')]), InteractionLoop( # both ScGeom and PolyhedraGeom, MortarMat and PolyhedraMat [Ig2_Polyhedra_Polyhedra_PolyhedraGeomOrScGeom(label='ig2')], [Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys(),Ip2_MortarMat_MortarMat_MortarPhys()], [Law2_PolyhedraGeom_PolyhedraPhys_Volumetric(),Law2_ScGeom_MortarPhys_Lourenco()], ), NewtonIntegrator(), PyRunner(iterPeriod=1,command='plotAddData()'), PyRunner(iterPeriod=1,command='checkpoint()'), ] ig2.ig2scGeom.interactionDetectionFactor = factor O.step() # after O.step, a cohesive interaction is created and we can change material of the bodies. It has no effect on existing interactions, but newly created interactions will be created form the new material for b in O.bodies: b.mat = polyMat ig2.createScGeom = False # also for new interactions, create PolyhedraGeom rather than ScGeom ig2.ig2scGeom.interactionDetectionFactor = bo1.aabbEnlargeFactor = 1 # deactivate interaction detection enlargement phys = O.interactions[0,1].phys phys.kn = young*2*x*2*y/(2*z) # sets correct kn of interaction phys.crossSection = 2*x*2*y plot.plots = {'dn':'fn','ds':'fs','i':('fn','fs')} plot.plot() b2.state.vel = (0,0,vDspl/(nSteps*O.dt)) O.run() trunk-2017.01a/examples/normalInelasticity-test.py000066400000000000000000000152361304022710500222100ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Script to test the constitutive law contained in NormalInelasticityLaw : consider two spheres moving one to each other (this script illustrates few different ways of moving spheres) #- first penetration of the contact evolves => Monitor of the normal force #- then, test in tangential direction #- finally for what concerns moment transfer, with relative orientation changes (use frictionAngle=0.0 in this case to study more easily what's going on) #Different graphs illustrate the effects of the different loadings. The run is paused at each plot window (so that there is time to observe them). Push on "Return", while being in the Yade terminal, to go ahead. # Comment/uncomment around l.18-19 and l.38 to execute the script with Law2_ScGeom_FrictPhys_CundallStrack, to see the difference #No crash warranty with r2676 and r2852 +/-2 from yade import plot #Def of the material which will be used O.materials.append(NormalInelasticMat(density=2600,young=4.0e9,poisson=.04,frictionAngle=.6,coeff_dech=3.0,label='Materiau1')) #O.materials.append(FrictMat(young=10e9,poisson=.25,frictionAngle=0.5,density=1e3)) #Def of the bodies of the simulations : 2 spheres, with names which will be useful after O.bodies.append(sphere([0,0,0], 1, fixed=True, wire=False, color=None, highlight=False)) #'Materiau1', as the latest material defined, will be used O.bodies.append(sphere([0,2,0], 1, fixed=True, wire=False, color=None, highlight=False)) lowerSphere=O.bodies[0] upperSphere=O.bodies[1] #Def of the engines taking part to the simulation loop O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()],verletDist=0),# use of verletDist>0 without NewtonIntegrator let crash ?? InteractionLoop( [Ig2_Sphere_Sphere_ScGeom6D()], [Ip2_2xNormalInelasticMat_NormalInelasticityPhys(betaR=0.24)], [Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity()] ), #InteractionLoop( #[Ig2_Sphere_Sphere_ScGeom()], #[Ip2_FrictMat_FrictMat_FrictPhys()], #[Law2_ScGeom_FrictPhys_CundallStrack()]), PyRunner(iterPeriod=1,command='letMove()') ] #Def of the python commands which will impose required displacements to the moving sphere def letMove():#Load for the first 10 iterations, unload for the 7 following iterations, then reload if mode=='normal': vImposed=[0,-1,0] if O.iter < 25 and O.iter>14: vImposed=[0,1,0] if mode=='tangential': vImposed=[1,0,0] upperSphere.state.vel=vImposed upperSphere.state.pos=upperSphere.state.pos+upperSphere.state.vel*O.dt #Def of the python command defData() : which will be used once the interaction will really exist def defData(): i=O.interactions[1,0] vecFn=i.phys.normalForce vecDist=upperSphere.state.pos-lowerSphere.state.pos plot.addData(normFn=vecFn.norm(),normFnBis=vecFn.norm(),fnY=vecFn[1],step=O.iter, unPerso=lowerSphere.shape.radius+upperSphere.shape.radius-vecDist.norm(),unTrue=i.geom.penetrationDepth, gamma=upperSphere.state.pos[0]-lowerSphere.state.pos[0],fx=O.forces.f(0)[0],torque=O.forces.t(1)[2]) #print i.geom.penetrationDepth # ------ Test of the law in the normal direction, using python commands to let move ------ # print 'Beginning of normal loading' mode='normal' O.dt=1e-5 #print 'Ok 1' #yade.qt.View() print 'Going to first cycles, for free' #stop O.run(2,True) #cycles "for free", so that the interaction between spheres will be defined (with his physics and so on) print 'First cycles done' O.engines=O.engines+[PyRunner(iterPeriod=1,command='defData()')] O.run(40,True) print 'End of normal loading' # define of the plots to be made : un(step), and Fn(un) plot.plots={'step':('unTrue','torque',),'unPerso':('normFn',),'unTrue':('normFnBis',)} plot.plot(noShow=False, subPlots=False) print 'Plotting curve. Type Return to go ahead' print '' raw_input() #-- Comments (r2851) --# # - different unTrue and unPerso illustrate the definition of penetrationDepth really used in the code (computed in Ig2_Sphere_Sphere_ScGeom6D) which is slightly different from R1 + R2 - Distance (because of this "shift2" in Distance computation). According to the really used penetrationDepth, Fn evolves as it should # - value of virgin slope is 4e9 N/m (r2851) corresponding indeed to input "young" (as it should be the case here with used radii) # - and unload-reload slope is correctly multiplied by three # ------ Test of the law in the tangential direction, still with python function ------ # print 'Beginning of tangential loading' mode='tangential' O.run(1000,True) print 'End of tangential loading' tOn0woLTM=O.forces.t(0) tOn1woLTM=O.forces.t(1) plot.plots={'step':('gamma','torque',),'gamma':('fx',)} plot.plot(subPlots=False) print 'Plotting curve. Type Return to go ahead' raw_input() plot.plots={'normFn':('fx',)} plot.plot(subPlots=False) print 'Plotting another curve. Type Return to go ahead' raw_input() #pylab.show() #to pause on the plot window. Effective only first time print '' #-- Comments (r2528) --# # - evolution of Fx with gamma normal (flat at the beginning because of the order of engines) # - waited value of initial slope of fx(gamma) equal to 1.6 e8 N/m confirmed by what can be measured (r2851) # - un decreases indeed during this shear, but maybe a zoom on the curves is needed to see it. # - We can observe that the force state of the sample decreases a line with a slope equal to tan(~34.5°)=tan(~0.602 rad). Why not strict equality ? Because of the measure of the slope or because something else ? To see... # - during this phase O.forces.t(0).norm() / O.forces.f(0)[0] seems to increase between 0.502 and 0.507 (according to r=[T[i]/F[i] for i in range(50,T.__len__()-20) ]) # Please note, to explain this, that Fx = O.forces.f(0)[0] is more and more different from Ft, from which we can expect Ft = Torque /Radius ## ------ Test of the law for the moment, using blockedDOF_s and NewtonIntegrator ------ # print 'Beginning of rotationnal loading' ##To use blockedDOF_s, the body has to be dynamic.... upperSphere.dynamic=True upperSphere.state.blockedDOFs='xyzXYZ' upperSphere.state.angVel=Vector3(0,0,1) upperSphere.state.vel=Vector3(0,0,0) i=O.interactions[1,0] O.engines=O.engines[:3]+[NewtonIntegrator()]+O.engines[4:]#+[PyRunner(iterPeriod=1,command='printInfo()')] def printInfo(): print O.iter print upperSphere.state.ori print i.geom.penetrationDepth O.run(4000,True) print 'End of rotationnal loading' tOn0withLTMonly=O.forces.t(0)- tOn0woLTM tOn1withLTMonly=O.forces.t(1)- tOn1woLTM plot.plots={'step':('torque',)} plot.plot(subPlots=False) print 'Type Return to go ahead' #-- Comments : (r2851) # - threshold of increment of torque corresponding to relative rotation corresponds to the threshold value which is expected : 1.0 (here) * Fn ~ 5.4e5 Nm trunk-2017.01a/examples/not-working/000077500000000000000000000000001304022710500172565ustar00rootroot00000000000000trunk-2017.01a/examples/not-working/Se3Interpolator.py000066400000000000000000000026671304022710500227000ustar00rootroot00000000000000# default parameters or from table # encoding: utf-8 """ THIS SCRIPT IS NOT WORKING! ERROR MESSAGE: Running script Se3Interpolator.py Traceback (most recent call last): File "/home/me/YADE/YADE3041/bin/yade-bzr3041", line 182, in runScript execfile(script,globals()) File "Se3Interpolator.py", line 8, in Se3Interpolator(ids=[0],goal=(Vector3(10,10,0),Quaternion(0,0,1,pi)),startIter=10,goalIter=1010,goalHook='print "Finished moving the thing!"; O.pause()'), NameError: name 'Se3Interpolator' is not defined """ O.bodies.append([ sphere([0,0,0],radius=.5), ]) O.engines=[ Se3Interpolator(ids=[0],goal=(Vector3(10,10,0),Quaternion(0,0,1,pi)),startIter=10,goalIter=1010,goalHook='print "Finished moving the thing!"; O.pause()'), ] O.dt=1e-6 print 'Initial se3:',O.bodies[0].phys['se3'] #O.saveTmp('init'); O.run(); O.wait(); #print 'Final se3:',O.bodies[0].phys['se3'] #quit() trunk-2017.01a/examples/not-working/facet-topo.py000066400000000000000000000053401304022710500216730ustar00rootroot00000000000000""" THIS SCRIPT IS NOT WORKING! ERROR MESSAGE: Running script facet-topo.py Traceback (most recent call last): File "/home/me/YADE/YADE3041/bin/yade-bzr3041", line 182, in runScript execfile(script,globals()) File "facet-topo.py", line 14, in O.step(); RuntimeError: FACET_TOPO was not enabled in Facet.hpp at compile-time. Do not use FacetTopologyAnalyzer or recompile. """ # Note: FacetTopologyAnalyzer is normally run as an initializer; # it is only for testing sake that it is in O.engines here. O.engines=[FacetTopologyAnalyzer(projectionAxis=(1,1,1),label='topo'),] # most simple case: no touch at all if 1: O.bodies.append([ facet([(0,0,0),(1,0,0),(0,1,0)]), facet([(0,0,1),(1,0,1),(0,1,1)]), ]) O.step(); assert(topo['commonEdgesFound']==0) if 1: O.bodies.clear() O.bodies.append([ facet([(0,0,0),(1,0,0),(0,1,0)]), facet([(1,1,0),(1,0,0),(0,1,0)]), ]) O.step() assert(O.bodies[0].shape['edgeAdjIds'][1]==0 and O.bodies[1].shape['edgeAdjIds'][1]==1) assert(topo['commonEdgesFound']==1) if 1: O.bodies.clear() O.bodies.append([ facet([(0,0,0),(1,0,0),(0,1,0)]), facet([(1,1,1),(1,0,0),(0,1,0)]), ]) O.step() assert(O.bodies[0].shape['edgeAdjIds'][1]==0 and O.bodies[1].shape['edgeAdjIds'][1]==1) assert(topo['commonEdgesFound']==1) assert(abs(O.bodies[0].shape['edgeAdjHalfAngle'][1]-(-.5*atan(2/sqrt(2))))<1e-6) if 1: O.bodies.clear() r=.5 # radius of the sphere nPoly=12; # try 128, it is still quite fast def sphPt(i,j): if i==0: return (0,0,-r) if i==nPoly/2: return (0,0,r) assert(i>0 and i=0 and j<=nPoly) theta=i*2*pi/nPoly rr=r*sin(theta) phi=j*2*pi/nPoly return rr*cos(phi),rr*sin(phi),-r*cos(theta) for i in range(0,nPoly/2): for j in range(0,nPoly): if i!=0: O.bodies.append(facet([sphPt(i,j),sphPt(i,j+1),sphPt(i+1,j)])) if i!=nPoly/2-1: O.bodies.append(facet([sphPt(i+1,j),sphPt(i,j+1),sphPt(i+1,j+1)])) print 'Sphere created, has',len(O.bodies),'facets' O.step() assert(topo['commonVerticesFound']==nPoly*(nPoly/2-1)+2) assert(topo['commonEdgesFound']==nPoly*((nPoly/2-1)+(nPoly/2-2)*2+2)) print topo['commonVerticesFound'],'vertices; ',topo['commonEdgesFound'],'edges' #quit() trunk-2017.01a/examples/not-working/insertion-sort-collider.py000066400000000000000000000025421304022710500244250ustar00rootroot00000000000000 """ NOTE Needs yade compiled with CGAL feature """ O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop([Ig2_Facet_Sphere_ScGeom()],[Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_ScGeom_FrictPhys_CundallStrack()],), NewtonIntegrator(damping=0.01,gravity=[0,0,-10]), ] mat=O.materials.append(FrictMat(young=1e3,poisson=.2,density=1000,frictionAngle=20)) O.bodies.append([ facet([[-1,-1,0],[1,-1,0],[0,1,0]],fixed=True,color=[1,0,0],material=mat), facet([[1,-1,0],[0,1,0,],[1,.5,.5]],fixed=True,material=mat) ]) import random if 1: for i in range(0,100): O.bodies.append(sphere([random.gauss(0,1),random.gauss(0,1),random.uniform(1,2)],random.uniform(.02,.05),material=mat)) O.bodies[len(O.bodies)-1].state.vel=Vector3(random.gauss(0,.1),random.gauss(0,.1),random.gauss(0,.1)) else: O.bodies.append(sphere([0,0,.6],.5),material=mat) O.dt=1e-4 O.saveTmp('init') # compare 2 colliders: if 1: O.timingEnabled=True from yade import timing for collider in InsertionSortCollider(),PersistentTriangulationCollider(haveDistantTransient=True): for i in range(2): O.loadTmp('init') replaceCollider(collider) O.run(100,True) timing.reset() O.run(50000,True) timing.stats() else: #O.run(100,True) O.step() print len(O.interactions) #O.bodies[2].phys['se3']=[-.6,0,.6,1,0,0,0] #O.step() trunk-2017.01a/examples/not-working/triax-identical-results.py000066400000000000000000000041601304022710500244110ustar00rootroot00000000000000# Test if different algorithm version give same results for TriaxialTest. # # The first run creates initial sphere packing, and saves resulting positions # after 2000 steps. Subsequent runs only save resulting positions. # # Compare output files with diff to see if the are 100% identical # """ THIS SCRIPT IS NOT WORKING! ERROR MESSAGE: Running script triax-identical-results.py Using new initial configuration in triax-identical-results-in.spheres Traceback (most recent call last): File "/home/me/YADE/YADE3041/bin/yade-bzr3041", line 182, in runScript execfile(script,globals()) File "triax-identical-results.py", line 20, in spheresToFile(inSph) AttributeError: 'module' object has no attribute 'spheresToFile' """ from os.path import exists sph='triax-identical-results' i=0; outSph='' while True: outSph='%s-out%02d.spheres'%(sph,i) if not exists(outSph): break i+=1 inSph='%s-in.spheres'%sph if exists(inSph): print "Using existing initial configuration",inSph else: TriaxialTest(noFiles=True).load() print "Using new initial configuration in",inSph spheresToFile(inSph) TriaxialTest(importFilename=inSph,noFiles=True).load() O.usesTimeStepper=False O.dt=PWaveTimeStep() # # uncomment this line to enable shear computation in ScGeom and then compare results with this line commented # [e for e in O.engines if e.name=='ElasticContactLaw'][0]['useShear']=True if 1: #for i in range(0,100): # # O.save('/tmp/a.%03d.xml'%O.iter) # O.step() O.run(2000,True) spheresToFile(outSph) print "Results saved to",outSph #quit() trunk-2017.01a/examples/packs/000077500000000000000000000000001304022710500161015ustar00rootroot00000000000000trunk-2017.01a/examples/packs/LSMGenGeo.geo000066400000000000000000000533511304022710500203240ustar00rootroot00000000000000LSMGeometry 1.2 BoundingBox -2 -2 -8 3.25 3.25 9.5 PeriodicBoundaries 0 0 0 Dimension 3D BeginParticles Simple 387 -0.9262759724 -1.058448624 0.5934789567 0.5934786407 430 0 -0.7337180112 -0.2941556215 0.261686305 0.261686205 443 0 -0.2919400221 -1.655024767 0.3194234863 0.3194233863 3362 0 -1.597798043 -0.7768410239 0.2233630403 0.2233624688 3367 0 -0.59999 -0.8958448116 2.12929564 0.5992200167 3 0 -1.391964921 -0.5277399199 1.443261338 0.5113506679 1199 0 -1.303523473 -0.378461522 2.213426408 0.2781175118 1595 0 -1.630891607 -0.7520024509 0.8072844866 0.2040833284 1701 0 -1.473634405 -0.8977706025 2.131635292 0.2744295438 2071 0 -1.738324669 -0.2735094727 2.475494346 0.2402896715 2617 0 -0.6897737455 -0.7386775455 1.317455977 0.2325528744 2779 0 -0.3255598021 -1.701021961 1.960099027 0.268103162 3298 0 -0.2514673246 -0.6440563051 1.28313265 0.2171613747 3740 0 -1.078967707 -1.293215633 1.458540899 0.3157851267 4199 0 -0.5685924975 -1.180008414 1.319693758 0.2251180157 4716 0 -0.7054084502 -1.608126148 1.185407932 0.2439615207 6427 0 -0.4924743105 -1.69433734 0.8010799675 0.203789093 6813 0 -1.754045077 -0.4038110588 2.055145099 0.2000719028 7175 0 -0.5151785117 -0.7012326592 3.043265842 0.3390804537 325 0 -0.962231283 -0.2756646064 4.013247769 0.5244118502 332 0 -1.335289698 -0.7016520479 2.911267504 0.4915853067 410 0 -0.7732274232 -1.395768394 2.982084169 0.4043646491 489 0 -0.5922428323 -1.505260376 4.111211711 0.3824212717 905 0 -0.2563610202 -1.18980911 3.72977573 0.2157576834 933 0 -1.208006186 -1.100419576 4.241440604 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-4.4408997959349 0 1.5190194235244 3.6142702934017 -4.5444332014752 0 2.543437469799 4.5063483206219 -6.3179572763921 0 -0.24526028715351 4.3733777215095 -5.1946081883281 0 -0.67793138703452 3.5122070514485 -4.058693376312 0 0.7668862216033 3.2470611761867 -3.7183727616168 0 -1.6984461402266 2.8565535692464 -3.6999186344499 0 1.8409712583355 2.9161694821589 -3.8771343271828 0 2.2155446444777 4.083484027652 -5.5701567524319 0 -1.0205678755183 5.0203546348214 -6.2450699717688 0 0.40220012269193 3.8864344298386 -4.5256017801011 0 1.579026917017 4.8451260122149 -6.2067429646 0 -1.4493085375803 4.1596393420579 -5.2294614041823 0 0.98778292819349 4.3919803804835 -5.3663500965282 0 -2.5020208457379 3.7585664236253 -5.3854412335108 0 -2.3401710969288 4.4762900020786 -6.1433287682438 0 Triangles 260 31 80 25 22 26 80 32 22 80 26 25 22 80 31 32 22 81 27 26 22 81 32 33 22 32 81 26 22 27 81 33 22 31 3 8 22 3 31 25 22 27 9 2 22 9 27 33 22 28 82 22 24 23 82 29 24 82 23 22 24 82 28 29 24 30 83 29 24 23 83 24 24 83 23 29 24 83 30 24 24 4 6 22 24 6 28 22 24 24 8 3 24 8 24 30 24 84 20 19 26 84 37 38 26 37 84 19 26 20 84 38 26 85 21 20 26 85 38 39 26 38 85 20 26 21 85 39 26 10 19 1 26 19 10 37 26 4 21 39 26 6 4 39 26 34 86 16 28 17 86 35 28 86 17 16 28 86 34 35 28 36 87 35 28 17 87 18 28 87 17 35 28 87 36 18 28 9 16 2 28 16 9 34 28 10 18 36 28 18 10 1 28 91 62 61 30 93 23 24 30 23 94 22 30 93 94 23 30 61 13 73 30 73 91 61 30 95 24 3 30 95 74 89 30 74 95 3 30 96 71 4 30 22 96 4 30 73 97 91 30 72 97 73 30 64 98 65 30 94 99 90 30 64 88 98 30 92 99 93 30 94 93 99 30 75 89 74 30 98 88 92 30 66 65 98 30 88 64 63 30 63 100 88 30 89 101 93 30 101 92 93 30 102 92 88 30 92 102 99 30 94 96 22 30 94 90 96 30 63 62 100 30 62 91 100 30 103 89 75 30 89 103 101 30 66 104 67 30 95 93 24 30 89 93 95 30 98 104 66 30 92 101 98 30 76 15 67 30 104 76 67 30 90 102 97 30 102 90 99 30 76 103 75 30 103 76 104 30 96 72 71 30 97 72 90 30 96 90 72 30 100 102 88 30 97 100 91 30 102 100 97 30 101 104 98 30 103 104 101 30 108 41 40 32 110 20 21 32 20 111 19 32 110 111 20 32 40 11 70 32 70 108 40 32 112 21 4 32 112 71 106 32 71 112 4 32 19 113 1 32 68 113 107 32 113 68 1 32 70 115 108 32 69 115 70 32 115 69 68 32 107 115 68 32 115 114 108 32 43 116 44 32 111 117 107 32 43 105 116 32 109 117 110 32 111 110 117 32 72 106 71 32 116 105 109 32 45 44 116 32 105 43 42 32 42 118 105 32 114 118 108 32 118 114 105 32 106 119 110 32 119 109 110 32 107 120 115 32 120 114 115 32 120 107 117 32 121 109 105 32 114 121 105 32 109 121 117 32 111 113 19 32 111 107 113 32 120 121 114 32 120 117 121 32 42 41 118 32 41 108 118 32 122 106 72 32 106 122 119 32 45 123 46 32 112 110 21 32 106 110 112 32 116 123 45 32 109 119 116 32 73 13 46 32 123 73 46 32 73 122 72 32 122 73 123 32 119 123 116 32 122 123 119 32 127 48 47 34 129 17 18 34 17 130 16 34 129 130 17 34 47 14 79 34 79 127 47 34 68 131 1 34 131 18 1 34 131 68 125 34 132 77 2 34 16 132 2 34 79 133 127 34 78 133 79 34 50 134 51 34 130 135 126 34 50 124 134 34 128 135 129 34 130 129 135 34 69 125 68 34 134 124 128 34 52 51 134 34 124 50 49 34 49 136 124 34 125 137 129 34 137 128 129 34 138 128 124 34 128 138 135 34 130 132 16 34 130 126 132 34 49 48 136 34 48 127 136 34 139 125 69 34 125 139 137 34 52 140 53 34 131 129 18 34 125 129 131 34 134 140 52 34 128 137 134 34 70 11 53 34 140 70 53 34 126 138 133 34 138 126 135 34 70 139 69 34 139 70 140 34 132 78 77 34 133 78 126 34 132 126 78 34 136 138 124 34 133 136 127 34 138 136 133 34 137 140 134 34 139 140 137 34 144 55 54 36 146 26 27 36 26 147 25 36 146 147 26 36 54 15 76 36 76 144 54 36 77 148 2 36 148 27 2 36 148 77 142 36 25 149 3 36 149 74 3 36 76 150 144 36 75 150 76 36 57 151 58 36 147 152 143 36 57 141 151 36 145 152 146 36 147 146 152 36 78 142 77 36 151 141 145 36 59 58 151 36 141 57 56 36 56 153 141 36 142 154 146 36 154 145 146 36 155 145 141 36 145 155 152 36 147 149 25 36 147 143 149 36 56 55 153 36 55 144 153 36 156 142 78 36 142 156 154 36 59 157 60 36 148 146 27 36 142 146 148 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Line(13) = {1, 18}; Line(14) = {6, 4}; Line(15) = {2, 13}; Line(16) = {3, 8}; Line(17) = {1, 19}; Line(18) = {4, 21}; Line(19) = {3, 29}; Line(20) = {2, 24}; Line Loop(21) = {6, -15, -4, 16}; Ruled Surface(22) = {21}; Line Loop(23) = {5, -16, -3, -14}; Ruled Surface(24) = {23}; Line Loop(25) = {8, 14, -2, 13}; Ruled Surface(26) = {25}; Line Loop(27) = {7, -13, -1, 15}; Ruled Surface(28) = {27}; Line Loop(29) = {3, 19, -12, -18}; Ruled Surface(30) = {29}; Line Loop(31) = {18, -9, -17, 2}; Ruled Surface(32) = {31}; Line Loop(33) = {17, -10, -20, 1}; Ruled Surface(34) = {33}; Line Loop(35) = {20, -11, -19, 4}; Ruled Surface(36) = {35}; trunk-2017.01a/examples/packs/packs.py000066400000000000000000000176771304022710500175760ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- from yade import pack,ymport,export,geom,bodiesHandling """ This script demonstrates how to use 2 components of creating packings: 1. packing generators pack.regularHexa, pack.regularOrtho etc. generate vertices and filter them using predicates. (Note that this will be enhanced to irregular packings in the future) 2. predicates are functors returning True/False for points that are given by the packing generator. Their names are mostly self-explanatory, see their docstrings for meaning of their arguments. Predicates can be combined using set arithmetics to get their Intersection (p1 & p2), union (p1 | p2), difference (p1 - p2) and symmetric difference (XOR, p1 ^ p2). This is demontrated on the head (which has sphere taken off at the back and also a notch) and the body (with cylidrical hole inside). """ rad,gap=.15,.02 #Add material O.materials.append(FrictMat(young=10e9,poisson=.25,frictionAngle=0.5,density=1e3)) #Parameters, which will be passed into spheres and facets creators kw={'material':0} kwBoxes={'color':[1,0,0],'wire':False,'dynamic':False,'material':0} kwMeshes={'color':[1,1,0],'wire':True,'dynamic':False,'material':0} O.bodies.append( pack.regularHexa( (pack.inSphere((0,0,4),2)-pack.inSphere((0,-2,5),2)) & pack.notInNotch(centerPoint=(0,0,4),edge=(0,1,0),normal=(-1,1,-1),aperture=.2) ,radius=rad,gap=gap,color=(0,1,0),material=0) # head +[sphere((.8,1.9,5),radius=.2,color=(.6,.6,.6),material=0),sphere((-.8,1.9,5),radius=.2,color=(.6,.6,.6),material=0),sphere((0,2.4,4),radius=.4,color=(1,0,0),material=0)] # eyes and nose +pack.regularHexa(pack.inCylinder((-1,2.2,3.3),(1,2.2,3.3),2*rad),radius=rad,gap=gap/3,color=(0.929,0.412,0.412),material=0) #mouth ) groundId=O.bodies.append(facet([(12,0,-6),(0,12,-6,),(-12,-12,-6)],dynamic=False)) # ground for part in [ pack.regularHexa ( pack.inAlignedBox((-2,-2,-2),(2,2,2))-pack.inCylinder((0,-2,0),(0,2,0),1), radius=1.5*rad,gap=2*gap,color=(1,0,1),**kw), # body, pack.regularOrtho(pack.inEllipsoid((-1,0,-4),(1,1,2)),radius=rad,gap=0,color=(0,1,1),**kw), # left leg pack.regularHexa (pack.inCylinder((+1,1,-2.5),(0,3,-5),1),radius=rad,gap=gap,color=(0,1,1),**kw), # right leg pack.regularHexa (pack.inHyperboloid((+2,0,1),(+6,0,0),1,.5),radius=rad,gap=gap,color=(0,0,1),**kw), # right hand pack.regularOrtho(pack.inCylinder((-2,0,2),(-5,0,4),1),radius=rad,gap=gap,color=(0,0,1),**kw) # left hand ]: O.bodies.appendClumped(part) # Example of geom.facetBox usage oriBody = Quaternion(Vector3(0,0,1),(pi/3)) O.bodies.append(geom.facetBox((12,0,-6+0.9),(1,0.7,0.9),oriBody,**kwBoxes)) oriBody = Quaternion(Vector3(0,0,1),(pi/2)) O.bodies.append(geom.facetBox((0,12,-6+0.9),(1,0.7,0.9),oriBody,**kwBoxes)) oriBody = Quaternion(Vector3(0,0,1),(pi)) O.bodies.append(geom.facetBox((-12,-12,-6+0.9),(1,0.7,0.9),oriBody,**kwBoxes)) # Example of geom.facetParallelepiped usage oriBody = Quaternion(Vector3(0,0,1),(pi/3)) O.bodies.append(geom.facetParallelepiped(center=Vector3(12,0,-6+2.7),extents=Vector3(1,0.7,0.9),height=0.5, orientation=oriBody,**kwBoxes)) oriBody = Quaternion(Vector3(0,0,1),(pi/2)) O.bodies.append(geom.facetParallelepiped(center=Vector3(0,12,-6+2.7),extents=Vector3(1,0.7,0.9),height=0.5, orientation=oriBody,**kwBoxes)) oriBody = Quaternion(Vector3(0,0,1),(pi)) O.bodies.append(geom.facetParallelepiped(center=Vector3(-12,-12,-6+2.7),extents=Vector3(1,0.7,0.9),height=0.5, orientation=oriBody,**kwBoxes)) # Example of geom.facetCylinder, facetHelix and RotationEngine usage example oriBody = Quaternion(Vector3(1,0,0),(pi/2.0)) rotateIDs=O.bodies.append(geom.facetHelix((-7.0,-6.0,-5.0),radiusOuter=2.0,radiusInner=0.1,pitch=2.0,orientation=oriBody,segmentsNumber=50,angleRange=[pi*8.0,0],**kwBoxes)) O.bodies.append(geom.facetCylinder((-7.0,-12.0,-5.0),radius=2.0,height=7.0,orientation=oriBody,segmentsNumber=10,wallMask=4,**kwMeshes)) O.bodies.append(geom.facetCylinder((-7.0,-7.0,-5.0),radius=2.0,height=4.0,segmentsNumber=10,wallMask=4,angleRange=[-pi*0.2,pi*1.2],**kwMeshes)) oriBody = Quaternion(Vector3(0,0,1),(pi/2)) O.bodies.append(ymport.gmsh('cone.mesh',orientation=oriBody,**kwMeshes))#generates facets from the mesh file SpheresID=[] oriBody = Quaternion(Vector3(0,0,1),(pi/2)) SpheresID+=O.bodies.append(ymport.gengeoFile('LSMGenGeo.geo',shift=Vector3(-7.0,-7.0,0.0),scale=1.0,orientation=oriBody,color=(1,0,1),**kw)) #Demonstration of spheresPackDimensions function. The "Edge" particles are colored with blue color geometryParameters = bodiesHandling.spheresPackDimensions(SpheresID) for v in [geometryParameters['minId'],geometryParameters['maxId']]: for i in v: O.bodies[int(i)].shape.color = Vector3(0,0,1) #Example of bodiesHandling.spheresModify() hat=O.bodies.append(pack.regularOrtho(pack.inCylinder((0,0,6),(0,0,7),20*rad),radius=0.2,gap=0,color=(1,0,0))) # hat oriBody = Quaternion(Vector3(0,1,0),(pi/8)) hat_upper=O.bodies.append(bodiesHandling.spheresModify(hat,shift=(0.0,0.0,1.4),scale=0.7,orientation=oriBody,copy=True)) #Duplicate the "heart", shifting, scaling and rotating it #change the color of upper part of the hat for hatTmp in hat_upper: O.bodies[hatTmp].shape.color=(0.9,0.5,0.59) #facetBunker Demonstration #Demonstration of HarmonicMotionEngine vibrationPlate = O.bodies.append(geom.facetBunker((-7.0,-7.0,-3.0),dBunker=geometryParameters['extends'][0]*1.1,dOutput=3.0,hBunker=11.0,hOutput=1.5,hPipe=0.8,wallMask=5,segmentsNumber=20,**kwMeshes)) # spheresToFile saves coordinates and radii of all spheres of the simulation into the text file, works but disabled. Please, uncomment it, if you need #print "Saved into the OutFile " + str (export.text("OutFile")) + " spheres"; # spheresFromFile function imports coordinates and radii of all spheres of the simulation into the text file O.bodies.append(ymport.text('foo.spheres',shift=Vector3(6.0,6.0,-2.9),scale=0.7,color=(1,1,1),**kw)) #Demonstration of HarmonicRotationEngine O.bodies.append(pack.regularHexa(pack.inSphere((-15,5,-5),1.5),radius=rad*2.0,gap=rad/3.0,color=(0.5,0.5,0.1),material=0)) O.bodies.append(geom.facetBox((-15,5,-5),(2,2,2),wallMask=15,**kwMeshes)) vibrationRotationPlate = O.bodies.append(geom.facetBox((-15,5,-5),(2,2,2),wallMask=16,**kwBoxes)) O.bodies.append(wall((0,0,-10),axis=2)) O.engines=[ #SubdomainBalancer(colorize=True,initRun=True,iterPeriod=100), ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb(),Bo1_Wall_Aabb()],label='collider'), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom(),Ig2_Wall_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), NewtonIntegrator(damping=.1,exactAsphericalRot=True,gravity=(1e-2,1e-2,-1000)), RotationEngine( ids=rotateIDs, angularVelocity=100.0, rotationAxis=[0,-1,0], rotateAroundZero=1, zeroPoint=[-7.0,-6.0,-5.0]), HarmonicMotionEngine(A=[0,0,0.5], f=[0,0,20.0], fi = [0.0,0.0,pi], ids = vibrationPlate), HarmonicRotationEngine(A=0.2, f=20.0, fi = pi, rotationAxis=[1.0,0.0,0.0], rotateAroundZero = True, zeroPoint = [-15.0,3.0,-7.0], ids = vibrationRotationPlate), BoxFactory(maxParticles=300, extents=(1.0,1.0,1.0),center=(0.0,12.0,0.0),vMin=200.0,vMax=250.0, PSDsizes=(0.1, 0.2, 0.3, 0.5, 0.7), PSDcum=(0.1, 0.5, 0.8, 1.0), PSDcalculateMass=True, exactDiam=False, vAngle=pi/3.0,massFlowRate=50000.0,normal=(0.0,0.0,1.0),label='factory',mask=7,silent=True,stopIfFailed=False) ] ''' Boxfactory is an example of usage SpheresFactory. Produces PSD-dispersion: Size: Mass, % Cumulative Cum. mass mass,% 0.5-0.7 20% 100% 1.0 0.3-0.5 30% 80% 0.8 0.2-0.3 40% 50% 0.5 0.1-0.2 10% 10% 0.1 ''' # we don't care about physical accuracy here, (over)critical step is fine as long as the simulation doesn't explode O.dt=PWaveTimeStep() O.run(1,True) try: from yade import qt qt.Controller() qt.View() except ImportError: pass O.saveTmp() O.timingEnabled=True #O.run(10000,True) #from yade import timing #timing.stats() #quit() trunk-2017.01a/examples/periodic-compress.py000066400000000000000000000022421304022710500210010ustar00rootroot00000000000000''' This example shows compression of a packing with a periodic cell. ''' O.periodic=True O.cell.setBox(20,20,10) from yade import pack,timing O.materials.append(FrictMat(young=30e9,density=2400)) p=pack.SpherePack() p.makeCloud(Vector3(0,0,0),Vector3(20,20,10),1,.5,700,True) for sph in p: O.bodies.append(sphere(sph[0],sph[1])) O.timingEnabled=True O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()],allowBiggerThanPeriod=True), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), PeriIsoCompressor(charLen=.5,stresses=[-50e9,-1e8],doneHook="print 'FINISHED'; O.pause() ",keepProportions=True), NewtonIntegrator(damping=.4) ] O.dt=PWaveTimeStep() O.saveTmp() #print O.cell.refSize from yade import qt; qt.Controller(); qt.View() O.run() O.wait() timing.stats() #while True: # O.step() # now take that packing and pad some larger volume with it #sp=pack.SpherePack() #sp.fromSimulation() # take spheres from simulation; cellSize is set as well #O.reset() #print sp.cellSize #sp.cellFill((30,30,30)) #print sp.cellSize #for s in sp: # O.bodies.append(sphere(s[0],s[1])) trunk-2017.01a/examples/periodic-grow.py000066400000000000000000000023661304022710500201330ustar00rootroot00000000000000"""Script that shrinks the periodic cell progressively. It prints strain and average stress (computed from total volume force) once in a while.""" from yade import timing O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()],allowBiggerThanPeriod=True), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), NewtonIntegrator(damping=.6) ] import random for i in xrange(250): O.bodies.append(sphere(Vector3(10*random.random(),10*random.random(),10*random.random()),.5+random.random())) cubeSize=20 # absolute positioning of the cell is not important O.periodic=True O.cell.setBox(cubeSize,cubeSize,cubeSize) O.dt=PWaveTimeStep() O.saveTmp() from yade import qt qt.Controller(); qt.View() O.run(200,True) rate=-1e-3*cubeSize/(O.dt*200)*Matrix3.Identity O.cell.velGrad=rate print 'Please be patient...' for i in range(0,25): O.run(2000,True) F,stiff=totalForceInVolume() dim=O.cell.refSize; A=Vector3(dim[1]*dim[2],dim[0]*dim[2],dim[0]*dim[1]) avgStress=sum([F[i]/A[i] for i in 0,1,2])/3. print 'strain',(cubeSize-dim[0])/cubeSize,'avg. stress ',avgStress,'unbalanced ',unbalancedForce() #O.timingEnabled=True; timing.reset(); O.run(200000,True); timing.stats() trunk-2017.01a/examples/periodicSandPile.py000066400000000000000000000033441304022710500205740ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # © 2012 Bruno Chareyre """Script showing how large bodies can be combined with periodic boundary conditions using InsertioSortCollider::allowBiggerThanPeriod=True (1).""" from yade import pack from pylab import rand from yade import qt O.periodic=True length=0.4 height=0.6 width=0.2 thickness=0.01 O.cell.hSize=Matrix3(length, 0, 0, 0 ,3.*height, 0, 0, 0, width) O.materials.append(FrictMat(density=1,young=1e5,poisson=0.3,frictionAngle=radians(30),label='boxMat')) lowBox = box( center=(length/2.0,height-thickness/2.0,width/2.0), extents=(length*1000.0,thickness/2.0,width*1000.0) ,fixed=True,wire=False) O.bodies.append(lowBox) radius=0.01 O.materials.append(FrictMat(density=1000,young=1e4,poisson=0.3,frictionAngle=radians(30),label='sphereMat')) sp=pack.SpherePack() sp.makeCloud((0.*length,height+1.2*radius,0.25*width),(0.5*length,2*height-1.2*radius,0.75*width),-1,.2,2000,periodic=True) O.bodies.append([sphere(s[0],s[1],color=(0.6+0.15*rand(),0.5+0.15*rand(),0.15+0.15*rand())) for s in sp]) O.dt=0.2*PWaveTimeStep() O.usesTimeStepper=True newton=NewtonIntegrator(damping=0.6,gravity=(0,-10,0)) O.engines=[ ForceResetter(), #(1) This is where we all big bodies, else it would crash due to the very large bottom box: InsertionSortCollider([Bo1_Box_Aabb(),Bo1_Sphere_Aabb()],allowBiggerThanPeriod=True), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), GlobalStiffnessTimeStepper(timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8,defaultDt=O.dt), newton ] Gl1_Sphere.stripes=1 from yade import qt qt.View() print('Press PLAY button') trunk-2017.01a/examples/pfacet/000077500000000000000000000000001304022710500162425ustar00rootroot00000000000000trunk-2017.01a/examples/pfacet/box.gts000066400000000000000000000004731304022710500175550ustar00rootroot000000000000008 18 12 GtsSurface GtsFace GtsEdge GtsVertex -0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 -0.5 0.5 0.5 -0.5 0.5 0.5 0.5 0.5 -0.5 0.5 -0.5 -0.5 -0.5 1 2 3 1 2 3 4 5 1 4 5 1 5 6 5 2 6 2 7 5 7 4 4 8 4 3 3 8 7 6 3 7 8 1 2 7 1 2 3 4 5 6 7 8 9 4 10 11 12 13 14 15 10 7 16 13 11 17 5 12 1 8 6 16 18 3 14 2 17 9 18 15 trunk-2017.01a/examples/pfacet/gts-pfacet.py000066400000000000000000000047431304022710500206610ustar00rootroot00000000000000from yade import qt from yade.gridpfacet import * import gts, os.path, locale locale.setlocale(locale.LC_ALL, 'en_US.UTF-8') # Note: gts is locale-dependend. If, for example, german locale is used, gts.read()-function does not import floats normally ''' if you get "Error: unsupported locale setting" -> type as root: "dpkg-reconfigure locales" -> choose "en_US.UTF-8" (press space to choose) ''' ################ ### ENGINES ### ################ O.engines=[ ForceResetter(), InsertionSortCollider([ Bo1_Wall_Aabb(), Bo1_PFacet_Aabb(), ],sortThenCollide=True), InteractionLoop( [ Ig2_GridNode_GridNode_GridNodeGeom6D(), Ig2_Wall_PFacet_ScGeom(),Ig2_Wall_Sphere_ScGeom() ], [ Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=True), Ip2_FrictMat_FrictMat_FrictPhys()], [ Law2_ScGeom6D_CohFrictPhys_CohesionMoment(), Law2_ScGeom_FrictPhys_CundallStrack(), Law2_ScGridCoGeom_FrictPhys_CundallStrack(), Law2_GridCoGridCoGeom_FrictPhys_CundallStrack() ]), GlobalStiffnessTimeStepper(timestepSafetyCoefficient=0.5,label='ts'), NewtonIntegrator(gravity=(0,-9.81,0),damping=0.1,label='newton') ] ################# ### MATERIAL ### ################# O.materials.append(CohFrictMat(young=1e8,poisson=0.3,density=2650,frictionAngle=radians(20),normalCohesion=1e100,shearCohesion=1e100,momentRotationLaw=True,label='gridNodeMat')) O.materials.append(FrictMat(young=1e8,poisson=0.3,density=2650,frictionAngle=radians(20),label='pFacetMat')) ################### ### IMPORT MESH ### ################### radius=1e-02 wire=False fixed=False z=-1.2 color=[0,0,1] nodesIds0,cylIds0,pfIds0 = gtsPFacet('octahedron.gts',shift=(0,0,0),scale=1.,radius=radius,wire=wire,fixed=fixed,materialNodes='gridNodeMat',material='pFacetMat',color=color) nodesIds1,cylIds1,pfIds1 = gtsPFacet('box.gts',shift=(3.,0.,0.),scale=2,radius=radius,wire=wire,fixed=fixed,materialNodes='gridNodeMat',material='pFacetMat',color=color) nodesIds2,cylIds2,pfIds2 = gtsPFacet('sphere.gts',shift=(6.,0.,0.),scale=1.0,radius=radius,wire=wire,fixed=fixed,materialNodes='gridNodeMat',material='pFacetMat',color=color) ##################### ##### Wall ### ##################### O.bodies.append(utils.wall(position=z,sense=0, axis=1,color=Vector3(1,0,0),material='pFacetMat')) ########## ## VIEW ## ########## qt.Controller() qtv = qt.View() qtr = qt.Renderer() qtr.light2=True qtr.lightPos=Vector3(1200,1500,500) qtr.bgColor=[1,1,1] qtv.ortho=True O.saveTmp() trunk-2017.01a/examples/pfacet/mesh-pfacet.py000066400000000000000000000064771304022710500210260ustar00rootroot00000000000000# -*- coding: utf-8 from yade import qt,plot from yade.gridpfacet import * ################## ### PARAMETERS ### ################## phi=20. E=3.*1e8 color=[255./255.,102./255.,0./255.] r=0.005 # position of imported mesh xpafet=0.22 ypafet=0.05 ################ ### ENGINES ### ################ O.engines=[ ForceResetter(), InsertionSortCollider([ Bo1_PFacet_Aabb(), ]), InteractionLoop([ Ig2_GridNode_GridNode_GridNodeGeom6D(), Ig2_GridConnection_GridConnection_GridCoGridCoGeom(), Ig2_Sphere_PFacet_ScGridCoGeom(), Ig2_PFacet_PFacet_ScGeom(), ], [ Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=True), Ip2_FrictMat_FrictMat_FrictPhys() ], [ Law2_ScGeom6D_CohFrictPhys_CohesionMoment(), Law2_ScGeom_FrictPhys_CundallStrack(), Law2_ScGridCoGeom_FrictPhys_CundallStrack(), Law2_GridCoGridCoGeom_FrictPhys_CundallStrack() ] ), GlobalStiffnessTimeStepper(timestepSafetyCoefficient=0.5,label='ts'), NewtonIntegrator(gravity=(0,-9.81,0),damping=0.0,label='newton'), PyRunner(iterPeriod=200,command='history()'), ] ################ ### MATERIAL ### ################ O.materials.append( CohFrictMat( young=E,poisson=0.3,density=2650,frictionAngle=radians(phi),normalCohesion=3e100,shearCohesion=3e100,momentRotationLaw=True,label='gridNodeMat' ) ) # material to create the gridConnections O.materials.append( FrictMat( young=E,poisson=0.3,density=2650,frictionAngle=radians(phi),label='pFacetMat' ) ) # material for general interactions ######################################## ### GENERATE THE WALL AND THE SPHERE ### ######################################## # FIXED WALL O.bodies.append( gridNode([-0.25,-0.22,-.25],r,wire=False,fixed=True,material='gridNodeMat',color=color) ) O.bodies.append( gridNode([.5,0.,-.25],r,wire=False,fixed=True,material='gridNodeMat',color=color) ) O.bodies.append( gridNode([-.25,-0.22,.25],r,wire=False,fixed=True,material='gridNodeMat',color=color) ) O.bodies.append( gridNode([.5,0.,.25],r,wire=False,fixed=True,material='gridNodeMat',color=color) ) O.bodies.append( gridConnection(0,1,r,color=color,material='gridNodeMat') ) O.bodies.append( gridConnection(2,3,r,color=color,material='gridNodeMat') ) O.bodies.append( gridConnection(2,1,r,color=color,material='gridNodeMat') ) O.bodies.append( gridConnection(2,0,r,color=color,material='gridNodeMat') ) O.bodies.append( gridConnection(3,1,r,color=color,material='gridNodeMat') ) O.bodies.append( pfacet(2,1,0,wire=False,material='pFacetMat',color=color) ) O.bodies.append( pfacet(2,3,1,wire=False,material='pFacetMat',color=color) ) # IMPORT MESH oriBody = Quaternion(Vector3(0,0,1),pi/2.) nodesIds,cylIds,pfIds = gmshPFacet( meshfile='sphere.mesh', shift=Vector3(xpafet,ypafet,0.), orientation=oriBody, radius=r, wire=False, fixed=False, materialNodes='gridNodeMat', material='pFacetMat', color=[1,0,0] ) ############ ### PLOT ### ############ def history(): xyz=[] for k in [0,1,2]: ksum=0 for i in nodesIds: ksum+=O.bodies[i].state.pos[k] xyz.append(ksum/len(nodesIds)) # take average value as reference plot.addData(i=O.iter,t=O.time,x=xyz[0],y=xyz[1],z=xyz[2]) plot.plots={'x':'y'} plot.plot() ########## ## VIEW ## ########## qt.Controller() qtv = qt.View() qtr = qt.Renderer() qtr.light2=True qtr.lightPos=Vector3(1200,1500,500) qtr.bgColor=[1,1,1] O.saveTmp() trunk-2017.01a/examples/pfacet/octahedron.gts000066400000000000000000000464161304022710500211220ustar00rootroot00000000000000258 768 512 GtsSurface GtsFace GtsEdge GtsVertex 0 0.625 0.625 0.1909179688 0.517578125 0.6655273438 0 0.4765625 0.7685546875 -0.3125 -0.890625 0 -0.1826171875 -0.91015625 0.1826171875 -0.3530273438 -0.8041992188 0.18359375 0.1826171875 0.91015625 0.1826171875 0 0.890625 0.3125 0.18359375 0.8041992188 0.3530273438 0 0.1494140625 0.97265625 -0.1826171875 0.1826171875 0.91015625 0 0.3125 0.890625 -0.3671875 -0.3671875 0.671875 -0.18359375 -0.3530273438 0.8041992188 -0.3530273438 -0.18359375 0.8041992188 0.625 0 0.625 0.7685546875 0 0.4765625 0.6655273438 -0.1909179688 0.517578125 -0.97265625 0 -0.1494140625 -1 0 0 -0.97265625 -0.1494140625 0 0 -0.4765625 -0.7685546875 -0.1909179688 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187 462 743 171 545 206 640 93 553 440 673 475 414 744 294 270 463 28 279 736 741 718 745 630 746 672 688 472 547 747 311 221 700 345 748 115 749 750 684 751 752 739 68 729 362 392 474 339 517 658 373 689 593 639 579 753 393 720 754 601 602 192 363 301 415 753 213 401 218 755 46 542 754 643 52 756 99 738 723 757 669 30 749 745 113 140 562 624 728 5 174 712 466 42 281 748 757 330 708 709 758 668 727 589 697 513 652 744 759 451 660 480 627 434 734 80 179 760 108 563 583 495 425 758 761 608 77 347 721 364 549 560 242 515 760 36 205 762 200 763 730 500 628 543 594 349 91 86 247 302 703 106 764 750 657 706 447 722 155 765 505 755 677 400 313 766 421 746 685 692 4 614 539 765 767 763 768 569 619 459 195 676 188 571 1 431 235 342 637 761 649 185 698 732 759 632 641 756 576 678 534 609 743 751 386 531 766 261 625 356 715 726 674 725 633 433 742 599 246 29 258 656 230 607 251 21 762 338 584 610 412 116 262 20 747 354 691 530 225 399 764 122 665 711 740 670 419 202 717 705 731 767 382 642 591 662 694 306 78 518 682 768 367 737 506 598 360 752 611 208 548 644 413 482 498 612 trunk-2017.01a/examples/pfacet/pfacetcreators.py000066400000000000000000000106071304022710500216250ustar00rootroot00000000000000# encoding: utf-8 from yade import qt from yade.gridpfacet import * ########################### ##### ENGINES ##### ########################### O.engines=[ ForceResetter(), InsertionSortCollider([ Bo1_Sphere_Aabb(), Bo1_Wall_Aabb(), Bo1_PFacet_Aabb(), ],sortThenCollide=True), InteractionLoop( [ Ig2_GridNode_GridNode_GridNodeGeom6D(), Ig2_Sphere_PFacet_ScGridCoGeom(), Ig2_Wall_PFacet_ScGeom(),Ig2_Wall_Sphere_ScGeom() ], [ Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=True), Ip2_FrictMat_FrictMat_FrictPhys()], [ Law2_ScGeom6D_CohFrictPhys_CohesionMoment(), Law2_ScGeom_FrictPhys_CundallStrack(), Law2_ScGridCoGeom_FrictPhys_CundallStrack(), Law2_GridCoGridCoGeom_FrictPhys_CundallStrack() ]), GlobalStiffnessTimeStepper(timestepSafetyCoefficient=0.8,label='ts'), NewtonIntegrator(gravity=(0,-9.81,0),damping=0.1,label='newton') ] O.materials.append(CohFrictMat(young=1e7,poisson=1,density=1e2,frictionAngle=radians(30),normalCohesion=3e7,shearCohesion=3e7,momentRotationLaw=True,label='gridNodeMat')) O.materials.append(FrictMat(young=1e7,poisson=1,density=1e2,frictionAngle=radians(30),label='gridConnectionMat')) ################################### ##### PFacet creators ##### ################################### fixed = False color=[255./255.,102./255.,0./255.] nodesIds=[] cylIds=[] #position of the node in the middle a=0.00 r=0.03 ## Option 1: pfacet(id1,id2,id3) -> based on 3 gridNodes already connected via 3 gridConnections nodesIds.append( O.bodies.append(gridNode([0,0,0],r,wire=False,fixed=fixed,material='gridNodeMat',color=color)) ) nodesIds.append( O.bodies.append(gridNode([1,0,0],r,wire=False,fixed=fixed,material='gridNodeMat',color=color)) ) nodesIds.append( O.bodies.append(gridNode([0.5,1,0],r,wire=False,fixed=fixed,material='gridNodeMat',color=color)) ) cylIds.append(O.bodies.append( gridConnection(0,1,r,color=color) )) cylIds.append(O.bodies.append( gridConnection(1,2,r,color=color) )) cylIds.append(O.bodies.append( gridConnection(2,0,r,color=color) )) O.bodies.append( pfacet(nodesIds[0],nodesIds[1],nodesIds[2],wire=False,color=color,highlight=False,material=O.materials[1]) ) ## Option 2: pfacetCreator1(vertices) -> based on 3 vertices v1=Vector3(2,0,0) v2=Vector3(3,0,0) v3=Vector3(2.5,1,0) vertices=[v1,v2,v3] pfacetCreator1(vertices,r,nodesIds=[],cylIds=[],pfIds=[],wire=False,color=color,fixed=fixed,materialNodes='gridNodeMat',material='gridConnectionMat') ## Option 3: pfacetCreator2(id1,id2,vertex) -> based on 2 gridNodes connected via a gridConnection and a vertex nodesIds.append( O.bodies.append(gridNode([4,0,0],r,wire=False,fixed=fixed,material='gridNodeMat',color=color)) ) nodesIds.append( O.bodies.append(gridNode([5,0,0],r,wire=False,fixed=fixed,material='gridNodeMat',color=color)) ) vertex=Vector3(4.5,1,0) cylIds.append(O.bodies.append( gridConnection(nodesIds[3],nodesIds[4],r,color=color) ) ) pfacetCreator2(nodesIds[3],nodesIds[4],vertex,r,nodesIds=nodesIds,wire=True,materialNodes='gridNodeMat',material='gridConnectionMat',color=color,fixed=fixed) ## Option 4: pfacetCreator3(id1,id2,id3) -> based on 3 gridNodes a = O.bodies.append(gridNode([6,0,0],r,wire=False,fixed=fixed,material='gridNodeMat',color=color)) b = O.bodies.append(gridNode([7,0,0],r,wire=False,fixed=fixed,material='gridNodeMat',color=color)) c = O.bodies.append(gridNode([6.5,1,0],r,wire=False,fixed=fixed,material='gridNodeMat',color=color)) pfacetCreator3(a,b,c,cylIds=[],pfIds=[],wire=False,material=-1,color=color) ## Option 4: pfacetCreator4(id1,id2,id3) -> based on 3 gridConnections a = O.bodies.append(gridNode([8,0,0],r,wire=False,fixed=fixed,material='gridNodeMat',color=color)) b = O.bodies.append(gridNode([9,0,0],r,wire=False,fixed=fixed,material='gridNodeMat',color=color)) c = O.bodies.append(gridNode([8.5,1,0],r,wire=False,fixed=fixed,material='gridNodeMat',color=color)) n=len(cylIds) cylIds.append(O.bodies.append( gridConnection(a,b,r,color=color) ) ) cylIds.append(O.bodies.append( gridConnection(b,c,r,color=color) ) ) cylIds.append(O.bodies.append( gridConnection(c,a,r,color=color) ) ) pfacetCreator4(cylIds[n],cylIds[n+1],cylIds[n+2],pfIds=[],wire=False,material=-1,color=color) ##################### ##### Wall ### ##################### O.bodies.append(utils.wall(position=-1,sense=0, axis=1,color=Vector3(1,0,0),material='gridConnectionMat')) qt.View() O.saveTmp() trunk-2017.01a/examples/pfacet/sphere.gts000066400000000000000000000050361304022710500202530ustar00rootroot0000000000000042 120 80 GtsSurface GtsFace GtsEdge GtsVertex 0 0 -1 -0.3090169728 0.5 -0.8090170026 0.3090169728 0.5 -0.8090170026 -1 0 0 -0.850650847 -0.5257311463 0 -0.8090170026 -0.3090169728 0.5 0.5 0.8090170026 0.3090169728 0.5 0.8090170026 -0.3090169728 0.850650847 0.5257311463 0 0 1 0 0 0.850650847 0.5257311463 -0.5 0.8090170026 0.3090169728 0 0.850650847 -0.5257311463 -0.5 0.8090170026 -0.3090169728 0 -0.850650847 0.5257311463 0 -1 0 0.5 -0.8090170026 0.3090169728 0.5257311463 0 -0.850650847 0.3090169728 -0.5 -0.8090170026 0.8090170026 -0.3090169728 -0.5 -0.5 -0.8090170026 -0.3090169728 0 -0.850650847 -0.5257311463 -0.3090169728 -0.5 -0.8090170026 -0.8090170026 -0.3090169728 -0.5 -0.5257311463 0 -0.850650847 -0.8090170026 0.3090169728 0.5 -0.8090170026 0.3090169728 -0.5 0.5 -0.8090170026 -0.3090169728 0.850650847 -0.5257311463 0 0 0 1 -0.5257311463 0 0.850650847 -0.3090169728 -0.5 0.8090170026 -0.850650847 0.5257311463 0 0.3090169728 0.5 0.8090170026 -0.3090169728 0.5 0.8090170026 -0.5 -0.8090170026 0.3090169728 0.5257311463 0 0.850650847 0.8090170026 0.3090169728 0.5 0.8090170026 -0.3090169728 0.5 0.3090169728 -0.5 0.8090170026 0.8090170026 0.3090169728 -0.5 1 0 0 1 2 2 3 3 1 4 5 5 6 4 6 7 8 7 9 9 8 10 11 12 10 12 11 13 10 13 14 10 14 15 16 17 16 17 15 18 19 20 18 19 20 21 22 23 21 22 23 24 23 25 24 23 25 6 26 26 4 27 24 27 25 28 17 28 29 29 17 30 31 31 32 30 32 33 4 26 33 34 35 34 11 11 35 1 25 25 2 36 21 36 5 5 21 21 24 11 7 10 7 16 22 21 16 2 27 27 14 14 2 19 23 19 22 37 34 38 37 34 38 38 7 7 34 35 12 17 39 39 40 40 17 15 36 16 36 8 13 3 8 13 3 41 3 18 41 3 18 9 42 41 42 41 9 32 15 36 32 6 36 38 39 37 39 39 29 6 31 31 26 42 20 20 41 14 12 14 33 33 12 24 4 24 5 42 29 39 42 16 28 4 27 8 10 20 28 29 20 28 19 22 28 33 27 37 30 40 30 40 37 32 40 15 40 35 30 35 31 30 34 42 38 1 19 23 1 18 1 2 13 9 38 32 6 26 35 12 26 8 41 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 6 28 29 30 31 26 32 33 34 35 36 37 38 29 39 40 41 42 43 44 1 45 46 47 48 25 23 10 49 50 51 52 22 53 54 55 56 57 24 58 59 60 60 61 62 12 63 42 64 65 66 16 67 68 69 70 71 72 73 74 44 31 53 75 76 77 78 79 67 80 5 46 81 59 82 34 83 64 28 84 85 86 87 76 88 89 90 68 45 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-0.044475395850498 0.044475395850498 23 0.044475395850283 0.044475395850283 0.077742384372498 25 0.044475395850498 0.077742384372253 0.044475395850498 25 0.077742384372375 0.044475395850299 0.044475395850482 25 -0.044475395850283 -0.044475395850283 0.077742384372498 27 -0.077742384372375 -0.044475395850299 0.044475395850482 27 -0.044475395850498 -0.077742384372253 0.044475395850498 27 -0.044475395850283 0.044475395850283 0.077742384372498 29 -0.044475395850299 0.077742384372375 0.044475395850482 29 -0.077742384372253 0.044475395850498 0.044475395850498 29 Edges 48 2 8 1 8 9 1 9 10 1 10 3 1 3 11 2 11 12 2 12 13 2 13 4 2 4 14 3 14 15 3 15 16 3 16 5 3 5 17 4 17 18 4 18 19 4 19 2 4 6 20 6 20 21 6 21 22 6 22 3 6 6 23 7 23 24 7 24 25 7 25 5 7 6 26 8 26 27 8 27 28 8 28 2 8 6 29 9 29 30 9 30 31 9 31 4 9 7 32 10 32 33 10 33 34 10 34 3 10 7 35 11 35 36 11 36 37 11 37 2 11 7 38 12 38 39 12 39 40 12 40 5 12 7 41 13 41 42 13 42 43 13 43 4 13 Triangles 128 2 8 37 15 8 44 37 15 8 9 44 15 37 44 36 15 36 45 35 15 45 32 35 15 45 33 32 15 35 32 7 15 36 44 45 15 44 46 45 15 44 9 46 15 45 46 33 15 9 10 46 15 10 34 46 15 10 3 34 15 46 34 33 15 5 17 40 17 17 47 40 17 17 18 47 17 40 47 39 17 39 48 38 17 48 35 38 17 48 36 35 17 38 35 7 17 39 47 48 17 47 49 48 17 47 18 49 17 48 49 36 17 18 19 49 17 19 37 49 17 19 2 37 17 49 37 36 17 7 38 41 19 38 50 41 19 38 39 50 19 41 50 42 19 42 51 43 19 51 14 43 19 51 15 14 19 43 14 4 19 39 52 50 19 52 51 50 19 52 15 51 19 50 51 42 19 5 16 40 19 16 52 40 19 16 15 52 19 40 52 39 19 7 41 32 21 41 53 32 21 41 42 53 21 32 53 33 21 33 54 34 21 54 11 34 21 54 12 11 21 34 11 3 21 12 55 13 21 55 43 13 21 55 42 43 21 13 43 4 21 12 54 55 21 54 53 55 21 54 33 53 21 55 53 42 21 5 17 25 23 17 56 25 23 17 18 56 23 25 56 24 23 24 57 23 23 57 26 23 23 57 27 26 23 23 26 6 23 27 58 28 23 58 19 28 23 58 18 19 23 28 19 2 23 27 57 58 23 57 56 58 23 57 24 56 23 58 56 18 23 6 26 20 25 26 59 20 25 26 27 59 25 20 59 21 25 21 60 22 25 60 10 22 25 60 9 10 25 22 10 3 25 9 61 8 25 61 28 8 25 61 27 28 25 8 28 2 25 21 59 60 25 59 61 60 25 59 27 61 25 60 61 9 25 6 23 29 27 23 62 29 27 23 24 62 27 29 62 30 27 30 63 31 27 63 14 31 27 63 15 14 27 31 14 4 27 30 62 63 27 62 64 63 27 62 24 64 27 63 64 15 27 24 25 64 27 25 16 64 27 25 5 16 27 64 16 15 27 6 29 20 29 29 65 20 29 29 30 65 29 20 65 21 29 21 66 22 29 66 11 22 29 66 12 11 29 22 11 3 29 21 65 66 29 65 67 66 29 65 30 67 29 66 67 12 29 30 31 67 29 31 13 67 29 31 4 13 29 67 13 12 29 End trunk-2017.01a/examples/polyhedra/000077500000000000000000000000001304022710500167675ustar00rootroot00000000000000trunk-2017.01a/examples/polyhedra/ball.py000066400000000000000000000023301304022710500202510ustar00rootroot00000000000000from yade import plot, polyhedra_utils from yade import qt m = PolyhedraMat() m.density = 2600 #kg/m^3 m.young = 1E6 #Pa m.poisson = 20000/1E6 m.frictionAngle = 0.6 #rad maxLoad = 3E6 minLoad = 1E3 O.bodies.append(utils.wall(0,axis=2,sense=1, material = m)) t = polyhedra_utils.polyhedralBall(0.025, 100, m, (0,0,0)) t.state.pos = (0,0,0.5) O.bodies.append(t) def checkUnbalanced(): print "unbalanced forces = %.5f, position %f, %f, %f"%(utils.unbalancedForce(), t.state.pos[0], t.state.pos[1], t.state.pos[2]) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Polyhedra_Aabb(),Bo1_Wall_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Wall_Polyhedra_PolyhedraGeom(), Ig2_Polyhedra_Polyhedra_PolyhedraGeom(), Ig2_Facet_Polyhedra_PolyhedraGeom()], [Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()], # collision "physics" [Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()] # contact law -- apply forces ), #GravityEngine(gravity=(0,0,-9.81)), NewtonIntegrator(damping=0.5,gravity=(0,0,-9.81)), PyRunner(command='checkUnbalanced()',realPeriod=3,label='checker') ] #O.dt=0.025*polyhedra_utils.PWaveTimeStep() O.dt=0.00025 qt.Controller() V = qt.View() O.saveTmp() #O.run() trunk-2017.01a/examples/polyhedra/clump.py000066400000000000000000000037201304022710500204630ustar00rootroot00000000000000m = PolyhedraMat() m.density = 2600 #kg/m^3 m.Ks = 20000 m.Kn = 1E9 #Pa m.frictionAngle = 0.6 #rad O.materials.append(m) ###################################################################### # basic test t1 = polyhedron(((0,0,0),(0,0,1),(0,1,0),(0,1,1),(1,0,0),(1,0,1),(1,1,0),(1,1,1))) t2 = polyhedron(((0,0,1),(0,0,2),(0,1,1),(0,1,2),(2,0,1),(2,0,2),(2,1,1),(2,1,2))) t1.state.mass = 1e-12 t1.state.inertia = (1e-12,1e-12,1e-12) t1.state.pos = (0,.5,0) t2.state.ori = ((1,2,3),1) t2.state.pos = (sqrt(2),.5,-sqrt(2)) clumpId,polys = O.bodies.appendClumped((t1,t2)) clump = O.bodies[clumpId] s = clump.state s2 = t2.state # if t1.mass and inertia are set to almost zero, clump properties should equal t2 properties print s.pos, s2.pos print s.mass, s2.mass print s.inertia, s2.inertia ###################################################################### ###################################################################### # something more real wire = False O.bodies.clear() t1 = polyhedron(((0,0,0),(0,0,1),(0,1,0),(0,1,1),(1,0,0),(1,0,1),(1,1,0),(1,1,1)),color=(0,1,0),wire=wire) t2 = polyhedron(((0,0,1),(0,0,2),(0,1,1),(0,1,2),(2,0,1),(2,0,2),(2,1,1),(2,1,2)),color=(0,1,0),wire=wire) bottom = polyhedron(((-5,-5,0),(5,-5,0),(5,5,0),(-5,5,0),(-5,-5,-1),(5,-5,-1),(5,5,-1),(-5,5,-1)),fixed=True,color=(0,1,1),wire=wire) O.bodies.append(bottom) clumpId,polys = O.bodies.appendClumped((t1,t2)) s = O.bodies[clumpId].state s.pos = (0,0,5) s.ori = Quaternion((1,1,.3),1.5) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Polyhedra_Aabb(),Bo1_Wall_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Polyhedra_Polyhedra_PolyhedraGeom()], [Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()], [Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()], ), NewtonIntegrator(label='newton'), ] O.dt=0.00001 try: from yade import qt qt.View() except: pass O.step() newton.gravity = (0,0,-9.81) ###################################################################### trunk-2017.01a/examples/polyhedra/free-fall.py000066400000000000000000000040231304022710500211750ustar00rootroot00000000000000from yade import plot, polyhedra_utils gravel = PolyhedraMat() gravel.density = 2600 #kg/m^3 gravel.young = 1E7 #Pa gravel.poisson = 20000/1E7 gravel.frictionAngle = 0.5 #rad steel = PolyhedraMat() steel.density = 7850 #kg/m^3 steel.young = 10*gravel.young steel.poisson = gravel.poisson steel.frictionAngle = 0.4 #rad rubber = PolyhedraMat() rubber.density = 1000 #kg/m^3 rubber.young = gravel.young/10 rubber.poisson = gravel.poisson rubber.frictionAngle = 0.7 #rad O.bodies.append(polyhedra_utils.polyhedra(gravel,v=((0,0,-0.05),(0.3,0,-0.05),(0.3,0.3,-0.05),(0,0.3,-0.05),(0,0,0),(0.3,0,0),(0.3,0.3,0),(0,0.3,0)),fixed=True, color=(0.35,0.35,0.35))) #O.bodies.append(utils.wall(0,axis=1,sense=1, material = gravel)) #O.bodies.append(utils.wall(0,axis=0,sense=1, material = gravel)) #O.bodies.append(utils.wall(0.3,axis=1,sense=-1, material = gravel)) #O.bodies.append(utils.wall(0.3,axis=0,sense=-1, material = gravel)) polyhedra_utils.fillBox((0,0,0), (0.3,0.3,0.3),gravel,sizemin=[0.025,0.025,0.025],sizemax=[0.05,0.05,0.05],seed=4) def checkUnbalancedI(): print "iter %d, time elapsed %f, time step %.5e, unbalanced forces = %.5f"%(O.iter, O.realtime, O.dt, utils.unbalancedForce()) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Polyhedra_Aabb(),Bo1_Wall_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Wall_Polyhedra_PolyhedraGeom(), Ig2_Polyhedra_Polyhedra_PolyhedraGeom(), Ig2_Facet_Polyhedra_PolyhedraGeom()], [Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()], # collision "physics" [Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()] # contact law -- apply forces ), #GravityEngine(gravity=(0,0,-9.81)), NewtonIntegrator(damping=0.3,gravity=(0,0,-9.81)), PyRunner(command='checkUnbalancedI()',realPeriod=5,label='checker') ] #O.dt=0.25*polyhedra_utils.PWaveTimeStep() O.dt=0.0025*polyhedra_utils.PWaveTimeStep() from yade import qt qt.Controller() V = qt.View() V.screenSize = (550,450) V.sceneRadius = 1 V.eyePosition = (0.7,0.5,0.1) V.upVector = (0,0,1) V.lookAt = (0.15,0.15,0.1) trunk-2017.01a/examples/polyhedra/horse.coarse.gts000066400000000000000000000723221304022710500221070ustar00rootroot00000000000000336 1002 668 GtsSurface GtsFace GtsEdge GtsVertex 0.01632376508 0.02011445965 0.03949959237 0.01658055601 0.02674922323 0.04300259797 0.01342358396 0.04386696349 0.0605453965 0.03001315348 0.01873622255 -0.04975389892 0.03116204225 0.01487261331 -0.04662516627 0.03463446561 0.01417249157 -0.06445953302 0.03853905253 -0.06858153453 -0.05929809 0.03482282022 -0.07347322551 -0.06009816584 0.03366937294 -0.06833041545 -0.06716035938 -0.00372101118 -0.05117824214 -0.005623645339 0.007895279935 -0.05575069912 -0.005892351915 -0.0051427155 -0.06231273516 -0.02069042783 -0.004407438103 0.0225899988 -0.0146861251 -0.0003199737081 0.02192630914 -0.02218160879 -0.00413713029 0.02296543695 -0.03588216291 0.03873458014 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trunk-2017.01a/examples/polyhedra/horse.py000066400000000000000000000021171304022710500204620ustar00rootroot00000000000000# modified script yade/examples/gts-horse/horse.py from yade import pack,ymport import gts surf=gts.read(open('horse.coarse.gts')) pred=pack.inGtsSurface(surf) aabb=pred.aabb() dim0=aabb[1][0]-aabb[0][0]; radius=dim0/40. O.bodies.append(pack.regularHexa(pred,radius=radius,gap=radius/4.)) tetras = ymport.ele('horse.node','horse.ele',shift=(0,0,-1*(aabb[1][2]-aabb[0][2])),wire=False,color=(0,1,1),fixed=True) O.bodies.append(tetras) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Polyhedra_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Sphere_Polyhedra_ScGeom(edgeCoeff=.1,vertexCoeff=.05)], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), NewtonIntegrator(damping=.1,gravity=(0,0,-5000)), PyRunner(iterPeriod=10,command='addPlotData()') ] O.dt=.4*PWaveTimeStep() O.saveTmp() O.timingEnabled=True O.trackEnergy=True from yade import plot plot.plots={'i':('total',O.energy.keys,)} def addPlotData(): plot.addData(i=O.iter,total=O.energy.total(),**O.energy) plot.plot(subPlots=False) from yade import qt qt.View() trunk-2017.01a/examples/polyhedra/irregular.py000066400000000000000000000036011304022710500213350ustar00rootroot00000000000000# gravity deposition, continuing with oedometric test after stabilization # shows also how to run parametric studies with yade-batch # The components of the batch are: # 1. table with parameters, one set of parameters per line (ccc.table) # 2. utils.readParamsFromTable which reads respective line from the parameter file # 3. the simulation muse be run using yade-batch, not yade # # $ yade-batch --job-threads=1 03-oedometric-test.table 03-oedometric-test.py # # create box with free top, and ceate loose packing inside the box from yade import plot, polyhedra_utils from yade import qt m = PolyhedraMat() m.density = 2600 #kg/m^3 m.young = 1E6 #Pa m.poisson = 20000/1E6 m.frictionAngle = 0.6 #rad O.bodies.append(utils.wall(0,axis=2,sense=1, material = m)) t = polyhedra_utils.polyhedra(m,size = (0.06,0.06,0.06),seed = 5) t.state.pos = (0.,0.,0.5) O.bodies.append(t) def checkUnbalanced(): # at the very start, unbalanced force can be low as there is only few contacts, but it does not mean the packing is stable print "unbalanced forces = %.5f, position %f, %f, %f"%(utils.unbalancedForce(), t.state.pos[0], t.state.pos[1], t.state.pos[2]) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Polyhedra_Aabb(),Bo1_Wall_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Wall_Polyhedra_PolyhedraGeom(), Ig2_Polyhedra_Polyhedra_PolyhedraGeom(), Ig2_Facet_Polyhedra_PolyhedraGeom()], [Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()], # collision "physics" [Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()] # contact law -- apply forces ), #GravityEngine(gravity=(0,0,-9.81)), NewtonIntegrator(damping=0.5,gravity=(0,0,-9.81)), PyRunner(command='checkUnbalanced()',realPeriod=3,label='checker') ] #O.dt=0.025*polyhedra_utils.PWaveTimeStep() O.dt=0.00025 qt.Controller() V = qt.View() O.saveTmp() #O.run() #O.save('./done') utils.waitIfBatch() trunk-2017.01a/examples/polyhedra/sphere-interaction.py000066400000000000000000000016051304022710500231460ustar00rootroot00000000000000from yade import polyhedra_utils import random polyMat = PolyhedraMat(young=1e10,poisson=.05) frictMat = FrictMat(young=1e9,poisson=.2) O.materials.append((polyMat,frictMat)) poly = polyhedra_utils.polyhedra(polyMat,(1,2,3)); poly.wire=False sph1 = sphere((2,2,2),.5,material=frictMat) sph2 = sphere((-2,0,0),.5,material=frictMat) sph3 = sphere((0,-2,0),.5,material=frictMat) O.bodies.append(( poly, sph1, sph2, sph3 )) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Polyhedra_Aabb(),Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Polyhedra_ScGeom()], [Ip2_FrictMat_PolyhedraMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), NewtonIntegrator(), ] O.dt = 1e-7 O.step() poly.state.blockedDOFs = 'xyzXYZ' for s in (sph1,sph2,sph3): r=random.random s.state.vel = -10*(s.state.pos+Vector3(r(),r(),r())) from yade import qt qt.View() trunk-2017.01a/examples/polyhedra/splitter.py000066400000000000000000000024161304022710500212120ustar00rootroot00000000000000from yade import polyhedra_utils gravel1 = PolyhedraMat() gravel1.IsSplitable = True gravel1.strength = 1e0 gravel2 = PolyhedraMat() gravel2.IsSplitable = True gravel2.strength = 2e0 gravel3 = PolyhedraMat() gravel3.IsSplitable = True gravel3.strength = 4e0 steel = PolyhedraMat() steel.young = 1e10 d = .05 p1 = polyhedra_utils.polyhedra(gravel1, size=(d,d,d), seed=1) p2 = polyhedra_utils.polyhedra(gravel2, size=(d,d,d), seed=1) p3 = polyhedra_utils.polyhedra(gravel3, size=(d,d,d), seed=1) p2.state.pos = (2*d,0,0) p3.state.pos = (4*d,0,0) p2.state.ori = p3.state.ori = p1.state.ori d = .035 w1 = utils.wall(+d, axis=1, sense=-1, material=steel) w2 = utils.wall(-d, axis=1, sense=+1, material=steel) v = 5e-1 w1.state.vel = (0,-v,0) w2.state.vel = (0,+v,0) O.bodies.append((p1,p2,p3,w1,w2)) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Polyhedra_Aabb(),Bo1_Wall_Aabb()]), InteractionLoop( [Ig2_Wall_Polyhedra_PolyhedraGeom(), Ig2_Polyhedra_Polyhedra_PolyhedraGeom()], [Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()], [Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()] ), NewtonIntegrator(), PolyhedraSplitter(iterPeriod=100), ] O.dt=1e-6 try: from yade import qt qt.Controller() v = qt.View() v.ortho = True except: pass O.run(30000) trunk-2017.01a/examples/polyhedra/tests/000077500000000000000000000000001304022710500201315ustar00rootroot00000000000000trunk-2017.01a/examples/polyhedra/tests/interactinDetectionFactor.py000066400000000000000000000012131304022710500256360ustar00rootroot00000000000000from yade import plot, polyhedra_utils from yade import qt m = PolyhedraMat() O.materials.append(m) t1,t2 = [polyhedra_utils.polyhedra(m,size=(1,1,1),seed=i) for i in (5,6)] O.bodies.append((t1,t2)) t2.state.pos = (3,0,0) t2.state.vel = (-1,0,0) factor = 2 O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Polyhedra_Aabb(aabbEnlargeFactor=factor)]), InteractionLoop( [Ig2_Polyhedra_Polyhedra_PolyhedraGeom(interactionDetectionFactor=factor)], [Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()], [Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()] ), NewtonIntegrator(), ] O.dt=0.00001 try: qt.View() except: pass trunk-2017.01a/examples/polyhedra/tests/scGeom.py000066400000000000000000000014701304022710500217220ustar00rootroot00000000000000from yade import plot, polyhedra_utils from yade import qt scGeom = 1 m = FrictMat() if scGeom else PolyhedraMat() O.materials.append(m) t1,t2 = [polyhedron(((-1,-1,-1),(+1,-1,-1),(-1,+1,-1),(+1,+1,-1),(-1,-1,+1),(+1,-1,+1),(-1,+1,+1),(+1,+1,+1))) for i in (0,1)] O.bodies.append((t1,t2)) t2.state.pos = (3,0,0) t2.state.vel = (-1,0,0) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Polyhedra_Aabb()]), InteractionLoop( [Ig2_Polyhedra_Polyhedra_ScGeom() if scGeom else Ig2_Polyhedra_Polyhedra_PolyhedraGeom()], [Ip2_FrictMat_FrictMat_FrictPhys() if scGeom else Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()], [Law2_ScGeom_FrictPhys_CundallStrack() if scGeom else Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()] ), NewtonIntegrator(), ] O.dt=0.00001 try: qt.View() except: pass trunk-2017.01a/examples/polyhedra/textExport.py000066400000000000000000000003251304022710500215270ustar00rootroot00000000000000from yade import polyhedra_utils,export polyhedra_utils.fillBox((0,0,0), (0.3,0.3,0.3),defaultMaterial(),sizemin=(0.025,0.025,0.025),sizemax=(0.05,0.05,0.05),seed=4) export.textPolyhedra('/tmp/textPolyhedra.txt') trunk-2017.01a/examples/polyhedra/wall.py000066400000000000000000000035641304022710500203100ustar00rootroot00000000000000from yade import qt import numpy as np import random from yade import polyhedra_utils m = PolyhedraMat() m.density = 1000 m.young = 5E8 m.poisson = 5E6/5E8 m.frictionAngle = 0.7 size = 0.1; vertices = [[0,0,0],[size,0,0],[size,size,0],[size,size,size],[0,size,0],[0,size,size],[0,0,size],[size,0,size]] for i in range(0,10): for j in range(0,10): t = polyhedra_utils.polyhedra(m,v=vertices) t.state.pos = (0,(i+0.5)*size-5*size,(j+0.5)*size*1) O.bodies.append(t) qt.Controller() V = qt.View() V.screenSize = (750,550) V.sceneRadius = 1 V.eyePosition = (-1.5,1.5,0.5) V.lookAt = (0,-0.5,0) V.upVector = (0,0,1) O.bodies.append(utils.wall(0,axis=2,sense=1,material=m)) def checkUnbalanced(): print ('iter %d, time elapsed %f, unbalanced forces = %f'%(O.iter, O.realtime, utils.unbalancedForce())) if O.iter<200: return if utils.unbalancedForce()>0.01: return AddBall() def AddBall(): ball = polyhedra_utils.polyhedralBall(size*1, 40, m, (-size*2.5,0,size*7),mask=1) ball.shape.color = (0,0,0.9) ball.state.vel = (15,0,0) O.bodies.append(ball) checker.dead = True O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Polyhedra_Aabb(),Bo1_Wall_Aabb()]), InteractionLoop( [Ig2_Wall_Polyhedra_PolyhedraGeom(), Ig2_Polyhedra_Polyhedra_PolyhedraGeom(), Ig2_Facet_Polyhedra_PolyhedraGeom()], [Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()], # collision "physics" [Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()] # contact law -- apply forces ), #GravityEngine(gravity=(0,0,-9.81)), NewtonIntegrator(damping=0.5,gravity=(0,0,-9.81)), PyRunner(command='checkUnbalanced()',realPeriod=3,label='checker')#, # wideo_recording #qt.SnapshotEngine(fileBase='W',iterPeriod=50,label='snapshot') ] #O.dt=.5*polyhedra_utils.PWaveTimeStep() O.dt = 0.000025 O.saveTmp() #O.run() #comment ball to see stability trunk-2017.01a/examples/ring2d/000077500000000000000000000000001304022710500161655ustar00rootroot00000000000000trunk-2017.01a/examples/ring2d/ring.stl000066400000000000000000000063241304022710500176550ustar00rootroot00000000000000Binary STL output from Blender: /home/sega/data/yade/tmp/ring.stl @>>L >>L=D>9>L= >>LD>9>L=2>9>L 2>9>LD>9>L=l>C>L= 2>9>Ll>C>L=^>C>L ^>C>Ll>C>L=>3=L= ^>C>L>3=L=>=L >=L>3=L=?ȪL= >=L?ȪL=?i!"3L ?i!"3L?ȪL=><ǽL= ?i!"3L><ǽL=>ǽL >ǽL><ǽL=U>BCL= >ǽLU>BCL=_>CL _>CLU>BCL='>9L= _>CL'>9L=2>9L 2>9L'>9L=>L= 2>9L>L=>L >L>L=9>4ԾL= >L9>4ԾL=9>2ԾL 9>2ԾL9>4ԾL=C>^L= 9>2ԾLC>^L=C>`L C>`LC>^L==L= C>`L=L==L =L=L=4L= =L4L=L.L L.L4L=kǽL= L.LkǽL=ǽL ǽLkǽL=CjL= ǽLCjL=$C[L $C[LCjL=9EԾL= $C[L9EԾL=9,ԾL 9,ԾL9EԾL=L= 9,ԾLL=L LL=Ծ:L= LԾ:L=8Ծ9L 8Ծ9LԾ:L=I|CL= 8Ծ9LI|CL=dCL dCLI|CL=ǽL= dCLǽL=ǽL ǽLǽL= L= ǽL L=5L 5L L==L= 5L=L==L =L=L=~}C>L= =L~}C>L=W8C>L W8C>L~}C>L=cԾ9>L= W8C>LcԾ9>L=&Ծ9>L &Ծ9>LcԾ9>L=7>L= &Ծ9>L7>L=>L >L7>L=/:>L= >L/:>L=9>>L 9>>L/:>L=C5>L= 9>>LC5>L=Ch>L Ch>LC5>L=ǽ>L= Ch>Lǽ>L=]ǽ>L ]ǽ>Lǽ>L=-Dt?L= ]ǽ>L-Dt?L=wW5?L wW5?L-Dt?L==>L= wW5?L=>L=1=>L 1=>L=>L=C>>L= 1=>LC>>L=LC>S>L LC>S>LC>>L=d9>>L= LC>S>Ld9>>L=9> >L >>L=>>L9> >L >>L=9> >Ld9>>L= trunk-2017.01a/examples/ring2d/ringCundallDamping.py000066400000000000000000000035401304022710500223030ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- from yade import ymport sphereRadius=0.05 ## Import wall's geometry walls = O.bodies.append(ymport.stl('ring.stl')) def fill_cylinder_with_spheres(sphereRadius,cylinderRadius,cylinderHeight,cylinderOrigin,cylinderSlope): spheresCount=0 for h in xrange(0,int(cylinderHeight/sphereRadius/2)): for r in xrange(1,int(cylinderRadius/sphereRadius/2)): dfi = asin(0.5/r)*2 for a in xrange(0,int(6.28/dfi)): x = cylinderOrigin[0]+2*r*sphereRadius*cos(dfi*a) y = cylinderOrigin[1]+2*r*sphereRadius*sin(dfi*a) z = cylinderOrigin[2]+h*2*sphereRadius s=sphere([x,y*cos(cylinderSlope)+z*sin(cylinderSlope),z*cos(cylinderSlope)-y*sin(cylinderSlope)],sphereRadius) O.bodies.append(s) spheresCount+=1 return spheresCount ## Spheres spheresCount=0 spheresCount+=fill_cylinder_with_spheres(sphereRadius,0.5,0.10,[0,0,0],radians(0)) print "Number of spheres: %d" % spheresCount ## Engines O.engines=[ ## Resets forces and momenta the act on bodies ForceResetter(), ## Using bounding boxes find possible body collisions. InsertionSortCollider([ Bo1_Sphere_Aabb(), Bo1_Facet_Aabb(), ]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), ## Apply gravity ## NOTE: Non zero Cundall damping affected a dynamic simulation! NewtonIntegrator(damping=0.3,gravity=[0,-9.81,0]), ## Apply kinematics to walls ## angularVelocity = 0.73 rad/sec = 7 rpm RotationEngine(ids=walls,rotationAxis=[0,0,1],rotateAroundZero=True,angularVelocity=0.73) ] for b in O.bodies: if isinstance(b.shape,Sphere): b.state.blockedDOFs='z' # blocked movement along Z O.dt=0.02*PWaveTimeStep() O.saveTmp('init'); from yade import qt renderer=qt.Renderer() renderer.wire=True #qt.Controller() qt.View() O.run() trunk-2017.01a/examples/ring2d/ringSimpleViscoelastic.py000066400000000000000000000044161304022710500232260ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- from yade import ymport ## Omega o=Omega() ## PhysicalParameters Density=2400 frictionAngle=radians(35) sphereRadius=0.05 tc = 0.001 en = 0.3 es = 0.3 ## Import wall's geometry facetMat=O.materials.append(ViscElMat(frictionAngle=frictionAngle,tc=tc,en=en,et=es)) sphereMat=O.materials.append(ViscElMat(density=Density,frictionAngle=frictionAngle,tc=tc,en=en,et=es)) walls = O.bodies.append(ymport.stl('ring.stl',material=facetMat)) def fill_cylinder_with_spheres(sphereRadius,cylinderRadius,cylinderHeight,cylinderOrigin,cylinderSlope): spheresCount=0 for h in xrange(0,int(cylinderHeight/sphereRadius/2)): for r in xrange(1,int(cylinderRadius/sphereRadius/2)): dfi = asin(0.5/r)*2 for a in xrange(0,int(6.28/dfi)): x = cylinderOrigin[0]+2*r*sphereRadius*cos(dfi*a) y = cylinderOrigin[1]+2*r*sphereRadius*sin(dfi*a) z = cylinderOrigin[2]+h*2*sphereRadius s=sphere([x,y*cos(cylinderSlope)+z*sin(cylinderSlope),z*cos(cylinderSlope)-y*sin(cylinderSlope)],sphereRadius,material=sphereMat) o.bodies.append(s) spheresCount+=1 return spheresCount # Spheres spheresCount=0 spheresCount+=fill_cylinder_with_spheres(sphereRadius,0.5,0.10,[0,0,0],radians(0)) print "Number of spheres: %d" % spheresCount ## Engines o.engines=[ ## Resets forces and momenta the act on bodies ForceResetter(), ## Using bounding boxes find possible body collisions. InsertionSortCollider([ Bo1_Sphere_Aabb(), Bo1_Facet_Aabb(), ]), # Interactions InteractionLoop( ## Create geometry information about each potential collision. [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom()], ## Create physical information about the interaction. [Ip2_ViscElMat_ViscElMat_ViscElPhys()], ## Constitutive law [Law2_ScGeom_ViscElPhys_Basic()], ), ## Apply gravity ## Cundall damping must been disabled! NewtonIntegrator(damping=0,gravity=[0,-9.81,0]), ## Apply kinematics to walls ## angularVelocity = 0.73 rad/sec = 7 rpm RotationEngine(ids=walls,rotationAxis=[0,0,1],rotateAroundZero=True,angularVelocity=0.73) ] for b in O.bodies: if isinstance(b.shape,Sphere): b.state.blockedDOFs='zXY' O.dt=0.02*tc O.saveTmp('init'); from yade import qt renderer=qt.Renderer() renderer.wire=True #qt.Controller() qt.View() O.run() trunk-2017.01a/examples/rod-penetration/000077500000000000000000000000001304022710500201125ustar00rootroot00000000000000trunk-2017.01a/examples/rod-penetration/model.py000066400000000000000000000037101304022710500215650ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- import random from yade import ymport ## PhysicalParameters ## Variant of mesh mesh = 'coarse' #mesh = 'fine' #mesh = 'tiny' ## Import geometry rod = O.bodies.append(ymport.stl('rod-'+mesh+'.stl',wire=True)) # Spheres sphereRadius = 0.01 nbSpheres = (32,11,32) print "Creating %d spheres..."%(nbSpheres[0]*nbSpheres[1]*nbSpheres[2]), for i in xrange(nbSpheres[0]): for j in xrange(nbSpheres[1]): for k in xrange(nbSpheres[2]): x = (i*2 - nbSpheres[0])*sphereRadius*1.1+sphereRadius*random.uniform(-0.1,0.1) y = -j*sphereRadius*2.2-0.01 z = (k*2 - nbSpheres[2])*sphereRadius*1.1+sphereRadius*random.uniform(-0.1,0.1) r = random.uniform(sphereRadius,sphereRadius*0.9) fixed = False color=[0.51,0.52,0.4] if (i==0 or i==nbSpheres[0]-1 or j==nbSpheres[1]-1 or k==0 or k==nbSpheres[2]-1): fixed = True color=[0.21,0.22,0.1] O.bodies.append(sphere([x,y,z],r,color=color,fixed=fixed)) print "done\n" ## Estimate time step #O.dt=PWaveTimeStep() O.dt=0.0001 ## Engines O.engines=[ ## Resets forces and momenta the act on bodies ForceResetter(), ## Using bounding boxes find possible body collisions. InsertionSortCollider([ Bo1_Sphere_Aabb(), Bo1_Facet_Aabb(), ]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), ## Apply gravity ## Motion equation NewtonIntegrator(damping=0.3,gravity=[0,-9.81,0]), ## Apply kinematics to rod TranslationEngine(ids=rod,translationAxis=[0,-1,0],velocity=0.075), ## Save force on rod #ForceRecorder(ids=rod,file='force-'+mesh+'.dat',iterPeriod=50), ] import sys,time print "Start simulation: " + mesh nbIter=10000 from yade import qt qt.View() O.stopAtIter=nbIter O.run() #for t in xrange(2): # start=time.time();O.run(nbIter);O.wait();finish=time.time() # speed=nbIter/(finish-start); print '%g iter/sec\n'%speed #print "FINISH" #quit() trunk-2017.01a/examples/rod-penetration/rod-coarse.stl000066400000000000000000000012541304022710500226760ustar00rootroot00000000000000Binary STL output from Blender: /home/sega/YADE/data/rod_penetration/rod.stl =?̽=À;̽̽`À;̽ 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>=d̽1 >=̽o&>=)Ľ>=tܦ[u')Ľ>=̽o&>=%>=d̽>=̽1 >=)Ľ>=S>=>=)Ľ>=Ua%$')Ľ>=%>=S>=:̽>=)Ľ>=>=trunk-2017.01a/examples/rotationalResistance.py000066400000000000000000000026711304022710500215550ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 from yade import utils, plot o = Omega() fr = 0.5;rho=2000 tc = 0.001; en = 0.7; et = 0.7; o.dt = 0.0002*tc r = 0.002 mat1 = O.materials.append(ViscElMat(frictionAngle=fr,mR = 0.05, mRtype = 1, density=rho,tc=tc,en=en,et=et)) mat2 = O.materials.append(ViscElMat(frictionAngle=fr,mR = 0.05, mRtype = 2, density=rho,tc=tc,en=en,et=et)) oriBody = Quaternion(Vector3(1,0,0),(pi/28)) id1 = O.bodies.append(sphere(center=[0,0,2*r],radius=r,material=mat1)) id2 = O.bodies.append(geom.facetBox(center=(0,-16.0*r,-2*r),orientation=oriBody,extents=(r,17.0*r,0), material=mat1,color=(0,0,1))) id3 = O.bodies.append(sphere(center=[10*r,0,2*r],radius=r,material=mat2)) id4 = O.bodies.append(geom.facetBox(center=(10*r,-16.0*r,-2*r),orientation=oriBody,extents=(r,17.0*r,0), material=mat2,color=(0,0,1))) o.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0,gravity=[0,0,-9.81]), PyRunner(command='addPlotData()',iterPeriod=10000, dead = False, label='graph'), ] def addPlotData(): f1 = [0,0,0] s1 = O.bodies[id1].state.pos[1] s2 = O.bodies[id3].state.pos[1] plot.addData(sc=O.time, fc1=s1, fc2=s2) plot.plots={'sc':('fc1','fc2')}; plot.plot() from yade import qt qt.View() trunk-2017.01a/examples/simple-scene/000077500000000000000000000000001304022710500173645ustar00rootroot00000000000000trunk-2017.01a/examples/simple-scene/2SpheresNormVisc.py000066400000000000000000000027511304022710500231170ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 # # This script plots the viscous and normal forces of the contact # of 2 spheres from yade import utils, plot, qt o = Omega() # Physical parameters fr = 0.5;rho=2000 tc = 0.0001; en = 0.7; et = 0.7; o.dt = 0.000002*tc Rad = 2.0e-3 # Add material mat1 = O.materials.append(ViscElMat(frictionAngle=fr,tc=tc,en=en,et=et)) # Add spheres id1 = O.bodies.append(sphere(center=[0,0,0],radius=Rad,material=mat1,fixed=True)) id2 = O.bodies.append(sphere(center=[0,0,(2.0*Rad)],radius=Rad,material=mat1,fixed=False)) O.bodies[id2].state.vel[2] = -1.0 # Add engines o.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0,gravity=[0,0,-9.81]), PyRunner(command='addPlotData()',iterPeriod=100), ] # Function to add data to plot def addPlotData(): try: delta = (O.bodies[id2].state.pos[2]-O.bodies[id1].state.pos[2])-(2*Rad) plot.addData(delta=delta, time1=O.time, time2=O.time, time3=O.time, time4=O.time, Fn = O.interactions[0,1].phys.Fn, Fv = O.interactions[0,1].phys.Fv, deltaDot = O.bodies[id2].state.vel[2] - O.bodies[id1].state.vel[2]) except: pass plot.plots={'time1':('delta'), 'time2':('deltaDot'), 'time3':('Fn'), 'time4':('Fv')}; plot.plot() O.run(1) qt.View() #O.wait() ; plot.saveGnuplot('sim-data_Sphere') trunk-2017.01a/examples/simple-scene/simple-scene-default-engines.py000066400000000000000000000007641304022710500254010ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- ## Demonstrate scene construction using the default list of engines ## Note that it is no longer necessary to define O.dt ## See simple-scene.py for the complete version with explicit engines definition typedEngine("NewtonIntegrator").gravity=(0,0,-9.81) typedEngine("NewtonIntegrator").damping=0.1 O.bodies.append(box(center=[0,0,0],extents=[.5,.5,.5],color=[0,0,1],fixed=True)) O.bodies.append(sphere([0,0,2],1,color=[0,1,0])) O.save('/tmp/a.xml.bz2'); trunk-2017.01a/examples/simple-scene/simple-scene-energy-tracking.py000066400000000000000000000112571304022710500254170ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- ############################################ ##### interesting parameters ##### ############################################ # Cundall non-viscous damping # try zero damping and watch total energy... damping = 0.2 # initial angular velocity angVel = 3.0 # use two spheres? two_spheres =True # sphere rotating more? rotate_in_two_directions = True ############################################ ##### material ##### ############################################ import matplotlib matplotlib.use('TkAgg') O.materials.append(CohFrictMat( young=3e8, poisson=0.3, frictionAngle=radians(30), density=2600, isCohesive=False, alphaKr=0.031, alphaKtw=0.031, momentRotationLaw=False, etaRoll=5.0, label='granular_material')) ############################################ ##### calculation loop ##### ############################################ law=Law2_ScGeom6D_CohFrictPhys_CohesionMoment(always_use_moment_law=False) g=9.81 O.trackEnergy=True O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom6D(),Ig2_Box_Sphere_ScGeom6D()], [Ip2_CohFrictMat_CohFrictMat_CohFrictPhys()], [law] ), GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=50,timestepSafetyCoefficient=.0001), NewtonIntegrator(damping=damping,kinSplit=True,gravity=(0,0,-g)), PyRunner(iterPeriod=20,command='myAddPlotData()') ] O.bodies.append(box(center=[0,0,0],extents=[.5,.5,.5],fixed=True,color=[1,0,0],material='granular_material')) O.bodies.append(sphere([0,0,2],1,color=[0,1,0],material='granular_material')) if(two_spheres): O.bodies.append(sphere([0,0,4],1,color=[0,1,0],material='granular_material')) O.dt=.002*PWaveTimeStep() O.bodies[1].state.angVel[1]=angVel if(rotate_in_two_directions): O.bodies[1].state.angVel[2]=angVel ############################################ ##### now the part pertaining to plots ##### ############################################ from yade import plot ## we will have 2 plots: ## 1. t as function of i (joke test function) ## 2. i as function of t on left y-axis ('|||' makes the separation) and z_sph, v_sph (as green circles connected with line) and z_sph_half again as function of t plot.labels={'t':'time [s]', 'normal_Work':'Normal work: W=kx^2/2', 'shear_Work':'Shear work: W=kx^2/2', 'E_kin_translation':'Translation energy: E_kin=m*V^2/2', 'E_kin_rotation':'Rotation energy: E_kin=I*$\omega$^2/2', 'E_pot':'Gravitational potential: E_pot=m*g*h', 'E_plastic':'Plastic dissipation on shearing: E_pl=F*$\Delta$F/k', 'total':'total', 'total_plus_damp':'total + damping'} plot.plots={'t':( ('normal_Work','b-'), ('shear_Work','r-'), ('E_kin_translation','b-.'), ('E_kin_rotation','r-.'), ('E_plastic','c-'), ('E_pot','y-'), ('total','k:'), ('total_plus_damp','k-') )} ## this function is called by plotDataCollector ## it should add data with the labels that we will plot ## if a datum is not specified (but exists), it will be NaN and will not be plotted def myAddPlotData(): normal_Work = law.normElastEnergy() shear_Work = law.shearElastEnergy() E_kin_translation = 0 E_kin_rotation = 0 E_pot = 0 E_plastic = 0 E_tracker = dict(O.energy.items()) if(two_spheres):## for more bodies we better use the energy tracker, because it's tracking all bodies E_kin_translation = E_tracker['kinTrans'] E_kin_rotation = E_tracker['kinRot'] E_pot = E_tracker['gravWork'] else: ## for one sphere we can just calculate, and it will be correct sph=O.bodies[1] h=sph.state.pos[2] V=sph.state.vel.norm() w=sph.state.angVel.norm() m=sph.state.mass I=sph.state.inertia[0] E_kin_translation = m*V**2.0/2.0 E_kin_rotation = I*w**2.0/2.0 E_pot = m*g*h if('plastDissip' in E_tracker): E_plastic = E_tracker['plastDissip'] total = normal_Work + shear_Work + E_plastic + E_kin_translation + E_kin_rotation + E_pot total_plus_damp = 0 if(damping!=0): total_plus_damp = total + E_tracker['nonviscDamp'] else: total_plus_damp = total plot.addData( t=O.time, normal_Work = normal_Work , shear_Work = shear_Work , E_kin_translation = E_kin_translation, E_kin_rotation = E_kin_rotation , E_pot = E_pot , E_plastic = E_plastic , total = total , total_plus_damp = total_plus_damp , ) print "Now calling plot.plot() to show the figures. The timestep is artificially low so that you can watch graphs being updated live." plot.liveInterval=2 plot.plot(subPlots=False) #from yade import qt #qt.View() O.run(int(20./O.dt)); #plot.saveGnuplot('/tmp/a') ## you can also access the data in plot.data['t'], etc, under the labels they were saved. trunk-2017.01a/examples/simple-scene/simple-scene-plot.py000066400000000000000000000037521304022710500233050ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- import matplotlib matplotlib.use('TkAgg') O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), NewtonIntegrator(damping=.2,gravity=(0,0,-9.81)), ### ### NOTE this extra engine: ### ### You want snapshot to be taken every 1 sec (realTimeLim) or every 50 iterations (iterLim), ### whichever comes soones. virtTimeLim attribute is unset, hence virtual time period is not taken into account. PyRunner(iterPeriod=20,command='myAddPlotData()') ] O.bodies.append(box(center=[0,0,0],extents=[.5,.5,.5],fixed=True,color=[1,0,0])) O.bodies.append(sphere([0,0,2],1,color=[0,1,0])) O.dt=.002*PWaveTimeStep() ############################################ ##### now the part pertaining to plots ##### ############################################ from yade import plot ## we will have 2 plots: ## 1. t as function of i (joke test function) ## 2. i as function of t on left y-axis ('|||' makes the separation) and z_sph, v_sph (as green circles connected with line) and z_sph_half again as function of t plot.plots={'i':('t'),'t':('z_sph',None,('v_sph','go-'),'z_sph_half')} ## this function is called by plotDataCollector ## it should add data with the labels that we will plot ## if a datum is not specified (but exists), it will be NaN and will not be plotted def myAddPlotData(): sph=O.bodies[1] ## store some numbers under some labels plot.addData(t=O.time,i=O.iter,z_sph=sph.state.pos[2],z_sph_half=.5*sph.state.pos[2],v_sph=sph.state.vel.norm()) print "Now calling plot.plot() to show the figures. The timestep is artificially low so that you can watch graphs being updated live." plot.liveInterval=.2 plot.plot(subPlots=False) O.run(int(2./O.dt)); #plot.saveGnuplot('/tmp/a') ## you can also access the data in plot.data['i'], plot.data['t'] etc, under the labels they were saved. trunk-2017.01a/examples/simple-scene/simple-scene.py000066400000000000000000000101651304022710500223250ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- ## Omega is the super-class that orchestrates the whole program. ## It holds the entire simulation (MetaBody), takes care of loading/saving, ## starting/stopping the simulation, loads plugins and more. o=Omega() # for advaned folks: this creates default MetaBody as well ## Engines are called consecutively at each iteration. Their order matters. ## ## Some of them work by themselves (GlobalEngine, PartialEngine - the difference of these two is unimportant). ## ## MetaEngines act as dispatchers and based on the type of objects they operate on, different EngineUnits are called. o.engines=[ ## Resets forces and momenta the act on bodies ForceResetter(), ## associates bounding volume - in this case, AxisAlignedBoundingBox (Aabb) - to each body. ## Using bounding boxes created, find possible body collisions. ## These possible collisions are inserted in O.interactions container (Scene::interactions in c++). InsertionSortCollider([ Bo1_Sphere_Aabb(), Bo1_Box_Aabb(), ]), InteractionLoop( ## Decide whether the potential collisions are real; if so, create geometry information about each potential collision. ## Here, the decision about which EngineUnit to use depends on types of _both_ bodies. ## Note that there is no EngineUnit for box-box collision. They are not implemented. [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], ## Create physical information about the interaction. ## This may consist in deriving contact rigidity from elastic moduli of each body, for example. ## The purpose is that the contact may be "solved" without reference to related bodies, ## only with the information contained in contact geometry and physics. [Ip2_FrictMat_FrictMat_FrictPhys()], ## "Solver" of the contact, also called (consitutive) law. ## Based on the information in interaction physics and geometry, it applies corresponding forces on bodies in interaction. [Law2_ScGeom_FrictPhys_CundallStrack()] ), ## Apply gravity: all bodies will have gravity applied on them. ## Note the engine parameter 'gravity', a vector that gives the acceleration. ## Forces acting on bodies are damped to artificially increase energy dissipation in simulation. ## (In this model, the restitution coefficient of interaction is 1, which is not realistic.) ## This MetaEngine acts on all PhysicalActions and selects the right EngineUnit base on type of the PhysicalAction. # # note that following 4 engines (till the end) can be replaced by an optimized monolithic version: NewtonIntegrator(damping=0.1,gravity=[0,0,-9.81]) ] ## The yade.utils module contains some handy functions, like yade.utils.box and yade.utils.sphere. ## After this import, they will be accessible as utils.box and utils.sphere. ### UPDATE: utils is loaded automatically, no longer need to import #from yade import utils ## create bodies in the simulation: one box in the origin and one floating above it. ## ## The box: ## * extents: half-size of the box. [.5,.5,.5] is unit cube ## * center: position of the center of the box ## * dynamic: it is not dynamic, i.e. will not move during simulation, even if forces are applied to it o.bodies.append(box(center=[0,0,0],extents=[.5,.5,.5],color=[0,0,1],fixed=True)) ## The sphere ## ## * First two arguments are radius and center, respectively. They are used as "positional arguments" here: ## python will deduce based on where they are what they mean. ## ## It could also be written without using sphere - see gui/py/utils.py for the code of the sphere function o.bodies.append(sphere([0,0,2],1,color=[0,1,0])) ## Estimate timestep from p-wave speed and multiply it by safety factor of .2 o.dt=.01*PWaveTimeStep() ## Save the scene to file, so that it can be loaded later. Supported extension are: .xml, .xml.gz, .xml.bz2. o.save('/tmp/a.xml.bz2'); #o.run(100000); o.wait(); print o.iter/o.realtime,'iterations/sec' def onBodySelect(id): print "Selected:",id highlightNone() for i in O.interactions.withBody(id): O.bodies[i.id2 if i.id1==id else i.id1].shape.highlight=True print i.id1,i.id2,i.phys,i.geom try: from yade import qt qt.View() qt.Controller() except ImportError: pass O.run(20000) trunk-2017.01a/examples/simple-shear/000077500000000000000000000000001304022710500173715ustar00rootroot00000000000000trunk-2017.01a/examples/simple-shear/simpleShear.py000066400000000000000000000132621304022710500222230ustar00rootroot00000000000000# -*- coding: utf-8 -*- # J. Duriez duriez@geo.hmg.inpg.fr # "PreProcessor" script to define a numerical model for simple shear box # In order to illustrate various Kinem...Engine which allow to perform different loadings on the box # There is here one § for each Kinem...Engine, comment/uncomment them to observe what you want #NB : the run of the script is paused at each plot window (so that there is time to observe it). Type "Return" in the Yade terminal to resume from yade import plot from yade.pack import * O=Omega() #Def of the material which will be used O.materials.append(NormalInelasticMat(density=2600,young=4.0e9,poisson=.04,frictionAngle=.6,coeff_dech=3.0,label='Material1')) #Def of dimensions of the box #length=5 #height=1 #width=2 length=0.1 height=0.02 width=0.04 thickness=0.001 porosity = 0.55 nSpheres=800 rMean = pow( ((1-porosity) * length * height * width) / (nSpheres * 4.0/3.0 * pi) , 1.0/3.0 ) #Definition of bodies constituing the numerical model : six boxes corresponding to sids of the simple shear box, containing a particle samples pred=inAlignedBox((0,0,-0.02),(0.1,0.02,0.02)) leftBox = box( center=(-thickness/2.0,(height)/2.0,0), extents=(thickness/2.0,5*(height/2.0+thickness),width/2.0) ,fixed=True,wire=True) lowBox = box( center=(length/2.0,-thickness/2.0,0), extents=(length/2.0,thickness/2.0,width/2.0) ,fixed=True,wire=True) rightBox = box( center=(length+thickness/2.0,height/2.0,0), extents=(thickness/2.0,5*(height/2.0+thickness),width/2.0) ,fixed=True,wire=True) upBox = box( center=(length/2.0,height+thickness/2.0,0), extents=(length/2.0,thickness/2.0,width/2.0) ,fixed=True,wire=True) behindBox = box( center=(length/2.0,height/2.0,-width/2.0-thickness/2.0), extents=(2.5*length/2.0,height/2.0+thickness,thickness/2.0), fixed=True,wire=True) inFrontBox = box( center=(length/2.0,height/2.0,width/2.0+thickness/2.0), extents=(2.5*length/2.0,height/2.0+thickness,thickness/2.0), fixed=True,wire=True) O.bodies.append([leftBox,lowBox,rightBox,upBox,behindBox,inFrontBox]) sp=SpherePack() #memoizeDb='/tmp/simpleshear-triax-packings.sqlite' #sp=randomDensePack(pred,radius=0.002,rRelFuzz=0.15,memoDbg=True,memoizeDb=memoizeDb,returnSpherePack=True) #sp=randomDensePack(pred,radius=0.002,rRelFuzz=0.15,memoDbg=True,memoizeDb=memoizeDb,spheresInCell=100,returnSpherePack=True) sp.makeCloud(Vector3(0,0.0,-width/2.0),Vector3(length,height,width/2.0),rMean,.15) sp.toSimulation() #---- Def of the engines ----# O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom6D(),Ig2_Box_Sphere_ScGeom6D()], [Ip2_2xNormalInelasticMat_NormalInelasticityPhys()], [Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity()] ), NewtonIntegrator(damping=.1) ,PyRunner(iterPeriod=50,command='defData()') ] def defData(): plot.addData(fy=O.forces.f(3)[1], # vertical component of the force sustained by the upper side of the shear box fx=O.forces.f(3)[0], # horizontal component of the force sustained by the upper side of the shear box step=O.iter, gamma=O.bodies[3].state.pos[0] - length/2.0, u=O.bodies[3].state.pos[1] - (height+thickness/2.0) ) fy=O.forces.f(3)[1] # The fy above exists only as a label in plot.data from yade import qt qt.View() #O.save("SimpleShearReady.xml") #O.saveTmp("InitialState") #---- Compression ---- O.engines = O.engines+[KinemCTDEngine(compSpeed=0.5,sigma_save=(),temoin_save=(),targetSigma=40000.0,LOG=False)] O.dt=.4*PWaveTimeStep() print '' print 'Be patient, running in progress (the shear box is being compressed)' O.run(14000,True) plot.plots={'step':('fy',)} plot.plot(subPlots=False) print 'Plotting curve (fy = normal force). Type Return to go ahead' print '' raw_input() plot.plots={'u':('fy',)} plot.plot(subPlots=False) print 'Plotting curve (u = normal displacement). Type Return to go ahead' print '' raw_input() #O.save('FinComp.xml') #---- Shear at constant normal displacement ---- nCycShear = 20000 O.engines=O.engines[:5]+[KinemCNDEngine(shearSpeed=(length/7.0)/(nCycShear*O.dt),gamma_save=(),temoin_save=(),gammalim=length/7.0,LOG=False)] print 'Be patient, running in progress (the shear box is being sheared)' O.run(int(1.15*nCycShear),True) plot.plots={'step':('gamma',)} plot.plot(subPlots=False) print 'Plotting curve (gamma = tangential displacement). Type Return to go ahead' print '' raw_input() plot.plots={'gamma':('fx','fy',)} plot.plot(subPlots=False) print 'Plotting curve (fx = tangential force). Type Return to go ahead' print '' raw_input() #---- A re-compression, from this initial sheared state ---- O.engines=O.engines[:5]+[KinemCTDEngine(compSpeed=0.5,sigma_save=(),temoin_save=(),targetSigma=80000.0,LOG=False)] print 'Be patient, running in progress (the sample is being again compressed, from this sheared state)' O.run(10000,True) plot.plots={'u':('fx','fy',)} plot.plot(subPlots=False) print 'Plotting curve. Type Return to go ahead' print '' raw_input() print 'End of script' ##---- Shear at constant normal load/stress ---- #nCycShear = 20000 #O.engines=O.engines[:6]+[KinemCNLEngine(shearSpeed=(length/10.0)/(nCycShear*O.dt),gamma_save=(),temoin_save=(),gammalim=length/10.0,LOG=False)] #O.run(int(1.15*nCycShear),True) #plot.plots={'step':('gamma','u',)} #plot.plot() #raw_input() #plot.plots={'gamma':('fx','fy',)} #plot.plot() #raw_input() #---- Shear at constant normal stifness ---- #nCycShear = 20000 #O.engines=O.engines[:6]+[KinemCNSEngine(shearSpeed=(length/10.0)/(nCycShear*O.dt),gammalim=length/10.0,LOG=False,KnC=1)] #O.run(int(1.15*nCycShear),True) #plot.plots={'step':('gamma','u',)} #plot.plot() #raw_input() #plot.plots={'gamma':('fx','fy',)} #plot.plot() #raw_input() #plot.plots={'u':('fy',)} #plot.plot() #raw_input() trunk-2017.01a/examples/sph/000077500000000000000000000000001304022710500155725ustar00rootroot00000000000000trunk-2017.01a/examples/sph/README000066400000000000000000000002011304022710500164430ustar00rootroot00000000000000This directory contains some scripits, which are using SPH method. This is highly experimental for the moment. <2014-04-09 Wed> trunk-2017.01a/examples/sph/box.geo000066400000000000000000000012341304022710500170560ustar00rootroot00000000000000acc = 300.0; hW = 2000.0; thickW = 50.0; Point(1) = {0, 300, 0, acc}; Point(2) = {0, -hW, 0, acc}; Point(3) = {1000.0, -hW, 0, acc}; Point(4) = {2000.0, -hW, 0, acc}; Point(5) = {2300, -hW+300, 0, acc}; Point(6) = {2300, -hW, 0, acc}; Point(7) = {3700, -hW, 0, acc}; Point(8) = {4000, -hW+300, 0, acc}; Point(9) = {4000, 300, 0, acc}; Line(1) = {1, 2}; Line(2) = {2, 3}; Line(3) = {3, 4}; Line(4) = {4, 5}; Line(5) = {5, 6}; Line(6) = {6, 7}; Line(7) = {7, 8}; Line(8) = {8, 9}; Line(9) = {9, 1}; Line Loop(10) = {1, 2, 3, 4, 5, 6, 7, 8, 9}; Plane Surface(11) = {10}; Extrude {0, 0, thickW} { Surface{11}; } trunk-2017.01a/examples/sph/box.mesh000066400000000000000000001267421304022710500172540ustar00rootroot00000000000000 MeshVersionFormatted 2 Dimension 3 Vertices 388 0 300 0 1 0 -2000 0 2 1000 -2000 0 3 2000 -2000 0 4 2300 -1700 0 5 2300 -2000 0 6 3700 -2000 0 7 4000 -1700 0 8 4000 300 0 9 0 300 50 10 0 -2000 50 11 1000 -2000 50 15 2000 -2000 50 19 2300 -1700 50 23 2300 -2000 50 27 3700 -2000 50 31 4000 -1700 50 35 4000 300 50 39 0 12.500000000903 0 1 0 -274.99999999796 0 1 0 -562.49999999681 0 1 0 -849.99999999633 0 1 0 -1137.4999999966 0 1 0 -1424.9999999969 0 1 0 -1712.4999999971 0 1 249.99999999967 -2000 0 2 499.99999999976 -2000 0 2 749.99999999991 -2000 0 2 1250 -2000 0 3 1500 -2000 0 3 1750 -2000 0 3 2150.0000000009 -1849.9999999991 0 4 2580 -2000 0 6 2860 -2000 0 6 3140 -2000 0 6 3420 -2000 0 6 3850 -1850 0 7 4000 -1414.2857142857 0 8 4000 -1128.5714285715 0 8 4000 -842.8571428572 0 8 4000 -557.1428571428 0 8 4000 -271.42857142853 0 8 4000 14.285714285733 0 8 3714.2857142857 300 0 9 3428.5714285715 300 0 9 3142.8571428572 300 0 9 2857.1428571429 300 0 9 2571.4285714287 300 0 9 2285.7142857144 300 0 9 2000.0000000001 300 0 9 1714.2857142856 300 0 9 1428.5714285713 300 0 9 1142.8571428571 300 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317 58 75 302 327 58 64 65 376 58 14 337 297 58 254 305 315 58 15 71 338 58 259 307 333 58 270 351 309 58 259 300 367 58 261 350 297 58 256 332 387 58 245 334 342 58 252 296 377 58 243 370 305 58 270 305 370 58 76 369 294 58 267 377 296 58 16 75 327 58 266 344 298 58 260 310 348 58 286 387 332 58 267 363 306 58 11 384 63 58 259 367 307 58 257 385 322 58 250 341 309 58 65 293 376 58 91 365 317 58 252 352 296 58 269 371 320 58 88 306 363 58 249 357 350 58 261 297 337 58 266 298 374 58 268 334 335 58 72 73 368 58 249 320 357 58 266 327 302 58 280 370 349 58 59 60 347 58 265 368 298 58 291 323 388 58 279 294 369 58 275 357 320 58 93 94 367 58 317 365 385 58 256 387 336 58 276 322 329 58 262 335 334 58 268 328 342 58 76 77 369 58 246 303 343 58 272 360 331 58 94 307 367 58 73 298 368 58 12 340 66 58 246 343 329 58 78 375 299 58 286 332 356 58 246 329 322 58 78 299 380 58 64 301 384 58 247 356 332 58 265 309 341 58 283 324 359 58 60 311 347 58 85 86 353 58 279 380 299 58 275 320 388 58 271 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355 58 266 374 327 58 81 355 366 58 270 370 351 58 279 369 380 58 286 373 387 58 282 387 373 58 77 380 369 58 End trunk-2017.01a/examples/sph/cpt/000077500000000000000000000000001304022710500163605ustar00rootroot00000000000000trunk-2017.01a/examples/sph/cpt/a000066400000000000000000000000001304022710500165110ustar00rootroot00000000000000trunk-2017.01a/examples/sph/dam_break.py000066400000000000000000000041701304022710500200530ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 from yade import utils, plot, qt o = Omega() # Physical parameters fr = 0.5; rho= 1000.0 k = 1000.0 mu = 10.0 tc = 0.01; en = 0.7; et = 0.7; vel = 0.0 #Rad = 0.006 #h = 0.011 Rad = 0.015 h = 0.03 #Rad = 0.02 #h = 0.04 o.dt = 0.0005 X = 4.0 Z = 3.0 yCoeff = 4.0 SpheresX = 1.0 SpheresZ = 2.0 # Add material mat1 = O.materials.append(ViscElMat(frictionAngle=fr,density=rho, SPHmode=True, h=h, mu=mu,tc=tc, en=en, et=et, KernFunctionPressure = 1, KernFunctionVisco = 1)) idBox = pack.regularHexa(pack.inAlignedBox((0.0,-Rad*yCoeff,0.0),(X,Rad*yCoeff,Z)),radius=Rad,gap=0.0,color=(0,1,1), material=mat1, mask = 1, fixed=True) idBoxAdd = [] idSpheresAdd = [] for i in range(len(idBox)): if (((idBox[i].state.pos[0])(X-yCoeff*Rad - 2.0*Rad)) or ((idBox[i].state.pos[2])<(yCoeff*Rad)) or ((idBox[i].state.pos[2])>(Z - 2.0*Rad))): idBoxAdd.append(idBox[i]) elif (((idBox[i].state.pos[0])-Rad) and ((idBox[i].state.pos[1])<2.0*Rad)): idBox[i].shape.color = Vector3(1,0,0) idBox[i].state.fixed = False idBox[i].state.blockedDOFs = 'y' idSpheresAdd.append(idBox[i]) O.bodies.append(idBoxAdd) idSpheres = O.bodies.append(idSpheresAdd) # Add engines o.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(label='is2aabb')],ompThreads=1), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(label='ss2sc')], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0.01,gravity=[0,0,-9.81]), SPHEngine(mask=1, k=k, rho0 = rho, h=h, KernFunctionDensity= 1), PyRunner(command='addPlotData()',iterPeriod=10,initRun=True,dead=False), ] enlargeF = h/Rad*1.1 print "enlargeF = %g"%enlargeF is2aabb.aabbEnlargeFactor = enlargeF ss2sc.interactionDetectionFactor = enlargeF # Function to add data to plot def addPlotData(): plot.addData(t = O.time, eKin = utils.kineticEnergy()) plot.plots={'t':('eKin')}; plot.plot() qt.View() trunk-2017.01a/examples/sph/sph_box.py000066400000000000000000000030261304022710500176070ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 # This script demonstrates SPH-engine in Yade # !!! Very experimental at the moment!!! from yade import utils, plot, qt o = Omega() # Physical parameters fr = 0.5; rho=1000.0 k = 2000.0 tc = 0.001; en = 0.5; et = 0.5; Rad = 7.0e-3 h = 2*7.0e-3 o.dt = 0.00025 # Add material mat1 = O.materials.append(ViscElMat(frictionAngle=fr,density=rho, SPHmode=True, h=h, tc=tc, en=en, et=et, KernFunctionPressure = 1, KernFunctionVisco = 1)) mat2 = O.materials.append(ViscElMat(frictionAngle=fr,density=rho, SPHmode=False,tc=tc, en=en, et=et)) # Add spheres d = 0.17 idSpheres = O.bodies.append( pack.regularHexa( pack.inAlignedBox( (-d*0.5,-d*0.5,-d), # lower angle (d*0.5,d*0.5,d)), # upper angle radius=Rad,gap=0.01*Rad, mask=3, material=mat1,color=(0,1,1))) id1 = O.bodies.append(geom.facetBox((Vector3(0.0,0,0.0)), (Vector3(0.2, 0.2, 0.2)), material=mat2, mask=5, color=(1,0,0), wire=True)) # Add engines o.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(label='is2aabb'),Bo1_Facet_Aabb(label='is3aabb')]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(label='ss2sc'),Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0.0,gravity=[0,0,-9.81]), SPHEngine(mask=3, k=k, rho0 = rho, h=h, KernFunctionDensity= 1), ] enlargeF = h/Rad*1.1 print "enlargeF = %g"%enlargeF is2aabb.aabbEnlargeFactor = enlargeF ss2sc.interactionDetectionFactor = enlargeF O.step() qt.View() trunk-2017.01a/examples/sph/testKernelFunc.py000066400000000000000000000076411304022710500211100ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 # This example allows to test different kernel functions from yade import utils, plot, qt o = Omega() # Physical parameters fr = 0.5; rho=1000.0 k = 1.0 mu = 100.0 tc = 0.0001; en = 0.7; et = 0.7; vel = 0.05 Rad = 15.0e-3 o.dt = 0.0001 shift = 1.0 # Add material mat1 = O.materials.append(ViscElMat(frictionAngle=fr,density=rho, SPHmode=True,mu=mu,tc=tc, en=en, et=et, KernFunctionPressure = 1, KernFunctionVisco = 1)) mat2 = O.materials.append(ViscElMat(frictionAngle=fr,density=rho, SPHmode=True,mu=mu,tc=tc, en=en, et=et, KernFunctionPressure = 1, KernFunctionVisco = 2)) mat3 = O.materials.append(ViscElMat(frictionAngle=fr,density=rho, SPHmode=True,mu=mu,tc=tc, en=en, et=et, KernFunctionPressure = 1, KernFunctionVisco = 3)) mat4 = O.materials.append(ViscElMat(frictionAngle=fr,density=rho, SPHmode=True,mu=mu,tc=tc, en=en, et=et, KernFunctionPressure = 1, KernFunctionVisco = 4)) mat5 = O.materials.append(ViscElMat(frictionAngle=fr,density=rho, SPHmode=True,mu=mu,tc=tc, en=en, et=et, KernFunctionPressure = 1, KernFunctionVisco = 5)) # Add spheres #inert = True inert = True id11 = O.bodies.append(sphere(center=[0,0,0],radius=Rad, material=mat1, mask = 1, fixed=True)) id12 = O.bodies.append(sphere(center=[0,0,(Rad*2.0*shift)],radius=Rad, material=mat1, mask = 1, fixed=inert)) id21 = O.bodies.append(sphere(center=[3.0*Rad,0,0],radius=Rad, material=mat2, mask = 1, fixed=True)) id22 = O.bodies.append(sphere(center=[3.0*Rad,0,(Rad*2.0*shift)],radius=Rad, material=mat2, mask = 1, fixed=inert)) id31 = O.bodies.append(sphere(center=[6.0*Rad,0,0],radius=Rad, material=mat3, mask = 1, fixed=True)) id32 = O.bodies.append(sphere(center=[6.0*Rad,0,(Rad*2.0*shift)],radius=Rad, material=mat3, mask = 1, fixed=inert)) id41 = O.bodies.append(sphere(center=[9.0*Rad,0,0],radius=Rad, material=mat4, mask = 1, fixed=True)) id42 = O.bodies.append(sphere(center=[9.0*Rad,0,(Rad*2.0*shift)],radius=Rad, material=mat4, mask = 1, fixed=inert)) id51 = O.bodies.append(sphere(center=[12.0*Rad,0,0],radius=Rad, material=mat5, mask = 1, fixed=True)) id52 = O.bodies.append(sphere(center=[12.0*Rad,0,(Rad*2.0*shift)],radius=Rad, material=mat5, mask = 1, fixed=inert)) vel = 0.1 O.bodies[id12].state.vel=Vector3(0,0,-vel) O.bodies[id22].state.vel=Vector3(0,0,-vel) O.bodies[id32].state.vel=Vector3(0,0,-vel) O.bodies[id42].state.vel=Vector3(0,0,-vel) O.bodies[id52].state.vel=Vector3(0,0,-vel) # Add engines o.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(label='is2aabb')]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(label='ss2sc')], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0,gravity=[0,0,-9.81]), SPHEngine(mask=1, k=k, rho0 = rho, KernFunctionDensity=1), PyRunner(command='addPlotData()',iterPeriod=1,dead=False), ] print "Time\tX\tRho\tP\tFpr " # Function to add data to plot def addPlotData(): #print "%.2f\t%.5f\t%.5f\t%.5f\t%.5f" % (O.time+O.dt, O.bodies[id2].state.pos[2], O.bodies[id2].rho, O.bodies[id2].press, O.forces.f(id2)[2]) s1 = (O.bodies[id12].state.pos[2]-O.bodies[id11].state.pos[2])-(Rad*2.0) s2 = (O.bodies[id22].state.pos[2]-O.bodies[id21].state.pos[2])-(Rad*2.0) s3 = (O.bodies[id32].state.pos[2]-O.bodies[id31].state.pos[2])-(Rad*2.0) s4 = (O.bodies[id42].state.pos[2]-O.bodies[id41].state.pos[2])-(Rad*2.0) s5 = (O.bodies[id52].state.pos[2]-O.bodies[id51].state.pos[2])-(Rad*2.0) f1 = O.forces.f(id12)[2] f2 = O.forces.f(id22)[2] f3 = O.forces.f(id32)[2] f4 = O.forces.f(id42)[2] f5 = O.forces.f(id52)[2] plot.addData(sc=O.iter, s1 = s1, s2 = s2, s3 = s3, s4 = s4, s5 = s5, fc=O.iter, f1 = f1, f2 = f2, f3 = f3, f4 = f4, f5 = f5) plot.plots={'sc':('s1', 's2', 's3', 's4', 's5'), 'fc':('f1', 'f2', 'f3', 'f4', 'f5')}; plot.plot() O.run(1, True) qt.View() O.run(1500) trunk-2017.01a/examples/sph/toystar.py000066400000000000000000000030321304022710500176470ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 # This script demonstrates SPH-engine in Yade # !!! Very experimental at the moment!!! from yade import utils, plot, qt o = Omega() # Physical parameters fr = 0.5; rho=1000.0 k = 1.0 tc = 0.0001; en = 0.7; et = 0.7; Rad = 10.0e-3 h = 2*Rad o.dt = 0.00001 # Add material mat1 = O.materials.append(ViscElMat(frictionAngle=fr,density=rho, SPHmode=True,h=h,tc=tc, en=en, et=et, KernFunctionPressure = 1, KernFunctionVisco = 1)) # Add spheres d = 0.8 idSpheres = O.bodies.append( pack.regularHexa( pack.inSphere( (0,0,0), d), radius=Rad,gap=10.5*Rad, material=mat1, mask=1, color=(0,1,1))) idCentralBody = O.bodies.append(sphere(center=[0,0,0],radius=0.1*Rad, mask = 2, color = [1,0,0], fixed=True)) # Add engines o.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(label='is2aabb'),Bo1_Facet_Aabb(label='is3aabb')]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(label='ss2sc'),Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), CentralGravityEngine(accel=50.0, label='gr', centralBody=idCentralBody), NewtonIntegrator(damping=0.1), SPHEngine(mask=1, k=k, rho0 = rho, h=h, KernFunctionDensity= 1), VTKRecorder(iterPeriod=1000, mask=1, fileName='./cpt/spheres-', recorders=['spheres','velocity','colors','intr','ids','mask','materialId','stress']), ] enlargeF = h/Rad*1.1 print "enlargeF = %g"%enlargeF is2aabb.aabbEnlargeFactor = enlargeF ss2sc.interactionDetectionFactor = enlargeF O.step() qt.View() trunk-2017.01a/examples/sph/watercolumn.py000066400000000000000000000036761304022710500205200ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 from yade import utils, plot, qt, ymport o = Omega() # Physical parameters fr = 0.0; rho=1000.0 k = 5000.0 tc = 0.001; en = 0.7; et = 0.7; vel = 0.05 Rad = 12.0e-3 h = 2*Rad o.dt = 0.0002 scaleF = 0.001 # Add material mat1 = O.materials.append(ViscElMat(frictionAngle=fr,density=rho, SPHmode=True,h=h,tc=tc, en=en, et=et, KernFunctionPressure = 1, KernFunctionVisco = 1)) mat2 = O.materials.append(ViscElMat(frictionAngle=fr,density=rho, SPHmode=False,h=h,tc=tc, en=en, et=et)) id1 = O.bodies.append(ymport.gmsh("box.mesh", scale=scaleF, material=mat2, color=(1,0,0), mask = 5, wire=True)) d = 15.0*scaleF print d idSpheres = O.bodies.append( pack.regularHexa( pack.inAlignedBox( (0, -2000.0*scaleF, 0.0), (1000*scaleF, 200*scaleF, 50.0*scaleF)), radius=d,gap=0.001*d, material=mat1, mask=3, color=(0,1,1))) print len(idSpheres) # Add engines o.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(label='is2aabb'),Bo1_Facet_Aabb(label='is3aabb')]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(label='ss2sc'),Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0.05,gravity=[0,-9.81,0]), SPHEngine(mask=3, k=k, rho0 = rho, h = h, KernFunctionDensity= 1), VTKRecorder(iterPeriod=100,fileName='./cpt/spheres-', recorders=['spheres','velocity','colors','intr','ids','mask','materialId','stress']), VTKRecorder(iterPeriod=100,fileName='./cpt/facet-', recorders=['facets'],label='VTK_box2'), PyRunner(command='addPlotData()',iterPeriod=50,dead=False), ] def addPlotData(): plot.addData(t=O.time, Ekin=utils.kineticEnergy()) plot.plots={'t':('Ekin')}; plot.plot() enlargeF = h/Rad*1.1 print "enlargeF = %g"%enlargeF is2aabb.aabbEnlargeFactor = enlargeF ss2sc.interactionDetectionFactor = enlargeF O.run(1, True) qt.View() #O.run(10000, True) #plot.saveGnuplot('sim-data_0.05') trunk-2017.01a/examples/spheresFactory.py000066400000000000000000000046551304022710500203650ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- """Simple script which shows how to create an inlet. """ shotsId,steelId=O.materials.append([ FrictMat(young=50e9,density=6000,poisson=.2,label='shots'), FrictMat(young=210e9,density=7800, poisson=.3,label='steel'), ]) ## same as # # shotsId,steelId=O.materials.index('shots'),O.materials.index('steel') # O.bodies.append(geom.facetBox(center=(0,0,0),extents=(30e-3,30e-3,0),wallMask=32,wire=False,material='steel',color=(0,1,.3))) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()],verletDist=.05*.29e-3), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_MindlinPhys( # define restitution coefficients between different pairs of material ids, see the functor's documentation for details #en=MatchMaker(fallback='zero',matches=((steelId,shotsId,.4),(shotsId,shotsId,1))) en=MatchMaker(matches=((steelId,shotsId,.4),(shotsId,shotsId,1))) )], [Law2_ScGeom_MindlinPhys_Mindlin(label='contactLaw')] ), NewtonIntegrator(damping=0), ## CircularFactory: disk if length=0 or cylinder if length>0 #CircularFactory(maxParticles=10000,radius=8e-3,length=16e-3,center=(0,-15e-3,15e-3),rMin=0.28e-3,rMax=0.29e-3,vMin=100,vMax=100,vAngle=0,massFlowRate=100./60,normal=(0,1.5,-1),label='factory',materialId=shotsId), ## BoxFactory: a line, plane or cuboid BoxFactory(maxParticles=10000,extents=(8e-3,8e-3,8e-3),center=(0,-15e-3,15e-3),rMin=0.28e-3,rMax=0.29e-3,vMin=100,vMax=100,vAngle=0,massFlowRate=100./60,normal=(0,1.5,-1),label='factory',materialId=shotsId), DomainLimiter(lo=(-30e-3,-30e-3,0),hi=(30e-3,30e-3,60e-3),iterPeriod=200), #VTKRecorder(recorders=['spheres','facets','velocity'],fileName='/tmp/nozzle-',iterPeriod=500), # run this every once in a while, to finalize the simulation at some point PyRunner(iterPeriod=10000,command='if factory.numParticles>=factory.maxParticles: O.stopAtIter=O.iter+8000; timing.stats()') ] # the timestep must be smaller because of high linear velocities of particles # we cannot use PWaveTimeStep directly, since there are no spheres generated yet O.dt=SpherePWaveTimeStep(factory.rMin,O.materials[factory.materialId].density,O.materials[factory.materialId].young) O.saveTmp() #O.timingEnabled=True from yade import timing try: from yade import qt # setup 3d view v=qt.View() v.upVector=(0,0,1); v.viewDir=(-1,0,-.3); v.center(median=False) except ImportError: pass O.run() trunk-2017.01a/examples/stl-gts/000077500000000000000000000000001304022710500163755ustar00rootroot00000000000000trunk-2017.01a/examples/stl-gts/README000066400000000000000000000004071304022710500172560ustar00rootroot00000000000000This example shows, how to perform the following conversion: GEO->STL->GTS->Yade(clumps) Then GTS-file (mesh) is importing into Yade-Script and new spheres are adding as a clump within the volume of this mesh. The script requires gmsh and libgts-bin installed. trunk-2017.01a/examples/stl-gts/cone.geo000066400000000000000000000016641304022710500200240ustar00rootroot00000000000000acc = 20.0/1000.0; D = 280.0/2.0/1000.0; d = 180.0/2.0/1000.0; h = 180.0/1000.0; Point(1) = {0.0, 0.0, 0.0, acc}; Point(2) = {0.0, D, 0.0, acc}; Point(3) = {0.0, -D, 0.0, acc}; Point(4) = {D, 0.0, 0.0, acc}; Point(5) = {-D, 0.0, 0.0, acc}; Point(6) = {0.0, 0.0, h, acc}; Circle(1) = {2, 1, 4}; Circle(2) = {4, 1, 3}; Circle(3) = {3, 1, 5}; Circle(4) = {5, 1, 2}; Line(5) = {2, 1}; Line(6) = {2, 6}; Line(7) = {4, 1}; Line(8) = {4, 6}; Line(9) = {3, 1}; Line(10) = {3, 6}; Line(11) = {5, 1}; Line(12) = {5, 6}; Line Loop(13) = {1, 7, -5}; Plane Surface(14) = {13}; Line Loop(15) = {2, 9, -7}; Plane Surface(16) = {15}; Line Loop(17) = {3, 11, -9}; Plane Surface(18) = {17}; Line Loop(19) = {4, 5, -11}; Plane Surface(20) = {19}; Line Loop(21) = {3, 12, -10}; Ruled Surface(22) = {21}; Line Loop(23) = {4, 6, -12}; Ruled Surface(24) = {23}; Line Loop(25) = {1, 8, -6}; Ruled Surface(26) = {25}; Line Loop(27) = {2, 10, -8}; Ruled Surface(28) = {27}; trunk-2017.01a/examples/stl-gts/convert2stl.sh000077500000000000000000000001121304022710500212130ustar00rootroot00000000000000#!/bin/bash gmsh -2 cone.geo -o cone.stl stl2gts -r < cone.stl > cone.gts trunk-2017.01a/examples/stl-gts/gts-stl.py000066400000000000000000000025651304022710500203540ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- # © 2009 Václav Šmilauer # © 2013 Anton Gladky from yade import pack import gts, os.path, locale surf=gts.read(open('cone.gts')) if surf.is_closed(): pred=pack.inGtsSurface(surf) aabb=pred.aabb() dim0=aabb[1][0]-aabb[0][0]; radius=dim0/70. # get some characteristic dimension, use it for radius O.bodies.appendClumped(pack.regularHexa(pred,radius=radius,gap=radius/4.)) surf.translate(0,-(aabb[1][1]-aabb[0][1])/2.0,-(aabb[1][2]-aabb[0][2])) # move surface down so that facets are underneath the falling spheres O.bodies.append(pack.gtsSurface2Facets(surf,wire=True)) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()],label='collider'), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), NewtonIntegrator(damping=.1,gravity=[0,0,-500.0]), PyRunner(iterPeriod=1000,command='timing.stats(); O.pause();'), PyRunner(iterPeriod=10,command='addPlotData()') ] O.dt=.7*PWaveTimeStep() O.saveTmp() O.timingEnabled=True O.trackEnergy=True from yade import plot plot.plots={'i':('total',O.energy.keys,)} def addPlotData(): plot.addData(i=O.iter,total=O.energy.total(),**O.energy) plot.plot(subPlots=False) from yade import timing from yade import qt qt.View() trunk-2017.01a/examples/tesselationwrapper/000077500000000000000000000000001304022710500207335ustar00rootroot00000000000000trunk-2017.01a/examples/tesselationwrapper/tesselationWrapper.py000066400000000000000000000020101304022710500251710ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- #2012 Bruno Chareyre """Example usage of a TesselationWrapper object for getting microscale quantities.""" # See Catalano2014a for the definition of micro-strain # (http://dx.doi.org/10.1002/nag.2198 or free-access at arxiv http://arxiv.org/pdf/1304.4895.pdf) tt=TriaxialTest() tt.generate("test.yade") O.load("test.yade") O.run(100,True) TW=TesselationWrapper() TW.triangulate() #compute regular Delaunay triangulation, don’t construct tesselation TW.computeVolumes() #will silently tesselate the packing, then compute volume of each Voronoi cell TW.volume(10) #get volume associated to sphere of id 10 TW.setState(0) #store current positions internaly for later use as the "0" state O.run(100,True) #make particles move a little (let's hope they will!) TW.setState(1) #store current positions internaly in the "1" (deformed) state #Now we can define strain by comparing states 0 and 1, and average them at the particles scale TW.defToVtk("strain.vtk")trunk-2017.01a/examples/test/000077500000000000000000000000001304022710500157575ustar00rootroot00000000000000trunk-2017.01a/examples/test/Damping_HM.py000066400000000000000000000061251304022710500203000ustar00rootroot00000000000000# encoding: utf-8 # 2010 Chiara Modenese # Script to test the contact damping in HM (both in the normal and shear direction) #__________________________________________________________________ # Geometry sphere and box r2=1e-2 # radii [m] p2=[r2,0,0] # center positions [m] center=[-r2/2.,0,0] # center [m] extents=[r2/2.,3*r2,3*r2] # half edge lenght [m] #__________________________________________________________________ # Material young=600.0e6 # [N/m^2] poisson=0.6 density=2.60e3 # [kg/m^3] frictionAngle=26 # [°] # Append geometry and material O.materials.append(FrictMat(young=young,poisson=poisson,density=density,frictionAngle=frictionAngle)) O.bodies.append(box(center=center,extents=extents,fixed=True,wire=True)) # body id=0 O.bodies.append(sphere(p2,r2,fixed=True,wire=True)) # body id=1 m_sphere=O.bodies[1].state.mass O.bodies[0].state.mass=m_sphere # set the mass of the box the same as the mass of the sphere O.bodies[1].state.blockedDOFs='XYZ' # block particles rotations #__________________________________________________________________ # list of engines O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_MindlinPhys(label='damping')], [Law2_ScGeom_MindlinPhys_Mindlin(label='contactLaw')] ), ForceEngine(force=(-20,0,0),ids=[1],label='force'), NewtonIntegrator(damping=0.0), PyRunner(iterPeriod=1,command='myAddPlotData()'), ] #__________________________________________________________________ # define contact damping coefficients damping.betan=0.5 # normal direction damping.betas=0.0 # shear direction damping.useDamping=True #__________________________________________________________________ # time step O.dt=.2*PWaveTimeStep() O.saveTmp('init') #__________________________________________________________________ from yade import qt qt.View() qt.Controller() #__________________________________________________________________ # plot some results from yade import plot plot.labels=dict(Fn='$Normal\,force$',un='$Overlapping$',time='$Time$',time_='$Time$',Fs='$Shear\,force$',t='$Time$') plot.plots={'time':('un',),'time_':('Fn',),'t':('Fs')} def myAddPlotData(): i=O.interactions[0,1] plot.addData(Fn=i.phys.normalForce[0],Fs=i.phys.shearForce[1],un=i.geom.penetrationDepth,time=O.time,time_=O.time,t=O.time) # We will have: # 1) data in graphs (if you call plot.plot()) # 2) data in file (if you call plot.saveGnuplot('/home/chia/Desktop/Output/out') # 3) data in memory as plot.data['un'], plot.data['fn'], etc. under the labels they were saved O.run(1000,True) # Now test the shear direction, having previously obtained a constant normal overlapping damping.betas=0.5 force.force=(-20,5,0) # assign a force also in the shear direction O.run(1000,True) plot.plot(subPlots=False) # NOTE about the results: # In the graphs, you will see the behaviour both of the normal and shear force. As expected from the damped solution, their values oscillate around the equilibrium position, which is eventually reached after few iterations. trunk-2017.01a/examples/test/WireMatPM/000077500000000000000000000000001304022710500175645ustar00rootroot00000000000000trunk-2017.01a/examples/test/WireMatPM/net-2part-displ-unloading.py000066400000000000000000000101121304022710500250340ustar00rootroot00000000000000# -*- coding: utf-8 -*- # encoding: utf-8 from yade import ymport, qt, plot ## definition of some colors for colored text output in terminal BLUE = '\033[94m' GREEN = '\033[92m' YELLOW = '\033[93m' RED = '\033[91m' BLACK = '\033[0m' #### short description of script print BLUE+''' Simple test for two particles to test the contact law for the WireMat by unsing the '''+RED+'''StepDisplacer'''+BLUE+''' with loading and unloading. '''+BLACK #### define parameters for the net # mesh opening size mos = 80./1000. a = mos/sqrt(3) # wire diameter d = 2.7/1000. # particle radius radius = d*5. # define piecewise lineare stress-strain curve strainStressValues=[(0.0019230769,2.5e8),(0.0192,3.2195e8),(0.05,3.8292e8),(0.15,5.1219e8),(0.25,5.5854e8),(0.3,5.6585e8),(0.35,5.6585e8)] # elastic material properties particleVolume = 4./3.*pow(radius,3)*pi particleMass = 3.9/1000. density = particleMass/particleVolume young = strainStressValues[0][1] / strainStressValues[0][0] poisson = 0.3 #### material definition netMat = O.materials.append(WireMat(young=young,poisson=poisson,frictionAngle=radians(30),density=density,isDoubleTwist=False,diameter=d,strainStressValues=strainStressValues,lambdaEps=0.4,lambdak=0.21)) #### create boddies, default: dynamic=True O.bodies.append( sphere([0,0,0], radius, wire=False, color=[1,0,0], highlight=False, material=netMat) ) O.bodies.append( sphere([0,a,0], radius, wire=False, color=[0,1,0], highlight=False, material=netMat) ) FixedSphere=O.bodies[0] MovingSphere=O.bodies[1] FixedSphere.dynamic=False MovingSphere.dynamic=False def addPlotData(): if O.iter < 1: plot.addData( Fn=0., un=0. ) #plot.saveGnuplot('net-2part-displ-unloading') else: try: i=O.interactions[FixedSphere.id,MovingSphere.id] plot.addData( Fn=i.phys.normalForce.norm(), un=(O.bodies[1].state.pos[1]-O.bodies[0].state.pos[1])-a ) #plot.saveGnuplot('net-2part-displ-unloading') except: print "No interaction!" O.pause() #### define simulation to create link interactionRadius=2. O.engines = [ ForceResetter(), InsertionSortCollider( [Bo1_Sphere_Aabb(aabbEnlargeFactor=interactionRadius,label='aabb')] ), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=interactionRadius,label='Ig2ssGeom')], [Ip2_WireMat_WireMat_WirePhys(linkThresholdIteration=1,label='interactionPhys')], [Law2_ScGeom_WirePhys_WirePM(linkThresholdIteration=1,label='interactionLaw')] ), NewtonIntegrator(damping=0.), PyRunner(initRun=True,iterPeriod=1,command='addPlotData()') ] #### plot some results plot.plots={'un':('Fn',)} plot.plot(noShow=False, subPlots=False) #### create link (no time step needed since loading is involved in this step) O.step() # create cohesive link (cohesiveTresholdIteration=1) #### initializes now the interaction detection factor aabb.aabbEnlargeFactor=-1. Ig2ssGeom.interactionDetectionFactor=-1. ## time step definition ## no time step definition is required since setVelocities=False in StepDisplacer #### define simulation loading O.engines = [StepDisplacer( ids=[1],mov=Vector3(0,+1e-5,0),rot=Quaternion().Identity,setVelocities=False )] + O.engines print 'Loading (press enter)' raw_input() O.run(100,True) #### define simulation unloading O.engines = [StepDisplacer( ids=[1],mov=Vector3(0,-1.3e-5,0),rot=Quaternion().Identity,setVelocities=False )] + O.engines[1:] print 'Unloading (press enter)' raw_input() O.run(50,True) #### define simulation reloading O.engines = [StepDisplacer( ids=[1],mov=Vector3(0,+1.6e-5,0),rot=Quaternion().Identity,setVelocities=False )] + O.engines[1:] print 'Reloading (press enter)' raw_input() O.run(500,True) #### define simulation unloading O.engines = [StepDisplacer( ids=[1],mov=Vector3(0,-1.45e-5,0),rot=Quaternion().Identity,setVelocities=False )] + O.engines[1:] print 'Reunloading (press enter)' raw_input() O.run(10,True) #### define simulation reloading O.engines = [StepDisplacer( ids=[1],mov=Vector3(0,+1.6e-5,0),rot=Quaternion().Identity,setVelocities=False )] + O.engines[1:] print 'Reloading (press enter)' raw_input() O.run(500,True) #### to see it v=qt.Controller() v=qt.View() rr=qt.Renderer() rr.intrAllWire=True trunk-2017.01a/examples/test/WireMatPM/net-2part-displ.py000066400000000000000000000061361304022710500230710ustar00rootroot00000000000000# -*- coding: utf-8 -*- # encoding: utf-8 from yade import ymport, qt, plot ## definition of some colors for colored text output in terminal BLUE = '\033[94m' GREEN = '\033[92m' YELLOW = '\033[93m' RED = '\033[91m' BLACK = '\033[0m' #### short description of script print BLUE+'Simple test for two particles to test contact law with '+RED+'StepDisplacer'+BLUE+'.'+BLACK #### define parameters for the net # mesh opening size mos = 80./1000. a = mos/sqrt(3) # wire diameter d = 2.7/1000. # particle radius radius = d*5. # define piecewise lineare stress-strain curve strainStressValues=[(0.0019230769,2.5e8),(0.0192,3.2195e8),(0.05,3.8292e8),(0.15,5.1219e8),(0.25,5.5854e8),(0.3,5.6585e8),(0.35,5.6585e8)] # elastic material properties particleVolume = 4./3.*pow(radius,3)*pi particleMass = 3.9/1000. density = particleMass/particleVolume young = strainStressValues[0][1] / strainStressValues[0][0] poisson = 0.3 #### material definition netMat = O.materials.append(WireMat(young=young,poisson=poisson,frictionAngle=radians(30),density=density,isDoubleTwist=False,diameter=d,strainStressValues=strainStressValues,lambdaEps=0.4,lambdak=0.21)) #### create boddies, default: dynamic=True O.bodies.append( sphere([0,0,0], radius, wire=False, color=[1,0,0], highlight=False, material=netMat, fixed=True) ) O.bodies.append( sphere([0,a,0], radius, wire=False, color=[0,1,0], highlight=False, material=netMat) ) FixedSphere=O.bodies[0] MovingSphere=O.bodies[1] FixedSphere.dynamic=False MovingSphere.dynamic=False #### define addPlotData def addPlotData(): if O.iter < 1: plot.addData( Fn=0., un=0. ) #plot.saveGnuplot('net-2part-displ') else: try: i=O.interactions[FixedSphere.id,MovingSphere.id] plot.addData( Fn=i.phys.normalForce.norm(), un=(O.bodies[1].state.pos[1]-O.bodies[0].state.pos[1])-a ) #plot.saveGnuplot('net-2part-displ') except: print "No interaction!" O.pause() #### define simulation to create link interactionRadius=2. O.engines = [ ForceResetter(), InsertionSortCollider( [Bo1_Sphere_Aabb(aabbEnlargeFactor=interactionRadius,label='aabb')] ), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=interactionRadius,label='Ig2ssGeom')], [Ip2_WireMat_WireMat_WirePhys(linkThresholdIteration=1,label='interactionPhys')], [Law2_ScGeom_WirePhys_WirePM(linkThresholdIteration=1,label='interactionLaw')] ), NewtonIntegrator(damping=0.), PyRunner(initRun=True,iterPeriod=1,command='addPlotData()') ] #### plot some results plot.plots={'un':('Fn',)} plot.plot(noShow=False, subPlots=False) #### create link (no time step needed since loading is involved in this step) O.step() # create link (cohesiveTresholdIteration=1) #### initializes now the interaction detection factor aabb.aabbEnlargeFactor=-1. Ig2ssGeom.interactionDetectionFactor=-1. #### time step definition ## no time step definition is required since setVelocities=False in StepDisplacer #### define simulation loading O.engines = [StepDisplacer( ids=[1],mov=Vector3(0,+1e-5,0),rot=Quaternion().Identity,setVelocities=False )] + O.engines #### to see it v=qt.Controller() v=qt.View() rr=qt.Renderer() rr.intrAllWire=True trunk-2017.01a/examples/test/WireMatPM/net-2part-strain.py000066400000000000000000000065061304022710500232570ustar00rootroot00000000000000# -*- coding: utf-8 -*- # encoding: utf-8 from yade import ymport, qt ## definition of some colors for colored text output in terminal BLUE = '\033[94m' GREEN = '\033[92m' YELLOW = '\033[93m' RED = '\033[91m' BLACK = '\033[0m' #### short description of script print BLUE+'Simple test for two particles to test contact law with '+RED+'UniaxialStrainer'+BLUE+'.'+BLACK #### define parameters for the net # mesh opening size mos = 80./1000. a = mos/sqrt(3) # wire diameter d = 2.7/1000. # particle radius radius = d*5. # define piecewise lineare stress-strain curve strainStressValues=[(0.0019230769,2.5e8),(0.0192,3.2195e8),(0.05,3.8292e8),(0.15,5.1219e8),(0.25,5.5854e8),(0.3,5.6585e8),(0.35,5.6585e8)] # elastic material properties particleVolume = 4./3.*pow(radius,3)*pi particleMass = 3.9/1000. density = particleMass/particleVolume young = strainStressValues[0][1] / strainStressValues[0][0] poisson = 0.3 #### material definition netMat = O.materials.append(WireMat(young=young,poisson=poisson,frictionAngle=radians(30),density=density,isDoubleTwist=False,diameter=d,strainStressValues=strainStressValues,lambdaEps=0.4,lambdak=0.21)) #### create boddies, default: dynamic=True O.bodies.append( sphere([0,0,0], radius, wire=False, color=[1,0,0], highlight=False, material=netMat) ) O.bodies.append( sphere([0,a,0], radius, wire=False, color=[0,1,0], highlight=False, material=netMat) ) FixedSphere=O.bodies[0] MovingSphere=O.bodies[1] FixedSphere.dynamic=True MovingSphere.dynamic=True #### initialize values for UniaxialStrainer bb = uniaxialTestFeatures(axis=1) negIds,posIds,axis,crossSectionArea=bb['negIds'],bb['posIds'],bb['axis'],bb['area'] strainRateTension = 1./a setSpeeds = True #### define simulation to create link interactionRadius=2. O.engines = [ ForceResetter(), InsertionSortCollider( [Bo1_Sphere_Aabb(aabbEnlargeFactor=interactionRadius,label='aabb')] ), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=interactionRadius,label='Ig2ssGeom')], [Ip2_WireMat_WireMat_WirePhys(linkThresholdIteration=1,label='interactionPhys')], [Law2_ScGeom_WirePhys_WirePM(linkThresholdIteration=1,label='interactionLaw')] ), NewtonIntegrator(damping=0.) ] #### create link (no time step needed since loading is involved in this step) O.step() # create cohesive link (cohesiveTresholdIteration=1) #### initializes now the interaction detection factor aabb.aabbEnlargeFactor=-1. Ig2ssGeom.interactionDetectionFactor=-1. ## time step definition O.dt = 1e-5 ## critical time step proposed by Bertrand #O.dt = 0.2*sqrt(particleMass/(2.*O.interactions[0,1].phys.kn)) #### plot some results from yade import plot plot.plots={'un':('Fn',)} plot.plot(noShow=False, subPlots=False) def addPlotData(): try: i=O.interactions[FixedSphere.id,MovingSphere.id] plot.addData( Fn=i.phys.normalForce.norm(), un=(O.bodies[1].state.pos[1]-O.bodies[0].state.pos[1])-a ) #plot.saveGnuplot('net-2part-strain') except: print "No interaction!" O.pause() #### define simulation O.engines += [UniaxialStrainer(strainRate=strainRateTension,axis=axis,asymmetry=1,posIds=posIds,negIds=negIds,crossSectionArea=crossSectionArea,blockDisplacements=True,blockRotations=True,setSpeeds=setSpeeds,label='strainer')] + [PyRunner(initRun=True,iterPeriod=1,command='addPlotData()')] #### to see it v=qt.Controller() v=qt.View() rr=qt.Renderer() rr.intrAllWire=True trunk-2017.01a/examples/test/batch/000077500000000000000000000000001304022710500170405ustar00rootroot00000000000000trunk-2017.01a/examples/test/batch/params.table000066400000000000000000000003001304022710500213250ustar00rootroot00000000000000!OMP_NUM_THREADS important! unimportant this! more # comment # comment and empty line 2 51 'hummm' 3.1415 'a' 1 51 'paaah' = 'b' = 52 = 'fff' = 'c' = = 'not' = 'd' 3 52 'yes' 2.71828 'e' trunk-2017.01a/examples/test/batch/sim.py000066400000000000000000000007131304022710500202030ustar00rootroot00000000000000 readParamsFromTable(unknownOk=True, important=6, unimportant='foo', this=-1, notInTable='notInTable' ) from yade.params import table #print O.tags['description'] print 'important',table.important print 'unimportant',table.unimportant #print O.tags['params'] #print O.tags['defaultParams'] import time #time.sleep(5) O.engines=[PyRunner(command='time.sleep(.005)',iterPeriod=1)] O.run(1000,True) print 'finished' import sys sys.stdout.flush() sys.exit(0) trunk-2017.01a/examples/test/beam-l6geom.py000066400000000000000000000026341304022710500204310ustar00rootroot00000000000000# # Demonstrate L6Geom class with suspended hook-shaped beam fixed at one side, subject to gravity # import numpy # radius, number and distance of spheres rad,num=1,6; dist=1.9999*rad # one arm O.bodies.append([sphere((0,y,0),rad,wire=True) for y in numpy.arange(0,2*num-1,dist)]) # the lateral arm O.bodies.append([sphere((x,(num-1)*2*rad,0),rad,wire=True) for x in numpy.arange(dist,1+num/2,dist)]) # support sphere O.bodies[0].state.blockedDOFs='xyzXYZ' # small dt to see in realtime how it swings; real critical is higher, but much less than p-wave O.dt=.01*PWaveTimeStep() O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop([Ig2_Sphere_Sphere_L6Geom(distFactor=-1)],[Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_L6Geom_FrictPhys_Linear(charLen=1)]), NewtonIntegrator(damping=0.1,gravity=(0,0,-9.81)), ] O.saveTmp() try: from yade import qt v=qt.View(); v.axes=True v.viewDir=Vector3(-0.888,-0.2,-0.4144) v.eyePosition=Vector3(18.16,8.235,5.12) v.sceneRadius=7.5 v.upVector=Vector3(-0.46,0.3885,0.798) v.screenSize=(900,900) rr=qt.Renderer() rr.intrGeom=True Gl1_L6Geom.phiScale=30; Gl1_L3Geom.uScale=20 #O.engines=O.engines+[ # qt.SnapshotEngine(fileBase=O.tmpFilename(),label='snapper',iterPeriod=300,deadTimeout=20), # PyRunner(iterPeriod=330000,command='makeVideo(snapper.snapshots,out="beam-l6geom.avi"); snapper.dead=True; O.pause()') #] except ImportError: pass O.run() trunk-2017.01a/examples/test/callback.py000066400000000000000000000011051304022710500200620ustar00rootroot00000000000000O.materials.append(FrictMat(young=30e9,poisson=.2,density=4000,frictionAngle=.5)) O.bodies.append([ sphere((0,0,0),1,fixed=True), sphere((0,0,2.1),1) ]) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), NewtonIntegrator(label='newton',gravity=(0,0,-9.81)) ] O.dt=PWaveTimeStep() disp=typedEngine('InteractionLoop') disp.callbacks=[SumIntrForcesCb()] #newton.callbacks=[SumBodyForcesCb()] print O.numThreads O.step() trunk-2017.01a/examples/test/clump-facet.py000066400000000000000000000017371304022710500205410ustar00rootroot00000000000000O.engines=[ ForceResetter(), InsertionSortCollider([ Bo1_Sphere_Aabb(), Bo1_Facet_Aabb(), ]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), NewtonIntegrator(), ] s1 = sphere((2,2,0),1) s2 = sphere((-2,2,0),1,fixed=True) f1 = facet(((0,0,-2),(0,0,2),(+5,0,0)),wire=False) f2 = facet(((0,0,-2),(0,0,2),(-5,0,0)),wire=False) # needs to assign (any) nonzero mass and inertia to facets. Total mass and inertia of clump itself can be assigned independently f1.state.mass = f2.state.mass = 1 f2.state.inertia = f2.state.inertia = (1,1,1) O.bodies.append((s1,s2)) clumpId,facetsId = O.bodies.appendClumped((f1,f2)) s = O.bodies[clumpId].state # now we can assign arbitrary inertia of the overall clump s.mass = 5000 s.inertia = 10000*Vector3(1,1,1) s.blockedDOFs = 'xyzXY' O.forces.setPermT(clumpId,(0,0,1e1)) O.dt = 5e-5 try: from yade import qt qt.View() except: pass trunk-2017.01a/examples/test/clump.py000066400000000000000000000017171304022710500174570ustar00rootroot00000000000000O.engines=[ ForceResetter(), InsertionSortCollider([ Bo1_Sphere_Aabb(), Bo1_Box_Aabb(), ]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), NewtonIntegrator(damping=.2,exactAsphericalRot=True,gravity=[0,0,-9.81]) ] # support O.bodies.append(box([0,0,-1.5],[3,3,.2],fixed=True)) # stand-alone sphere O.bodies.append(sphere([0,0,0],.5)) # clumps relPos=[(0,-.5,-.5),(0,.5,0),(.5,0,0),(0,0,.5)] coords=[(-2,0,0),(2,0,0),(0,2,0),(0,-2,0)] for i,cc in enumerate(coords): # This shorthand command does something like this: # O.bodies.appendClumped([sphere(...),sphere(...),sphere(...)]) # and returns tuple of clumpId,[bodyId1,bodyId2,bodyId3] clump,spheres=O.bodies.appendClumped([sphere([relPos[j][0]+coords[i][0],relPos[j][1]+coords[i][1],relPos[j][2]+coords[i][2]],.5) for j in range(0,i+1)]) print clump,spheres O.dt=PWaveTimeStep() O.saveTmp('init') trunk-2017.01a/examples/test/clumpPack.py000066400000000000000000000013411304022710500202470ustar00rootroot00000000000000# create a few clump configurations by hand from yade import pack c1=pack.SpherePack([((0,0,0),.5),((.5,0,0),.5),((0,.5,0),.3)]) c2=pack.SpherePack([((0,0,0),.5),((.7,0,0),.3),((.9,0,0),.2)]) sp=pack.SpherePack() print 'Generated # of clumps:',sp.makeClumpCloud((0,0,0),(15,15,15),[c1,c2],periodic=False) sp.toSimulation() O.bodies.append(wall(position=0,axis=2)) O.engines=[ #SubdomainBalancer(), ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Wall_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Wall_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), NewtonIntegrator(damping=.4,gravity=(0,0,-100)) ] O.dt=.7*PWaveTimeStep() O.saveTmp() O.step() trunk-2017.01a/examples/test/collider-stride-triax.py000066400000000000000000000021461304022710500225460ustar00rootroot00000000000000""" Playground for tuning collider strides depending on maximum velocity. """ from yade import timing import os.path loadFrom='/tmp/triax.xml' #if not os.path.exists(loadFrom): TriaxialTest(numberOfGrains=2000,noFiles=True).generate(loadFrom) O.load(loadFrom) collider=typedEngine('InsertionSortCollider') newton=typedEngine('NewtonIntegrator') # use striding; say "if 0:" to disable striding and compare to regular runs if 1: # length by which bboxes will be made larger collider.verletDist=.2*O.bodies[100].shape.radius O.step() # filter out initialization O.timingEnabled=True totalTime=0 # run a few times 500 steps, show timings to see what is the trend # notably, the percentage of collider time should decrease as the max velocity decreases as well for i in range(0,5): O.run(1000,True) timing.stats() totalTime+=sum([e.execTime for e in O.engines]) print 'Number of interactions: %d (real ratio: %g)'%(len(O.interactions),float(O.interactions.countReal())/len(O.interactions)) print '=======================================================' timing.reset() print 'Total time: %g s'%(totalTime/1e9) #quit() trunk-2017.01a/examples/test/collider-stride.py000066400000000000000000000015131304022710500214160ustar00rootroot00000000000000# # check visually whether swept bounding boxes work as expected # mat=O.materials.append(FrictMat(young=30e9,poisson=.2,density=4000,frictionAngle=.5)) O.bodies.append([ facet([[1,0,0],[-1,2,0],[-1,-2,0]],material=mat), sphere([0,0,2],.5,color=(0,1,0),material=mat) ]) O.bodies[1].state.vel=Vector3(0,0,-1) O.dt=PWaveTimeStep() O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()],label='isc'), InteractionLoop( [Ig2_Facet_Sphere_ScGeom(),Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), NewtonIntegrator(damping=0,gravity=[0,0,-100]) ] from yade import timing,qt try: renderer=qt.Renderer() #renderer['Body_bounding_volume']=True qt.Controller(); qt.View() except ImportError: pass O.timingEnabled=True O.saveTmp() O.step() trunk-2017.01a/examples/test/collider-sweep-simple.py000066400000000000000000000013251304022710500225370ustar00rootroot00000000000000O.bodies.append(sphere([0,0,10],.5)) #O.bodies.append(sphere([0,0,0],.5,fixed=True)) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()],label='collider'), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), NewtonIntegrator(damping=.1,gravity=[0,0,-1e4]) ] collider.verletDist=.5 O.dt=8e-2*PWaveTimeStep() O.saveTmp() from yade import timing O.timingEnabled=True from yade import qt r=qt.Renderer() #r['Body_bounding_volume']=True v=qt.View(); qt.Controller() v.ortho=True; #v.viewDir=O.bodies[0].phys.pos; v.lookAt=O.bodies[0].phys.pos; v.upVector=(0,0,1); O.run(2,True) trunk-2017.01a/examples/test/combined-kinematic-engine.py000066400000000000000000000030621304022710500233170ustar00rootroot00000000000000box = geom.facetBox(center=(0,0,0),extents=(1,2,3), color=(0,1,0)) O.bodies.append(box) ids = [b.id for b in box] # set this parameter according to your computer power to make the simulation vizualization slower of faster coeff = 5.0 nIterPerOneCycle = int(50000/coeff) vel = 10000*coeff angVel = 8000*coeff # function for changing motion, sets transEngine.translationAxis, rotEngine.angularVelocity and rotEngine.zeroPoint def updateKinematicEngines(): part = (O.iter / nIterPerOneCycle) % 4 if part == 0: # fist part v = Vector3(1,0,0) av = 0 elif part == 1: # second part v = Vector3(0,1,0) av = angVel elif part == 2: # third part v = Vector3(-1,0,0) av = -2*angVel elif part == 3: # fourth part v = Vector3(0,-1,0) av = angVel transEngine.translationAxis = v rotEngine.angularVelocity = av rotEngine.zeroPoint += v*vel*O.dt O.engines = [ ForceResetter(), PyRunner(iterPeriod=1, command="updateKinematicEngines()" ), # construct CombinedKinematicEngine with label, add (with +) TranslationEngine and RotationEngine CombinedKinematicEngine(ids=ids,label='combEngine') + TranslationEngine(translationAxis=(1,0,0),velocity=vel) + RotationEngine(rotationAxis=(0,0,1), angularVelocity=0, rotateAroundZero=True, zeroPoint=(0,0,0)), NewtonIntegrator(), ] # get TranslationEngine and RotationEngine from CombinedKinematicEngine transEngine, rotEngine = combEngine.comb[0], combEngine.comb[1] print print 'transEngine:', transEngine print 'rotEngine:', rotEngine print try: from yade import qt qt.View() except: print 'No graphics, sorry..' O.run() trunk-2017.01a/examples/test/energy.py000066400000000000000000000032421304022710500176230ustar00rootroot00000000000000from yade import pack,plot readParamsFromTable(useL3Geom=True,nonviscDamp=0,frictAngle=0,useClumps=False,noTableOk=True) from yade.params import table if 1: sp=pack.SpherePack(); # bunch of balls, with an infinite plane just underneath if not table.useClumps: sp.makeCloud((0,0,0),(1,1,1),.05,.5); # use clumps of 2 spheres instead, to have rotation without friction else: sp.makeClumpCloud((0,0,0),(1,1,1),[pack.SpherePack([((0,0,0),.05),((0,0,.08),.02)])],periodic=False) sp.toSimulation() else: O.bodies.append(sphere((0,0,2),radius=.5)) # one single bouncing ball O.bodies.append(wall(position=0,axis=2,sense=1)) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Wall_Aabb()]), InteractionLoop([Ig2_Sphere_Sphere_L3Geom(approxMask=0),Ig2_Wall_Sphere_L3Geom(approxMask=0)],[Ip2_FrictMat_FrictMat_FrictPhys(frictAngle=table.frictAngle)],[Law2_L3Geom_FrictPhys_ElPerfPl(noSlip=False,noBreak=False)]) if table.useL3Geom else InteractionLoop([Ig2_Sphere_Sphere_ScGeom(),Ig2_Wall_Sphere_ScGeom()],[Ip2_FrictMat_FrictMat_FrictPhys(frictAngle=table.frictAngle)],[Law2_ScGeom_FrictPhys_CundallStrack()]), NewtonIntegrator(damping=table.nonviscDamp,kinSplit=True,gravity=(0,0,-9.81)), PyRunner(iterPeriod=1,command='addPlotData()'), ] O.dt=.1*PWaveTimeStep() def addPlotData(): Ek,maxId=kineticEnergy(findMaxId=True) plot.addData(i=O.iter,total=O.energy.total(),maxId=maxId,**O.energy) # turn on energy tracking O.trackEnergy=True O.saveTmp() # the callable should return list of strings, plots will be updated automatically plot.plots={'i':[O.energy.keys,None,'total']} #from yade import timing #O.timingEnabled=True #timing.stats() plot.plot(subPlots=False) trunk-2017.01a/examples/test/exact-rot-facet.py000066400000000000000000000014701304022710500213210ustar00rootroot00000000000000# -*- encoding=utf-8 -*- ## ## TODO: verify that the code for facet & hasShear is physically correct! ## O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb(),Bo1_Facet_Aabb()]), IGeomDispatcher([ Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom(), ]), IPhysDispatcher([Ip2_FrictMat_FrictMat_FrictPhys()]), ElasticContactLaw(), RotationEngine(ids=[1],rotationAxis=[1,0,0],angularVelocity=.01), NewtonIntegrator(damping=0.2) ] scale=.1 O.bodies.append(facet([[scale,0,0],[-scale,-scale,0],[-scale,scale,0]],fixed=True,color=[1,0,0])) O.bodies.append(sphere([0,0,.99*scale],1*scale,color=[0,1,0],wire=True,fixed=True)) O.dt=.4*PWaveTimeStep() from yade import qt qt.View() renderer=qt.Renderer() renderer.intrGeom=True qt.Controller() O.step(); O.step(); O.step() O.run(20000) trunk-2017.01a/examples/test/exact-rot.py000066400000000000000000000015141304022710500202400ustar00rootroot00000000000000# -*- encoding=utf-8 -*- O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), IGeomDispatcher([ Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom(), ]), IPhysDispatcher([Ip2_FrictMat_FrictMat_FrictPhys()]), ElasticContactLaw(), RotationEngine(ids=[1],rotationAxis=(1,0,0),angularVelocity=.01), RotationEngine(ids=[0],rotationAxis=(1,1,1),angularVelocity=-.02), NewtonIntegrator(damping=.2,gravity=(0,0,-9.81)) ] O.bodies.append(sphere([0,0,0],1,fixed=True,color=[1,0,0],wire=True)) O.bodies.append(sphere([0,sqrt(2),sqrt(2)],1,color=[0,1,0],wire=True)) O.dt=.01*PWaveTimeStep() O.saveTmp() #o.run(100000); o.wait(); print o.iter/o.realtime,'iterations/sec' from yade import qt qt.View() renderer=qt.Renderer() renderer.intrGeom=True qt.Controller() O.step(); O.step(); O.step() O.run(20000) trunk-2017.01a/examples/test/facet-box.py000066400000000000000000000003171304022710500202020ustar00rootroot00000000000000O.bodies.append(geom.facetBox((0,0,0),(10,5,2))) O.bodies.append(geom.facetBox((0,0,10),(10,5,2),wallMask=0b110011,wire=False)) O.bodies.append(geom.facetBox((0,10,5),(10,5,2),wallMask=0b101010,wire=False)) trunk-2017.01a/examples/test/facet-sphere-ViscElBasic-peri.py000066400000000000000000000023361304022710500237650ustar00rootroot00000000000000# -*- coding: utf-8 # Testing facet-sphere interaction in periodic case. # Pass, if the sphere is rolling from left to right through the period. sphereRadius=0.1 tc=0.001# collision time en=0.3 # normal restitution coefficient es=0.3 # tangential restitution coefficient density=2700 frictionAngle=radians(35)# facetMat=O.materials.append(ViscElMat(frictionAngle=frictionAngle,tc=tc,en=en,et=es)) sphereMat=O.materials.append(ViscElMat(density=density,frictionAngle=frictionAngle,tc=tc,en=en,et=es)) #floor n=5 s=1./n for i in range(0,n): for j in range(0,n): O.bodies.append([ facet( [(i*s,j*s,0.1),(i*s,(j+1)*s,0.1),((i+1)*s,(j+1)*s,0.1)],material=facetMat), facet( [(i*s,j*s,0.1),((i+1)*s,j*s,0.1),((i+1)*s,(j+1)*s,0.1)],material=facetMat), ]) # Spheres sphId=O.bodies.append([sphere((0.5,0.5,0.2), 0.1, material=sphereMat)]) O.bodies[sphId[-1]].state.vel=(0.5,0,0) ## Engines O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0,gravity=[0,0,-9.81]), ] O.periodic=True O.cell.refSize=(1,1,1) O.dt=.01*tc O.saveTmp() trunk-2017.01a/examples/test/facet-sphere-ViscElBasic.py000066400000000000000000000026351304022710500230320ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Testing facet-sphere interaction. # A facet is rotated around Z axis. Test pass, if a sphere at (0,0) position is not moving (because in this case no transfer moment from the facet to the sphere), but a sphere at facet's edge moves with the facet (for this sphere blocked the rotation DOFs in order to remove rolling). ## PhysicalParameters Density=2400 frictionAngle=radians(35) tc = 0.001 en = 0.3 es = 0.3 ## Import wall's geometry facetMat=O.materials.append(ViscElMat(frictionAngle=frictionAngle,tc=tc,en=en,et=es)) sphereMat=O.materials.append(ViscElMat(density=Density,frictionAngle=frictionAngle,tc=tc,en=en,et=es)) facetId=O.bodies.append(facet( [ (-1,0,0), (1,1,0), (1,-1,0)], material=facetMat,color=(1,0,0))) sphIds=O.bodies.append([ sphere( (0,0,0.1),0.1, material=sphereMat,color=(0,1,0)), sphere( (0.9,0,0.1),0.1, material=sphereMat,color=(0,1,0)) ]) O.bodies[sphIds[1]].state.blockedDOFs='XYZ' ## Timestep O.dt=.1*tc ## Engines O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0,gravity=[0,0,-9.81]), RotationEngine(ids=[facetId],rotationAxis=[0,0,1],rotateAroundZero=True,angularVelocity=0.1) ] from yade import qt qt.View() O.saveTmp() #O.run() trunk-2017.01a/examples/test/facet-sphere.py000066400000000000000000000021741304022710500207030ustar00rootroot00000000000000# -*- coding: utf-8 -*- # © Václav Šmilauer # # Test case for sphere-facet interaction. O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), #SpatialQuickSortCollider(), InteractionLoop( [Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), NewtonIntegrator(damping=0.01,gravity=[0,0,-10]), ] O.bodies.append([ facet([[-1,-1,0],[1,-1,0],[0,1,0]],fixed=True,color=[1,0,0]), facet([[1,-1,0],[0,1,0,],[1,.5,.5]],fixed=True) ]) import random for i in range(0,100): s=sphere([random.gauss(0,1),random.gauss(0,1),random.uniform(1,2)],random.uniform(.02,.05)) s.state.vel=Vector3(random.gauss(0,.1),random.gauss(0,.1),random.gauss(0,.1)) O.bodies.append(s) O.dt=PWaveTimeStep() O.run() O.saveTmp('init') if 0: from yade import qt renderer=qt.Renderer() renderer['Interaction_geometry']=True qt.Controller() #except ImportError: pass O.saveTmp() O.loadTmp() if 0: O.timingEnabled=True from yade import timing for i in range(4): timing.reset() O.loadTmp('init') O.run(100000,True) timing.stats() quit() trunk-2017.01a/examples/test/flat-collider.py000066400000000000000000000016341304022710500210560ustar00rootroot00000000000000from yade import pack,timing #O.bodies.append([ sphere((0.2,0,0),.5,fixed=True), sphere((0.2,0.0,1.01),.5), ]) O.bodies.append(pack.regularHexa(pack.inAlignedBox((0,0,0),(10,10,1)),radius=.5,gap=0,fixed=True)) O.bodies.append(pack.regularOrtho(pack.inAlignedBox((3,3,3),(7,7,4)),radius=.05,gap=0)) O.engines=[ ForceResetter(), FlatGridCollider(step=.2,aabbMin=(0,0,0),aabbMax=(10,10,5),verletDist=0.005), # InsertionSortCollider([Bo1_Sphere_Aabb()],sweepLength=0.005), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), NewtonIntegrator(damping=0.4,gravity=[0,0,-10]), ] O.dt=.6*PWaveTimeStep() O.saveTmp() #O.step() #while True: # O.step() # if len(O.interactions)>0 or O.bodies[1].state.pos[2]<.97: break print('This will take a while, drink a coffee ;)') O.timingEnabled=True O.run(5000,True) timing.stats() import sys #sys.exit(0) trunk-2017.01a/examples/test/force-move.py000066400000000000000000000003711304022710500203740ustar00rootroot00000000000000O.bodies.append(sphere([0,0,0],1,fixed=False)) O.engines=[ ForceResetter(), PyRunner(command='O.forces.addMove(0,(1e-2,0,0))',iterPeriod=1), NewtonIntegrator() ] for i in xrange(0,20): O.step() print O.forces.f(0),O.bodies[0].state.pos quit() trunk-2017.01a/examples/test/force-network-video.py000066400000000000000000000024411304022710500222230ustar00rootroot00000000000000print 30*'*'+' WARNING '+30*'*'+'\nFor hardware/driver/...? reasons related to 3d, this script might\nsometimes crash when the first snapshot is taken with message such as\n\n\tQGLContext::makeCurrent(): Failed.\n\nor\n\n\tFatal IO error 11 (Resource temporarily unavailable) on X server :0.0.\n\nA workaround is to open the 3d view by hand, rather than having it\nopen by SnapshotEngine automatically when the first snapshot is\nabout to be taken. Sometimes only the message is displayed,\nwithout crash.\n'+25*'*'+' This is a known bug. '+25*'*' TriaxialTest(noFiles=True).load() from yade import qt O.engines=O.engines+[ qt.SnapshotEngine(fileBase=O.tmpFilename(),label='snapshotter',iterPeriod=5,ignoreErrors=False), PyRunner(iterPeriod=500,command='finito()') ] rr=qt.Renderer() rr.shape,rr.intrPhys=False,True def finito(): """This function will be called after 500 steps. Since SnapshotEngine waits for a new 3d view to open, it must run after the script has finished and the command line appears (see https://bugs.launchpad.net/yade/+bug/622669). For that reason, O.run() is at the end of the script and this function will be called once we want to exit really. """ makeVideo(snapshotter.snapshots,out='/tmp/video.avi') print "Video saved in /tmp/video.avi" import sys sys.exit(0) O.run() trunk-2017.01a/examples/test/genCylLSM.py000066400000000000000000000034261304022710500201330ustar00rootroot00000000000000""" This example shows how LSMGenGeo generates Cylinder with given parameters. Be sure LSMGenGeo library is installed. The result is: 2 files: "cyl.geo" is the geometry file which can be imported into YADE with ymport.gengeoFile() function "cyl.vtk" is the VTK-filed which can be opened by any VTK-based software, for example Paraview spheres, imported into the YADE simulation, according to generated geometry http://www.access.edu.au/lsmgengeo_python_doc/current/pythonapi/html/GenGeo-module.html https://svn.esscc.uq.edu.au/svn/esys3/lsm/contrib/LSMGenGeo/ """ from yade import pack,ymport try: from GenGeo import * except ImportError: from gengeo import * import sys fileName="cyl" radius=15 length=100 minRadius=0.5 maxRadius=2.0 origin=Vector3(0.0,0.0,0.0) axis=Vector3(0.0,0.0,1.0) minPoint=Vector3(-radius,-radius,-length) maxPoint=Vector3(radius,radius,length) box=CylinderVol ( origin = origin, axis = axis, radius = radius, length = 2.0*length ) mntable=MNTable3D ( minPoint=minPoint, maxPoint=maxPoint, gridSize=2.5*maxRadius, numGroups=1 ) packer=InsertGenerator3D( minRadius=minRadius, maxRadius=maxRadius, insertFails=1000, maxIterations=1000, tolerance=1.0e-6, seed=0 ) packer.generatePacking ( volume=box, ntable=mntable, groupID=0 ) #Write data to files mntable.write(fileName+".geo",1) mntable.write(fileName+".vtu",2) #Add material O.materials.append(FrictMat(young=1e9,poisson=.25,frictionAngle=0.5,density=1e3)) #Parameters, which will be passed into spheres and facets creators kw={'material':0} #Import the GenGeo geometry directly into the YADE simulation O.bodies.append(ymport.gengeo(mntable,shift=[-1.0,-1.0,-1.0],scale=2.0,color=(1,1,0),**kw)) try: from yade import qt qt.Controller() qt.View() except ImportError: pass trunk-2017.01a/examples/test/helix.py000066400000000000000000000007141304022710500174440ustar00rootroot00000000000000# script for testing InterpolatingHelixEngine: sphere going in a sphere-like motion around bar O.bodies.append([box([0,0,0],[.005,.005,1],fixed=True),sphere([0,.1,-1],.04,fixed=False)]) O.engines=[ InterpolatingHelixEngine(ids=[1],times=[10,20,30,40,50,60,70,80,90,100],angularVelocities=[1,2,3,4,5,3,1,-1,-3,0],rotationAxis=[0,0,1],zeroPoint=[0,0,0], wrap=True,slope=.003,label='spiral'), ] O.dt=4e-6 O.saveTmp('initial') from yade import qt qt.Controller() trunk-2017.01a/examples/test/interpolating-force.py000066400000000000000000000045131304022710500223070ustar00rootroot00000000000000# encoding: utf-8 # 2009 Václav Šmilauer # script showing how to use InterpolatingDirectedForceEngine, # simply pushing one free sphere agains a fixed one with varying force # # The force evolution is sine wave, but it could really be any data from numpy import arange nPulses=4 # run for total of 4 pulses freq=10. # 5 pulses per second times=arange(0,1/freq,.01/freq) # generate 100 points equally distributed over the period (can be much more) maxMag=1e5 # maximum magnitude of applied force magnitudes=[.5*maxMag*(sin(t*(freq*2*pi))+1) for t in times] # generate points on sine wave over 1 period, but shifted up to be ∈(0,2) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), # ids: what bodies is force applied to # direction: direction of the force (normalized automatically), constant # magnitudes: series of force magnitude # times: time points at which magnitudes are defined # wrap: continue from t0 once t_last is reached # label: automatically defines python variable of that name pointing to this engine InterpolatingDirectedForceEngine(ids=[1],direction=[0,0,-1],magnitudes=magnitudes,times=times,wrap=True,label='forcer'), # without damping, the interaction never stabilizes and oscillates wildly… try it NewtonIntegrator(damping=0.01), # collect some data to plot periodically (every 50 steps) PyRunner(iterPeriod=1,command='myAddPlotData()') ] O.bodies.append([ sphere([0,0,0],1,fixed=True,color=[1,0,0]), sphere([0,0,2],1,color=[0,1,0]) ]) # elastic timestep O.dt=.5*PWaveTimeStep() # callback for plotDataCollector import yade.plot as yp def myAddPlotData(): yp.addData(t=O.time,F_applied=forcer.force[2],supportReaction=O.forces.f(0)[2]) O.saveTmp() # try open 3d view, if not running in pure console mode try: import yade.qt yade.qt.View() except ImportError: pass # run so many steps such that prescribed number of pulses is done O.run(int((nPulses/freq)/O.dt),True) # plot the time-series of force magnitude import pylab pylab.plot(times,magnitudes,label='Force magnitude over 1 pulse'); pylab.legend(('Force magnitude',)); pylab.xlabel('t'); pylab.grid(True) # plot some recorded data yp.plots={'t':('F_applied','supportReaction')} yp.plot() trunk-2017.01a/examples/test/kinematic.py000066400000000000000000000014761304022710500203050ustar00rootroot00000000000000# Deomonstrate composition of KinematicEngine's with +: # The first engine is composed (from translation and 2 independent rotations, one global and one local) # The second engine does the same on body #1 as the first one does on #0 (the local rotation is not present) O.bodies.append([ sphere((-1,0,0),.3,color=(1,0,.5),fixed=False,wire=True), sphere((1,0,0),.3,color=(0,1,0),fixed=False,wire=True) ]) O.engines=[ # only ids of the 1st engine are used TranslationEngine(ids=[0],translationAxis=(0,0,1),velocity=.1) + RotationEngine(rotationAxis=(0,0,1),angularVelocity=1,rotateAroundZero=True) + RotationEngine(rotationAxis=(1,0,0),angularVelocity=.3,rotateAroundZero=False), HelixEngine(ids=[1],rotationAxis=(0,0,1),angularVelocity=1,linearVelocity=.1), NewtonIntegrator(warnNoForceReset=False), ] O.dt=1e-6 O.saveTmp() trunk-2017.01a/examples/test/mindlin.py000066400000000000000000000042041304022710500177630ustar00rootroot00000000000000#!/usr/bin/python # -*- coding: utf-8 -*- ## ## SCRIPT TO TEST A NEW CONSTITUTIVE LAW (MINDLIN - nonlinear elastic model) ## list of engines O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_MindlinPhys()], [Law2_ScGeom_MindlinPhys_Mindlin()] ), NewtonIntegrator(damping=0.0,gravity=(10,0,0)), ### ### NOTE this extra engine: ### ### You want snapshot to be taken every 1 sec (realTimeLim) or every 50 iterations (iterLim), ### whichever comes soones. virtTimeLim attribute is unset, hence virtual time period is not taken into account. PyRunner(iterPeriod=1,command='myAddPlotData()') ] ## define and append material mat=FrictMat(young=600.0e6,poisson=0.6,density=2.60e3,frictionAngle=26,label='Friction') O.materials.append(mat) ## create two spheres (one will be fixed) and append them s0=sphere([0,0,0],1,color=[0,1,0],fixed=False,wire=True,material='Friction') s1=sphere([2,0,0],1,color=[0,2,0],fixed=True,wire=True,material='Friction') O.bodies.append(s0) O.bodies.append(s1) ## time step O.dt=.2*PWaveTimeStep() O.saveTmp('Mindlin') from yade import qt qt.View() qt.Controller() ############################################ ##### now the part pertaining to plots ##### ############################################ from yade import plot ## make one plot: step as function of fn plot.plots={'un':('fn')} ## this function is called by plotDataCollector ## it should add data with the labels that we will plot ## if a datum is not specified (but exists), it will be NaN and will not be plotted def myAddPlotData(): if O.interactions[0,1].isReal: i=O.interactions[0,1] ## store some numbers under some labels plot.addData(fn=i.phys.normalForce[0],step=O.iter,un=2*s0.shape.radius-s1.state.pos[0]+s0.state.pos[0],kn=i.phys.kn) O.run(100,True); plot.plot(subPlots=False) ## We will have: ## 1) data in graphs (if you call plot.plot()) ## 2) data in file (if you call plot.saveGnuplot('/tmp/a') ## 3) data in memory as plot.data['step'], plot.data['fn'], plot.data['un'], etc. under the labels they were saved trunk-2017.01a/examples/test/multi/000077500000000000000000000000001304022710500171115ustar00rootroot00000000000000trunk-2017.01a/examples/test/multi/multi.out000066400000000000000000000000541304022710500207730ustar00rootroot00000000000000-9.81 2400 10 18.6013 -9.81 2400 10 18.6013 trunk-2017.01a/examples/test/multi/multi.py000066400000000000000000000031501304022710500206140ustar00rootroot00000000000000# # https://yade-dem.org/wiki/ScriptParametricStudy # ## read parameters from table here from yade import plot readParamsFromTable(gravity=-9.81,density=2400,initialSpeed=10,noTableOk=True) from yade.params.table import * print gravity,density,initialSpeed O.materials.append(FrictMat(young=30e9,density=density,poisson=.3)) ## use the 'density' parameter here O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb(),]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys(),], [Law2_ScGeom_FrictPhys_CundallStrack(),] ), PyRunner(iterPeriod=100,command='myAddPlotData()',label='plotDataCollector'), NewtonIntegrator(damping=0.4,gravity=(0,0,gravity))## here we use the 'gravity' parameter ] O.bodies.append([ box([0,50,0],extents=[1,50,1],fixed=True,color=[1,0,0]), sphere([0,0,10],1,color=[0,1,0]) ]) O.bodies[1].state.vel=(0,initialSpeed,0) ## assign initial velocity O.dt=.8*PWaveTimeStep() ## o.saveTmp('initial') def myAddPlotData(): s=O.bodies[1] plot.addData({'t':O.time,'y_sph':s.state.pos[1],'z_sph':s.state.pos[2]}) plot.plots={'y_sph':('z_sph',)} # run 30000 iterations O.run(20000,True) # write some results to a common file # (we rely on the fact that 2 processes will not write results at exactly the same time) # 'a' means to open for appending #file('multi.out','a').write('%s %g %g %g %g\n'%(O.tags['description'],gravity,density,initialSpeed,O.bodies[1].state.pos[1])) file('multi.out','a').write('%g %g %g %g\n'%(gravity,density,initialSpeed,O.bodies[1].state.pos[1])) print 'gnuplot',plot.saveGnuplot(O.tags['id']) trunk-2017.01a/examples/test/multi/multi.table000066400000000000000000000003431304022710500212540ustar00rootroot00000000000000description density initialSpeed ## comment here reference 2400 10 hi_v 2400 20 lo_v 2400 5 # comment there hi_rho 5000 10 hi_rho_v 5000 20 hi_rh0_lo_v 5000 5 # comment-only line trunk-2017.01a/examples/test/pack-cloud.py000066400000000000000000000005251304022710500203550ustar00rootroot00000000000000""" Generate random periodic sphere packing using SpherePack::makeCloud """ from yade import pack p=pack.SpherePack() O.cellSize=Vector3(10,10,10) print p.makeCloud(Vector3(0,0,0),Vector3(10,10,10),.5,.5,200,True) for s in p: O.bodies.append(sphere(s[0],s[1])) O.engines=[BoundDispatcher([Bo1_Sphere_Aabb()])] from yade import qt qt.View() trunk-2017.01a/examples/test/pack-inConvexPolyhedron.py000066400000000000000000000026101304022710500231010ustar00rootroot00000000000000from yade import pack import random random.seed(1) # a cube p1 = Vector3(-9,-2,-2) p2 = p1 + (1,1,1) pred1 = pack.inConvexPolyhedron(( (p1, (+1, 0, 0)), (p1, ( 0,+1, 0)), (p1, ( 0, 0,+1)), (p2, (-1, 0, 0)), (p2, ( 0,-1, 0)), (p2, ( 0, 0,-1)), )) # a tetrahedron p1 = Vector3(-7,-2,-2) p2 = p1 + (1,1,1) pred2 = pack.inConvexPolyhedron(( (p1, (+1, 0, 0)), (p1, ( 0,+1, 0)), (p1, ( 0, 0,+1)), (p2, (-1,-1,-1)), )) # random polyhedron center = Vector3(-2,-2,-2) dMin = 1 dMax = 1.2 n = 20 planes = [] for i in xrange(n): d = random.random()*(dMax-dMin) + dMin # distance of plane from center, random number in range (dMin,dMax) # http://mathworld.wolfram.com/HyperspherePointPicking.html normal = Vector3([random.gauss(0,10) for _ in xrange(3)]) # random normal vector normal.normalize() planes.append((center-d*normal,normal)) pred3 = pack.inConvexPolyhedron(planes) try: # should be ValueError, since the 3 planes does not form closed polyhedron and finding its bounds should fail pred4 = pack.inConvexPolyhedron(( ((0,0,0), (+1, 0, 0)), ((0,0,0), ( 0,+1, 0)), ((0,0,0), ( 0, 0,+1)), )) except ValueError: print 'ValueError successfully detected' else: raise RuntimeError, "ValueError should have been detected..." r = .05 for p in (pred1,pred2,pred3): O.bodies.append(pack.regularHexa(p,r,0,color=randomColor())) try: from yade import qt v = qt.View() v.axes = True except: pass trunk-2017.01a/examples/test/pack-predicates.py000066400000000000000000000005771304022710500214010ustar00rootroot00000000000000from yade.pack import * s1=inSphere((0,0,0),1) s2=inSphere((0,0,1),1) # construct using explicit composition s12=PredicateUnion(s1,s2) print s12.aabb(), s12((0,0,.5),0) # constuct the same predicate with operators print (s1|s2).aabb(), (s1|s2)((0,0,.5),0) # predicate difference: points in s1 and not in s2 print (s1-s2).aabb() print (s1-s2)((0,0,1.5),0) print (s1-s2)((0,0,-0.5),0) trunk-2017.01a/examples/test/paraview-spheres-solid-section/000077500000000000000000000000001304022710500240165ustar00rootroot00000000000000trunk-2017.01a/examples/test/paraview-spheres-solid-section/export_text.py000066400000000000000000000014211304022710500267530ustar00rootroot00000000000000from yade import pack, export pred = pack.inAlignedBox((0,0,0),(10,10,10)) O.bodies.append(pack.randomDensePack(pred,radius=1.,rRelFuzz=.5,spheresInCell=500,memoizeDb='/tmp/pack.db')) export.textExt('/tmp/test.txt',format='x_y_z_r_attrs',attrs=('b.state.pos.norm()','b.state.pos'),comment='dstN dstV_x dstV_y dstV_z') # text2vtk and text2vtkSection function can be copy-pasted from yade/py/export.py into separate py file to avoid executing yade or to use pure python export.text2vtk('/tmp/test.txt','/tmp/test.vtk') export.text2vtkSection('/tmp/test.txt','/tmp/testSection.vtk',point=(5,5,5),normal=(1,1,1)) # now open paraview, click "Tools" menu -> "Python Shell", click "Run Script", choose "pv_section.py" from this directiory # or just run python pv_section.py # and enjoy :-) trunk-2017.01a/examples/test/paraview-spheres-solid-section/pv_section.py000066400000000000000000000754601304022710500265550ustar00rootroot00000000000000try: paraview.simple except: from paraview.simple import * paraview.simple._DisableFirstRenderCameraReset() RenderView1 = CreateRenderView() RenderView1.LightSpecularColor = [1.0, 1.0, 1.0] RenderView1.KeyLightAzimuth = 10.0 RenderView1.UseTexturedBackground = 0 RenderView1.UseLight = 1 RenderView1.CameraPosition = [-10.901121443539559, -17.271355476388358, 4.309974877565033] RenderView1.FillLightKFRatio = 3.0 RenderView1.Background2 = [0.0, 0.0, 0.165] RenderView1.FillLightAzimuth = -10.0 RenderView1.LODResolution = 50.0 RenderView1.BackgroundTexture = [] RenderView1.InteractionMode = '3D' RenderView1.StencilCapable = 1 RenderView1.LightIntensity = 1.0 RenderView1.CameraFocalPoint = [4.732498500000004, 5.045734999999994, 4.874767500000023] RenderView1.ImageReductionFactor = 2 RenderView1.CameraViewAngle = 30.0 RenderView1.CameraParallelScale = 7.0538593576100945 RenderView1.EyeAngle = 2.0 RenderView1.HeadLightKHRatio = 3.0 RenderView1.StereoRender = 0 RenderView1.KeyLightIntensity = 0.75 RenderView1.BackLightAzimuth = 110.0 RenderView1.OrientationAxesInteractivity = 0 RenderView1.UseInteractiveRenderingForSceenshots = 0 RenderView1.UseOffscreenRendering = 0 RenderView1.Background = [1.0, 1.0, 1.0] RenderView1.UseOffscreenRenderingForScreenshots = 0 RenderView1.NonInteractiveRenderDelay = 2 RenderView1.CenterOfRotation = [4.7324985, 5.045735, 4.8747675] RenderView1.CameraParallelProjection = 0 RenderView1.CompressorConfig = 'vtkSquirtCompressor 0 3' RenderView1.HeadLightWarmth = 0.5 RenderView1.MaximumNumberOfPeels = 4 RenderView1.LightDiffuseColor = [1.0, 1.0, 1.0] RenderView1.StereoType = 'Red-Blue' RenderView1.DepthPeeling = 1 RenderView1.BackLightKBRatio = 3.5 RenderView1.StereoCapableWindow = 1 RenderView1.CameraViewUp = [-0.818931483577863, 0.5738512869077476, -0.006776851723502143] RenderView1.LightType = 'HeadLight' RenderView1.LightAmbientColor = [1.0, 1.0, 1.0] RenderView1.RemoteRenderThreshold = 3.0 RenderView1.CacheKey = 0.0 RenderView1.UseCache = 0 RenderView1.KeyLightElevation = 50.0 RenderView1.CenterAxesVisibility = 0 RenderView1.MaintainLuminance = 0 RenderView1.StillRenderImageReductionFactor = 1 RenderView1.BackLightWarmth = 0.5 RenderView1.FillLightElevation = -75.0 RenderView1.MultiSamples = 0 RenderView1.FillLightWarmth = 0.4 RenderView1.AlphaBitPlanes = 1 RenderView1.LightSwitch = 0 RenderView1.OrientationAxesVisibility = 0 RenderView1.CameraClippingRange = [14.893135346284218, 43.89470107765568] RenderView1.BackLightElevation = 0.0 RenderView1.ViewTime = 0.0 RenderView1.OrientationAxesOutlineColor = [1.0, 1.0, 1.0] RenderView1.LODThreshold = 5.0 RenderView1.CollectGeometryThreshold = 100.0 RenderView1.UseGradientBackground = 0 RenderView1.KeyLightWarmth = 0.6 RenderView1.OrientationAxesLabelColor = [1.0, 1.0, 1.0] test_vtk = LegacyVTKReader( guiName="test.vtk", FileNames=['/tmp/test.vtk'] ) Glyph1 = Glyph( guiName="Glyph1", RandomMode=1, GlyphTransform="Transform2", GlyphType="Sphere", MaximumNumberofPoints=5000, ScaleMode='scalar', MaskPoints=0, Vectors=['POINTS', ''], SetScaleFactor=1.0, Scalars=['POINTS', 'radius'], Orient=1 ) Glyph1.GlyphType.StartTheta = 0.0 Glyph1.GlyphType.ThetaResolution = 12 Glyph1.GlyphTransform.Rotate = [0.0, 0.0, 0.0] Glyph1.GlyphTransform.Translate = [0.0, 0.0, 0.0] Glyph1.GlyphType.PhiResolution = 12 Glyph1.GlyphType.EndTheta = 360.0 Glyph1.GlyphType.EndPhi = 180.0 Glyph1.GlyphType.Center = [0.0, 0.0, 0.0] Glyph1.GlyphType.Radius = 1.0 Glyph1.GlyphTransform.Scale = [1.0, 1.0, 1.0] Glyph1.GlyphType.StartPhi = 0.0 Clip2 = Clip( guiName="Clip2", InsideOut=0, UseValueAsOffset=0, Scalars=['POINTS', 'radius'], Value=0.0, ClipType="Plane" ) Clip2.ClipType.Normal = [1.0, 1.0, 1.0] Clip2.ClipType.Origin = [5.0, 5.0, 5.0] Clip2.ClipType.Offset = 0.0 testSection_vtk = LegacyVTKReader( guiName="testSection.vtk", FileNames=['/tmp/testSection.vtk'] ) Glyph3 = Glyph( guiName="Glyph3", ScaleMode='scalar', GlyphType="Cylinder", MaskPoints=0, RandomMode=1, Vectors=['POINTS', 'normal'], GlyphTransform="Transform2", Scalars=['POINTS', 'radius'], MaximumNumberofPoints=5000, SetScaleFactor=1.0, Orient=1 ) Glyph3.GlyphType.Capping = 1 Glyph3.GlyphType.Height = 0.01 Glyph3.GlyphTransform.Rotate = [0.0, 0.0, -90.0] Glyph3.GlyphType.Radius = 1.0 Glyph3.GlyphTransform.Translate = [0.0, 0.0, 0.0] Glyph3.GlyphType.Center = [0.0, 0.0, 0.0] Glyph3.GlyphType.Resolution = 18 Glyph3.GlyphTransform.Scale = [1.0, 1.0, 1.0] a1_radius_PiecewiseFunction = CreatePiecewiseFunction( Points=[0.0, 0.0, 0.5, 0.0, 1.0, 1.0, 0.5, 0.0] ) a1_radiusOrig_PiecewiseFunction = CreatePiecewiseFunction( Points=[0.0, 0.0, 0.5, 0.0, 1.0, 1.0, 0.5, 0.0] ) a1_radius_PVLookupTable = GetLookupTableForArray( "radius", 1, Discretize=1, RGBPoints=[0.522954, 0.0, 0.0, 1.0, 1.42914, 1.0, 0.0, 0.0], UseLogScale=0, VectorComponent=0, NanColor=[0.498039, 0.498039, 0.498039], NumberOfTableValues=256, ColorSpace='HSV', VectorMode='Magnitude', HSVWrap=0, ScalarRangeInitialized=1.0, LockScalarRange=1 ) a1_radiusOrig_PVLookupTable = GetLookupTableForArray( "radiusOrig", 1, Discretize=1, RGBPoints=[0.54491, 0.0, 0.0, 1.0, 1.41118, 1.0, 0.0, 0.0], UseLogScale=0, VectorComponent=0, NanColor=[0.498039, 0.498039, 0.498039], NumberOfTableValues=256, ColorSpace='HSV', VectorMode='Magnitude', HSVWrap=0, ScalarRangeInitialized=1.0, LockScalarRange=1 ) SetActiveSource(test_vtk) DataRepresentation1 = Show() DataRepresentation1.CubeAxesZAxisVisibility = 1 DataRepresentation1.SelectionPointLabelColor = [0.5, 0.5, 0.5] DataRepresentation1.SelectionPointFieldDataArrayName = 'radius' DataRepresentation1.SuppressLOD = 0 DataRepresentation1.CubeAxesXGridLines = 0 DataRepresentation1.CubeAxesYAxisTickVisibility = 1 DataRepresentation1.CubeAxesColor = [1.0, 1.0, 1.0] DataRepresentation1.Position = [0.0, 0.0, 0.0] DataRepresentation1.BackfaceRepresentation = 'Follow Frontface' DataRepresentation1.SelectionOpacity = 1.0 DataRepresentation1.SelectionPointLabelShadow = 0 DataRepresentation1.CubeAxesYGridLines = 0 DataRepresentation1.CubeAxesZAxisRange = [0.0, 1.0] DataRepresentation1.OrientationMode = 'Direction' DataRepresentation1.Source.TipResolution = 6 DataRepresentation1.ScaleMode = 'No Data Scaling Off' DataRepresentation1.Diffuse = 1.0 DataRepresentation1.SelectionUseOutline = 0 DataRepresentation1.CubeAxesZTitle = 'Z-Axis' DataRepresentation1.Specular = 0.1 DataRepresentation1.SelectionVisibility = 1 DataRepresentation1.InterpolateScalarsBeforeMapping = 1 DataRepresentation1.CubeAxesZAxisTickVisibility = 1 DataRepresentation1.Origin = [0.0, 0.0, 0.0] DataRepresentation1.CubeAxesVisibility = 0 DataRepresentation1.Scale = [1.0, 1.0, 1.0] DataRepresentation1.SelectionCellLabelJustification = 'Left' DataRepresentation1.DiffuseColor = [1.0, 1.0, 1.0] DataRepresentation1.SelectionCellLabelOpacity = 1.0 DataRepresentation1.Source = "Arrow" DataRepresentation1.Source.Invert = 0 DataRepresentation1.Masking = 0 DataRepresentation1.Opacity = 1.0 DataRepresentation1.LineWidth = 1.0 DataRepresentation1.MeshVisibility = 0 DataRepresentation1.Visibility = 1 DataRepresentation1.SelectionCellLabelFontSize = 18 DataRepresentation1.CubeAxesCornerOffset = 0.0 DataRepresentation1.SelectionPointLabelJustification = 'Left' DataRepresentation1.SelectionPointLabelVisibility = 0 DataRepresentation1.SelectOrientationVectors = '' DataRepresentation1.CubeAxesTickLocation = 'Inside' DataRepresentation1.CubeAxesXAxisMinorTickVisibility = 1 DataRepresentation1.CubeAxesYAxisVisibility = 1 DataRepresentation1.SelectionPointLabelFontFamily = 'Arial' DataRepresentation1.Source.ShaftResolution = 6 DataRepresentation1.CubeAxesFlyMode = 'Closest Triad' DataRepresentation1.SelectScaleArray = '' DataRepresentation1.CubeAxesYTitle = 'Y-Axis' DataRepresentation1.ColorAttributeType = 'POINT_DATA' DataRepresentation1.SpecularPower = 100.0 DataRepresentation1.Texture = [] DataRepresentation1.SelectionCellLabelShadow = 0 DataRepresentation1.AmbientColor = [1.0, 1.0, 1.0] DataRepresentation1.MapScalars = 1 DataRepresentation1.PointSize = 2.0 DataRepresentation1.Source.TipLength = 0.35 DataRepresentation1.SelectionCellLabelFormat = '' DataRepresentation1.Scaling = 0 DataRepresentation1.StaticMode = 0 DataRepresentation1.SelectionCellLabelColor = [0.0, 1.0, 0.0] DataRepresentation1.Source.TipRadius = 0.1 DataRepresentation1.EdgeColor = [0.0, 0.0, 0.5000076295109483] DataRepresentation1.CubeAxesXAxisTickVisibility = 1 DataRepresentation1.SelectionCellLabelVisibility = 0 DataRepresentation1.NonlinearSubdivisionLevel = 1 DataRepresentation1.CubeAxesXAxisRange = [0.0, 1.0] DataRepresentation1.Representation = 'Surface' DataRepresentation1.CubeAxesYAxisRange = [0.0, 1.0] DataRepresentation1.CustomBounds = [0.0, 1.0, 0.0, 1.0, 0.0, 1.0] DataRepresentation1.Orientation = [0.0, 0.0, 0.0] DataRepresentation1.CubeAxesEnableCustomAxisRange = 0 DataRepresentation1.CubeAxesXTitle = 'X-Axis' DataRepresentation1.CubeAxesInertia = 1 DataRepresentation1.BackfaceOpacity = 1.0 DataRepresentation1.SelectionCellFieldDataArrayName = 'vtkOriginalCellIds' DataRepresentation1.SelectionColor = [1.0, 0.0, 1.0] DataRepresentation1.Ambient = 0.0 DataRepresentation1.SelectionPointLabelFontSize = 18 DataRepresentation1.ScaleFactor = 0.8360145000000001 DataRepresentation1.BackfaceAmbientColor = [1.0, 1.0, 1.0] DataRepresentation1.Source.ShaftRadius = 0.03 DataRepresentation1.SelectMaskArray = '' DataRepresentation1.SelectionLineWidth = 2.0 DataRepresentation1.CubeAxesZAxisMinorTickVisibility = 1 DataRepresentation1.CubeAxesXAxisVisibility = 1 DataRepresentation1.Interpolation = 'Gouraud' DataRepresentation1.SelectionCellLabelFontFamily = 'Arial' DataRepresentation1.SelectionCellLabelItalic = 0 DataRepresentation1.CubeAxesYAxisMinorTickVisibility = 1 DataRepresentation1.CubeAxesZGridLines = 0 DataRepresentation1.SelectionPointLabelFormat = '' DataRepresentation1.SelectionPointLabelOpacity = 1.0 DataRepresentation1.BackfaceDiffuseColor = [1.0, 1.0, 1.0] DataRepresentation1.Pickable = 1 DataRepresentation1.CustomBoundsActive = [0, 0, 0] DataRepresentation1.SelectionRepresentation = 'Wireframe' DataRepresentation1.SelectionPointLabelBold = 0 DataRepresentation1.ColorArrayName = 'radius' DataRepresentation1.SelectionPointLabelItalic = 0 DataRepresentation1.AllowSpecularHighlightingWithScalarColoring = 0 DataRepresentation1.SpecularColor = [1.0, 1.0, 1.0] DataRepresentation1.LookupTable = a1_radius_PVLookupTable DataRepresentation1.SelectionPointSize = 5.0 DataRepresentation1.SelectionCellLabelBold = 0 DataRepresentation1.Orient = 0 SetActiveSource(Glyph1) DataRepresentation3 = Show() DataRepresentation3.CubeAxesZAxisVisibility = 1 DataRepresentation3.SelectionPointLabelColor = [0.5, 0.5, 0.5] DataRepresentation3.SelectionPointFieldDataArrayName = 'radius' DataRepresentation3.SuppressLOD = 0 DataRepresentation3.CubeAxesXGridLines = 0 DataRepresentation3.CubeAxesYAxisTickVisibility = 1 DataRepresentation3.CubeAxesColor = [1.0, 1.0, 1.0] DataRepresentation3.Position = [0.0, 0.0, 0.0] DataRepresentation3.BackfaceRepresentation = 'Follow Frontface' DataRepresentation3.SelectionOpacity = 1.0 DataRepresentation3.SelectionPointLabelShadow = 0 DataRepresentation3.CubeAxesYGridLines = 0 DataRepresentation3.CubeAxesZAxisRange = [0.0, 1.0] DataRepresentation3.OrientationMode = 'Direction' DataRepresentation3.Source.TipResolution = 6 DataRepresentation3.ScaleMode = 'No Data Scaling Off' DataRepresentation3.Diffuse = 1.0 DataRepresentation3.SelectionUseOutline = 0 DataRepresentation3.CubeAxesZTitle = 'Z-Axis' DataRepresentation3.Specular = 0.1 DataRepresentation3.SelectionVisibility = 1 DataRepresentation3.InterpolateScalarsBeforeMapping = 1 DataRepresentation3.CubeAxesZAxisTickVisibility = 1 DataRepresentation3.Origin = [0.0, 0.0, 0.0] DataRepresentation3.CubeAxesVisibility = 0 DataRepresentation3.Scale = [1.0, 1.0, 1.0] DataRepresentation3.SelectionCellLabelJustification = 'Left' DataRepresentation3.DiffuseColor = [1.0, 1.0, 1.0] DataRepresentation3.SelectionCellLabelOpacity = 1.0 DataRepresentation3.Source = "Arrow" DataRepresentation3.Source.Invert = 0 DataRepresentation3.Masking = 0 DataRepresentation3.Opacity = 1.0 DataRepresentation3.LineWidth = 1.0 DataRepresentation3.MeshVisibility = 0 DataRepresentation3.Visibility = 0 DataRepresentation3.SelectionCellLabelFontSize = 18 DataRepresentation3.CubeAxesCornerOffset = 0.0 DataRepresentation3.SelectionPointLabelJustification = 'Left' DataRepresentation3.SelectionPointLabelVisibility = 0 DataRepresentation3.SelectOrientationVectors = '' DataRepresentation3.CubeAxesTickLocation = 'Inside' DataRepresentation3.CubeAxesXAxisMinorTickVisibility = 1 DataRepresentation3.CubeAxesYAxisVisibility = 1 DataRepresentation3.SelectionPointLabelFontFamily = 'Arial' DataRepresentation3.Source.ShaftResolution = 6 DataRepresentation3.CubeAxesFlyMode = 'Closest Triad' DataRepresentation3.SelectScaleArray = '' DataRepresentation3.CubeAxesYTitle = 'Y-Axis' DataRepresentation3.ColorAttributeType = 'POINT_DATA' DataRepresentation3.SpecularPower = 100.0 DataRepresentation3.Texture = [] DataRepresentation3.SelectionCellLabelShadow = 0 DataRepresentation3.AmbientColor = [1.0, 1.0, 1.0] DataRepresentation3.MapScalars = 1 DataRepresentation3.PointSize = 2.0 DataRepresentation3.Source.TipLength = 0.35 DataRepresentation3.SelectionCellLabelFormat = '' DataRepresentation3.Scaling = 0 DataRepresentation3.StaticMode = 0 DataRepresentation3.SelectionCellLabelColor = [0.0, 1.0, 0.0] DataRepresentation3.Source.TipRadius = 0.1 DataRepresentation3.EdgeColor = [0.0, 0.0, 0.5000076295109483] DataRepresentation3.CubeAxesXAxisTickVisibility = 1 DataRepresentation3.SelectionCellLabelVisibility = 0 DataRepresentation3.NonlinearSubdivisionLevel = 1 DataRepresentation3.CubeAxesXAxisRange = [0.0, 1.0] DataRepresentation3.Representation = 'Surface' DataRepresentation3.CubeAxesYAxisRange = [0.0, 1.0] DataRepresentation3.CustomBounds = [0.0, 1.0, 0.0, 1.0, 0.0, 1.0] DataRepresentation3.Orientation = [0.0, 0.0, 0.0] DataRepresentation3.CubeAxesEnableCustomAxisRange = 0 DataRepresentation3.CubeAxesXTitle = 'X-Axis' DataRepresentation3.CubeAxesInertia = 1 DataRepresentation3.BackfaceOpacity = 1.0 DataRepresentation3.SelectionCellFieldDataArrayName = 'vtkOriginalCellIds' DataRepresentation3.SelectionColor = [1.0, 0.0, 1.0] DataRepresentation3.Ambient = 0.0 DataRepresentation3.SelectionPointLabelFontSize = 18 DataRepresentation3.ScaleFactor = 0.9713980622589589 DataRepresentation3.BackfaceAmbientColor = [1.0, 1.0, 1.0] DataRepresentation3.Source.ShaftRadius = 0.03 DataRepresentation3.SelectMaskArray = '' DataRepresentation3.SelectionLineWidth = 2.0 DataRepresentation3.CubeAxesZAxisMinorTickVisibility = 1 DataRepresentation3.CubeAxesXAxisVisibility = 1 DataRepresentation3.Interpolation = 'Gouraud' DataRepresentation3.SelectionCellLabelFontFamily = 'Arial' DataRepresentation3.SelectionCellLabelItalic = 0 DataRepresentation3.CubeAxesYAxisMinorTickVisibility = 1 DataRepresentation3.CubeAxesZGridLines = 0 DataRepresentation3.SelectionPointLabelFormat = '' DataRepresentation3.SelectionPointLabelOpacity = 1.0 DataRepresentation3.BackfaceDiffuseColor = [1.0, 1.0, 1.0] DataRepresentation3.Pickable = 1 DataRepresentation3.CustomBoundsActive = [0, 0, 0] DataRepresentation3.SelectionRepresentation = 'Wireframe' DataRepresentation3.SelectionPointLabelBold = 0 DataRepresentation3.ColorArrayName = 'radius' DataRepresentation3.SelectionPointLabelItalic = 0 DataRepresentation3.AllowSpecularHighlightingWithScalarColoring = 0 DataRepresentation3.SpecularColor = [1.0, 1.0, 1.0] DataRepresentation3.LookupTable = a1_radius_PVLookupTable DataRepresentation3.SelectionPointSize = 5.0 DataRepresentation3.SelectionCellLabelBold = 0 DataRepresentation3.Orient = 0 SetActiveSource(Clip2) DataRepresentation5 = Show() DataRepresentation5.CubeAxesZAxisVisibility = 1 DataRepresentation5.SelectionPointLabelColor = [0.5, 0.5, 0.5] DataRepresentation5.SelectionPointFieldDataArrayName = 'radius' DataRepresentation5.SuppressLOD = 0 DataRepresentation5.CubeAxesXGridLines = 0 DataRepresentation5.CubeAxesYAxisTickVisibility = 1 DataRepresentation5.CubeAxesColor = [1.0, 1.0, 1.0] DataRepresentation5.Position = [0.0, 0.0, 0.0] DataRepresentation5.BackfaceRepresentation = 'Follow Frontface' DataRepresentation5.SelectionOpacity = 1.0 DataRepresentation5.SelectionPointLabelShadow = 0 DataRepresentation5.CubeAxesYGridLines = 0 DataRepresentation5.CubeAxesZAxisRange = [0.0, 1.0] DataRepresentation5.OrientationMode = 'Direction' DataRepresentation5.Source.TipResolution = 6 DataRepresentation5.ScaleMode = 'No Data Scaling Off' DataRepresentation5.Diffuse = 1.0 DataRepresentation5.SelectionUseOutline = 0 DataRepresentation5.SelectionPointLabelFormat = '' DataRepresentation5.CubeAxesZTitle = 'Z-Axis' DataRepresentation5.Specular = 0.1 DataRepresentation5.SelectionVisibility = 1 DataRepresentation5.InterpolateScalarsBeforeMapping = 1 DataRepresentation5.CubeAxesZAxisTickVisibility = 1 DataRepresentation5.Origin = [0.0, 0.0, 0.0] DataRepresentation5.CubeAxesVisibility = 0 DataRepresentation5.Scale = [1.0, 1.0, 1.0] DataRepresentation5.SelectionCellLabelJustification = 'Left' DataRepresentation5.DiffuseColor = [1.0, 1.0, 1.0] DataRepresentation5.SelectionCellLabelOpacity = 1.0 DataRepresentation5.CubeAxesInertia = 1 DataRepresentation5.Source = "Arrow" DataRepresentation5.Source.Invert = 0 DataRepresentation5.Masking = 0 DataRepresentation5.Opacity = 1.0 DataRepresentation5.LineWidth = 1.0 DataRepresentation5.MeshVisibility = 0 DataRepresentation5.Visibility = 1 DataRepresentation5.SelectionCellLabelFontSize = 18 DataRepresentation5.CubeAxesCornerOffset = 0.0 DataRepresentation5.SelectionPointLabelJustification = 'Left' DataRepresentation5.SelectionPointLabelVisibility = 0 DataRepresentation5.SelectOrientationVectors = '' DataRepresentation5.CubeAxesTickLocation = 'Inside' DataRepresentation5.BackfaceDiffuseColor = [1.0, 1.0, 1.0] DataRepresentation5.CubeAxesYAxisVisibility = 1 DataRepresentation5.SelectionPointLabelFontFamily = 'Arial' DataRepresentation5.Source.ShaftResolution = 6 DataRepresentation5.CubeAxesFlyMode = 'Closest Triad' DataRepresentation5.SelectScaleArray = '' DataRepresentation5.CubeAxesYTitle = 'Y-Axis' DataRepresentation5.ColorAttributeType = 'POINT_DATA' DataRepresentation5.SpecularPower = 100.0 DataRepresentation5.Texture = [] DataRepresentation5.SelectionCellLabelShadow = 0 DataRepresentation5.AmbientColor = [1.0, 1.0, 1.0] DataRepresentation5.MapScalars = 1 DataRepresentation5.PointSize = 2.0 DataRepresentation5.Source.TipLength = 0.35 DataRepresentation5.SelectionCellLabelFormat = '' DataRepresentation5.Scaling = 0 DataRepresentation5.StaticMode = 0 DataRepresentation5.SelectionCellLabelColor = [0.0, 1.0, 0.0] DataRepresentation5.Source.TipRadius = 0.1 DataRepresentation5.EdgeColor = [0.0, 0.0, 0.5000076295109483] DataRepresentation5.CubeAxesXAxisTickVisibility = 1 DataRepresentation5.SelectionCellLabelVisibility = 0 DataRepresentation5.NonlinearSubdivisionLevel = 1 DataRepresentation5.CubeAxesXAxisRange = [0.0, 1.0] DataRepresentation5.Representation = 'Surface' DataRepresentation5.CubeAxesYAxisRange = [0.0, 1.0] DataRepresentation5.CustomBounds = [0.0, 1.0, 0.0, 1.0, 0.0, 1.0] DataRepresentation5.Orientation = [0.0, 0.0, 0.0] DataRepresentation5.CubeAxesEnableCustomAxisRange = 0 DataRepresentation5.CubeAxesXTitle = 'X-Axis' DataRepresentation5.ScalarOpacityUnitDistance = 1.1040324233388048 DataRepresentation5.BackfaceOpacity = 1.0 DataRepresentation5.SelectionPointLabelFontSize = 18 DataRepresentation5.SelectionCellFieldDataArrayName = 'vtkOriginalCellIds' DataRepresentation5.SelectionColor = [1.0, 0.0, 1.0] DataRepresentation5.Ambient = 0.0 DataRepresentation5.CubeAxesXAxisMinorTickVisibility = 1 DataRepresentation5.ScaleFactor = 0.8981979608535767 DataRepresentation5.BackfaceAmbientColor = [1.0, 1.0, 1.0] DataRepresentation5.Source.ShaftRadius = 0.03 DataRepresentation5.ScalarOpacityFunction = a1_radius_PiecewiseFunction DataRepresentation5.SelectMaskArray = '' DataRepresentation5.SelectionLineWidth = 2.0 DataRepresentation5.CubeAxesZAxisMinorTickVisibility = 1 DataRepresentation5.CubeAxesXAxisVisibility = 1 DataRepresentation5.Interpolation = 'Gouraud' DataRepresentation5.SelectMapper = 'Projected tetra' DataRepresentation5.SelectionCellLabelFontFamily = 'Arial' DataRepresentation5.SelectionCellLabelItalic = 0 DataRepresentation5.CubeAxesYAxisMinorTickVisibility = 1 DataRepresentation5.CubeAxesZGridLines = 0 DataRepresentation5.ExtractedBlockIndex = 0 DataRepresentation5.SelectionPointLabelOpacity = 1.0 DataRepresentation5.Pickable = 1 DataRepresentation5.CustomBoundsActive = [0, 0, 0] DataRepresentation5.SelectionRepresentation = 'Wireframe' DataRepresentation5.SelectionPointLabelBold = 0 DataRepresentation5.ColorArrayName = 'radius' DataRepresentation5.SelectionPointLabelItalic = 0 DataRepresentation5.AllowSpecularHighlightingWithScalarColoring = 0 DataRepresentation5.SpecularColor = [1.0, 1.0, 1.0] DataRepresentation5.LookupTable = a1_radius_PVLookupTable DataRepresentation5.SelectionPointSize = 5.0 DataRepresentation5.SelectionCellLabelBold = 0 DataRepresentation5.Orient = 0 SetActiveSource(testSection_vtk) DataRepresentation7 = Show() DataRepresentation7.CubeAxesZAxisVisibility = 1 DataRepresentation7.SelectionPointLabelColor = [0.5, 0.5, 0.5] DataRepresentation7.SelectionPointFieldDataArrayName = 'radius' DataRepresentation7.SuppressLOD = 0 DataRepresentation7.CubeAxesXGridLines = 0 DataRepresentation7.CubeAxesYAxisTickVisibility = 1 DataRepresentation7.CubeAxesColor = [1.0, 1.0, 1.0] DataRepresentation7.Position = [0.0, 0.0, 0.0] DataRepresentation7.BackfaceRepresentation = 'Follow Frontface' DataRepresentation7.SelectionOpacity = 1.0 DataRepresentation7.SelectionPointLabelShadow = 0 DataRepresentation7.CubeAxesYGridLines = 0 DataRepresentation7.CubeAxesZAxisRange = [0.0, 1.0] DataRepresentation7.OrientationMode = 'Direction' DataRepresentation7.Source.TipResolution = 6 DataRepresentation7.ScaleMode = 'No Data Scaling Off' DataRepresentation7.Diffuse = 1.0 DataRepresentation7.SelectionUseOutline = 0 DataRepresentation7.CubeAxesZTitle = 'Z-Axis' DataRepresentation7.Specular = 0.1 DataRepresentation7.SelectionVisibility = 1 DataRepresentation7.InterpolateScalarsBeforeMapping = 1 DataRepresentation7.CubeAxesZAxisTickVisibility = 1 DataRepresentation7.Origin = [0.0, 0.0, 0.0] DataRepresentation7.CubeAxesVisibility = 0 DataRepresentation7.Scale = [1.0, 1.0, 1.0] DataRepresentation7.SelectionCellLabelJustification = 'Left' DataRepresentation7.DiffuseColor = [1.0, 1.0, 1.0] DataRepresentation7.SelectionCellLabelOpacity = 1.0 DataRepresentation7.Source = "Arrow" DataRepresentation7.Source.Invert = 0 DataRepresentation7.Masking = 0 DataRepresentation7.Opacity = 1.0 DataRepresentation7.LineWidth = 1.0 DataRepresentation7.MeshVisibility = 0 DataRepresentation7.Visibility = 1 DataRepresentation7.SelectionCellLabelFontSize = 18 DataRepresentation7.CubeAxesCornerOffset = 0.0 DataRepresentation7.SelectionPointLabelJustification = 'Left' DataRepresentation7.SelectionPointLabelVisibility = 0 DataRepresentation7.SelectOrientationVectors = '' DataRepresentation7.CubeAxesTickLocation = 'Inside' DataRepresentation7.CubeAxesXAxisMinorTickVisibility = 1 DataRepresentation7.CubeAxesYAxisVisibility = 1 DataRepresentation7.SelectionPointLabelFontFamily = 'Arial' DataRepresentation7.Source.ShaftResolution = 6 DataRepresentation7.CubeAxesFlyMode = 'Closest Triad' DataRepresentation7.SelectScaleArray = '' DataRepresentation7.CubeAxesYTitle = 'Y-Axis' DataRepresentation7.ColorAttributeType = 'POINT_DATA' DataRepresentation7.SpecularPower = 100.0 DataRepresentation7.Texture = [] DataRepresentation7.SelectionCellLabelShadow = 0 DataRepresentation7.AmbientColor = [1.0, 1.0, 1.0] DataRepresentation7.MapScalars = 1 DataRepresentation7.PointSize = 2.0 DataRepresentation7.Source.TipLength = 0.35 DataRepresentation7.SelectionCellLabelFormat = '' DataRepresentation7.Scaling = 0 DataRepresentation7.StaticMode = 0 DataRepresentation7.SelectionCellLabelColor = [0.0, 1.0, 0.0] DataRepresentation7.Source.TipRadius = 0.1 DataRepresentation7.EdgeColor = [0.0, 0.0, 0.5000076295109483] DataRepresentation7.CubeAxesXAxisTickVisibility = 1 DataRepresentation7.SelectionCellLabelVisibility = 0 DataRepresentation7.NonlinearSubdivisionLevel = 1 DataRepresentation7.CubeAxesXAxisRange = [0.0, 1.0] DataRepresentation7.Representation = 'Surface' DataRepresentation7.CubeAxesYAxisRange = [0.0, 1.0] DataRepresentation7.CustomBounds = [0.0, 1.0, 0.0, 1.0, 0.0, 1.0] DataRepresentation7.Orientation = [0.0, 0.0, 0.0] DataRepresentation7.CubeAxesEnableCustomAxisRange = 0 DataRepresentation7.CubeAxesXTitle = 'X-Axis' DataRepresentation7.CubeAxesInertia = 1 DataRepresentation7.BackfaceOpacity = 1.0 DataRepresentation7.SelectionCellFieldDataArrayName = 'vtkOriginalCellIds' DataRepresentation7.SelectionColor = [1.0, 0.0, 1.0] DataRepresentation7.Ambient = 0.0 DataRepresentation7.SelectionPointLabelFontSize = 18 DataRepresentation7.ScaleFactor = 0.73055 DataRepresentation7.BackfaceAmbientColor = [1.0, 1.0, 1.0] DataRepresentation7.Source.ShaftRadius = 0.03 DataRepresentation7.SelectMaskArray = '' DataRepresentation7.SelectionLineWidth = 2.0 DataRepresentation7.CubeAxesZAxisMinorTickVisibility = 1 DataRepresentation7.CubeAxesXAxisVisibility = 1 DataRepresentation7.Interpolation = 'Gouraud' DataRepresentation7.SelectionCellLabelFontFamily = 'Arial' DataRepresentation7.SelectionCellLabelItalic = 0 DataRepresentation7.CubeAxesYAxisMinorTickVisibility = 1 DataRepresentation7.CubeAxesZGridLines = 0 DataRepresentation7.SelectionPointLabelFormat = '' DataRepresentation7.SelectionPointLabelOpacity = 1.0 DataRepresentation7.BackfaceDiffuseColor = [1.0, 1.0, 1.0] DataRepresentation7.Pickable = 1 DataRepresentation7.CustomBoundsActive = [0, 0, 0] DataRepresentation7.SelectionRepresentation = 'Wireframe' DataRepresentation7.SelectionPointLabelBold = 0 DataRepresentation7.ColorArrayName = 'radius' DataRepresentation7.SelectionPointLabelItalic = 0 DataRepresentation7.AllowSpecularHighlightingWithScalarColoring = 0 DataRepresentation7.SpecularColor = [1.0, 1.0, 1.0] DataRepresentation7.LookupTable = a1_radius_PVLookupTable DataRepresentation7.SelectionPointSize = 5.0 DataRepresentation7.SelectionCellLabelBold = 0 DataRepresentation7.Orient = 0 SetActiveSource(Glyph3) DataRepresentation8 = Show() DataRepresentation8.CubeAxesZAxisVisibility = 1 DataRepresentation8.SelectionPointLabelColor = [0.5, 0.5, 0.5] DataRepresentation8.SelectionPointFieldDataArrayName = 'radius' DataRepresentation8.SuppressLOD = 0 DataRepresentation8.CubeAxesXGridLines = 0 DataRepresentation8.CubeAxesYAxisTickVisibility = 1 DataRepresentation8.CubeAxesColor = [1.0, 1.0, 1.0] DataRepresentation8.Position = [0.0, 0.0, 0.0] DataRepresentation8.BackfaceRepresentation = 'Follow Frontface' DataRepresentation8.SelectionOpacity = 1.0 DataRepresentation8.SelectionPointLabelShadow = 0 DataRepresentation8.CubeAxesYGridLines = 0 DataRepresentation8.CubeAxesZAxisRange = [0.0, 1.0] DataRepresentation8.OrientationMode = 'Direction' DataRepresentation8.Source.TipResolution = 6 DataRepresentation8.ScaleMode = 'No Data Scaling Off' DataRepresentation8.Diffuse = 1.0 DataRepresentation8.SelectionUseOutline = 0 DataRepresentation8.CubeAxesZTitle = 'Z-Axis' DataRepresentation8.Specular = 0.1 DataRepresentation8.SelectionVisibility = 1 DataRepresentation8.InterpolateScalarsBeforeMapping = 1 DataRepresentation8.CubeAxesZAxisTickVisibility = 1 DataRepresentation8.Origin = [0.0, 0.0, 0.0] DataRepresentation8.CubeAxesVisibility = 0 DataRepresentation8.Scale = [1.0, 1.0, 1.0] DataRepresentation8.SelectionCellLabelJustification = 'Left' DataRepresentation8.DiffuseColor = [1.0, 1.0, 1.0] DataRepresentation8.SelectionCellLabelOpacity = 1.0 DataRepresentation8.Source = "Arrow" DataRepresentation8.Source.Invert = 0 DataRepresentation8.Masking = 0 DataRepresentation8.Opacity = 1.0 DataRepresentation8.LineWidth = 1.0 DataRepresentation8.MeshVisibility = 0 DataRepresentation8.Visibility = 1 DataRepresentation8.SelectionCellLabelFontSize = 18 DataRepresentation8.CubeAxesCornerOffset = 0.0 DataRepresentation8.SelectionPointLabelJustification = 'Left' DataRepresentation8.SelectionPointLabelVisibility = 0 DataRepresentation8.SelectOrientationVectors = '' DataRepresentation8.CubeAxesTickLocation = 'Inside' DataRepresentation8.CubeAxesXAxisMinorTickVisibility = 1 DataRepresentation8.CubeAxesYAxisVisibility = 1 DataRepresentation8.SelectionPointLabelFontFamily = 'Arial' DataRepresentation8.Source.ShaftResolution = 6 DataRepresentation8.CubeAxesFlyMode = 'Closest Triad' DataRepresentation8.SelectScaleArray = '' DataRepresentation8.CubeAxesYTitle = 'Y-Axis' DataRepresentation8.ColorAttributeType = 'POINT_DATA' DataRepresentation8.SpecularPower = 100.0 DataRepresentation8.Texture = [] DataRepresentation8.SelectionCellLabelShadow = 0 DataRepresentation8.AmbientColor = [1.0, 1.0, 1.0] DataRepresentation8.MapScalars = 1 DataRepresentation8.PointSize = 2.0 DataRepresentation8.Source.TipLength = 0.35 DataRepresentation8.SelectionCellLabelFormat = '' DataRepresentation8.Scaling = 0 DataRepresentation8.StaticMode = 0 DataRepresentation8.SelectionCellLabelColor = [0.0, 1.0, 0.0] DataRepresentation8.Source.TipRadius = 0.1 DataRepresentation8.EdgeColor = [0.0, 0.0, 0.5000076295109483] DataRepresentation8.CubeAxesXAxisTickVisibility = 1 DataRepresentation8.SelectionCellLabelVisibility = 0 DataRepresentation8.NonlinearSubdivisionLevel = 1 DataRepresentation8.CubeAxesXAxisRange = [0.0, 1.0] DataRepresentation8.Representation = 'Surface' DataRepresentation8.CubeAxesYAxisRange = [0.0, 1.0] DataRepresentation8.CustomBounds = [0.0, 1.0, 0.0, 1.0, 0.0, 1.0] DataRepresentation8.Orientation = [0.0, 0.0, 0.0] DataRepresentation8.CubeAxesEnableCustomAxisRange = 0 DataRepresentation8.CubeAxesXTitle = 'X-Axis' DataRepresentation8.CubeAxesInertia = 1 DataRepresentation8.BackfaceOpacity = 1.0 DataRepresentation8.SelectionCellFieldDataArrayName = 'vtkOriginalCellIds' DataRepresentation8.SelectionColor = [1.0, 0.0, 1.0] DataRepresentation8.Ambient = 0.0 DataRepresentation8.SelectionPointLabelFontSize = 18 DataRepresentation8.ScaleFactor = 0.8328240185976029 DataRepresentation8.BackfaceAmbientColor = [1.0, 1.0, 1.0] DataRepresentation8.Source.ShaftRadius = 0.03 DataRepresentation8.SelectMaskArray = '' DataRepresentation8.SelectionLineWidth = 2.0 DataRepresentation8.CubeAxesZAxisMinorTickVisibility = 1 DataRepresentation8.CubeAxesXAxisVisibility = 1 DataRepresentation8.Interpolation = 'Gouraud' DataRepresentation8.SelectionCellLabelFontFamily = 'Arial' DataRepresentation8.SelectionCellLabelItalic = 0 DataRepresentation8.CubeAxesYAxisMinorTickVisibility = 1 DataRepresentation8.CubeAxesZGridLines = 0 DataRepresentation8.SelectionPointLabelFormat = '' DataRepresentation8.SelectionPointLabelOpacity = 1.0 DataRepresentation8.BackfaceDiffuseColor = [1.0, 1.0, 1.0] DataRepresentation8.Pickable = 1 DataRepresentation8.CustomBoundsActive = [0, 0, 0] DataRepresentation8.SelectionRepresentation = 'Wireframe' DataRepresentation8.SelectionPointLabelBold = 0 DataRepresentation8.ColorArrayName = 'radiusOrig' DataRepresentation8.SelectionPointLabelItalic = 0 DataRepresentation8.AllowSpecularHighlightingWithScalarColoring = 0 DataRepresentation8.SpecularColor = [1.0, 1.0, 1.0] DataRepresentation8.LookupTable = a1_radiusOrig_PVLookupTable DataRepresentation8.SelectionPointSize = 5.0 DataRepresentation8.SelectionCellLabelBold = 0 DataRepresentation8.Orient = 0 Render() trunk-2017.01a/examples/test/performance/000077500000000000000000000000001304022710500202605ustar00rootroot00000000000000trunk-2017.01a/examples/test/performance/checkPerf.py000066400000000000000000000115551304022710500225330ustar00rootroot00000000000000# -*- coding: utf-8 from yade import pack,export,geom,timing,bodiesHandling import time,numpy radRAD=[ 23.658, #5000 elements 40.455, #25000 elements 50.97, #50000 elements 64.218, #100000 elements 80.91, #200000 elements #109.811, #500000 elements ] iterN=[ 12000, #5000 elements 2500, #25000 elements 1400, #50000 elements 800, #100000 elements 200, #200000 elements #10, #500000 elements ] coefCor=[ 110, 28, 18, 9, 2, #0.1, ] iterVel=[] testTime=[] particlesNumber=[] data=[] numberTests = 3 initIter = 1 # number of initial iterations excluded from performance check (e.g. Collider is initialised in first step therefore exclude first step from performance check) tStartAll=time.time() for z in range(numberTests): for i in range(len(radRAD)): rR = radRAD[i] nbIter=iterN[i] O.reset() tc=0.001 en=.003 es=.003 frictionAngle=radians(35) density=2300 defMat=O.materials.append(ViscElMat(density=density,frictionAngle=frictionAngle,tc=tc,en=en,et=es)) O.dt=.1*tc # time step rad=0.5 # particle radius tolerance = 0.0001 SpheresID=[] SpheresID+=O.bodies.append(pack.regularHexa(pack.inSphere((Vector3(0.0,0.0,0.0)),rad),radius=rad/rR,gap=rad/rR*0.5,material=defMat)) geometryParameters = bodiesHandling.spheresPackDimensions(SpheresID) print len(SpheresID) floorId=[] floorId+=O.bodies.append(geom.facetBox(geometryParameters['center'],geometryParameters['extends']/2.0*1.05,material=defMat)) #Floor #Calculate the mass of spheres sphMass = getSpheresVolume()*density # Create engines O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0,gravity=[0,0,-9.81]), ] print "number of bodies %d"%len(O.bodies) # Initialize the collider else it is not possible to compare the results with different nbIter O.run(initIter,1) O.timingEnabled=True timing.reset() tStart=time.time() # run nbIter iterations O.run(nbIter) O.wait() tEnd=time.time() print print 'Elapsed ', tEnd-tStart, ' sec' print 'Performance ', nbIter/(tEnd-tStart), ' iter/sec' print 'Extrapolation on 1e5 iters ', (tEnd-tStart)/nbIter*1e5/3600., ' hours' print "=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*=*" timing.stats() iterVel += [nbIter/(tEnd-tStart)] testTime += [tEnd-tStart] particlesNumber += [len(O.bodies)] tEndAll=time.time() commonTime = tEndAll-tStartAll print "Common time ", commonTime, "s" print print print "___________________________________________________" print print "SUMMARY" print scoreIterVel=0.0 for i in range(len(radRAD)): iterAv=0.0 iterVelNumpy=numpy.empty(numberTests) for z in range(numberTests): iterVelNumpy[z]=iterVel[z*len(radRAD)+i] avgVel = numpy.average(iterVelNumpy) dispVel = numpy.std(iterVelNumpy)/numpy.average(iterVelNumpy)*100.0 if (dispVel>10.): print "Calculation velocity is unstable, try to close all programs and start performance tests again" print particlesNumber[i]," spheres, calculation velocity=",avgVel, "iter/sec +/-",dispVel,"%" data+=[[particlesNumber[i],avgVel,avgVel*dispVel/100.]] scoreIterVel+=avgVel/coefCor[i]*1000.0 print scoreIterVel = int(scoreIterVel) ## write output file for graph import subprocess cmd = "cat /proc/cpuinfo | grep \'model name\' | uniq" #processor = subprocess.check_output(cmd, shell=True).lstrip('model name\t:').strip() # needs python >=2.7.0 process = subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True) processor = process.communicate()[0].lstrip('model name\t:').strip() cmd = "cat /proc/cpuinfo | grep processor | wc -l" #cores = subprocess.check_output("cat /proc/cpuinfo | grep processor | wc -l", shell=True).strip() # needs python >=2.7.0 process = subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True) cores = process.communicate()[0].strip() header='# '+ processor + ' ('+cores+' cores)' numThreads=os.environ['OMP_NUM_THREADS'] if (len(os.environ['OMP_NUM_THREADS'])==2) else ('0'+os.environ['OMP_NUM_THREADS']) filename=version+"_j"+numThreads+".dat" #numpy.savetxt(filename,numpy.array(data),fmt=['%i','%g','%g'], header=header) # needs numpy >=1.7.0 fid = open( filename, 'w' ) fid.write(header+"\n") for l in data: fid.write("%d %f %f\n"%(l[0],l[1],l[2])) fid.close() print "Summary saved to "+filename print print "SCORE: " + str(scoreIterVel) print "Number of threads: ", os.environ['OMP_NUM_THREADS'] print "___________________________________________________" print print "CPU info:" cmd = "lscpu" #cpuinfo=subprocess.check_output(cmd, shell=True) # needs python >=2.7.0 process = subprocess.Popen(cmd, stdout=subprocess.PIPE, shell=True) cpuinfo = process.communicate()[0].lstrip('model name\t:').strip() print cpuinfo sys.exit(0) trunk-2017.01a/examples/test/performance/performance.db000066400000000000000000000100001304022710500230570ustar00rootroot00000000000000** This file contains an SQLite 2.1 database **(upW Wtablecpuscpus3CREATE TABLE cpus (id INTEGER PRIMARY KEY, CPUname MEDIUMTEXT) $&tableperformanceperformance4CREATE TABLE performance (id INTEGER PRIMARY KEY, j INTEGER, cpu INTEGER, rev INTEGER, score INTEGER, date )|L33Intel(R) Core(TM) i7 CPU 920 @ 2.67GHzAMD Phenom(tm) II X6 1090TH0 1127835262X 2127836800 3127837647 4127838042 1227834317 2227835222  3227835488 2227835222trunk-2017.01a/examples/test/peri3dController_example1.py000066400000000000000000000053001304022710500233550ustar00rootroot00000000000000# peri3dController_example1.py # script, that explains funcionality and input parameters of Peri3dController from yade import pack, plot # create some material O.materials.append(CpmMat(neverDamage=True,young=25e9,frictionAngle=.7,poisson=.2,sigmaT=3e6,epsCrackOnset=1e-4,relDuctility=30)) # create periodic assembly of particles initSize=1.2 sp=pack.randomPeriPack(radius=.05,initSize=Vector3(initSize,initSize,initSize),memoizeDb='/tmp/packDb.sqlite') sp.toSimulation() # plotting #plot.live=False plot.plots={'progress':('sx','sy','sz','syz','szx','sxy',),'progress_':('ex','ey','ez','eyz','ezx','exy',)} def plotAddData(): plot.addData( progress=p3d.progress,progress_=p3d.progress, sx=p3d.stress[0],sy=p3d.stress[1],sz=p3d.stress[2], syz=p3d.stress[3],szx=p3d.stress[4],sxy=p3d.stress[5], ex=p3d.strain[0],ey=p3d.strain[1],ez=p3d.strain[2], eyz=p3d.strain[3],ezx=p3d.strain[4],exy=p3d.strain[5], ) # in how many time steps should be the goal state reached nSteps=4000 O.dt=PWaveTimeStep()/2 EnlargeFactor=1.5 EnlargeFactor=1.0 O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=EnlargeFactor,label='bo1s')]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=EnlargeFactor,label='ig2ss')], [Ip2_CpmMat_CpmMat_CpmPhys()],[Law2_ScGeom_CpmPhys_Cpm()]), NewtonIntegrator(), Peri3dController( goal=(20e-4,-6e-4,0, -2e6,3e-4,2e6), # Vector6 of prescribed final values (xx,yy,zz, yz,zx,xy) stressMask=0b101100, # prescribed ex,ey,sz,syz,ezx,sxy; e..strain; s..stress nSteps=nSteps, # how many time steps the simulation will last # after reaching nSteps do doneHook action doneHook='print "Simulation with Peri3dController finished."; O.pause()', # the prescribed path (step,value of stress/strain) can be defined in absolute values xxPath=[(465,5e-4),(934,-5e-4),(1134,10e-4)], # or in relative values yyPath=[(2,4),(7,-2),(11,0),(14,4)], # if the goal value is 0, the absolute stress/strain values are always considered (step values remain relative) zzPath=[(5,-1e7),(10,0)], # if ##Path is not explicitly defined, it is considered as linear function between (0,0) and (nSteps,goal) # as in yzPath and xyPath # the relative values are really relative (zxPath gives the same - except of the sign from goal value - result as yyPath) zxPath=[(4,2),(14,-1),(22,0),(28,2)], xyPath=[(1,1),(2,-1),(3,1),(4,-1),(5,1)], # variables used in the first step label='p3d' ), PyRunner(command='plotAddData()',iterPeriod=1), ] O.step() bo1s.aabbEnlargeFactor=ig2ss.interactionDetectionFactor=1. O.run(); #O.wait() plot.plot(subPlots=False) trunk-2017.01a/examples/test/peri3dController_shear.py000066400000000000000000000041561304022710500227530ustar00rootroot00000000000000# peri3dController_shear.py # script, that explains funcionality and input parameters of Peri3dController on the example of # shear test with rotated periodic cell (that enables strain localization). # The simulation is run on rotated cell to enable localization and strain softening # (you can also try simulation with different angles of rotation to pbtain different results. from yade import pack,plot,qt # define material O.materials.append(CpmMat(young=25e9,poisson=.2,sigmaT=3e6,epsCrackOnset=1e-4,relDuctility=1e-6)) # create periodic assembly of particles initSize=1.2 sp=pack.randomPeriPack(radius=.05,initSize=Vector3(initSize,initSize,initSize),memoizeDb='/tmp/packDb.sqlite') angle=0. #angle=pi/4 rot=Matrix3(cos(angle),-sin(angle),0, sin(angle),cos(angle),0, 0,0,1) sp.toSimulation(rot=rot) # plotting plot.live=False plot.plots={'iter':('sx','sy','sz','syz','szx','sxy',),'iter_':('ex','ey','ez','eyz','ezx','exy',),'exy':('sxy',)} def plotAddData(): plot.addData( iter=O.iter,iter_=O.iter, sx=p3d.stress[0],sy=p3d.stress[1],sz=p3d.stress[2], syz=p3d.stress[3],szx=p3d.stress[4],sxy=p3d.stress[5], ex=p3d.strain[0],ey=p3d.strain[1],ez=p3d.strain[2], eyz=p3d.strain[3],ezx=p3d.strain[4],exy=p3d.strain[5], ) O.dt=PWaveTimeStep()/2 # define the first part of simulation, hydrostatic compression enlargeFactor=1.5 O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=enlargeFactor,label='bo1s')]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=enlargeFactor,label='ig2ss')], [Ip2_CpmMat_CpmMat_CpmPhys()],[Law2_ScGeom_CpmPhys_Cpm()]), NewtonIntegrator(), Peri3dController( goal=(0,0,0, 0,0,5e-3), # Vector6 of prescribed final values stressMask=0b011111, nSteps=2000, doneHook='print "Simulation with Peri3dController finished."; O.pause()', maxStrain=.5, label='p3d' ), PyRunner(command='plotAddData()',iterPeriod=1), ] O.step() bo1s.aabbEnlargeFactor=ig2ss.interactionDetectionFactor=1.0 renderer=qt.Renderer() renderer.intrPhys,renderer.shape=True,False Gl1_CpmPhys.dmgLabel=False qt.View() O.run() #plot.plot() trunk-2017.01a/examples/test/peri3dController_triaxialCompression.py000066400000000000000000000057321304022710500257110ustar00rootroot00000000000000# peri3dController_triaxialCompression.py # script, that explains funcionality and input parameters of Peri3dController on the example of # triaxial compression. # Firstly, a hydrostatic preassure is applied, then a strain along z axis is increasing # while x- and y- stress is constant # The simulation is run on rotated cell to enable localization and strain softening # (you can also try simulation with command sp.toSimulation() with no rotation, # in this case there is almost no difference, but in script peri3dController_shear, # the cell rotation has significant effect) from yade import pack,plot,qt # define material O.materials.append(FrictMat()) # create periodic assembly of particles initSize=1.2 sp=pack.randomPeriPack(radius=.05,initSize=Vector3(initSize,initSize,initSize),memoizeDb='/tmp/packDb.sqlite') angle=0 rot=Matrix3(cos(angle),0,-sin(angle), 0,1,0, sin(angle),0,cos(angle)) sp.toSimulation(rot=rot) # plotting plot.live=False plot.plots={'iter':('sx','sy','sz','syz','szx','sxy',),'iter_':('ex','ey','ez','eyz','ezx','exy',),'ez':('sz',)} def plotAddData(): plot.addData( iter=O.iter,iter_=O.iter, sx=p3d.stress[0],sy=p3d.stress[1],sz=p3d.stress[2], syz=p3d.stress[3],szx=p3d.stress[4],sxy=p3d.stress[5], ex=p3d.strain[0],ey=p3d.strain[1],ez=p3d.strain[2], eyz=p3d.strain[3],ezx=p3d.strain[4],exy=p3d.strain[5], ) O.dt=PWaveTimeStep()/2 # define the first part of simulation, hydrostatic compression O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_ScGeom_FrictPhys_CundallStrack()]), NewtonIntegrator(), Peri3dController( goal=(-1e7,-1e7,-1e7, 0,0,0), # Vector6 of prescribed final values stressMask=0b000111, nSteps=500, doneHook='print "Hydrostatic load reached."; O.pause()', youngEstimation=.5e9, # needed, when only nonzero prescribed values are stress maxStrain=.5, label='p3d' ), PyRunner(command='plotAddData()',iterPeriod=1), ] O.run(); O.wait() # second part, z-axis straining and constant transversal stress O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_ScGeom_FrictPhys_CundallStrack()]), NewtonIntegrator(), Peri3dController( goal=(-1e7,-1e7,-4e-1, 0,0,0), # Vector6 of prescribed final values stressMask=0b000011, nSteps=1000, xxPath=[(0,1),(1,1)], # the first (time) zero defines the initial value of stress considered nonzero yyPath=[(0,1),(1,1)], doneHook='print "Simulation with Peri3dController finished."; O.pause()', maxStrain=.5, label='p3d', strain=p3d.strain, # continue from value reached in previous part stressIdeal=Vector6(-1e7,-1e7,0, 0,0,0), # continue from value reached in previous part ), PyRunner(command='plotAddData()',iterPeriod=1), ] O.run();O.wait() plot.plot(subPlots=False) trunk-2017.01a/examples/test/periodic-geom-compare.py000066400000000000000000000027541304022710500225100ustar00rootroot00000000000000# coding: utf-8 # 2009 © Václav Šmilauer "Test and demonstrate use of PeriTriaxController." from yade import pack O.periodic=True O.cell.setBox(.1,.1,.1) O.cell.trsf=Matrix3().Identity; sp=pack.SpherePack() radius=5e-3 num=sp.makeCloud(Vector3().Zero,O.cell.refSize,radius,.6,-1,periodic=True) # min,max,radius,rRelFuzz,spheresInCell,periodic sp.toSimulation() # specify which family of geometry functors to use readParamsFromTable(noTableOk=True,geom='sc') from yade.params.table import geom if geom=='sc': loop=InteractionLoop([Ig2_Sphere_Sphere_ScGeom()],[Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_ScGeom_FrictPhys_CundallStrack()]) elif geom=='l3': loop=InteractionLoop([Ig2_Sphere_Sphere_L3Geom()],[Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_L3Geom_FrictPhys_ElPerfPl()]) elif geom=='l3a': loop=InteractionLoop([Ig2_Sphere_Sphere_L3Geom(approxMask=63)],[Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_L3Geom_FrictPhys_ElPerfPl()]) else: raise ValueError('geom must be one of sc, d3d, l3, l3a (not %s)'%geom) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()],verletDist=.05*radius), loop, NewtonIntegrator(damping=.6), ] O.dt=0.5*PWaveTimeStep() try: from yade import qt qt.View() except: pass O.cell.velGrad=Matrix3(-.1,.03,0, 0,-.1,0, 0,0,-.1) O.saveTmp() #O.run(10000,True); #rrr=qt.Renderer(); rrr.intrAllWire,rrr.intrGeom=True,False if runningInBatch(): O.timingEnabled=True O.run(300000,True) O.timingEnabled from yade import timing timing.stats() trunk-2017.01a/examples/test/periodic-shear.py000066400000000000000000000021151304022710500212260ustar00rootroot00000000000000O.periodic=True O.cell.setBox(.55,.55,.55) O.bodies.append(facet([[.4,.0001,.3],[.2,.0001,.3],[.3,.2,.2]])) O.bodies.append(sphere([.3,.1,.4],.05,fixed=False)) O.bodies.append(sphere([.200001,.2000001,.4],.05,fixed=True)) O.bodies.append(sphere([.3,0,0],.1,fixed=True)) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()],label='isc'), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), NewtonIntegrator(gravity=(0,0,-10)), #PyRunner(command='doCellFlip()',realPeriod=5) ] def doCellFlip(): flip=1 if O.cell.trsf[1,2]<0 else -1; flipCell(Matrix3(0,0,0, 0,0,flip, 0,0,0)) #g=0. #while False: # O.cellShear=Vector3(.2*sin(g),.2*cos(pi*g),.2*sin(2*g)+.2*cos(3*g)) # time.sleep(0.001) # g+=1e-3 O.cell.trsf=Matrix3(1,0,0, 0,1,.5, 0,0,1) O.dt=2e-2*PWaveTimeStep() O.step() O.saveTmp() rrr=yade.qt.Renderer() rrr.intrAllWire,rrr.bound=True,True #isc.watch1,isc.watch2=0,-1 #import yade.qt,time #v=yade.qt.View() #v.axes=True #v.grid=(True,True,True) trunk-2017.01a/examples/test/periodic-simple-shear.py000066400000000000000000000031271304022710500225210ustar00rootroot00000000000000# coding: utf-8 # 2009 © Václav Šmilauer # 2011 ©Bruno Chareyre "Test and demonstrate use of PeriTriaxController." from yade import pack,qt O.periodic=True O.cell.setBox(.1,.1,.1) #O.cell.Hsize=Matrix3(0.1,0,0, 0,0.1,0, 0,0,0.1) sp=pack.SpherePack() radius=5e-3 num=sp.makeCloud((0,0,0),(.1,.1,.1),radius,.2,500,periodic=True) # min,max,radius,rRelFuzz,spheresInCell,periodic O.bodies.append([sphere(s[0],s[1]) for s in sp]) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()],verletDist=.05*radius), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), PeriTriaxController(dynCell=True,mass=0.2,maxUnbalanced=0.01,relStressTol=0.02,goal=[-1e4,-1e4,0],stressMask=3,globUpdate=5,maxStrainRate=[1.,1.,1.],doneHook='triaxDone()',label='triax'), NewtonIntegrator(damping=.2), ] phase=0 def triaxDone(): global phase if phase==0: print 'Here we are: stress',triax.stress,'strain',triax.strain,'stiffness',triax.stiff print 'Now shearing.' O.cell.velGrad=Matrix3(0,6,0, 0,0,0, 0,0,0) triax.stressMask=7 triax.goal=[-1e4,-1e4,-1e4] phase+=1 O.pause() #elif phase==1: #print 'Here we are: stress',triax.stress,'strain',triax.strain,'stiffness',triax.stiff #phase+=1 ##print 'Done, pausing now.' ##O.pause() O.dt=PWaveTimeStep() #O.run(7000); #qt.View() ##r=qt.Renderer() ##r.bgColor=1,1,1 #O.wait() #O.saveTmp() #O.cell.velGrad=Matrix3(0,0,0, -6,0,0, 0,0,0) #O.run(5000); #O.wait() #O.cell.velGrad=Matrix3(0,6,0, 0,0,0, 0,0,0) #O.run(5000); trunk-2017.01a/examples/test/periodic-simple.py000066400000000000000000000020131304022710500214120ustar00rootroot00000000000000"""Simple test of periodic collider. A few spheres falling down in gravity field and one moving accross. Includes a clump. """ from yade import timing O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()],label='collider'), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), TranslationEngine(translationAxis=(1,0,0),velocity=10,ids=[0]), NewtonIntegrator(damping=.4,gravity=[0,0,-10]) ] O.bodies.append(sphere([-4,0,11],2,fixed=True)) O.bodies.append(sphere([0,-2,5.5],2)) O.bodies.append(sphere([0,2,5.5],2)) O.bodies.appendClumped([sphere([0,4,8],.8),sphere([0,5,7],.6)]) # sets up the periodic cell O.periodic=True O.cell.setBox(10,10,10) # normally handled in by the simulation... but we want to have the rendering right before start #O.cell.postProcessAttributes() O.dt=.1*PWaveTimeStep() O.saveTmp() from yade import qt qt.Controller() qt.View() #O.timingEnabled=True; timing.reset(); O.run(200000,True); timing.stats() trunk-2017.01a/examples/test/periodic-triax-settingHsize.py000066400000000000000000000030671304022710500237400ustar00rootroot00000000000000# coding: utf-8 # 2011 ©Bruno Chareyre "Demonstrate the compression of a periodic cell with non-trivial initial geometry." from yade import pack,qt O.periodic=True O.cell.hSize=Matrix3(1.0, -0.15, -0.10, -0.2 ,1.5, 0.3, 0.3, -0.3, 1.0) sp=pack.SpherePack() num=sp.makeCloud(hSize=O.cell.hSize, rMean=-0.01,rRelFuzz=.2, num=500,periodic=True, porosity=0.52,distributeMass=False) O.bodies.append([sphere(s[0],s[1]) for s in sp]) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), #We compress the packing isotropicaly first PeriTriaxController( dynCell=True,mass=0.2,maxUnbalanced=0.01, relStressTol=0.01,goal=(-1e4,-1e4,-1e4), stressMask=7,globUpdate=5, maxStrainRate=(1.,1.,1.), doneHook='triaxDone()', label='triax'), NewtonIntegrator(damping=.2), #PyRunner(iterPeriod=500,command='print "strain: ",triax.strain," stress: ",triax.stress') ] O.dt=0.5*PWaveTimeStep() qt.View() phase=0 def triaxDone(): global phase if phase==0: print 'Here we are: stress',triax.stress,'strain',triax.strain #Here we reset the transformation, the compressed packing corresponds to null strain O.cell.trsf=Matrix3.Identity print 'Now εxx will go from 0 to .4 while σzz and σyy will be kept the same.' triax.stressMask=6 triax.goal=(-0.4,-1e4,-1e4) phase+=1 elif phase==1: print 'Here we are: stress',triax.stress,'strain',triax.strain print 'Done, pausing now.' O.pause() trunk-2017.01a/examples/test/periodic-triax.py000066400000000000000000000030021304022710500212470ustar00rootroot00000000000000# coding: utf-8 # 2009 © Václav Šmilauer "Test and demonstrate use of PeriTriaxController." from yade import pack,qt O.periodic=True O.cell.hSize=Matrix3(0.1, 0, 0, 0 ,0.1, 0, 0, 0, 0.1) sp=pack.SpherePack() radius=5e-3 num=sp.makeCloud(Vector3().Zero,O.cell.refSize,radius,.2,500,periodic=True) # min,max,radius,rRelFuzz,spheresInCell,periodic O.bodies.append([sphere(s[0],s[1]) for s in sp]) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()],verletDist=.05*radius), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), #PeriTriaxController(maxUnbalanced=0.01,relStressTol=0.02,goal=[-1e4,-1e4,0],stressMask=3,globUpdate=5,maxStrainRate=[1.,1.,1.],doneHook='triaxDone()',label='triax'), #using cell inertia PeriTriaxController(dynCell=True,mass=0.2,maxUnbalanced=0.01,relStressTol=0.02,goal=(-1e4,-1e4,0),stressMask=3,globUpdate=5,maxStrainRate=(1.,1.,1.),doneHook='triaxDone()',label='triax'), NewtonIntegrator(damping=.2), ] O.dt=PWaveTimeStep() O.run(); qt.View() phase=0 def triaxDone(): global phase if phase==0: print 'Here we are: stress',triax.stress,'strain',triax.strain,'stiffness',triax.stiff print 'Now εz will go from 0 to .2 while σx and σy will be kept the same.' triax.goal=(-1e4,-1e4,-0.2) phase+=1 elif phase==1: print 'Here we are: stress',triax.stress,'strain',triax.strain,'stiffness',triax.stiff print 'Done, pausing now.' O.pause() trunk-2017.01a/examples/test/psd.py000066400000000000000000000034021304022710500171160ustar00rootroot00000000000000# encoding: utf-8 # # demonstrate how to generate sphere packing based on arbitrary PSD (particle size distribution) # show the difference between size-based and mass-based (≡ volume-based in our case) PSD # import matplotlib; matplotlib.rc('axes',grid=True) from yade import pack import pylab # PSD given as points of piecewise-linear function psdSizes,psdCumm=[.02,0.04,0.045,.05,.06,.08,.12],[0.,0.1,0.3,0.3,.3,.7,1.] pylab.plot(psdSizes,psdCumm,label='precribed mass PSD') sp0=pack.SpherePack(); sp0.makeCloud((0,0,0),(1,1,1),psdSizes=psdSizes,psdCumm=psdCumm,distributeMass=True) sp1=pack.SpherePack(); sp1.makeCloud((0,0,0),(1,1,1),psdSizes=psdSizes,psdCumm=psdCumm,distributeMass=True,num=5000) sp2=pack.SpherePack(); sp2.makeCloud((0,0,0),(1,1,1),psdSizes=psdSizes,psdCumm=psdCumm,distributeMass=True,num=20000) pylab.semilogx(*sp0.psd(bins=30,mass=True),label='Mass PSD of (free) %d random spheres'%len(sp0)) pylab.semilogx(*sp1.psd(bins=30,mass=True),label='Mass PSD of (imposed) %d random spheres'%len(sp1)) pylab.semilogx(*sp2.psd(bins=30,mass=True),label='Mass PSD of (imposed) %d random spheres (scaled down)'%len(sp2)) pylab.legend() # uniform distribution of size (sp3) and of mass (sp4) sp3=pack.SpherePack(); sp3.makeCloud((0,0,0),(1,1,1),rMean=0.03,rRelFuzz=2/3.,distributeMass=False); sp4=pack.SpherePack(); sp4.makeCloud((0,0,0),(1,1,1),rMean=0.03,rRelFuzz=2/3.,distributeMass=True); pylab.figure() pylab.plot(*(sp3.psd(mass=True)+('g',)+sp4.psd(mass=True)+('r',))) pylab.legend(['Mass PSD of size-uniform distribution','Mass PSD of mass-uniform distribution']) pylab.figure() pylab.plot(*(sp3.psd(mass=False)+('g',)+sp4.psd(mass=False)+('r',))) pylab.legend(['Size PSD of size-uniform distribution','Size PSD of mass-uniform distribution']) pylab.show() pylab.show()trunk-2017.01a/examples/test/qt4-attributes.py000066400000000000000000000152131304022710500212270ustar00rootroot00000000000000from PyQt4.QtCore import * from PyQt4.QtGui import * from PyQt4 import QtGui #from PyQt4 import Qwt5 import re import logging logging.basicConfig(level=logging.INFO) #from logging import debug,info,warning,error class AttrEditor(): def __init__(self,ser,attr): self.ser,self.attr=ser,attr self.hot=False self.widget=None def refresh(self): pass def update(self): pass def isHot(self,hot=True): "Called when the widget gets focus; mark it hot, change colors etc." if hot==self.hot: return self.hot=hot p=QPalette(); if hot: p.setColor(QPalette.WindowText,Qt.red); self.setPalette(p) self.repaint() print self.attr,('hot' if hot else 'cold') def sizeHint(self): return QSize(180,12) class AttrEditor_Bool(AttrEditor,QCheckBox): def __init__(self,parent,ser,attr): AttrEditor.__init__(self,ser,attr) QCheckBox.__init__(self,parent) self.clicked.connect(self.update) def refresh(self): self.setChecked(getattr(self.ser,self.attr)) def update(self): setattr(self.ser,self.attr,self.isChecked()) class AttrEditor_Int(AttrEditor,QSpinBox): def __init__(self,parent,ser,attr): AttrEditor.__init__(self,ser,attr) QSpinBox.__init__(self,parent) self.setRange(int(-1e10),int(1e10)); self.setSingleStep(1); self.valueChanged.connect(self.update) def refresh(self): self.setValue(getattr(self.ser,self.attr)) def update(self): setattr(self.ser,self.attr,self.value()); self.isHot(False) class AttrEditor_Str(AttrEditor,QLineEdit): def __init__(self,parent,ser,attr): AttrEditor.__init__(self,ser,attr) QLineEdit.__init__(self,parent) self.textEdited.connect(self.isHot) self.editingFinished.connect(self.update) def refresh(self): self.setText(getattr(self.ser,self.attr)) def update(self): setattr(self.ser,self.attr,str(self.text())); self.isHot(False) class AttrEditor_Float(AttrEditor,QLineEdit): def __init__(self,parent,ser,attr): AttrEditor.__init__(self,ser,attr) QLineEdit.__init__(self,parent) self.textEdited.connect(self.isHot) self.editingFinished.connect(self.update) def refresh(self): self.setText(str(getattr(self.ser,self.attr))) def update(self): try: setattr(self.ser,self.attr,float(self.text())) except ValueError: self.refresh() self.isHot(False) class AttrEditor_Vector3(AttrEditor,QFrame): def __init__(self,parent,ser,attr): AttrEditor.__init__(self,ser,attr) QFrame.__init__(self,parent) self.setContentsMargins(0,0,0,0) self.box=QHBoxLayout(self); self.box.setSpacing(0); self.box.setMargin(0) self.widgets=[] for i in range(3): w=QLineEdit(''); self.box.addWidget(w); self.widgets.append(w) w.textEdited.connect(self.isHot) w.editingFinished.connect(self.update) def refresh(self): val=getattr(self.ser,self.attr) for i in range(3): self.widgets[i].setText(str(val[i])) def update(self): try: val=getattr(self.ser,self.attr) for i in range(3): if self.widgets[i].isModified(): val[i]=float(self.widgets[i].text()) print 'setting',val setattr(self.ser,self.attr,val) except ValueError: self.refresh() self.isHot(False) class AttrEditor_ListStr(AttrEditor,QPlainTextEdit): def __init__(self,parent,ser,attr): AttrEditor.__init__(self,ser,attr) QPlainTextEdit.__init__(self,parent) self.setLineWrapMode(QPlainTextEdit.NoWrap) self.setFixedHeight(80) self.textChanged.connect(self.update) def refresh(self): lst=getattr(self.ser,self.attr) self.setPlainText('\n'.join(lst)) def update(self): if self.hasFocus(): self.isHot() t=self.toPlainText() setattr(self.ser,self.attr,str(t).strip().split('\n')) if not self.hasFocus(): self.isHot(False) class SerializableEditor(QWidget): "Class displaying and modifying serializable attributes of a yade object." import collections import logging # each attribute has one entry associated with itself class EntryData: def __init__(self,name,T): self.name,self.T=name,T self.lineNo,self.widget=None,None def __init__(self,ser,parent=None): "Construct window, *ser* is the object we want to show." QtGui.QWidget.__init__(self,parent) self.ser=ser self.entries=[] logging.debug('New Serializable of type %s'%ser.__class__.__name__) self.setWindowTitle(str(ser)) self.mkWidgets() self.refreshTimer=QTimer() self.refreshTimer.timeout.connect(self.refreshEvent) self.refreshTimer.start(500) def getListTypeFromDocstring(self,attr): "Guess type of array by scanning docstring for :yattrtype: and parsing its argument; ugly, but works." doc=getattr(self.ser.__class__,attr).__doc__ if doc==None: error("Attribute %s has no docstring."%attr) return None m=re.search(r':yattrtype:`([^`]*)`',doc) if not m: error("Attribute %s does not contain :yattrtype:`....` (docstring is '%s'"%(attr,doc)) return None cxxT=m.group(1) logging.debug('Got type "%s" from :yattrtype:'%cxxT) def vecTest(T,cxxT): regexp=r'^\s*(std\s*::)?\s*vector\s*<\s*(std\s*::)?\s*('+T+r')\s*>\s*$' m=re.match(regexp,cxxT) return m vecMap={ 'int':int,'long':int,'Body::id_t':long,'size_t':long, 'Real':float,'float':float,'double':float, 'Vector3r':Vector3,'Matrix3r':Matrix3, 'string':str } for T,ret in vecMap.items(): if vecTest(T,cxxT): logging.debug("Got type %s from cxx type %s"%(ret.__name__,cxxT)) return (ret,) error("Unable to guess python type from cxx type '%s'"%cxxT) return None def mkAttrEntries(self): d=self.ser.dict() for attr,val in self.ser.dict().items(): if isinstance(val,list): if len(val)==0: t=self.getListTypeFromDocstring(attr) else: t=(val[0].__class__,) # 1-tuple is list of the contained type else: t=val.__class__ #logging.debug('Attr %s is of type %s'%(attr,((t[0].__name__,) if isinstance(t,tuple) else t.__name__))) self.entries.append(self.EntryData(name=attr,T=t)) def mkWidget(self,entry): typeMap={bool:AttrEditor_Bool,str:AttrEditor_Str,int:AttrEditor_Int,float:AttrEditor_Float,Vector3:AttrEditor_Vector3,(str,):AttrEditor_ListStr} Klass=typeMap.get(entry.T,None) if not Klass: return None widget=Klass(self,self.ser,entry.name) widget.setFocusPolicy(Qt.StrongFocus) return widget def mkWidgets(self): self.mkAttrEntries() grid=QtGui.QGridLayout() for lineNo,entry in enumerate(self.entries): grid.addWidget(QtGui.QLabel(entry.name),lineNo,0) entry.widget=self.mkWidget(entry) if entry.widget: grid.addWidget(entry.widget,lineNo,1) else: grid.addWidget(QtGui.QLabel('unhandled type'),lineNo,1) self.setLayout(grid) self.refreshEvent() def refreshEvent(self): for e in self.entries: if e.widget and not e.widget.hot: e.widget.refresh() vr=VTKRecorder() s1=SerializableEditor(vr) s1.show() s2=SerializableEditor(OpenGLRenderer()) s2.show() #import time #def aa(): # print vr.dict(); time.sleep(1) trunk-2017.01a/examples/test/qt4-pyqglviewer.py000066400000000000000000000006771304022710500214270ustar00rootroot00000000000000# install pyqglviewer from https://launchpad.net/~nakednous/+ppa-packages from PyQGLViewer import * class Viewer(QGLViewer): def __init__(self): QGLViewer.__init__(self) self.renderer=OpenGLRenderer() def init(self): self.setAxisIsDrawn(True) self.setGridIsDrawn(True) def draw(self): self.renderer.render() O.bodies.append([sphere((0,0,-.4),.3),sphere((0,0,.4),.3)]) viewer=Viewer() viewer.setWindowTitle('Yade') viewer.show() trunk-2017.01a/examples/test/remove-body.py000066400000000000000000000023641304022710500205660ustar00rootroot00000000000000# -*- coding: utf-8 -*- # © Václav Šmilauer # # Test case for sphere-facet interaction. #O.bodyContainer="BodyVector" O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()],nBins=5,sweepLength=5e-3), #SpatialQuickSortCollider(), InteractionLoop( [Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), NewtonIntegrator(damping=0.01,gravity=[0,0,-10]), ] O.bodies.append([ facet([[-1,-1,0],[1,-1,0],[0,1,0]],fixed=True,color=[1,0,0]), facet([[1,-1,0],[0,1,0,],[1,.5,.5]],fixed=True) ]) #Gl1_Facet(normals=True) import random,sys def addRandomSphere(): return O.bodies.append(sphere([random.gauss(0,1),random.gauss(0,1),random.uniform(1,2)],random.uniform(.02,.05))) O.bodies[len(O.bodies)-1].state.vel=[random.gauss(0,.1),random.gauss(0,.1),random.gauss(0,.1)] for i in range(0,100): addRandomSphere() O.dt=1e-4 #O.run() O.saveTmp('init') from yade import qt qt.Controller() qt.View() if 1: for i in range(0,1000): O.run(50,True); if random.choice([True,False]): idOld=random.randint(2,len(O.bodies)-1) O.bodies.erase(idOld) print "-%d"%idOld, else: idNew=addRandomSphere() print "+%d"%idNew, sys.stdout.flush() trunk-2017.01a/examples/test/shear.py000066400000000000000000000022211304022710500174300ustar00rootroot00000000000000# # script for testing ScGeom shear computation # Runs the same 2-sphere setup for useShear=False and for useShear=True # O.bodies.append([ sphere([0,0,0],.5000001,fixed=True,color=(1,0,0)), sphere([0,0,1],.5000001,fixed=False,color=(0,0,1)) ]) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), IGeomDispatcher([Ig2_Sphere_Sphere_ScGeom()]), IPhysDispatcher([Ip2_FrictMat_FrictMat_FrictPhys()]), RotationEngine(rotationAxis=[1,1,0],angularVelocity=.001,ids=[1]), ElasticContactLaw(label='elasticLaw'), PyRunner(iterPeriod=10000,command='interInfo()'), NewtonIntegrator() ] O.dt=1e-8 O.saveTmp('init') def interInfo(): i=O.interactions[0,1] if 1: print O.time,i.phys.shearForce else: r1,r2=O.bodies[0].shape.radius,O.bodies[1].shape.radius theta=[e['angularVelocity'] for e in O.engines if e.name=='RotationEngine'][0] f=.5*(r1+r2)*theta*O.time*i.phys['ks'] print O.time,i.phys.shearForce,f,i.phys.shearForce[0]/f print '=========== no shear ============' O.run(100000,True) nIter=O.iter print '============= shear =============' O.loadTmp('init') #elasticLaw['useShear']=True O.run(nIter,True) quit() trunk-2017.01a/examples/test/sphere-sphere-ViscElBasic-peri.py000066400000000000000000000017231304022710500241700ustar00rootroot00000000000000# -*- coding: utf-8 # Testing sphere-sphere interaction in periodic case. # Pass, if the spheres moves along the X axis, interacting through the period. sphereRadius=0.1 tc=0.001# collision time en=1 # normal restitution coefficient es=1 # tangential restitution coefficient density=2700 frictionAngle=radians(35)# sphereMat=O.materials.append(ViscElMat(density=density,frictionAngle=frictionAngle,tc=tc,en=en,et=es)) # Spheres sphId=O.bodies.append([ sphere( (0.4,0.5,0.5), 0.1, material=sphereMat), sphere( (0.6,0.5,0.5), 0.1, material=sphereMat) ]) O.bodies[sphId[-1]].state.vel=(0.5,0,0) O.bodies[sphId[0]].state.vel=(-0.5,0,0) ## Engines O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0), ] O.periodic=True O.cell.setBox(1,1,1) O.dt=.01*tc O.saveTmp() trunk-2017.01a/examples/test/subdomain-balancer.py000066400000000000000000000017641304022710500220670ustar00rootroot00000000000000from yade import pack,timing readParamsFromTable(noTableOk=True,num=12000) import yade.params.table sp=pack.SpherePack() sp.makeCloud((0,0,0),(1,1,1),.03*((12000./yade.params.table.num)**(1/3.)),.5) sp.toSimulation() O.bodies.append(wall((0,0,0),axis=2)) O.bodies.append(wall((0,0,0),axis=1)) #O.bodies.append(wall((0,0,0),axis=0)) #O.bodies.append(wall((0,2,0),axis=1)) #O.bodies.append(wall((2,0,0),axis=0)) O.engines=([SubdomainBalancer(axesOrder='xyz',colorize=True)] if 'SubdomainBalancer' in dir() else [])+[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Wall_Aabb()],verletDist=.05*.05), InteractionLoop([Ig2_Sphere_Sphere_ScGeom(),Ig2_Wall_Sphere_ScGeom()],[Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_ScGeom_FrictPhys_CundallStrack()]), NewtonIntegrator(gravity=(0,0,-10)), #PyRunner(iterPeriod=5000,command='O.pause(); timing.stats();') ] O.dt=PWaveTimeStep() O.timingEnabled=True #O.step(); #O.run(10000,True) timing.stats() from yade import qt qt.View() #O.step() #O.run(5000,True) trunk-2017.01a/examples/test/test-sphere-facet-corner.py000066400000000000000000000016541304022710500231500ustar00rootroot00000000000000# -*- encoding=utf-8 -*- ## PhysicalParameters Young = 7e6 Poisson = 0.2 Density=2700 # Append a material mat=O.materials.append(FrictMat(young=Young,poisson=Poisson,density=Density,frictionAngle=26)) O.bodies.append([ sphere([0,0,0.6],0.25,material=mat), facet([[-0.707,-0.707,0.1],[0,1.414,0],[1.414,0,0]],dynamic=False,color=[1,0,0],material=mat), facet([[0,1.414,0],[1.414,0,0],[0.707,0.707,-2.0]],dynamic=False,color=[1,0,0],material=mat)]) ## Engines O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), NewtonIntegrator(damping=.3,gravity=(0,0,-10)) ] ## Timestep O.dt=5e-6 O.saveTmp() try: from yade import qt renderer=qt.Renderer() renderer.wire=True renderer.intrPhys=True qt.Controller() except ImportError: pass trunk-2017.01a/examples/test/test-sphere-facet.py000066400000000000000000000043601304022710500216570ustar00rootroot00000000000000# -*- coding: utf-8 -*- # © Václav Šmilauer # # Test case for sphere-facet interaction preserving the original contact orientation. # Z-gravity is being increased every 4000 iterations, the sphere dives more into the facet and stabilizes, # etc. This process continues even if the sphere center passes on the other side of the facet and, # (if distant transient interactions are allowed in the collider) if the sphere passes in its entirety to # the other side of the facet. The interaction, however, still pushes in the same sense. # # After the gravity reaches some value, it is reset and the sphere should be pushed from the facet towards # its original position. When the contact on the original side is lost, the interaction should be deleted. # # # The only tunable sign places the sphere either on the top ot at the bottom of the facet # and sets gravity accordingly. It can be +1 or -1 # sign=-1 # ## PhysicalParameters Young = 7e6 Poisson = 0.2 Density=2700 # Append a material mat=O.materials.append(FrictMat(young=Young,poisson=Poisson,density=Density,frictionAngle=26)) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), NewtonIntegrator(damping=.3,gravity=(0,0,-10),label='integrator'), PyRunner(iterPeriod=4000,command='setGravity()'), ] O.bodies.append([ facet([[-1,-1,0],[1,-1,0],[0,1,0]],fixed=True,color=[1,0,0],material=mat), sphere([0,0,sign*.49999],radius=.5,wire=True,material=mat), ]) O.timingEnabled=True O.saveTmp() O.dt=1e-4 print '** virgin dispatch matrix:' O.engines[2].lawDispatcher.dispMatrix() print '** class indices' O.run(1000,True) print '** used dispatch matrix' O.engines[2].lawDispatcher.dispMatrix() def setGravity(): gz=integrator.gravity[2] integrator.gravity=[0,0,1.05*gz] if abs(gz)>=2500: print "Gravity reset & slow down" O.dt=1e-6; integrator.gravity=[0,0,0] if abs(gz)>0: print gz try: from yade import qt renderer=qt.Renderer() renderer.intrGeom=True qt.Controller() except ImportError: pass from yade import timing O.run(100000,True) timing.stats() timing.reset() O.loadTmp() O.run(100000,True) timing.stats() trunk-2017.01a/examples/test/test_Ip2_FrictMat_CpmMat_FrictPhys.py000066400000000000000000000023601304022710500250500ustar00rootroot00000000000000from yade import * from yade import plot,qt import sys young=25e9 poisson=.2 sigmaT=3e6 frictionAngle=atan(1) density=4800 ## 4800 # twice the density, since porosity is about .5 (.62) epsCrackOnset=1e-4 relDuctility=300 intRadius=1.5 concMat = O.materials.append(CpmMat(young=young,poisson=poisson,density=4800,sigmaT=3e6,relDuctility=30,epsCrackOnset=1e-4,neverDamage=False)) frictMat = O.materials.append(FrictMat(young=young,poisson=poisson,density=4800)) b1 = sphere((0,0,0),1,material=concMat) b1.state.vel = Vector3(1,0,0) b2 = sphere((0,5,0),1,material=concMat) b2.state.vel = Vector3(2,-2,0) b3 = sphere((0,-4,0),1,material=frictMat) b3.state.vel = Vector3(1,3,0) b4 = facet(((2,-5,-5),(2,-5,10),(2,10,-5)),material=frictMat) O.bodies.append((b1,b2,b3,b4)) O.dt = 5e-6 O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [ Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom() ], [ Ip2_CpmMat_CpmMat_CpmPhys(), Ip2_FrictMat_CpmMat_FrictPhys(), Ip2_FrictMat_FrictMat_FrictPhys(), ], [ Law2_ScGeom_CpmPhys_Cpm(), Law2_ScGeom_FrictPhys_CundallStrack() ] ), NewtonIntegrator(label='newton'), ] O.step() try: from yade import qt qt.View() except: O.run() trunk-2017.01a/examples/test/triax-basic.py000066400000000000000000000044241304022710500205430ustar00rootroot00000000000000# encoding: utf-8 # the script demonstrates a simple case of triaxial simulation using TriaxialCompressionEngine. More elaborated examples can be found in the triax-tutorial folder from yade import pack sp=pack.SpherePack() ## corners of the initial packing mn,mx=Vector3(0,0,0),Vector3(10,10,10) ## box between mn and mx, avg radius ± ½(20%), 2k spheres sp.makeCloud(minCorner=mn,maxCorner=mx,rRelFuzz=.2,num=2000) ## create material #0, which will be used as default O.materials.append(FrictMat(young=15e6,poisson=.4,frictionAngle=radians(30),density=2600,label='spheres')) O.materials.append(FrictMat(young=15e6,poisson=.4,frictionAngle=0,density=0,label='frictionless')) ## copy spheres from the packing into the scene ## use default material, don't care about that for now O.bodies.append([sphere(center,rad,material='spheres') for center,rad in sp]) ## create walls around the packing walls=aabbWalls(thickness=1e-10,material='frictionless') wallIds=O.bodies.append(walls) triax=TriaxialCompressionEngine( wall_bottom_id=wallIds[2], wall_top_id=wallIds[3], wall_left_id=wallIds[0], wall_right_id=wallIds[1], wall_back_id=wallIds[4], wall_front_id=wallIds[5], internalCompaction=False, ## define the rest of triax params here ## see in pkg/dem/PreProcessor/TriaxialTest.cpp:524 etc ## which are assigned in the c++ preprocessor actually sigmaIsoCompaction=-50e3, sigmaLateralConfinement=-50e3, max_vel=10, strainRate=0.01, label="triax" ) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8), triax, # you can add TriaxialStateRecorder and such here… NewtonIntegrator(damping=.4) ] from yade import plot O.engines=O.engines[0:5]+[PyRunner(iterPeriod=20,command='history()',label='recorder')]+O.engines[5:7] def history(): plot.addData(e11=-triax.strain[0], e22=-triax.strain[1], e33=-triax.strain[2], s11=-triax.stress(0)[0], s22=-triax.stress(2)[1], s33=-triax.stress(4)[2], i=O.iter) plot.plots={'i':('e11','e22','e33',None,'s11','s22','s33')} O.saveTmp() plot.plot()trunk-2017.01a/examples/test/triax-cohesive.py000066400000000000000000000067361304022710500212770ustar00rootroot00000000000000# encoding: utf-8 # 2012 ©Bruno Chareyre # This variant of triax-basic.py shows the usage of cohesive contact laws and moments at contacts from yade import pack sp=pack.SpherePack() ## corners of the initial packing mn,mx=Vector3(0,0,0),Vector3(10,10,10) ## box between mn and mx, avg radius ± ½(20%), 2k spheres sp.makeCloud(minCorner=mn,maxCorner=mx,rRelFuzz=.2,num=600) ## create material #0, which will be used as default O.materials.append(CohFrictMat(young=15e6,poisson=0.4,density=2600,frictionAngle=radians(30),normalCohesion=1e6,shearCohesion=1e6,momentRotationLaw=True,etaRoll=0.1,label='spheres')) O.materials.append(FrictMat(young=15e6,poisson=.4,frictionAngle=0,density=0,label='frictionlessWalls')) ## copy spheres from the packing into the scene O.bodies.append([sphere(center,rad,material='spheres') for center,rad in sp]) ## create walls around the packing walls=aabbWalls(material='frictionlessWalls') wallIds=O.bodies.append(walls) triax=TriaxialCompressionEngine( wall_bottom_id=wallIds[2], wall_top_id=wallIds[3], wall_left_id=wallIds[0], wall_right_id=wallIds[1], wall_back_id=wallIds[4], wall_front_id=wallIds[5], internalCompaction=False, sigmaIsoCompaction=-50e3, sigmaLateralConfinement=-50e3, max_vel=10, strainRate=0.03, label="triax" ) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( #box-sphere interactions will be the simple normal-shear law, we use ScGeom for them [Ig2_Sphere_Sphere_ScGeom6D(),Ig2_Box_Sphere_ScGeom()], #Boxes will be frictional (FrictMat), so the sphere-box physics is FrictMat vs. CohFrictMat, the Ip type will be found via the inheritance tree (CohFrictMat is a FrictMat) and will result in FrictPhys interaction physics #and will result in a FrictPhys [Ip2_FrictMat_FrictMat_FrictPhys(),Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(label="cohesiveIp")], #Finally, two different contact laws for sphere-box and sphere-sphere [Law2_ScGeom_FrictPhys_CundallStrack(),Law2_ScGeom6D_CohFrictPhys_CohesionMoment( useIncrementalForm=True, #useIncrementalForm is turned on as we want plasticity on the contact moments always_use_moment_law=False, #if we want "rolling" friction even if the contact is not cohesive (or cohesion is broken), we will have to turn this true somewhere label='cohesiveLaw')] ), GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.5), triax, NewtonIntegrator(damping=.4) ] from yade import plot O.engines=O.engines[0:5]+[PyRunner(iterPeriod=20,command='history()',label='recorder')]+O.engines[5:7] def history(): plot.addData(e11=-O.engines[4].strain[0], e22=-O.engines[4].strain[1], e33=-O.engines[4].strain[2], s11=-O.engines[4].stress(0)[0], s22=-O.engines[4].stress(2)[1], s33=-O.engines[4].stress(4)[2], i=O.iter) plot.plots={'i':(('e11',"bo"),('e22',"ro"),('e33',"go"),None,('s11',"bx"),('s22',"rx"),('s33',"gx"))} plot.plot() print "computing, be patient..." #First run without moment and without cohesion O.run(7000,True) #This will reload the autosaved compacted sample O.reload() #second run with rolling friction O.engines[2].lawDispatcher.functors[1].always_use_moment_law = True O.run(6000,True) O.reload() #third run with rolling friction + cohesion O.engines[2].lawDispatcher.functors[1].always_use_moment_law = True #We assign cohesion to all contacts at the next iteration O.engines[2].physDispatcher.functors[1].setCohesionNow = True O.run(6000,True) trunk-2017.01a/examples/test/unstructuredGrid.py000066400000000000000000000011501304022710500217030ustar00rootroot00000000000000################################################################################ # # TODO # ################################################################################ O.engines = [ InsertionSortCollider([Bo1_Tetra_Aabb(),Bo1_Facet_Aabb()]), ] ug = utils.UnstructuredGrid() v = { 1: (0,0,0), 3: (1,0,0), 5: (0,1,0), 6: (0,0,1), 2: (-1,0,0), } ct = { 1: (1,3,5), 4: (1,3,6), 8: (1,5,2,6), } ug.setup(v,ct,wire=False) ug.toSimulation() O.step() from yade import qt qt.View() def setNewCoords(): ug.setPositionsOfNodes({ 1: (-1,-1,-1), 3: (2,0,.5), 5: (0,3,0), 6: (0,0,.5), 2: (-1,0,1) }) trunk-2017.01a/examples/test/unv-read/000077500000000000000000000000001304022710500175005ustar00rootroot00000000000000trunk-2017.01a/examples/test/unv-read/shell.unv000066400000000000000000000434151304022710500213500ustar00rootroot00000000000000 -1 2411 1 0 0 11 2.0000000000000000E+00 2.0000000000000000E+00 0.0000000000000000E+00 2 0 0 11 -2.0000000000000000E+00 2.0000000000000000E+00 0.0000000000000000E+00 3 0 0 11 -2.0000000000000000E+00 -2.0000000000000000E+00 0.0000000000000000E+00 4 0 0 11 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11 2 1 7 2 0 0 0 4 12 8 11 2 1 7 2 0 0 0 12 1 9 11 2 1 7 2 0 0 0 3 13 10 11 2 1 7 2 0 0 0 13 14 11 11 2 1 7 2 0 0 0 14 5 12 11 2 1 7 2 0 0 0 5 15 13 11 2 1 7 2 0 0 0 15 6 14 11 2 1 7 2 0 0 0 6 16 15 11 2 1 7 2 0 0 0 16 17 16 11 2 1 7 2 0 0 0 17 4 17 11 2 1 7 2 0 0 0 6 18 18 11 2 1 7 2 0 0 0 18 7 19 11 2 1 7 2 0 0 0 7 19 20 11 2 1 7 2 0 0 0 19 20 21 11 2 1 7 2 0 0 0 20 1 22 11 2 1 7 2 0 0 0 8 21 23 11 2 1 7 2 0 0 0 21 22 24 11 2 1 7 2 0 0 0 22 2 25 11 2 1 7 2 0 0 0 7 23 26 11 2 1 7 2 0 0 0 23 8 27 11 2 1 7 2 0 0 0 8 24 28 11 2 1 7 2 0 0 0 24 5 29 41 2 1 7 3 10 26 3 30 41 2 1 7 3 4 25 12 31 41 2 1 7 3 25 4 11 32 41 2 1 7 3 11 27 25 33 41 2 1 7 3 26 27 11 34 41 2 1 7 3 11 3 26 35 41 2 1 7 3 25 28 12 36 41 2 1 7 3 12 28 1 37 41 2 1 7 3 2 29 10 38 41 2 1 7 3 29 26 10 39 41 2 1 7 3 27 26 29 40 41 2 1 7 3 28 29 9 41 41 2 1 7 3 29 2 9 42 41 2 1 7 3 1 28 9 43 41 2 1 7 3 25 27 28 44 41 2 1 7 3 29 28 27 45 41 2 1 7 3 31 15 5 46 41 2 1 7 3 31 5 14 47 41 2 1 7 3 30 11 17 48 41 2 1 7 3 13 3 30 49 41 2 1 7 3 30 3 11 50 41 2 1 7 3 33 30 17 51 41 2 1 7 3 31 14 32 52 41 2 1 7 3 32 14 13 53 41 2 1 7 3 32 13 30 54 41 2 1 7 3 31 34 15 55 41 2 1 7 3 17 11 4 56 41 2 1 7 3 32 34 31 57 41 2 1 7 3 34 6 15 58 41 2 1 7 3 16 6 34 59 41 2 1 7 3 33 16 32 60 41 2 1 7 3 17 16 33 61 41 2 1 7 3 30 33 32 62 41 2 1 7 3 34 32 16 63 41 2 1 7 3 36 18 6 64 41 2 1 7 3 36 6 16 65 41 2 1 7 3 35 12 20 66 41 2 1 7 3 35 17 4 67 41 2 1 7 3 35 4 12 68 41 2 1 7 3 17 35 37 69 41 2 1 7 3 38 35 20 70 41 2 1 7 3 36 16 37 71 41 2 1 7 3 37 16 17 72 41 2 1 7 3 36 39 18 73 41 2 1 7 3 20 12 1 74 41 2 1 7 3 37 39 36 75 41 2 1 7 3 39 7 18 76 41 2 1 7 3 19 7 39 77 41 2 1 7 3 38 19 37 78 41 2 1 7 3 20 19 38 79 41 2 1 7 3 35 38 37 80 41 2 1 7 3 39 37 19 81 41 2 1 7 3 19 41 7 82 41 2 1 7 3 21 42 43 83 41 2 1 7 3 42 44 43 84 41 2 1 7 3 42 21 8 85 41 2 1 7 3 41 23 7 86 41 2 1 7 3 21 43 22 87 41 2 1 7 3 2 22 40 88 41 2 1 7 3 40 9 2 89 41 2 1 7 3 23 41 8 90 41 2 1 7 3 20 1 44 91 41 2 1 7 3 42 8 41 92 41 2 1 7 3 40 44 9 93 41 2 1 7 3 20 44 42 94 41 2 1 7 3 42 41 19 95 41 2 1 7 3 40 43 44 96 41 2 1 7 3 1 9 44 97 41 2 1 7 3 40 22 43 98 41 2 1 7 3 42 19 20 99 41 2 1 7 3 46 24 8 100 41 2 1 7 3 46 5 24 101 41 2 1 7 3 45 48 10 102 41 2 1 7 3 45 10 3 103 41 2 1 7 3 47 14 46 104 41 2 1 7 3 47 45 13 105 41 2 1 7 3 45 3 13 106 41 2 1 7 3 48 2 10 107 41 2 1 7 3 5 46 14 108 41 2 1 7 3 47 13 14 109 41 2 1 7 3 48 22 2 110 41 2 1 7 3 22 47 21 111 41 2 1 7 3 46 8 21 112 41 2 1 7 3 46 21 47 113 41 2 1 7 3 48 47 22 114 41 2 1 7 3 45 47 48 115 41 2 1 7 3 15 6 50 116 41 2 1 7 3 50 6 18 117 41 2 1 7 3 49 15 50 118 41 2 1 7 3 8 24 51 119 41 2 1 7 3 49 24 5 120 41 2 1 7 3 49 5 15 121 41 2 1 7 3 50 18 7 122 41 2 1 7 3 49 51 24 123 41 2 1 7 3 51 23 8 124 41 2 1 7 3 50 7 51 125 41 2 1 7 3 51 7 23 126 41 2 1 7 3 51 49 50 -1 trunk-2017.01a/examples/test/unv-read/unvRead.py000066400000000000000000000002501304022710500214530ustar00rootroot00000000000000from yade import ymport facets = ymport.unv('shell.unv',shift=(100,200,300),scale=1000) O.bodies.append([f for f in facets]) try: import qt qt.View() except: pass trunk-2017.01a/examples/test/unv-read/unvReadVTKExport.py000066400000000000000000000002551304022710500232470ustar00rootroot00000000000000from yade import ymport,export f,n,e = ymport.unv('shell.unv',returnElementMap=True) O.bodies.append(f) vtk = export.VTKExporter('test') vtk.exportFacetsAsMesh(elements=e) trunk-2017.01a/examples/test/vtk-exporter/000077500000000000000000000000001304022710500204315ustar00rootroot00000000000000trunk-2017.01a/examples/test/vtk-exporter/vtkExporter.py000066400000000000000000000017571304022710500233520ustar00rootroot00000000000000from yade import export,polyhedra_utils mat = PolyhedraMat() O.bodies.append(( polyhedra_utils.polyhedra(mat,(1,2,3),0), polyhedra_utils.polyhedralBall(2,20,mat,(-2,-2,4)), )) O.bodies[-1].state.pos = (-2,-2,-2) O.bodies[-1].state.ori = Quaternion((1,1,2),1) O.bodies[-2].state.pos = (-2,-2,3) O.bodies[-2].state.ori = Quaternion((1,2,0),1) O.step() O.bodies.append(( sphere((0,0,0),1), sphere((0,3,0),1), sphere((0,2,4),2), sphere((0,5,2),1.5), facet([Vector3(0,-3,-1),Vector3(0,-2,5),Vector3(5,4,0)]), facet([Vector3(0,-3,-1),Vector3(0,-2,5),Vector3(-5,4,0)]), )) for i,j in ((0,1),(0,2),(0,3),(1,2),(1,3),(2,3)): createInteraction(i+2,j+2) vtkExporter = export.VTKExporter('/tmp/vtkExporterTesting') vtkExporter.exportSpheres(what=[('dist','b.state.pos.norm()')]) vtkExporter.exportFacets(what=[('pos','b.state.pos')]) vtkExporter.exportInteractions(what=[('kn','i.phys.kn')]) vtkExporter.exportContactPoints(what=[('nn','i.geom.normal')]) vtkExporter.exportPolyhedra(what=[('n','b.id')]) trunk-2017.01a/examples/test/vtkPeriodicCell.py000066400000000000000000000015411304022710500214150ustar00rootroot00000000000000###################################################################### # Simple script to test VTK export of periodic cell ###################################################################### # enable periodic cell O.periodic=True # insert some bodies sp = randomPeriPack(radius=1,initSize=(10,20,30),memoizeDb='/tmp/vtkPeriodicCell.sqlite') sp.toSimulation() # transform the cell a bit O.cell.hSize *= Matrix3(1,.1,.1, .1,1,0, .1,0,1) # skew the cell in xy and xz plane O.cell.hSize *= Matrix3(1,0,0, 0,.8,.6, 0,-.6,.8) # rotate it along x axis O.step() # test of export.VTKExporter from yade import export vtk1 = export.VTKExporter('/tmp/vtkPeriodicCell-VTKExporter') vtk1.exportSpheres() vtk1.exportPeriodicCell() # test of VTKReorder vtk2 = VTKRecorder(fileName='/tmp/vtkPeriodicCell-VTKRecorder-',recorders=['spheres','pericell']) vtk2() # do the export trunk-2017.01a/examples/test/wall.py000066400000000000000000000017071304022710500172750ustar00rootroot00000000000000""" Show basic wall functionality (infinite axis-aligned planes). """ O.materials.append(FrictMat(young=30e9,density=1000,poisson=.2,frictionAngle=.5)) O.bodies.append([ wall(1,axis=2,sense=-1), wall(-5,axis=0,sense=1), wall(1,axis=1), wall((1,0,0),0), sphere([0,0,0],.5), sphere([-4,-4,-3],.5) ]) Gl1_Wall(div=10) from yade import qt qt.Controller() qt.View() O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb(),Bo1_Wall_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom(),Ig2_Wall_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()], ), NewtonIntegrator(damping=0.01,gravity=[1e2,1e2,1e2]), ] O.dt=PWaveTimeStep() O.save('/tmp/a.xml') O.saveTmp() O.run() #O.bodies.append([ # facet([[-1,-1,0],[1,-1,0],[0,1,0]],dynamic=False,color=[1,0,0],young=1e3), # facet([[1,-1,0],[0,1,0,],[1,.5,.5]],dynamic=False,young=1e3) #]) #import random trunk-2017.01a/examples/test/wm3-wrap.py000066400000000000000000000011441304022710500200060ustar00rootroot00000000000000# constructors, constants as static objects x,y,z,one=Vector3.UnitX,Vector3.UnitY,Vector3.UnitZ,Vector3(1,1,1) x2=Vector3(x) # conversions to sequence types list(x2) tuple(x2) # operations and operators x+y+z==one x.dot(y)==0 x.cross(y)==z # methods one.norm() # quaternions # construction (implicit conversion of 3-tuple or list of length 3 to Vector3) q1=Quaternion((0,0,1),pi/2) q2=Quaternion(Vector3(0,0,1),pi/2) q1==q2 # rotating vector q1*x==y # almost, due to rounding # rotation composition q1*q1*x # inverse rotation q1.conjugate() # convert to axis-angle representation axis,angle=q1.toAxisAngle() trunk-2017.01a/examples/tetra/000077500000000000000000000000001304022710500161175ustar00rootroot00000000000000trunk-2017.01a/examples/tetra/oneTetra.py000066400000000000000000000015261304022710500202560ustar00rootroot00000000000000################################################################################ # # Script to test tetra gl functions and prescribed motion # ################################################################################ v1 = (0,0,0) v2 = (1,0,0) v3 = (0,1,0) v4 = (0,0,1) t1 = tetra((v1,v2,v3,v4),color=(0,1,0)) O.bodies.append((t1)) def changeVelocity(): if O.iter == 50000: t1.state.vel = (-1,0,0) if O.iter == 100000: t1.state.vel = (0,1,-1) if O.iter == 150000: t1.state.vel = (0,0,0) t1.state.angMom = (0,0,10) if O.iter == 200000: O.pause() O.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Tetra_Aabb()]), InteractionLoop([],[],[]), NewtonIntegrator(), PyRunner(iterPeriod=1,command="changeVelocity()"), ] O.step() try: from yade import qt qt.View() except: pass O.dt = 1e-5 t1.state.vel = (1,0,0) O.run() trunk-2017.01a/examples/tetra/oneTetraPoly.py000066400000000000000000000015361304022710500211230ustar00rootroot00000000000000################################################################################ # # Script to test tetra gl functions and prescribed motion # ################################################################################ v1 = (0,0,0) v2 = (1,0,0) v3 = (0,1,0) v4 = (0,0,1) t1 = tetraPoly((v1,v2,v3,v4),color=(0,1,0)) O.bodies.append((t1)) def changeVelocity(): if O.iter == 50000: t1.state.vel = (-1,0,0) if O.iter == 100000: t1.state.vel = (0,1,-1) if O.iter == 150000: t1.state.vel = (0,0,0) t1.state.angMom = (0,0,10) if O.iter == 200000: O.pause() O.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Polyhedra_Aabb()]), InteractionLoop([],[],[]), NewtonIntegrator(), PyRunner(iterPeriod=1,command="changeVelocity()"), ] O.step() try: from yade import qt qt.View() except: pass O.dt = 1e-5 t1.state.vel = (1,0,0) O.run() trunk-2017.01a/examples/tetra/twoTetras.py000066400000000000000000000100771304022710500204720ustar00rootroot00000000000000################################################################################ # # Python script to test tetra-tetra contact detection for different possible # contact modes. Some tests are run twice to test the symmetry of the law. # # It runs several tests, making pause before each one. If run with GUI, you can # adjust the viewer # # During the test, momentum, angular momentum and kinetic energy is tracked in # plot.data. You can use plot.plot() to see the results (in sime modes the # energy is not conserved for instace). # ################################################################################ from yade import qt,plot O.materials.append(ElastMat(young=1e10)) O.dt = 4e-5 O.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Tetra_Aabb()]), InteractionLoop( [Ig2_Tetra_Tetra_TTetraSimpleGeom()], [Ip2_ElastMat_ElastMat_NormPhys()], [Law2_TTetraSimpleGeom_NormPhys_Simple()] ), NewtonIntegrator(damping=0), PyRunner(iterPeriod=500,command="addPlotData()"), PyRunner(iterPeriod=1,command="runExamples()"), ] def addPlotData(): p = utils.momentum() l = utils.angularMomentum() plot.addData( i = O.iter, e = utils.kineticEnergy(), px = p[0], py = p[1], pz = p[2], lx = l[0], ly = l[1], lz = l[2], ) def prepareExample(vertices1,vertices2,vel1=(0,0,0),vel2=(0,0,0),amom1=(0,0,0),amom2=(0,0,0),label=''): O.interactions.clear() O.bodies.clear() t1 = tetra(vertices1,color=(0,1,0),wire=False) t2 = tetra(vertices2,color=(0,1,1),wire=False) O.bodies.append((t1,t2)) t1.state.vel = vel1 t2.state.vel = vel2 t1.state.angMom = amom1 t2.state.angMom = amom2 if label: print label O.pause() O.step() def runExamples(): dt = 20000 if O.iter == 1: vertices1 = ((0,0,0),(2,0,0),(0,2,0),(0,0,2)) vertices2 = ((1,1,1),(3,1,1),(1,3,1),(1,1,3)) prepareExample(vertices1,vertices2,vel2=(-1,-1,-1),label='\ntesting vertex-triangle contact...\n') if O.iter == 1*dt: plot.data = {} vertices1 = ((1,1,1),(3,1,1),(1,3,1),(1,1,3)) vertices2 = ((0,0,0),(2,0,0),(0,2,0),(0,0,2)) prepareExample(vertices1,vertices2,vel1=(-1,-1,-1),label='\ntesting vertex-triangle contact 2...\n') elif O.iter == 2*dt: vertices1 = ((0,0,0),(0,0,1.1),(1,0,1),(0,1,.9)) vertices2 = ((0,.5,1.4),(-.5,.5,.6),(-1.6,0,1),(-1.6,1.1,1)) prepareExample(vertices1,vertices2,vel2=(1,0,0),amom2=(0,10,0),label='\ntesting edge-edge contact\n') elif O.iter == 3*dt: vertices1 = ((0,0,0),(0,0,1.1),(1,0,1),(0,1,.9)) vertices2 = ((-.5,.5,.6),(0,.5,1.4),(-1.6,1.1,1),(-1.6,0,1)) prepareExample(vertices1,vertices2,vel2=(1,0,0),amom2=(0,10,0),label='\ntesting edge-edge contact\n') elif O.iter == 4*dt: vertices1 = ((.1,-.4,-.3),(-.3,-.4,2),(3,-.2,2),(-.1,3,2)) vertices2 = ((.5,1.5,2.3),(1.5,.5,2.3),(2,2,3),(0,0,3)) prepareExample(vertices1,vertices2,vel2=(0,0,-1),amom2=(0,0,0),label='\ntesting edge-triangle contact\n') elif O.iter == 5*dt: vertices1 = ((.1,-.4,-.3),(-.3,-.4,2),(3,-.2,2),(-.1,3,2)) vertices2 = ((-.5,2.5,2.3),(2.5,-.5,2.3),(2,2,3),(0,0,3)) prepareExample(vertices1,vertices2,vel2=(0,0,-1),amom2=(0,0,0),label='\ntesting edge-triangle contact 2\n') elif O.iter == 6*dt: vertices1 = ((1,0,0),(0,1,0),(0,0,1),(1,1,1)) vertices2 = ((.5,.5,1.2),(0,.1,2),(2,0,2),(0,1,2)) prepareExample(vertices1,vertices2,vel2=(0,0,-1),label='\ntesting vertex-edge contact\n') elif O.iter == 7*dt: vertices1 = ((.5,.5,1.2),(0,.1,2),(2,0,2),(0,1,2)) vertices2 = ((1,0,0),(0,1,0),(0,0,1),(1,1,1)) prepareExample(vertices1,vertices2,vel1=(0,0,-1),label='\ntesting vertex-edge contact 2\n') elif O.iter == 8*dt: vertices1 = ((0,0,0),(1,0,0),(0,1,0),(0,0,1)) vertices2 = ((0,0,1.2),(.9,.8,2),(-.7,.61,2.3),(0,-.7,2.1)) prepareExample(vertices1,vertices2,vel2=(0,0,-1),label='\ntesting vertex-edge contact\n') elif O.iter == 9*dt: vertices1 = ((0,0,1.2),(.9,.8,2),(-.7,.61,2.3),(0,-.7,2.1)) vertices2 = ((0,0,0),(1,0,0),(0,1,0),(0,0,1)) prepareExample(vertices1,vertices2,vel1=(0,0,-1),label='\ntesting vertex-edge contact 2\n') elif O.iter == 10*dt: O.pause() viewer = qt.View() plot.plots = {'i':'e','i ':('px','py','pz'),'i ':('lx','ly','lz')} O.step() O.step() O.step() trunk-2017.01a/examples/tetra/twoTetrasPoly.py000066400000000000000000000103031304022710500213260ustar00rootroot00000000000000################################################################################ # # Python script to test tetra-tetra contact detection for different possible # contact modes. Some tests are run twice to test the symmetry of the law. # # It runs several tests, making pause before each one. If run with GUI, you can # adjust the viewer # # During the test, momentum, angular momentum and kinetic energy is tracked in # plot.data. You can use plot.plot() to see the results (in sime modes the # energy is not conserved for instace). # ################################################################################ from yade import qt,plot mat = PolyhedraMat() mat.density = 2600 #kg/m^3 mat.Ks = 2000000 mat.Kn = 1E9 #Pa mat.frictionAngle = 0.5 #rad O.materials.append(mat) O.dt = 4e-5 O.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Polyhedra_Aabb()]), InteractionLoop( [Ig2_Polyhedra_Polyhedra_PolyhedraGeom()], [Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()], [Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()] ), NewtonIntegrator(damping=0), PyRunner(iterPeriod=500,command="addPlotData()"), PyRunner(iterPeriod=1,command="runExamples()"), ] def addPlotData(): p = utils.momentum() l = utils.angularMomentum() plot.addData( i = O.iter, e = utils.kineticEnergy(), px = p[0], py = p[1], pz = p[2], lx = l[0], ly = l[1], lz = l[2], ) def prepareExample(vertices1,vertices2,vel1=(0,0,0),vel2=(0,0,0),amom1=(0,0,0),amom2=(0,0,0),label=''): O.interactions.clear() O.bodies.clear() t1 = tetraPoly(vertices1,color=(0,1,0),wire=False) t2 = tetraPoly(vertices2,color=(0,1,1),wire=False) O.bodies.append((t1,t2)) t1.state.vel = vel1 t2.state.vel = vel2 t1.state.angMom = amom1 t2.state.angMom = amom2 if label: print label O.pause() O.step() def runExamples(): dt = 20000 if O.iter == 1: vertices1 = ((0,0,0),(2,0,0),(0,2,0),(0,0,2)) vertices2 = ((1,1,1),(3,1,1),(1,3,1),(1,1,3)) prepareExample(vertices1,vertices2,vel2=(-1,-1,-1),label='\ntesting vertex-triangle contact...\n') if O.iter == 1*dt: plot.data = {} vertices1 = ((1,1,1),(3,1,1),(1,3,1),(1,1,3)) vertices2 = ((0,0,0),(2,0,0),(0,2,0),(0,0,2)) prepareExample(vertices1,vertices2,vel1=(-1,-1,-1),label='\ntesting vertex-triangle contact 2...\n') elif O.iter == 2*dt: vertices1 = ((0,0,0),(0,0,1.1),(1,0,1),(0,1,.9)) vertices2 = ((0,.5,1.4),(-.5,.5,.6),(-1.6,0,1),(-1.6,1.1,1)) prepareExample(vertices1,vertices2,vel2=(1,0,0),amom2=(0,10,0),label='\ntesting edge-edge contact\n') elif O.iter == 3*dt: vertices1 = ((0,0,0),(0,0,1.1),(1,0,1),(0,1,.9)) vertices2 = ((-.5,.5,.6),(0,.5,1.4),(-1.6,1.1,1),(-1.6,0,1)) prepareExample(vertices1,vertices2,vel2=(1,0,0),amom2=(0,10,0),label='\ntesting edge-edge contact\n') elif O.iter == 4*dt: vertices1 = ((.1,-.4,-.3),(-.3,-.4,2),(3,-.2,2),(-.1,3,2)) vertices2 = ((.5,1.5,2.3),(1.5,.5,2.3),(2,2,3),(0,0,3)) prepareExample(vertices1,vertices2,vel2=(0,0,-1),amom2=(0,0,0),label='\ntesting edge-triangle contact\n') elif O.iter == 5*dt: vertices1 = ((.1,-.4,-.3),(-.3,-.4,2),(3,-.2,2),(-.1,3,2)) vertices2 = ((-.5,2.5,2.3),(2.5,-.5,2.3),(2,2,3),(0,0,3)) prepareExample(vertices1,vertices2,vel2=(0,0,-1),amom2=(0,0,0),label='\ntesting edge-triangle contact 2\n') elif O.iter == 6*dt: vertices1 = ((1,0,0),(0,1,0),(0,0,1),(1,1,1)) vertices2 = ((.5,.5,1.2),(0,.1,2),(2,0,2),(0,1,2)) prepareExample(vertices1,vertices2,vel2=(0,0,-1),label='\ntesting vertex-edge contact\n') elif O.iter == 7*dt: vertices1 = ((.5,.5,1.2),(0,.1,2),(2,0,2),(0,1,2)) vertices2 = ((1,0,0),(0,1,0),(0,0,1),(1,1,1)) prepareExample(vertices1,vertices2,vel1=(0,0,-1),label='\ntesting vertex-edge contact 2\n') elif O.iter == 8*dt: vertices1 = ((0,0,0),(1,0,0),(0,1,0),(0,0,1)) vertices2 = ((0,0,1.2),(.9,.8,2),(-.7,.61,2.3),(0,-.7,2.1)) prepareExample(vertices1,vertices2,vel2=(0,0,-1),label='\ntesting vertex-edge contact\n') elif O.iter == 9*dt: vertices1 = ((0,0,1.2),(.9,.8,2),(-.7,.61,2.3),(0,-.7,2.1)) vertices2 = ((0,0,0),(1,0,0),(0,1,0),(0,0,1)) prepareExample(vertices1,vertices2,vel1=(0,0,-1),label='\ntesting vertex-edge contact 2\n') elif O.iter == 10*dt: O.pause() viewer = qt.View() plot.plots = {'i':'e','i ':('px','py','pz'),'i ':('lx','ly','lz')} O.step() O.step() O.step() trunk-2017.01a/examples/timeStepperUsage.py000066400000000000000000000134251304022710500206450ustar00rootroot00000000000000# coding: utf-8 # 2012 © Bruno Chareyre "Test and demonstrate the use of timestepper and density scaling." from yade import pack,qt,timing O.periodic=True O.cell.hSize=Matrix3(0.1, 0, 0, 0 ,0.1, 0, 0, 0, 0.1) n=1000 sp=pack.SpherePack() num=sp.makeCloud(Vector3().Zero,O.cell.refSize,rRelFuzz=.5,num=n,periodic=True,seed=1) O.bodies.append([sphere(s[0],s[1]) for s in sp]) #make the problem more interesting by giving a smaller mass to one of the bodies, different stiffness present similar difficulties O.bodies[3].state.mass = O.bodies[n-1].state.mass*0.01 O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), GlobalStiffnessTimeStepper(label='ts'), PeriTriaxController(dynCell=True,mass=0.2,maxUnbalanced=0.001, relStressTol=0.01,goal=(-1e4,-1e4,0),stressMask=3,globUpdate=5, maxStrainRate=(10.,10.,10.),doneHook='triaxDone()',label='triax'), NewtonIntegrator(damping=.2,label="newton"), ] phase=0 def triaxDone(): global phase if phase==0: O.pause() O.timingEnabled=1 qt.View() O.saveTmp() #====== First, we won't use a timestepper at all, we fix O.dt using PWave timestep =========# timing.reset() O.dt=0.8*PWaveTimeStep() #for fair comparison, we use the same safety factor as in GS timestepper, allthough many scripts use 0.5 or even 0.1*PWaveTimeStep() ts.active=False O.run(100000,True);#it will actually stop before 100k iterations as soon as the packing is stable print "--------------------------------" print "Fixed dt = 0.8 * PWave timestep:" print "--------------------------------" timing.stats() #====== Now we use the timestepper to adjust dt dynamicaly =========# O.reload() timing.reset() O.dt=100000000 #or whatever ts.active=True O.run(100000,True); print "--------------------------------------------------" print "dt dynamicaly set with GlobalStiffness timesteper:" print "--------------------------------------------------" timing.stats() #====== And finaly, the timestepper with density scaling =========# O.reload() timing.reset() O.dt=1000000 #or whatever #We force dt=1. The inertia of bodies will adjusted automatically... newton.densityScaling=True #... but not that of cell, hence we have to adjust it or the problem becomes unstable triax.mass=triax.mass*(1e4)**2 O.run(1000000,True); print "--------------------------------------------------------------------" print "dt dynamicaly set with GlobalStiffness timesteper + density scaling:" print "--------------------------------------------------------------------" timing.stats() #_____ TYPICAL RESULTS (n=1000)____ #-------------------------------- #Fixed dt = 0.8 * PWave timestep: #-------------------------------- #Name Count Time Rel. time #------------------------------------------------------------------------------------------------------- #ForceResetter 77246 326813us 0.24% #InsertionSortCollider 23571 29447986us 21.73% #InteractionLoop 77246 65954607us 48.67% #"ts" 0 0us 0.00% #"triax" 77246 11876934us 8.76% #"newton" 77246 27914757us 20.60% #TOTAL 135521099us 100.00% #-------------------------------------------------- #dt dynamicaly set with GlobalStiffness timesteper: #-------------------------------------------------- #Name Count Time Rel. time #------------------------------------------------------------------------------------------------------- #ForceResetter 45666 193813us 0.23% #InsertionSortCollider 6727 9456709us 11.09% #InteractionLoop 45666 44245384us 51.87% #"ts" 45666 6267682us 7.35% #"triax" 45666 8234896us 9.65% #"newton" 45666 16906118us 19.82% #TOTAL 85304605us 100.00% #-------------------------------------------------------------------- #dt dynamicaly set with GlobalStiffness timesteper + density scaling: #-------------------------------------------------------------------- #Name Count Time Rel. time #------------------------------------------------------------------------------------------------------- #ForceResetter 23936 102435us 0.25% #InsertionSortCollider 305 534572us 1.29% #InteractionLoop 23936 23748011us 57.11% #"ts" 23936 3520397us 8.47% #"triax" 23936 4623106us 11.12% #"newton" 23936 9051032us 21.77% #TOTAL 41579556us 100.00% trunk-2017.01a/examples/triax-tutorial/000077500000000000000000000000001304022710500177705ustar00rootroot00000000000000trunk-2017.01a/examples/triax-tutorial/README000066400000000000000000000006351304022710500206540ustar00rootroot00000000000000The material in this folder was used for the numerical sessions of Alert's "Olek Zinkiewicz" course on discrete mechanics, Grenoble, 2011. They show basic simulation of triaxial tests (session 1) and advanced boundary conditions for stress-strain probing (session 2). Authors: Nejib Hada, Luc Sibille, Bruno Chareyre. Yade's version should be bzr2830 or later, although some earlier versions could work as well. trunk-2017.01a/examples/triax-tutorial/script-session1.py000066400000000000000000000237511304022710500234200ustar00rootroot00000000000000# -*- coding: utf-8 -*- #************************************************************************* # Copyright (C) 2010 by Bruno Chareyre * # bruno.chareyre_at_grenoble-inp.fr * # * # This program is free software; it is licensed under the terms of the * # GNU General Public License v2 or later. See file LICENSE for details. * #*************************************************************************/ ## This script details the simulation of a triaxial test on sphere packings using Yade ## See the associated pdf file for detailed exercises ## the algorithms presented here have been used in published papers, namely: ## * Chareyre et al. 2002 (http://www.geosyntheticssociety.org/Resources/Archive/GI/src/V9I2/GI-V9-N2-Paper1.pdf) ## * Chareyre and Villard 2005 (https://yade-dem.org/w/images/1/1b/Chareyre&Villard2005_licensed.pdf) ## * Scholtès et al. 2009 (http://dx.doi.org/10.1016/j.ijengsci.2008.07.002) ## * Tong et al.2012 (http://dx.doi.org/10.2516/ogst/2012032) ## ## Most of the ideas were actually developped during my PhD. ## If you want to know more on micro-macro relations evaluated by triaxial simulations ## AND if you can read some french, it is here: http://tel.archives-ouvertes.fr/docs/00/48/68/07/PDF/Thesis.pdf from yade import pack ############################################ ### DEFINING VARIABLES AND MATERIALS ### ############################################ # The following 5 lines will be used later for batch execution nRead=readParamsFromTable( num_spheres=1000,# number of spheres compFricDegree = 30, # contact friction during the confining phase key='_triax_base_', # put you simulation's name here unknownOk=True ) from yade.params import table num_spheres=table.num_spheres# number of spheres key=table.key targetPorosity = 0.43 #the porosity we want for the packing compFricDegree = table.compFricDegree # initial contact friction during the confining phase (will be decreased during the REFD compaction process) finalFricDegree = 30 # contact friction during the deviatoric loading rate=-0.02 # loading rate (strain rate) damp=0.2 # damping coefficient stabilityThreshold=0.01 # we test unbalancedForce against this value in different loops (see below) young=5e6 # contact stiffness mn,mx=Vector3(0,0,0),Vector3(1,1,1) # corners of the initial packing ## create materials for spheres and plates O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),density=2600,label='spheres')) O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls')) ## create walls around the packing walls=aabbWalls([mn,mx],thickness=0,material='walls') wallIds=O.bodies.append(walls) ## use a SpherePack object to generate a random loose particles packing sp=pack.SpherePack() clumps=False #turn this true for the same example with clumps if clumps: ## approximate mean rad of the futur dense packing for latter use volume = (mx[0]-mn[0])*(mx[1]-mn[1])*(mx[2]-mn[2]) mean_rad = pow(0.09*volume/num_spheres,0.3333) ## define a unique clump type (we could have many, see clumpCloud documentation) c1=pack.SpherePack([((-0.2*mean_rad,0,0),0.5*mean_rad),((0.2*mean_rad,0,0),0.5*mean_rad)]) ## generate positions and input them in the simulation sp.makeClumpCloud(mn,mx,[c1],periodic=False) sp.toSimulation(material='spheres') O.bodies.updateClumpProperties()#get more accurate clump masses/volumes/inertia else: sp.makeCloud(mn,mx,-1,0.3333,num_spheres,False, 0.95,seed=1) #"seed" make the "random" generation always the same O.bodies.append([sphere(center,rad,material='spheres') for center,rad in sp]) #or alternatively (higher level function doing exactly the same): #sp.toSimulation(material='spheres') ############################ ### DEFINING ENGINES ### ############################ triax=TriaxialStressController( ## TriaxialStressController will be used to control stress and strain. It controls particles size and plates positions. ## this control of boundary conditions was used for instance in http://dx.doi.org/10.1016/j.ijengsci.2008.07.002 maxMultiplier=1.+2e4/young, # spheres growing factor (fast growth) finalMaxMultiplier=1.+2e3/young, # spheres growing factor (slow growth) thickness = 0, ## switch stress/strain control using a bitmask. What is a bitmask, huh?! ## Say x=1 if stess is controlled on x, else x=0. Same for for y and z, which are 1 or 0. ## Then an integer uniquely defining the combination of all these tests is: mask = x*1 + y*2 + z*4 ## to put it differently, the mask is the integer whose binary representation is xyz, i.e. ## "100" (1) means "x", "110" (3) means "x and y", "111" (7) means "x and y and z", etc. stressMask = 7, internalCompaction=True, # If true the confining pressure is generated by growing particles ) newton=NewtonIntegrator(damping=damp) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), ## We will use the global stiffness of each body to determine an optimal timestep (see https://yade-dem.org/w/images/1/1b/Chareyre&Villard2005_licensed.pdf) GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8), triax, TriaxialStateRecorder(iterPeriod=100,file='WallStresses'+table.key), newton ] #Display spheres with 2 colors for seeing rotations better Gl1_Sphere.stripes=0 if nRead==0: yade.qt.Controller(), yade.qt.View() ## UNCOMMENT THE FOLLOWING SECTIONS ONE BY ONE ## DEPENDING ON YOUR EDITOR, IT COULD BE DONE ## BY SELECTING THE CODE BLOCKS BETWEEN THE SUBTITLES ## AND PRESSING CTRL+SHIFT+D ####################################### ### APPLYING CONFINING PRESSURE ### ####################################### #the value of (isotropic) confining stress defines the target stress to be applied in all three directions triax.goal1=triax.goal2=triax.goal3=-10000 #while 1: #O.run(1000, True) ##the global unbalanced force on dynamic bodies, thus excluding boundaries, which are not at equilibrium #unb=unbalancedForce() #print 'unbalanced force:',unb,' mean stress: ',triax.meanStress #if unbtargetPorosity: ## we decrease friction value and apply it to all the bodies and contacts #compFricDegree = 0.95*compFricDegree #setContactFriction(radians(compFricDegree)) #print "\r Friction: ",compFricDegree," porosity:",triax.porosity, #sys.stdout.flush() ## while we run steps, triax will tend to grow particles as the packing ## keeps shrinking as a consequence of decreasing friction. Consequently ## porosity will decrease #O.run(500,1) #O.save('compactedState'+key+'.yade.gz') #print "### Compacted state saved ###" ############################## ### DEVIATORIC LOADING ### ############################## ##We move to deviatoric loading, let us turn internal compaction off to keep particles sizes constant #triax.internalCompaction=False ## Change contact friction (remember that decreasing it would generate instantaneous instabilities) #setContactFriction(radians(finalFricDegree)) ##set stress control on x and z, we will impose strain rate on y #triax.stressMask = 5 ##now goal2 is the target strain rate #triax.goal2=rate ## we define the lateral stresses during the test, here the same 10kPa as for the initial confinement. #triax.goal1=-10000 #triax.goal3=-10000 ##we can change damping here. What is the effect in your opinion? #newton.damping=0.1 ##Save temporary state in live memory. This state will be reloaded from the interface with the "reload" button. #O.saveTmp() ##################################################### ### Example of how to record and plot data ### ##################################################### #from yade import plot ### a function saving variables #def history(): #plot.addData(e11=-triax.strain[0], e22=-triax.strain[1], e33=-triax.strain[2], #ev=-triax.strain[0]-triax.strain[1]-triax.strain[2], #s11=-triax.stress(triax.wall_right_id)[0], #s22=-triax.stress(triax.wall_top_id)[1], #s33=-triax.stress(triax.wall_front_id)[2], #i=O.iter) #if 1: ## include a periodic engine calling that function in the simulation loop #O.engines=O.engines[0:5]+[PyRunner(iterPeriod=20,command='history()',label='recorder')]+O.engines[5:7] ##O.engines.insert(4,PyRunner(iterPeriod=20,command='history()',label='recorder')) #else: ## With the line above, we are recording some variables twice. We could in fact replace the previous ## TriaxialRecorder ## by our periodic engine. Uncomment the following line: #O.engines[4]=PyRunner(iterPeriod=20,command='history()',label='recorder') #O.run(100,True) ### declare what is to plot. "None" is for separating y and y2 axis #plot.plots={'i':('e11','e22','e33',None,'s11','s22','s33')} ### the traditional triaxial curves would be more like this: ##plot.plots={'e22':('s11','s22','s33',None,'ev')} ## display on the screen (doesn't work on VMware image it seems) #plot.plot() ##### PLAY THE SIMULATION HERE WITH "PLAY" BUTTON OR WITH THE COMMAND O.run(N) ##### ## In that case we can still save the data to a text file at the the end of the simulation, with: #plot.saveDataTxt('results'+key) ##or even generate a script for gnuplot. Open another terminal and type "gnuplot plotScriptKEY.gnuplot: #plot.saveGnuplot('plotScript'+key) trunk-2017.01a/examples/triax-tutorial/script-session2.py000066400000000000000000000175671304022710500234310ustar00rootroot00000000000000# -*- coding: utf-8 -*- from yade import pack num_spheres=500 ## corners of the initial packing mn,mx=Vector3(0,0,0),Vector3(1,1,1) thick = 0.01 compFricDegree = 2 rate=0.2 damp=0.1 stabilityThreshold=0.001 key='_define_a_name_' ## create material #0, which will be used as default O.materials.append(FrictMat(young=5e6,poisson=0.5,frictionAngle=radians(compFricDegree),density=2600,label='spheres')) O.materials.append(FrictMat(young=5e6,poisson=0.5,frictionAngle=0,density=0,label='walls')) ## create walls around the packing walls=aabbWalls([mn,mx],thickness=thick,material='walls') wallIds=O.bodies.append(walls) sp=pack.SpherePack() sp.makeCloud(mn,mx,-1,0.3333,num_spheres,False, 0.95) volume = (mx[0]-mn[0])*(mx[1]-mn[1])*(mx[2]-mn[2]) mean_rad = pow(0.09*volume/num_spheres,0.3333) clumps=False if clumps: c1=pack.SpherePack([((-0.2*mean_rad,0,0),0.5*mean_rad),((0.2*mean_rad,0,0),0.5*mean_rad)]) sp.makeClumpCloud((0,0,0),(1,1,1),[c1],periodic=False) O.bodies.append([sphere(center,rad,material='spheres') for center,rad in sp]) standalone,clumps=sp.getClumps() for clump in clumps: O.bodies.clump(clump) for i in clump[1:]: O.bodies[i].shape.color=O.bodies[clump[0]].shape.color #sp.toSimulation() else: O.bodies.append([sphere(center,rad,material='spheres') for center,rad in sp]) O.dt=.5*PWaveTimeStep() # initial timestep, to not explode right away O.usesTimeStepper=True triax=ThreeDTriaxialEngine( maxMultiplier=1.005, finalMaxMultiplier=1.002, thickness = thick, stressControl_1 = False, stressControl_2 = False, stressControl_3 = False, ## Independant stress values for anisotropic loadings sigma1=-10000, sigma2=-10000, sigma3=-10000, internalCompaction=True, Key=key, ) newton=NewtonIntegrator(damping=damp) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()],verletDist=-mean_rad*0.06), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8, defaultDt=4*PWaveTimeStep()), triax, TriaxialStateRecorder(iterPeriod=100,file='WallStresses'+key), newton ] #Display spheres with 2 colors for seeing rotations better Gl1_Sphere.stripes=0 yade.qt.Controller(), yade.qt.View() while 1: O.run(1000, True) #the global unbalanced force on dynamic bodies, thus excluding boundaries, which are not at equilibrium unb=unbalancedForce() #average stress #note: triax.stress(k) returns a stress vector, so we need to keep only the normal component meanS=(triax.stress(triax.wall_right_id)[0]+triax.stress(triax.wall_top_id)[1]+triax.stress(triax.wall_front_id)[2])/3 print 'unbalanced force:',unb,' mean stress: ',meanS if unb>/Type/Annot/Rect[345.6 320.7 381.7 334.5]>> endobj 3 0 obj <>/Type/Annot/Rect[223.9 265.5 260 279.3]>> endobj 7 0 obj <>stream x]M0 c`W"eC?l'EjrȿyV!af0; sn>¥2L׷KZ{m,m pW,ݖa6x ܅.4 0,kӅs󹙾4אk󡋏K%|<`-Uڱ i bmV: C߳*f6Eבrr ʮʵ+(׌; WƵvCֽSx=+l #n_c/&LZI+0+eW[0k܏מC9/q^G3t0=<]t_ѿ=8xG=55NRӿĻsmHǝ /S\WX+e  Dq_pB8?c 0˴yì3iwާqB~u endstream endobj 9 0 obj <>stream xݼ{|SǙ?<Ϝs$]e[|mc`|;e m 8BI 5iЍ4%M۸IvIЖMҸ-/%a4o6>s$sI}޿^:gg<3yG = Wo$:2>5#o@wf_WE[B,a"awz1n; de Uycm#cƽ7fjFJ +$t}]CH?q*/Q&lg+ם_f¢PYyErfUfں9s>NbB1zÇ;N\~7^Ӌ|e-4CIrO~Ez $N֑-H#SOtɾQqr3|Ir<7$'X_Lahȝ,#EEQ#^uԷɣt?YHٸ|01ŒDZ_mܿ*t/ZGh߈x?Uw.2l.K#()t:J*Y~yY0-+;;˗-/Y|Ӣ bm-ɍцsjgϪY(/+.* 3|Y2 :Q@ZIo0 X9!"F7yo䔑ssrS w.[^m{So4ki'o+ᛔ0_D 0%gm7IoKu}-f,N;?P[^FNhua(U9QPe J4lHŗv4}e RFD+ETSjH:Vu{lr}%*oLqwײoޔ9*7Jv-+}_{$ FJ J!,؊ݷmݗ*W;iA x':}{ݩVZmluiwg[k~_g^9[@|OdFRK;3q/Y~M{KN=l_޹/ [PSp<ʺ/}}.Rb B >eDgnB[bX9-d,[^2]L}r29E뚕K#)jj[ީdfKHru6W*̞mٗlT_\:Quj1;*l90$8ӆn_J^9 4P>Χ<1E':ۗۗvuf+I`tg!5NV"o+MsR5P զNpinF2؜c p.MŢX۷җQLf94L$.iQHL9l{;ޔdmcQ"l_%n]',at 3r_/T}.ytw߾|+ܟ-`r٭~68qF+y Yfsy- wUQe!Оh*/Cet,=!=˻:_@':?ٴD:_"+Tʨ"^a%-ÈFw 2 A> Dii@V4MH34YRZ1/\/q@?E'))71z#7f*FW'S,ۤ/B_58$<959_uB%39bY`*G>sg5So: >̿A C"솠jr5T4 mr-qv^r\pכ.n&ӹ71CrL c&'îg1.>θîFwg\ tq^B_b eo|p]X7+.먋tAq6+oWɿ.V +܇.E`cHhUh=yj: W"S ..SEnV80Hc5ᢞLñ~BOy=/oh"(ڸ>b!?@{d?gT^5jjz0<㾚f 8BE\N;"빠{>X;hh^GXڑeٙvTqC)P`-haWy._V2)_3ʽB6G{ y;˷@O^jߵ.ڥ5.9_YܽAhU& {?-}E83>WLm!'V_gs ;Gnn/ޗWUvXAe dw6f,Ŗl5O˳ q_uas!-,IR\58t:G:nIOhpGB(RTq@jVMu:"s88Ag PE^^

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    '%D.basename outStr+=str(table) print outStr quit() trunk-2017.01a/scripts/checks-and-tests/law-test.py000066400000000000000000000057771304022710500221430ustar00rootroot00000000000000# # demonstrate capabilities of LawTester # # The contact is loaded as described by LawTester.path triplets: # # 1. Push spheres together, then shear, then release in the normal sense, # while keeping shear constant; slipping is taking place along the # Mohr-Coulomb plasticity surface # # 2. Load in the normal direction, then go around a square in the shear plane # # The sphere couple is oriented randomly, but the result should always be the same. # from yade import utils,plot import random random.seed() # sphere's radii r1,r2=.1,.2 # place sphere 1 at the origin pt1=Vector3(0,0,0) # random orientation of the interaction normal=Vector3(random.random()-.5,random.random()-.5,random.random()-.5) normal=Vector3.UnitX O.bodies.append([ utils.sphere(pt1,r1,wire=True,color=(.7,.7,.7)), utils.sphere(pt1+.999999*(r1+r2)*normal.normalized(),r2,wire=True,color=(0,0,0)) ]) O.engines=[ ForceResetter(), PyRunner(iterPeriod=1,command='import time; time.sleep(.05)'), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( #[Ig2_Sphere_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] # ScGeom #[Ig2_Sphere_Sphere_L3Geom(approxMask=63)],[Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_L3Geom_FrictPhys_ElPerfPl(noBreak=True,noSlip=False)] # L3Geom [Ig2_Sphere_Sphere_L6Geom(approxMask=63)],[Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_L6Geom_FrictPhys_Linear(charLen=1)] # L6Geom ), LawTester(ids=[0,1],disPath=[(0,0,0)]*7+[(-1e-5,0,0),(-1e-5,.1,.1)],rotPath=[(0,.2,0),(0,0,0),(0,0,.2),(0,0,0),(.2,0,0),(-.2,0,0),(0,0,0)],pathSteps=[10],doneHook='tester.dead=True; O.pause();',label='tester',rotWeight=0), #LawTester(ids=[0,1],path=[ # (-1e-5,0,0),(-.1,0,0),(-.1,.1,0),(-1e-5,.1,0), # towards, shear, back to intial normal distance # (-.02,.1,.1),(-.02,-.1,.1),(-.02,-.1,-.1),(-.02,.1,-.1),(-.02,.1,.1), # go in square in the shear plane without changing normal deformation # (-1e-4,0,0) # back to the origin, but keep some overlap to not delete the interaction # ],pathSteps=[100],doneHook='tester.dead=True; O.pause()',label='tester',rotWeight=.2,idWeight=.2), NewtonIntegrator(), PyRunner(iterPeriod=1,command='addPlotData()'), ] def addPlotData(): i=O.interactions[0,1] plot.addData( un=tester.uTest[0],us1=tester.uTest[1],us2=tester.uTest[2], ung=tester.uGeom[0],us1g=tester.uGeom[1],us2g=tester.uGeom[2], phiX=tester.uTest[3],phiY=tester.uTest[4],phiZ=tester.uTest[5], phiXg=tester.uGeom[3],phiYg=tester.uGeom[4],phiZg=tester.uGeom[5], i=O.iter,Fs=i.phys.shearForce.norm(),Fn=i.phys.normalForce.norm(),Tx=O.forces.t(0)[0],Tyz=sqrt(O.forces.t(0)[1]**2+O.forces.t(0)[2]**2) ) plot.plots={'us1':('us2',),'Fn':('Fs',),'i':('un','us1','us2'),' i':('Fs','Fn','Tx','Tyz'),' i':('ung','us1g','us2g'),'i ':('phiX','phiXg','phiY','phiYg','phiZ','phiZg')} #'ung','us1g','us2g' plot.plot(subPlots=True) try: from yade import qt qt.Controller(); v=qt.View() rr=qt.Renderer() rr.extraDrawers=[GlExtra_LawTester()] rr.intrGeom=True except ImportError: pass O.dt=1 O.saveTmp() #O.run() trunk-2017.01a/scripts/checks-and-tests/serialization-benchmark.py000066400000000000000000000014201304022710500251650ustar00rootroot00000000000000import time # change this line to load your reference simulation O.load2('ref.boost.bin.gz') base='~sim~' # http://blogmag.net/blog/read/38/Print_human_readable_file_size def sizeof_fmt(num): for x in ['bytes','KB','MB','GB','TB']: if num<1024.0: return "%3.1f%s"%(num,x) num/=1024.0 def io(ext,load,noBoost=False): t0=time.time() f=base+('.yade.' if noBoost else '.boost.')+ext ((O.load if noBoost else O.load2) if load else (O.save if noBoost else O.save2))(f) print ('Loaded' if load else 'Saved '),('yade ' if noBoost else 'boost'),'%-7s '%ext,'%7s'%sizeof_fmt(os.path.getsize(f)),'%.1fs'%(time.time()-t0) for ext in ['xml','xml.bz2']: io(ext,False,True) io(ext,True,True) for ext in ['xml','xml.gz','xml.bz2','bin','bin.gz','bin.bz2']: io(ext,False) io(ext,True) trunk-2017.01a/scripts/checks-and-tests/triax-perf/000077500000000000000000000000001304022710500220725ustar00rootroot00000000000000trunk-2017.01a/scripts/checks-and-tests/triax-perf/mkTextTable.sh000066400000000000000000000006551304022710500246600ustar00rootroot00000000000000#!/bin/sh # run this to get nice text to paste into the openoffice sheet TMPS=/tmp/a$$ /tmp/b$$ /tmp/c$$ /tmp/d$$ ls *.ser?.log awk '/TOTAL/ { print $2}' *.ser?.log > /tmp/a$$ awk '/Collider/ { print $4}' *.ser?.log > /tmp/b$$ awk '/TOTAL/ { print $2}' *.par?.log > /tmp/c$$ awk '/Collider/ { print $4}' *.par?.log > /tmp/d$$ paste /tmp/a$$ /tmp/b$$ /tmp/c$$ /tmp/d$$ | sed 's/us//g' | sed 's/%//g' | sed 's/\./,/g' rm -rf $TMPS trunk-2017.01a/scripts/checks-and-tests/triax-perf/triax-perf.ods000066400000000000000000000463671304022710500247020ustar00rootroot00000000000000PK9:l9..mimetypeapplication/vnd.oasis.opendocument.spreadsheetPK9: content.xml]6Oa٢]XL$.Z4md ŀ#Ѷ]\J>bOŔo#ʖg?\<lÆKsyK!4]mUQ $a aˌ1qN=]ƐB,(E;VwmMmtOZ lZ`qQ4UԻIQwӥj?c)`k _(>dƦÄQ30ZMv`ޓ}3f);B?*3eWlCبAۤ з=5gb46-]L՚>ʦ9a_HP|9:AgivIlPQD%e'%8Z%_B,(#`Ì$`LR ҳ\bES KsTa) R QNki1؉]:TY$V%^2-rjOcC1q6[AcL(Gа\[+GO@Ĭ+wIASѸ{@Dlio}\x;޹N;՗|;w83<׼pSM՞BNsyyK$ nסQT+JfД*=v1*J={v+/ALK"I}5G @+rjkwDEqAc@3v[/IwePxlXp4@Hrd̊WTp+ ~yR~ $'gXyb}}b}W^iR$`DljUvO([ ĝ1a~]fyyMI6I@d2|AG~`/g uAlt%CÑrZou$_~<H,iRbp HjIw4X01=kfsps2;J>j=`Q?ivE@6(qm7#H9-,GR_Oʼn""ٝ1?y4JаLΡݵӂCPUҏ=d!9F?tq5ƪi'LFdϞnNktL$VQhYѲC !OLXQғ=W5l;2%54ϱuMâ'{H5Z3B"%=,H(xn},q(LfxcՋۈC5Os]Kâ8T[虡lɞ=8ؓt55OC,m]vK-nf|y'7<>hQ7?M}s>960&=l{ܭ^!r3f&P2<1?iog4#Sz~HߔCQTd蹖 隞r֠]k${sȄ9,ImjmN'A2liv YCu5ґ#l1=͜\y6(ŜWSOG(œY9zk̎>2τY2$m9҄FniɢR!yCbR,vcQ~ Qtu~3Tȸ",MwL<$\~7Ҽ^ & ( 58sBܐdEt8bZrlD een.%q'`,hOe`q iq\3.l{ݎ&s[ {]!=FP,Fmwڊ6 'h*%mQM +p'Sm۰mI*T&>T&~7lK q+%h+J̨BU%Tw8szK%AR"z=yq4Nڜ‚;%OmSLXH_w*~e8%I `k%"l4Y*csryE-z]]eT g|n5ǹQt Q /+ $njn1p^i1:~WU t\g݇D$:`|7d0T%C1_.C) $ ]7D8N-Q)sLx-&/"1oF1l-d#%iENMLؔ, reD-ҋ9)_%^lwJ31kDF)FC11W."m}RꭣߐDv)фLzj6$x~OJ *+A~l~HɪBFі`-$քZ&0 ɳ pOHο{b (knA/^~@F 0#cu sgoͮh҃bP̾0P/X~f9M?A0bbg~ucKnѡWjn{I G{dǏw>>\!RpȸM`&O !bGW}>NUtzlul}q>'#k=ȿ2C&z ҟ0 Q~Q=)+"SJٝG T7e?/`ͼ}~{Ś3{;YtӽWu!ǃnyqE׿ 9p1\M&\~r؞~~>'O[X{Oav%b6\ T"f{KC1lwr# T[.'a=ċHP(T`7tPo^`9N,| Ikh k!TO3v|`t%GeT⩈Y-,,Kq".kܬTkCvӫ[vإ<P쮓ݏӸVƬ[vɮn#|&oUcT/b'7Ih(AE 6 wP䞓[5[78Aީ:VWo܉? 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Regular TriaxialTest with 3 independent dispatchers (geom, phys, constitutive law) # 2. TriaxialTest with InteractionLoop (common loop and functor cache) # # Run the test like this: # # yade-trunk-opt-multi -j1 triax-perf.table triax-perf.py # # The -j1 ensures that only 1 job will run at time # (even if other cores are free, access to memory is limiting if running multiple jobs at time) # # You have to collect the results by hand from log files, or run sh mkTextTable.sh and use # triax-perf.ods to get comparison # utils.readParamsFromTable(fast=False,noTableOk=True) TriaxialTest(numberOfGrains=50000,fast=fast,noFiles=True).load() O.run(10,True) # filter out initialization O.timingEnabled=True O.run(200,True) from yade import timing timing.stats() print 'ForceContainer synced %d times'%(O.bexSyncCount) trunk-2017.01a/scripts/checks-and-tests/triax-perf/triax-perf.table000066400000000000000000000002371304022710500251660ustar00rootroot00000000000000!OMP_NUM_THREADS fast description 1 False ser1 2 False ser2 3 False ser3 4 False ser4 5 False ser5 1 True par1 2 True par2 3 True par3 4 True par4 5 True par5 trunk-2017.01a/scripts/erskine3-apply.sh000077500000000000000000000042541304022710500200630ustar00rootroot00000000000000#!/bin/sh #set -x ERSKINE=./erskine3.py YADE=../ # erskine3 accepts scons variables smuggled as @VARIABLE and resulting in $VARIABLE in generated scripts; do that for $PREFIX (ac scons var) export YADE_QMAKE_PATH=@PREFIX YADECOMPILATIONPATH=$YADE ENGINE=--scons; SCRIPT=SConscript #ENGINE=--waf; SCRIPT=wscript_build # erskine2.py syntax: ### project-file [--waf|--scons] buildscript-dir > buildscript # projects are traversed recursively and corresponding waf wscript_build files are sent to the standard output $ERSKINE $ENGINE $YADE/yade-libs/*/src/*.pro $YADE/yade-libs > $YADE/yade-libs/$SCRIPT $ERSKINE $ENGINE $YADE/yade-core/src/yade.pro $YADE/yade-core > $YADE/yade-core/$SCRIPT $ERSKINE $ENGINE $YADE/yade-guis/yade-gui-qt/src/QtGUI.pro $YADE/yade-guis > $YADE/yade-guis/$SCRIPT $ERSKINE $ENGINE $YADE/yade-extra/yade-spherical-dem-simulator/src/yade-spherical-dem-simulator.pro $YADE/yade-extra > $YADE/yade-extra/$SCRIPT # packages are have separated buildscripts each $ERSKINE $ENGINE $YADE/yade-packages/yade-package-common/src/yade-package-common.pro $YADE/yade-packages/yade-package-common > $YADE/yade-packages/yade-package-common/$SCRIPT $ERSKINE $ENGINE $YADE/yade-packages/yade-package-dem/src/yade-package-dem.pro $YADE/yade-packages/yade-package-dem > $YADE/yade-packages/yade-package-dem/$SCRIPT $ERSKINE $ENGINE $YADE/yade-packages/yade-package-fem/src/yade-package-fem.pro $YADE/yade-packages/yade-package-fem > $YADE/yade-packages/yade-package-fem/$SCRIPT $ERSKINE $ENGINE $YADE/yade-packages/yade-package-lattice/src/yade-package-lattice.pro $YADE/yade-packages/yade-package-lattice > $YADE/yade-packages/yade-package-lattice/$SCRIPT $ERSKINE $ENGINE $YADE/yade-packages/yade-package-mass-spring/src/yade-package-mass-spring.pro $YADE/yade-packages/yade-package-mass-spring > $YADE/yade-packages/yade-package-mass-spring/$SCRIPT $ERSKINE $ENGINE $YADE/yade-packages/yade-package-realtime-rigidbody/src/yade-package-realtime-rigidbody.pro $YADE/yade-packages/yade-package-realtime-rigidbody > $YADE/yade-packages/yade-package-realtime-rigidbody/$SCRIPT echo Creating entry for yade-extra/Clump in $YADE/yade-extra/$SCRIPT echo "env.SConscript(dirs=['clump'])" >> $YADE/yade-extra/$SCRIPT trunk-2017.01a/scripts/erskine3.py000066400000000000000000000332701304022710500167530ustar00rootroot00000000000000#!/usr/bin/env python # -*- Encoding: utf-8 -*- """ This program should really be run by the erskine3-apply.sh script Erskine is Watt's colleague in the house of Mr. Nutting. """ import sys,pprint,string,os from logging import * from os.path import * from re import * from copy import deepcopy import pprint def warning2(msg): warning(currentPro+' '+msg) bgroup=('(','{','[') egroup=(')','}',']') # variables that do not propagate to sub-builds localVars=['TEMPLATE','SUBDIRS','HEADERS','SOURCES','FORMS','LEXSOURCES','YACCSOURCES','TARGET','DESTDIR','PROJECT'] # variables / function that are ignored if undefined (replaced by ''); for all other, a warning is printed (and are ignored anyway) undefOK=['CXXPATH','CXX','CXXFLAGS','INCPATH','IDL_COMPILER'] # internal qmake variables that may be replace with the environment ones without warning replaceOK=['YADECOMPILATIONPATH'] discardedStatements=['^isEmpty\s*\(\s*YADE_QMAKE_PATH\s*\).*$'] #discardedStatements=[] targetLangType={'yade-lib-serialization-qt':'qt3','QtGUI':'qt3'} # used to be yadeQt, but it was dropped... targetEnv={'yade-lib-serialization-qt':'env','QtGUI':'env'} # was: yade defaultEnv='env' currentPro='[none]' allEnvs=[defaultEnv] for t in targetEnv.keys(): if not targetEnv[t] in allEnvs: allEnvs.append(targetEnv[t]) allSystemLibs=['glut','boost_date_time','boost_filesystem','boost_thread'] def splitgroup(s,delims=' '): "Split string at delims, but do not break parenthesized/bracketed/curly-bracketed groups" nest=0;ret=[];lastsplit=0 for i in range(0,len(s)): if s[i] in bgroup: nest+=1 elif s[i] in egroup: nest-=1 elif (nest==0 and s[i] in delims): ret.append(s[lastsplit:i]) lastsplit=i+1 ret.append(s[lastsplit:len(s)]) return ret def parseProject(proFile,inheritedVariables={}): """Returns dictionary of variables defined in this qmake project, replacing variables, that may propagate from parent project. No functions, only a few conditionals are expanded. An important 'parser' difference is that qmake obviously allows \\ continuation _after_ #. Since it is not nice at all, it doesn't work here. Also, it would be difficult to add.""" vars=inheritedVariables # sanitize input: no comments, no \\ linebreaks (join lines), no empty lines, no leading/trailing whitespace qm=[]; l=''; nest=0 for line in proFile: m=match(r'^\s*([^#]*)(#.*)?$',line[:-1]) l+=m.group(1) l=l.rstrip() beginnest=nest if len(l)==0: continue for c in l: if c in bgroup:nest+=1 elif c in egroup:nest-=1 if l[-1]!='\\' and nest==0: qm.append(l) l='' else: if l[-1]=='\\': l=l[:-1] nest=beginnest #pprint.pprint(qm) # process statements sequentially, replace variables / functions for stat in qm: # discard what should be discarded discard=False for pat in discardedStatements: if match(pat,stat): discard=True; break if discard: continue #replace environment and qmake variables while True: m=search(r'\$\$?([a-zA-Z0-9_]+\b|\([a-zA-Z0-9_]+\)|\{[a-zA-Z0-9_]+\})',stat) # possible patters of variables if not m: break v=m.group(1) if v[0]=='{': v=v[1:-1] if os.environ.has_key(v): repl=os.environ[v] info("Substituting environment variable `%s` → `%s`"%(v,repl)) else: if not v in undefOK: warning2("Undefined environment variable `%s'."%(v)) repl='' else: if v[0]=='(': v=v[1:-1] if vars.has_key(v): repl=vars[v] else: if not v in undefOK: if os.environ.has_key(v): repl=os.environ[v] if not v in replaceOK: warning2("Undefined internal variable `%s', using environment variable instead."%(v)) else: warning2("Undefined internal variable `%s'."%(v)) repl='' else: repl='' stat=stat[:m.start()]+repl+stat[m.end():] # scons variables (namely, $PREFIX, were smuggled unexpanded by using @PREFIX instead. Change it to what it should be now. stat=stat.replace('@','$') conditional=match(r'^\s*(!?[a-zA-Z0-9_]+)\s*{(.*)}$',stat) # this is a (possibly negated) conditional; nothing complicated, please; specifically, nested conditionals do not work if conditional: cond,then=conditional.group(1,2) if cond=='win32': continue # windows stuff is discarded completely elif cond=='!win32': stat=then # otherwise we pass the whole then-clause to further treatment else: warning2("Unknown condition `%s'."%cond) assign=match(r'^\s*([a-zA-Z0-9_.]+)\s*(=|\+=)\s*(.*)$',stat) # this line is an assignment call=match(r'^\s*(!?[a-z][a-zA-Z0-9_]+)\s*(\(.*)$',stat) # this line is a "function call" if assign: param,action,val=assign.group(1,2,3) val=sub('\s+$','',val) val=splitgroup(sub('\s+',' ',val)) if not vars.has_key(param): vars[param]=[] if action =='=' or action=='+=': vars[param]+=val elif call: func,rest=call.group(1,2) if not func in undefOK: warning2("Function `%s' not implemented; arguments `%s'.\n"%(func,rest)) else: warning2("Line not parsed: `%s'.\n"%(stat)) return vars def proProcess(filename,_vars={},dir='.',nest=0): info("(%s) Processing project file `%s'."%(nest,filename)) global currentPro currentPro=filename posterityVars=[] vars=deepcopy(_vars) for l in localVars: if vars.has_key(l): del vars[l] # these are NOT propagated to sub-builds childVars=parseProject(open(filename,'r'),vars) childVars['PROJECT']=filename assert(childVars.has_key('TEMPLATE')) # otherwise the file is broken assert(len(childVars['TEMPLATE'])==1) # dtto template=childVars['TEMPLATE'][0] if template=='subdirs': # if not childVars.has_key('SUBDIRS'): #warning("Template is `subdirs' but SUBDIRS is empty.") return None for subdir in childVars['SUBDIRS']: #print "dir=%s,subdir=%s"%(dir,subdir) subPro=dir+'/'+subdir+'/'+subdir.split('/')[-1]+'.pro' # .pro file is named the same as its immediate parent directory + .pro posterityVars.append(proProcess(subPro,_vars=childVars,dir=dir+'/'+subdir,nest=nest+1)) # recurse return [posterityVars] elif template=='app' or 'lib': guessedTarget=os.path.split(filename)[-1].split('.')[0] # garbage/foo.pro -> foo explicitTarget=None if childVars.has_key('TARGET'): explicitTarget=os.path.split(childVars['TARGET'][0])[1].split('.')[0] if explicitTarget: childVars['TARGET']=explicitTarget else: childVars['TARGET']=guessedTarget #if oldTarget!=newTarget: warning("Old and new target differ: `%s' vs. `%s' (using new one)."%(oldTarget,newTarget)) return [childVars] else: warning2("%s: Unknown TEMPLATE `%s'"%(currentPro,template)) return None def listUnique(List): if len(List)<=1: return List List.sort() last=List[-1] for i in range(len(List)-2, -1, -1): if last==List[i]: del List[i] else: last=List[i] return List def processVars(V,dir): ret="" for v in V: if isinstance(v,list): ret+=processVars(v,dir) if isinstance(v,dict): ret+=scriptGen(v,dir) return ret def pythonicTarget(t): #return target name such that it is acceptable as python identifier return sub('(^[0-9]|^|[^a-zA-Z0-9_])','_',t) def scriptGen(v,dir): project=v['PROJECT'] global currentPro currentPro=project target=v['TARGET'] commentOut=False # waf doesn't like targetless sources; scons is fine with that template=v['TEMPLATE'][0] ################### ### PATHS projAbsPath=realpath(normpath(dirname(project))) dirAbsPath=realpath(normpath(dir)) prefix=commonprefix([projAbsPath,dirAbsPath]) relPath=projAbsPath[len(prefix)+1:] #warning("PATHS:\n%s\n%s →\n%s"%(projAbsPath,dirAbsPath,relPath)) assert(not isabs(relPath)) #return 'PROJECT=%s\nTARGET=%s\nSOURCES=%s\nINCLUDES=%s\nrelPath=%s\n'%(v['PROJECT'],v['TARGET'],string.join(v['SOURCES']),string.join(v['INCLUDEPATH']),relPath) ################### ### SOURCES if v.has_key('SOURCES'): sources=v['SOURCES'] else: sources=[]; if v.has_key('FORMS'): sources+=v['FORMS'] #if v.has_key('IDLS'): sources+=v['IDLS'] sources=listUnique(sources) ################### ### LIBRARIES def prependDirFile(d,f): return map(lambda x: join(d,x),f) def listLibs(ll): ret=[] for l in ll: if l[0:2]=='-l': ret.append(l[2:]) elif l=='-rdynamic': pass else: warning2("Unknown LIBS item `%s'."%l) return ret libs=[] if v.has_key('LIBS'): libs=listLibs(v['LIBS']) ################### ### INCLUDE PATHS # waf/scons don't compile from the current directory, make sure it is there; duplicata removed later if not v.has_key('INCLUDEPATH'): includePath=['.'] else: includePath=v['INCLUDEPATH']+['.'] includePath=listUnique(includePath) #print "relPath=%s,INCLUDEPATH=%s"%(relPath,includePath) def prependDirFileIfRelative(d,f): def prepIf(ff): if not isabs(ff) and ff[0]!='$': return join(d,ff) return ff return map(prepIf,f) includePath=prependDirFileIfRelative(relPath,includePath) # filter out non-existent paths; without warning, it could be a short lambda... def DelAndWarnNonexistentPath(x): if not exists(normpath(join(dirAbsPath,x))) and x[0]!='$': warning2("Include path `%s' is invalid, removed!"%(normpath(join(dirAbsPath,x)))) return False return True includePath=filter(DelAndWarnNonexistentPath,includePath) includePath=[normpath(p) for p in includePath] # remove duplicates... http://stinkpot.afraid.org:8080/tricks/index.php/2006/05/find-all-the-unique-elements-in-a-python-list/ includePath=dict([(i,1) for i in includePath]).keys() # begin building the actual script ret="## %s\n"%v['PROJECT'] if template=='lib': if v.has_key('CONFIG') and 'dll' in v['CONFIG']: targetType='shlib' else: targetType='staticlib' elif template=='app': targetType='program' if buildEngine=='waf': assert(targetType) # "TEMPLATE is neither `lib' nor `app'. if not len(sources)==0: warning2("Project `%s' has empty source list, build rule will be commented out."%project) commentOut=True langType='cpp' localLibs,systemLibs=[],[] if target in targetLangType: langType=targetLangType[target] if langType=='qt3': systemLibs.append('QT3') ret+="obj=bld.create_obj('%s','%s')\n"%(langType,targetType) ret+="obj.name='%s'\n"%target ret+="obj.target='%s'\n"%target ret+="obj.source='%s'\n"%string.join(prependDirFile(relPath,sources)) # FIXME: install not yet there #ret+="obj.install_in='%s'\n"% #includePath=filter(lambda x: exists(normpath(join(dirAbsPath,x))),includePath) ret+="obj.includes='%s'\n"%string.join(includePath) # libs if len(libs)>0: for l in libs: if l in allSystemLibs: systemLibs.append(l) else: localLibs.append(ll) if len(localLibs)>0: ret+="obj.uselib_local='%s'\n"%(string.join(localLibs)) if len(systemLibs)>0: ret+="obj.uselib='%s'\n"%(string.join(systemLibs)) elif buildEngine=='scons': env=defaultEnv if target in targetEnv: env=targetEnv[target] ret+="%s.%s('%s',%s%s"%(env,{'program':'Program','shlib':'SharedLibrary','staticlib':'StaticLibrary'}[targetType], target,fieldSep,toStr(prependDirFile(relPath,sources))) if installable.has_key((env,targetType)): installable[(env,targetType)].append(pythonicTarget(target)) else: installable[(env,targetType)]=[pythonicTarget(target),] if len(libs)>0: ret+=",%sLIBS=%s['LIBS']+%s"%(fieldSep,env,toStr(libs)) if len(includePath)>0: # using CPPPATH would override top-level settings (question posted on scons ML how to avoid this) # for now, put all paths prefixed with -I to CPPFLAGS as workaround #ret+=",%sCPPFLAGS=%s"%(fieldSep,toStr(map(lambda x: '-I'+x,includePath))) ### NO, that doesn't work since CPPPATH is relative to SConscript dir, whereas CPPFLAGS are not prepended (logically) ### try the inverse: ret+=",%sCPPPATH=%s['CPPPATH']+%s"%(fieldSep,env,toStr(includePath)) ret+=')' instDir=installDirs[targetType] if instDirTargets.has_key((env,instDir)): instDirTargets[(env,instDir)].append((ret,target)) else: instDirTargets[(env,instDir)]=[(ret,target)] else: raise ValueError('buildEngine must be waf or scons (--waf or --scons)'); if commentOut: ret='# This rule is commented out because it has no source'+sub('(^|\n)','\n#',ret) ret+='\n' return ret def masterScriptGen(V,dir): # s='' if buildEngine=='scons': s+="Import('*')\n" processVars(V,dir) # return value of processVars discarded, results passed in instDirTarget instead for env,dir in instDirTargets.keys(): idt=instDirTargets[(env,dir)] #binary targets are handles specially: they install under _filename_ postfixed if match('.*/bin$',dir): ## warhing: this is OS-specific to tell binary target! s+="%s.InstallAs(["%env+','.join(["'%s$POSTFIX'"%(join(dir,tgSpec[1])) for tgSpec in idt])+"],[\n" s+=',\n'.join([sub(r'(?m)^','\t',tgSpec[0]) for tgSpec in idt]) s+='\n])' #whereas other targets install under _filename_ into a dir that has been postfixed already else: s+="%s.Install('%s',[\n"%(env,dir) s+=',\n'.join([sub(r'(?m)^','\t',tgSpec[0]) for tgSpec in idt])+'\n])\n' #for tgSpec in idt: print tgSpec[0] elif buildEngine=='waf': s+=processVars(V,dir) return s assert(len(sys.argv)>=3) buildEngine,projects,scriptDir=sys.argv[1][2:],sys.argv[2:-1],sys.argv[-1] assert(buildEngine in ['waf','scons']) allVars=[] for project in projects: allVars.append(proProcess(project,dir=dirname(project))) # HACK: useful stuff to pass down via globals... pretty=True if pretty: def toStr(what): ret=pprint.pformat(what); n=1 # replace leading spaces (nesting) by tabs... while n: ret,n=subn(r'(?m)^(\t*) ',r'\1\t',ret) # indent all lines by one more tab ret=sub(r'(?m)^','\t',ret) # de-indent the first one return ret[1:] fieldSep='\n\t' else: toStr=str; fieldSep=''; installable={} # hash indexed by (env,targetType)->pythonicTargetName instDirTargets={} # hash indexed by (env,targetDir)->str_target_spec installDirs={'shlib':join('$PREFIX','lib','yade$POSTFIX',string.split(scriptDir,os.sep)[-1]),'staticlib':join('$PREFIX','lib','yade$POSTFIX'),'program':join('$PREFIX','bin')} print masterScriptGen(allVars,scriptDir) trunk-2017.01a/scripts/fix-plugin-names.py000066400000000000000000000010701304022710500204040ustar00rootroot00000000000000import os,re for root, dirs, files in os.walk('.'): for name in files: if not name.endswith('.cpp'): continue #if name!='BssSnowGrain.cpp': continue modified=False new=[] for l in open(root+'/'+name): m=re.match('(.*)YADE_PLUGIN\(([^)]*)\)(.*)',l) if m: modified=True plugins=''.join(['('+pl.strip()[1:-1]+')' for pl in m.group(2).split(',')]) new.append(m.group(1)+'YADE_PLUGIN('+plugins+')'+m.group(3)) else: new.append(l) if modified: print root+'/'+name f=open(root+'/'+name,'w') for l in new: f.write(l) f.close() trunk-2017.01a/scripts/gl-test.py000066400000000000000000000026621304022710500166100ustar00rootroot00000000000000# # Test script for OpenGL from python (and from other threads in general) # With GL locking, 1 view seems to work reliably, not two views, though. # # Some drivers (nvidia) raise XBadAccess if there is an attempt to access # OpenGL context concurrently from different threads. # Other drivers (intel, at least on my laptop) freeze the videocard completely # if that is the case. # # You can enable the "if False:" part (say "if True:" instead) to see what # it does in your case. # from yade import qt from yade import utils O.bodies.append(utils.box([0,0,0],[1,1,1],color=[1,0,0])) O.bodies.append(utils.sphere([0,2,0],1,color=[0,1,0])) print 'Begin here.' qt.View(); print 'Created view' glv0=qt.GLViewer(); print 'view #0' # get GLViewer instance for the primary view glv0.grid=True,True,False; print 'grid x,y' glv0.axes=True; print 'axes shown' glv0.screenSize=200,200; print 'screen size set to 200x200' glv0.center(True); print 'median center' # median center - will fallback since there are only 2 bodies ## ## !!! If you enable this, you may crash your machine !!! ## if False: glv1=qt.View(); print 'Created 2nd view' # create new view glv1.fps=True; print 'fps shown' glv1.lookAt=(0,1,0); print 'lookAt set' glv1.viewDirection=(0,-1,0); print 'viewDirection set' glv1.center(); print 'center' print 'list of views:',qt.views() # list all views we have print "CONGRATULATIONS! You passed the OpenGL test without crash or freeze :-)" trunk-2017.01a/scripts/linkdeps.py000066400000000000000000000057161304022710500170450ustar00rootroot00000000000000#!/usr/bin/python from sys import * import os,re from string import * srcRoot='./' from os.path import sep import shutil def getModule(dir): m=re.match('^.*?'+sep+'((extra|core)|((gui|lib|pkg)'+sep+'.*?))(|'+sep+'.*)$',dir) assert(m) return m.group(1).replace(sep,'-') def walkSourceFiles(): ret=[] for root, dirs, files in os.walk(srcRoot,topdown=True): for d in ('.svn','QGLViewer','triangulation','sqlite3x','miniWm3','py'): try: dirs.remove(d) except ValueError: pass for f in files: if f in ('stdafx.cpp',): continue if f.split('.')[-1] in ('cpp','cc','C'): ret+=((root,f),) return ret sources=walkSourceFiles() plugins=set() for dir,f in sources: for l in open(dir+sep+f): if 'YADE_PLUGIN' in l and getModule(dir) not in ('core',): plugins.add(f.split('.')[0]) maxIncludeLevel=4 def grepCpp(path,f,level=0): fullF=path+sep+f; baseName=f.split('.')[0] linkDeps,featureDeps=set(),set() if level==maxIncludeLevel: return set(),set() #print path,f for l in open(fullF): m=re.match('^#include<([^/]*)/(.*)>.*$',l) if m: incMod=m.group(1); incHead=m.group(2); baseName=incHead.split('.')[0]; assert(len(incHead.split('.'))==2) if incMod=='core': continue #if baseName not in plugins: print f,incHead linkDeps.add(incHead.split('.')[0]) continue m=re.match('^#include\s*"([^/]*)".*$',l) if m: inc=m.group(1); incBaseName=m.group(1).split('.')[0] if not os.path.exists(path+sep+m.group(1)): print "WARNING: file %s included from %s doesn't exist"%(m.group(1),fullF) pass else: if m.group(1).split('.')[0] not in plugins or incBaseName==baseName: linkDeps.update(grepCpp(path,m.group(1),level=level+1)[0]) continue m=re.match('^YADE_REQUIRE_FEATURE\((.*)\).*',l) if m: featureDeps.add(m.group(1)) return linkDeps,featureDeps pluginLinks,pluginFeats,pluginSrcs={},{},{} for dir,f in sources: if getModule(dir) in ('core',): continue if not getModule(dir).startswith('pkg'): continue link,feats=grepCpp(dir,f) plugin='.'.join(f.split('.')[:-1]) pluginLinks[plugin],pluginFeats[plugin],pluginSrcs[plugin]=link,feats,dir+'/'+f import shelve cache=shelve.open('linkdeps.cache') cache['pluginLinks'],cache['pluginFeats'],cache['pluginSrcs']=pluginLinks,pluginFeats,pluginSrcs pluginLinks,pluginFeats,pluginSrcs=cache['pluginLinks'],cache['pluginFeats'],cache['pluginSrcs'] pluginObjs={} for p in pluginLinks.keys(): pluginObjs[p]='packages' cache.close() def getPluginLibs(plugin): libs=set() myObj=pluginObjs[plugin] for lib in pluginLinks[plugin]: if pluginObjs[plugin]==myObj: continue try: libs.add(pluginObjs[lib]) except KeyError: print 'WARNING: plugin %s, missing lib %s'%(plugin,lib) return libs allLibs=set(); for p in pluginSrcs.keys(): allLibs.update(getPluginLibs(p)) print "\tenv.SharedLibrary('packages',Split('"+' '.join(pluginSrcs.values())+"'),LIBS=env['LIBS']+Split('"+' '.join(allLibs)+"'),CXXFLAGS=env['CXXFLAGS']+['--combine'])" #print plugin,' '.join(feats) #print f ,' '.join(feats) trunk-2017.01a/scripts/pbuilder-test-distributions.sh000066400000000000000000000015661304022710500227000ustar00rootroot00000000000000# # grab latest trunk, try building packages for various distributions # see http://yade.wikia.com/wiki/DebianPackages for configuration of the pbuilder environment # set -x TMP=/tmp/pbuild-yade-$$ mkdir $TMP cd $TMP bzr checkout --lightweight lp:yade trunk cd trunk; scripts/debian-prep jaunty; cd .. # distro not important here dpkg-source -b -I trunk DSC=yade-`cat trunk/VERSION`_1.dsc for DIST in lenny squeeze hardy jaunty karmic; do echo ============================================= TESTING $DIST =================================== echo =============================================================================================== BASETGZ=/var/cache/pbuilder/$DIST.tgz sudo pbuilder --build --basetgz $BASETGZ --debbuildopts "-j5 -Zlzma" $DSC || FAILED="$FAILED $DIST" done rm -rf $TMP if [ '$FAILED' ]; then echo "***************** Build failed for $FAILED"; exit 1; fi trunk-2017.01a/scripts/ppa/000077500000000000000000000000001304022710500154315ustar00rootroot00000000000000trunk-2017.01a/scripts/ppa/.dput.cf000066400000000000000000000002521304022710500167740ustar00rootroot00000000000000[mini] fqdn = localhost method = local incoming = /home/USER/M/Temp/archive/mini-dinstall/incoming allow_unsigned_uploads = 1 post_upload_command = mini-dinstall --batch trunk-2017.01a/scripts/ppa/.mini-dinstall.conf000066400000000000000000000006011304022710500211170ustar00rootroot00000000000000[DEFAULT] architectures = all, i386, amd64 incoming_permissions = 0750 archivedir = /home/USER/archive/ mail_on_success = 0 dynamic_reindex = 1 archive_style = flat generate_release = 1 trigger_reindex = 1 keep_old = 0 release_description = YADE Debian/Ubuntu daily packages [wheezy] [jessie] [stretch] [unstable] [precise] [saucy] [trusty] [utopic] [vivid] [wily] [xenial] trunk-2017.01a/scripts/ppa/buildppa.py000077500000000000000000000131751304022710500176150ustar00rootroot00000000000000#!/usr/bin/env python3 import argparse, os, git, shutil, sys, time parser = argparse.ArgumentParser(description='Process some integers.') parser.add_argument("-i", help="config file") parser.add_argument("-u","--update", help="update tarballs, if they are exist", action='store_true') parser.add_argument("-j", help="number of processors to build",dest='jobsNumber',default=6, type=int) args = parser.parse_args() configfile = args.i jobsNumber = args.jobsNumber infileconf = open(configfile, 'r') linesconf = infileconf.readlines() gitdebdir = linesconf[1].strip() pbdir = linesconf[4].strip() gitupsdir = linesconf[7].strip() userg = linesconf[10].strip() groupg = linesconf[13].strip() dputg = linesconf[16].strip() keyg = linesconf[19].strip() keypasspath = linesconf[22].strip() keysecrpath = linesconf[25].strip() patharchive = linesconf[28].strip() if not(os.path.isdir(gitdebdir)): raise RuntimeError('Git-debian-directory does not exists') if not(os.path.isdir(gitupsdir)): raise RuntimeError('Git-upstream-directory does not exists') if not(os.path.isdir(pbdir)): print ('Pbuilder-directory does not exists. Creating') os.mkdir(pbdir) repodeb = git.Repo(gitdebdir) repoups = git.Repo(gitupsdir) assert repodeb.bare == False assert repoups.bare == False if (repodeb.is_dirty()): print (repodeb.untracked_files) raise RuntimeError('Git-debian-repo has an uncommitted changes. Exiting.') if (repoups.is_dirty()): print (repoups.untracked_files) raise RuntimeError('Git-upstream-repo has an uncommitted changes. Exiting.') for branch in repodeb.branches: branchstr = str(branch) if (branchstr!='master'): print ("Switching to branch %s"%(branch)) repodeb.git.checkout(branch) infile = open(gitdebdir+"/pbuilder", 'r') lines = infile.readlines() mirror = lines[0].strip() components = lines[1].strip() archs = lines[2].split() keyringuse = lines[3].strip() othermirror = lines[4].strip() infile.close() for a in archs: tarball = "%s/%s_%s.tgz"%(pbdir, branchstr, a.strip()) addAllowuntrusted = "" if (othermirror!="#"): addAllowuntrusted = " --allow-untrusted " if not(os.path.isfile(tarball)): createPbTar = ('sudo pbuilder --create --distribution %s --mirror %s --components "%s" --architecture %s --debootstrapopts "--keyring=%s" --basetgz %s'% (branchstr, mirror, components, a, keyringuse, tarball)) if (othermirror!="#"): createPbTar += ' --othermirror "' + othermirror + '"' addAllowuntrusted = " --allow-untrusted " print (createPbTar) print ("Creating tarball %s"%(tarball)) os.system(createPbTar) else: print ("Tarball %s exists"%(tarball)) if (args.update): print ("Updating %s as requested" %(tarball)) updatePbTar = ('sudo pbuilder --update --basetgz %s'%(tarball)) os.system(updatePbTar) # Creating dir for building builddirup="%s_%s/"%(branchstr, a) builddirdeb="%s/build/"%(builddirup) builddirres="%s/result/"%(builddirup) #shutil.rmtree(builddirdeb,ignore_errors=True) shutil.rmtree(builddirup,ignore_errors=True) shutil.copytree(gitupsdir, builddirdeb ) shutil.rmtree(builddirdeb+".git") # Get package version versiondebian = repoups.git.describe()[0:-8] + repoups.head.commit.hexsha[0:7] + "~" + branchstr # Get package name infilepname = open(gitdebdir+"/changelog", 'r'); sourcePackName = infilepname.readlines()[0].split()[0] print (sourcePackName) os.system('cd %s; apack %s_%s.orig.tar.xz build'%(builddirup,sourcePackName,versiondebian)) shutil.copytree(gitdebdir, builddirdeb+"/debian") os.system('sed -i.bak -e s/VERSION/%s/ -e s/DISTRIBUTION/%s/ %s/debian/changelog'%(versiondebian,branch,builddirdeb)) os.system('sed -i.bak -e s/VERSIONYADEREPLACE/%s/ %s/debian/rules'%(versiondebian,builddirdeb)) os.system('cd %s; dpkg-source -b -I build'%(builddirup)) os.mkdir(builddirres) buildarch = '' if (len(archs)>1 and a != archs[0]): buildarch = '--binary-arch' #Build only arch-packages print ("Building package %s_%s"%(sourcePackName, versiondebian)) buildPackage = ('sudo pbuilder --build --architecture %s --basetgz %s %s --logfile %s/pbuilder.log --debbuildopts "-j%d" --buildresult %s %s %s/*.dsc'% (a, tarball, addAllowuntrusted, builddirup, jobsNumber, builddirres, buildarch, builddirup)) print (buildPackage) os.system(buildPackage) os.system('sudo chown %s:%s %s * -R'%(userg, groupg, builddirup)) os.system('sudo chown %s:%s %s * -R'%(userg, groupg, gitdebdir)) os.system('sudo chown %s:%s %s * -R'%(userg, groupg, gitupsdir)) os.system('cd %s ; su %s -c \'dput %s *.changes\''%(builddirres, userg, dputg)) for branch in repodeb.branches: branchstr = str(branch) if (branchstr!='master'): os.system('rm -rf %s/%s/Release.gpg ; su %s -c \'gpg --no-tty --digest-algo SHA512 --batch --default-key "%s" --detach-sign --passphrase-fd=0 --passphrase-file=%s -o %s/%s/Release.gpg %s/%s/Release\''%(patharchive, branch, userg, keyg, keypasspath, patharchive, branch, patharchive, branch)) trunk-2017.01a/scripts/ppa/ppa.config000066400000000000000000000007321304022710500174020ustar00rootroot00000000000000# git debian-directory /home/USER/dem/yade/yadedaily/ # directory, where will be created pbuilder tarballs /home/USER/dem/yade/ppa/pbuilder_new # git upstream-directrory /home/USER/dem/yade/trunk # user USER # group USER # name of dput ppa mini # Key to sign packages AA915EEB # Path to passphrase key /home/USER/dem/yade/ppa/gpg/pwdonly # Path to key secret part /home/USER/dem/yade/ppa/gpg/yadedev_sec.gpg # Path to archive (deb-repo) /home/USER/M/Temp/archive trunk-2017.01a/scripts/py2wiki.py000066400000000000000000000047351304022710500166320ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 # # 2008 © Václav Šmilauer """ Import commented python source, format it for yade.wikia.com by interspersing and literal text in comments. If given a second files (which is a c++ file), the comments will be taken from the python source, but the code from the c++ file. There are special marks for comments in python: "##" for empty line or "## some text" for non-empty line (the first space is stripped) Special marks for c++ comments are //@, but their contents is flushed; they serve merely to synchronize with python comments. Adjacent comment lines and adjacent code lines will be merged. Leading tabs in the code are replaced by unicode non-breakable spaces ( would otherwise eat leading spaces of the first line) Usage 1: generate simple-scene.py formatted for wiki ./py2wiki simple-scene.py Usasge 2: generate SimpleScene.cpp formatted for wiki with comments from simple-scene.py ./py2wiki simple-scene.py ../extra/SimpleScene.cpp """ import sys,re class Text: def __init__(self,txt): self.text=[txt] class Code(Text): pass class Comment(Text): pass pg=[] commentPatterns=(r'\s*##($|\s(.*)$)',r'\s*//@((.*))$') codeLangs=('python','cpp') assert(len(sys.argv)<=3) for i in range(0,len(sys.argv)-1): pg.append([Comment('')]) sys.stderr.write(str(i)+': '+sys.argv[i+1]+'\n') for l in open(sys.argv[i+1]): l=l[:-1] m=re.match(commentPatterns[i],l) if m: ll=Comment(m.group(1)[1:] if (len(m.group(1))>0 and m.group(1)[0]==' ') else m.group(1)) else: ll=Code(l) if pg[i][-1].__class__==ll.__class__: pg[i][-1].text.append(ll.text[0]) else: pg[i].append(ll) # replace tabs by 8 _nonbreakable_ spaces (\xc2 in utf-8) in code # strip leading/trailing blank lines for p in pg: for l in p: if l.__class__==Code('').__class__: l.text=[ll.replace('\t',8*' ') for ll in l.text] while len(l.text)>0 and l.text[-1]=='': l.text=l.text[:-1] while len(l.text)>0 and l.text[0]=='': l.text=l.text[1:] table=False showCode=len(pg)-1 for i in range(len(pg[0])): ll=pg[0][i] if ll.__class__==Comment('').__class__: for l in ll.text: print l if ll.__class__==Code('').__class__: if table: print '' for j in (range(len(pg)) if table else [showCode]): print '%s'%('' if table else '') if table: print '
    ' if table else '',codeLangs[j]) #if pg[j][i].text[0][0]==' ': print ' ', for l in pg[j][i].text: print l print '%s'%('
    ' trunk-2017.01a/scripts/rename-class.py000066400000000000000000000037251304022710500176040ustar00rootroot00000000000000#!/usr/bin/python import os,re,sys,os.path if not os.path.exists('SConstruct'): raise 'Must be run from the top-level source directory' oldClass,newClass=sys.argv[1],sys.argv[2] replCnt,moveCnt,moveDirCnt=0,0,0 for root, dirs, files in os.walk('.'): for name in files: if os.path.isdir(root+'/'+name): continue if not name.endswith('pp') and name!='SConscript': continue modified=False; new=[]; fullName=root+'/'+name if fullName.startswith('./lib/') or fullName.startswith('./extra'): continue for l in open(fullName): nl,cnt=re.subn(r'\b'+oldClass+r'\b',newClass,l) if cnt>0: new.append(nl); modified=True; replCnt+=1 else: new.append(l) # write back the file if it was modified if modified: print 'Updated: ',root+'/'+name f=open(root+'/'+name,'w') for l in new: f.write(l) f.close() # try to replace the class within the filename, move using bzr if it has changed newName,cnt=re.subn(r'\b'+oldClass+r'\b',newClass,name) if cnt>0: newFullName=root+'/'+newName os.system('bzr mv '+fullName+' '+newFullName) moveCnt+=1 # walk directories and change them with bzr if they match exactly (rarely useful) for root, dirs, files in os.walk('.'): for d in dirs: if d==oldClass: os.system('bzr mv %s/%s %s/%s'%(root,oldClass,root,newClass)) moveDirCnt+=1 print "Replaced %d occurences, moved %d files and %d directories"%(replCnt,moveCnt,moveDirCnt) print "Update python scripts (if wanted) by running: perl -pi -e 's/\\b%s\\b/%s/g' `ls **/*.py **/*.rst |grep -v py/system.py`"%(oldClass,newClass) import time,pwd,socket # update python deprecation records if replCnt+moveCnt+moveDirCnt==0: print "No replaces, not updating py/system.py deprecated names map." if True: new=[] for l in open('py/system.py'): if 'END_RENAMED_CLASSES_LIST' in l: new+="\t'%s':'%s', # %s, %s@%s\n"%(oldClass,newClass,time.asctime(),pwd.getpwuid(os.getuid())[0],socket.gethostname()) new+=l f=open('py/system.py','w') for l in new: f.write(l) f.close() trunk-2017.01a/scripts/update_names.sh000077500000000000000000000054141304022710500176610ustar00rootroot00000000000000#!/bin/sh # The script modifies authors names not to get duplicated names # Modifies the git directory! git filter-branch --commit-filter ' if [ "$GIT_AUTHOR_EMAIL" = "gladk@debian.org" ]; then GIT_AUTHOR_EMAIL="gladky.anton@gmail.com"; git commit-tree "$@"; elif [ "$GIT_AUTHOR_EMAIL" = "bruno.chareyre@grenoble-inp.fr" ] then GIT_AUTHOR_EMAIL="bruno.chareyre@hmg.inpg.fr"; git commit-tree "$@"; elif [ "$GIT_AUTHOR_EMAIL" = "christian@localhost.localdomain" ] then GIT_AUTHOR_NAME="Christian Jakob"; GIT_AUTHOR_EMAIL="jakob@ifgt.tu-freiberg.de"; git commit-tree "$@"; elif [ "$GIT_AUTHOR_EMAIL" = "donia.marzougui@3sr-grenoble.fr" ] || [ "$GIT_AUTHOR_NAME" = "dmarzougui" ] || [ "$GIT_AUTHOR_NAME" = "Donia" ] || [ "$GIT_AUTHOR_EMAIL" = "marzougui.donia@hotmail.fr" ] then GIT_AUTHOR_NAME="Donia Marzougui"; GIT_AUTHOR_EMAIL="donia.marzougui@hmg.inpg.fr"; git commit-tree "$@"; elif [ "$GIT_AUTHOR_NAME" = "Francois" ] ||[ "$GIT_AUTHOR_NAME" = "françois" ] || [ "$GIT_AUTHOR_NAME" = "Francois Kneib" ] || [ "$GIT_AUTHOR_NAME" = "François Kneib" ] then GIT_AUTHOR_NAME="Francois Kneib"; GIT_AUTHOR_EMAIL="francois.kneib@gmail.com"; git commit-tree "$@"; elif [ "$GIT_AUTHOR_NAME" = "Jan Stransky" ] ||[ "$GIT_AUTHOR_NAME" = "Jan Stránský" ] || [ "$GIT_AUTHOR_NAME" = "Jan Stransky" ] || [ "$GIT_AUTHOR_NAME" = "Jan Stránský" ] then GIT_AUTHOR_NAME="Jan Stransky"; GIT_AUTHOR_EMAIL="jan.stransky@fsv.cvut.cz"; git commit-tree "$@"; elif [ "$GIT_AUTHOR_NAME" = "Jerome Duriez" ] then GIT_AUTHOR_NAME="Jerome Duriez"; GIT_AUTHOR_EMAIL="duriez@geo.hmg.inpg.fr"; git commit-tree "$@"; elif [ "$GIT_AUTHOR_NAME" = "Luc Scholtes" ] || [ "$GIT_AUTHOR_NAME" = "scholtes" ] then GIT_AUTHOR_NAME="Luc Scholtes"; GIT_AUTHOR_EMAIL="lscholtes63@gmail.com"; git commit-tree "$@"; elif [ "$GIT_AUTHOR_NAME" = "Luc Sibille" ] then GIT_AUTHOR_NAME="Luc Sibille"; GIT_AUTHOR_EMAIL="luc.sibille@3sr-grenoble.fr"; git commit-tree "$@"; elif [ "$GIT_AUTHOR_NAME" = "Raphael Maurin" ] then GIT_AUTHOR_NAME="Raphaël Maurin"; GIT_AUTHOR_EMAIL="raphael.maurin@irstea.fr"; git commit-tree "$@"; elif [ "$GIT_AUTHOR_NAME" = "Raphael Maurin" ] then GIT_AUTHOR_NAME="Raphaël Maurin"; GIT_AUTHOR_EMAIL="raphael.maurin@irstea.fr"; git commit-tree "$@"; elif [ "$GIT_AUTHOR_NAME" = "Kubeu" ] then GIT_AUTHOR_NAME="Alexander Eulitz"; GIT_AUTHOR_EMAIL="alexander.eulitz@iwf.tu-berlin.de"; git commit-tree "$@"; else git commit-tree "$@"; fi' HEAD

    Yade is located at www.yade-dem.org, which contains this documentation and wiki. Development is kindly hosted on launchpad and GitHub ; they are used for source code, bug tracking and source downloads and more.

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The tunnel is difference between an axis-aligned box and cylinder, or which axis is going through the bottom wall (-z) of the box. The tunnel hole is oriented along +y, the face is in the xz plane. The first you run this scipt, a few minutes is neede to generate the packing. It is saved in /tmp/triaxPackCache.sqlite and at next time it will be only loaded (fast). """ # set some geometry parameters: domain box size, tunnel radius, radius of particles boxSize=Vector3(5,8,5) tunnelRad=2 rSphere=.1 # construct spatial predicate as difference of box and cylinder: # (see examples/test/pack-predicates.py for details) # # https://yade-dem.org/doc/yade.pack.html?highlight=inalignedbox#yade._packPredicates.inAlignedBox # https://yade-dem.org/doc/yade.pack.html?highlight=incylinder#yade._packPredicates.inCylinder pred=pack.inAlignedBox((-.5*boxSize[0],-.5*boxSize[1],0),(.5*boxSize[0],.5*boxSize[1],boxSize[2])) - pack.inCylinder((-.5*boxSize[0],0,0),(.5*boxSize[0],0,0),tunnelRad) # Use the predicate to generate sphere packing inside # # https://yade-dem.org/doc/yade.pack.html?highlight=randomdensepack#yade.pack.randomDensePack sp=SpherePack() sp=pack.randomDensePack(pred,radius=rSphere,rRelFuzz=.3,memoizeDb='/tmp/triaxPackCache.sqlite',spheresInCell=3000,returnSpherePack=True) sp.toSimulation() # to see it from yade import qt qt.Controller() qt.View() trunk-2017.01a/gui/000077500000000000000000000000001304022710500137465ustar00rootroot00000000000000trunk-2017.01a/gui/CMakeLists.txt000066400000000000000000000101511304022710500165040ustar00rootroot00000000000000IF(${ENABLE_GUI}) INCLUDE_DIRECTORIES(${QGLVIEWER_INCLUDE_DIR}) IF(USE_QT5) SET(CMAKE_AUTOMOC ON) SET(_GLViewer_SOURCE_FILES qt5/GLViewer.cpp;qt5/_GLViewer.cpp;qt5/OpenGLManager.cpp;qt5/GLViewerDisplay.cpp;qt5/GLViewerMouse.cpp) ADD_LIBRARY(_GLViewer SHARED ${_GLViewer_SOURCE_FILES}) SET_TARGET_PROPERTIES(_GLViewer PROPERTIES PREFIX "") TARGET_LINK_LIBRARIES(_GLViewer Qt5::Widgets Qt5::Xml Qt5::OpenGL ${GLUT_LIBRARY} ${OPENGL_LIBRARY} ${QGLVIEWER_LIBRARIES} ${Boost_LIBRARIES} ${PYTHON_LIBRARIES}) IF(GL2PS_FOUND AND ENABLE_GL2PS) TARGET_LINK_LIBRARIES(_GLViewer ${GL2PS_LIBRARIES}) ENDIF(GL2PS_FOUND AND ENABLE_GL2PS) INSTALL(TARGETS _GLViewer DESTINATION ${YADE_PY_PATH}/yade/qt) FILE(GLOB filesPYQT "${CMAKE_CURRENT_SOURCE_DIR}/qt5/*.py") INSTALL(FILES ${filesPYQT} DESTINATION ${YADE_PY_PATH}/yade/qt) EXECUTE_PROCESS( COMMAND "pyrcc5" "-o" "${CMAKE_BINARY_DIR}/img_rc.py" "img.qrc" WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/qt5 RESULT_VARIABLE rv ) EXECUTE_PROCESS( COMMAND "pyuic5" "-o" "${CMAKE_BINARY_DIR}/ui_controller.py" "controller.ui" WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/qt5 RESULT_VARIABLE rv ) INSTALL(FILES ${CMAKE_BINARY_DIR}/img_rc.py ${CMAKE_BINARY_DIR}/ui_controller.py DESTINATION ${YADE_PY_PATH}/yade/qt) TARGET_LINK_LIBRARIES(_GLViewer Qt5::Widgets Qt5::Xml Qt5::OpenGL ${GLUT_LIBRARY} ${OPENGL_LIBRARY} ${QGLVIEWER_LIBRARIES} ${Boost_LIBRARIES} ${PYTHON_LIBRARIES}) IF(GL2PS_FOUND AND ENABLE_GL2PS) TARGET_LINK_LIBRARIES(_GLViewer ${GL2PS_LIBRARIES}) ENDIF(GL2PS_FOUND AND ENABLE_GL2PS) INSTALL(TARGETS _GLViewer DESTINATION ${YADE_PY_PATH}/yade/qt) FILE(GLOB filesPYQT "${CMAKE_CURRENT_SOURCE_DIR}/qt5/*.py") INSTALL(FILES ${filesPYQT} DESTINATION ${YADE_PY_PATH}/yade/qt) EXECUTE_PROCESS( COMMAND "pyrcc5" "-o" "${CMAKE_BINARY_DIR}/img_rc.py" "img.qrc" WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/qt5 RESULT_VARIABLE rv ) EXECUTE_PROCESS( COMMAND "pyuic5" "-o" "${CMAKE_BINARY_DIR}/ui_controller.py" "controller.ui" WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/qt5 RESULT_VARIABLE rv ) INSTALL(FILES ${CMAKE_BINARY_DIR}/img_rc.py ${CMAKE_BINARY_DIR}/ui_controller.py DESTINATION ${YADE_PY_PATH}/yade/qt) ELSE(USE_QT5) INCLUDE(${QT_USE_FILE}) SET(_GLViewer_MOC_HEADERS qt4/GLViewer.hpp;qt4/OpenGLManager.hpp) SET(_GLViewer_SOURCE_FILES qt4/GLViewer.cpp;qt4/_GLViewer.cpp;qt4/OpenGLManager.cpp;qt4/GLViewerDisplay.cpp;qt4/GLViewerMouse.cpp) QT4_WRAP_CPP(_GLViewer_MOC_OUTFILES ${_GLViewer_MOC_HEADERS}) ADD_LIBRARY(_GLViewer SHARED ${_GLViewer_SOURCE_FILES} ${_GLViewer_MOC_OUTFILES}) SET_TARGET_PROPERTIES(_GLViewer PROPERTIES PREFIX "") TARGET_LINK_LIBRARIES(_GLViewer ${GLUT_LIBRARY} ${OPENGL_LIBRARY} ${QT_LIBRARIES} ${QGLVIEWER_LIBRARIES} ${Boost_LIBRARIES} ${PYTHON_LIBRARIES}) IF(GL2PS_FOUND AND ENABLE_GL2PS) TARGET_LINK_LIBRARIES(_GLViewer ${GL2PS_LIBRARIES}) ENDIF(GL2PS_FOUND AND ENABLE_GL2PS) INSTALL(TARGETS _GLViewer DESTINATION ${YADE_PY_PATH}/yade/qt) FILE(GLOB filesPYQT "${CMAKE_CURRENT_SOURCE_DIR}/qt4/*.py") INSTALL(FILES ${filesPYQT} DESTINATION ${YADE_PY_PATH}/yade/qt) EXECUTE_PROCESS( COMMAND "pyrcc4" "-o" "${CMAKE_BINARY_DIR}/img_rc.py" "img.qrc" WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/qt4 RESULT_VARIABLE rv ) EXECUTE_PROCESS( COMMAND "pyuic4" "-o" "${CMAKE_BINARY_DIR}/ui_controller.py" "controller.ui" WORKING_DIRECTORY ${CMAKE_CURRENT_SOURCE_DIR}/qt4 RESULT_VARIABLE rv ) INSTALL(FILES ${CMAKE_BINARY_DIR}/img_rc.py ${CMAKE_BINARY_DIR}/ui_controller.py DESTINATION ${YADE_PY_PATH}/yade/qt) ENDIF(USE_QT5) ENDIF(${ENABLE_GUI}) trunk-2017.01a/gui/qt4/000077500000000000000000000000001304022710500144565ustar00rootroot00000000000000trunk-2017.01a/gui/qt4/GLViewer.cpp000066400000000000000000000556471304022710500166670ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2005 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include"GLViewer.hpp" #include"OpenGLManager.hpp" #include #include #include #include #include #include #include #include #include #include #include #include #include #ifdef YADE_GL2PS #include #endif static unsigned initBlocked(State::DOF_NONE); CREATE_LOGGER(GLViewer); GLLock::GLLock(GLViewer* _glv): boost::try_mutex::scoped_lock(Omega::instance().renderMutex), glv(_glv){ glv->makeCurrent(); } GLLock::~GLLock(){ glv->doneCurrent(); } #define _W3 setw(3)<emitCloseView(viewId); e->accept(); } GLViewer::GLViewer(int _viewId, const shared_ptr& _renderer, QGLWidget* shareWidget): QGLViewer(/*parent*/(QWidget*)NULL,shareWidget), renderer(_renderer), viewId(_viewId) { isMoving=false; drawGrid=0; drawScale=true; timeDispMask=TIME_REAL|TIME_VIRT|TIME_ITER; cut_plane = 0; cut_plane_delta = -2; gridSubdivide = false; resize(550,550); last=-1; if(viewId==0) setWindowTitle("Primary view"); else setWindowTitle(("Secondary view #"+boost::lexical_cast(viewId)).c_str()); show(); mouseMovesCamera(); manipulatedClipPlane=-1; if(manipulatedFrame()==0) setManipulatedFrame(new qglviewer::ManipulatedFrame()); xyPlaneConstraint=shared_ptr(new qglviewer::LocalConstraint()); manipulatedFrame()->setConstraint(NULL); setKeyDescription(Qt::Key_Return,"Run simulation."); setKeyDescription(Qt::Key_A,"Toggle visibility of global axes."); setKeyDescription(Qt::Key_C,"Set scene center so that all bodies are visible; if a body is selected, center around this body."); setKeyDescription(Qt::Key_C & Qt::AltModifier,"Set scene center to median body position (same as space)"); setKeyDescription(Qt::Key_D,"Toggle time display mask"); setKeyDescription(Qt::Key_G,"Toggle grid visibility; g turns on and cycles"); setKeyDescription(Qt::Key_G & Qt::ShiftModifier ,"Hide grid."); setKeyDescription(Qt::Key_M, "Move selected object."); setKeyDescription(Qt::Key_X,"Show the xz [shift: xy] (up-right) plane (clip plane: align normal with +x)"); setKeyDescription(Qt::Key_Y,"Show the yx [shift: yz] (up-right) plane (clip plane: align normal with +y)"); setKeyDescription(Qt::Key_Z,"Show the zy [shift: zx] (up-right) plane (clip plane: align normal with +z)"); setKeyDescription(Qt::Key_Period,"Toggle grid subdivision by 10"); setKeyDescription(Qt::Key_S,"Save QGLViewer state to /tmp/qglviewerState.xml"); setKeyDescription(Qt::Key_T,"Switch orthographic / perspective camera"); setKeyDescription(Qt::Key_O,"Set narrower field of view"); setKeyDescription(Qt::Key_P,"Set wider field of view"); setKeyDescription(Qt::Key_R,"Revolve around scene center"); setKeyDescription(Qt::Key_V,"Save PDF of the current view to /tmp/yade-snapshot-0001.pdf (whichever number is available first). (Must be compiled with the gl2ps feature.)"); setPathKey(-Qt::Key_F1); setPathKey(-Qt::Key_F2); setKeyDescription(Qt::Key_Escape,"Manipulate scene (default)"); setKeyDescription(Qt::Key_F1,"Manipulate clipping plane #1"); setKeyDescription(Qt::Key_F2,"Manipulate clipping plane #2"); setKeyDescription(Qt::Key_F3,"Manipulate clipping plane #3"); setKeyDescription(Qt::Key_1,"Make the manipulated clipping plane parallel with plane #1"); setKeyDescription(Qt::Key_2,"Make the manipulated clipping plane parallel with plane #2"); setKeyDescription(Qt::Key_2,"Make the manipulated clipping plane parallel with plane #3"); setKeyDescription(Qt::Key_1 & Qt::AltModifier,"Add/remove plane #1 to/from the bound group"); setKeyDescription(Qt::Key_2 & Qt::AltModifier,"Add/remove plane #2 to/from the bound group"); setKeyDescription(Qt::Key_3 & Qt::AltModifier,"Add/remove plane #3 to/from the bound group"); setKeyDescription(Qt::Key_0,"Clear the bound group"); setKeyDescription(Qt::Key_7,"Load [Alt: save] view configuration #0"); setKeyDescription(Qt::Key_8,"Load [Alt: save] view configuration #1"); setKeyDescription(Qt::Key_9,"Load [Alt: save] view configuration #2"); setKeyDescription(Qt::Key_Space,"Center scene (same as Alt-C); clip plane: activate/deactivate"); centerScene(); } bool GLViewer::isManipulating(){ return isMoving || manipulatedClipPlane>=0; } void GLViewer::resetManipulation(){ mouseMovesCamera(); setSelectedName(-1); isMoving=false; manipulatedClipPlane=-1; } void GLViewer::startClipPlaneManipulation(int planeNo){ assert(planeNonumClipPlanes); resetManipulation(); mouseMovesManipulatedFrame(xyPlaneConstraint.get()); manipulatedClipPlane=planeNo; const Se3r se3(renderer->clipPlaneSe3[planeNo]); manipulatedFrame()->setPositionAndOrientation(qglviewer::Vec(se3.position[0],se3.position[1],se3.position[2]),qglviewer::Quaternion(se3.orientation.x(),se3.orientation.y(),se3.orientation.z(),se3.orientation.w())); string grp=strBoundGroup(); displayMessage("Manipulating clip plane #"+boost::lexical_cast(planeNo+1)+(grp.empty()?grp:" (bound planes:"+grp+")")); } string GLViewer::getState(){ QString origStateFileName=stateFileName(); string tmpFile=Omega::instance().tmpFilename(); setStateFileName(QString(tmpFile.c_str())); saveStateToFile(); setStateFileName(origStateFileName); LOG_WARN("State saved to temp file "<>ss; ret+=" "+ss;}; in.close(); boost::filesystem::remove(boost::filesystem::path(tmpFile)); return ret; } void GLViewer::setState(string state){ string tmpFile=Omega::instance().tmpFilename(); std::ofstream out(tmpFile.c_str()); if(!out.good()){ LOG_ERROR("Error opening temp file `"<key()==Qt::Key_A){ toggleAxisIsDrawn(); return; } else if(e->key()==Qt::Key_Escape){ if(!isManipulating()){ setSelectedName(-1); return; } else { resetManipulation(); displayMessage("Manipulating scene."); } } else if(e->key()==Qt::Key_Space){ if(manipulatedClipPlane>=0) {displayMessage("Clip plane #"+boost::lexical_cast(manipulatedClipPlane+1)+(renderer->clipPlaneActive[manipulatedClipPlane]?" de":" ")+"activated"); renderer->clipPlaneActive[manipulatedClipPlane]=!renderer->clipPlaneActive[manipulatedClipPlane]; } else{ centerMedianQuartile(); } } /* function keys */ else if(e->key()==Qt::Key_F1 || e->key()==Qt::Key_F2 || e->key()==Qt::Key_F3 /* || ... */ ){ int n=0; if(e->key()==Qt::Key_F1) n=1; else if(e->key()==Qt::Key_F2) n=2; else if(e->key()==Qt::Key_F3) n=3; assert(n>0); int planeId=n-1; if(planeId>=renderer->numClipPlanes) return; if(planeId!=manipulatedClipPlane) startClipPlaneManipulation(planeId); } /* numbers */ else if(e->key()==Qt::Key_0 && (e->modifiers() & Qt::AltModifier)) { boundClipPlanes.clear(); displayMessage("Cleared bound planes group.");} else if(e->key()==Qt::Key_1 || e->key()==Qt::Key_2 || e->key()==Qt::Key_3 /* || ... */ ){ int n=0; if(e->key()==Qt::Key_1) n=1; else if(e->key()==Qt::Key_2) n=2; else if(e->key()==Qt::Key_3) n=3; assert(n>0); int planeId=n-1; if(planeId>=renderer->numClipPlanes) return; // no such clipping plane if(e->modifiers() & Qt::AltModifier){ if(boundClipPlanes.count(planeId)==0) {boundClipPlanes.insert(planeId); displayMessage("Added plane #"+boost::lexical_cast(planeId+1)+" to the bound group: "+strBoundGroup());} else {boundClipPlanes.erase(planeId); displayMessage("Removed plane #"+boost::lexical_cast(planeId+1)+" from the bound group: "+strBoundGroup());} } else if(manipulatedClipPlane>=0 && manipulatedClipPlane!=planeId) { const Quaternionr& o=renderer->clipPlaneSe3[planeId].orientation; manipulatedFrame()->setOrientation(qglviewer::Quaternion(o.x(),o.y(),o.z(),o.w())); displayMessage("Copied orientation from plane #1"); } } else if(e->key()==Qt::Key_7 || e->key()==Qt::Key_8 || e->key()==Qt::Key_9){ int nn=-1; if(e->key()==Qt::Key_7)nn=0; else if(e->key()==Qt::Key_8)nn=1; else if(e->key()==Qt::Key_9)nn=2; assert(nn>=0); size_t n=(size_t)nn; if(e->modifiers() & Qt::AltModifier) saveDisplayParameters(n); else useDisplayParameters(n); } /* letters alphabetically */ else if(e->key()==Qt::Key_C && (e->modifiers() & Qt::AltModifier)){ displayMessage("Median centering"); centerMedianQuartile(); } else if(e->key()==Qt::Key_C){ // center around selected body if(selectedName() >= 0 && (*(Omega::instance().getScene()->bodies)).exists(selectedName())) setSceneCenter(manipulatedFrame()->position()); // make all bodies visible else centerScene(); } else if(e->key()==Qt::Key_D &&(e->modifiers() & Qt::AltModifier)){ Body::id_t id; if((id=Omega::instance().getScene()->selectedBody)>=0){ const shared_ptr& b=Body::byId(id); b->setDynamic(!b->isDynamic()); LOG_INFO("Body #"<isDynamic()?"":"NOT")<<" dynamic"); } } else if(e->key()==Qt::Key_D) {timeDispMask+=1; if(timeDispMask>(TIME_REAL|TIME_VIRT|TIME_ITER))timeDispMask=0; } else if(e->key()==Qt::Key_G) { if(e->modifiers() & Qt::ShiftModifier){ drawGrid=0; return; } else drawGrid++; if(drawGrid>=8) drawGrid=0; } else if (e->key()==Qt::Key_M && selectedName() >= 0){ if(!(isMoving=!isMoving)){ displayMessage("Moving done."); if (last>=0) {Body::byId(Body::id_t(last))->state->blockedDOFs=initBlocked; last=-1;} mouseMovesCamera();} else{ displayMessage("Moving selected object"); long selection = Omega::instance().getScene()->selectedBody; initBlocked=Body::byId(Body::id_t(selection))->state->blockedDOFs; last=selection; Body::byId(Body::id_t(selection))->state->blockedDOFs=State::DOF_ALL; Quaternionr& q = Body::byId(selection)->state->ori; Vector3r& v = Body::byId(selection)->state->pos; manipulatedFrame()->setPositionAndOrientation(qglviewer::Vec(v[0],v[1],v[2]),qglviewer::Quaternion(q.x(),q.y(),q.z(),q.w())); mouseMovesManipulatedFrame();} } else if (e->key() == Qt::Key_T) camera()->setType(camera()->type()==qglviewer::Camera::ORTHOGRAPHIC ? qglviewer::Camera::PERSPECTIVE : qglviewer::Camera::ORTHOGRAPHIC); else if(e->key()==Qt::Key_O) camera()->setFieldOfView(camera()->fieldOfView()*0.9); else if(e->key()==Qt::Key_P) camera()->setFieldOfView(camera()->fieldOfView()*1.1); else if(e->key()==Qt::Key_R){ // reverse the clipping plane; revolve around scene center if no clipping plane selected if(manipulatedClipPlane>=0 && manipulatedClipPlanenumClipPlanes){ /* here, we must update both manipulatedFrame orientation and renderer->clipPlaneSe3 orientation in the same way */ Quaternionr& ori=renderer->clipPlaneSe3[manipulatedClipPlane].orientation; ori=Quaternionr(AngleAxisr(Mathr::PI,Vector3r(0,1,0)))*ori; manipulatedFrame()->setOrientation(qglviewer::Quaternion(qglviewer::Vec(0,1,0),Mathr::PI)*manipulatedFrame()->orientation()); displayMessage("Plane #"+boost::lexical_cast(manipulatedClipPlane+1)+" reversed."); } else { camera()->setRevolveAroundPoint(sceneCenter()); } } else if(e->key()==Qt::Key_S){ LOG_INFO("Saving QGLViewer state to /tmp/qglviewerState.xml"); setStateFileName("/tmp/qglviewerState.xml"); saveStateToFile(); setStateFileName(QString::null); } else if(e->key()==Qt::Key_L){ LOG_INFO("Loading QGLViewer state from /tmp/qglviewerState.xml"); setStateFileName("/tmp/qglviewerState.xml"); restoreStateFromFile(); setStateFileName(QString::null); } else if(e->key()==Qt::Key_X || e->key()==Qt::Key_Y || e->key()==Qt::Key_Z){ int axisIdx=(e->key()==Qt::Key_X?0:(e->key()==Qt::Key_Y?1:2)); if(manipulatedClipPlane<0){ qglviewer::Vec up(0,0,0), vDir(0,0,0); bool alt=(e->modifiers() && Qt::ShiftModifier); up[axisIdx]=1; vDir[(axisIdx+(alt?2:1))%3]=alt?1:-1; camera()->setViewDirection(vDir); camera()->setUpVector(up); centerMedianQuartile(); } else{ // align clipping normal plane with world axis // x: (0,1,0),pi/2; y: (0,0,1),pi/2; z: (1,0,0),0 qglviewer::Vec axis(0,0,0); axis[(axisIdx+1)%3]=1; Real angle=axisIdx==2?0:Mathr::PI/2; manipulatedFrame()->setOrientation(qglviewer::Quaternion(axis,angle)); } } else if(e->key()==Qt::Key_Period) gridSubdivide = !gridSubdivide; else if(e->key()==Qt::Key_Return){ if (Omega::instance().isRunning()) Omega::instance().pause(); else Omega::instance().run(); LOG_INFO("Running..."); } #ifdef YADE_GL2PS else if(e->key()==Qt::Key_V){ for(int i=0; ;i++){ std::ostringstream fss; fss<<"/tmp/yade-snapshot-"<key()==Qt::Key_Plus ){ cut_plane = std::min(1.0, cut_plane + std::pow(10.0,(double)cut_plane_delta)); static_cast(camera())->setCuttingDistance(cut_plane); displayMessage("Cut plane: "+boost::lexical_cast(cut_plane)); }else if( e->key()==Qt::Key_Minus ){ cut_plane = std::max(0.0, cut_plane - std::pow(10.0,(double)cut_plane_delta)); static_cast(camera())->setCuttingDistance(cut_plane); displayMessage("Cut plane: "+boost::lexical_cast(cut_plane)); }else if( e->key()==Qt::Key_Slash ){ cut_plane_delta -= 1; displayMessage("Cut plane increment: 1e"+(cut_plane_delta>0?std::string("+"):std::string(""))+boost::lexical_cast(cut_plane_delta)); }else if( e->key()==Qt::Key_Asterisk ){ cut_plane_delta = std::min(1+cut_plane_delta,-1); displayMessage("Cut plane increment: 1e"+(cut_plane_delta>0?std::string("+"):std::string(""))+boost::lexical_cast(cut_plane_delta)); } #endif else if(e->key()!=Qt::Key_Escape && e->key()!=Qt::Key_Space) QGLViewer::keyPressEvent(e); updateGL(); } /* Center the scene such that periodic cell is contained in the view */ void GLViewer::centerPeriodic(){ Scene* scene=Omega::instance().getScene().get(); assert(scene->isPeriodic); Vector3r center=.5*scene->cell->getSize(); Vector3r halfSize=.5*scene->cell->getSize(); float radius=std::max(halfSize[0],std::max(halfSize[1],halfSize[2])); LOG_DEBUG("Periodic scene center="<isPeriodic){ centerPeriodic(); return; } long nBodies=scene->bodies->size(); if(nBodies<4) { LOG_DEBUG("Less than 4 bodies, median makes no sense; calling centerScene() instead."); return centerScene(); } std::vector coords[3]; for(int i=0;i<3;i++)coords[i].reserve(nBodies); FOREACH(shared_ptr b, *scene->bodies){ if(!b) continue; for(int i=0; i<3; i++) coords[i].push_back(b->state->pos[i]); } Vector3r median,interQuart; for(int i=0;i<3;i++){ sort(coords[i].begin(),coords[i].end()); median[i]=*(coords[i].begin()+nBodies/2); interQuart[i]=*(coords[i].begin()+3*nBodies/4)-*(coords[i].begin()+nBodies/4); } LOG_DEBUG("Median position is"<isPeriodic){ centerPeriodic(); return; } LOG_INFO("Select with shift, press 'm' to move."); Vector3r min,max; if(not(rb->bound)){ rb->updateBound();} min=rb->bound->min; max=rb->bound->max; bool hasNan=(std::isnan(min[0])||std::isnan(min[1])||std::isnan(min[2])||std::isnan(max[0])||std::isnan(max[1])||std::isnan(max[2])); Real minDim=std::min(max[0]-min[0],std::min(max[1]-min[1],max[2]-min[2])); if(minDim<=0 || hasNan){ // Aabb is not yet calculated... LOG_DEBUG("scene's bound not yet calculated or has zero or nan dimension(s), attempt get that from bodies' positions."); Real inf=std::numeric_limits::infinity(); min=Vector3r(inf,inf,inf); max=Vector3r(-inf,-inf,-inf); FOREACH(const shared_ptr& b, *rb->bodies){ if(!b) continue; max=max.cwiseMax(b->state->pos); min=min.cwiseMin(b->state->pos); } if(std::isinf(min[0])||std::isinf(min[1])||std::isinf(min[2])||std::isinf(max[0])||std::isinf(max[1])||std::isinf(max[2])){ LOG_DEBUG("No min/max computed from bodies either, setting cube (-1,-1,-1)×(1,1,1)"); min=-Vector3r::Ones(); max=Vector3r::Ones(); } } else {LOG_DEBUG("Using scene's Aabb");} LOG_DEBUG("Got scene box min="<=0) { Body::byId(Body::id_t(last))->state->blockedDOFs=initBlocked; last=-1; Omega::instance().getScene()->selectedBody = -1;} if(isMoving){ displayMessage("Moving finished"); mouseMovesCamera(); isMoving=false; Omega::instance().getScene()->selectedBody = -1; } return; } if(selection>=0 && (*(Omega::instance().getScene()->bodies)).exists(selection)){ resetManipulation(); if (last>=0) {Body::byId(Body::id_t(last))->state->blockedDOFs=initBlocked; last=-1;} if(Body::byId(Body::id_t(selection))->isClumpMember()){ // select clump (invisible) instead of its member LOG_DEBUG("Clump member #"<clumpId; } setSelectedName(selection); LOG_DEBUG("New selection "<(selection)+(Body::byId(selection)->isClump()?" (clump)":"")); Omega::instance().getScene()->selectedBody = selection; PyGILState_STATE gstate; gstate = PyGILState_Ensure(); boost::python::object main=boost::python::import("__main__"); boost::python::object global=main.attr("__dict__"); // the try/catch block must be properly nested inside PyGILState_Ensure and PyGILState_Release try{ boost::python::eval(string("onBodySelect("+boost::lexical_cast(selection)+")").c_str(),global,global); } catch (boost::python::error_already_set const &) { LOG_DEBUG("unable to call onBodySelect. Not defined?"); } PyGILState_Release(gstate); // see https://svn.boost.org/trac/boost/ticket/2781 for exception handling } } // maybe new object will be selected. // if so, then set isDynamic of previous selection, to old value void GLViewer::endSelection(const QPoint &point){ manipulatedClipPlane=-1; QGLViewer::endSelection(point); } string GLViewer::getRealTimeString(){ ostringstream oss; boost::posix_time::time_duration t=Omega::instance().getRealTime_duration(); unsigned d=t.hours()/24,h=t.hours()%24,m=t.minutes(),s=t.seconds(); oss<<"clock "; if(d>0) oss<0) oss<<_W2<=0x020603 qreal YadeCamera::zNear() const #else float YadeCamera::zNear() const #endif { float z = distanceToSceneCenter() - zClippingCoefficient()*sceneRadius()*(1.f-2*cuttingDistance); // Prevents negative or null zNear values. const float zMin = zNearCoefficient() * zClippingCoefficient() * sceneRadius(); if (z < zMin) /* switch (type()) { case Camera::PERSPECTIVE :*/ z = zMin; /*break; case Camera::ORTHOGRAPHIC : z = 0.0; break; }*/ return z; } trunk-2017.01a/gui/qt4/GLViewer.hpp000066400000000000000000000124141304022710500166550ustar00rootroot00000000000000// Copyright (C) 2004 by Olivier Galizzi, Janek Kozicki * // © 2008 Václav Šmilauer #pragma once #ifndef Q_MOC_RUN #include #include #include #include #endif #include #include #include using std::setw; using std::setfill; using std::setprecision; /*! Class handling user interaction with the openGL rendering of simulation. * * Clipping planes: * ================ * * Clipping plane is manipulated after hitting F1, F2, .... To end the manipulation, press Escape. * * Keystrokes during clipping plane manipulation: * * space activates/deactives the clipping plane * * x,y,z aligns the plane with yz, xz, xy planes * * left-double-click aligns the plane with world coordinates system (canonical planes + 45˚ interpositions) * * 1,2,... will align the current plane with #1, #2, ... (same orientation) * * r reverses the plane (normal*=-1)a * * Keystrokes that work regardless of whether a clipping plane is being manipulated: * * Alt-1,Alt-2,... adds/removes the respective plane to bound group: * mutual positions+orientations of planes in the group are maintained when one of those planes is manipulated * * Clip plane number is 3; change YADE_RENDERER_NUM_CLIP_PLANE, complete switches "|| ..." in keyPressEvent * and recompile to have more. */ class GLViewer : public QGLViewer { Q_OBJECT friend class QGLThread; protected: shared_ptr renderer; private : bool isMoving; bool wasDynamic; float cut_plane; int cut_plane_delta; bool gridSubdivide; long last; int manipulatedClipPlane; set boundClipPlanes; shared_ptr xyPlaneConstraint; string strBoundGroup(){string ret;FOREACH(int i, boundClipPlanes) ret+=" "+boost::lexical_cast(i+1);return ret;} boost::posix_time::ptime last_user_event; public: //virtual void updateGL(void); const int viewId; void centerMedianQuartile(); int drawGrid; bool drawScale; int timeDispMask; enum{TIME_REAL=1,TIME_VIRT=2,TIME_ITER=4}; GLViewer(int viewId, const shared_ptr& renderer, QGLWidget* shareWidget=0); virtual ~GLViewer(); #if 0 virtual void paintGL(); #endif virtual void draw(); virtual void drawWithNames(); void displayMessage(const std::string& s){ QGLViewer::displayMessage(QString(s.c_str()));} void centerScene(); void centerPeriodic(); void mouseMovesCamera(); void mouseMovesManipulatedFrame(qglviewer::Constraint* c=NULL); void resetManipulation(); bool isManipulating(); void startClipPlaneManipulation(int planeNo); //! get QGLViewer state as string (XML); QGLViewer normally only supports saving state to file. string getState(); //! set QGLViewer state from string (XML); QGLVIewer normally only supports loading state from file. void setState(string); //! Load display parameters (QGLViewer and OpenGLRenderer) from Scene::dispParams[n] and use them void useDisplayParameters(size_t n); //! Save display parameters (QGOViewer and OpenGLRenderer) to Scene::dispParams[n] void saveDisplayParameters(size_t n); //! Get radius of the part of scene that fits the current view float displayedSceneRadius(); //! Get center of the part of scene that fits the current view qglviewer::Vec displayedSceneCenter(); //! Adds our attributes to the QGLViewer state that can be saved QDomElement domElement(const QString& name, QDomDocument& document) const; //! Adds our attributes to the QGLViewer state that can be restored void initFromDOMElement(const QDomElement& element); // if defined, snapshot will be saved to this file right after being drawn and the string will be reset. // this way the caller will be notified of the frame being saved successfully. string nextFrameSnapshotFilename; #ifdef YADE_GL2PS // output stream for gl2ps; initialized as needed FILE* gl2psStream; #endif boost::posix_time::ptime getLastUserEvent(); DECLARE_LOGGER; protected : virtual void keyPressEvent(QKeyEvent *e); virtual void postDraw(); // overridden in the player that doesn't get time from system clock but from the db virtual string getRealTimeString(); virtual void closeEvent(QCloseEvent *e); virtual void postSelection(const QPoint& point); virtual void endSelection(const QPoint &point); virtual void mouseDoubleClickEvent(QMouseEvent *e); virtual void wheelEvent(QWheelEvent* e); virtual void mouseMoveEvent(QMouseEvent *e); virtual void mousePressEvent(QMouseEvent *e); }; /*! Get unconditional lock on a GL view. Use if you need to manipulate GL context in some way. The ctor doesn't return until the lock has been acquired and the lock is released when the GLLock object is desctructed; */ class GLLock: public boost::try_mutex::scoped_lock{ GLViewer* glv; public: GLLock(GLViewer* _glv); ~GLLock(); }; class YadeCamera : public qglviewer::Camera { Q_OBJECT private: float cuttingDistance; public : YadeCamera():cuttingDistance(0){}; #if QGLVIEWER_VERSION>=0x020603 virtual qreal zNear() const; #else virtual float zNear() const; #endif virtual void setCuttingDistance(float s){cuttingDistance=s;}; }; trunk-2017.01a/gui/qt4/GLViewerDisplay.cpp000066400000000000000000000327751304022710500202120ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2005 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include"GLViewer.hpp" #include"OpenGLManager.hpp" #include #include #include #include #include #include #include #include #include #include #include #include #ifdef YADE_GL2PS #include #endif void GLViewer::useDisplayParameters(size_t n){ LOG_DEBUG("Loading display parameters from #"< >& dispParams=Omega::instance().getScene()->dispParams; if(dispParams.size()<=(size_t)n){ throw std::invalid_argument(("Display parameters #"+boost::lexical_cast(n)+" don't exist (number of entries "+boost::lexical_cast(dispParams.size())+")").c_str());; return;} const shared_ptr& dp=dispParams[n]; string val; if(dp->getValue("OpenGLRenderer",val)){ istringstream oglre(val); yade::ObjectIO::load(oglre,"renderer",renderer); } else { LOG_WARN("OpenGLRenderer configuration not found in display parameters, skipped.");} if(dp->getValue("GLViewer",val)){ GLViewer::setState(val); displayMessage("Loaded view configuration #"+boost::lexical_cast(n)); } else { LOG_WARN("GLViewer configuration not found in display parameters, skipped."); } } void GLViewer::saveDisplayParameters(size_t n){ LOG_DEBUG("Saving display parameters to #"< >& dispParams=Omega::instance().getScene()->dispParams; if(dispParams.size()<=n){while(dispParams.size()<=n) dispParams.push_back(shared_ptr(new DisplayParameters));} assert(n& dp=dispParams[n]; ostringstream oglre; yade::ObjectIO::save(oglre,"renderer",renderer); dp->setValue("OpenGLRenderer",oglre.str()); dp->setValue("GLViewer",GLViewer::getState()); displayMessage("Saved view configuration ot #"+boost::lexical_cast(n)); } void GLViewer::draw() { #ifdef YADE_GL2PS if(!nextFrameSnapshotFilename.empty() && boost::algorithm::ends_with(nextFrameSnapshotFilename,".pdf")){ gl2psStream=fopen(nextFrameSnapshotFilename.c_str(),"wb"); if(!gl2psStream){ int err=errno; throw runtime_error(string("Error opening file ")+nextFrameSnapshotFilename+": "+strerror(err)); } LOG_DEBUG("Start saving snapshot to "<bodies->size(); int sortAlgo=(nBodies<100 ? GL2PS_BSP_SORT : GL2PS_SIMPLE_SORT); gl2psBeginPage(/*const char *title*/"Some title", /*const char *producer*/ "Yade", /*GLint viewport[4]*/ NULL, /*GLint format*/ GL2PS_PDF, /*GLint sort*/ sortAlgo, /*GLint options*/GL2PS_SIMPLE_LINE_OFFSET|GL2PS_USE_CURRENT_VIEWPORT|GL2PS_TIGHT_BOUNDING_BOX|GL2PS_COMPRESS|GL2PS_OCCLUSION_CULL|GL2PS_NO_BLENDING, /*GLint colormode*/ GL_RGBA, /*GLint colorsize*/0, /*GL2PSrgba *colortable*/NULL, /*GLint nr*/0, /*GLint ng*/0, /*GLint nb*/0, /*GLint buffersize*/4096*4096 /* 16MB */, /*FILE *stream*/ gl2psStream, /*const char *filename*/NULL); } #endif qglviewer::Vec vd=camera()->viewDirection(); renderer->viewDirection=Vector3r(vd[0],vd[1],vd[2]); if(Omega::instance().getScene()){ const shared_ptr& scene=Omega::instance().getScene(); int selection = selectedName(); if(selection!=-1 && (*(Omega::instance().getScene()->bodies)).exists(selection) && isMoving){ static Real lastTimeMoved(0); #if QGLVIEWER_VERSION>=0x020603 qreal v0,v1,v2; manipulatedFrame()->getPosition(v0,v1,v2); #else float v0,v1,v2; manipulatedFrame()->getPosition(v0,v1,v2); #endif if(last == selection) // delay by one redraw, so the body will not jump into 0,0,0 coords { Quaternionr& q = (*(Omega::instance().getScene()->bodies))[selection]->state->ori; Vector3r& v = (*(Omega::instance().getScene()->bodies))[selection]->state->pos; Vector3r& vel = (*(Omega::instance().getScene()->bodies))[selection]->state->vel; Vector3r& angVel = (*(Omega::instance().getScene()->bodies))[selection]->state->angVel; angVel=Vector3r::Zero(); Real dt=(scene->time-lastTimeMoved); lastTimeMoved=scene->time; if (dt!=0) { vel[0]=-(v[0]-v0)/dt; vel[1]=-(v[1]-v1)/dt; vel[2]=-(v[2]-v2)/dt;} else vel[0]=vel[1]=vel[2]=0; //FIXME: should update spin like velocity above, when the body is rotated: double q0,q1,q2,q3; manipulatedFrame()->getOrientation(q0,q1,q2,q3); q.x()=q0;q.y()=q1;q.z()=q2;q.w()=q3; } (*(Omega::instance().getScene()->bodies))[selection]->userForcedDisplacementRedrawHook(); } if(manipulatedClipPlane>=0){ assert(manipulatedClipPlanenumClipPlanes); #if QGLVIEWER_VERSION>=0x020603 qreal v0,v1,v2; manipulatedFrame()->getPosition(v0,v1,v2); #else float v0,v1,v2; manipulatedFrame()->getPosition(v0,v1,v2); #endif double q0,q1,q2,q3; manipulatedFrame()->getOrientation(q0,q1,q2,q3); Se3r newSe3(Vector3r(v0,v1,v2),Quaternionr(q0,q1,q2,q3)); newSe3.orientation.normalize(); const Se3r& oldSe3=renderer->clipPlaneSe3[manipulatedClipPlane]; FOREACH(int planeId, boundClipPlanes){ if(planeId>=renderer->numClipPlanes || !renderer->clipPlaneActive[planeId] || planeId==manipulatedClipPlane) continue; Se3r& boundSe3=renderer->clipPlaneSe3[planeId]; Quaternionr relOrient=oldSe3.orientation.conjugate()*boundSe3.orientation; relOrient.normalize(); Vector3r relPos=oldSe3.orientation.conjugate()*(boundSe3.position-oldSe3.position); boundSe3.position=newSe3.position+newSe3.orientation*relPos; boundSe3.orientation=newSe3.orientation*relOrient; boundSe3.orientation.normalize(); } renderer->clipPlaneSe3[manipulatedClipPlane]=newSe3; } scene->renderer=renderer; renderer->render(scene, selectedName()); } } void GLViewer::drawWithNames(){ qglviewer::Vec vd=camera()->viewDirection(); renderer->viewDirection=Vector3r(vd[0],vd[1],vd[2]); const shared_ptr scene(Omega::instance().getScene()); scene->renderer=renderer; renderer->scene=scene; renderer->renderShape(); } qglviewer::Vec GLViewer::displayedSceneCenter(){ return camera()->unprojectedCoordinatesOf(qglviewer::Vec(width()/2 /* pixels */ ,height()/2 /* pixels */, /*middle between near plane and far plane*/ .5)); } float GLViewer::displayedSceneRadius(){ return (camera()->unprojectedCoordinatesOf(qglviewer::Vec(width()/2,height()/2,.5))-camera()->unprojectedCoordinatesOf(qglviewer::Vec(0,0,.5))).norm(); } void GLViewer::postDraw(){ Real wholeDiameter=QGLViewer::camera()->sceneRadius()*2; renderer->viewInfo.sceneRadius=QGLViewer::camera()->sceneRadius(); qglviewer::Vec c=QGLViewer::camera()->sceneCenter(); renderer->viewInfo.sceneCenter=Vector3r(c[0],c[1],c[2]); Real dispDiameter=min(wholeDiameter,max((Real)displayedSceneRadius()*2,wholeDiameter/1e3)); // limit to avoid drawing 1e5 lines with big zoom level //qglviewer::Vec center=QGLViewer::camera()->sceneCenter(); Real gridStep=pow(10,(floor(log10(dispDiameter)-.7))); Real scaleStep=pow(10,(floor(log10(displayedSceneRadius()*2)-.7))); // unconstrained int nSegments=((int)(wholeDiameter/gridStep))+1; Real realSize=nSegments*gridStep; //LOG_TRACE("nSegments="<projectedCoordinatesOf(center+delta)-camera()->projectedCoordinatesOf(center); for(int xy=0;xy<2;xy++)extremalDxDy[xy]=(axis>0 ? min(extremalDxDy[xy],(int)screenDxDy[axis][xy]) : screenDxDy[axis][xy]); } //LOG_DEBUG("Screen offsets for axes: "<<" x("<=0){ for(int planeId=0; planeIdnumClipPlanes; planeId++){ if(!renderer->clipPlaneActive[planeId] && planeId!=manipulatedClipPlane) continue; glPushMatrix(); const Se3r& se3=renderer->clipPlaneSe3[planeId]; AngleAxisr aa(se3.orientation); glTranslatef(se3.position[0],se3.position[1],se3.position[2]); glRotated(aa.angle()*Mathr::RAD_TO_DEG,aa.axis()[0],aa.axis()[1],aa.axis()[2]); Real cff=1; if(!renderer->clipPlaneActive[planeId]) cff=.4; glColor3f(max((Real)0.,cff*cos(planeId)),max((Real)0.,cff*sin(planeId)),planeId==manipulatedClipPlane); // variable colors QGLViewer::drawGrid(realSize,2*nSegments); drawArrow(wholeDiameter/6); glPopMatrix(); } } Scene* rb=Omega::instance().getScene().get(); #define _W3 setw(3)<time; unsigned min=((unsigned)t/60),sec=(((unsigned)t)%60),msec=((unsigned)(1e3*t))%1000,usec=((unsigned long)(1e6*t))%1000,nsec=((unsigned long)(1e9*t))%1000; if(min>0) oss<<_W2<0) oss<<_W2<0) oss<<_W3<0) oss<<_W3<iter; if(rb->stopAtIter>rb->iter) oss<<" ("<iter)/rb->stopAtIter<<"%)"; QGLViewer::drawText(x,y,oss.str().c_str()); y-=lineHt; } if(drawGrid){ glColor3v(Vector3r(1,1,0)); ostringstream oss; oss<<"grid: "< #include #include #include #include #include #include #include #include #include #include #include #include #ifdef YADE_GL2PS #include #endif void GLViewer::mouseMovesCamera(){ setWheelBinding(Qt::ShiftModifier , FRAME, ZOOM); setWheelBinding(Qt::NoModifier, CAMERA, ZOOM); #if QGLVIEWER_VERSION>=0x020500 setMouseBinding(Qt::ShiftModifier, Qt::RightButton, FRAME, ZOOM); setMouseBinding(Qt::ShiftModifier, Qt::MidButton, FRAME, TRANSLATE); setMouseBinding(Qt::ShiftModifier, Qt::RightButton, FRAME, ROTATE); setMouseBinding(Qt::NoModifier, Qt::MidButton, CAMERA, ZOOM); setMouseBinding(Qt::NoModifier, Qt::LeftButton, CAMERA, ROTATE); setMouseBinding(Qt::NoModifier, Qt::RightButton, CAMERA, TRANSLATE); #else setMouseBinding(Qt::SHIFT + Qt::LeftButton, SELECT); setMouseBinding(Qt::SHIFT + Qt::LeftButton + Qt::RightButton, FRAME, ZOOM); setMouseBinding(Qt::SHIFT + Qt::MidButton, FRAME, TRANSLATE); setMouseBinding(Qt::SHIFT + Qt::RightButton, FRAME, ROTATE); setMouseBinding(Qt::LeftButton + Qt::RightButton, CAMERA, ZOOM); setMouseBinding(Qt::MidButton, CAMERA, ZOOM); setMouseBinding(Qt::LeftButton, CAMERA, ROTATE); setMouseBinding(Qt::RightButton, CAMERA, TRANSLATE); camera()->frame()->setWheelSensitivity(-1.0f); #endif }; void GLViewer::mouseMovesManipulatedFrame(qglviewer::Constraint* c){ setMouseBinding(Qt::LeftButton + Qt::RightButton, FRAME, ZOOM); setMouseBinding(Qt::MidButton, FRAME, ZOOM); setMouseBinding(Qt::LeftButton, FRAME, ROTATE); setMouseBinding(Qt::RightButton, FRAME, TRANSLATE); setWheelBinding(Qt::NoModifier , FRAME, ZOOM); manipulatedFrame()->setConstraint(c); } void GLViewer::mouseMoveEvent(QMouseEvent *e){ last_user_event = boost::posix_time::second_clock::local_time(); QGLViewer::mouseMoveEvent(e); } void GLViewer::mousePressEvent(QMouseEvent *e){ last_user_event = boost::posix_time::second_clock::local_time(); QGLViewer::mousePressEvent(e); } /* Handle double-click event; if clipping plane is manipulated, align it with the global coordinate system. * Otherwise pass the event to QGLViewer to handle it normally. * * mostly copied over from ManipulatedFrame::mouseDoubleClickEvent */ void GLViewer::mouseDoubleClickEvent(QMouseEvent *event){ last_user_event = boost::posix_time::second_clock::local_time(); if(manipulatedClipPlane<0) { /* LOG_DEBUG("Double click not on clipping plane"); */ QGLViewer::mouseDoubleClickEvent(event); return; } #if QT_VERSION >= 0x040000 if (event->modifiers() == Qt::NoModifier) #else if (event->state() == Qt::NoButton) #endif switch (event->button()){ case Qt::LeftButton: manipulatedFrame()->alignWithFrame(NULL,true); LOG_DEBUG("Aligning cutting plane"); break; default: break; // avoid warning } } void GLViewer::wheelEvent(QWheelEvent* event){ last_user_event = boost::posix_time::second_clock::local_time(); if(manipulatedClipPlane<0){ QGLViewer::wheelEvent(event); return; } assert(manipulatedClipPlanenumClipPlanes); float distStep=1e-3*sceneRadius(); float dist=event->delta()*manipulatedFrame()->wheelSensitivity()*distStep; Vector3r normal=renderer->clipPlaneSe3[manipulatedClipPlane].orientation*Vector3r(0,0,1); qglviewer::Vec newPos=manipulatedFrame()->position()+qglviewer::Vec(normal[0],normal[1],normal[2])*dist; manipulatedFrame()->setPosition(newPos); renderer->clipPlaneSe3[manipulatedClipPlane].position=Vector3r(newPos[0],newPos[1],newPos[2]); updateGL(); /* in draw, bound cutting planes will be moved as well */ } trunk-2017.01a/gui/qt4/Inspector.py000066400000000000000000000273111304022710500170020ustar00rootroot00000000000000# encoding: utf-8 from PyQt4.QtCore import * from PyQt4.QtGui import * from yade import * from yade.qt.SerializableEditor import * import yade.qt class EngineInspector(QWidget): def __init__(self,parent=None): QWidget.__init__(self,parent) grid=QGridLayout(self); grid.setSpacing(0); grid.setMargin(0) self.serEd=SeqSerializable(parent=None,getter=lambda:O.engines,setter=lambda x:setattr(O,'engines',x),serType=Engine,path='O.engines') grid.addWidget(self.serEd) self.setLayout(grid) #class MaterialsInspector(QWidget): # def __init__(self,parent=None): # QWidget.__init__(self,parent) # grid=QGridLayout(self); grid.setSpacing(0); grid.setMargin(0) # self.serEd=SeqSerializable(parent=None,getter=lambda:O.materials,setter=lambda x:setattr(O,'materials',x),serType=Engine) # grid.addWidget(self.serEd) # self.setLayout(grid) class CellInspector(QWidget): def __init__(self,parent=None): QWidget.__init__(self,parent) self.layout=QVBoxLayout(self) #; self.layout.setSpacing(0); self.layout.setMargin(0) self.periCheckBox=QCheckBox('periodic boundary',self) self.periCheckBox.clicked.connect(self.update) self.layout.addWidget(self.periCheckBox) self.scroll=QScrollArea(self); self.scroll.setWidgetResizable(True) self.layout.addWidget(self.scroll) self.setLayout(self.layout) self.refresh() self.refreshTimer=QTimer(self) self.refreshTimer.timeout.connect(self.refresh) self.refreshTimer.start(1000) def refresh(self): self.periCheckBox.setChecked(O.periodic) editor=self.scroll.widget() if not O.periodic and editor: self.scroll.takeWidget() if (O.periodic and not editor) or (editor and editor.ser!=O.cell): self.scroll.setWidget(SerializableEditor(O.cell,parent=self,showType=True,path='O.cell')) def update(self): self.scroll.takeWidget() # do this before changing periodicity, otherwise the SerializableEditor will raise exception about None object O.periodic=self.periCheckBox.isChecked() self.refresh() def makeBodyLabel(b): ret=unicode(b.id)+u' ' if not b.shape: ret+=u'⬚' else: typeMap={'Sphere':u'⚫','Facet':u'△','Wall':u'┃','Box':u'⎕','Cylinder':u'⌭','ChainedCylinder':u'☡','Clump':u'☍'} ret+=typeMap.get(b.shape.__class__.__name__,u'﹖') if not b.dynamic: ret+=u'⚓' elif b.state.blockedDOFs: ret+=u'⎈' return ret def getBodyIdFromLabel(label): try: return int(unicode(label).split()[0]) except ValueError: print 'Error with label:',unicode(label) return -1 class BodyInspector(QWidget): def __init__(self,bodyId=-1,parent=None,bodyLinkCallback=None,intrLinkCallback=None): QWidget.__init__(self,parent) v=yade.qt.views() self.bodyId=bodyId if bodyId<0 and len(v)>0 and v[0].selection>0: self.bodyId=v[0].selection self.idGlSync=self.bodyId self.bodyLinkCallback,self.intrLinkCallback=bodyLinkCallback,intrLinkCallback self.bodyIdBox=QSpinBox(self) self.bodyIdBox.setMinimum(0) self.bodyIdBox.setMaximum(100000000) self.bodyIdBox.setValue(self.bodyId) self.intrWithCombo=QComboBox(self); self.gotoBodyButton=QPushButton(u'→ #',self) self.gotoIntrButton=QPushButton(u'→ #+#',self) # id selector topBoxWidget=QWidget(self); topBox=QHBoxLayout(topBoxWidget); topBox.setMargin(0); #topBox.setSpacing(0); hashLabel=QLabel('#',self); hashLabel.setFixedWidth(8) topBox.addWidget(hashLabel) topBox.addWidget(self.bodyIdBox) self.plusLabel=QLabel('+',self); topBox.addWidget(self.plusLabel) hashLabel2=QLabel('#',self); hashLabel2.setFixedWidth(8); topBox.addWidget(hashLabel2) topBox.addWidget(self.intrWithCombo) topBox.addStretch() topBox.addWidget(self.gotoBodyButton) topBox.addWidget(self.gotoIntrButton) topBoxWidget.setLayout(topBox) # forces display forcesWidget=QFrame(self); forcesWidget.setFrameShape(QFrame.Box); self.forceGrid=QGridLayout(forcesWidget); self.forceGrid.setVerticalSpacing(0); self.forceGrid.setHorizontalSpacing(9); self.forceGrid.setMargin(4); for i,j in itertools.product((0,1,2,3),(-1,0,1,2)): lab=QLabel(''+('force','torque','move','rot')[i]+'' if j==-1 else ''); self.forceGrid.addWidget(lab,i,j+1); if j>=0: lab.setAlignment(Qt.AlignRight) if i>1: lab.hide() # do not show forced moves and rotations by default (they will appear if non-zero) self.showMovRot=False # self.grid=QGridLayout(self); self.grid.setSpacing(0); self.grid.setMargin(0) self.grid.addWidget(topBoxWidget) self.grid.addWidget(forcesWidget) self.scroll=QScrollArea(self) self.scroll.setWidgetResizable(True) self.grid.addWidget(self.scroll) self.tryShowBody() self.bodyIdBox.valueChanged.connect(self.bodyIdSlot) self.gotoBodyButton.clicked.connect(self.gotoBodySlot) self.gotoIntrButton.clicked.connect(self.gotoIntrSlot) self.refreshTimer=QTimer(self) self.refreshTimer.timeout.connect(self.refreshEvent) self.refreshTimer.start(1000) self.intrWithCombo.addItems(['0']); self.intrWithCombo.setCurrentIndex(0); self.intrWithCombo.setMinimumWidth(80) self.setWindowTitle('Body #%d'%self.bodyId) self.gotoBodySlot() def displayForces(self): if self.bodyId<0: return try: val=[O.forces.f(self.bodyId),O.forces.t(self.bodyId),O.forces.move(self.bodyId),O.forces.rot(self.bodyId)] hasMovRot=(val[2]!=Vector3.Zero or val[3]!=Vector3.Zero) if hasMovRot!=self.showMovRot: for i,j in itertools.product((2,3),(-1,0,1,2)): if hasMovRot: self.forceGrid.itemAtPosition(i,j+1).widget().show() else: self.forceGrid.itemAtPosition(i,j+1).widget().hide() self.showMovRot=hasMovRot rows=((0,1,2,3) if hasMovRot else (0,1)) for i,j in itertools.product(rows,(0,1,2)): self.forceGrid.itemAtPosition(i,j+1).widget().setText(''+str(val[i][j])+'') except IndexError:pass def tryShowBody(self): try: b=O.bodies[self.bodyId] self.serEd=SerializableEditor(b,showType=True,parent=self,path='O.bodies[%d]'%self.bodyId) except IndexError: self.serEd=QFrame(self) self.bodyId=-1 self.scroll.setWidget(self.serEd) def changeIdSlot(self,newId): self.bodyIdBox.setValue(newId); self.bodyIdSlot() def bodyIdSlot(self): self.bodyId=self.bodyIdBox.value() self.tryShowBody() self.setWindowTitle('Body #%d'%self.bodyId) self.refreshEvent() def gotoBodySlot(self): try: id=int(getBodyIdFromLabel(self.intrWithCombo.currentText())) except ValueError: return # empty id if not self.bodyLinkCallback: self.bodyIdBox.setValue(id); self.bodyId=id else: self.bodyLinkCallback(id) def gotoIntrSlot(self): ids=self.bodyIdBox.value(),getBodyIdFromLabel(self.intrWithCombo.currentText()) if not self.intrLinkCallback: self.ii=InteractionInspector(ids) self.ii.show() else: self.intrLinkCallback(ids) def refreshEvent(self): try: O.bodies[self.bodyId] except: self.bodyId=-1 # invalidate deleted body # no body shown yet, try to get the first one... if self.bodyId<0 and len(O.bodies)>0: try: print 'SET ZERO' b=O.bodies[0]; self.bodyIdBox.setValue(0) except IndexError: pass v=yade.qt.views() if len(v)>0 and v[0].selection!=self.bodyId: if self.idGlSync==self.bodyId: # changed in the viewer, reset ourselves self.bodyId=self.idGlSync=v[0].selection; self.changeIdSlot(self.bodyId) return else: v[0].selection=self.idGlSync=self.bodyId # changed here, set in the viewer meId=self.bodyIdBox.value(); pos=self.intrWithCombo.currentIndex() try: meLabel=makeBodyLabel(O.bodies[meId]) except IndexError: meLabel=u'…' self.plusLabel.setText(' '.join(meLabel.split()[1:])+' +') # do not repeat the id self.bodyIdBox.setMaximum(len(O.bodies)-1) others=[(i.id1 if i.id1!=meId else i.id2) for i in O.interactions.withBody(self.bodyIdBox.value()) if i.isReal] others.sort() self.intrWithCombo.clear() self.intrWithCombo.addItems([makeBodyLabel(O.bodies[i]) for i in others]) if pos>self.intrWithCombo.count() or pos<0: pos=0 self.intrWithCombo.setCurrentIndex(pos); other=self.intrWithCombo.itemText(pos) if other=='': self.gotoBodyButton.setEnabled(False); self.gotoIntrButton.setEnabled(False) other=u'∅' else: self.gotoBodyButton.setEnabled(True); self.gotoIntrButton.setEnabled(True) self.gotoBodyButton.setText(u'→ %s'%other) self.gotoIntrButton.setText(u'→ %s + %s'%(meLabel,other)) self.displayForces() class InteractionInspector(QWidget): def __init__(self,ids=None,parent=None,bodyLinkCallback=None): QWidget.__init__(self,parent) self.bodyLinkCallback=bodyLinkCallback self.ids=ids self.gotoId1Button=QPushButton(u'#…',self) self.gotoId2Button=QPushButton(u'#…',self) self.gotoId1Button.clicked.connect(self.gotoId1Slot) self.gotoId2Button.clicked.connect(self.gotoId2Slot) topBoxWidget=QWidget(self) topBox=QHBoxLayout(topBoxWidget) topBox.addWidget(self.gotoId1Button) labelPlus=QLabel('+',self); labelPlus.setAlignment(Qt.AlignHCenter) topBox.addWidget(labelPlus) topBox.addWidget(self.gotoId2Button) topBoxWidget.setLayout(topBox) self.setWindowTitle(u'No interaction') self.grid=QGridLayout(self); self.grid.setSpacing(0); self.grid.setMargin(0) self.grid.addWidget(topBoxWidget,0,0) self.scroll=QScrollArea(self) self.scroll.setWidgetResizable(True) self.grid.addWidget(self.scroll) self.refreshTimer=QTimer(self) self.refreshTimer.timeout.connect(self.refreshEvent) self.refreshTimer.start(1000) if self.ids: self.setupInteraction() def setupInteraction(self): try: intr=O.interactions[self.ids[0],self.ids[1]] self.serEd=SerializableEditor(intr,showType=True,parent=self.scroll,path='O.interactions[%d,%d]'%(self.ids[0],self.ids[1])) self.scroll.setWidget(self.serEd) self.gotoId1Button.setText('#'+makeBodyLabel(O.bodies[self.ids[0]])) self.gotoId2Button.setText('#'+makeBodyLabel(O.bodies[self.ids[1]])) self.setWindowTitle('Interaction #%d + #%d'%(self.ids[0],self.ids[1])) except IndexError: if self.ids: # reset view (there was an interaction) self.ids=None self.serEd=QFrame(self.scroll); self.scroll.setWidget(self.serEd) self.setWindowTitle('No interaction') self.gotoId1Button.setText(u'#…'); self.gotoId2Button.setText(u'#…'); def gotoId(self,bodyId): if self.bodyLinkCallback: self.bodyLinkCallback(bodyId) else: self.bi=BodyInspector(bodyId); self.bi.show() def gotoId1Slot(self): self.gotoId(self.ids[0]) def gotoId2Slot(self): self.gotoId(self.ids[1]) def refreshEvent(self): # no ids yet -- try getting the first interaction, if it exists if not self.ids: try: i=O.interactions.nth(0) self.ids=i.id1,i.id2 self.setupInteraction() return except IndexError: return # no interaction exists at all try: # try to fetch an existing interaction O.interactions[self.ids[0],self.ids[1]] except IndexError: self.ids=None class SimulationInspector(QWidget): def __init__(self,parent=None): QWidget.__init__(self,parent) self.setWindowTitle("Simulation Inspection") self.tabWidget=QTabWidget(self) self.engineInspector=EngineInspector(parent=None) self.bodyInspector=BodyInspector(parent=None,intrLinkCallback=self.changeIntrIds) self.intrInspector=InteractionInspector(parent=None,bodyLinkCallback=self.changeBodyId) self.cellInspector=CellInspector(parent=None) for i,name,widget in [(0,'Engines',self.engineInspector),(1,'Bodies',self.bodyInspector),(2,'Interactions',self.intrInspector),(3,'Cell',self.cellInspector)]: self.tabWidget.addTab(widget,name) grid=QGridLayout(self); grid.setSpacing(0); grid.setMargin(0) grid.addWidget(self.tabWidget) self.setLayout(grid) def changeIntrIds(self,ids): self.tabWidget.removeTab(2); self.intrInspector.close() self.intrInspector=InteractionInspector(ids=ids,parent=None,bodyLinkCallback=self.changeBodyId) self.tabWidget.insertTab(2,self.intrInspector,'Interactions') self.tabWidget.setCurrentIndex(2) def changeBodyId(self,id): self.bodyInspector.changeIdSlot(id) self.tabWidget.setCurrentIndex(1) trunk-2017.01a/gui/qt4/OpenGLManager.cpp000066400000000000000000000051631304022710500176060ustar00rootroot00000000000000#include"OpenGLManager.hpp" CREATE_LOGGER(OpenGLManager); OpenGLManager* OpenGLManager::self=NULL; OpenGLManager::OpenGLManager(QObject* parent): QObject(parent){ if(self) throw runtime_error("OpenGLManager instance already exists, uses OpenGLManager::self to retrieve it."); self=this; renderer=shared_ptr(new OpenGLRenderer); renderer->init(); connect(this,SIGNAL(createView()),this,SLOT(createViewSlot())); connect(this,SIGNAL(resizeView(int,int,int)),this,SLOT(resizeViewSlot(int,int,int))); connect(this,SIGNAL(closeView(int)),this,SLOT(closeViewSlot(int))); connect(this,SIGNAL(startTimerSignal()),this,SLOT(startTimerSlot()),Qt::QueuedConnection); } void OpenGLManager::timerEvent(QTimerEvent* event){ //cerr<<"."; boost::mutex::scoped_lock lock(viewsMutex); // when sharing the 0th view widget, it should be enough to update the primary view only //if(views.size()>0) views[0]->updateGL(); #if 1 FOREACH(const shared_ptr& view, views){ if(view) view->updateGL(); } #endif } void OpenGLManager::createViewSlot(){ boost::mutex::scoped_lock lock(viewsMutex); if(views.size()==0){ views.push_back(shared_ptr(new GLViewer(0,renderer,/*shareWidget*/(QGLWidget*)0))); } else { throw runtime_error("Secondary views not supported"); //views.push_back(shared_ptr(new GLViewer(views.size(),renderer,views[0].get()))); } } void OpenGLManager::resizeViewSlot(int id, int wd, int ht){ views[id]->resize(wd,ht); } void OpenGLManager::closeViewSlot(int id){ boost::mutex::scoped_lock lock(viewsMutex); for(size_t i=views.size()-1; (!views[i]); i--){ views.resize(i); } // delete empty views from the end if(id<0){ // close the last one existing assert(*views.rbegin()); // this should have been sanitized by the loop above views.resize(views.size()-1); // releases the pointer as well } if(id==0){ LOG_DEBUG("Closing primary view."); if(views.size()==1) views.clear(); else{ LOG_INFO("Cannot close primary view, secondary views still exist."); } } } void OpenGLManager::centerAllViews(){ boost::mutex::scoped_lock lock(viewsMutex); FOREACH(const shared_ptr& g, views){ if(!g) continue; g->centerScene(); } } void OpenGLManager::startTimerSlot(){ startTimer(50); } int OpenGLManager::waitForNewView(float timeout,bool center){ size_t origViewCount=views.size(); emitCreateView(); float t=0; while(views.size()!=origViewCount+1){ usleep(50000); t+=.05; // wait at most 5 secs if(t>=timeout) { LOG_ERROR("Timeout waiting for the new view to open, giving up."); return -1; } } if(center)(*views.rbegin())->centerScene(); return (*views.rbegin())->viewId; } trunk-2017.01a/gui/qt4/OpenGLManager.hpp000066400000000000000000000027601304022710500176130ustar00rootroot00000000000000#pragma once //#include #ifndef Q_MOC_RUN #include"GLViewer.hpp" #endif #include #include /* Singleton class managing OpenGL views, a renderer instance and timer to refresh the display. */ class OpenGLManager: public QObject{ Q_OBJECT DECLARE_LOGGER; public: static OpenGLManager* self; OpenGLManager(QObject *parent=0); // manipulation must lock viewsMutex! std::vector > views; shared_ptr renderer; // signals are protected, emitting them is therefore wrapped with such funcs void emitResizeView(int id, int wd, int ht){ emit resizeView(id,wd,ht); } void emitCreateView(){ emit createView(); } void emitStartTimer(){ emit startTimerSignal(); } void emitCloseView(int id){ emit closeView(id); } // create a new view and wait for it to become available; return the view number // if timout (in seconds) elapses without the view to come up, reports error and returns -1 int waitForNewView(float timeout=5., bool center=true); signals: void createView(); void resizeView(int id, int wd, int ht); void closeView(int id); // this is used to start timer from the main thread via postEvent (ugly) void startTimerSignal(); public slots: virtual void createViewSlot(); virtual void resizeViewSlot(int id, int wd, int ht); virtual void closeViewSlot(int id=-1); virtual void timerEvent(QTimerEvent* event); virtual void startTimerSlot(); void centerAllViews(); private: boost::mutex viewsMutex; }; trunk-2017.01a/gui/qt4/SerializableEditor.py000066400000000000000000001107221304022710500206100ustar00rootroot00000000000000# encoding: utf-8 from PyQt4.QtCore import * from PyQt4.QtGui import * from PyQt4 import QtGui import re,itertools import logging logging.trace=logging.debug logging.basicConfig(level=logging.INFO) from yade import * import yade.qt from minieigen import * seqSerializableShowType=True # show type headings in serializable sequences (takes vertical space, but makes the type hyperlinked) # BUG: cursor is moved to the beginning of the input field even if it has focus # checking for focus seems to return True always and cursor is never moved # the 'True or' part effectively disables the condition (so that the cursor is moved always), but it might be fixed in the future somehow # if True or w.hasFocus(): w.home(False) # Janek: It looks like I've fixed this BUG, please do more testing. # def makeWrapperHref(text,className,attr=None,static=False): """Create clickable HTML hyperlink to a Yade class or its attribute. :param className: name of the class to link to. :param attr: attribute to link to. If given, must exist directly in given *className*; if not given or empty, link to the class itself is created and *attr* is ignored. :return: HTML with the hyperref. """ if not static: return '%s'%(yade.qt.sphinxDocWrapperPage,className,(('.'+attr) if attr else ''),text) else: return '%s'%(yade.qt.sphinxDocWrapperPage,className,attr,text) def serializableHref(ser,attr=None,text=None): """Return HTML href to a *ser* optionally to the attribute *attr*. The class hierarchy is crawled upwards to find out in which parent class is *attr* defined, so that the href target is a valid link. In that case, only single inheritace is assumed and the first class from the top defining *attr* is used. :param ser: object of class deriving from :yref:`Serializable`, or string; if string, *attr* must be empty. :param attr: name of the attribute to link to; if empty, linke to the class itself is created. :param text: visible text of the hyperlink; if not given, either class name or attribute name without class name (when *attr* is not given) is used. :returns: HTML with the hyperref. """ # klass is a class name given as string if isinstance(ser,str): if attr: raise InvalidArgument("When *ser* is a string, *attr* must be empty (only class link can be created)") return makeWrapperHref(text if text else ser,ser) # klass is a type object if attr: klass=ser.__class__ while attr in dir(klass.__bases__[0]): klass=klass.__bases__[0] if not text: text=attr else: klass=ser.__class__ if not text: text=klass.__name__ return makeWrapperHref(text,klass.__name__,attr,static=(attr and getattr(klass,attr)==getattr(ser,attr))) class AttrEditor(): """Abstract base class handing some aspects common to all attribute editors. Holds exacly one attribute which is updated whenever it changes.""" def __init__(self,getter=None,setter=None): self.getter,self.setter=getter,setter self.hot,self.focused=False,False self.widget=None def refresh(self): pass def update(self): pass def isHot(self,hot=True): "Called when the widget gets focus; mark it hot, change colors etc." if hot==self.hot: return self.hot=hot if hot: self.setStyleSheet('QWidget { background: red }') else: self.setStyleSheet('QWidget { background: none }') def sizeHint(self): return QSize(150,12) def trySetter(self,val): try: self.setter(val) except AttributeError: self.setEnabled(False) self.isHot(False) class AttrEditor_Bool(AttrEditor,QFrame): def __init__(self,parent,getter,setter): AttrEditor.__init__(self,getter,setter) QFrame.__init__(self,parent) self.checkBox=QCheckBox(self) lay=QVBoxLayout(self); lay.setSpacing(0); lay.setMargin(0); lay.addStretch(1); lay.addWidget(self.checkBox); lay.addStretch(1) self.checkBox.clicked.connect(self.update) def refresh(self): self.checkBox.setChecked(self.getter()) def update(self): self.trySetter(self.checkBox.isChecked()) class AttrEditor_Int(AttrEditor,QSpinBox): def __init__(self,parent,getter,setter): AttrEditor.__init__(self,getter,setter) QSpinBox.__init__(self,parent) self.setRange(int(-1e9),int(1e9)); self.setSingleStep(1); self.valueChanged.connect(self.update) def refresh(self): if (not self.hasFocus()): self.setValue(self.getter()) def update(self): self.trySetter(self.value()) class AttrEditor_Str(AttrEditor,QLineEdit): def __init__(self,parent,getter,setter): AttrEditor.__init__(self,getter,setter) QLineEdit.__init__(self,parent) self.textEdited.connect(self.isHot) self.selectionChanged.connect(self.isHot) self.editingFinished.connect(self.update) def refresh(self): if (not self.hasFocus()): self.setText(self.getter()) def update(self): self.trySetter(str(self.text())) class AttrEditor_Float(AttrEditor,QLineEdit): def __init__(self,parent,getter,setter): AttrEditor.__init__(self,getter,setter) QLineEdit.__init__(self,parent) self.textEdited.connect(self.isHot) self.selectionChanged.connect(self.isHot) self.editingFinished.connect(self.update) def refresh(self): #if True or not self.hasFocus(): self.home(False) if (not self.hasFocus()): self.setText(str(self.getter())); self.home(False) def update(self): try: self.trySetter(float(self.text())) except ValueError: self.refresh() class AttrEditor_Complex(AttrEditor,QLineEdit): def __init__(self,parent,getter,setter): AttrEditor.__init__(self,getter,setter) QFrame.__init__(self,parent) self.rows,self.cols=1,2 self.setContentsMargins(0,0,0,0) self.first=True val=self.getter() self.grid=QGridLayout(self); self.grid.setSpacing(0); self.grid.setMargin(0) for row,col in itertools.product(range(self.rows),range(self.cols)): w=QLineEdit('') self.grid.addWidget(w,row,col); w.textEdited.connect(self.isHot) w.selectionChanged.connect(self.isHot) w.editingFinished.connect(self.update) def refresh(self,force=False): val=self.getter() for row,col in itertools.product(range(self.rows),range(self.cols)): w=self.grid.itemAtPosition(row,col).widget() if(self.first or force): w.setText(str(val.real if col==0 else val.imag)) #if True or not w.hasFocus: w.home(False) # make the left-most part visible, if the text is wider than the widget if (not w.hasFocus): w.setText(str(val.real if col==0 else val.imag)) w.home(False) # make the left-most part visible, if the text is wider than the widget self.first=False def update(self): try: val=self.getter() w1=self.grid.itemAtPosition(0,0).widget() w2=self.grid.itemAtPosition(0,1).widget() if w1.isModified() or w2.isModified(): val=complex(float(w1.text()),float(w2.text())) logging.debug('setting'+str(val)) self.trySetter(val) except ValueError: self.refresh(force=True) def setFocus(self): self.grid.itemAtPosition(0,0).widget().setFocus() class AttrEditor_Quaternion(AttrEditor,QFrame): def __init__(self,parent,getter,setter): AttrEditor.__init__(self,getter,setter) QFrame.__init__(self,parent) self.grid=QHBoxLayout(self); self.grid.setSpacing(0); self.grid.setMargin(0) for i in range(4): if i==3: # add vertical divider (axis | angle) f=QFrame(self); f.setFrameShape(QFrame.VLine); f.setFrameShadow(QFrame.Sunken); f.setFixedWidth(4) self.grid.addWidget(f) w=QLineEdit('') self.grid.addWidget(w); w.textEdited.connect(self.isHot) w.selectionChanged.connect(self.isHot) w.editingFinished.connect(self.update) def refresh(self): val=self.getter(); axis,angle=val.toAxisAngle() for i in (0,1,2,4): #if True or not w.hasFocus(): w.home(False) w=self.grid.itemAt(i).widget(); if (not w.hasFocus()): w.setText(str(axis[i] if i<3 else angle)); w.home(False) def update(self): try: x=[float((self.grid.itemAt(i).widget().text())) for i in (0,1,2,4)] except ValueError: self.refresh() return q=Quaternion(Vector3(x[0],x[1],x[2]),x[3]); q.normalize() # from axis-angle self.trySetter(q) def setFocus(self): self.grid.itemAt(0).widget().setFocus() class AttrEditor_Se3(AttrEditor,QFrame): def __init__(self,parent,getter,setter): AttrEditor.__init__(self,getter,setter) QFrame.__init__(self,parent) self.grid=QGridLayout(self); self.grid.setSpacing(0); self.grid.setMargin(0) for row,col in itertools.product(range(2),range(5)): # one additional column for vertical line in quaternion if (row,col)==(0,3): continue if (row,col)==(0,4): self.grid.addWidget(QLabel(u'←pos ↙ori',self),row,col); continue if (row,col)==(1,3): f=QFrame(self); f.setFrameShape(QFrame.VLine); f.setFrameShadow(QFrame.Sunken); f.setFixedWidth(4); self.grid.addWidget(f,row,col); continue w=QLineEdit('') self.grid.addWidget(w,row,col); w.textEdited.connect(self.isHot) w.selectionChanged.connect(self.isHot) w.editingFinished.connect(self.update) def refresh(self): pos,ori=self.getter(); axis,angle=ori.toAxisAngle() for i in (0,1,2,4): #if True or not w.hasFocus(): w.home(False) w=self.grid.itemAtPosition(1,i).widget(); if (not w.hasFocus()): w.setText(str(axis[i] if i<3 else angle)); w.home(False) for i in (0,1,2): #if True or not w.hasFocus(): w.home(False) w=self.grid.itemAtPosition(0,i).widget(); if (not w.hasFocus()): w.setText(str(pos[i])); w.home(False) def update(self): try: q=[float((self.grid.itemAtPosition(1,i).widget().text())) for i in (0,1,2,4)] v=[float((self.grid.itemAtPosition(0,i).widget().text())) for i in (0,1,2)] except ValueError: self.refresh() return qq=Quaternion(Vector3(q[0],q[1],q[2]),q[3]); qq.normalize() # from axis-angle self.trySetter((v,qq)) def setFocus(self): self.grid.itemAtPosition(0,0).widget().setFocus() class AttrEditor_MatrixX(AttrEditor,QFrame): def __init__(self,parent,getter,setter,rows,cols,idxConverter): 'idxConverter converts row,col tuple to either (row,col), (col) etc depending on what access is used for []' AttrEditor.__init__(self,getter,setter) QFrame.__init__(self,parent) self.rows,self.cols=rows,cols self.idxConverter=idxConverter self.setContentsMargins(0,0,0,0) self.first=True val=self.getter() self.grid=QGridLayout(self); self.grid.setSpacing(0); self.grid.setMargin(0) for row,col in itertools.product(range(self.rows),range(self.cols)): w=QLineEdit('') self.grid.addWidget(w,row,col); w.textEdited.connect(self.isHot) w.selectionChanged.connect(self.isHot) w.editingFinished.connect(self.update) def refresh(self,force=False): val=self.getter() for row,col in itertools.product(range(self.rows),range(self.cols)): w=self.grid.itemAtPosition(row,col).widget() if(self.first or force): w.setText(str(val[self.idxConverter(row,col)])) if (not w.hasFocus): w.setText(str(val[self.idxConverter(row,col)])) w.home(False) # make the left-most part visible, if the text is wider than the widget self.first=False def update(self): try: val=self.getter() for row,col in itertools.product(range(self.rows),range(self.cols)): w=self.grid.itemAtPosition(row,col).widget() if w.isModified(): val[self.idxConverter(row,col)]=float(w.text()) logging.debug('setting'+str(val)) self.trySetter(val) except ValueError: self.refresh(force=True) def setFocus(self): self.grid.itemAtPosition(0,0).widget().setFocus() class AttrEditor_MatrixXi(AttrEditor,QFrame): def __init__(self,parent,getter,setter,rows,cols,idxConverter): 'idxConverter converts row,col tuple to either (row,col), (col) etc depending on what access is used for []' AttrEditor.__init__(self,getter,setter) QFrame.__init__(self,parent) self.rows,self.cols=rows,cols self.idxConverter=idxConverter self.setContentsMargins(0,0,0,0) self.grid=QGridLayout(self); self.grid.setSpacing(0); self.grid.setMargin(0) for row,col in itertools.product(range(self.rows),range(self.cols)): w=QSpinBox() w.setRange(int(-1e9),int(1e9)); w.setSingleStep(1); self.grid.addWidget(w,row,col); self.refresh() # refresh before connecting signals! for row,col in itertools.product(range(self.rows),range(self.cols)): self.grid.itemAtPosition(row,col).widget().valueChanged.connect(self.update) def refresh(self): val=self.getter() for row,col in itertools.product(range(self.rows),range(self.cols)): w=self.grid.itemAtPosition(row,col).widget().setValue(val[self.idxConverter(row,col)]) def update(self): val=self.getter(); modified=False for row,col in itertools.product(range(self.rows),range(self.cols)): w=self.grid.itemAtPosition(row,col).widget() if w.value()!=val[self.idxConverter(row,col)]: modified=True; val[self.idxConverter(row,col)]=w.value() if not modified: return logging.debug('setting'+str(val)) self.trySetter(val) def setFocus(self): self.grid.itemAtPosition(0,0).widget().setFocus() class AttrEditor_Vector6i(AttrEditor_MatrixXi): def __init__(self,parent,getter,setter): AttrEditor_MatrixXi.__init__(self,parent,getter,setter,1,6,lambda r,c:c) class AttrEditor_Vector3i(AttrEditor_MatrixXi): def __init__(self,parent,getter,setter): AttrEditor_MatrixXi.__init__(self,parent,getter,setter,1,3,lambda r,c:c) class AttrEditor_Vector2i(AttrEditor_MatrixXi): def __init__(self,parent,getter,setter): AttrEditor_MatrixXi.__init__(self,parent,getter,setter,1,2,lambda r,c:c) class AttrEditor_Vector6(AttrEditor_MatrixX): def __init__(self,parent,getter,setter): AttrEditor_MatrixX.__init__(self,parent,getter,setter,1,6,lambda r,c:c) class AttrEditor_Vector3(AttrEditor_MatrixX): def __init__(self,parent,getter,setter): AttrEditor_MatrixX.__init__(self,parent,getter,setter,1,3,lambda r,c:c) class AttrEditor_Vector2(AttrEditor_MatrixX): def __init__(self,parent,getter,setter): AttrEditor_MatrixX.__init__(self,parent,getter,setter,1,2,lambda r,c:c) class AttrEditor_Matrix3(AttrEditor_MatrixX): def __init__(self,parent,getter,setter): AttrEditor_MatrixX.__init__(self,parent,getter,setter,3,3,lambda r,c:(r,c)) class Se3FakeType: pass _fundamentalEditorMap={bool:AttrEditor_Bool,str:AttrEditor_Str,int:AttrEditor_Int,float:AttrEditor_Float,complex:AttrEditor_Complex,Quaternion:AttrEditor_Quaternion,Vector2:AttrEditor_Vector2,Vector3:AttrEditor_Vector3,Vector6:AttrEditor_Vector6,Matrix3:AttrEditor_Matrix3,Vector6i:AttrEditor_Vector6i,Vector3i:AttrEditor_Vector3i,Vector2i:AttrEditor_Vector2i,Se3FakeType:AttrEditor_Se3} _fundamentalInitValues={bool:True,str:'',int:0,float:0.0,complex:0.0j,Quaternion:Quaternion((0,1,0),0.0),Vector3:Vector3.Zero,Matrix3:Matrix3.Zero,Vector6:Vector6.Zero,Vector6i:Vector6i.Zero,Vector3i:Vector3i.Zero,Vector2i:Vector2i.Zero,Vector2:Vector2.Zero,Se3FakeType:(Vector3.Zero,Quaternion((0,1,0),0.0))} class SerQLabel(QLabel): def __init__(self,parent,label,tooltip,path): QLabel.__init__(self,parent) self.path=path self.setText(label) if tooltip or path: self.setToolTip((''+path+'
    ' if self.path else '')+(tooltip if tooltip else '')) self.linkActivated.connect(yade.qt.openUrl) def mousePressEvent(self,event): if event.button()!=Qt.MidButton: event.ignore(); return # middle button clicked, paste pasteText to clipboard cb=QApplication.clipboard() cb.setText(self.path,mode=QClipboard.Clipboard) cb.setText(self.path,mode=QClipboard.Selection) # X11 global selection buffer event.accept() class SerializableEditor(QFrame): "Class displaying and modifying serializable attributes of a yade object." import collections import logging # each attribute has one entry associated with itself class EntryData: def __init__(self,name,T,flags=0): self.name,self.T,self.flags=name,T,flags self.lineNo,self.widget=None,None def __init__(self,ser,parent=None,ignoredAttrs=set(),showType=False,path=None): "Construct window, *ser* is the object we want to show." QtGui.QFrame.__init__(self,parent) self.ser=ser self.path=(ser.label if (hasattr(ser,'label') and ser.label) else path) self.showType=showType self.hot=False self.entries=[] self.ignoredAttrs=ignoredAttrs logging.debug('New Serializable of type %s'%ser.__class__.__name__) self.setWindowTitle(str(ser)) self.mkWidgets() self.refreshTimer=QTimer(self) self.refreshTimer.timeout.connect(self.refreshEvent) self.refreshTimer.start(500) def getListTypeFromDocstring(self,attr): "Guess type of array by scanning docstring for :yattrtype: and parsing its argument; ugly, but works." doc=getattr(self.ser.__class__,attr).__doc__ if doc==None: logging.error("Attribute %s has no docstring."%attr) return None m=re.search(r':yattrtype:`([^`]*)`',doc) if not m: logging.error("Attribute %s does not contain :yattrtype:`....` (docstring is '%s'"%(attr,doc)) return None cxxT=m.group(1) logging.debug('Got type "%s" from :yattrtype:'%cxxT) def vecTest(T,cxxT): #regexp=r'^\s*(std\s*::)?\s*vector\s*<\s*(std\s*::)?\s*('+T+r')\s*>\s*$' regexp=r'^\s*(std\s*::)?\s*vector\s*<\s*(shared_ptr\s*<\s*)?\s*(std\s*::)?\s*('+T+r')(\s*>)?\s*>\s*$' m=re.match(regexp,cxxT) return m vecMap={ 'bool':bool,'int':int,'long':int,'Body::id_t':long,'size_t':long, 'Real':float,'float':float,'double':float,'complex':complex,'std::complex':complex, 'Vector6r':Vector6,'Vector6i':Vector6i,'Vector3i':Vector3i,'Vector2r':Vector2,'Vector2i':Vector2i, 'Vector3r':Vector3,'Matrix3r':Matrix3,'Se3r':Se3FakeType, 'string':str, #'BodyCallback':BodyCallback, 'IntrCallback':IntrCallback,'BoundFunctor':BoundFunctor,'IGeomFunctor':IGeomFunctor,'IPhysFunctor':IPhysFunctor,'LawFunctor':LawFunctor,'KinematicEngine':KinematicEngine, 'GlShapeFunctor':GlShapeFunctor,'GlStateFunctor':GlStateFunctor,'GlIGeomFunctor':GlIGeomFunctor,'GlIPhysFunctor':GlIPhysFunctor,'GlBoundFunctor':GlBoundFunctor,'GlExtraDrawer':GlExtraDrawer } for T,ret in vecMap.items(): if vecTest(T,cxxT): logging.debug("Got type %s from cxx type %s"%(repr(ret),cxxT)) return (ret,) logging.error("Unable to guess python type from cxx type '%s'"%cxxT) return None def mkAttrEntries(self): if self.ser==None: return try: d=self.ser.dict() except TypeError: logging.error('TypeError when getting attributes of '+str(self.ser)+',skipping. ') import traceback traceback.print_exc() attrs=self.ser.dict().keys(); attrs.sort() for attr in attrs: val=getattr(self.ser,attr) # get the value using serattr, as it might be different from what the dictionary provides (e.g. Body.blockedDOFs) t=None doc=getattr(self.ser.__class__,attr).__doc__; # some attributes are not shown if '|yhidden|' in doc: continue if attr in self.ignoredAttrs: continue # FIXME: (Janek) Implementing Quantum Mechanics makes some DEM assumptions # invalid. I think that we should rethink what base class Body contains, so # that in QM we would not need to use this hack to hide some variables. # However it is great to note that only this little 'cosmetic' hack is needed # to make Quantum Mechanics possible in yade # See also: class QuantumMechanicalState, class QuantumMechanicalBody, gui/qt4/SerializableEditor.py if hasattr(self.ser,"qtHide") and (attr in getattr(self.ser,"qtHide").split()): continue if isinstance(val,list): t=self.getListTypeFromDocstring(attr) if not t and len(val)==0: t=(val[0].__class__,) # 1-tuple is list of the contained type #if not t: raise RuntimeError('Unable to guess type of '+str(self.ser)+'.'+attr) # hack for Se3, which is returned as (Vector3,Quaternion) in python elif isinstance(val,tuple) and len(val)==2 and val[0].__class__==Vector3 and val[1].__class__==Quaternion: t=Se3FakeType else: t=val.__class__ match=re.search(':yattrflags:`\s*([0-9]+)\s*`',doc) # non-empty attribute flags=int(match.group(1)) if match else 0 #logging.debug('Attr %s is of type %s'%(attr,((t[0].__name__,) if isinstance(t,tuple) else t.__name__))) self.entries.append(self.EntryData(name=attr,T=t)) #print("name: "+str(attr)+"\tflag: "+str(flags)) def getDocstring(self,attr=None): "If attr is *None*, return docstring of the Serializable itself" doc=(getattr(self.ser.__class__,attr).__doc__ if attr else self.ser.__class__.__doc__) if not doc: return '' doc=re.sub(':y(attrtype|default|attrflags):`[^`]*`','',doc) statAttr=re.compile('^.. ystaticattr::.*$',re.MULTILINE|re.DOTALL) doc=re.sub(statAttr,'',doc) # static classes have their proper docs at the beginning, discard static memeber docs # static: attribute of the type is the same object as attribute of the instance # in that case, get docstring from the class documentation by parsing it if attr and getattr(self.ser.__class__,attr)==getattr(self.ser,attr): doc=self.getStaticAttrDocstring(attr) doc=re.sub(':yref:`([^`]*)`','\\1',doc) import textwrap wrapper=textwrap.TextWrapper(replace_whitespace=False) return wrapper.fill(textwrap.dedent(doc)) def getStaticAttrDocstring(self,attr): ret=''; c=self.ser.__class__ while hasattr(c,attr) and hasattr(c.__base__,attr): c=c.__base__ start='.. ystaticattr:: %s.%s('%(c.__name__,attr) if start in c.__doc__: ll=c.__doc__.split('\n') for i in range(len(ll)): if ll[i].startswith(start): break for i in range(i+1,len(ll)): if len(ll[i])>0 and ll[i][0] not in ' \t': break ret+=ll[i] return ret else: return '[no documentation found]' def mkWidget(self,entry): if not entry.T: return None # single fundamental object Klass=_fundamentalEditorMap.get(entry.T,None) getter,setter=lambda: getattr(self.ser,entry.name), lambda x: setattr(self.ser,entry.name,x) if Klass: widget=Klass(self,getter=getter,setter=setter) widget.setFocusPolicy(Qt.StrongFocus) if (entry.flags & AttrFlags.readonly): widget.setEnabled(False) return widget # sequences if entry.T.__class__==tuple: assert(len(entry.T)==1) # we don't handle tuples of other lenghts # sequence of serializables T=entry.T[0] if (issubclass(T,Serializable) or T==Serializable): widget=SeqSerializable(self,getter,setter,T,path=(self.path+'.'+entry.name if self.path else None),shrink=True) return widget if (T in _fundamentalEditorMap): widget=SeqFundamentalEditor(self,getter,setter,T) return widget return None # a serializable if issubclass(entry.T,Serializable) or entry.T==Serializable: obj=getattr(self.ser,entry.name) if hasattr(obj,'label') and obj.label: path=obj.label elif self.path: path=self.path+'.'+entry.name else: path=None widget=SerializableEditor(getattr(self.ser,entry.name),parent=self,showType=self.showType,path=(self.path+'.'+entry.name if self.path else None)) widget.setFrameShape(QFrame.Box); widget.setFrameShadow(QFrame.Raised); widget.setLineWidth(1) return widget return None def mkWidgets(self): self.mkAttrEntries() grid=QFormLayout() grid.setContentsMargins(2,2,2,2) grid.setVerticalSpacing(0) grid.setLabelAlignment(Qt.AlignRight) if self.showType: lab=SerQLabel(self,makeSerializableLabel(self.ser,addr=True,href=True),tooltip=self.getDocstring(),path=self.path) lab.setFrameShape(QFrame.Box); lab.setFrameShadow(QFrame.Sunken); lab.setLineWidth(2); lab.setAlignment(Qt.AlignHCenter); lab.linkActivated.connect(yade.qt.openUrl) grid.setWidget(0,QFormLayout.SpanningRole,lab) for entry in self.entries: entry.widget=self.mkWidget(entry) objPath=(self.path+'.'+entry.name) if self.path else None label=SerQLabel(self,serializableHref(self.ser,entry.name),tooltip=self.getDocstring(entry.name),path=objPath) grid.addRow(label,entry.widget if entry.widget else QLabel('unhandled type')) self.setLayout(grid) self.refreshEvent() def refreshEvent(self): for e in self.entries: if e.widget and not e.widget.hot: e.widget.refresh() def refresh(self): pass def makeSerializableLabel(ser,href=False,addr=True,boldHref=True,num=-1,count=-1): ret=u'' if num>=0: if count>=0: ret+=u'%d/%d. '%(num,count) else: ret+=u'%d. '%num if href: ret+=(u' ' if boldHref else u' ')+serializableHref(ser)+(u' ' if boldHref else u' ') else: ret+=ser.__class__.__name__+' ' if hasattr(ser,'label') and ser.label: ret+=u' “'+unicode(ser.label)+u'”' # do not show address if there is a label already elif addr: import re ss=unicode(ser); m=re.match(u'<(.*) instance at (0x.*)>',ss) if m: ret+=m.group(2) else: logging.warning(u"Serializable converted to str ('%s') does not contain 'instance at 0x…'"%ss) return ret class SeqSerializableComboBox(QFrame): def __init__(self,parent,getter,setter,serType,path=None,shrink=False): QFrame.__init__(self,parent) self.getter,self.setter,self.serType,self.path,self.shrink=getter,setter,serType,path,shrink self.layout=QVBoxLayout(self) topLineFrame=QFrame(self) topLineLayout=QHBoxLayout(topLineFrame); for l in self.layout, topLineLayout: l.setSpacing(0); l.setContentsMargins(0,0,0,0) topLineFrame.setLayout(topLineLayout) buttons=(self.newButton,self.killButton,self.upButton,self.downButton)=[QPushButton(label,self) for label in (u'☘',u'☠',u'↑',u'↓')] buttonSlots=(self.newSlot,self.killSlot,self.upSlot,self.downSlot) # same order as buttons for b in buttons: b.setStyleSheet('QPushButton { font-size: 15pt; }'); b.setFixedWidth(30); b.setFixedHeight(30) self.combo=QComboBox(self) self.combo.setSizeAdjustPolicy(QComboBox.AdjustToContents) for w in buttons[0:2]+[self.combo,]+buttons[2:4]: topLineLayout.addWidget(w) self.layout.addWidget(topLineFrame) # nested layout self.scroll=QScrollArea(self); self.scroll.setWidgetResizable(True) self.layout.addWidget(self.scroll) self.seqEdit=None # currently edited serializable self.setLayout(self.layout) self.hot=None # API compat with SerializableEditor self.setFrameShape(QFrame.Box); self.setFrameShadow(QFrame.Raised); self.setLineWidth(1) # signals for b,slot in zip(buttons,buttonSlots): b.clicked.connect(slot) self.combo.currentIndexChanged.connect(self.comboIndexSlot) self.refreshEvent() # periodic refresh self.refreshTimer=QTimer(self) self.refreshTimer.timeout.connect(self.refreshEvent) self.refreshTimer.start(1000) # 1s should be enough #print 'SeqSerializable path is',self.path def comboIndexSlot(self,ix): # different seq item selected currSeq=self.getter(); if len(currSeq)==0: ix=-1 logging.debug('%s comboIndexSlot len=%d, ix=%d'%(self.serType.__name__,len(currSeq),ix)) self.downButton.setEnabled(ix0) self.combo.setEnabled(ix>=0) if ix>=0: ser=currSeq[ix] self.seqEdit=SerializableEditor(ser,parent=self,showType=seqSerializableShowType,path=(self.path+'['+str(ix)+']') if self.path else None) self.scroll.setWidget(self.seqEdit) if self.shrink: self.sizeHint=lambda: QSize(100,1000) self.scroll.sizeHint=lambda: QSize(100,1000) self.sizePolicy().setVerticalPolicy(QSizePolicy.Expanding) self.scroll.sizePolicy().setVerticalPolicy(QSizePolicy.Expanding) self.setMinimumHeight(min(300,self.seqEdit.height()+self.combo.height()+10)) self.setMaximumHeight(100000) self.scroll.setMaximumHeight(100000) else: self.scroll.setWidget(QFrame()) if self.shrink: self.setMaximumHeight(self.combo.height()+10); self.scroll.setMaximumHeight(0) def serLabel(self,ser,i=-1): return ('' if i<0 else str(i)+'. ')+str(ser)[1:-1].replace('instance at ','') def refreshEvent(self,forceIx=-1): currSeq=self.getter() comboEnabled=self.combo.isEnabled() if comboEnabled and len(currSeq)==0: self.comboIndexSlot(-1) # force refresh, otherwise would not happen from the initially empty state ix,cnt=self.combo.currentIndex(),self.combo.count() # serializable currently being edited (which can be absent) or the one of which index is forced ser=(self.seqEdit.ser if self.seqEdit else None) if forceIx<0 else currSeq[forceIx] if comboEnabled and len(currSeq)==cnt and (ix<0 or ser==currSeq[ix]): return if not comboEnabled and len(currSeq)==0: return logging.debug(self.serType.__name__+' rebuilding list from scratch') self.combo.clear() if len(currSeq)>0: prevIx=-1 for i,s in enumerate(currSeq): self.combo.addItem(makeSerializableLabel(s,num=i,count=len(currSeq),addr=False)) if s==ser: prevIx=i if forceIx>=0: newIx=forceIx # force the index (used from newSlot to make the new element active) elif prevIx>=0: newIx=prevIx # if found what was active before, use it elif ix>=0: newIx=ix # otherwise use the previous index (e.g. after deletion) else: newIx=0 # fallback to 0 logging.debug('%s setting index %d'%(self.serType.__name__,newIx)) self.combo.setCurrentIndex(newIx) else: logging.debug('%s EMPTY, setting index 0'%(self.serType.__name__)) self.combo.setCurrentIndex(-1) self.killButton.setEnabled(len(currSeq)>0) def newSlot(self): dialog=NewSerializableDialog(self,self.serType.__name__) if not dialog.exec_(): return # cancelled ser=dialog.result() ix=self.combo.currentIndex() currSeq=self.getter(); currSeq.insert(ix,ser); self.setter(currSeq) logging.debug('%s new item created at index %d'%(self.serType.__name__,ix)) self.refreshEvent(forceIx=ix) def killSlot(self): ix=self.combo.currentIndex() currSeq=self.getter(); del currSeq[ix]; self.setter(currSeq) self.refreshEvent() def upSlot(self): i=self.combo.currentIndex() assert(i>0) currSeq=self.getter(); prev,curr=currSeq[i-1:i+1]; currSeq[i-1],currSeq[i]=curr,prev; self.setter(currSeq) self.refreshEvent(forceIx=i-1) def downSlot(self): i=self.combo.currentIndex() currSeq=self.getter(); assert(i=0 else None menu=QMenu(self) actNew,actKill,actUp,actDown=[menu.addAction(name) for name in (u'☘ New',u'☠ Remove',u'↑ Up',u'↓ Down')] if index<0: [a.setEnabled(False) for a in actKill,actUp,actDown] if index==len(seq)-1: actDown.setEnabled(False) if index==0: actUp.setEnabled(False) if field: field.setStyleSheet('QWidget { background: green }') act=menu.exec_(self.mapToGlobal(event.pos())) if field: field.setStyleSheet('QWidget { background: none }') if not act: return if act==actNew: self.newSlot(index) elif act==actKill: self.killSlot(index) elif act==actUp: self.upSlot(index) elif act==actDown: self.downSlot(index) def localPositionToIndex(self,pos): gp=self.mapToGlobal(pos) for row in range(self.form.count()/2): w,i=self.form.itemAt(row,QFormLayout.FieldRole),self.form.itemAt(row,QFormLayout.LabelRole) for wi in w.widget(),i.widget(): x0,y0,x1,y1=wi.geometry().getCoords(); globG=QRect(self.mapToGlobal(QPoint(x0,y0)),self.mapToGlobal(QPoint(x1,y1))) if globG.contains(gp): return row return -1 def newSlot(self,i): seq=self.getter(); seq.insert(i,_fundamentalInitValues.get(self.itemType,self.itemType())) self.setter(seq) self.rebuild() def killSlot(self,i): seq=self.getter(); assert(iError',errMsg) return class ItemGetter(): def __init__(self,getter,index): self.getter,self.index=getter,index def __call__(self): return self.getter()[self.index] class ItemSetter(): def __init__(self,getter,setter,index): self.getter,self.setter,self.index=getter,setter,index def __call__(self,val): seq=self.getter(); seq[self.index]=val; self.setter(seq) for i,item in enumerate(currSeq): widget=Klass(self,ItemGetter(self.getter,i),ItemSetter(self.getter,self.setter,i)) #proxy,'value') self.form.insertRow(i,'%d. '%i,widget) logging.debug('added item %d %s'%(i,str(widget))) if len(currSeq)==0: self.form.insertRow(0,'empty',QLabel('(right-click for menu)')) logging.debug('rebuilt, will refresh now') self.refreshEvent(dontRebuild=True) # avoid infinite recursion it the length would change meanwhile def refreshEvent(self,dontRebuild=False,forceIx=-1): currSeq=self.getter() if len(currSeq)!=self.form.count()/2: #rowCount(): if dontRebuild: return # length changed behind our back, just pretend nothing happened and update next time instead self.rebuild() currSeq=self.getter() for i in range(len(currSeq)): item=self.form.itemAt(i,QFormLayout.FieldRole) logging.trace('got item #%d %s'%(i,str(item.widget()))) widget=item.widget() if not widget.hot: widget.refresh() if forceIx>=0 and forceIx==i: widget.setFocus() def refresh(self): pass # SerializableEditor API trunk-2017.01a/gui/qt4/XYZ.png000066400000000000000000000007011304022710500156540ustar00rootroot00000000000000PNG  IHDR((msRGBbKGD pHYs  tIME ($`iAIDATXؿ.DAߊxD JT$^-- :DOH$!H(p.{WK$79>(/b0X@)LG+X_P 0 J8-"3fS-DO5'Nҏ1&f}ѣKqń`f , y{Bkyj땎p2,} 4tɾ>4k-$ow⼁5kl`W7 ^X'~qVɣ= ʭ"ymj^462jO0u)%P .rbIENDB`trunk-2017.01a/gui/qt4/YZX.xpm000066400000000000000000000034571304022710500157070ustar00rootroot00000000000000/* XPM */ static char * YZX_xpm[] = { "40 40 2 1", " c None", ". c #000000", " ...... ", " .. ", " .. ", " .. ", " . ", " .. ", " .. ", " ...... ", " ", " . ", " . ", " ... ", " ... ", " ... ", " ..... ", " ..... ", " . ", " . ", " . ", " . ", " . ", " . ", " . ", " . ", " . ", " . ", " ........... ", " . . ", " . .. .. . .. .. ", " . . . . .. . . ", " . .... . ..... .... ", " . .. .................... .... ", " . .. . ..... .. ", " . .... . ... .. ", " . . . . .. ", " . .. .. . .. ", " . . ", " ........... ", " ", " "}; trunk-2017.01a/gui/qt4/ZXY.png000066400000000000000000000007111304022710500156550ustar00rootroot00000000000000PNG  IHDR((msRGBbKGD pHYs  tIME )EZIIDATXؽJCAJXhi kKS 쵉 "hM".rYvc1bѠ7a=MaEI<$R)OZ 6alf6&-\WߒPy $bW)C,)R(`j3`"&h|5Q^ky )>UP*u8ݬP=/ `^b]78` .; *r Sjk+6HǠ։mcotlbo96`7LGeǨL:uV@&~mԕI 'tAIENDB`trunk-2017.01a/gui/qt4/ZXY.xpm000066400000000000000000000034571304022710500157070ustar00rootroot00000000000000/* XPM */ static char * ZXY_xpm[] = { "40 40 2 1", " c None", ". c #000000", " .. .. ", " . . ", " .... ", " .. ", " .. ", " .... ", " . . ", " .. .. ", " ", " . ", " . ", " ... ", " ... ", " ... ", " ..... ", " ..... ", " . ", " . ", " . ", " . ", " . ", " . ", " . ", " . ", " . ", " . ", " ........... ", " . . ", " . .. .. . ...... ", " . . . . .. .. ", " . .... . ..... .. ", " . .... .................... .. ", " . .. . ..... . ", " . .. . ... .. ", " . .. . .. ", " . .. . ...... ", " . . ", " ........... ", " ", " "}; trunk-2017.01a/gui/qt4/_GLViewer.cpp000066400000000000000000000214451304022710500170130ustar00rootroot00000000000000#include"GLViewer.hpp" #include"OpenGLManager.hpp" #include #include #include #include namespace py=boost::python; qglviewer::Vec tuple2vec(py::tuple t){ qglviewer::Vec ret; for(int i=0;i<3;i++){py::extract e(t[i]); if(!e.check()) throw invalid_argument("Element #"+boost::lexical_cast(i)+" is not a number"); ret[i]=e();} return ret;}; py::tuple vec2tuple(qglviewer::Vec v){return py::make_tuple(v[0],v[1],v[2]);}; class pyGLViewer{ const size_t viewNo; public: #define GLV if((OpenGLManager::self->views.size()<=viewNo) || !(OpenGLManager::self->views[viewNo])) throw runtime_error("No view #"+boost::lexical_cast(viewNo)); GLViewer* glv=OpenGLManager::self->views[viewNo].get(); pyGLViewer(size_t _viewNo=0): viewNo(_viewNo){} void close(){ GLV; QCloseEvent* e(new QCloseEvent); QApplication::postEvent(glv,e); } py::tuple get_grid(){GLV; return py::make_tuple(bool(glv->drawGrid & 1),bool(glv->drawGrid & 2),bool(glv->drawGrid & 4));} void set_grid(py::tuple t){GLV; glv->drawGrid=0; for(int i=0;i<3;i++) if(py::extract(t[i])()) glv->drawGrid+=1<camera()->upVector,glv->camera()->setUpVector); VEC_GET_SET(lookAt,glv->camera()->position()+glv->camera()->viewDirection,glv->camera()->lookAt); VEC_GET_SET(viewDir,glv->camera()->viewDirection,glv->camera()->setViewDirection); VEC_GET_SET(eyePosition,glv->camera()->position,glv->camera()->setPosition); #define BOOL_GET_SET(property,getter,setter)void set_##property(bool b){GLV; setter(b);} bool get_##property(){GLV; return getter();} BOOL_GET_SET(axes,glv->axisIsDrawn,glv->setAxisIsDrawn); BOOL_GET_SET(fps,glv->FPSIsDisplayed,glv->setFPSIsDisplayed); bool get_scale(){GLV; return glv->drawScale;} void set_scale(bool b){GLV; glv->drawScale=b;} bool get_orthographic(){GLV; return glv->camera()->type()==qglviewer::Camera::ORTHOGRAPHIC;} void set_orthographic(bool b){GLV; return glv->camera()->setType(b ? qglviewer::Camera::ORTHOGRAPHIC : qglviewer::Camera::PERSPECTIVE);} int get_selection(void){ GLV; return glv->selectedName(); } void set_selection(int s){ GLV; glv->setSelectedName(s); } #define FLOAT_GET_SET(property,getter,setter)void set_##property(Real r){GLV; setter(r);} Real get_##property(){GLV; return getter();} FLOAT_GET_SET(sceneRadius,glv->sceneRadius,glv->setSceneRadius); void fitAABB(const Vector3r& min, const Vector3r& max){GLV; glv->camera()->fitBoundingBox(qglviewer::Vec(min[0],min[1],min[2]),qglviewer::Vec(max[0],max[1],max[2]));} void fitSphere(const Vector3r& center,Real radius){GLV; glv->camera()->fitSphere(qglviewer::Vec(center[0],center[1],center[2]),radius);} void showEntireScene(){GLV; glv->camera()->showEntireScene();} void center(bool median){GLV; if(median)glv->centerMedianQuartile(); else glv->centerScene();} Vector2i get_screenSize(){GLV; return Vector2i(glv->width(),glv->height());} void set_screenSize(Vector2i t){ /*GLV;*/ OpenGLManager::self->emitResizeView(viewNo,t[0],t[1]);} string pyStr(){return string("(viewNo)+">";} void saveDisplayParameters(size_t n){GLV; glv->saveDisplayParameters(n);} void useDisplayParameters(size_t n){GLV; glv->useDisplayParameters(n);} void loadState(string filename){GLV; QString origStateFileName=glv->stateFileName(); glv->setStateFileName(QString(filename.c_str())); glv->restoreStateFromFile(); glv->saveStateToFile(); glv->setStateFileName(origStateFileName);} void saveState(string filename){GLV; QString origStateFileName=glv->stateFileName(); glv->setStateFileName(QString(filename.c_str())); glv->saveStateToFile(); glv->setStateFileName(origStateFileName);} string get_timeDisp(){GLV; const int& m(glv->timeDispMask); string ret; if(m&GLViewer::TIME_REAL) ret+='r'; if(m&GLViewer::TIME_VIRT) ret+="v"; if(m&GLViewer::TIME_ITER) ret+="i"; return ret;} void set_timeDisp(string s){GLV; int& m(glv->timeDispMask); m=0; FOREACH(char c, s){switch(c){case 'r': m|=GLViewer::TIME_REAL; break; case 'v': m|=GLViewer::TIME_VIRT; break; case 'i': m|=GLViewer::TIME_ITER; break; default: throw invalid_argument(string("Invalid flag for timeDisp: `")+c+"'");}}} void set_bgColor(const Vector3r& c){ QColor cc(255*c[0],255*c[1],255*c[2]); GLV; glv->setBackgroundColor(cc);} Vector3r get_bgColor(){ GLV; QColor c(glv->backgroundColor()); return Vector3r(c.red()/255.,c.green()/255.,c.blue()/255.);} void saveSnapshot(string filename) {GLV; glv->nextFrameSnapshotFilename = filename;} #undef GLV #undef VEC_GET_SET #undef BOOL_GET_SET #undef FLOAT_GET_SET }; // ask to create a new view and wait till it exists pyGLViewer createView(){ int id=OpenGLManager::self->waitForNewView(); if(id<0) throw std::runtime_error("Unable to open new 3d view."); return pyGLViewer((*OpenGLManager::self->views.rbegin())->viewId); } py::list getAllViews(){ py::list ret; FOREACH(const shared_ptr& v, OpenGLManager::self->views){ if(v) ret.append(pyGLViewer(v->viewId)); } return ret; }; void centerViews(void){ OpenGLManager::self->centerAllViews(); } shared_ptr getRenderer(){ return OpenGLManager::self->renderer; } BOOST_PYTHON_MODULE(_GLViewer){ YADE_SET_DOCSTRING_OPTS; OpenGLManager* glm=new OpenGLManager(); // keep this singleton object forever glm->emitStartTimer(); py::def("View",createView,"Create a new 3d view."); py::def("center",centerViews,"Center all views."); py::def("views",getAllViews,"Return list of all open :yref:`yade.qt.GLViewer` objects"); py::def("Renderer",&getRenderer,"Return the active :yref:`OpenGLRenderer` object."); py::class_("GLViewer",py::no_init) .add_property("upVector",&pyGLViewer::get_upVector,&pyGLViewer::set_upVector,"Vector that will be shown oriented up on the screen.") .add_property("lookAt",&pyGLViewer::get_lookAt,&pyGLViewer::set_lookAt,"Point at which camera is directed.") .add_property("viewDir",&pyGLViewer::get_viewDir,&pyGLViewer::set_viewDir,"Camera orientation (as vector).") .add_property("eyePosition",&pyGLViewer::get_eyePosition,&pyGLViewer::set_eyePosition,"Camera position.") .add_property("grid",&pyGLViewer::get_grid,&pyGLViewer::set_grid,"Display square grid in zero planes, as 3-tuple of bools for yz, xz, xy planes.") .add_property("fps",&pyGLViewer::get_fps,&pyGLViewer::set_fps,"Show frames per second indicator.") .add_property("axes",&pyGLViewer::get_axes,&pyGLViewer::set_axes,"Show arrows for axes.") .add_property("scale",&pyGLViewer::get_scale,&pyGLViewer::set_scale,"Scale of the view (?)") .add_property("sceneRadius",&pyGLViewer::get_sceneRadius,&pyGLViewer::set_sceneRadius,"Visible scene radius.") .add_property("ortho",&pyGLViewer::get_orthographic,&pyGLViewer::set_orthographic,"Whether orthographic projection is used; if false, use perspective projection.") .add_property("screenSize",&pyGLViewer::get_screenSize,&pyGLViewer::set_screenSize,"Size of the viewer's window, in scree pixels") .add_property("timeDisp",&pyGLViewer::get_timeDisp,&pyGLViewer::set_timeDisp,"Time displayed on in the vindow; is a string composed of characters *r*, *v*, *i* standing respectively for real time, virtual time, iteration number.") // .add_property("bgColor",&pyGLViewer::get_bgColor,&pyGLViewer::set_bgColor) // useless: OpenGLRenderer::Background_color is used via openGL directly, bypassing QGLViewer background property .def("fitAABB",&pyGLViewer::fitAABB,(py::arg("mn"),py::arg("mx")),"Adjust scene bounds so that Axis-aligned bounding box given by its lower and upper corners *mn*, *mx* fits in.") .def("fitSphere",&pyGLViewer::fitSphere,(py::arg("center"),py::arg("radius")),"Adjust scene bounds so that sphere given by *center* and *radius* fits in.") .def("showEntireScene",&pyGLViewer::showEntireScene) .def("center",&pyGLViewer::center,(py::arg("median")=true),"Center view. View is centered either so that all bodies fit inside (*median* = False), or so that 75\% of bodies fit inside (*median* = True).") .def("saveState",&pyGLViewer::saveState,(py::arg("stateFilename")=".qglviewer.xml"),"Save display parameters into a file. Saves state for both :yref:`GLViewer` and associated :yref:`OpenGLRenderer`.") .def("loadState",&pyGLViewer::loadState,(py::arg("stateFilename")=".qglviewer.xml"),"Load display parameters from file saved previously into.") .def("__repr__",&pyGLViewer::pyStr).def("__str__",&pyGLViewer::pyStr) .def("close",&pyGLViewer::close) .def("saveSnapshot",&pyGLViewer::saveSnapshot,(py::arg("filename")),"Save the current view to image file") .add_property("selection",&pyGLViewer::get_selection,&pyGLViewer::set_selection) ; } trunk-2017.01a/gui/qt4/__init__.py000066400000000000000000000251221304022710500165710ustar00rootroot00000000000000# encoding: utf-8 import yade.runtime if not yade.runtime.hasDisplay: msg = "Connecting to DISPLAY at Yade startup failed, unable to activate the qt4 interface." import os if 'YADE_BATCH' in os.environ: msg += "\nDo not import qt when running in batch mode." raise ImportError(msg) from PyQt4.QtGui import * from PyQt4 import QtCore from yade.qt.ui_controller import Ui_Controller from yade.qt.Inspector import * from yade import * import yade.system, yade.config from yade.qt._GLViewer import * maxWebWindows=1 "Number of webkit windows that will be cycled to show help on clickable objects" webWindows=[] "holds instances of QtWebKit windows; clicking an url will open it in the window that was the least recently updated" sphinxOnlineDocPath='https://www.yade-dem.org/doc/' "Base URL for the documentation. Packaged versions should change to the local installation directory." import os.path # find if we have docs installed locally from package sphinxLocalDocPath=yade.config.prefix+'/share/doc/yade'+yade.config.suffix+'-doc/html/' sphinxBuildDocPath=yade.config.sourceRoot+'/doc/sphinx/_build/html/' # we prefer the packaged documentation for this version, if installed if os.path.exists(sphinxLocalDocPath+'/index.html'): sphinxPrefix='file://'+sphinxLocalDocPath # otherwise look for documentation generated in the source tree elif os.path.exists(sphinxBuildDocPath+'/index.html'): sphinxPrefix='file://'+sphinxBuildDocPath # fallback to online docs else: sphinxPrefix=sphinxOnlineDocPath sphinxDocWrapperPage=sphinxPrefix+'/yade.wrapper.html' def openUrl(url): from PyQt4 import QtWebKit global maxWebWindows,webWindows reuseLast=False # use the last window if the class is the same and only the attribute differs try: reuseLast=(len(webWindows)>0 and str(webWindows[-1].url()).split('#')[-1].split('.')[2]==url.split('#')[-1].split('.')[2]) #print str(webWindows[-1].url()).split('#')[-1].split('.')[2],url.split('#')[-1].split('.')[2] except: pass if not reuseLast: if len(webWindows)0: self.displayCombo.insertSeparator(10000); afterSep=0 for c in yade.system.childClasses(bc) | set([bc]): inst=eval(c+'()'); if len(set(inst.dict().keys())-set(['label']))>0: self.displayCombo.addItem(c); afterSep+=1 def inspectSlot(self): self.inspector=SimulationInspector(parent=None) self.inspector.show() def setTabActive(self,what): if what=='simulation': ix=0 elif what=='display': ix=1 elif what=='generator': ix=2 elif what=='python': ix=3 else: raise ValueErorr("No such tab: "+what) self.controllerTabs.setCurrentIndex(ix) def generatorComboSlot(self,genStr): "update generator parameters when a new one is selected" gen=eval(str(genStr)+'()') self.generator=gen se=SerializableEditor(gen,parent=self.generatorArea,showType=True) self.generatorArea.setWidget(se) def pythonComboSlot(self,cmd): try: code=compile(str(cmd),'','exec') exec code in globals() except: import traceback traceback.print_exc() def generateSlot(self): filename=str(self.generatorFilenameEdit.text()) if self.generatorMemoryCheck.isChecked(): filename=':memory:'+filename print 'BUG: Saving to memory slots freezes Yade (cause unknown). Cross fingers.' #print 'Will save to ',filename self.generator.generate(filename) if self.generatorAutoCheck: O.load(filename) self.setTabActive('simulation') if len(views())==0: v=View(); v.center() def displayComboSlot(self,dispStr): ser=(self.renderer if dispStr=='OpenGLRenderer' else eval(str(dispStr)+'()')) path='yade.qt.Renderer()' if dispStr=='OpenGLRenderer' else dispStr se=SerializableEditor(ser,parent=self.displayArea,ignoredAttrs=set(['label']),showType=True,path=path) self.displayArea.setWidget(se) def loadSlot(self): f=QFileDialog.getOpenFileName(self,'Load simulation','','Yade simulations (*.xml *.xml.bz2 *.xml.gz *.yade *.yade.gz *.yade.bz2);; *.*') f=str(f) if not f: return # cancelled self.deactivateControls() O.load(f) def saveSlot(self): f=QFileDialog.getSaveFileName(self,'Save simulation','','Yade simulations (*.xml *.xml.bz2 *.xml.gz *.yade *.yade.gz *.yade.bz2);; *.*') f=str(f) if not f: return # cancelled O.save(f) def reloadSlot(self): self.deactivateControls() from yade import plot plot.splitData() O.reload() def dtFixedSlot(self): O.dt=O.dt O.dynDt=False def dtDynSlot(self): O.dt=-O.dt def dtEditNoupdateSlot(self): self.dtEditUpdate=False def dtEditedSlot(self): try: t=float(self.dtEdit.text()) O.dt=t except ValueError: pass self.dtEdit.setText(str(O.dt)) self.dtEditUpdate=True def playSlot(self): O.run() def pauseSlot(self): O.pause() def stepSlot(self): O.step() def subStepSlot(self,value): O.subStepping=bool(value) def show3dSlot(self, show): vv=views() assert(len(vv) in (0,1)) if show: if len(vv)==0: View() else: if len(vv)>0: vv[0].close() def setReferenceSlot(self): # sets reference periodic cell as well utils.setRefSe3() def centerSlot(self): for v in views(): v.center() def setViewAxes(self,dir,up): try: v=views()[0] v.viewDir=dir v.upVector=up v.center() except IndexError: pass def xyzSlot(self): self.setViewAxes((0,0,-1),(0,1,0)) def yzxSlot(self): self.setViewAxes((-1,0,0),(0,0,1)) def zxySlot(self): self.setViewAxes((0,-1,0),(1,0,0)) def refreshEvent(self): self.refreshValues() self.activateControls() def deactivateControls(self): self.realTimeLabel.setText('') self.virtTimeLabel.setText('') self.iterLabel.setText('') self.fileLabel.setText('[loading]') self.playButton.setEnabled(False) self.pauseButton.setEnabled(False) self.stepButton.setEnabled(False) self.subStepCheckbox.setEnabled(False) self.reloadButton.setEnabled(False) self.dtFixedRadio.setEnabled(False) self.dtDynRadio.setEnabled(False) self.dtEdit.setEnabled(False) self.dtEdit.setText('') self.dtEditUpdate=True def activateControls(self): hasSim=len(O.engines)>0 running=O.running if hasSim: self.playButton.setEnabled(not running) self.pauseButton.setEnabled(running) self.reloadButton.setEnabled(O.filename is not None) self.stepButton.setEnabled(not running) self.subStepCheckbox.setEnabled(not running) else: self.playButton.setEnabled(False) self.pauseButton.setEnabled(False) self.reloadButton.setEnabled(False) self.stepButton.setEnabled(False) self.subStepCheckbox.setEnabled(False) self.dtFixedRadio.setEnabled(True) self.dtDynRadio.setEnabled(O.dynDtAvailable) dynDt=O.dynDt self.dtFixedRadio.setChecked(not dynDt) self.dtDynRadio.setChecked(dynDt) if dynDt or self.dtEditUpdate: self.dtEdit.setText(str(O.dt)) if dynDt: self.dtEditUpdate=True self.dtEdit.setEnabled(not dynDt) fn=O.filename self.fileLabel.setText(fn if fn else '[no file]') def refreshValues(self): rt=int(O.realtime); t=O.time; iter=O.iter; assert(len(self.iterTimes)==len(self.iterValues)) if len(self.iterTimes)==0: self.iterTimes.append(rt); self.iterValues.append(iter); self.iterPerSec=0 # update always for the first time elif rt-self.iterTimes[-1]>self.iterPerSecTimeout: # update after a timeout if len(self.iterTimes)==1: self.iterTimes.append(self.iterTimes[0]); self.iterValues.append(self.iterValues[0]) # 2 values, first one is bogus self.iterTimes[0]=self.iterTimes[1]; self.iterValues[0]=self.iterValues[1] self.iterTimes[1]=rt; self.iterValues[1]=iter; self.iterPerSec=(self.iterValues[-1]-self.iterValues[-2])/(self.iterTimes[-1]-self.iterTimes[-2]) if not O.running: self.iterPerSec=0 stopAtIter=O.stopAtIter subStepInfo='' if O.subStepping: subStep=O.subStep if subStep==-1: subStepInfo=u'→ prologue' elif subStep>=0 and subStepepilogue    ' else: raise RuntimeError("Invalid O.subStep value %d, should be ∈{-1,…,len(o.engines)}"%subStep) subStepInfo="
    sub %d/%d [%s]"%(subStep,len(O.engines),subStepInfo) self.subStepCheckbox.setChecked(O.subStepping) # might have been changed async if stopAtIter<=iter: self.realTimeLabel.setText('%02d:%02d:%02d'%(rt//3600,(rt%3600)//60,rt%60)) self.iterLabel.setText('#%ld, %.1f/s %s'%(iter,self.iterPerSec,subStepInfo)) else: e=int((stopAtIter-iter)*self.iterPerSec) self.realTimeLabel.setText('%02d:%02d:%02d (ETA %02d:%02d:%02d)'%(rt//3600,rt//60,rt%60,e//3600,e//60,e%60)) self.iterLabel.setText('#%ld / %ld, %.1f/s %s'%(O.iter,stopAtIter,self.iterPerSec,subStepInfo)) if t!=float('inf'): s=int(t); ms=int(t*1000)%1000; us=int(t*1000000)%1000; ns=int(t*1000000000)%1000 self.virtTimeLabel.setText(u'%03ds%03dm%03dμ%03dn'%(s,ms,us,ns)) else: self.virtTimeLabel.setText(u'[ ∞ ] ?!') self.show3dButton.setChecked(len(views())>0) def Generator(): global controller if not controller: controller=ControllerClass(); controller.show(); controller.raise_() controller.setTabActive('generator') def Controller(): global controller if not controller: controller=ControllerClass(); controller.show(); controller.raise_() controller.setTabActive('simulation') def Inspector(): global controller if not controller: controller=ControllerClass(); controller.inspectSlot() #if __name__=='__main__': # from PyQt4 import QtGui # import sys # qapp=QtGui.QApplication(sys.argv) # c=Controller().show() # qapp.exec_() trunk-2017.01a/gui/qt4/controller.ui000066400000000000000000001000301304022710500171720ustar00rootroot00000000000000 Controller 0 0 290 495 0 0 Yade :/img/yade-favicon.xpm:/img/yade-favicon.xpm 0 0 0 0 0 Simulation 0 0 6 QLayout::SetMinAndMaxSize true 0 0 0 0 Load true 0 0 0 0 Save Inspect QLayout::SetMinimumSize QFormLayout::AllNonFixedFieldsGrow 6 6 6 real 00:00:00 virt 00:000.000m000μ000n iter #0, 0.0/s true Δt fixed true false time stepper false Qt::ClickFocus Qt::Horizontal 40 20 [no file] Qt::Horizontal 40 20 6 6 0 false 5 0 18 ▶ 32 32 true false false 4 0 18 ▮▮ 32 32 0 0 0 false 2 0 12 ▶▮ 32 32 7 sub-step false 5 0 22 ↻ 32 32 Show 3D true Reference Center 48 48 :/img/XYZ.xpm:/img/XYZ.xpm 40 40 48 48 :/img/YZX.xpm:/img/YZX.xpm 40 40 48 48 :/img/ZXY.xpm:/img/ZXY.xpm 40 40 Display 0 0 true 0 0 284 433 Generate 0 0 200 200 0 0 true 0 0 500 500 0 0 500 500 398 336 false memory slot false false /tmp/scene.yade.gz open automatically true Generate Python Monospace IBeamCursor Qt::StrongFocus false true QComboBox::InsertAtTop 1 false <i>(Output appears in the terminal)</i> Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter Qt::Vertical 20 40 loadButton clicked() Controller loadSlot() 93 64 284 0 saveButton clicked() Controller saveSlot() 184 64 284 0 dtFixedRadio clicked() Controller dtFixedSlot() 143 170 284 0 dtDynRadio clicked() Controller dtDynSlot() 268 176 284 4 dtEdit editingFinished() Controller dtEditedSlot() 147 204 284 43 playButton clicked() Controller playSlot() 116 304 3 309 pauseButton clicked() Controller pauseSlot() 268 304 284 311 referenceButton clicked() Controller setReferenceSlot() 184 429 5 469 centerButton clicked() Controller centerSlot() 275 429 284 469 xyzButton clicked() Controller xyzSlot() 93 460 0 469 yzxButton clicked() Controller yzxSlot() 184 485 243 469 zxyButton clicked() Controller zxySlot() 275 485 284 469 generateButton clicked() Controller generateSlot() 101 60 284 469 dtEdit textEdited(QString) Controller dtEditNoupdateSlot() 147 204 284 205 dtEdit cursorPositionChanged(int,int) Controller dtEditNoupdateSlot() 147 204 284 181 generatorCombo currentIndexChanged(QString) Controller generatorComboSlot() 101 60 284 130 displayCombo currentIndexChanged(QString) Controller displayComboSlot() 101 45 284 108 pythonCombo activated(QString) Controller pythonComboSlot() 107 66 284 68 inspectButton clicked() Controller inspectSlot() 247 54 0 58 reloadButton clicked() Controller reloadSlot() 194 363 284 437 stepButton clicked() Controller stepSlot() 79 363 6 450 subStepCheckbox stateChanged(int) Controller subStepSlot() 42 376 -2 381 show3dButton toggled(bool) Controller show3dSlot(bool) 42 418 -2 422 loadSlot() saveSlot() reloadSlot() playSlot() pauseSlot() stepSlot() setReferenceSlot() centerSlot() dtFixedSlot() dtDynSlot() dtEditedSlot() xyzSlot() yzxSlot() zxySlot() generateSlot() dtEditNoupdateSlot() generatorComboSlot() displayComboSlot() pythonComboSlot() pythonEditSlot() inspectSlot() subStepSlot() show3dSlot(bool) trunk-2017.01a/gui/qt4/img.qrc000066400000000000000000000002441304022710500157410ustar00rootroot00000000000000 yade-favicon.xpm XYZ.xpm YZX.xpm ZXY.xpm trunk-2017.01a/gui/qt4/yade-favicon.png000066400000000000000000000022211304022710500175260ustar00rootroot00000000000000PNG  IHDRasRGBbKGD pHYs  tIME 65tEXtCommentCreated with GIMPWIDAT8{lu]w}\6Qa6c-É6DMϑh_&8KY1&g[u׻ |zY*#Oq羪hdOr,0ͬY8[/HG+i+wG~N7:f_~5W+LZ.67vu~yIQ=ˣqx* cD2o1y4(>7!D߻ |aj= ]^BQs/yv8ql1zqy͜68xDwـ1- 4vt؁>tb>l"q4Qyk?񸥴w"Bv]j9pgMQ++.꒎9n)CEyGv{ёy+BEHrxnְVw5uP+s0_Cs!g'O-G~.g3V FM Clbu#ċS7o",`d0h1N,2B7 wochج f61hS>qd ȵk]]!M'H̬NOwԔh4 @n,Iy8* yӹ/9um,Ox6ze-E"utA Hy9 YU.j1‘Oip㭂%b*10@N -4dD`3@TIމH2%tŎ4Q0R_DtCp},y L f=U\:gsl 8ڋVp)CM;;;G|6 PV'L@WTlSS&cfY6F4P [H8ǞN [^.E"" ʄ Tne [Z A3$Tc˻\c[?\~ZՐ[guyʀi9Iڼщk|IENDB`trunk-2017.01a/gui/qt4/yade-favicon.xpm000066400000000000000000000076341304022710500175630ustar00rootroot00000000000000/* XPM */ static char * yade_favicon_xpm[] = { "16 16 210 2", " c None", ". c #F47372", "+ c #F1B4B5", "@ c #909092", "# c #EA5A5A", "$ c #8E4D3C", "% c #746C35", "& c #616233", "* c #4B4B0E", "= c #939191", "- c #8A8A8A", "; 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", "@.#.$.%.&.*.=.-.;.>.,. '. ", ").!.~.{.].^./.(._.:.<.[.}.|. ", "1.2.3.4.5.6.7.8.9.0.a. b. ", "c.d.e.f.g.h.i.j.k.l.m.n.o. p.q.", "r.s.t.u.v.w.x.y.z.A.B.C.D.E.F.G.", "H.I.J.K.L.M.N.O.P.Q.R.S.T.U.V.W.", "X.Y.Z.`. +.+++@+#+$+%+&+*+=+ ", "-+;+>+,+'+)+!+~+{+]+^+/+(+_+:+<+"}; trunk-2017.01a/gui/qt5/000077500000000000000000000000001304022710500144575ustar00rootroot00000000000000trunk-2017.01a/gui/qt5/GLViewer.cpp000066400000000000000000000556501304022710500166620ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2005 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include"GLViewer.hpp" #include"OpenGLManager.hpp" #include #include #include #include #include #include #include #include #include #include #include #include #include #ifdef YADE_GL2PS #include #endif static unsigned initBlocked(State::DOF_NONE); CREATE_LOGGER(GLViewer); GLLock::GLLock(GLViewer* _glv): boost::try_mutex::scoped_lock(Omega::instance().renderMutex), glv(_glv){ glv->makeCurrent(); } GLLock::~GLLock(){ glv->doneCurrent(); } #define _W3 setw(3)<emitCloseView(viewId); e->accept(); } GLViewer::GLViewer(int _viewId, const shared_ptr& _renderer, QGLWidget* shareWidget): QGLViewer(/*parent*/(QWidget*)NULL,shareWidget), renderer(_renderer), viewId(_viewId) { isMoving=false; drawGrid=0; drawScale=true; timeDispMask=TIME_REAL|TIME_VIRT|TIME_ITER; cut_plane = 0; cut_plane_delta = -2; gridSubdivide = false; resize(550,550); last=-1; if(viewId==0) setWindowTitle("Primary view"); else setWindowTitle(("Secondary view #"+boost::lexical_cast(viewId)).c_str()); show(); mouseMovesCamera(); manipulatedClipPlane=-1; if(manipulatedFrame()==0) setManipulatedFrame(new qglviewer::ManipulatedFrame()); xyPlaneConstraint=shared_ptr(new qglviewer::LocalConstraint()); manipulatedFrame()->setConstraint(NULL); setKeyDescription(Qt::Key_Return,"Run simulation."); setKeyDescription(Qt::Key_A,"Toggle visibility of global axes."); setKeyDescription(Qt::Key_C,"Set scene center so that all bodies are visible; if a body is selected, center around this body."); setKeyDescription(Qt::Key_C & Qt::AltModifier,"Set scene center to median body position (same as space)"); setKeyDescription(Qt::Key_D,"Toggle time display mask"); setKeyDescription(Qt::Key_G,"Toggle grid visibility; g turns on and cycles"); setKeyDescription(Qt::Key_G & Qt::ShiftModifier ,"Hide grid."); setKeyDescription(Qt::Key_M, "Move selected object."); setKeyDescription(Qt::Key_X,"Show the xz [shift: xy] (up-right) plane (clip plane: align normal with +x)"); setKeyDescription(Qt::Key_Y,"Show the yx [shift: yz] (up-right) plane (clip plane: align normal with +y)"); setKeyDescription(Qt::Key_Z,"Show the zy [shift: zx] (up-right) plane (clip plane: align normal with +z)"); setKeyDescription(Qt::Key_Period,"Toggle grid subdivision by 10"); setKeyDescription(Qt::Key_S,"Save QGLViewer state to /tmp/qglviewerState.xml"); setKeyDescription(Qt::Key_T,"Switch orthographic / perspective camera"); setKeyDescription(Qt::Key_O,"Set narrower field of view"); setKeyDescription(Qt::Key_P,"Set wider field of view"); setKeyDescription(Qt::Key_R,"Revolve around scene center"); setKeyDescription(Qt::Key_V,"Save PDF of the current view to /tmp/yade-snapshot-0001.pdf (whichever number is available first). (Must be compiled with the gl2ps feature.)"); setPathKey(-Qt::Key_F1); setPathKey(-Qt::Key_F2); setKeyDescription(Qt::Key_Escape,"Manipulate scene (default)"); setKeyDescription(Qt::Key_F1,"Manipulate clipping plane #1"); setKeyDescription(Qt::Key_F2,"Manipulate clipping plane #2"); setKeyDescription(Qt::Key_F3,"Manipulate clipping plane #3"); setKeyDescription(Qt::Key_1,"Make the manipulated clipping plane parallel with plane #1"); setKeyDescription(Qt::Key_2,"Make the manipulated clipping plane parallel with plane #2"); setKeyDescription(Qt::Key_2,"Make the manipulated clipping plane parallel with plane #3"); setKeyDescription(Qt::Key_1 & Qt::AltModifier,"Add/remove plane #1 to/from the bound group"); setKeyDescription(Qt::Key_2 & Qt::AltModifier,"Add/remove plane #2 to/from the bound group"); setKeyDescription(Qt::Key_3 & Qt::AltModifier,"Add/remove plane #3 to/from the bound group"); setKeyDescription(Qt::Key_0,"Clear the bound group"); setKeyDescription(Qt::Key_7,"Load [Alt: save] view configuration #0"); setKeyDescription(Qt::Key_8,"Load [Alt: save] view configuration #1"); setKeyDescription(Qt::Key_9,"Load [Alt: save] view configuration #2"); setKeyDescription(Qt::Key_Space,"Center scene (same as Alt-C); clip plane: activate/deactivate"); centerScene(); } bool GLViewer::isManipulating(){ return isMoving || manipulatedClipPlane>=0; } void GLViewer::resetManipulation(){ mouseMovesCamera(); setSelectedName(-1); isMoving=false; manipulatedClipPlane=-1; } void GLViewer::startClipPlaneManipulation(int planeNo){ assert(planeNonumClipPlanes); resetManipulation(); mouseMovesManipulatedFrame(xyPlaneConstraint.get()); manipulatedClipPlane=planeNo; const Se3r se3(renderer->clipPlaneSe3[planeNo]); manipulatedFrame()->setPositionAndOrientation(qglviewer::Vec(se3.position[0],se3.position[1],se3.position[2]),qglviewer::Quaternion(se3.orientation.x(),se3.orientation.y(),se3.orientation.z(),se3.orientation.w())); string grp=strBoundGroup(); displayMessage("Manipulating clip plane #"+boost::lexical_cast(planeNo+1)+(grp.empty()?grp:" (bound planes:"+grp+")")); } string GLViewer::getState(){ QString origStateFileName=stateFileName(); string tmpFile=Omega::instance().tmpFilename(); setStateFileName(QString(tmpFile.c_str())); saveStateToFile(); setStateFileName(origStateFileName); LOG_WARN("State saved to temp file "<>ss; ret+=" "+ss;}; in.close(); boost::filesystem::remove(boost::filesystem::path(tmpFile)); return ret; } void GLViewer::setState(string state){ string tmpFile=Omega::instance().tmpFilename(); std::ofstream out(tmpFile.c_str()); if(!out.good()){ LOG_ERROR("Error opening temp file `"<key()==Qt::Key_A){ toggleAxisIsDrawn(); return; } else if(e->key()==Qt::Key_Escape){ if(!isManipulating()){ setSelectedName(-1); return; } else { resetManipulation(); displayMessage("Manipulating scene."); } } else if(e->key()==Qt::Key_Space){ if(manipulatedClipPlane>=0) {displayMessage("Clip plane #"+boost::lexical_cast(manipulatedClipPlane+1)+(renderer->clipPlaneActive[manipulatedClipPlane]?" de":" ")+"activated"); renderer->clipPlaneActive[manipulatedClipPlane]=!renderer->clipPlaneActive[manipulatedClipPlane]; } else{ centerMedianQuartile(); } } /* function keys */ else if(e->key()==Qt::Key_F1 || e->key()==Qt::Key_F2 || e->key()==Qt::Key_F3 /* || ... */ ){ int n=0; if(e->key()==Qt::Key_F1) n=1; else if(e->key()==Qt::Key_F2) n=2; else if(e->key()==Qt::Key_F3) n=3; assert(n>0); int planeId=n-1; if(planeId>=renderer->numClipPlanes) return; if(planeId!=manipulatedClipPlane) startClipPlaneManipulation(planeId); } /* numbers */ else if(e->key()==Qt::Key_0 && (e->modifiers() & Qt::AltModifier)) { boundClipPlanes.clear(); displayMessage("Cleared bound planes group.");} else if(e->key()==Qt::Key_1 || e->key()==Qt::Key_2 || e->key()==Qt::Key_3 /* || ... */ ){ int n=0; if(e->key()==Qt::Key_1) n=1; else if(e->key()==Qt::Key_2) n=2; else if(e->key()==Qt::Key_3) n=3; assert(n>0); int planeId=n-1; if(planeId>=renderer->numClipPlanes) return; // no such clipping plane if(e->modifiers() & Qt::AltModifier){ if(boundClipPlanes.count(planeId)==0) {boundClipPlanes.insert(planeId); displayMessage("Added plane #"+boost::lexical_cast(planeId+1)+" to the bound group: "+strBoundGroup());} else {boundClipPlanes.erase(planeId); displayMessage("Removed plane #"+boost::lexical_cast(planeId+1)+" from the bound group: "+strBoundGroup());} } else if(manipulatedClipPlane>=0 && manipulatedClipPlane!=planeId) { const Quaternionr& o=renderer->clipPlaneSe3[planeId].orientation; manipulatedFrame()->setOrientation(qglviewer::Quaternion(o.x(),o.y(),o.z(),o.w())); displayMessage("Copied orientation from plane #1"); } } else if(e->key()==Qt::Key_7 || e->key()==Qt::Key_8 || e->key()==Qt::Key_9){ int nn=-1; if(e->key()==Qt::Key_7)nn=0; else if(e->key()==Qt::Key_8)nn=1; else if(e->key()==Qt::Key_9)nn=2; assert(nn>=0); size_t n=(size_t)nn; if(e->modifiers() & Qt::AltModifier) saveDisplayParameters(n); else useDisplayParameters(n); } /* letters alphabetically */ else if(e->key()==Qt::Key_C && (e->modifiers() & Qt::AltModifier)){ displayMessage("Median centering"); centerMedianQuartile(); } else if(e->key()==Qt::Key_C){ // center around selected body if(selectedName() >= 0 && (*(Omega::instance().getScene()->bodies)).exists(selectedName())) setSceneCenter(manipulatedFrame()->position()); // make all bodies visible else centerScene(); } else if(e->key()==Qt::Key_D &&(e->modifiers() & Qt::AltModifier)){ Body::id_t id; if((id=Omega::instance().getScene()->selectedBody)>=0){ const shared_ptr& b=Body::byId(id); b->setDynamic(!b->isDynamic()); LOG_INFO("Body #"<isDynamic()?"":"NOT")<<" dynamic"); } } else if(e->key()==Qt::Key_D) {timeDispMask+=1; if(timeDispMask>(TIME_REAL|TIME_VIRT|TIME_ITER))timeDispMask=0; } else if(e->key()==Qt::Key_G) { if(e->modifiers() & Qt::ShiftModifier){ drawGrid=0; return; } else drawGrid++; if(drawGrid>=8) drawGrid=0; } else if (e->key()==Qt::Key_M && selectedName() >= 0){ if(!(isMoving=!isMoving)){ displayMessage("Moving done."); if (last>=0) {Body::byId(Body::id_t(last))->state->blockedDOFs=initBlocked; last=-1;} mouseMovesCamera();} else{ displayMessage("Moving selected object"); long selection = Omega::instance().getScene()->selectedBody; initBlocked=Body::byId(Body::id_t(selection))->state->blockedDOFs; last=selection; Body::byId(Body::id_t(selection))->state->blockedDOFs=State::DOF_ALL; Quaternionr& q = Body::byId(selection)->state->ori; Vector3r& v = Body::byId(selection)->state->pos; manipulatedFrame()->setPositionAndOrientation(qglviewer::Vec(v[0],v[1],v[2]),qglviewer::Quaternion(q.x(),q.y(),q.z(),q.w())); mouseMovesManipulatedFrame();} } else if (e->key() == Qt::Key_T) camera()->setType(camera()->type()==qglviewer::Camera::ORTHOGRAPHIC ? qglviewer::Camera::PERSPECTIVE : qglviewer::Camera::ORTHOGRAPHIC); else if(e->key()==Qt::Key_O) camera()->setFieldOfView(camera()->fieldOfView()*0.9); else if(e->key()==Qt::Key_P) camera()->setFieldOfView(camera()->fieldOfView()*1.1); else if(e->key()==Qt::Key_R){ // reverse the clipping plane; revolve around scene center if no clipping plane selected if(manipulatedClipPlane>=0 && manipulatedClipPlanenumClipPlanes){ /* here, we must update both manipulatedFrame orientation and renderer->clipPlaneSe3 orientation in the same way */ Quaternionr& ori=renderer->clipPlaneSe3[manipulatedClipPlane].orientation; ori=Quaternionr(AngleAxisr(Mathr::PI,Vector3r(0,1,0)))*ori; manipulatedFrame()->setOrientation(qglviewer::Quaternion(qglviewer::Vec(0,1,0),Mathr::PI)*manipulatedFrame()->orientation()); displayMessage("Plane #"+boost::lexical_cast(manipulatedClipPlane+1)+" reversed."); } else { camera()->setRevolveAroundPoint(sceneCenter()); } } else if(e->key()==Qt::Key_S){ LOG_INFO("Saving QGLViewer state to /tmp/qglviewerState.xml"); setStateFileName("/tmp/qglviewerState.xml"); saveStateToFile(); setStateFileName(QString::null); } else if(e->key()==Qt::Key_L){ LOG_INFO("Loading QGLViewer state from /tmp/qglviewerState.xml"); setStateFileName("/tmp/qglviewerState.xml"); restoreStateFromFile(); setStateFileName(QString::null); } else if(e->key()==Qt::Key_X || e->key()==Qt::Key_Y || e->key()==Qt::Key_Z){ int axisIdx=(e->key()==Qt::Key_X?0:(e->key()==Qt::Key_Y?1:2)); if(manipulatedClipPlane<0){ qglviewer::Vec up(0,0,0), vDir(0,0,0); bool alt=(e->modifiers() && Qt::ShiftModifier); up[axisIdx]=1; vDir[(axisIdx+(alt?2:1))%3]=alt?1:-1; camera()->setViewDirection(vDir); camera()->setUpVector(up); centerMedianQuartile(); } else{ // align clipping normal plane with world axis // x: (0,1,0),pi/2; y: (0,0,1),pi/2; z: (1,0,0),0 qglviewer::Vec axis(0,0,0); axis[(axisIdx+1)%3]=1; Real angle=axisIdx==2?0:Mathr::PI/2; manipulatedFrame()->setOrientation(qglviewer::Quaternion(axis,angle)); } } else if(e->key()==Qt::Key_Period) gridSubdivide = !gridSubdivide; else if(e->key()==Qt::Key_Return){ if (Omega::instance().isRunning()) Omega::instance().pause(); else Omega::instance().run(); LOG_INFO("Running..."); } #ifdef YADE_GL2PS else if(e->key()==Qt::Key_V){ for(int i=0; ;i++){ std::ostringstream fss; fss<<"/tmp/yade-snapshot-"<key()==Qt::Key_Plus ){ cut_plane = std::min(1.0, cut_plane + std::pow(10.0,(double)cut_plane_delta)); static_cast(camera())->setCuttingDistance(cut_plane); displayMessage("Cut plane: "+boost::lexical_cast(cut_plane)); }else if( e->key()==Qt::Key_Minus ){ cut_plane = std::max(0.0, cut_plane - std::pow(10.0,(double)cut_plane_delta)); static_cast(camera())->setCuttingDistance(cut_plane); displayMessage("Cut plane: "+boost::lexical_cast(cut_plane)); }else if( e->key()==Qt::Key_Slash ){ cut_plane_delta -= 1; displayMessage("Cut plane increment: 1e"+(cut_plane_delta>0?std::string("+"):std::string(""))+boost::lexical_cast(cut_plane_delta)); }else if( e->key()==Qt::Key_Asterisk ){ cut_plane_delta = std::min(1+cut_plane_delta,-1); displayMessage("Cut plane increment: 1e"+(cut_plane_delta>0?std::string("+"):std::string(""))+boost::lexical_cast(cut_plane_delta)); } #endif else if(e->key()!=Qt::Key_Escape && e->key()!=Qt::Key_Space) QGLViewer::keyPressEvent(e); updateGL(); } /* Center the scene such that periodic cell is contained in the view */ void GLViewer::centerPeriodic(){ Scene* scene=Omega::instance().getScene().get(); assert(scene->isPeriodic); Vector3r center=.5*scene->cell->getSize(); Vector3r halfSize=.5*scene->cell->getSize(); float radius=std::max(halfSize[0],std::max(halfSize[1],halfSize[2])); LOG_DEBUG("Periodic scene center="<isPeriodic){ centerPeriodic(); return; } long nBodies=scene->bodies->size(); if(nBodies<4) { LOG_DEBUG("Less than 4 bodies, median makes no sense; calling centerScene() instead."); return centerScene(); } std::vector coords[3]; for(int i=0;i<3;i++)coords[i].reserve(nBodies); FOREACH(shared_ptr b, *scene->bodies){ if(!b) continue; for(int i=0; i<3; i++) coords[i].push_back(b->state->pos[i]); } Vector3r median,interQuart; for(int i=0;i<3;i++){ sort(coords[i].begin(),coords[i].end()); median[i]=*(coords[i].begin()+nBodies/2); interQuart[i]=*(coords[i].begin()+3*nBodies/4)-*(coords[i].begin()+nBodies/4); } LOG_DEBUG("Median position is"<isPeriodic){ centerPeriodic(); return; } LOG_INFO("Select with shift, press 'm' to move."); Vector3r min,max; if(not(rb->bound)){ rb->updateBound();} min=rb->bound->min; max=rb->bound->max; bool hasNan=(std::isnan(min[0])||std::isnan(min[1])||std::isnan(min[2])||std::isnan(max[0])||std::isnan(max[1])||std::isnan(max[2])); Real minDim=std::min(max[0]-min[0],std::min(max[1]-min[1],max[2]-min[2])); if(minDim<=0 || hasNan){ // Aabb is not yet calculated... LOG_DEBUG("scene's bound not yet calculated or has zero or nan dimension(s), attempt get that from bodies' positions."); Real inf=std::numeric_limits::infinity(); min=Vector3r(inf,inf,inf); max=Vector3r(-inf,-inf,-inf); FOREACH(const shared_ptr& b, *rb->bodies){ if(!b) continue; max=max.cwiseMax(b->state->pos); min=min.cwiseMin(b->state->pos); } if(std::isinf(min[0])||std::isinf(min[1])||std::isinf(min[2])||std::isinf(max[0])||std::isinf(max[1])||std::isinf(max[2])){ LOG_DEBUG("No min/max computed from bodies either, setting cube (-1,-1,-1)×(1,1,1)"); min=-Vector3r::Ones(); max=Vector3r::Ones(); } } else {LOG_DEBUG("Using scene's Aabb");} LOG_DEBUG("Got scene box min="<=0) { Body::byId(Body::id_t(last))->state->blockedDOFs=initBlocked; last=-1; Omega::instance().getScene()->selectedBody = -1;} if(isMoving){ displayMessage("Moving finished"); mouseMovesCamera(); isMoving=false; Omega::instance().getScene()->selectedBody = -1; } return; } if(selection>=0 && (*(Omega::instance().getScene()->bodies)).exists(selection)){ resetManipulation(); if (last>=0) {Body::byId(Body::id_t(last))->state->blockedDOFs=initBlocked; last=-1;} if(Body::byId(Body::id_t(selection))->isClumpMember()){ // select clump (invisible) instead of its member LOG_DEBUG("Clump member #"<clumpId; } setSelectedName(selection); LOG_DEBUG("New selection "<(selection)+(Body::byId(selection)->isClump()?" (clump)":"")); Omega::instance().getScene()->selectedBody = selection; PyGILState_STATE gstate; gstate = PyGILState_Ensure(); boost::python::object main=boost::python::import("__main__"); boost::python::object global=main.attr("__dict__"); // the try/catch block must be properly nested inside PyGILState_Ensure and PyGILState_Release try{ boost::python::eval(string("onBodySelect("+boost::lexical_cast(selection)+")").c_str(),global,global); } catch (boost::python::error_already_set const &) { LOG_DEBUG("unable to call onBodySelect. Not defined?"); } PyGILState_Release(gstate); // see https://svn.boost.org/trac/boost/ticket/2781 for exception handling } } // maybe new object will be selected. // if so, then set isDynamic of previous selection, to old value void GLViewer::endSelection(const QPoint &point){ manipulatedClipPlane=-1; QGLViewer::endSelection(point); } string GLViewer::getRealTimeString(){ ostringstream oss; boost::posix_time::time_duration t=Omega::instance().getRealTime_duration(); unsigned d=t.hours()/24,h=t.hours()%24,m=t.minutes(),s=t.seconds(); oss<<"clock "; if(d>0) oss<0) oss<<_W2<=0x020603 qreal YadeCamera::zNear() const #else float YadeCamera::zNear() const #endif { float z = distanceToSceneCenter() - zClippingCoefficient()*sceneRadius()*(1.f-2*cuttingDistance); // Prevents negative or null zNear values. const float zMin = zNearCoefficient() * zClippingCoefficient() * sceneRadius(); if (z < zMin) /* switch (type()) { case Camera::PERSPECTIVE :*/ z = zMin; /*break; case Camera::ORTHOGRAPHIC : z = 0.0; break; }*/ return z; } trunk-2017.01a/gui/qt5/GLViewer.hpp000066400000000000000000000124171304022710500166610ustar00rootroot00000000000000// Copyright (C) 2004 by Olivier Galizzi, Janek Kozicki * // © 2008 Václav Šmilauer #pragma once #ifndef Q_MOC_RUN #include #include #include #include #endif #include #include #include using std::setw; using std::setfill; using std::setprecision; /*! Class handling user interaction with the openGL rendering of simulation. * * Clipping planes: * ================ * * Clipping plane is manipulated after hitting F1, F2, .... To end the manipulation, press Escape. * * Keystrokes during clipping plane manipulation: * * space activates/deactives the clipping plane * * x,y,z aligns the plane with yz, xz, xy planes * * left-double-click aligns the plane with world coordinates system (canonical planes + 45˚ interpositions) * * 1,2,... will align the current plane with #1, #2, ... (same orientation) * * r reverses the plane (normal*=-1)a * * Keystrokes that work regardless of whether a clipping plane is being manipulated: * * Alt-1,Alt-2,... adds/removes the respective plane to bound group: * mutual positions+orientations of planes in the group are maintained when one of those planes is manipulated * * Clip plane number is 3; change YADE_RENDERER_NUM_CLIP_PLANE, complete switches "|| ..." in keyPressEvent * and recompile to have more. */ class GLViewer : public QGLViewer { Q_OBJECT friend class QGLThread; protected: shared_ptr renderer; private : bool isMoving; bool wasDynamic; float cut_plane; int cut_plane_delta; bool gridSubdivide; long last; int manipulatedClipPlane; set boundClipPlanes; shared_ptr xyPlaneConstraint; string strBoundGroup(){string ret;FOREACH(int i, boundClipPlanes) ret+=" "+boost::lexical_cast(i+1);return ret;} boost::posix_time::ptime last_user_event; public: //virtual void updateGL(void); const int viewId; void centerMedianQuartile(); int drawGrid; bool drawScale; int timeDispMask; enum{TIME_REAL=1,TIME_VIRT=2,TIME_ITER=4}; GLViewer(int viewId, const shared_ptr& renderer, QGLWidget* shareWidget=0); virtual ~GLViewer(); #if 0 virtual void paintGL(); #endif virtual void draw(); virtual void drawWithNames(); void displayMessage(const std::string& s){ QGLViewer::displayMessage(QString(s.c_str()));} void centerScene(); void centerPeriodic(); void mouseMovesCamera(); void mouseMovesManipulatedFrame(qglviewer::Constraint* c=NULL); void resetManipulation(); bool isManipulating(); void startClipPlaneManipulation(int planeNo); //! get QGLViewer state as string (XML); QGLViewer normally only supports saving state to file. string getState(); //! set QGLViewer state from string (XML); QGLVIewer normally only supports loading state from file. void setState(string); //! Load display parameters (QGLViewer and OpenGLRenderer) from Scene::dispParams[n] and use them void useDisplayParameters(size_t n); //! Save display parameters (QGOViewer and OpenGLRenderer) to Scene::dispParams[n] void saveDisplayParameters(size_t n); //! Get radius of the part of scene that fits the current view float displayedSceneRadius(); //! Get center of the part of scene that fits the current view qglviewer::Vec displayedSceneCenter(); //! Adds our attributes to the QGLViewer state that can be saved QDomElement domElement(const QString& name, QDomDocument& document) const; //! Adds our attributes to the QGLViewer state that can be restored void initFromDOMElement(const QDomElement& element); // if defined, snapshot will be saved to this file right after being drawn and the string will be reset. // this way the caller will be notified of the frame being saved successfully. string nextFrameSnapshotFilename; #ifdef YADE_GL2PS // output stream for gl2ps; initialized as needed FILE* gl2psStream; #endif boost::posix_time::ptime getLastUserEvent(); DECLARE_LOGGER; protected : virtual void keyPressEvent(QKeyEvent *e); virtual void postDraw(); // overridden in the player that doesn't get time from system clock but from the db virtual string getRealTimeString(); virtual void closeEvent(QCloseEvent *e); virtual void postSelection(const QPoint& point); virtual void endSelection(const QPoint &point); virtual void mouseDoubleClickEvent(QMouseEvent *e); virtual void wheelEvent(QWheelEvent* e); virtual void mouseMoveEvent(QMouseEvent *e); virtual void mousePressEvent(QMouseEvent *e); }; /*! Get unconditional lock on a GL view. Use if you need to manipulate GL context in some way. The ctor doesn't return until the lock has been acquired and the lock is released when the GLLock object is desctructed; */ class GLLock: public boost::try_mutex::scoped_lock{ GLViewer* glv; public: GLLock(GLViewer* _glv); ~GLLock(); }; class YadeCamera : public qglviewer::Camera { Q_OBJECT private: float cuttingDistance; public : YadeCamera():cuttingDistance(0){}; #if QGLVIEWER_VERSION>=0x020603 virtual qreal zNear() const; #else virtual float zNear() const; #endif virtual void setCuttingDistance(float s){cuttingDistance=s;}; }; trunk-2017.01a/gui/qt5/GLViewerDisplay.cpp000066400000000000000000000327751304022710500202130ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2005 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include"GLViewer.hpp" #include"OpenGLManager.hpp" #include #include #include #include #include #include #include #include #include #include #include #include #ifdef YADE_GL2PS #include #endif void GLViewer::useDisplayParameters(size_t n){ LOG_DEBUG("Loading display parameters from #"< >& dispParams=Omega::instance().getScene()->dispParams; if(dispParams.size()<=(size_t)n){ throw std::invalid_argument(("Display parameters #"+boost::lexical_cast(n)+" don't exist (number of entries "+boost::lexical_cast(dispParams.size())+")").c_str());; return;} const shared_ptr& dp=dispParams[n]; string val; if(dp->getValue("OpenGLRenderer",val)){ istringstream oglre(val); yade::ObjectIO::load(oglre,"renderer",renderer); } else { LOG_WARN("OpenGLRenderer configuration not found in display parameters, skipped.");} if(dp->getValue("GLViewer",val)){ GLViewer::setState(val); displayMessage("Loaded view configuration #"+boost::lexical_cast(n)); } else { LOG_WARN("GLViewer configuration not found in display parameters, skipped."); } } void GLViewer::saveDisplayParameters(size_t n){ LOG_DEBUG("Saving display parameters to #"< >& dispParams=Omega::instance().getScene()->dispParams; if(dispParams.size()<=n){while(dispParams.size()<=n) dispParams.push_back(shared_ptr(new DisplayParameters));} assert(n& dp=dispParams[n]; ostringstream oglre; yade::ObjectIO::save(oglre,"renderer",renderer); dp->setValue("OpenGLRenderer",oglre.str()); dp->setValue("GLViewer",GLViewer::getState()); displayMessage("Saved view configuration ot #"+boost::lexical_cast(n)); } void GLViewer::draw() { #ifdef YADE_GL2PS if(!nextFrameSnapshotFilename.empty() && boost::algorithm::ends_with(nextFrameSnapshotFilename,".pdf")){ gl2psStream=fopen(nextFrameSnapshotFilename.c_str(),"wb"); if(!gl2psStream){ int err=errno; throw runtime_error(string("Error opening file ")+nextFrameSnapshotFilename+": "+strerror(err)); } LOG_DEBUG("Start saving snapshot to "<bodies->size(); int sortAlgo=(nBodies<100 ? GL2PS_BSP_SORT : GL2PS_SIMPLE_SORT); gl2psBeginPage(/*const char *title*/"Some title", /*const char *producer*/ "Yade", /*GLint viewport[4]*/ NULL, /*GLint format*/ GL2PS_PDF, /*GLint sort*/ sortAlgo, /*GLint options*/GL2PS_SIMPLE_LINE_OFFSET|GL2PS_USE_CURRENT_VIEWPORT|GL2PS_TIGHT_BOUNDING_BOX|GL2PS_COMPRESS|GL2PS_OCCLUSION_CULL|GL2PS_NO_BLENDING, /*GLint colormode*/ GL_RGBA, /*GLint colorsize*/0, /*GL2PSrgba *colortable*/NULL, /*GLint nr*/0, /*GLint ng*/0, /*GLint nb*/0, /*GLint buffersize*/4096*4096 /* 16MB */, /*FILE *stream*/ gl2psStream, /*const char *filename*/NULL); } #endif qglviewer::Vec vd=camera()->viewDirection(); renderer->viewDirection=Vector3r(vd[0],vd[1],vd[2]); if(Omega::instance().getScene()){ const shared_ptr& scene=Omega::instance().getScene(); int selection = selectedName(); if(selection!=-1 && (*(Omega::instance().getScene()->bodies)).exists(selection) && isMoving){ static Real lastTimeMoved(0); #if QGLVIEWER_VERSION>=0x020603 qreal v0,v1,v2; manipulatedFrame()->getPosition(v0,v1,v2); #else float v0,v1,v2; manipulatedFrame()->getPosition(v0,v1,v2); #endif if(last == selection) // delay by one redraw, so the body will not jump into 0,0,0 coords { Quaternionr& q = (*(Omega::instance().getScene()->bodies))[selection]->state->ori; Vector3r& v = (*(Omega::instance().getScene()->bodies))[selection]->state->pos; Vector3r& vel = (*(Omega::instance().getScene()->bodies))[selection]->state->vel; Vector3r& angVel = (*(Omega::instance().getScene()->bodies))[selection]->state->angVel; angVel=Vector3r::Zero(); Real dt=(scene->time-lastTimeMoved); lastTimeMoved=scene->time; if (dt!=0) { vel[0]=-(v[0]-v0)/dt; vel[1]=-(v[1]-v1)/dt; vel[2]=-(v[2]-v2)/dt;} else vel[0]=vel[1]=vel[2]=0; //FIXME: should update spin like velocity above, when the body is rotated: double q0,q1,q2,q3; manipulatedFrame()->getOrientation(q0,q1,q2,q3); q.x()=q0;q.y()=q1;q.z()=q2;q.w()=q3; } (*(Omega::instance().getScene()->bodies))[selection]->userForcedDisplacementRedrawHook(); } if(manipulatedClipPlane>=0){ assert(manipulatedClipPlanenumClipPlanes); #if QGLVIEWER_VERSION>=0x020603 qreal v0,v1,v2; manipulatedFrame()->getPosition(v0,v1,v2); #else float v0,v1,v2; manipulatedFrame()->getPosition(v0,v1,v2); #endif double q0,q1,q2,q3; manipulatedFrame()->getOrientation(q0,q1,q2,q3); Se3r newSe3(Vector3r(v0,v1,v2),Quaternionr(q0,q1,q2,q3)); newSe3.orientation.normalize(); const Se3r& oldSe3=renderer->clipPlaneSe3[manipulatedClipPlane]; FOREACH(int planeId, boundClipPlanes){ if(planeId>=renderer->numClipPlanes || !renderer->clipPlaneActive[planeId] || planeId==manipulatedClipPlane) continue; Se3r& boundSe3=renderer->clipPlaneSe3[planeId]; Quaternionr relOrient=oldSe3.orientation.conjugate()*boundSe3.orientation; relOrient.normalize(); Vector3r relPos=oldSe3.orientation.conjugate()*(boundSe3.position-oldSe3.position); boundSe3.position=newSe3.position+newSe3.orientation*relPos; boundSe3.orientation=newSe3.orientation*relOrient; boundSe3.orientation.normalize(); } renderer->clipPlaneSe3[manipulatedClipPlane]=newSe3; } scene->renderer=renderer; renderer->render(scene, selectedName()); } } void GLViewer::drawWithNames(){ qglviewer::Vec vd=camera()->viewDirection(); renderer->viewDirection=Vector3r(vd[0],vd[1],vd[2]); const shared_ptr scene(Omega::instance().getScene()); scene->renderer=renderer; renderer->scene=scene; renderer->renderShape(); } qglviewer::Vec GLViewer::displayedSceneCenter(){ return camera()->unprojectedCoordinatesOf(qglviewer::Vec(width()/2 /* pixels */ ,height()/2 /* pixels */, /*middle between near plane and far plane*/ .5)); } float GLViewer::displayedSceneRadius(){ return (camera()->unprojectedCoordinatesOf(qglviewer::Vec(width()/2,height()/2,.5))-camera()->unprojectedCoordinatesOf(qglviewer::Vec(0,0,.5))).norm(); } void GLViewer::postDraw(){ Real wholeDiameter=QGLViewer::camera()->sceneRadius()*2; renderer->viewInfo.sceneRadius=QGLViewer::camera()->sceneRadius(); qglviewer::Vec c=QGLViewer::camera()->sceneCenter(); renderer->viewInfo.sceneCenter=Vector3r(c[0],c[1],c[2]); Real dispDiameter=min(wholeDiameter,max((Real)displayedSceneRadius()*2,wholeDiameter/1e3)); // limit to avoid drawing 1e5 lines with big zoom level //qglviewer::Vec center=QGLViewer::camera()->sceneCenter(); Real gridStep=pow(10,(floor(log10(dispDiameter)-.7))); Real scaleStep=pow(10,(floor(log10(displayedSceneRadius()*2)-.7))); // unconstrained int nSegments=((int)(wholeDiameter/gridStep))+1; Real realSize=nSegments*gridStep; //LOG_TRACE("nSegments="<projectedCoordinatesOf(center+delta)-camera()->projectedCoordinatesOf(center); for(int xy=0;xy<2;xy++)extremalDxDy[xy]=(axis>0 ? min(extremalDxDy[xy],(int)screenDxDy[axis][xy]) : screenDxDy[axis][xy]); } //LOG_DEBUG("Screen offsets for axes: "<<" x("<=0){ for(int planeId=0; planeIdnumClipPlanes; planeId++){ if(!renderer->clipPlaneActive[planeId] && planeId!=manipulatedClipPlane) continue; glPushMatrix(); const Se3r& se3=renderer->clipPlaneSe3[planeId]; AngleAxisr aa(se3.orientation); glTranslatef(se3.position[0],se3.position[1],se3.position[2]); glRotated(aa.angle()*Mathr::RAD_TO_DEG,aa.axis()[0],aa.axis()[1],aa.axis()[2]); Real cff=1; if(!renderer->clipPlaneActive[planeId]) cff=.4; glColor3f(max((Real)0.,cff*cos(planeId)),max((Real)0.,cff*sin(planeId)),planeId==manipulatedClipPlane); // variable colors QGLViewer::drawGrid(realSize,2*nSegments); drawArrow(wholeDiameter/6); glPopMatrix(); } } Scene* rb=Omega::instance().getScene().get(); #define _W3 setw(3)<time; unsigned min=((unsigned)t/60),sec=(((unsigned)t)%60),msec=((unsigned)(1e3*t))%1000,usec=((unsigned long)(1e6*t))%1000,nsec=((unsigned long)(1e9*t))%1000; if(min>0) oss<<_W2<0) oss<<_W2<0) oss<<_W3<0) oss<<_W3<iter; if(rb->stopAtIter>rb->iter) oss<<" ("<iter)/rb->stopAtIter<<"%)"; QGLViewer::drawText(x,y,oss.str().c_str()); y-=lineHt; } if(drawGrid){ glColor3v(Vector3r(1,1,0)); ostringstream oss; oss<<"grid: "< #include #include #include #include #include #include #include #include #include #include #include #include #ifdef YADE_GL2PS #include #endif void GLViewer::mouseMovesCamera(){ setWheelBinding(Qt::ShiftModifier , FRAME, ZOOM); setWheelBinding(Qt::NoModifier, CAMERA, ZOOM); #if QGLVIEWER_VERSION>=0x020500 setMouseBinding(Qt::ShiftModifier, Qt::RightButton, FRAME, ZOOM); setMouseBinding(Qt::ShiftModifier, Qt::MidButton, FRAME, TRANSLATE); setMouseBinding(Qt::ShiftModifier, Qt::RightButton, FRAME, ROTATE); setMouseBinding(Qt::NoModifier, Qt::MidButton, CAMERA, ZOOM); setMouseBinding(Qt::NoModifier, Qt::LeftButton, CAMERA, ROTATE); setMouseBinding(Qt::NoModifier, Qt::RightButton, CAMERA, TRANSLATE); #else setMouseBinding(Qt::SHIFT + Qt::LeftButton, SELECT); setMouseBinding(Qt::SHIFT + Qt::LeftButton + Qt::RightButton, FRAME, ZOOM); setMouseBinding(Qt::SHIFT + Qt::MidButton, FRAME, TRANSLATE); setMouseBinding(Qt::SHIFT + Qt::RightButton, FRAME, ROTATE); setMouseBinding(Qt::LeftButton + Qt::RightButton, CAMERA, ZOOM); setMouseBinding(Qt::MidButton, CAMERA, ZOOM); setMouseBinding(Qt::LeftButton, CAMERA, ROTATE); setMouseBinding(Qt::RightButton, CAMERA, TRANSLATE); camera()->frame()->setWheelSensitivity(-1.0f); #endif }; void GLViewer::mouseMovesManipulatedFrame(qglviewer::Constraint* c){ setMouseBinding(Qt::LeftButton + Qt::RightButton, FRAME, ZOOM); setMouseBinding(Qt::MidButton, FRAME, ZOOM); setMouseBinding(Qt::LeftButton, FRAME, ROTATE); setMouseBinding(Qt::RightButton, FRAME, TRANSLATE); setWheelBinding(Qt::NoModifier , FRAME, ZOOM); manipulatedFrame()->setConstraint(c); } void GLViewer::mouseMoveEvent(QMouseEvent *e){ last_user_event = boost::posix_time::second_clock::local_time(); QGLViewer::mouseMoveEvent(e); } void GLViewer::mousePressEvent(QMouseEvent *e){ last_user_event = boost::posix_time::second_clock::local_time(); QGLViewer::mousePressEvent(e); } /* Handle double-click event; if clipping plane is manipulated, align it with the global coordinate system. * Otherwise pass the event to QGLViewer to handle it normally. * * mostly copied over from ManipulatedFrame::mouseDoubleClickEvent */ void GLViewer::mouseDoubleClickEvent(QMouseEvent *event){ last_user_event = boost::posix_time::second_clock::local_time(); if(manipulatedClipPlane<0) { /* LOG_DEBUG("Double click not on clipping plane"); */ QGLViewer::mouseDoubleClickEvent(event); return; } #if QT_VERSION >= 0x040000 if (event->modifiers() == Qt::NoModifier) #else if (event->state() == Qt::NoButton) #endif switch (event->button()){ case Qt::LeftButton: manipulatedFrame()->alignWithFrame(NULL,true); LOG_DEBUG("Aligning cutting plane"); break; default: break; // avoid warning } } void GLViewer::wheelEvent(QWheelEvent* event){ last_user_event = boost::posix_time::second_clock::local_time(); if(manipulatedClipPlane<0){ QGLViewer::wheelEvent(event); return; } assert(manipulatedClipPlanenumClipPlanes); float distStep=1e-3*sceneRadius(); float dist=event->delta()*manipulatedFrame()->wheelSensitivity()*distStep; Vector3r normal=renderer->clipPlaneSe3[manipulatedClipPlane].orientation*Vector3r(0,0,1); qglviewer::Vec newPos=manipulatedFrame()->position()+qglviewer::Vec(normal[0],normal[1],normal[2])*dist; manipulatedFrame()->setPosition(newPos); renderer->clipPlaneSe3[manipulatedClipPlane].position=Vector3r(newPos[0],newPos[1],newPos[2]); updateGL(); /* in draw, bound cutting planes will be moved as well */ } trunk-2017.01a/gui/qt5/Inspector.py000066400000000000000000000275011304022710500170040ustar00rootroot00000000000000# encoding: utf-8 from PyQt5.QtCore import * from PyQt5.QtGui import * from yade import * from yade.qt.SerializableEditor import * import yade.qt class EngineInspector(QWidget): def __init__(self,parent=None): QWidget.__init__(self,parent) grid=QGridLayout(self); grid.setSpacing(0); grid.setContentsMargins(0,0,0,0) self.serEd=SeqSerializable(parent=None,getter=lambda:O.engines,setter=lambda x:setattr(O,'engines',x),serType=Engine,path='O.engines') grid.addWidget(self.serEd) self.setLayout(grid) #class MaterialsInspector(QWidget): # def __init__(self,parent=None): # QWidget.__init__(self,parent) # grid=QGridLayout(self); grid.setSpacing(0); grid.setContentsMargins(0,0,0,0) # self.serEd=SeqSerializable(parent=None,getter=lambda:O.materials,setter=lambda x:setattr(O,'materials',x),serType=Engine) # grid.addWidget(self.serEd) # self.setLayout(grid) class CellInspector(QWidget): def __init__(self,parent=None): QWidget.__init__(self,parent) self.layout=QVBoxLayout(self) #; self.layout.setSpacing(0); self.layout.setContentsMargins(0,0,0,0) self.periCheckBox=QCheckBox('periodic boundary',self) self.periCheckBox.clicked.connect(self.update) self.layout.addWidget(self.periCheckBox) self.scroll=QScrollArea(self); self.scroll.setWidgetResizable(True) self.layout.addWidget(self.scroll) self.setLayout(self.layout) self.refresh() self.refreshTimer=QTimer(self) self.refreshTimer.timeout.connect(self.refresh) self.refreshTimer.start(1000) def refresh(self): self.periCheckBox.setChecked(O.periodic) editor=self.scroll.widget() if not O.periodic and editor: self.scroll.takeWidget() if (O.periodic and not editor) or (editor and editor.ser!=O.cell): self.scroll.setWidget(SerializableEditor(O.cell,parent=self,showType=True,path='O.cell')) def update(self): self.scroll.takeWidget() # do this before changing periodicity, otherwise the SerializableEditor will raise exception about None object O.periodic=self.periCheckBox.isChecked() self.refresh() def makeBodyLabel(b): ret=unicode(b.id)+u' ' if not b.shape: ret+=u'⬚' else: typeMap={'Sphere':u'⚫','Facet':u'△','Wall':u'┃','Box':u'⎕','Cylinder':u'⌭','ChainedCylinder':u'☡','Clump':u'☍'} ret+=typeMap.get(b.shape.__class__.__name__,u'﹖') if not b.dynamic: ret+=u'⚓' elif b.state.blockedDOFs: ret+=u'⎈' return ret def getBodyIdFromLabel(label): try: return int(unicode(label).split()[0]) except ValueError: print 'Error with label:',unicode(label) return -1 class BodyInspector(QWidget): def __init__(self,bodyId=-1,parent=None,bodyLinkCallback=None,intrLinkCallback=None): QWidget.__init__(self,parent) v=yade.qt.views() self.bodyId=bodyId if bodyId<0 and len(v)>0 and v[0].selection>0: self.bodyId=v[0].selection self.idGlSync=self.bodyId self.bodyLinkCallback,self.intrLinkCallback=bodyLinkCallback,intrLinkCallback self.bodyIdBox=QSpinBox(self) self.bodyIdBox.setMinimum(0) self.bodyIdBox.setMaximum(100000000) self.bodyIdBox.setValue(self.bodyId) self.intrWithCombo=QComboBox(self); self.gotoBodyButton=QPushButton(u'→ #',self) self.gotoIntrButton=QPushButton(u'→ #+#',self) # id selector topBoxWidget=QWidget(self); topBox=QHBoxLayout(topBoxWidget); topBox.setContentsMargins(0,0,0,0); #topBox.setSpacing(0); hashLabel=QLabel('#',self); hashLabel.setFixedWidth(8) topBox.addWidget(hashLabel) topBox.addWidget(self.bodyIdBox) self.plusLabel=QLabel('+',self); topBox.addWidget(self.plusLabel) hashLabel2=QLabel('#',self); hashLabel2.setFixedWidth(8); topBox.addWidget(hashLabel2) topBox.addWidget(self.intrWithCombo) topBox.addStretch() topBox.addWidget(self.gotoBodyButton) topBox.addWidget(self.gotoIntrButton) topBoxWidget.setLayout(topBox) # forces display forcesWidget=QFrame(self); forcesWidget.setFrameShape(QFrame.Box); self.forceGrid=QGridLayout(forcesWidget); self.forceGrid.setVerticalSpacing(0); self.forceGrid.setHorizontalSpacing(9); self.forceGrid.setContentsMargins(4,4,4,4); for i,j in itertools.product((0,1,2,3),(-1,0,1,2)): lab=QLabel(''+('force','torque','move','rot')[i]+'' if j==-1 else ''); self.forceGrid.addWidget(lab,i,j+1); if j>=0: lab.setAlignment(Qt.AlignRight) if i>1: lab.hide() # do not show forced moves and rotations by default (they will appear if non-zero) self.showMovRot=False # self.grid=QGridLayout(self); self.grid.setSpacing(0); self.grid.setContentsMargins(0,0,0,0) self.grid.addWidget(topBoxWidget) self.grid.addWidget(forcesWidget) self.scroll=QScrollArea(self) self.scroll.setWidgetResizable(True) self.grid.addWidget(self.scroll) self.tryShowBody() self.bodyIdBox.valueChanged.connect(self.bodyIdSlot) self.gotoBodyButton.clicked.connect(self.gotoBodySlot) self.gotoIntrButton.clicked.connect(self.gotoIntrSlot) self.refreshTimer=QTimer(self) self.refreshTimer.timeout.connect(self.refreshEvent) self.refreshTimer.start(1000) self.intrWithCombo.addItems(['0']); self.intrWithCombo.setCurrentIndex(0); self.intrWithCombo.setMinimumWidth(80) self.setWindowTitle('Body #%d'%self.bodyId) self.gotoBodySlot() def displayForces(self): if self.bodyId<0: return try: val=[O.forces.f(self.bodyId),O.forces.t(self.bodyId),O.forces.move(self.bodyId),O.forces.rot(self.bodyId)] hasMovRot=(val[2]!=Vector3.Zero or val[3]!=Vector3.Zero) if hasMovRot!=self.showMovRot: for i,j in itertools.product((2,3),(-1,0,1,2)): if hasMovRot: self.forceGrid.itemAtPosition(i,j+1).widget().show() else: self.forceGrid.itemAtPosition(i,j+1).widget().hide() self.showMovRot=hasMovRot rows=((0,1,2,3) if hasMovRot else (0,1)) for i,j in itertools.product(rows,(0,1,2)): self.forceGrid.itemAtPosition(i,j+1).widget().setText(''+str(val[i][j])+'') except IndexError:pass def tryShowBody(self): try: b=O.bodies[self.bodyId] self.serEd=SerializableEditor(b,showType=True,parent=self,path='O.bodies[%d]'%self.bodyId) except IndexError: self.serEd=QFrame(self) self.bodyId=-1 self.scroll.setWidget(self.serEd) def changeIdSlot(self,newId): self.bodyIdBox.setValue(newId); self.bodyIdSlot() def bodyIdSlot(self): self.bodyId=self.bodyIdBox.value() self.tryShowBody() self.setWindowTitle('Body #%d'%self.bodyId) self.refreshEvent() def gotoBodySlot(self): try: id=int(getBodyIdFromLabel(self.intrWithCombo.currentText())) except ValueError: return # empty id if not self.bodyLinkCallback: self.bodyIdBox.setValue(id); self.bodyId=id else: self.bodyLinkCallback(id) def gotoIntrSlot(self): ids=self.bodyIdBox.value(),getBodyIdFromLabel(self.intrWithCombo.currentText()) if not self.intrLinkCallback: self.ii=InteractionInspector(ids) self.ii.show() else: self.intrLinkCallback(ids) def refreshEvent(self): try: O.bodies[self.bodyId] except: self.bodyId=-1 # invalidate deleted body # no body shown yet, try to get the first one... if self.bodyId<0 and len(O.bodies)>0: try: print 'SET ZERO' b=O.bodies[0]; self.bodyIdBox.setValue(0) except IndexError: pass v=yade.qt.views() if len(v)>0 and v[0].selection!=self.bodyId: if self.idGlSync==self.bodyId: # changed in the viewer, reset ourselves self.bodyId=self.idGlSync=v[0].selection; self.changeIdSlot(self.bodyId) return else: v[0].selection=self.idGlSync=self.bodyId # changed here, set in the viewer meId=self.bodyIdBox.value(); pos=self.intrWithCombo.currentIndex() try: meLabel=makeBodyLabel(O.bodies[meId]) except IndexError: meLabel=u'…' self.plusLabel.setText(' '.join(meLabel.split()[1:])+' +') # do not repeat the id self.bodyIdBox.setMaximum(len(O.bodies)-1) others=[(i.id1 if i.id1!=meId else i.id2) for i in O.interactions.withBody(self.bodyIdBox.value()) if i.isReal] others.sort() self.intrWithCombo.clear() self.intrWithCombo.addItems([makeBodyLabel(O.bodies[i]) for i in others]) if pos>self.intrWithCombo.count() or pos<0: pos=0 self.intrWithCombo.setCurrentIndex(pos); other=self.intrWithCombo.itemText(pos) if other=='': self.gotoBodyButton.setEnabled(False); self.gotoIntrButton.setEnabled(False) other=u'∅' else: self.gotoBodyButton.setEnabled(True); self.gotoIntrButton.setEnabled(True) self.gotoBodyButton.setText(u'→ %s'%other) self.gotoIntrButton.setText(u'→ %s + %s'%(meLabel,other)) self.displayForces() class InteractionInspector(QWidget): def __init__(self,ids=None,parent=None,bodyLinkCallback=None): QWidget.__init__(self,parent) self.bodyLinkCallback=bodyLinkCallback self.ids=ids self.gotoId1Button=QPushButton(u'#…',self) self.gotoId2Button=QPushButton(u'#…',self) self.gotoId1Button.clicked.connect(self.gotoId1Slot) self.gotoId2Button.clicked.connect(self.gotoId2Slot) topBoxWidget=QWidget(self) topBox=QHBoxLayout(topBoxWidget) topBox.addWidget(self.gotoId1Button) labelPlus=QLabel('+',self); labelPlus.setAlignment(Qt.AlignHCenter) topBox.addWidget(labelPlus) topBox.addWidget(self.gotoId2Button) topBoxWidget.setLayout(topBox) self.setWindowTitle(u'No interaction') self.grid=QGridLayout(self); self.grid.setSpacing(0); self.grid.setContentsMargins(0,0,0,0) self.grid.addWidget(topBoxWidget,0,0) self.scroll=QScrollArea(self) self.scroll.setWidgetResizable(True) self.grid.addWidget(self.scroll) self.refreshTimer=QTimer(self) self.refreshTimer.timeout.connect(self.refreshEvent) self.refreshTimer.start(1000) if self.ids: self.setupInteraction() def setupInteraction(self): try: intr=O.interactions[self.ids[0],self.ids[1]] self.serEd=SerializableEditor(intr,showType=True,parent=self.scroll,path='O.interactions[%d,%d]'%(self.ids[0],self.ids[1])) self.scroll.setWidget(self.serEd) self.gotoId1Button.setText('#'+makeBodyLabel(O.bodies[self.ids[0]])) self.gotoId2Button.setText('#'+makeBodyLabel(O.bodies[self.ids[1]])) self.setWindowTitle('Interaction #%d + #%d'%(self.ids[0],self.ids[1])) except IndexError: if self.ids: # reset view (there was an interaction) self.ids=None self.serEd=QFrame(self.scroll); self.scroll.setWidget(self.serEd) self.setWindowTitle('No interaction') self.gotoId1Button.setText(u'#…'); self.gotoId2Button.setText(u'#…'); def gotoId(self,bodyId): if self.bodyLinkCallback: self.bodyLinkCallback(bodyId) else: self.bi=BodyInspector(bodyId); self.bi.show() def gotoId1Slot(self): self.gotoId(self.ids[0]) def gotoId2Slot(self): self.gotoId(self.ids[1]) def refreshEvent(self): # no ids yet -- try getting the first interaction, if it exists if not self.ids: try: i=O.interactions.nth(0) self.ids=i.id1,i.id2 self.setupInteraction() return except IndexError: return # no interaction exists at all try: # try to fetch an existing interaction O.interactions[self.ids[0],self.ids[1]] except IndexError: self.ids=None class SimulationInspector(QWidget): def __init__(self,parent=None): QWidget.__init__(self,parent) self.setWindowTitle("Simulation Inspection") self.tabWidget=QTabWidget(self) self.engineInspector=EngineInspector(parent=None) self.bodyInspector=BodyInspector(parent=None,intrLinkCallback=self.changeIntrIds) self.intrInspector=InteractionInspector(parent=None,bodyLinkCallback=self.changeBodyId) self.cellInspector=CellInspector(parent=None) for i,name,widget in [(0,'Engines',self.engineInspector),(1,'Bodies',self.bodyInspector),(2,'Interactions',self.intrInspector),(3,'Cell',self.cellInspector)]: self.tabWidget.addTab(widget,name) grid=QGridLayout(self); grid.setSpacing(0); grid.setContentsMargins(0,0,0,0) grid.addWidget(self.tabWidget) self.setLayout(grid) def changeIntrIds(self,ids): self.tabWidget.removeTab(2); self.intrInspector.close() self.intrInspector=InteractionInspector(ids=ids,parent=None,bodyLinkCallback=self.changeBodyId) self.tabWidget.insertTab(2,self.intrInspector,'Interactions') self.tabWidget.setCurrentIndex(2) def changeBodyId(self,id): self.bodyInspector.changeIdSlot(id) self.tabWidget.setCurrentIndex(1) trunk-2017.01a/gui/qt5/OpenGLManager.cpp000066400000000000000000000051631304022710500176070ustar00rootroot00000000000000#include"OpenGLManager.hpp" CREATE_LOGGER(OpenGLManager); OpenGLManager* OpenGLManager::self=NULL; OpenGLManager::OpenGLManager(QObject* parent): QObject(parent){ if(self) throw runtime_error("OpenGLManager instance already exists, uses OpenGLManager::self to retrieve it."); self=this; renderer=shared_ptr(new OpenGLRenderer); renderer->init(); connect(this,SIGNAL(createView()),this,SLOT(createViewSlot())); connect(this,SIGNAL(resizeView(int,int,int)),this,SLOT(resizeViewSlot(int,int,int))); connect(this,SIGNAL(closeView(int)),this,SLOT(closeViewSlot(int))); connect(this,SIGNAL(startTimerSignal()),this,SLOT(startTimerSlot()),Qt::QueuedConnection); } void OpenGLManager::timerEvent(QTimerEvent* event){ //cerr<<"."; boost::mutex::scoped_lock lock(viewsMutex); // when sharing the 0th view widget, it should be enough to update the primary view only //if(views.size()>0) views[0]->updateGL(); #if 1 FOREACH(const shared_ptr& view, views){ if(view) view->updateGL(); } #endif } void OpenGLManager::createViewSlot(){ boost::mutex::scoped_lock lock(viewsMutex); if(views.size()==0){ views.push_back(shared_ptr(new GLViewer(0,renderer,/*shareWidget*/(QGLWidget*)0))); } else { throw runtime_error("Secondary views not supported"); //views.push_back(shared_ptr(new GLViewer(views.size(),renderer,views[0].get()))); } } void OpenGLManager::resizeViewSlot(int id, int wd, int ht){ views[id]->resize(wd,ht); } void OpenGLManager::closeViewSlot(int id){ boost::mutex::scoped_lock lock(viewsMutex); for(size_t i=views.size()-1; (!views[i]); i--){ views.resize(i); } // delete empty views from the end if(id<0){ // close the last one existing assert(*views.rbegin()); // this should have been sanitized by the loop above views.resize(views.size()-1); // releases the pointer as well } if(id==0){ LOG_DEBUG("Closing primary view."); if(views.size()==1) views.clear(); else{ LOG_INFO("Cannot close primary view, secondary views still exist."); } } } void OpenGLManager::centerAllViews(){ boost::mutex::scoped_lock lock(viewsMutex); FOREACH(const shared_ptr& g, views){ if(!g) continue; g->centerScene(); } } void OpenGLManager::startTimerSlot(){ startTimer(50); } int OpenGLManager::waitForNewView(float timeout,bool center){ size_t origViewCount=views.size(); emitCreateView(); float t=0; while(views.size()!=origViewCount+1){ usleep(50000); t+=.05; // wait at most 5 secs if(t>=timeout) { LOG_ERROR("Timeout waiting for the new view to open, giving up."); return -1; } } if(center)(*views.rbegin())->centerScene(); return (*views.rbegin())->viewId; } trunk-2017.01a/gui/qt5/OpenGLManager.hpp000066400000000000000000000027601304022710500176140ustar00rootroot00000000000000#pragma once //#include #ifndef Q_MOC_RUN #include"GLViewer.hpp" #endif #include #include /* Singleton class managing OpenGL views, a renderer instance and timer to refresh the display. */ class OpenGLManager: public QObject{ Q_OBJECT DECLARE_LOGGER; public: static OpenGLManager* self; OpenGLManager(QObject *parent=0); // manipulation must lock viewsMutex! std::vector > views; shared_ptr renderer; // signals are protected, emitting them is therefore wrapped with such funcs void emitResizeView(int id, int wd, int ht){ emit resizeView(id,wd,ht); } void emitCreateView(){ emit createView(); } void emitStartTimer(){ emit startTimerSignal(); } void emitCloseView(int id){ emit closeView(id); } // create a new view and wait for it to become available; return the view number // if timout (in seconds) elapses without the view to come up, reports error and returns -1 int waitForNewView(float timeout=5., bool center=true); signals: void createView(); void resizeView(int id, int wd, int ht); void closeView(int id); // this is used to start timer from the main thread via postEvent (ugly) void startTimerSignal(); public slots: virtual void createViewSlot(); virtual void resizeViewSlot(int id, int wd, int ht); virtual void closeViewSlot(int id=-1); virtual void timerEvent(QTimerEvent* event); virtual void startTimerSlot(); void centerAllViews(); private: boost::mutex viewsMutex; }; trunk-2017.01a/gui/qt5/SerializableEditor.py000066400000000000000000001107751304022710500206210ustar00rootroot00000000000000# encoding: utf-8 from PyQt5.QtCore import * from PyQt5.QtGui import * from PyQt5 import QtGui from PyQt5 import QtWidgets from PyQt5.QtWidgets import * import re,itertools import logging logging.trace=logging.debug logging.basicConfig(level=logging.INFO) from yade import * import yade.qt from minieigen import * seqSerializableShowType=True # show type headings in serializable sequences (takes vertical space, but makes the type hyperlinked) # BUG: cursor is moved to the beginning of the input field even if it has focus # checking for focus seems to return True always and cursor is never moved # the 'True or' part effectively disables the condition (so that the cursor is moved always), but it might be fixed in the future somehow # if True or w.hasFocus(): w.home(False) # Janek: It looks like I've fixed this BUG, please do more testing. # def makeWrapperHref(text,className,attr=None,static=False): """Create clickable HTML hyperlink to a Yade class or its attribute. :param className: name of the class to link to. :param attr: attribute to link to. If given, must exist directly in given *className*; if not given or empty, link to the class itself is created and *attr* is ignored. :return: HTML with the hyperref. """ if not static: return '%s'%(yade.qt.sphinxDocWrapperPage,className,(('.'+attr) if attr else ''),text) else: return '%s'%(yade.qt.sphinxDocWrapperPage,className,attr,text) def serializableHref(ser,attr=None,text=None): """Return HTML href to a *ser* optionally to the attribute *attr*. The class hierarchy is crawled upwards to find out in which parent class is *attr* defined, so that the href target is a valid link. In that case, only single inheritace is assumed and the first class from the top defining *attr* is used. :param ser: object of class deriving from :yref:`Serializable`, or string; if string, *attr* must be empty. :param attr: name of the attribute to link to; if empty, linke to the class itself is created. :param text: visible text of the hyperlink; if not given, either class name or attribute name without class name (when *attr* is not given) is used. :returns: HTML with the hyperref. """ # klass is a class name given as string if isinstance(ser,str): if attr: raise InvalidArgument("When *ser* is a string, *attr* must be empty (only class link can be created)") return makeWrapperHref(text if text else ser,ser) # klass is a type object if attr: klass=ser.__class__ while attr in dir(klass.__bases__[0]): klass=klass.__bases__[0] if not text: text=attr else: klass=ser.__class__ if not text: text=klass.__name__ return makeWrapperHref(text,klass.__name__,attr,static=(attr and getattr(klass,attr)==getattr(ser,attr))) class AttrEditor(): """Abstract base class handing some aspects common to all attribute editors. Holds exacly one attribute which is updated whenever it changes.""" def __init__(self,getter=None,setter=None): self.getter,self.setter=getter,setter self.hot,self.focused=False,False self.widget=None def refresh(self): pass def update(self): pass def isHot(self,hot=True): "Called when the widget gets focus; mark it hot, change colors etc." if hot==self.hot: return self.hot=hot if hot: self.setStyleSheet('QWidget { background: red }') else: self.setStyleSheet('QWidget { background: none }') def sizeHint(self): return QSize(150,12) def trySetter(self,val): try: self.setter(val) except AttributeError: self.setEnabled(False) self.isHot(False) class AttrEditor_Bool(AttrEditor,QFrame): def __init__(self,parent,getter,setter): AttrEditor.__init__(self,getter,setter) QFrame.__init__(self,parent) self.checkBox=QCheckBox(self) lay=QVBoxLayout(self); lay.setSpacing(0); lay.addStretch(1); lay.addWidget(self.checkBox); lay.addStretch(1) self.checkBox.clicked.connect(self.update) def refresh(self): self.checkBox.setChecked(self.getter()) def update(self): self.trySetter(self.checkBox.isChecked()) class AttrEditor_Int(AttrEditor,QSpinBox): def __init__(self,parent,getter,setter): AttrEditor.__init__(self,getter,setter) QSpinBox.__init__(self,parent) self.setRange(int(-1e9),int(1e9)); self.setSingleStep(1); self.valueChanged.connect(self.update) def refresh(self): if (not self.hasFocus()): self.setValue(self.getter()) def update(self): self.trySetter(self.value()) class AttrEditor_Str(AttrEditor,QLineEdit): def __init__(self,parent,getter,setter): AttrEditor.__init__(self,getter,setter) QLineEdit.__init__(self,parent) self.textEdited.connect(self.isHot) self.selectionChanged.connect(self.isHot) self.editingFinished.connect(self.update) def refresh(self): if (not self.hasFocus()): self.setText(self.getter()) def update(self): self.trySetter(str(self.text())) class AttrEditor_Float(AttrEditor,QLineEdit): def __init__(self,parent,getter,setter): AttrEditor.__init__(self,getter,setter) QLineEdit.__init__(self,parent) self.textEdited.connect(self.isHot) self.selectionChanged.connect(self.isHot) self.editingFinished.connect(self.update) def refresh(self): #if True or not self.hasFocus(): self.home(False) if (not self.hasFocus()): self.setText(str(self.getter())); self.home(False) def update(self): try: self.trySetter(float(self.text())) except ValueError: self.refresh() class AttrEditor_Complex(AttrEditor,QLineEdit): def __init__(self,parent,getter,setter): AttrEditor.__init__(self,getter,setter) QFrame.__init__(self,parent) self.rows,self.cols=1,2 self.setContentsMargins(0,0,0,0) self.first=True val=self.getter() self.grid=QGridLayout(self); self.grid.setSpacing(0); self.grid.setContentsMargins(0,0,0,0) for row,col in itertools.product(range(self.rows),range(self.cols)): w=QLineEdit('') self.grid.addWidget(w,row,col); w.textEdited.connect(self.isHot) w.selectionChanged.connect(self.isHot) w.editingFinished.connect(self.update) def refresh(self,force=False): val=self.getter() for row,col in itertools.product(range(self.rows),range(self.cols)): w=self.grid.itemAtPosition(row,col).widget() if(self.first or force): w.setText(str(val.real if col==0 else val.imag)) #if True or not w.hasFocus: w.home(False) # make the left-most part visible, if the text is wider than the widget if (not w.hasFocus): w.setText(str(val.real if col==0 else val.imag)) w.home(False) # make the left-most part visible, if the text is wider than the widget self.first=False def update(self): try: val=self.getter() w1=self.grid.itemAtPosition(0,0).widget() w2=self.grid.itemAtPosition(0,1).widget() if w1.isModified() or w2.isModified(): val=complex(float(w1.text()),float(w2.text())) logging.debug('setting'+str(val)) self.trySetter(val) except ValueError: self.refresh(force=True) def setFocus(self): self.grid.itemAtPosition(0,0).widget().setFocus() class AttrEditor_Quaternion(AttrEditor,QFrame): def __init__(self,parent,getter,setter): AttrEditor.__init__(self,getter,setter) QFrame.__init__(self,parent) self.grid=QHBoxLayout(self); self.grid.setSpacing(0); self.grid.setContentsMargins(0,0,0,0) for i in range(4): if i==3: # add vertical divider (axis | angle) f=QFrame(self); f.setFrameShape(QFrame.VLine); f.setFrameShadow(QFrame.Sunken); f.setFixedWidth(4) self.grid.addWidget(f) w=QLineEdit('') self.grid.addWidget(w); w.textEdited.connect(self.isHot) w.selectionChanged.connect(self.isHot) w.editingFinished.connect(self.update) def refresh(self): val=self.getter(); axis,angle=val.toAxisAngle() for i in (0,1,2,4): #if True or not w.hasFocus(): w.home(False) w=self.grid.itemAt(i).widget(); if (not w.hasFocus()): w.setText(str(axis[i] if i<3 else angle)); w.home(False) def update(self): try: x=[float((self.grid.itemAt(i).widget().text())) for i in (0,1,2,4)] except ValueError: self.refresh() return q=Quaternion(Vector3(x[0],x[1],x[2]),x[3]); q.normalize() # from axis-angle self.trySetter(q) def setFocus(self): self.grid.itemAt(0).widget().setFocus() class AttrEditor_Se3(AttrEditor,QFrame): def __init__(self,parent,getter,setter): AttrEditor.__init__(self,getter,setter) QFrame.__init__(self,parent) self.grid=QGridLayout(self); self.grid.setSpacing(0); for row,col in itertools.product(range(2),range(5)): # one additional column for vertical line in quaternion if (row,col)==(0,3): continue if (row,col)==(0,4): self.grid.addWidget(QLabel(u'←pos ↙ori',self),row,col); continue if (row,col)==(1,3): f=QFrame(self); f.setFrameShape(QFrame.VLine); f.setFrameShadow(QFrame.Sunken); f.setFixedWidth(4); self.grid.addWidget(f,row,col); continue w=QLineEdit('') self.grid.addWidget(w,row,col); w.textEdited.connect(self.isHot) w.selectionChanged.connect(self.isHot) w.editingFinished.connect(self.update) def refresh(self): pos,ori=self.getter(); axis,angle=ori.toAxisAngle() for i in (0,1,2,4): #if True or not w.hasFocus(): w.home(False) w=self.grid.itemAtPosition(1,i).widget(); if (not w.hasFocus()): w.setText(str(axis[i] if i<3 else angle)); w.home(False) for i in (0,1,2): #if True or not w.hasFocus(): w.home(False) w=self.grid.itemAtPosition(0,i).widget(); if (not w.hasFocus()): w.setText(str(pos[i])); w.home(False) def update(self): try: q=[float((self.grid.itemAtPosition(1,i).widget().text())) for i in (0,1,2,4)] v=[float((self.grid.itemAtPosition(0,i).widget().text())) for i in (0,1,2)] except ValueError: self.refresh() return qq=Quaternion(Vector3(q[0],q[1],q[2]),q[3]); qq.normalize() # from axis-angle self.trySetter((v,qq)) def setFocus(self): self.grid.itemAtPosition(0,0).widget().setFocus() class AttrEditor_MatrixX(AttrEditor,QFrame): def __init__(self,parent,getter,setter,rows,cols,idxConverter): 'idxConverter converts row,col tuple to either (row,col), (col) etc depending on what access is used for []' AttrEditor.__init__(self,getter,setter) QFrame.__init__(self,parent) self.rows,self.cols=rows,cols self.idxConverter=idxConverter self.setContentsMargins(0,0,0,0) self.first=True val=self.getter() self.grid=QGridLayout(self); self.grid.setSpacing(0); for row,col in itertools.product(range(self.rows),range(self.cols)): w=QLineEdit('') self.grid.addWidget(w,row,col); w.textEdited.connect(self.isHot) w.selectionChanged.connect(self.isHot) w.editingFinished.connect(self.update) def refresh(self,force=False): val=self.getter() for row,col in itertools.product(range(self.rows),range(self.cols)): w=self.grid.itemAtPosition(row,col).widget() if(self.first or force): w.setText(str(val[self.idxConverter(row,col)])) if (not w.hasFocus): w.setText(str(val[self.idxConverter(row,col)])) w.home(False) # make the left-most part visible, if the text is wider than the widget self.first=False def update(self): try: val=self.getter() for row,col in itertools.product(range(self.rows),range(self.cols)): w=self.grid.itemAtPosition(row,col).widget() if w.isModified(): val[self.idxConverter(row,col)]=float(w.text()) logging.debug('setting'+str(val)) self.trySetter(val) except ValueError: self.refresh(force=True) def setFocus(self): self.grid.itemAtPosition(0,0).widget().setFocus() class AttrEditor_MatrixXi(AttrEditor,QFrame): def __init__(self,parent,getter,setter,rows,cols,idxConverter): 'idxConverter converts row,col tuple to either (row,col), (col) etc depending on what access is used for []' AttrEditor.__init__(self,getter,setter) QFrame.__init__(self,parent) self.rows,self.cols=rows,cols self.idxConverter=idxConverter self.setContentsMargins(0,0,0,0) self.grid=QGridLayout(self); self.grid.setSpacing(0); self.grid.setContentsMargins(0,0,0,0) for row,col in itertools.product(range(self.rows),range(self.cols)): w=QSpinBox() w.setRange(int(-1e9),int(1e9)); w.setSingleStep(1); self.grid.addWidget(w,row,col); self.refresh() # refresh before connecting signals! for row,col in itertools.product(range(self.rows),range(self.cols)): self.grid.itemAtPosition(row,col).widget().valueChanged.connect(self.update) def refresh(self): val=self.getter() for row,col in itertools.product(range(self.rows),range(self.cols)): w=self.grid.itemAtPosition(row,col).widget().setValue(val[self.idxConverter(row,col)]) def update(self): val=self.getter(); modified=False for row,col in itertools.product(range(self.rows),range(self.cols)): w=self.grid.itemAtPosition(row,col).widget() if w.value()!=val[self.idxConverter(row,col)]: modified=True; val[self.idxConverter(row,col)]=w.value() if not modified: return logging.debug('setting'+str(val)) self.trySetter(val) def setFocus(self): self.grid.itemAtPosition(0,0).widget().setFocus() class AttrEditor_Vector6i(AttrEditor_MatrixXi): def __init__(self,parent,getter,setter): AttrEditor_MatrixXi.__init__(self,parent,getter,setter,1,6,lambda r,c:c) class AttrEditor_Vector3i(AttrEditor_MatrixXi): def __init__(self,parent,getter,setter): AttrEditor_MatrixXi.__init__(self,parent,getter,setter,1,3,lambda r,c:c) class AttrEditor_Vector2i(AttrEditor_MatrixXi): def __init__(self,parent,getter,setter): AttrEditor_MatrixXi.__init__(self,parent,getter,setter,1,2,lambda r,c:c) class AttrEditor_Vector6(AttrEditor_MatrixX): def __init__(self,parent,getter,setter): AttrEditor_MatrixX.__init__(self,parent,getter,setter,1,6,lambda r,c:c) class AttrEditor_Vector3(AttrEditor_MatrixX): def __init__(self,parent,getter,setter): AttrEditor_MatrixX.__init__(self,parent,getter,setter,1,3,lambda r,c:c) class AttrEditor_Vector2(AttrEditor_MatrixX): def __init__(self,parent,getter,setter): AttrEditor_MatrixX.__init__(self,parent,getter,setter,1,2,lambda r,c:c) class AttrEditor_Matrix3(AttrEditor_MatrixX): def __init__(self,parent,getter,setter): AttrEditor_MatrixX.__init__(self,parent,getter,setter,3,3,lambda r,c:(r,c)) class Se3FakeType: pass _fundamentalEditorMap={bool:AttrEditor_Bool,str:AttrEditor_Str,int:AttrEditor_Int,float:AttrEditor_Float,complex:AttrEditor_Complex,Quaternion:AttrEditor_Quaternion,Vector2:AttrEditor_Vector2,Vector3:AttrEditor_Vector3,Vector6:AttrEditor_Vector6,Matrix3:AttrEditor_Matrix3,Vector6i:AttrEditor_Vector6i,Vector3i:AttrEditor_Vector3i,Vector2i:AttrEditor_Vector2i,Se3FakeType:AttrEditor_Se3} _fundamentalInitValues={bool:True,str:'',int:0,float:0.0,complex:0.0j,Quaternion:Quaternion((0,1,0),0.0),Vector3:Vector3.Zero,Matrix3:Matrix3.Zero,Vector6:Vector6.Zero,Vector6i:Vector6i.Zero,Vector3i:Vector3i.Zero,Vector2i:Vector2i.Zero,Vector2:Vector2.Zero,Se3FakeType:(Vector3.Zero,Quaternion((0,1,0),0.0))} class SerQLabel(QLabel): def __init__(self,parent,label,tooltip,path): QLabel.__init__(self,parent) self.path=path self.setText(label) if tooltip or path: self.setToolTip((''+path+'
    ' if self.path else '')+(tooltip if tooltip else '')) self.linkActivated.connect(yade.qt.openUrl) def mousePressEvent(self,event): if event.button()!=Qt.MidButton: event.ignore(); return # middle button clicked, paste pasteText to clipboard cb=QApplication.clipboard() cb.setText(self.path,mode=QClipboard.Clipboard) cb.setText(self.path,mode=QClipboard.Selection) # X11 global selection buffer event.accept() class SerializableEditor(QFrame): "Class displaying and modifying serializable attributes of a yade object." import collections import logging # each attribute has one entry associated with itself class EntryData: def __init__(self,name,T,flags=0): self.name,self.T,self.flags=name,T,flags self.lineNo,self.widget=None,None def __init__(self,ser,parent=None,ignoredAttrs=set(),showType=False,path=None): "Construct window, *ser* is the object we want to show." QtWidgets.QFrame.__init__(self,parent) self.ser=ser self.path=(ser.label if (hasattr(ser,'label') and ser.label) else path) self.showType=showType self.hot=False self.entries=[] self.ignoredAttrs=ignoredAttrs logging.debug('New Serializable of type %s'%ser.__class__.__name__) self.setWindowTitle(str(ser)) self.mkWidgets() self.refreshTimer=QTimer(self) self.refreshTimer.timeout.connect(self.refreshEvent) self.refreshTimer.start(500) def getListTypeFromDocstring(self,attr): "Guess type of array by scanning docstring for :yattrtype: and parsing its argument; ugly, but works." doc=getattr(self.ser.__class__,attr).__doc__ if doc==None: logging.error("Attribute %s has no docstring."%attr) return None m=re.search(r':yattrtype:`([^`]*)`',doc) if not m: logging.error("Attribute %s does not contain :yattrtype:`....` (docstring is '%s'"%(attr,doc)) return None cxxT=m.group(1) logging.debug('Got type "%s" from :yattrtype:'%cxxT) def vecTest(T,cxxT): #regexp=r'^\s*(std\s*::)?\s*vector\s*<\s*(std\s*::)?\s*('+T+r')\s*>\s*$' regexp=r'^\s*(std\s*::)?\s*vector\s*<\s*(shared_ptr\s*<\s*)?\s*(std\s*::)?\s*('+T+r')(\s*>)?\s*>\s*$' m=re.match(regexp,cxxT) return m vecMap={ 'bool':bool,'int':int,'long':int,'Body::id_t':long,'size_t':long, 'Real':float,'float':float,'double':float,'complex':complex,'std::complex':complex, 'Vector6r':Vector6,'Vector6i':Vector6i,'Vector3i':Vector3i,'Vector2r':Vector2,'Vector2i':Vector2i, 'Vector3r':Vector3,'Matrix3r':Matrix3,'Se3r':Se3FakeType, 'string':str, #'BodyCallback':BodyCallback, 'IntrCallback':IntrCallback,'BoundFunctor':BoundFunctor,'IGeomFunctor':IGeomFunctor,'IPhysFunctor':IPhysFunctor,'LawFunctor':LawFunctor,'KinematicEngine':KinematicEngine, 'GlShapeFunctor':GlShapeFunctor,'GlStateFunctor':GlStateFunctor,'GlIGeomFunctor':GlIGeomFunctor,'GlIPhysFunctor':GlIPhysFunctor,'GlBoundFunctor':GlBoundFunctor,'GlExtraDrawer':GlExtraDrawer } for T,ret in vecMap.items(): if vecTest(T,cxxT): logging.debug("Got type %s from cxx type %s"%(repr(ret),cxxT)) return (ret,) logging.error("Unable to guess python type from cxx type '%s'"%cxxT) return None def mkAttrEntries(self): if self.ser==None: return try: d=self.ser.dict() except TypeError: logging.error('TypeError when getting attributes of '+str(self.ser)+',skipping. ') import traceback traceback.print_exc() attrs=self.ser.dict().keys(); attrs.sort() for attr in attrs: val=getattr(self.ser,attr) # get the value using serattr, as it might be different from what the dictionary provides (e.g. Body.blockedDOFs) t=None doc=getattr(self.ser.__class__,attr).__doc__; # some attributes are not shown if '|yhidden|' in doc: continue if attr in self.ignoredAttrs: continue # FIXME: (Janek) Implementing Quantum Mechanics makes some DEM assumptions # invalid. I think that we should rethink what base class Body contains, so # that in QM we would not need to use this hack to hide some variables. # However it is great to note that only this little 'cosmetic' hack is needed # to make Quantum Mechanics possible in yade # See also: class QuantumMechanicalState, class QuantumMechanicalBody, gui/qt4/SerializableEditor.py if hasattr(self.ser,"qtHide") and (attr in getattr(self.ser,"qtHide").split()): continue if isinstance(val,list): t=self.getListTypeFromDocstring(attr) if not t and len(val)==0: t=(val[0].__class__,) # 1-tuple is list of the contained type #if not t: raise RuntimeError('Unable to guess type of '+str(self.ser)+'.'+attr) # hack for Se3, which is returned as (Vector3,Quaternion) in python elif isinstance(val,tuple) and len(val)==2 and val[0].__class__==Vector3 and val[1].__class__==Quaternion: t=Se3FakeType else: t=val.__class__ match=re.search(':yattrflags:`\s*([0-9]+)\s*`',doc) # non-empty attribute flags=int(match.group(1)) if match else 0 #logging.debug('Attr %s is of type %s'%(attr,((t[0].__name__,) if isinstance(t,tuple) else t.__name__))) self.entries.append(self.EntryData(name=attr,T=t)) #print("name: "+str(attr)+"\tflag: "+str(flags)) def getDocstring(self,attr=None): "If attr is *None*, return docstring of the Serializable itself" doc=(getattr(self.ser.__class__,attr).__doc__ if attr else self.ser.__class__.__doc__) if not doc: return '' doc=re.sub(':y(attrtype|default|attrflags):`[^`]*`','',doc) statAttr=re.compile('^.. ystaticattr::.*$',re.MULTILINE|re.DOTALL) doc=re.sub(statAttr,'',doc) # static classes have their proper docs at the beginning, discard static memeber docs # static: attribute of the type is the same object as attribute of the instance # in that case, get docstring from the class documentation by parsing it if attr and getattr(self.ser.__class__,attr)==getattr(self.ser,attr): doc=self.getStaticAttrDocstring(attr) doc=re.sub(':yref:`([^`]*)`','\\1',doc) import textwrap wrapper=textwrap.TextWrapper(replace_whitespace=False) return wrapper.fill(textwrap.dedent(doc)) def getStaticAttrDocstring(self,attr): ret=''; c=self.ser.__class__ while hasattr(c,attr) and hasattr(c.__base__,attr): c=c.__base__ start='.. ystaticattr:: %s.%s('%(c.__name__,attr) if start in c.__doc__: ll=c.__doc__.split('\n') for i in range(len(ll)): if ll[i].startswith(start): break for i in range(i+1,len(ll)): if len(ll[i])>0 and ll[i][0] not in ' \t': break ret+=ll[i] return ret else: return '[no documentation found]' def mkWidget(self,entry): if not entry.T: return None # single fundamental object Klass=_fundamentalEditorMap.get(entry.T,None) getter,setter=lambda: getattr(self.ser,entry.name), lambda x: setattr(self.ser,entry.name,x) if Klass: widget=Klass(self,getter=getter,setter=setter) widget.setFocusPolicy(Qt.StrongFocus) if (entry.flags & AttrFlags.readonly): widget.setEnabled(False) return widget # sequences if entry.T.__class__==tuple: assert(len(entry.T)==1) # we don't handle tuples of other lenghts # sequence of serializables T=entry.T[0] if (issubclass(T,Serializable) or T==Serializable): widget=SeqSerializable(self,getter,setter,T,path=(self.path+'.'+entry.name if self.path else None),shrink=True) return widget if (T in _fundamentalEditorMap): widget=SeqFundamentalEditor(self,getter,setter,T) return widget return None # a serializable if issubclass(entry.T,Serializable) or entry.T==Serializable: obj=getattr(self.ser,entry.name) if hasattr(obj,'label') and obj.label: path=obj.label elif self.path: path=self.path+'.'+entry.name else: path=None widget=SerializableEditor(getattr(self.ser,entry.name),parent=self,showType=self.showType,path=(self.path+'.'+entry.name if self.path else None)) widget.setFrameShape(QFrame.Box); widget.setFrameShadow(QFrame.Raised); widget.setLineWidth(1) return widget return None def mkWidgets(self): self.mkAttrEntries() grid=QFormLayout() grid.setContentsMargins(2,2,2,2) grid.setVerticalSpacing(0) grid.setLabelAlignment(Qt.AlignRight) if self.showType: lab=SerQLabel(self,makeSerializableLabel(self.ser,addr=True,href=True),tooltip=self.getDocstring(),path=self.path) lab.setFrameShape(QFrame.Box); lab.setFrameShadow(QFrame.Sunken); lab.setLineWidth(2); lab.setAlignment(Qt.AlignHCenter); lab.linkActivated.connect(yade.qt.openUrl) grid.setWidget(0,QFormLayout.SpanningRole,lab) for entry in self.entries: entry.widget=self.mkWidget(entry) objPath=(self.path+'.'+entry.name) if self.path else None label=SerQLabel(self,serializableHref(self.ser,entry.name),tooltip=self.getDocstring(entry.name),path=objPath) grid.addRow(label,entry.widget if entry.widget else QLabel('unhandled type')) self.setLayout(grid) self.refreshEvent() def refreshEvent(self): for e in self.entries: if e.widget and not e.widget.hot: e.widget.refresh() def refresh(self): pass def makeSerializableLabel(ser,href=False,addr=True,boldHref=True,num=-1,count=-1): ret=u'' if num>=0: if count>=0: ret+=u'%d/%d. '%(num,count) else: ret+=u'%d. '%num if href: ret+=(u' ' if boldHref else u' ')+serializableHref(ser)+(u' ' if boldHref else u' ') else: ret+=ser.__class__.__name__+' ' if hasattr(ser,'label') and ser.label: ret+=u' “'+unicode(ser.label)+u'”' # do not show address if there is a label already elif addr: import re ss=unicode(ser); m=re.match(u'<(.*) instance at (0x.*)>',ss) if m: ret+=m.group(2) else: logging.warning(u"Serializable converted to str ('%s') does not contain 'instance at 0x…'"%ss) return ret class SeqSerializableComboBox(QFrame): def __init__(self,parent,getter,setter,serType,path=None,shrink=False): QFrame.__init__(self,parent) self.getter,self.setter,self.serType,self.path,self.shrink=getter,setter,serType,path,shrink self.layout=QVBoxLayout(self) topLineFrame=QFrame(self) topLineLayout=QHBoxLayout(topLineFrame); for l in self.layout, topLineLayout: l.setSpacing(0); l.setContentsMargins(0,0,0,0) topLineFrame.setLayout(topLineLayout) buttons=(self.newButton,self.killButton,self.upButton,self.downButton)=[QPushButton(label,self) for label in (u'☘',u'☠',u'↑',u'↓')] buttonSlots=(self.newSlot,self.killSlot,self.upSlot,self.downSlot) # same order as buttons for b in buttons: b.setStyleSheet('QPushButton { font-size: 15pt; }'); b.setFixedWidth(30); b.setFixedHeight(30) self.combo=QComboBox(self) self.combo.setSizeAdjustPolicy(QComboBox.AdjustToContents) for w in buttons[0:2]+[self.combo,]+buttons[2:4]: topLineLayout.addWidget(w) self.layout.addWidget(topLineFrame) # nested layout self.scroll=QScrollArea(self); self.scroll.setWidgetResizable(True) self.layout.addWidget(self.scroll) self.seqEdit=None # currently edited serializable self.setLayout(self.layout) self.hot=None # API compat with SerializableEditor self.setFrameShape(QFrame.Box); self.setFrameShadow(QFrame.Raised); self.setLineWidth(1) # signals for b,slot in zip(buttons,buttonSlots): b.clicked.connect(slot) self.combo.currentIndexChanged.connect(self.comboIndexSlot) self.refreshEvent() # periodic refresh self.refreshTimer=QTimer(self) self.refreshTimer.timeout.connect(self.refreshEvent) self.refreshTimer.start(1000) # 1s should be enough #print 'SeqSerializable path is',self.path def comboIndexSlot(self,ix): # different seq item selected currSeq=self.getter(); if len(currSeq)==0: ix=-1 logging.debug('%s comboIndexSlot len=%d, ix=%d'%(self.serType.__name__,len(currSeq),ix)) self.downButton.setEnabled(ix0) self.combo.setEnabled(ix>=0) if ix>=0: ser=currSeq[ix] self.seqEdit=SerializableEditor(ser,parent=self,showType=seqSerializableShowType,path=(self.path+'['+str(ix)+']') if self.path else None) self.scroll.setWidget(self.seqEdit) if self.shrink: self.sizeHint=lambda: QSize(100,1000) self.scroll.sizeHint=lambda: QSize(100,1000) self.sizePolicy().setVerticalPolicy(QSizePolicy.Expanding) self.scroll.sizePolicy().setVerticalPolicy(QSizePolicy.Expanding) self.setMinimumHeight(min(300,self.seqEdit.height()+self.combo.height()+10)) self.setMaximumHeight(100000) self.scroll.setMaximumHeight(100000) else: self.scroll.setWidget(QFrame()) if self.shrink: self.setMaximumHeight(self.combo.height()+10); self.scroll.setMaximumHeight(0) def serLabel(self,ser,i=-1): return ('' if i<0 else str(i)+'. ')+str(ser)[1:-1].replace('instance at ','') def refreshEvent(self,forceIx=-1): currSeq=self.getter() comboEnabled=self.combo.isEnabled() if comboEnabled and len(currSeq)==0: self.comboIndexSlot(-1) # force refresh, otherwise would not happen from the initially empty state ix,cnt=self.combo.currentIndex(),self.combo.count() # serializable currently being edited (which can be absent) or the one of which index is forced ser=(self.seqEdit.ser if self.seqEdit else None) if forceIx<0 else currSeq[forceIx] if comboEnabled and len(currSeq)==cnt and (ix<0 or ser==currSeq[ix]): return if not comboEnabled and len(currSeq)==0: return logging.debug(self.serType.__name__+' rebuilding list from scratch') self.combo.clear() if len(currSeq)>0: prevIx=-1 for i,s in enumerate(currSeq): self.combo.addItem(makeSerializableLabel(s,num=i,count=len(currSeq),addr=False)) if s==ser: prevIx=i if forceIx>=0: newIx=forceIx # force the index (used from newSlot to make the new element active) elif prevIx>=0: newIx=prevIx # if found what was active before, use it elif ix>=0: newIx=ix # otherwise use the previous index (e.g. after deletion) else: newIx=0 # fallback to 0 logging.debug('%s setting index %d'%(self.serType.__name__,newIx)) self.combo.setCurrentIndex(newIx) else: logging.debug('%s EMPTY, setting index 0'%(self.serType.__name__)) self.combo.setCurrentIndex(-1) self.killButton.setEnabled(len(currSeq)>0) def newSlot(self): dialog=NewSerializableDialog(self,self.serType.__name__) if not dialog.exec_(): return # cancelled ser=dialog.result() ix=self.combo.currentIndex() currSeq=self.getter(); currSeq.insert(ix,ser); self.setter(currSeq) logging.debug('%s new item created at index %d'%(self.serType.__name__,ix)) self.refreshEvent(forceIx=ix) def killSlot(self): ix=self.combo.currentIndex() currSeq=self.getter(); del currSeq[ix]; self.setter(currSeq) self.refreshEvent() def upSlot(self): i=self.combo.currentIndex() assert(i>0) currSeq=self.getter(); prev,curr=currSeq[i-1:i+1]; currSeq[i-1],currSeq[i]=curr,prev; self.setter(currSeq) self.refreshEvent(forceIx=i-1) def downSlot(self): i=self.combo.currentIndex() currSeq=self.getter(); assert(i=0 else None menu=QMenu(self) actNew,actKill,actUp,actDown=[menu.addAction(name) for name in (u'☘ New',u'☠ Remove',u'↑ Up',u'↓ Down')] if index<0: [a.setEnabled(False) for a in actKill,actUp,actDown] if index==len(seq)-1: actDown.setEnabled(False) if index==0: actUp.setEnabled(False) if field: field.setStyleSheet('QWidget { background: green }') act=menu.exec_(self.mapToGlobal(event.pos())) if field: field.setStyleSheet('QWidget { background: none }') if not act: return if act==actNew: self.newSlot(index) elif act==actKill: self.killSlot(index) elif act==actUp: self.upSlot(index) elif act==actDown: self.downSlot(index) def localPositionToIndex(self,pos): gp=self.mapToGlobal(pos) for row in range(self.form.count()/2): w,i=self.form.itemAt(row,QFormLayout.FieldRole),self.form.itemAt(row,QFormLayout.LabelRole) for wi in w.widget(),i.widget(): x0,y0,x1,y1=wi.geometry().getCoords(); globG=QRect(self.mapToGlobal(QPoint(x0,y0)),self.mapToGlobal(QPoint(x1,y1))) if globG.contains(gp): return row return -1 def newSlot(self,i): seq=self.getter(); seq.insert(i,_fundamentalInitValues.get(self.itemType,self.itemType())) self.setter(seq) self.rebuild() def killSlot(self,i): seq=self.getter(); assert(iError',errMsg) return class ItemGetter(): def __init__(self,getter,index): self.getter,self.index=getter,index def __call__(self): return self.getter()[self.index] class ItemSetter(): def __init__(self,getter,setter,index): self.getter,self.setter,self.index=getter,setter,index def __call__(self,val): seq=self.getter(); seq[self.index]=val; self.setter(seq) for i,item in enumerate(currSeq): widget=Klass(self,ItemGetter(self.getter,i),ItemSetter(self.getter,self.setter,i)) #proxy,'value') self.form.insertRow(i,'%d. '%i,widget) logging.debug('added item %d %s'%(i,str(widget))) if len(currSeq)==0: self.form.insertRow(0,'empty',QLabel('(right-click for menu)')) logging.debug('rebuilt, will refresh now') self.refreshEvent(dontRebuild=True) # avoid infinite recursion it the length would change meanwhile def refreshEvent(self,dontRebuild=False,forceIx=-1): currSeq=self.getter() if len(currSeq)!=self.form.count()/2: #rowCount(): if dontRebuild: return # length changed behind our back, just pretend nothing happened and update next time instead self.rebuild() currSeq=self.getter() for i in range(len(currSeq)): item=self.form.itemAt(i,QFormLayout.FieldRole) logging.trace('got item #%d %s'%(i,str(item.widget()))) widget=item.widget() if not widget.hot: widget.refresh() if forceIx>=0 and forceIx==i: widget.setFocus() def refresh(self): pass # SerializableEditor API trunk-2017.01a/gui/qt5/XYZ.png000066400000000000000000000007011304022710500156550ustar00rootroot00000000000000PNG  IHDR((msRGBbKGD pHYs  tIME ($`iAIDATXؿ.DAߊxD JT$^-- :DOH$!H(p.{WK$79>(/b0X@)LG+X_P 0 J8-"3fS-DO5'Nҏ1&f}ѣKqń`f , y{Bkyj땎p2,} 4tɾ>4k-$ow⼁5kl`W7 ^X'~qVɣ= ʭ"ymj^462jO0u)%P .rbIENDB`trunk-2017.01a/gui/qt5/YZX.xpm000066400000000000000000000034571304022710500157100ustar00rootroot00000000000000/* XPM */ static char * YZX_xpm[] = { "40 40 2 1", " c None", ". c #000000", " ...... ", " .. ", " .. ", " .. ", " . ", " .. ", " .. ", " ...... ", " ", " . ", " . ", " ... ", " ... ", " ... ", " ..... ", " ..... ", " . ", " . ", " . ", " . ", " . ", " . ", " . ", " . ", " . ", " . ", " ........... ", " . . ", " . .. .. . .. .. ", " . . . . .. . . ", " . .... . ..... .... ", " . .. .................... .... ", " . .. . ..... .. ", " . .... . ... .. ", " . . . . .. ", " . .. .. . .. ", " . . ", " ........... ", " ", " "}; trunk-2017.01a/gui/qt5/ZXY.png000066400000000000000000000007111304022710500156560ustar00rootroot00000000000000PNG  IHDR((msRGBbKGD pHYs  tIME )EZIIDATXؽJCAJXhi kKS 쵉 "hM".rYvc1bѠ7a=MaEI<$R)OZ 6alf6&-\WߒPy $bW)C,)R(`j3`"&h|5Q^ky )>UP*u8ݬP=/ `^b]78` .; *r Sjk+6HǠ։mcotlbo96`7LGeǨL:uV@&~mԕI 'tAIENDB`trunk-2017.01a/gui/qt5/ZXY.xpm000066400000000000000000000034571304022710500157100ustar00rootroot00000000000000/* XPM */ static char * ZXY_xpm[] = { "40 40 2 1", " c None", ". c #000000", " .. .. ", " . . ", " .... ", " .. ", " .. ", " .... ", " . . ", " .. .. ", " ", " . ", " . ", " ... ", " ... ", " ... ", " ..... ", " ..... ", " . ", " . ", " . ", " . ", " . ", " . ", " . ", " . ", " . ", " . ", " ........... ", " . . ", " . .. .. . ...... ", " . . . . .. .. ", " . .... . ..... .. ", " . .... .................... .. ", " . .. . ..... . ", " . .. . ... .. ", " . .. . .. ", " . .. . ...... ", " . . ", " ........... ", " ", " "}; trunk-2017.01a/gui/qt5/_GLViewer.cpp000066400000000000000000000214451304022710500170140ustar00rootroot00000000000000#include"GLViewer.hpp" #include"OpenGLManager.hpp" #include #include #include #include namespace py=boost::python; qglviewer::Vec tuple2vec(py::tuple t){ qglviewer::Vec ret; for(int i=0;i<3;i++){py::extract e(t[i]); if(!e.check()) throw invalid_argument("Element #"+boost::lexical_cast(i)+" is not a number"); ret[i]=e();} return ret;}; py::tuple vec2tuple(qglviewer::Vec v){return py::make_tuple(v[0],v[1],v[2]);}; class pyGLViewer{ const size_t viewNo; public: #define GLV if((OpenGLManager::self->views.size()<=viewNo) || !(OpenGLManager::self->views[viewNo])) throw runtime_error("No view #"+boost::lexical_cast(viewNo)); GLViewer* glv=OpenGLManager::self->views[viewNo].get(); pyGLViewer(size_t _viewNo=0): viewNo(_viewNo){} void close(){ GLV; QCloseEvent* e(new QCloseEvent); QApplication::postEvent(glv,e); } py::tuple get_grid(){GLV; return py::make_tuple(bool(glv->drawGrid & 1),bool(glv->drawGrid & 2),bool(glv->drawGrid & 4));} void set_grid(py::tuple t){GLV; glv->drawGrid=0; for(int i=0;i<3;i++) if(py::extract(t[i])()) glv->drawGrid+=1<camera()->upVector,glv->camera()->setUpVector); VEC_GET_SET(lookAt,glv->camera()->position()+glv->camera()->viewDirection,glv->camera()->lookAt); VEC_GET_SET(viewDir,glv->camera()->viewDirection,glv->camera()->setViewDirection); VEC_GET_SET(eyePosition,glv->camera()->position,glv->camera()->setPosition); #define BOOL_GET_SET(property,getter,setter)void set_##property(bool b){GLV; setter(b);} bool get_##property(){GLV; return getter();} BOOL_GET_SET(axes,glv->axisIsDrawn,glv->setAxisIsDrawn); BOOL_GET_SET(fps,glv->FPSIsDisplayed,glv->setFPSIsDisplayed); bool get_scale(){GLV; return glv->drawScale;} void set_scale(bool b){GLV; glv->drawScale=b;} bool get_orthographic(){GLV; return glv->camera()->type()==qglviewer::Camera::ORTHOGRAPHIC;} void set_orthographic(bool b){GLV; return glv->camera()->setType(b ? qglviewer::Camera::ORTHOGRAPHIC : qglviewer::Camera::PERSPECTIVE);} int get_selection(void){ GLV; return glv->selectedName(); } void set_selection(int s){ GLV; glv->setSelectedName(s); } #define FLOAT_GET_SET(property,getter,setter)void set_##property(Real r){GLV; setter(r);} Real get_##property(){GLV; return getter();} FLOAT_GET_SET(sceneRadius,glv->sceneRadius,glv->setSceneRadius); void fitAABB(const Vector3r& min, const Vector3r& max){GLV; glv->camera()->fitBoundingBox(qglviewer::Vec(min[0],min[1],min[2]),qglviewer::Vec(max[0],max[1],max[2]));} void fitSphere(const Vector3r& center,Real radius){GLV; glv->camera()->fitSphere(qglviewer::Vec(center[0],center[1],center[2]),radius);} void showEntireScene(){GLV; glv->camera()->showEntireScene();} void center(bool median){GLV; if(median)glv->centerMedianQuartile(); else glv->centerScene();} Vector2i get_screenSize(){GLV; return Vector2i(glv->width(),glv->height());} void set_screenSize(Vector2i t){ /*GLV;*/ OpenGLManager::self->emitResizeView(viewNo,t[0],t[1]);} string pyStr(){return string("(viewNo)+">";} void saveDisplayParameters(size_t n){GLV; glv->saveDisplayParameters(n);} void useDisplayParameters(size_t n){GLV; glv->useDisplayParameters(n);} void loadState(string filename){GLV; QString origStateFileName=glv->stateFileName(); glv->setStateFileName(QString(filename.c_str())); glv->restoreStateFromFile(); glv->saveStateToFile(); glv->setStateFileName(origStateFileName);} void saveState(string filename){GLV; QString origStateFileName=glv->stateFileName(); glv->setStateFileName(QString(filename.c_str())); glv->saveStateToFile(); glv->setStateFileName(origStateFileName);} string get_timeDisp(){GLV; const int& m(glv->timeDispMask); string ret; if(m&GLViewer::TIME_REAL) ret+='r'; if(m&GLViewer::TIME_VIRT) ret+="v"; if(m&GLViewer::TIME_ITER) ret+="i"; return ret;} void set_timeDisp(string s){GLV; int& m(glv->timeDispMask); m=0; FOREACH(char c, s){switch(c){case 'r': m|=GLViewer::TIME_REAL; break; case 'v': m|=GLViewer::TIME_VIRT; break; case 'i': m|=GLViewer::TIME_ITER; break; default: throw invalid_argument(string("Invalid flag for timeDisp: `")+c+"'");}}} void set_bgColor(const Vector3r& c){ QColor cc(255*c[0],255*c[1],255*c[2]); GLV; glv->setBackgroundColor(cc);} Vector3r get_bgColor(){ GLV; QColor c(glv->backgroundColor()); return Vector3r(c.red()/255.,c.green()/255.,c.blue()/255.);} void saveSnapshot(string filename) {GLV; glv->nextFrameSnapshotFilename = filename;} #undef GLV #undef VEC_GET_SET #undef BOOL_GET_SET #undef FLOAT_GET_SET }; // ask to create a new view and wait till it exists pyGLViewer createView(){ int id=OpenGLManager::self->waitForNewView(); if(id<0) throw std::runtime_error("Unable to open new 3d view."); return pyGLViewer((*OpenGLManager::self->views.rbegin())->viewId); } py::list getAllViews(){ py::list ret; FOREACH(const shared_ptr& v, OpenGLManager::self->views){ if(v) ret.append(pyGLViewer(v->viewId)); } return ret; }; void centerViews(void){ OpenGLManager::self->centerAllViews(); } shared_ptr getRenderer(){ return OpenGLManager::self->renderer; } BOOST_PYTHON_MODULE(_GLViewer){ YADE_SET_DOCSTRING_OPTS; OpenGLManager* glm=new OpenGLManager(); // keep this singleton object forever glm->emitStartTimer(); py::def("View",createView,"Create a new 3d view."); py::def("center",centerViews,"Center all views."); py::def("views",getAllViews,"Return list of all open :yref:`yade.qt.GLViewer` objects"); py::def("Renderer",&getRenderer,"Return the active :yref:`OpenGLRenderer` object."); py::class_("GLViewer",py::no_init) .add_property("upVector",&pyGLViewer::get_upVector,&pyGLViewer::set_upVector,"Vector that will be shown oriented up on the screen.") .add_property("lookAt",&pyGLViewer::get_lookAt,&pyGLViewer::set_lookAt,"Point at which camera is directed.") .add_property("viewDir",&pyGLViewer::get_viewDir,&pyGLViewer::set_viewDir,"Camera orientation (as vector).") .add_property("eyePosition",&pyGLViewer::get_eyePosition,&pyGLViewer::set_eyePosition,"Camera position.") .add_property("grid",&pyGLViewer::get_grid,&pyGLViewer::set_grid,"Display square grid in zero planes, as 3-tuple of bools for yz, xz, xy planes.") .add_property("fps",&pyGLViewer::get_fps,&pyGLViewer::set_fps,"Show frames per second indicator.") .add_property("axes",&pyGLViewer::get_axes,&pyGLViewer::set_axes,"Show arrows for axes.") .add_property("scale",&pyGLViewer::get_scale,&pyGLViewer::set_scale,"Scale of the view (?)") .add_property("sceneRadius",&pyGLViewer::get_sceneRadius,&pyGLViewer::set_sceneRadius,"Visible scene radius.") .add_property("ortho",&pyGLViewer::get_orthographic,&pyGLViewer::set_orthographic,"Whether orthographic projection is used; if false, use perspective projection.") .add_property("screenSize",&pyGLViewer::get_screenSize,&pyGLViewer::set_screenSize,"Size of the viewer's window, in scree pixels") .add_property("timeDisp",&pyGLViewer::get_timeDisp,&pyGLViewer::set_timeDisp,"Time displayed on in the vindow; is a string composed of characters *r*, *v*, *i* standing respectively for real time, virtual time, iteration number.") // .add_property("bgColor",&pyGLViewer::get_bgColor,&pyGLViewer::set_bgColor) // useless: OpenGLRenderer::Background_color is used via openGL directly, bypassing QGLViewer background property .def("fitAABB",&pyGLViewer::fitAABB,(py::arg("mn"),py::arg("mx")),"Adjust scene bounds so that Axis-aligned bounding box given by its lower and upper corners *mn*, *mx* fits in.") .def("fitSphere",&pyGLViewer::fitSphere,(py::arg("center"),py::arg("radius")),"Adjust scene bounds so that sphere given by *center* and *radius* fits in.") .def("showEntireScene",&pyGLViewer::showEntireScene) .def("center",&pyGLViewer::center,(py::arg("median")=true),"Center view. View is centered either so that all bodies fit inside (*median* = False), or so that 75\% of bodies fit inside (*median* = True).") .def("saveState",&pyGLViewer::saveState,(py::arg("stateFilename")=".qglviewer.xml"),"Save display parameters into a file. Saves state for both :yref:`GLViewer` and associated :yref:`OpenGLRenderer`.") .def("loadState",&pyGLViewer::loadState,(py::arg("stateFilename")=".qglviewer.xml"),"Load display parameters from file saved previously into.") .def("__repr__",&pyGLViewer::pyStr).def("__str__",&pyGLViewer::pyStr) .def("close",&pyGLViewer::close) .def("saveSnapshot",&pyGLViewer::saveSnapshot,(py::arg("filename")),"Save the current view to image file") .add_property("selection",&pyGLViewer::get_selection,&pyGLViewer::set_selection) ; } trunk-2017.01a/gui/qt5/__init__.py000066400000000000000000000254721304022710500166020ustar00rootroot00000000000000# encoding: utf-8 import yade.runtime if not yade.runtime.hasDisplay: msg = "Connecting to DISPLAY at Yade startup failed, unable to activate the qt5 interface." import os if 'YADE_BATCH' in os.environ: msg += "\nDo not import qt when running in batch mode." raise ImportError(msg) from PyQt5.QtGui import * from PyQt5 import QtCore from PyQt5 import QtGui from PyQt5.QtCore import * from PyQt5.QtWidgets import * from PyQt5 import QtWebKit, QtWebKitWidgets from yade.qt.ui_controller import Ui_Controller from yade.qt.Inspector import * from yade.qt._GLViewer import * from yade import * import yade.system, yade.config maxWebWindows=1 "Number of webkit windows that will be cycled to show help on clickable objects" webWindows=[] "holds instances of QtWebKit windows; clicking an url will open it in the window that was the least recently updated" sphinxOnlineDocPath='https://www.yade-dem.org/doc/' "Base URL for the documentation. Packaged versions should change to the local installation directory." import os.path # find if we have docs installed locally from package sphinxLocalDocPath=yade.config.prefix+'/share/doc/yade'+yade.config.suffix+'-doc/html/' sphinxBuildDocPath=yade.config.sourceRoot+'/doc/sphinx/_build/html/' # we prefer the packaged documentation for this version, if installed if os.path.exists(sphinxLocalDocPath+'/index.html'): sphinxPrefix='file://'+sphinxLocalDocPath # otherwise look for documentation generated in the source tree elif os.path.exists(sphinxBuildDocPath+'/index.html'): sphinxPrefix='file://'+sphinxBuildDocPath # fallback to online docs else: sphinxPrefix=sphinxOnlineDocPath sphinxDocWrapperPage=sphinxPrefix+'/yade.wrapper.html' def sslErrorHandler(reply, errorList): reply.ignoreSslErrors() def openUrl(url): global maxWebWindows,webWindows reuseLast=False # use the last window if the class is the same and only the attribute differs try: reuseLast=(len(webWindows)>0 and str(webWindows[-1].url()).split('#')[-1].split('.')[2]==url.split('#')[-1].split('.')[2]) #print str(webWindows[-1].url()).split('#')[-1].split('.')[2],url.split('#')[-1].split('.')[2] except: pass if not reuseLast: if len(webWindows)0: self.displayCombo.insertSeparator(10000); afterSep=0 for c in yade.system.childClasses(bc) | set([bc]): inst=eval(c+'()'); if len(set(inst.dict().keys())-set(['label']))>0: self.displayCombo.addItem(c); afterSep+=1 def inspectSlot(self): self.inspector=SimulationInspector(parent=None) self.inspector.show() def setTabActive(self,what): if what=='simulation': ix=0 elif what=='display': ix=1 elif what=='generator': ix=2 elif what=='python': ix=3 else: raise ValueErorr("No such tab: "+what) self.controllerTabs.setCurrentIndex(ix) def generatorComboSlot(self,genStr): "update generator parameters when a new one is selected" gen=eval(str(genStr)+'()') self.generator=gen se=SerializableEditor(gen,parent=self.generatorArea,showType=True) self.generatorArea.setWidget(se) def pythonComboSlot(self,cmd): try: code=compile(str(cmd),'','exec') exec code in globals() except: import traceback traceback.print_exc() def generateSlot(self): filename=str(self.generatorFilenameEdit.text()) if self.generatorMemoryCheck.isChecked(): filename=':memory:'+filename print 'BUG: Saving to memory slots freezes Yade (cause unknown). Cross fingers.' #print 'Will save to ',filename self.generator.generate(filename) if self.generatorAutoCheck: O.load(filename) self.setTabActive('simulation') if len(views())==0: v=View(); v.center() def displayComboSlot(self,dispStr): ser=(self.renderer if dispStr=='OpenGLRenderer' else eval(str(dispStr)+'()')) path='yade.qt.Renderer()' if dispStr=='OpenGLRenderer' else dispStr se=SerializableEditor(ser,parent=self.displayArea,ignoredAttrs=set(['label']),showType=True,path=path) self.displayArea.setWidget(se) def loadSlot(self): f=QFileDialog.getOpenFileName(self,'Load simulation','','Yade simulations (*.xml *.xml.bz2 *.xml.gz *.yade *.yade.gz *.yade.bz2);; *.*') f=str(f[0]) if not f: return # cancelled self.deactivateControls() O.load(f) def saveSlot(self): f=QFileDialog.getSaveFileName(self,'Save simulation','','Yade simulations (*.xml *.xml.bz2 *.xml.gz *.yade *.yade.gz *.yade.bz2);; *.*') f=str(f[0]) splf = f.split('.') if (len(splf) == 1): print('No extension is found in the file name! Added .xml.bz2') f = f+'.xml.bz2' if not f: return # cancelled O.save(f) def reloadSlot(self): self.deactivateControls() from yade import plot plot.splitData() O.reload() def dtFixedSlot(self): O.dt=O.dt O.dynDt=False def dtDynSlot(self): O.dt=-O.dt def dtEditNoupdateSlot(self): self.dtEditUpdate=False def dtEditedSlot(self): try: t=float(self.dtEdit.text()) O.dt=t except ValueError: pass self.dtEdit.setText(str(O.dt)) self.dtEditUpdate=True def playSlot(self): O.run() def pauseSlot(self): O.pause() def stepSlot(self): O.step() def subStepSlot(self,value): O.subStepping=bool(value) def show3dSlot(self, show): vv=views() assert(len(vv) in (0,1)) if show: if len(vv)==0: View() else: if len(vv)>0: vv[0].close() def setReferenceSlot(self): # sets reference periodic cell as well utils.setRefSe3() def centerSlot(self): for v in views(): v.center() def setViewAxes(self,dir,up): try: v=views()[0] v.viewDir=dir v.upVector=up v.center() except IndexError: pass def xyzSlot(self): self.setViewAxes((0,0,-1),(0,1,0)) def yzxSlot(self): self.setViewAxes((-1,0,0),(0,0,1)) def zxySlot(self): self.setViewAxes((0,-1,0),(1,0,0)) def refreshEvent(self): self.refreshValues() self.activateControls() def deactivateControls(self): self.realTimeLabel.setText('') self.virtTimeLabel.setText('') self.iterLabel.setText('') self.fileLabel.setText('[loading]') self.playButton.setEnabled(False) self.pauseButton.setEnabled(False) self.stepButton.setEnabled(False) self.subStepCheckbox.setEnabled(False) self.reloadButton.setEnabled(False) self.dtFixedRadio.setEnabled(False) self.dtDynRadio.setEnabled(False) self.dtEdit.setEnabled(False) self.dtEdit.setText('') self.dtEditUpdate=True def activateControls(self): hasSim=len(O.engines)>0 running=O.running if hasSim: self.playButton.setEnabled(not running) self.pauseButton.setEnabled(running) self.reloadButton.setEnabled(O.filename is not None) self.stepButton.setEnabled(not running) self.subStepCheckbox.setEnabled(not running) else: self.playButton.setEnabled(False) self.pauseButton.setEnabled(False) self.reloadButton.setEnabled(False) self.stepButton.setEnabled(False) self.subStepCheckbox.setEnabled(False) self.dtFixedRadio.setEnabled(True) self.dtDynRadio.setEnabled(O.dynDtAvailable) dynDt=O.dynDt self.dtFixedRadio.setChecked(not dynDt) self.dtDynRadio.setChecked(dynDt) if dynDt or self.dtEditUpdate: self.dtEdit.setText(str(O.dt)) if dynDt: self.dtEditUpdate=True self.dtEdit.setEnabled(not dynDt) fn=O.filename self.fileLabel.setText(fn if fn else '[no file]') def refreshValues(self): rt=int(O.realtime); t=O.time; iter=O.iter; assert(len(self.iterTimes)==len(self.iterValues)) if len(self.iterTimes)==0: self.iterTimes.append(rt); self.iterValues.append(iter); self.iterPerSec=0 # update always for the first time elif rt-self.iterTimes[-1]>self.iterPerSecTimeout: # update after a timeout if len(self.iterTimes)==1: self.iterTimes.append(self.iterTimes[0]); self.iterValues.append(self.iterValues[0]) # 2 values, first one is bogus self.iterTimes[0]=self.iterTimes[1]; self.iterValues[0]=self.iterValues[1] self.iterTimes[1]=rt; self.iterValues[1]=iter; self.iterPerSec=(self.iterValues[-1]-self.iterValues[-2])/(self.iterTimes[-1]-self.iterTimes[-2]) if not O.running: self.iterPerSec=0 stopAtIter=O.stopAtIter subStepInfo='' if O.subStepping: subStep=O.subStep if subStep==-1: subStepInfo=u'→ prologue' elif subStep>=0 and subStepepilogue' else: raise RuntimeError("Invalid O.subStep value %d, should be ∈{-1,…,len(o.engines)}"%subStep) subStepInfo="
    sub %d/%d [%s]"%(subStep,len(O.engines),subStepInfo) self.subStepCheckbox.setChecked(O.subStepping) # might have been changed async if stopAtIter<=iter: self.realTimeLabel.setText('%02d:%02d:%02d'%(rt//3600,(rt%3600)//60,rt%60)) self.iterLabel.setText('#%ld, %.1f/s %s'%(iter,self.iterPerSec,subStepInfo)) else: e=int((stopAtIter-iter)*self.iterPerSec) self.realTimeLabel.setText('%02d:%02d:%02d (ETA %02d:%02d:%02d)'%(rt//3600,rt//60,rt%60,e//3600,e//60,e%60)) self.iterLabel.setText('#%ld / %ld, %.1f/s %s'%(O.iter,stopAtIter,self.iterPerSec,subStepInfo)) if t!=float('inf'): s=int(t); ms=int(t*1000)%1000; us=int(t*1000000)%1000; ns=int(t*1000000000)%1000 self.virtTimeLabel.setText(u'%03ds%03dm%03dμ%03dn'%(s,ms,us,ns)) else: self.virtTimeLabel.setText(u'[ ∞ ] ?!') self.show3dButton.setChecked(len(views())>0) def Generator(): global controller if not controller: controller=ControllerClass(); controller.show(); controller.raise_() controller.setTabActive('generator') def Controller(): global controller if not controller: controller=ControllerClass(); controller.show(); controller.raise_() controller.setTabActive('simulation') def Inspector(): global controller if not controller: controller=ControllerClass(); controller.inspectSlot() trunk-2017.01a/gui/qt5/controller.ui000066400000000000000000001000301304022710500171730ustar00rootroot00000000000000 Controller 0 0 290 495 0 0 Yade :/img/yade-favicon.xpm:/img/yade-favicon.xpm 0 0 0 0 0 Simulation 0 0 6 QLayout::SetMinAndMaxSize true 0 0 0 0 Load true 0 0 0 0 Save Inspect QLayout::SetMinimumSize QFormLayout::AllNonFixedFieldsGrow 6 6 6 real 00:00:00 virt 00:000.000m000μ000n iter #0, 0.0/s true Δt fixed true false time stepper false Qt::ClickFocus Qt::Horizontal 40 20 [no file] Qt::Horizontal 40 20 6 6 0 false 5 0 18 ▶ 32 32 true false false 4 0 18 ▮▮ 32 32 0 0 0 false 2 0 12 ▶▮ 32 32 7 sub-step false 5 0 22 ↻ 32 32 Show 3D true Reference Center 48 48 :/img/XYZ.xpm:/img/XYZ.xpm 40 40 48 48 :/img/YZX.xpm:/img/YZX.xpm 40 40 48 48 :/img/ZXY.xpm:/img/ZXY.xpm 40 40 Display 0 0 true 0 0 284 433 Generate 0 0 200 200 0 0 true 0 0 500 500 0 0 500 500 398 336 false memory slot false false /tmp/scene.yade.gz open automatically true Generate Python Monospace IBeamCursor Qt::StrongFocus false true QComboBox::InsertAtTop 1 false <i>(Output appears in the terminal)</i> Qt::AlignRight|Qt::AlignTrailing|Qt::AlignVCenter Qt::Vertical 20 40 loadButton clicked() Controller loadSlot() 93 64 284 0 saveButton clicked() Controller saveSlot() 184 64 284 0 dtFixedRadio clicked() Controller dtFixedSlot() 143 170 284 0 dtDynRadio clicked() Controller dtDynSlot() 268 176 284 4 dtEdit editingFinished() Controller dtEditedSlot() 147 204 284 43 playButton clicked() Controller playSlot() 116 304 3 309 pauseButton clicked() Controller pauseSlot() 268 304 284 311 referenceButton clicked() Controller setReferenceSlot() 184 429 5 469 centerButton clicked() Controller centerSlot() 275 429 284 469 xyzButton clicked() Controller xyzSlot() 93 460 0 469 yzxButton clicked() Controller yzxSlot() 184 485 243 469 zxyButton clicked() Controller zxySlot() 275 485 284 469 generateButton clicked() Controller generateSlot() 101 60 284 469 dtEdit textEdited(QString) Controller dtEditNoupdateSlot() 147 204 284 205 dtEdit cursorPositionChanged(int,int) Controller dtEditNoupdateSlot() 147 204 284 181 generatorCombo currentIndexChanged(QString) Controller generatorComboSlot() 101 60 284 130 displayCombo currentIndexChanged(QString) Controller displayComboSlot() 101 45 284 108 pythonCombo activated(QString) Controller pythonComboSlot() 107 66 284 68 inspectButton clicked() Controller inspectSlot() 247 54 0 58 reloadButton clicked() Controller reloadSlot() 194 363 284 437 stepButton clicked() Controller stepSlot() 79 363 6 450 subStepCheckbox stateChanged(int) Controller subStepSlot() 42 376 -2 381 show3dButton toggled(bool) Controller show3dSlot(bool) 42 418 -2 422 loadSlot() saveSlot() reloadSlot() playSlot() pauseSlot() stepSlot() setReferenceSlot() centerSlot() dtFixedSlot() dtDynSlot() dtEditedSlot() xyzSlot() yzxSlot() zxySlot() generateSlot() dtEditNoupdateSlot() generatorComboSlot() displayComboSlot() pythonComboSlot() pythonEditSlot() inspectSlot() subStepSlot() show3dSlot(bool) trunk-2017.01a/gui/qt5/img.qrc000066400000000000000000000002441304022710500157420ustar00rootroot00000000000000 yade-favicon.xpm XYZ.xpm YZX.xpm ZXY.xpm trunk-2017.01a/gui/qt5/yade-favicon.png000066400000000000000000000022211304022710500175270ustar00rootroot00000000000000PNG  IHDRasRGBbKGD pHYs  tIME 65tEXtCommentCreated with GIMPWIDAT8{lu]w}\6Qa6c-É6DMϑh_&8KY1&g[u׻ |zY*#Oq羪hdOr,0ͬY8[/HG+i+wG~N7:f_~5W+LZ.67vu~yIQ=ˣqx* cD2o1y4(>7!D߻ |aj= ]^BQs/yv8ql1zqy͜68xDwـ1- 4vt؁>tb>l"q4Qyk?񸥴w"Bv]j9pgMQ++.꒎9n)CEyGv{ёy+BEHrxnְVw5uP+s0_Cs!g'O-G~.g3V FM Clbu#ċS7o",`d0h1N,2B7 wochج f61hS>qd ȵk]]!M'H̬NOwԔh4 @n,Iy8* yӹ/9um,Ox6ze-E"utA Hy9 YU.j1‘Oip㭂%b*10@N -4dD`3@TIމH2%tŎ4Q0R_DtCp},y L f=U\:gsl 8ڋVp)CM;;;G|6 PV'L@WTlSS&cfY6F4P [H8ǞN [^.E"" ʄ Tne [Z A3$Tc˻\c[?\~ZՐ[guyʀi9Iڼщk|IENDB`trunk-2017.01a/gui/qt5/yade-favicon.xpm000066400000000000000000000076341304022710500175640ustar00rootroot00000000000000/* XPM */ static char * yade_favicon_xpm[] = { "16 16 210 2", " c None", ". c #F47372", "+ c #F1B4B5", "@ c #909092", "# c #EA5A5A", "$ c #8E4D3C", "% c #746C35", "& c #616233", "* c #4B4B0E", "= c #939191", "- c #8A8A8A", "; 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", "@.#.$.%.&.*.=.-.;.>.,. '. ", ").!.~.{.].^./.(._.:.<.[.}.|. ", "1.2.3.4.5.6.7.8.9.0.a. b. ", "c.d.e.f.g.h.i.j.k.l.m.n.o. p.q.", "r.s.t.u.v.w.x.y.z.A.B.C.D.E.F.G.", "H.I.J.K.L.M.N.O.P.Q.R.S.T.U.V.W.", "X.Y.Z.`. +.+++@+#+$+%+&+*+=+ ", "-+;+>+,+'+)+!+~+{+]+^+/+(+_+:+<+"}; trunk-2017.01a/lib/000077500000000000000000000000001304022710500137305ustar00rootroot00000000000000trunk-2017.01a/lib/base/000077500000000000000000000000001304022710500146425ustar00rootroot00000000000000trunk-2017.01a/lib/base/Logging.hpp000066400000000000000000000033511304022710500167430ustar00rootroot00000000000000// 2006-2008 © Václav Šmilauer #pragma once /* * This file defines various useful logging-related macros - userspace stuff is * - LOG_* for actual logging, * - DECLARE_LOGGER; that should be used in class header to create separate logger for that class, * - CREATE_LOGGER(className); that must be used in class implementation file to create the static variable. * * Note that the latter 2 may change their name to something like LOG_DECLARE and LOG_CREATE, to be consistent. * Some other macros will be very likely added, to allow for easy variable tracing etc. Suggestions welcome. * * * Yade has the logging config file by default in ~/.yade-$VERSION/logging.conf. * */ #include # define _POOR_MANS_LOG(level,msg) {std::cerr< template<> const Real Math::EPSILON = DBL_EPSILON; template<> const Real Math::ZERO_TOLERANCE = 1e-20; template<> const Real Math::MAX_REAL = DBL_MAX; template<> const Real Math::PI = 4.0*atan(1.0); template<> const Real Math::TWO_PI = 2.0*Math::PI; template<> const Real Math::HALF_PI = 0.5*Math::PI; template<> const Real Math::DEG_TO_RAD = Math::PI/180.0; template<> const Real Math::RAD_TO_DEG = 180.0/Math::PI; template<> int ZeroInitializer(){ return (int)0; } template<> Real ZeroInitializer(){ return (Real)0; } #ifdef YADE_MASK_ARBITRARY bool operator==(const mask_t& g, int i) { return g == mask_t(i); } bool operator==(int i, const mask_t& g) { return g == i; } bool operator!=(const mask_t& g, int i) { return !(g == i); } bool operator!=(int i, const mask_t& g) { return g != i; } mask_t operator&(const mask_t& g, int i) { return g & mask_t(i); } mask_t operator&(int i, const mask_t& g) { return g & i; } mask_t operator|(const mask_t& g, int i) { return g | mask_t(i); } mask_t operator|(int i, const mask_t& g) { return g | i; } bool operator||(const mask_t& g, bool b) { return (g != 0) || b; } bool operator||(bool b, const mask_t& g) { return g || b; } bool operator&&(const mask_t& g, bool b) { return (g != 0) && b; } bool operator&&(bool b, const mask_t& g) { return g && b; } #endif trunk-2017.01a/lib/base/Math.hpp000066400000000000000000000334411304022710500162510ustar00rootroot00000000000000// © 2010 Václav Šmilauer #pragma once #ifdef QUAD_PRECISION using quad = long double; using Real = quad; #else using Real = double; #endif #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include using std::endl; using std::cout; using std::cerr; using std::vector; using std::string; using std::list; using std::pair; using std::min; using std::max; using std::set; using std::map; using std::type_info; using std::ifstream; using std::ofstream; using std::runtime_error; using std::logic_error; using std::invalid_argument; using std::ios; using std::ios_base; using std::fstream; using std::ostream; using std::ostringstream; using std::istringstream; using std::swap; using std::make_pair; #include #include #include #include #include #include #include #include #include #include #include using boost::shared_ptr; #ifndef FOREACH #define FOREACH BOOST_FOREACH #endif #ifndef YADE_PTR_CAST #define YADE_PTR_CAST boost::static_pointer_cast #endif #ifndef YADE_CAST #define YADE_CAST static_cast #endif #ifndef YADE_PTR_DYN_CAST #define YADE_PTR_DYN_CAST boost::dynamic_pointer_cast #endif #define EIGEN_DONT_PARALLELIZE #ifdef YADE_MASK_ARBITRARY #include #endif #include #include #include #include template using Vector2 = Eigen::Matrix; using Vector2i = Vector2; using Vector2r = Vector2; template using Vector3 = Eigen::Matrix; using Vector3i = Vector3; using Vector3r = Vector3; template using Vector6 = Eigen::Matrix; using Vector6i = Vector6; using Vector6r = Vector6; template using Matrix3 = Eigen::Matrix; using Matrix3i = Matrix3; using Matrix3r = Matrix3; template using Matrix6 = Eigen::Matrix; using Matrix6i = Matrix6; using Matrix6r = Matrix6; using Quaternionr = Eigen::Quaternion; using AngleAxisr = Eigen::AngleAxis; using AlignedBox2r = Eigen::AlignedBox; using AlignedBox3r = Eigen::AlignedBox; using Eigen::AngleAxis; using Eigen::Quaternion; // in some cases, we want to initialize types that have no default constructor (OpenMPAccumulator, for instance) // template specialization will help us here template EigenMatrix ZeroInitializer(){ return EigenMatrix::Zero(); }; template<> int ZeroInitializer(); template<> Real ZeroInitializer(); // io template std::ostream & operator<<(std::ostream &os, const Vector2& v) { os << v.x()<<" "< std::ostream & operator<<(std::ostream &os, const Vector3& v) { os << v.x()<<" "< std::ostream & operator<<(std::ostream &os, const Vector6& v) { os << v[0]<<" "< std::ostream & operator<<(std::ostream &os, const Eigen::Quaternion& q) { os< struct Math{ static const Scalar PI; static const Scalar HALF_PI; static const Scalar TWO_PI; static const Scalar MAX_REAL; static const Scalar DEG_TO_RAD; static const Scalar RAD_TO_DEG; static const Scalar EPSILON; static const Scalar ZERO_TOLERANCE; static Scalar Sign(Scalar f){ if(f<0) return -1; if(f>0) return 1; return 0; } static Scalar UnitRandom(){ return ((double)rand()/((double)(RAND_MAX))); } static Scalar SymmetricRandom(){ return 2.*(((double)rand())/((double)(RAND_MAX)))-1.; } static Scalar FastInvCos0(Scalar fValue) { Scalar fRoot = sqrt(((Scalar)1.0)-fValue); Scalar fResult = -(Scalar)0.0187293; fResult *= fValue; fResult += (Scalar)0.0742610; fResult *= fValue; fResult -= (Scalar)0.2121144; fResult *= fValue; fResult += (Scalar)1.5707288; fResult *= fRoot; return fResult; } }; using Mathr = Math; /* this was removed in eigen3, see http://forum.kde.org/viewtopic.php?f=74&t=90914 */ template void Matrix_computeUnitaryPositive(const MatrixT& in, MatrixT* unitary, MatrixT* positive){ assert(unitary); assert(positive); //Eigen::JacobiSVD svd(in, Eigen::ComputeThinU | Eigen::ComputeThinV); Eigen::JacobiSVD svd(in, Eigen::ComputeFullU | Eigen::ComputeFullV); MatrixT mU, mV, mS; mU = svd.matrixU(); mV = svd.matrixV(); mS = svd.singularValues().asDiagonal(); *unitary=mU * mV.adjoint(); *positive=mV * mS * mV.adjoint(); } template void matrixEigenDecomposition(const MatrixT& m, MatrixT& mRot, MatrixT& mDiag){ //assert(mRot); assert(mDiag); Eigen::SelfAdjointEigenSolver a(m); mRot=a.eigenvectors(); mDiag=a.eigenvalues().asDiagonal(); } /* convert Vector6r in the Voigt notation to corresponding 2nd order symmetric tensor (stored as Matrix3r) if strain is true, then multiply non-diagonal parts by .5 */ template Matrix3 voigt_toSymmTensor(const Vector6& v, bool strain=false){ Real k=(strain?.5:1.); Matrix3 ret; ret< Vector6 tensor_toVoigt(const Matrix3& m, bool strain=false){ int k=(strain?2:1); Vector6 ret; ret<::signaling_NaN()); // void quaternionToEulerAngles (const Quaternionr& q, Vector3r& eulerAngles,Real threshold=1e-6f); template void quaterniontoGLMatrix(const Quaternion& q, Scalar m[16]){ Scalar w2=2.*q.w(), x2=2.*q.x(), y2=2.*q.y(), z2=2.*q.z(); Scalar x2w=w2*q.w(), y2w=y2*q.w(), z2w=z2*q.w(); Scalar x2x=x2*q.x(), y2x=y2*q.x(), z2x=z2*q.x(); Scalar x2y=y2*q.y(), y2y=y2*q.y(), z2y=z2*q.y(); Scalar x2z=z2*q.z(), y2z=y2*q.z(), z2z=z2*q.z(); m[0]=1.-(y2y+z2z); m[4]=y2x-z2w; m[8]=z2x+y2w; m[12]=0; m[1]=y2x+z2w; m[5]=1.-(x2x+z2z); m[9]=z2y-x2w; m[13]=0; m[2]=z2x-y2w; m[6]=z2y+x2w; m[10]=1.-(x2x+y2y); m[14]=0; m[3]=0.; m[7]=0.; m[11]=0.; m[15]=1.; } // se3 template class Se3 { public : Vector3 position; Quaternion orientation; Se3(){}; Se3(Vector3 rkP, Quaternion qR){ position = rkP; orientation = qR; } Se3(const Se3& s){position = s.position;orientation = s.orientation;} Se3(Se3& a,Se3& b){ position = b.orientation.inverse()*(a.position - b.position); orientation = b.orientation.inverse()*a.orientation; } Se3 inverse(){ return Se3(-(orientation.inverse()*position), orientation.inverse());} void toGLMatrix(float m[16]){ orientation.toGLMatrix(m); m[12] = position[0]; m[13] = position[1]; m[14] = position[2];} Vector3 operator * (const Vector3& b ){return orientation*b+position;} Se3 operator * (const Quaternion& b ){return Se3(position , orientation*b);} Se3 operator * (const Se3& b ){return Se3(orientation*b.position+position,orientation*b.orientation);} }; // functions template Scalar unitVectorsAngle(const Vector3& a, const Vector3& b){ return acos(a.dot(b)); } // operators /* * Mask */ #ifdef YADE_MASK_ARBITRARY using mask_t = std::bitset; bool operator==(const mask_t& g, int i); bool operator==(int i, const mask_t& g); bool operator!=(const mask_t& g, int i); bool operator!=(int i, const mask_t& g); mask_t operator&(const mask_t& g, int i); mask_t operator&(int i, const mask_t& g); mask_t operator|(const mask_t& g, int i); mask_t operator|(int i, const mask_t& g); bool operator||(const mask_t& g, bool b); bool operator||(bool b, const mask_t& g); bool operator&&(const mask_t& g, bool b); bool operator&&(bool b, const mask_t& g); #else using mask_t = int; #endif using Se3r = Se3; /* * Serialization of math classes */ #include #include // fast serialization (no version infor and no tracking) for basic math types // http://www.boost.org/doc/libs/1_42_0/libs/serialization/doc/traits.html#bitwise BOOST_IS_BITWISE_SERIALIZABLE(Vector2r); BOOST_IS_BITWISE_SERIALIZABLE(Vector2i); BOOST_IS_BITWISE_SERIALIZABLE(Vector3r); BOOST_IS_BITWISE_SERIALIZABLE(Vector3i); BOOST_IS_BITWISE_SERIALIZABLE(Vector6r); BOOST_IS_BITWISE_SERIALIZABLE(Vector6i); BOOST_IS_BITWISE_SERIALIZABLE(Quaternionr); BOOST_IS_BITWISE_SERIALIZABLE(Se3r); BOOST_IS_BITWISE_SERIALIZABLE(Matrix3r); BOOST_IS_BITWISE_SERIALIZABLE(Matrix6r); namespace boost { namespace serialization { template void serialize(Archive & ar, Vector2r & g, const unsigned int version){ Real &x=g[0], &y=g[1]; ar & BOOST_SERIALIZATION_NVP(x) & BOOST_SERIALIZATION_NVP(y); } template void serialize(Archive & ar, Vector2i & g, const unsigned int version){ int &x=g[0], &y=g[1]; ar & BOOST_SERIALIZATION_NVP(x) & BOOST_SERIALIZATION_NVP(y); } template void serialize(Archive & ar, Vector3r & g, const unsigned int version) { Real &x=g[0], &y=g[1], &z=g[2]; ar & BOOST_SERIALIZATION_NVP(x) & BOOST_SERIALIZATION_NVP(y) & BOOST_SERIALIZATION_NVP(z); } template void serialize(Archive & ar, Vector3i & g, const unsigned int version){ int &x=g[0], &y=g[1], &z=g[2]; ar & BOOST_SERIALIZATION_NVP(x) & BOOST_SERIALIZATION_NVP(y) & BOOST_SERIALIZATION_NVP(z); } template void serialize(Archive & ar, Vector6r & g, const unsigned int version){ Real &v0=g[0], &v1=g[1], &v2=g[2], &v3=g[3], &v4=g[4], &v5=g[5]; ar & BOOST_SERIALIZATION_NVP(v0) & BOOST_SERIALIZATION_NVP(v1) & BOOST_SERIALIZATION_NVP(v2) & BOOST_SERIALIZATION_NVP(v3) & BOOST_SERIALIZATION_NVP(v4) & BOOST_SERIALIZATION_NVP(v5); } template void serialize(Archive & ar, Vector6i & g, const unsigned int version){ int &v0=g[0], &v1=g[1], &v2=g[2], &v3=g[3], &v4=g[4], &v5=g[5]; ar & BOOST_SERIALIZATION_NVP(v0) & BOOST_SERIALIZATION_NVP(v1) & BOOST_SERIALIZATION_NVP(v2) & BOOST_SERIALIZATION_NVP(v3) & BOOST_SERIALIZATION_NVP(v4) & BOOST_SERIALIZATION_NVP(v5); } template void serialize(Archive & ar, Quaternionr & g, const unsigned int version) { Real &w=g.w(), &x=g.x(), &y=g.y(), &z=g.z(); ar & BOOST_SERIALIZATION_NVP(w) & BOOST_SERIALIZATION_NVP(x) & BOOST_SERIALIZATION_NVP(y) & BOOST_SERIALIZATION_NVP(z); } template void serialize(Archive & ar, Se3r & g, const unsigned int version){ Vector3r& position=g.position; Quaternionr& orientation=g.orientation; ar & BOOST_SERIALIZATION_NVP(position) & BOOST_SERIALIZATION_NVP(orientation); } template void serialize(Archive & ar, Matrix3r & m, const unsigned int version){ Real &m00=m(0,0), &m01=m(0,1), &m02=m(0,2), &m10=m(1,0), &m11=m(1,1), &m12=m(1,2), &m20=m(2,0), &m21=m(2,1), &m22=m(2,2); ar & BOOST_SERIALIZATION_NVP(m00) & BOOST_SERIALIZATION_NVP(m01) & BOOST_SERIALIZATION_NVP(m02) & BOOST_SERIALIZATION_NVP(m10) & BOOST_SERIALIZATION_NVP(m11) & BOOST_SERIALIZATION_NVP(m12) & BOOST_SERIALIZATION_NVP(m20) & BOOST_SERIALIZATION_NVP(m21) & BOOST_SERIALIZATION_NVP(m22); } template void serialize(Archive & ar, Matrix6r & m, const unsigned int version){ Real &m00=m(0,0), &m01=m(0,1), &m02=m(0,2), &m03=m(0,3), &m04=m(0,4), &m05=m(0,5); Real &m10=m(1,0), &m11=m(1,1), &m12=m(1,2), &m13=m(1,3), &m14=m(1,4), &m15=m(1,5); Real &m20=m(2,0), &m21=m(2,1), &m22=m(2,2), &m23=m(2,3), &m24=m(2,4), &m25=m(2,5); Real &m30=m(3,0), &m31=m(3,1), &m32=m(3,2), &m33=m(3,3), &m34=m(3,4), &m35=m(3,5); Real &m40=m(4,0), &m41=m(4,1), &m42=m(4,2), &m43=m(4,3), &m44=m(4,4), &m45=m(4,5); Real &m50=m(5,0), &m51=m(5,1), &m52=m(5,2), &m53=m(5,3), &m54=m(5,4), &m55=m(5,5); ar & BOOST_SERIALIZATION_NVP(m00) & BOOST_SERIALIZATION_NVP(m01) & BOOST_SERIALIZATION_NVP(m02) & BOOST_SERIALIZATION_NVP(m03) & BOOST_SERIALIZATION_NVP(m04) & BOOST_SERIALIZATION_NVP(m05) & BOOST_SERIALIZATION_NVP(m10) & BOOST_SERIALIZATION_NVP(m11) & BOOST_SERIALIZATION_NVP(m12) & BOOST_SERIALIZATION_NVP(m13) & BOOST_SERIALIZATION_NVP(m14) & BOOST_SERIALIZATION_NVP(m15) & BOOST_SERIALIZATION_NVP(m20) & BOOST_SERIALIZATION_NVP(m21) & BOOST_SERIALIZATION_NVP(m22) & BOOST_SERIALIZATION_NVP(m23) & BOOST_SERIALIZATION_NVP(m24) & BOOST_SERIALIZATION_NVP(m25) & BOOST_SERIALIZATION_NVP(m30) & BOOST_SERIALIZATION_NVP(m31) & BOOST_SERIALIZATION_NVP(m32) & BOOST_SERIALIZATION_NVP(m33) & BOOST_SERIALIZATION_NVP(m34) & BOOST_SERIALIZATION_NVP(m35) & BOOST_SERIALIZATION_NVP(m40) & BOOST_SERIALIZATION_NVP(m41) & BOOST_SERIALIZATION_NVP(m42) & BOOST_SERIALIZATION_NVP(m43) & BOOST_SERIALIZATION_NVP(m44) & BOOST_SERIALIZATION_NVP(m45) & BOOST_SERIALIZATION_NVP(m50) & BOOST_SERIALIZATION_NVP(m51) & BOOST_SERIALIZATION_NVP(m52) & BOOST_SERIALIZATION_NVP(m53) & BOOST_SERIALIZATION_NVP(m54) & BOOST_SERIALIZATION_NVP(m55); } #ifdef YADE_MASK_ARBITRARY template void serialize(Archive & ar, mask_t& v, const unsigned int version){ std::string str = v.to_string(); ar & BOOST_SERIALIZATION_NVP(str); v = mask_t(str); } #endif } // namespace serialization } // namespace boost trunk-2017.01a/lib/base/Singleton.hpp000066400000000000000000000013161304022710500173160ustar00rootroot00000000000000// 2009 © Václav Šmilauer #pragma once #include #define FRIEND_SINGLETON(Class) friend class Singleton; // use to instantiate the self static member. #define SINGLETON_SELF(Class) template<> Class* Singleton::self=NULL; namespace { boost::mutex singleton_constructor_mutex; } template class Singleton{ protected: static T* self; // must not be method-local static variable, since it gets created in different translation units multiple times. public: static T& instance(){ if(!self) { boost::mutex::scoped_lock lock(singleton_constructor_mutex); if(!self) self=new T; } return *self; } }; trunk-2017.01a/lib/base/openmp-accu.hpp000066400000000000000000000234501304022710500175660ustar00rootroot00000000000000// 2010 © Václav Šmilauer #pragma once #include #include #include #ifdef YADE_OPENMP #include "omp.h" // O(1) access container which stores data in contiguous chunks of memory // each chunk belonging to one thread template class OpenMPArrayAccumulator{ int CLS; size_t nThreads; int perCL; // number of elements fitting inside cache line std::vector chunks; // array with pointers to the chunks of memory we have allocated; each item for one thread size_t sz; // current number of elements size_t nCL; // current number of allocated cache lines int nCL_for_N(size_t n){ return n/perCL+(n%perCL==0 ? 0 : 1); } // return number of cache lines to allocate for given number of elements public: OpenMPArrayAccumulator() : CLS(sysconf(_SC_LEVEL1_DCACHE_LINESIZE)>0 ? sysconf(_SC_LEVEL1_DCACHE_LINESIZE) : 64), nThreads(omp_get_max_threads()), perCL(CLS/sizeof(T)), chunks(nThreads,NULL), sz(0), nCL(0) { } OpenMPArrayAccumulator(size_t n): CLS(sysconf(_SC_LEVEL1_DCACHE_LINESIZE)>0 ? sysconf(_SC_LEVEL1_DCACHE_LINESIZE) : 64), nThreads(omp_get_max_threads()), perCL(CLS/sizeof(T)), chunks(nThreads,NULL), sz(0), nCL(0) { resize(n); } // change number of elements void resize(size_t n){ if(n==sz) return; // nothing to do size_t nCL_new=nCL_for_N(n); if(nCL_new>nCL){ for(size_t th=0; th(); } sz=n; } // clear (does not deallocate storage, anyway) void clear() { resize(0); } // return number of elements size_t size() const { return sz; } // get value of one element, by summing contributions of all threads T operator[](size_t ix) const { return get(ix); } T get(size_t ix) const { T ret(ZeroInitializer()); for(size_t th=0; th()); } // reset one element to ZeroInitializer void add(size_t ix, const T& diff){ chunks[omp_get_thread_num()][ix]+=diff; } void reset(size_t ix){ set(ix,ZeroInitializer()); } // get all stored data, organized first by index, then by threads; only used for debugging std::vector > getPerThreadData() const { std::vector > ret; for(size_t ix=0; ix vi; for(size_t th=0; th class OpenMPAccumulator{ // in the ctor, assume 64 bytes (arbitrary, but safe) if sysconf does not report anything meaningful // that might happen on newer proc models not yet reported by sysconf (?) // e.g. https://lists.launchpad.net/yade-dev/msg06294.html // where zero was reported, leading to FPU exception at startup int CLS; // cache line size int nThreads; int eSize; // size of an element, computed from cache line size and sizeof(T) char* data; // use void* rather than T*, since with T* the pointer arithmetics has sizeof(T) as unit, which is confusing; char* takes one byte public: // initialize storage with _zeroValue, depending on number of threads OpenMPAccumulator(): CLS(sysconf(_SC_LEVEL1_DCACHE_LINESIZE)>0 ? sysconf(_SC_LEVEL1_DCACHE_LINESIZE) : 64), nThreads(omp_get_max_threads()), eSize(CLS*(sizeof(T)/CLS+(sizeof(T)%CLS==0 ? 0 :1))) { int succ=posix_memalign(/*where allocated*/(void**)&data,/*alignment*/CLS,/*size*/ nThreads*eSize); if(succ!=0) throw std::runtime_error("OpenMPAccumulator: posix_memalign failed to allocate memory."); reset(); } ~OpenMPAccumulator() { free((void*)data); } // lock-free addition void operator+=(const T& val){ *((T*)(data+omp_get_thread_num()*eSize))+=val; } void operator-=(const T& val){ *((T*)(data+omp_get_thread_num()*eSize))-=val; } // return summary value; must not be used concurrently operator T() const { return get(); } // reset to zeroValue; must NOT be used concurrently void reset(){ for(int i=0; i(); } // this can be used to get the value from python, something like // .def_readonly("myAccu",&OpenMPAccumulator::get,"documentation") T get() const { T ret(ZeroInitializer()); for(int i=0; i getPerThreadData() const { std::vector ret; for(int i=0; i class OpenMPVector{ std::vector > vals; size_t sizeV; public: OpenMPVector() {sizeV = omp_get_max_threads(); vals.resize(sizeV);}; void push_back (const T& val) {vals[omp_get_thread_num()].push_back(val);}; size_t size() const { size_t sumSize = 0; for (size_t i=0; i= sizeV) { std::cerr<< ("Index is out of range.")<= size()) { std::cerr<< ("Index is out of range.")<= vals[t].size()) { ix-=vals[t].size(); t+=1; } return vals[t][ix]; } } void clear() { for (size_t i=0; i class OpenMPArrayAccumulator{ std::vector data; public: OpenMPArrayAccumulator(){} OpenMPArrayAccumulator(size_t n){ resize(n); } void resize(size_t s){ data.resize(s,ZeroInitializer()); } void clear(){ data.clear(); } size_t size() const { return data.size(); } T operator[](size_t ix) const { return get(ix); } T get(size_t ix) const { return data[ix]; } void add (size_t ix, const T& diff){ data[ix]+=diff; } void set(size_t ix, const T& val){ data[ix]=val; } void reset(size_t ix){ data[ix]=ZeroInitializer(); } std::vector > getPerThreadData() const { std::vector > ret; for(size_t ix=0; ix vi; vi.push_back(data[ix]); ret.push_back(vi); } return ret; } }; // single-threaded version of the accumulator above template class OpenMPAccumulator{ T data; public: void operator+=(const T& val){ data+=val; } void operator-=(const T& val){ data-=val; } operator T() const { return get(); } void reset(){ data=ZeroInitializer(); } T get() const { return data; } void set(const T& val){ data=val; } // debugging only std::vector getPerThreadData() const { std::vector ret; ret.push_back(data); return ret; } }; template using OpenMPVector=std::vector ; #endif // boost serialization BOOST_SERIALIZATION_SPLIT_FREE(OpenMPAccumulator); template void save(Archive &ar, const OpenMPAccumulator& a, unsigned int version){ int value=a.get(); ar & BOOST_SERIALIZATION_NVP(value); } template void load(Archive &ar, OpenMPAccumulator& a, unsigned int version){ int value; ar & BOOST_SERIALIZATION_NVP(value); a.set(value); } BOOST_SERIALIZATION_SPLIT_FREE(OpenMPAccumulator); template void save(Archive &ar, const OpenMPAccumulator& a, unsigned int version){ Real value=a.get(); ar & BOOST_SERIALIZATION_NVP(value); } template void load(Archive &ar, OpenMPAccumulator& a, unsigned int version){ Real value; ar & BOOST_SERIALIZATION_NVP(value); a.set(value); } BOOST_SERIALIZATION_SPLIT_FREE(OpenMPArrayAccumulator); template void save(Archive &ar, const OpenMPArrayAccumulator& a, unsigned int version){ size_t size=a.size(); ar & BOOST_SERIALIZATION_NVP(size); for(size_t i=0; i(i)).c_str(),item); } } template void load(Archive &ar, OpenMPArrayAccumulator& a, unsigned int version){ size_t size; ar & BOOST_SERIALIZATION_NVP(size); a.resize(size); for(size_t i=0; i(i)).c_str(),item); a.set(i,item); } } trunk-2017.01a/lib/computational-geometry/000077500000000000000000000000001304022710500204405ustar00rootroot00000000000000trunk-2017.01a/lib/computational-geometry/Hull2d.hpp000066400000000000000000000050151304022710500223040ustar00rootroot00000000000000// 2009 © Václav Šmilauer #include /*! Computing convex hull of a 2d cloud of points passed to the constructor, using Graham scan algorithm. Use the operator() to launch computation and get the hull as std::list. The source http://marknelson.us/2007/08/22/convex/ is gratefully acknowledged. Look there for detailed description and more information. */ class ConvexHull2d{ list raw_points, lower_partition_points, upper_partition_points, hull; Vector2r left, right; static Real direction(const Vector2r& p0, const Vector2r& p1, const Vector2r& p2) { return ((p0[0]-p1[0])*(p2[1]-p1[1]))-((p2[0]-p1[0])*(p0[1]-p1[1])); } struct Vector2r_xComparator{ bool operator()(const Vector2r& p1, const Vector2r& p2){return p1[0] build_half_hull(list& in, int factor){ vector out; in.push_back(right); out.push_back(left); while(in.size()>0){ out.push_back(in.front()); in.pop_front(); while(out.size()>=3){ size_t end=out.size()-1; if(factor*direction(out[end-2],out[end],out[end-1])<=0) out.erase(out.begin()+end-1); else break; } } return out; } public: ConvexHull2d(const list& pts){raw_points.assign(pts.begin(),pts.end());}; ConvexHull2d(const vector& pts){raw_points.assign(pts.begin(),pts.end());}; vector operator()(void){ partition_points(); vector lower_hull=build_half_hull(lower_partition_points,1); vector upper_hull=build_half_hull(upper_partition_points,-1); vector ret; ret.reserve(lower_hull.size()+upper_hull.size()-2); for(size_t i=upper_hull.size()-1; i>0; i--) ret.push_back(upper_hull[i]); size_t lsize=lower_hull.size(); for(size_t i=0; i P){ Real ret=0.; size_t n=P.size(); for(size_t i=0; i > >& scalarField, int sx, int sy, int sz) { sizeX = sx; sizeY = sy; sizeZ = sz; scalarField.resize(sx); for(int i=0;i > >& scalarField, Real iso) { isoValue = iso; nbTriangles = 0; for(int i=1;i > >& scalarField, int x,int y,int z) { static vector cellValues(8); static vector cellPositions(8); static vector vertexList(12); cellValues[0] = scalarField[x][y][z]; cellValues[1] = scalarField[x+1][y][z]; cellValues[2] = scalarField[x+1][y][z+1]; cellValues[3] = scalarField[x][y][z+1]; cellValues[4] = scalarField[x][y+1][z]; cellValues[5] = scalarField[x+1][y+1][z]; cellValues[6] = scalarField[x+1][y+1][z+1]; cellValues[7] = scalarField[x][y+1][z+1]; cellPositions[0] = positions[x][y][z]; cellPositions[1] = positions[x+1][y][z]; cellPositions[2] = positions[x+1][y][z+1]; cellPositions[3] = positions[x][y][z+1]; cellPositions[4] = positions[x][y+1][z]; cellPositions[5] = positions[x+1][y+1][z]; cellPositions[6] = positions[x+1][y+1][z+1]; cellPositions[7] = positions[x][y+1][z+1]; /* compute index in edgeArray that tells how the surface intersect the cell */ int index = 0; if (cellValues[0]>isoValue) index |= 1; if (cellValues[1]>isoValue) index |= 2; if (cellValues[2]>isoValue) index |= 4; if (cellValues[3]>isoValue) index |= 8; if (cellValues[4]>isoValue) index |= 16; if (cellValues[5]>isoValue) index |= 32; if (cellValues[6]>isoValue) index |= 64; if (cellValues[7]>isoValue) index |= 128; /* compute position of vertices where the surface interesct the cell*/ int config = edgeArray[index]; if (config == 0) /* the cell is not intersected by surface */ return; if (config & 1) interpolate(cellPositions[0], cellPositions[1], cellValues[0], cellValues[1], vertexList[0]); if (config & 2) interpolate(cellPositions[1], cellPositions[2], cellValues[1], cellValues[2], vertexList[1]); if (config & 4) interpolate(cellPositions[2], cellPositions[3], cellValues[2], cellValues[3], vertexList[2]); if (config & 8) interpolate(cellPositions[3], cellPositions[0], cellValues[3], cellValues[0], vertexList[3]); if (config & 16) interpolate(cellPositions[4], cellPositions[5], cellValues[4], cellValues[5], vertexList[4]); if (config & 32) interpolate(cellPositions[5], cellPositions[6], cellValues[5], cellValues[6], vertexList[5]); if (config & 64) interpolate(cellPositions[6], cellPositions[7], cellValues[6], cellValues[7], vertexList[6]); if (config & 128) interpolate(cellPositions[7], cellPositions[4], cellValues[7], cellValues[4], vertexList[7]); if (config & 256) interpolate(cellPositions[0], cellPositions[4], cellValues[0], cellValues[4], vertexList[8]); if (config & 512) interpolate(cellPositions[1], cellPositions[5], cellValues[1], cellValues[5], vertexList[9]); if (config & 1024) interpolate(cellPositions[2], cellPositions[6], cellValues[2], cellValues[6], vertexList[10]); if (config & 2048) interpolate(cellPositions[3], cellPositions[7], cellValues[3], cellValues[7], vertexList[11]); /* compute triangles and normals*/ int offset,i; const int * tri = triTable[index]; for (i=0; tri[i]!=-1; ++i) { offset = nbTriangles*3; index = tri[i]; triangles[offset] = vertexList[index]; computeNormal(scalarField,x,y,z,offset,index); offset++; index = tri[++i]; triangles[offset] = vertexList[index]; computeNormal(scalarField,x,y,z,offset,index); offset++; index = tri[++i]; triangles[offset] = vertexList[index]; computeNormal(scalarField,x,y,z,offset,index); nbTriangles++; } } void MarchingCube::computeNormal(const vector > >& scalarField, int x, int y, int z,int offset, int triangleNum) { switch (triangleNum) { case 0 : normals[offset] = computeNormalX(scalarField,x, y, z); break; case 1 : normals[offset] = computeNormalZ(scalarField,x+1, y, z); break; case 2 : normals[offset] = computeNormalX(scalarField,x, y, z+1); break; case 3 : normals[offset] = computeNormalZ(scalarField,x, y, z); break; case 4 : normals[offset] = computeNormalX(scalarField,x, y+1, z); break; case 5 : normals[offset] = computeNormalZ(scalarField,x+1, y+1, z); break; case 6 : normals[offset] = computeNormalX(scalarField,x, y+1, z+1); break; case 7 : normals[offset] = computeNormalZ(scalarField,x, y+1, z); break; case 8 : normals[offset] = computeNormalY(scalarField,x, y, z); break; case 9 : normals[offset] = computeNormalY(scalarField,x+1, y, z); break; case 10 : normals[offset] = computeNormalY(scalarField,x+1, y, z+1); break; case 11 : normals[offset] = computeNormalY(scalarField,x, y, z+1); break; } } void MarchingCube::interpolate(const Vector3r& vect1, const Vector3r& vect2, Real val1, Real val2, Vector3r& vect) { vect[0] = interpolateValue(val1, val2, vect1[0], vect2[0]); vect[1] = interpolateValue(val1, val2, vect1[1], vect2[1]); vect[2] = interpolateValue(val1, val2, vect1[2], vect2[2]); } Real MarchingCube::interpolateValue( Real val1, Real val2, Real val_cible1, Real val_cible2) { Real a = (val_cible2-val_cible1)/(val2-val1); Real b = val_cible1-a*val1; return a*isoValue+b; } const Vector3r& MarchingCube::computeNormalX(const vector > >& scalarField, int x, int y, int z) { static Vector3r normal; Real xyz = scalarField[x][y][z]; Real xp1yz = scalarField[x+1][y][z]; normal[0] = interpolateValue( xp1yz, xyz, scalarField[x+2][y][z]-xyz, xp1yz-scalarField[x-1][y][z] ); normal[1] = interpolateValue( xyz, xp1yz, scalarField[x][y+1][z], scalarField[x+1][y+1][z] ) - interpolateValue( xyz, xp1yz, scalarField[x][y-1][z], scalarField[x+1][y-1][z] ); normal[2] = interpolateValue( xyz, xp1yz, scalarField[x][y][z+1], scalarField[x+1][y][z+1] ) - interpolateValue( xyz, xp1yz, scalarField[x][y][z-1], scalarField[x+1][y][z-1] ); normal.normalize(); return normal; } const Vector3r& MarchingCube::computeNormalY(const vector > >& scalarField, int x, int y, int z ) { static Vector3r normal; Real xyz = scalarField[x][y][z]; Real xyp1z = scalarField[x][y+1][z]; normal[0] = interpolateValue( xyz, xyp1z, scalarField[x+1][y][z], scalarField[x+1][y+1][z] ) - interpolateValue( xyz, xyp1z, scalarField[x-1][y][z], scalarField[x-1][y+1][z] ); normal[1] = interpolateValue( xyp1z, xyz, scalarField[x][y+2][z]-xyz, xyp1z-scalarField[x][y-1][z] ); normal[2] = interpolateValue( xyz, xyp1z, scalarField[x][y][z+1], scalarField[x][y+1][z+1] ) - interpolateValue( xyz, xyp1z, scalarField[x][y][z-1], scalarField[x][y+1][z-1] ); normal.normalize(); return normal; } const Vector3r& MarchingCube::computeNormalZ(const vector > >& scalarField, int x, int y, int z) { static Vector3r normal; Real xyz = scalarField[x][y][z]; Real xyzp1 = scalarField[x][y][z+1]; normal[0] = interpolateValue( xyz, xyzp1, scalarField[x+1][y][z], scalarField[x+1][y][z+1] ) - interpolateValue( xyz, xyzp1, scalarField[x-1][y][z], scalarField[x-1][y][z+1] ); normal[1] = interpolateValue( xyz, xyzp1, scalarField[x][y+1][z], scalarField[x][y+1][z+1] ) - interpolateValue( xyz, xyzp1, scalarField[x][y-1][z], scalarField[x][y-1][z+1] ); normal[2] = interpolateValue( xyzp1, xyz, scalarField[x][y][z+2]-xyz, xyzp1-scalarField[x][y][z-1] ); normal.normalize(); return normal; } const int MarchingCube::edgeArray[256] = { 0x0 , 0x109, 0x203, 0x30a, 0x406, 0x50f, 0x605, 0x70c, 0x80c, 0x905, 0xa0f, 0xb06, 0xc0a, 0xd03, 0xe09, 0xf00, 0x190, 0x99 , 0x393, 0x29a, 0x596, 0x49f, 0x795, 0x69c, 0x99c, 0x895, 0xb9f, 0xa96, 0xd9a, 0xc93, 0xf99, 0xe90, 0x230, 0x339, 0x33 , 0x13a, 0x636, 0x73f, 0x435, 0x53c, 0xa3c, 0xb35, 0x83f, 0x936, 0xe3a, 0xf33, 0xc39, 0xd30, 0x3a0, 0x2a9, 0x1a3, 0xaa , 0x7a6, 0x6af, 0x5a5, 0x4ac, 0xbac, 0xaa5, 0x9af, 0x8a6, 0xfaa, 0xea3, 0xda9, 0xca0, 0x460, 0x569, 0x663, 0x76a, 0x66 , 0x16f, 0x265, 0x36c, 0xc6c, 0xd65, 0xe6f, 0xf66, 0x86a, 0x963, 0xa69, 0xb60, 0x5f0, 0x4f9, 0x7f3, 0x6fa, 0x1f6, 0xff , 0x3f5, 0x2fc, 0xdfc, 0xcf5, 0xfff, 0xef6, 0x9fa, 0x8f3, 0xbf9, 0xaf0, 0x650, 0x759, 0x453, 0x55a, 0x256, 0x35f, 0x55 , 0x15c, 0xe5c, 0xf55, 0xc5f, 0xd56, 0xa5a, 0xb53, 0x859, 0x950, 0x7c0, 0x6c9, 0x5c3, 0x4ca, 0x3c6, 0x2cf, 0x1c5, 0xcc , 0xfcc, 0xec5, 0xdcf, 0xcc6, 0xbca, 0xac3, 0x9c9, 0x8c0, 0x8c0, 0x9c9, 0xac3, 0xbca, 0xcc6, 0xdcf, 0xec5, 0xfcc, 0xcc , 0x1c5, 0x2cf, 0x3c6, 0x4ca, 0x5c3, 0x6c9, 0x7c0, 0x950, 0x859, 0xb53, 0xa5a, 0xd56, 0xc5f, 0xf55, 0xe5c, 0x15c, 0x55 , 0x35f, 0x256, 0x55a, 0x453, 0x759, 0x650, 0xaf0, 0xbf9, 0x8f3, 0x9fa, 0xef6, 0xfff, 0xcf5, 0xdfc, 0x2fc, 0x3f5, 0xff , 0x1f6, 0x6fa, 0x7f3, 0x4f9, 0x5f0, 0xb60, 0xa69, 0x963, 0x86a, 0xf66, 0xe6f, 0xd65, 0xc6c, 0x36c, 0x265, 0x16f, 0x66 , 0x76a, 0x663, 0x569, 0x460, 0xca0, 0xda9, 0xea3, 0xfaa, 0x8a6, 0x9af, 0xaa5, 0xbac, 0x4ac, 0x5a5, 0x6af, 0x7a6, 0xaa , 0x1a3, 0x2a9, 0x3a0, 0xd30, 0xc39, 0xf33, 0xe3a, 0x936, 0x83f, 0xb35, 0xa3c, 0x53c, 0x435, 0x73f, 0x636, 0x13a, 0x33 , 0x339, 0x230, 0xe90, 0xf99, 0xc93, 0xd9a, 0xa96, 0xb9f, 0x895, 0x99c, 0x69c, 0x795, 0x49f, 0x596, 0x29a, 0x393, 0x99 , 0x190, 0xf00, 0xe09, 0xd03, 0xc0a, 0xb06, 0xa0f, 0x905, 0x80c, 0x70c, 0x605, 0x50f, 0x406, 0x30a, 0x203, 0x109, 0x0 }; const int MarchingCube::triTable[256][16] = { {-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 0, 8, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 0, 1, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 1, 8, 3, 9, 8, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 1, 2, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 0, 8, 3, 1, 2, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 9, 2, 10, 0, 2, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 2, 8, 3, 2, 10, 8, 10, 9, 8, -1, -1, -1, -1, -1, -1, -1}, { 3, 11, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 0, 11, 2, 8, 11, 0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 1, 9, 0, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 1, 11, 2, 1, 9, 11, 9, 8, 11, -1, -1, -1, -1, -1, -1, -1}, { 3, 10, 1, 11, 10, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 0, 10, 1, 0, 8, 10, 8, 11, 10, -1, -1, -1, -1, -1, -1, -1}, { 3, 9, 0, 3, 11, 9, 11, 10, 9, -1, -1, -1, -1, -1, -1, -1}, { 9, 8, 10, 10, 8, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 4, 7, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 4, 3, 0, 7, 3, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 0, 1, 9, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 4, 1, 9, 4, 7, 1, 7, 3, 1, -1, -1, -1, -1, -1, -1, -1}, { 1, 2, 10, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 3, 4, 7, 3, 0, 4, 1, 2, 10, -1, -1, -1, -1, -1, -1, -1}, { 9, 2, 10, 9, 0, 2, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1}, { 2, 10, 9, 2, 9, 7, 2, 7, 3, 7, 9, 4, -1, -1, -1, -1}, { 8, 4, 7, 3, 11, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, {11, 4, 7, 11, 2, 4, 2, 0, 4, -1, -1, -1, -1, -1, -1, -1}, { 9, 0, 1, 8, 4, 7, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1}, { 4, 7, 11, 9, 4, 11, 9, 11, 2, 9, 2, 1, -1, -1, -1, -1}, { 3, 10, 1, 3, 11, 10, 7, 8, 4, -1, -1, -1, -1, -1, -1, -1}, { 1, 11, 10, 1, 4, 11, 1, 0, 4, 7, 11, 4, -1, -1, -1, -1}, { 4, 7, 8, 9, 0, 11, 9, 11, 10, 11, 0, 3, -1, -1, -1, -1}, { 4, 7, 11, 4, 11, 9, 9, 11, 10, -1, -1, -1, -1, -1, -1, -1}, { 9, 5, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 9, 5, 4, 0, 8, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 0, 5, 4, 1, 5, 0, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 8, 5, 4, 8, 3, 5, 3, 1, 5, -1, -1, -1, -1, -1, -1, -1}, { 1, 2, 10, 9, 5, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 3, 0, 8, 1, 2, 10, 4, 9, 5, -1, -1, -1, -1, -1, -1, -1}, { 5, 2, 10, 5, 4, 2, 4, 0, 2, -1, -1, -1, -1, -1, -1, -1}, { 2, 10, 5, 3, 2, 5, 3, 5, 4, 3, 4, 8, -1, -1, -1, -1}, { 9, 5, 4, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 0, 11, 2, 0, 8, 11, 4, 9, 5, -1, -1, -1, -1, -1, -1, -1}, { 0, 5, 4, 0, 1, 5, 2, 3, 11, -1, -1, -1, -1, -1, -1, -1}, { 2, 1, 5, 2, 5, 8, 2, 8, 11, 4, 8, 5, -1, -1, -1, -1}, {10, 3, 11, 10, 1, 3, 9, 5, 4, -1, -1, -1, -1, -1, -1, -1}, { 4, 9, 5, 0, 8, 1, 8, 10, 1, 8, 11, 10, -1, -1, -1, -1}, { 5, 4, 0, 5, 0, 11, 5, 11, 10, 11, 0, 3, -1, -1, -1, -1}, { 5, 4, 8, 5, 8, 10, 10, 8, 11, -1, -1, -1, -1, -1, -1, -1}, { 9, 7, 8, 5, 7, 9, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 9, 3, 0, 9, 5, 3, 5, 7, 3, -1, -1, -1, -1, -1, -1, -1}, { 0, 7, 8, 0, 1, 7, 1, 5, 7, -1, -1, -1, -1, -1, -1, -1}, { 1, 5, 3, 3, 5, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 9, 7, 8, 9, 5, 7, 10, 1, 2, -1, -1, -1, -1, -1, -1, -1}, {10, 1, 2, 9, 5, 0, 5, 3, 0, 5, 7, 3, -1, -1, -1, -1}, { 8, 0, 2, 8, 2, 5, 8, 5, 7, 10, 5, 2, -1, -1, -1, -1}, { 2, 10, 5, 2, 5, 3, 3, 5, 7, -1, -1, -1, -1, -1, -1, -1}, { 7, 9, 5, 7, 8, 9, 3, 11, 2, -1, -1, -1, -1, -1, -1, -1}, { 9, 5, 7, 9, 7, 2, 9, 2, 0, 2, 7, 11, -1, -1, -1, -1}, { 2, 3, 11, 0, 1, 8, 1, 7, 8, 1, 5, 7, -1, -1, -1, -1}, {11, 2, 1, 11, 1, 7, 7, 1, 5, -1, -1, -1, -1, -1, -1, -1}, { 9, 5, 8, 8, 5, 7, 10, 1, 3, 10, 3, 11, -1, -1, -1, -1}, { 5, 7, 0, 5, 0, 9, 7, 11, 0, 1, 0, 10, 11, 10, 0, -1}, {11, 10, 0, 11, 0, 3, 10, 5, 0, 8, 0, 7, 5, 7, 0, -1}, {11, 10, 5, 7, 11, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, {10, 6, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 0, 8, 3, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 9, 0, 1, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 1, 8, 3, 1, 9, 8, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1}, { 1, 6, 5, 2, 6, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 1, 6, 5, 1, 2, 6, 3, 0, 8, -1, -1, -1, -1, -1, -1, -1}, { 9, 6, 5, 9, 0, 6, 0, 2, 6, -1, -1, -1, -1, -1, -1, -1}, { 5, 9, 8, 5, 8, 2, 5, 2, 6, 3, 2, 8, -1, -1, -1, -1}, { 2, 3, 11, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, {11, 0, 8, 11, 2, 0, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1}, { 0, 1, 9, 2, 3, 11, 5, 10, 6, -1, -1, -1, -1, -1, -1, -1}, { 5, 10, 6, 1, 9, 2, 9, 11, 2, 9, 8, 11, -1, -1, -1, -1}, { 6, 3, 11, 6, 5, 3, 5, 1, 3, -1, -1, -1, -1, -1, -1, -1}, { 0, 8, 11, 0, 11, 5, 0, 5, 1, 5, 11, 6, -1, -1, -1, -1}, { 3, 11, 6, 0, 3, 6, 0, 6, 5, 0, 5, 9, -1, -1, -1, -1}, { 6, 5, 9, 6, 9, 11, 11, 9, 8, -1, -1, -1, -1, -1, -1, -1}, { 5, 10, 6, 4, 7, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 4, 3, 0, 4, 7, 3, 6, 5, 10, -1, -1, -1, -1, -1, -1, -1}, { 1, 9, 0, 5, 10, 6, 8, 4, 7, -1, -1, -1, -1, -1, -1, -1}, {10, 6, 5, 1, 9, 7, 1, 7, 3, 7, 9, 4, -1, -1, -1, -1}, { 6, 1, 2, 6, 5, 1, 4, 7, 8, -1, -1, -1, -1, -1, -1, -1}, { 1, 2, 5, 5, 2, 6, 3, 0, 4, 3, 4, 7, -1, -1, -1, -1}, { 8, 4, 7, 9, 0, 5, 0, 6, 5, 0, 2, 6, -1, -1, -1, -1}, { 7, 3, 9, 7, 9, 4, 3, 2, 9, 5, 9, 6, 2, 6, 9, -1}, { 3, 11, 2, 7, 8, 4, 10, 6, 5, -1, -1, -1, -1, -1, -1, -1}, { 5, 10, 6, 4, 7, 2, 4, 2, 0, 2, 7, 11, -1, -1, -1, -1}, { 0, 1, 9, 4, 7, 8, 2, 3, 11, 5, 10, 6, -1, -1, -1, -1}, { 9, 2, 1, 9, 11, 2, 9, 4, 11, 7, 11, 4, 5, 10, 6, -1}, { 8, 4, 7, 3, 11, 5, 3, 5, 1, 5, 11, 6, -1, -1, -1, -1}, { 5, 1, 11, 5, 11, 6, 1, 0, 11, 7, 11, 4, 0, 4, 11, -1}, { 0, 5, 9, 0, 6, 5, 0, 3, 6, 11, 6, 3, 8, 4, 7, -1}, { 6, 5, 9, 6, 9, 11, 4, 7, 9, 7, 11, 9, -1, -1, -1, -1}, { 10, 4, 9, 6, 4, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 4, 10, 6, 4, 9, 10, 0, 8, 3, -1, -1, -1, -1, -1, -1, -1}, {10, 0, 1, 10, 6, 0, 6, 4, 0, -1, -1, -1, -1, -1, -1, -1}, { 8, 3, 1, 8, 1, 6, 8, 6, 4, 6, 1, 10, -1, -1, -1, -1}, { 1, 4, 9, 1, 2, 4, 2, 6, 4, -1, -1, -1, -1, -1, -1, -1}, { 3, 0, 8, 1, 2, 9, 2, 4, 9, 2, 6, 4, -1, -1, -1, -1}, { 0, 2, 4, 4, 2, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 8, 3, 2, 8, 2, 4, 4, 2, 6, -1, -1, -1, -1, -1, -1, -1}, {10, 4, 9, 10, 6, 4, 11, 2, 3, -1, -1, -1, -1, -1, -1, -1}, { 0, 8, 2, 2, 8, 11, 4, 9, 10, 4, 10, 6, -1, -1, -1, -1}, { 3, 11, 2, 0, 1, 6, 0, 6, 4, 6, 1, 10, -1, -1, -1, -1}, { 6, 4, 1, 6, 1, 10, 4, 8, 1, 2, 1, 11, 8, 11, 1, -1}, { 9, 6, 4, 9, 3, 6, 9, 1, 3, 11, 6, 3, -1, -1, -1, -1}, { 8, 11, 1, 8, 1, 0, 11, 6, 1, 9, 1, 4, 6, 4, 1, -1}, { 3, 11, 6, 3, 6, 0, 0, 6, 4, -1, -1, -1, -1, -1, -1, -1}, { 6, 4, 8, 11, 6, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 7, 10, 6, 7, 8, 10, 8, 9, 10, -1, -1, -1, -1, -1, -1, -1}, { 0, 7, 3, 0, 10, 7, 0, 9, 10, 6, 7, 10, -1, -1, -1, -1}, {10, 6, 7, 1, 10, 7, 1, 7, 8, 1, 8, 0, -1, -1, -1, -1}, {10, 6, 7, 10, 7, 1, 1, 7, 3, -1, -1, -1, -1, -1, -1, -1}, { 1, 2, 6, 1, 6, 8, 1, 8, 9, 8, 6, 7, -1, -1, -1, -1}, { 2, 6, 9, 2, 9, 1, 6, 7, 9, 0, 9, 3, 7, 3, 9, -1}, { 7, 8, 0, 7, 0, 6, 6, 0, 2, -1, -1, -1, -1, -1, -1, -1}, { 7, 3, 2, 6, 7, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 2, 3, 11, 10, 6, 8, 10, 8, 9, 8, 6, 7, -1, -1, -1, -1}, { 2, 0, 7, 2, 7, 11, 0, 9, 7, 6, 7, 10, 9, 10, 7, -1}, { 1, 8, 0, 1, 7, 8, 1, 10, 7, 6, 7, 10, 2, 3, 11, -1}, {11, 2, 1, 11, 1, 7, 10, 6, 1, 6, 7, 1, -1, -1, -1, -1}, { 8, 9, 6, 8, 6, 7, 9, 1, 6, 11, 6, 3, 1, 3, 6, -1}, { 0, 9, 1, 11, 6, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 7, 8, 0, 7, 0, 6, 3, 11, 0, 11, 6, 0, -1, -1, -1, -1}, { 7, 11, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 7, 6, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 3, 0, 8, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 0, 1, 9, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 8, 1, 9, 8, 3, 1, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1}, {10, 1, 2, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 1, 2, 10, 3, 0, 8, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1}, { 2, 9, 0, 2, 10, 9, 6, 11, 7, -1, -1, -1, -1, -1, -1, -1}, { 6, 11, 7, 2, 10, 3, 10, 8, 3, 10, 9, 8, -1, -1, -1, -1}, { 7, 2, 3, 6, 2, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 7, 0, 8, 7, 6, 0, 6, 2, 0, -1, -1, -1, -1, -1, -1, -1}, { 2, 7, 6, 2, 3, 7, 0, 1, 9, -1, -1, -1, -1, -1, -1, -1}, { 1, 6, 2, 1, 8, 6, 1, 9, 8, 8, 7, 6, -1, -1, -1, -1}, {10, 7, 6, 10, 1, 7, 1, 3, 7, -1, -1, -1, -1, -1, -1, -1}, {10, 7, 6, 1, 7, 10, 1, 8, 7, 1, 0, 8, -1, -1, -1, -1}, { 0, 3, 7, 0, 7, 10, 0, 10, 9, 6, 10, 7, -1, -1, -1, -1}, { 7, 6, 10, 7, 10, 8, 8, 10, 9, -1, -1, -1, -1, -1, -1, -1}, { 6, 8, 4, 11, 8, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 3, 6, 11, 3, 0, 6, 0, 4, 6, -1, -1, -1, -1, -1, -1, -1}, { 8, 6, 11, 8, 4, 6, 9, 0, 1, -1, -1, -1, -1, -1, -1, -1}, { 9, 4, 6, 9, 6, 3, 9, 3, 1, 11, 3, 6, -1, -1, -1, -1}, { 6, 8, 4, 6, 11, 8, 2, 10, 1, -1, -1, -1, -1, -1, -1, -1}, { 1, 2, 10, 3, 0, 11, 0, 6, 11, 0, 4, 6, -1, -1, -1, -1}, { 4, 11, 8, 4, 6, 11, 0, 2, 9, 2, 10, 9, -1, -1, -1, -1}, {10, 9, 3, 10, 3, 2, 9, 4, 3, 11, 3, 6, 4, 6, 3, -1}, { 8, 2, 3, 8, 4, 2, 4, 6, 2, -1, -1, -1, -1, -1, -1, -1}, { 0, 4, 2, 4, 6, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 1, 9, 0, 2, 3, 4, 2, 4, 6, 4, 3, 8, -1, -1, -1, -1}, { 1, 9, 4, 1, 4, 2, 2, 4, 6, -1, -1, -1, -1, -1, -1, -1}, { 8, 1, 3, 8, 6, 1, 8, 4, 6, 6, 10, 1, -1, -1, -1, -1}, {10, 1, 0, 10, 0, 6, 6, 0, 4, -1, -1, -1, -1, -1, -1, -1}, { 4, 6, 3, 4, 3, 8, 6, 10, 3, 0, 3, 9, 10, 9, 3, -1}, {10, 9, 4, 6, 10, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 4, 9, 5, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 0, 8, 3, 4, 9, 5, 11, 7, 6, -1, -1, -1, -1, -1, -1, -1}, { 5, 0, 1, 5, 4, 0, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1}, {11, 7, 6, 8, 3, 4, 3, 5, 4, 3, 1, 5, -1, -1, -1, -1}, { 9, 5, 4, 10, 1, 2, 7, 6, 11, -1, -1, -1, -1, -1, -1, -1}, { 6, 11, 7, 1, 2, 10, 0, 8, 3, 4, 9, 5, -1, -1, -1, -1}, { 7, 6, 11, 5, 4, 10, 4, 2, 10, 4, 0, 2, -1, -1, -1, -1}, { 3, 4, 8, 3, 5, 4, 3, 2, 5, 10, 5, 2, 11, 7, 6, -1}, { 7, 2, 3, 7, 6, 2, 5, 4, 9, -1, -1, -1, -1, -1, -1, -1}, { 9, 5, 4, 0, 8, 6, 0, 6, 2, 6, 8, 7, -1, -1, -1, -1}, { 3, 6, 2, 3, 7, 6, 1, 5, 0, 5, 4, 0, -1, -1, -1, -1}, { 6, 2, 8, 6, 8, 7, 2, 1, 8, 4, 8, 5, 1, 5, 8, -1}, { 9, 5, 4, 10, 1, 6, 1, 7, 6, 1, 3, 7, -1, -1, -1, -1}, { 1, 6, 10, 1, 7, 6, 1, 0, 7, 8, 7, 0, 9, 5, 4, -1}, { 4, 0, 10, 4, 10, 5, 0, 3, 10, 6, 10, 7, 3, 7, 10, -1}, { 7, 6, 10, 7, 10, 8, 5, 4, 10, 4, 8, 10, -1, -1, -1, -1}, { 6, 9, 5, 6, 11, 9, 11, 8, 9, -1, -1, -1, -1, -1, -1, -1}, { 3, 6, 11, 0, 6, 3, 0, 5, 6, 0, 9, 5, -1, -1, -1, -1}, { 0, 11, 8, 0, 5, 11, 0, 1, 5, 5, 6, 11, -1, -1, -1, -1}, { 6, 11, 3, 6, 3, 5, 5, 3, 1, -1, -1, -1, -1, -1, -1, -1}, { 1, 2, 10, 9, 5, 11, 9, 11, 8, 11, 5, 6, -1, -1, -1, -1}, { 0, 11, 3, 0, 6, 11, 0, 9, 6, 5, 6, 9, 1, 2, 10, -1}, {11, 8, 5, 11, 5, 6, 8, 0, 5, 10, 5, 2, 0, 2, 5, -1}, { 6, 11, 3, 6, 3, 5, 2, 10, 3, 10, 5, 3, -1, -1, -1, -1}, { 5, 8, 9, 5, 2, 8, 5, 6, 2, 3, 8, 2, -1, -1, -1, -1}, { 9, 5, 6, 9, 6, 0, 0, 6, 2, -1, -1, -1, -1, -1, -1, -1}, { 1, 5, 8, 1, 8, 0, 5, 6, 8, 3, 8, 2, 6, 2, 8, -1}, { 1, 5, 6, 2, 1, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 1, 3, 6, 1, 6, 10, 3, 8, 6, 5, 6, 9, 8, 9, 6, -1}, {10, 1, 0, 10, 0, 6, 9, 5, 0, 5, 6, 0, -1, -1, -1, -1}, { 0, 3, 8, 5, 6, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, {10, 5, 6, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, {11, 5, 10, 7, 5, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, {11, 5, 10, 11, 7, 5, 8, 3, 0, -1, -1, -1, -1, -1, -1, -1}, { 5, 11, 7, 5, 10, 11, 1, 9, 0, -1, -1, -1, -1, -1, -1, -1}, {10, 7, 5, 10, 11, 7, 9, 8, 1, 8, 3, 1, -1, -1, -1, -1}, {11, 1, 2, 11, 7, 1, 7, 5, 1, -1, -1, -1, -1, -1, -1, -1}, { 0, 8, 3, 1, 2, 7, 1, 7, 5, 7, 2, 11, -1, -1, -1, -1}, { 9, 7, 5, 9, 2, 7, 9, 0, 2, 2, 11, 7, -1, -1, -1, -1}, { 7, 5, 2, 7, 2, 11, 5, 9, 2, 3, 2, 8, 9, 8, 2, -1}, { 2, 5, 10, 2, 3, 5, 3, 7, 5, -1, -1, -1, -1, -1, -1, -1}, { 8, 2, 0, 8, 5, 2, 8, 7, 5, 10, 2, 5, -1, -1, -1, -1}, { 9, 0, 1, 5, 10, 3, 5, 3, 7, 3, 10, 2, -1, -1, -1, -1}, { 9, 8, 2, 9, 2, 1, 8, 7, 2, 10, 2, 5, 7, 5, 2, -1}, { 1, 3, 5, 3, 7, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 0, 8, 7, 0, 7, 1, 1, 7, 5, -1, -1, -1, -1, -1, -1, -1}, { 9, 0, 3, 9, 3, 5, 5, 3, 7, -1, -1, -1, -1, -1, -1, -1}, { 9, 8, 7, 5, 9, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 5, 8, 4, 5, 10, 8, 10, 11, 8, -1, -1, -1, -1, -1, -1, -1}, { 5, 0, 4, 5, 11, 0, 5, 10, 11, 11, 3, 0, -1, -1, -1, -1}, { 0, 1, 9, 8, 4, 10, 8, 10, 11, 10, 4, 5, -1, -1, -1, -1}, {10, 11, 4, 10, 4, 5, 11, 3, 4, 9, 4, 1, 3, 1, 4, -1}, { 2, 5, 1, 2, 8, 5, 2, 11, 8, 4, 5, 8, -1, -1, -1, -1}, { 0, 4, 11, 0, 11, 3, 4, 5, 11, 2, 11, 1, 5, 1, 11, -1}, { 0, 2, 5, 0, 5, 9, 2, 11, 5, 4, 5, 8, 11, 8, 5, -1}, { 9, 4, 5, 2, 11, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 2, 5, 10, 3, 5, 2, 3, 4, 5, 3, 8, 4, -1, -1, -1, -1}, { 5, 10, 2, 5, 2, 4, 4, 2, 0, -1, -1, -1, -1, -1, -1, -1}, { 3, 10, 2, 3, 5, 10, 3, 8, 5, 4, 5, 8, 0, 1, 9, -1}, { 5, 10, 2, 5, 2, 4, 1, 9, 2, 9, 4, 2, -1, -1, -1, -1}, { 8, 4, 5, 8, 5, 3, 3, 5, 1, -1, -1, -1, -1, -1, -1, -1}, { 0, 4, 5, 1, 0, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 8, 4, 5, 8, 5, 3, 9, 0, 5, 0, 3, 5, -1, -1, -1, -1}, { 9, 4, 5, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 4, 11, 7, 4, 9, 11, 9, 10, 11, -1, -1, -1, -1, -1, -1, -1}, { 0, 8, 3, 4, 9, 7, 9, 11, 7, 9, 10, 11, -1, -1, -1, -1}, { 1, 10, 11, 1, 11, 4, 1, 4, 0, 7, 4, 11, -1, -1, -1, -1}, { 3, 1, 4, 3, 4, 8, 1, 10, 4, 7, 4, 11, 10, 11, 4, -1}, { 4, 11, 7, 9, 11, 4, 9, 2, 11, 9, 1, 2, -1, -1, -1, -1}, { 9, 7, 4, 9, 11, 7, 9, 1, 11, 2, 11, 1, 0, 8, 3, -1}, {11, 7, 4, 11, 4, 2, 2, 4, 0, -1, -1, -1, -1, -1, -1, -1}, {11, 7, 4, 11, 4, 2, 8, 3, 4, 3, 2, 4, -1, -1, -1, -1}, { 2, 9, 10, 2, 7, 9, 2, 3, 7, 7, 4, 9, -1, -1, -1, -1}, { 9, 10, 7, 9, 7, 4, 10, 2, 7, 8, 7, 0, 2, 0, 7, -1}, { 3, 7, 10, 3, 10, 2, 7, 4, 10, 1, 10, 0, 4, 0, 10, -1}, { 1, 10, 2, 8, 7, 4, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 4, 9, 1, 4, 1, 7, 7, 1, 3, -1, -1, -1, -1, -1, -1, -1}, { 4, 9, 1, 4, 1, 7, 0, 8, 1, 8, 7, 1, -1, -1, -1, -1}, { 4, 0, 3, 7, 4, 3, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 4, 8, 7, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 9, 10, 8, 10, 11, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 3, 0, 9, 3, 9, 11, 11, 9, 10, -1, -1, -1, -1, -1, -1, -1}, { 0, 1, 10, 0, 10, 8, 8, 10, 11, -1, -1, -1, -1, -1, -1, -1}, { 3, 1, 10, 11, 3, 10, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 1, 2, 11, 1, 11, 9, 9, 11, 8, -1, -1, -1, -1, -1, -1, -1}, { 3, 0, 9, 3, 9, 11, 1, 2, 9, 2, 11, 9, -1, -1, -1, -1}, { 0, 2, 11, 8, 0, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 3, 2, 11, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 2, 3, 8, 2, 8, 10, 10, 8, 9, -1, -1, -1, -1, -1, -1, -1}, { 9, 10, 2, 0, 9, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 2, 3, 8, 2, 8, 10, 0, 1, 8, 1, 10, 8, -1, -1, -1, -1}, { 1, 10, 2, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 1, 3, 8, 9, 1, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 0, 9, 1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, { 0, 3, 8, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1}, {-1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1, -1} }; trunk-2017.01a/lib/computational-geometry/MarchingCube.hpp000066400000000000000000000054371304022710500235110ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include class MarchingCube { /// ATTRIBUTES private : vector triangles; public : const vector& getTriangles() { return triangles; } private : vector normals; public : const vector& getNormals() { return normals; } private : int nbTriangles; public : int getNbTriangles() { return nbTriangles; } private : int sizeX,sizeY,sizeZ; private : Real isoValue; private : vector > > positions; private : static const int edgeArray[256]; private : static const int triTable[256][16]; Vector3r aNormal; /// PRIVATE METHOD /** triangulate cell (x,y,z) **/ private : void polygonize (const vector > >& scalarField, int x, int y, int z); /** compute normals of the triangles previously found with polygonizecalcule les normales des triangles trouver dans la case (x,y,z) @param n : indice of the first triangle to process **/ private : void computeNormal(const vector > >& scalarField, int x, int y, int z,int offset, int triangleNum); /** interpolate coordinates of point vect (that is on isosurface) from coordinates of points vect1 et vect2 **/ private : void interpolate (const Vector3r& vect1, const Vector3r& vect2, Real val1, Real val2,Vector3r& vect); /** Same as interpolate but in 1D **/ private : Real interpolateValue(Real val1, Real val2, Real val_cible1, Real val_cible2); /** Compute normal to vertice or triangle inside cell (x,y,z) **/ private : const Vector3r& computeNormalX(const vector > >& scalarField, int x, int y, int z); private : const Vector3r& computeNormalY(const vector > >& scalarField, int x, int y, int z); private : const Vector3r& computeNormalZ(const vector > >& scalarField, int x, int y, int z); /// CONSTRUCTOR/DESTRUCTOR public : MarchingCube (); public : ~MarchingCube (); /// PULIC METHODS public : void computeTriangulation(const vector > >& scalarField, Real iso); public : void init(int sx, int sy, int sz, const Vector3r& min, const Vector3r& max); public : void resizeScalarField(vector > >& scalarField, int sx, int sy, int sz); }; trunk-2017.01a/lib/factory/000077500000000000000000000000001304022710500153775ustar00rootroot00000000000000trunk-2017.01a/lib/factory/ClassFactory.cpp000066400000000000000000000077261304022710500205140ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "ClassFactory.hpp" #include #include CREATE_LOGGER(ClassFactory); SINGLETON_SELF(ClassFactory); class Factorable; bool ClassFactory::registerFactorable( std::string name , CreateFactorableFnPtr create, CreateSharedFactorableFnPtr createShared, CreatePureCustomFnPtr createPureCustom) { bool tmp = map.insert( FactorableCreatorsMap::value_type( name , FactorableCreators(create,createShared, createPureCustom) )).second; return tmp; } shared_ptr ClassFactory::createShared( std::string name ) { FactorableCreatorsMap::const_iterator i = map.find( name ); if( i == map.end() ) { dlm.load(name); if (dlm.isLoaded(name)) { if( map.find( name ) == map.end() ) { // Well, exception are also a way to return value, right? // This throws at startup for every .so that doesn't contain class named the same as the library. // I.e. almost everything in yade-libs and some others installed locally... // Don't log that, it would confuse users. //LOG_FATAL("Can't create class "< second.createShared ) (); } Factorable* ClassFactory::createPure( std::string name ) { FactorableCreatorsMap::const_iterator i = map.find( name ); if( i == map.end() ) { dlm.load(name); if (dlm.isLoaded(name)) { if( map.find( name ) == map.end() ) { throw std::runtime_error(("Class "+name+" not registered in the ClassFactory.").c_str()); } return createPure(name); } throw std::runtime_error(("Class "+name+" could not be factored in the ClassFactory.").c_str()); } return ( i -> second.create ) (); } void * ClassFactory::createPureCustom( std::string name ) { FactorableCreatorsMap::const_iterator i = map.find( name ); if( i == map.end() ) throw std::runtime_error(("Class "+name+" could not be factored in the ClassFactory.").c_str()); return ( i -> second.createPureCustom ) (); } bool ClassFactory::load(const string& name) { return dlm.load(name); } string ClassFactory::lastError() { return dlm.lastError(); } void ClassFactory::registerPluginClasses(const char* fileAndClasses[]){ assert(fileAndClasses[0]!=NULL); // must be file name // only filename given, no classes names explicitly if(fileAndClasses[1]==NULL){ /* strip leading path (if any; using / as path separator) and strip one suffix (if any) to get the contained class name */ string heldClass=boost::algorithm::replace_regex_copy(string(fileAndClasses[0]),boost::regex("^(.*/)?(.*?)(\\.[^.]*)?$"),string("\\2")); #ifdef YADE_DEBUG if(getenv("YADE_DEBUG")) cerr<<__FILE__<<":"<<__LINE__<<": Plugin "< #include #include "DynLibManager.hpp" /*! define the following macro to enable experimenta boost::serialization support Slows the compilation down about 2×. Python wrapper defines O.saveXML('file.xml') to try it out. Loading is not yet implemented (should be easy) */ #include #include #include #include #include // must come after all supported archive types #include #include #include #include #include #define REGISTER_FACTORABLE(name) \ inline shared_ptr< Factorable > CreateShared##name() \ { \ return shared_ptr< name > ( new name ); \ } \ inline Factorable* Create##name() \ { \ return new name; \ } \ inline void * CreatePureCustom##name() \ { \ return new name; \ } \ const bool registered##name __attribute__ ((unused)) = \ ClassFactory::instance().registerFactorable( #name , \ Create##name , \ CreateShared##name , \ CreatePureCustom##name); class Factorable; /*! \brief The class factory of Yade used for serialization purpose and also as a dynamic library loader. All classes that call the macro REGISTER_FACTORABLE in their header are registered inside the factory so it is possible to ask the factory to create an instance of that class. This is automatic because the macro should be outside the class definition, so it is called automatically when the class is loaded by the program or when a dynamic library is loaded. This ClassFactory also acts as a dynamic library loader : when you ask for an instance, either the class already exists inside the factory and a new instance is created, or the class doesn't exist inside the factory and the ClassFactory will look on the hard drive to know if your class exists inside a dynamic library. If so the library is loaded and a new instance of the class can be created. \note ClassFactory is a singleton so you can't create an instance of it because its constructor is private. You should instead use ClassFactory::instance().createShared("Rigidbody") for example. */ class ClassFactory : public Singleton { private : /// Pointer on a function that create an instance of a serializable class an return a shared pointer on it typedef shared_ptr ( *CreateSharedFactorableFnPtr )(); /// Pointer on a function that create an instance of a serializable class an return a C pointer on it typedef Factorable* ( *CreateFactorableFnPtr )(); /// Pointer on a function that create an instance of a custom class (i.e. not serializable) and return a void C pointer on it typedef void* ( *CreatePureCustomFnPtr )(); /// Description of a class that is stored inside the factory. struct FactorableCreators { CreateFactorableFnPtr create; /// Used to create a C pointer on the class (if serializable) CreateSharedFactorableFnPtr createShared; /// Used to create a shared pointer on the class (if serializable) CreatePureCustomFnPtr createPureCustom; /// Used to create a void C pointer on the class FactorableCreators() {}; FactorableCreators( CreateFactorableFnPtr c, CreateSharedFactorableFnPtr cs, CreatePureCustomFnPtr cpc) { create = c; createShared = cs; createPureCustom = cpc; }; }; /// Type of a Stl map used to map the registered class name with their FactorableCreators typedef std::map< std::string , FactorableCreators > FactorableCreatorsMap; /// The internal dynamic library manager used to load dynamic libraries when an instance of a non loaded class is ask DynLibManager dlm; /// Map that contains the name of the registered class and their description FactorableCreatorsMap map; ClassFactory() { if(getenv("YADE_DEBUG")) fprintf(stderr,"Constructing ClassFactory.\n"); } ClassFactory(const ClassFactory&); ClassFactory& operator=(const ClassFactory&); virtual ~ClassFactory() {}; DECLARE_LOGGER; public : /*! This method is used to register a Factorable class into the factory. It is called only from macro REGISTER_CLASS_TO_FACTORY \param name the name of the class \param create a pointer to a function that is able to return a C pointer on the given class \param createPureCustom a pointer to a function that is able to return a void C pointer on the given class \param verify a pointer to a function that is able to return the type_info of the given class \param type type of the class (SERIALIZABLE or CUSTOM) \param f is true is the class is a fundamental one (Vector3, Quaternion) \return true if registration is succesfull */ bool registerFactorable( std::string name , CreateFactorableFnPtr create, CreateSharedFactorableFnPtr createShared, CreatePureCustomFnPtr createPureCustom); /// Create a shared pointer on a serializable class of the given name shared_ptr createShared( std::string name ); /// Create a C pointer on a serializable class of the given name Factorable* createPure( std::string name ); /// Create a void C pointer on a class of the given name void * createPureCustom( std::string name ); /*! Mainly used by the method findType for serialization purpose. Tells if a given type is a serilializable class \param tp type info of the type to test \param fundamental is true if the given type is fundamental (Vector3,Quaternion ...) */ bool load(const string& fullFileName); std::string lastError(); void registerPluginClasses(const char* fileAndClasses[]); list pluginClasses; virtual string getClassName() const { return "Factorable"; }; virtual string getBaseClassName(int ) const { return "";}; FRIEND_SINGLETON(ClassFactory); }; /*! Macro defining what classes can be found in this plugin -- must always be used in the respective .cpp file. * A function registerThisPluginClasses_FirstPluginName is generated at every occurence. The identifier should * be unique and avoids use of __COUNTER__ which didn't appear in gcc until 4.3. */ #define _YADE_PLUGIN_BOOST_REGISTER(x,y,z) BOOST_CLASS_EXPORT_IMPLEMENT(z); BOOST_SERIALIZATION_FACTORY_0(z); #define _YADE_PLUGIN_REPEAT(x,y,z) BOOST_PP_STRINGIZE(z), // priority 500 is greater than priority for log4cxx initialization (in core/main/pyboot.cpp); therefore lo5cxx will be initialized before plugins are registered #define YADE_PLUGIN(plugins) namespace{ __attribute__((constructor)) void BOOST_PP_CAT(registerThisPluginClasses_,BOOST_PP_SEQ_HEAD(plugins)) (void){ const char* info[]={__FILE__ , BOOST_PP_SEQ_FOR_EACH(_YADE_PLUGIN_REPEAT,~,plugins) NULL}; ClassFactory::instance().registerPluginClasses(info);} } BOOST_PP_SEQ_FOR_EACH(_YADE_PLUGIN_BOOST_REGISTER,~,plugins) trunk-2017.01a/lib/factory/DynLibManager.cpp000066400000000000000000000041201304022710500205540ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * with help from Bronek Kozicki * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "DynLibManager.hpp" #include "ClassFactory.hpp" CREATE_LOGGER(DynLibManager); DynLibManager::DynLibManager () { autoUnload = true; } DynLibManager::~DynLibManager () { if(autoUnload) unloadAll(); } // load plugin with given filename bool DynLibManager::load (const string& lib){ if (lib.empty()) throw std::runtime_error(__FILE__ ": got empty library name to load."); void* handle = dlopen(lib.c_str(),RTLD_GLOBAL | RTLD_NOW); if (!handle) return !error(); handles[lib] = handle; return true; } // unload plugin, given full filename bool DynLibManager::unload (const string& libName) { if (isLoaded(libName)) return closeLib(libName); else return false; } bool DynLibManager::unloadAll () { std::map::iterator ith = handles.begin(); std::map::iterator ithEnd = handles.end(); for( ; ith!=ithEnd ; ++ith) if ((*ith).first.length()!=0) unload((*ith).first); return false; } bool DynLibManager::isLoaded (const string& libName) { std::map::iterator ith = handles.find(libName); return (ith!= handles.end() && (*ith).second!=NULL); } void DynLibManager::setAutoUnload ( bool enabled ) { autoUnload = enabled; } bool DynLibManager::closeLib(const string libName) { dlclose(handles[libName]); return !error(); } std::string DynLibManager::lastError() { return lastError_; } bool DynLibManager::error() { char * error = dlerror(); if (error != NULL) { lastError_ = error; } return (error!=NULL); } trunk-2017.01a/lib/factory/DynLibManager.hpp000066400000000000000000000023301304022710500205620ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2004 by Bronek Kozicki * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include class DynLibManager { private : std::map handles; bool autoUnload; public : DynLibManager (); ~DynLibManager (); void addBaseDirectory(const std::string& dir); bool load(const std::string& libName); bool unload (const std::string& libName); bool isLoaded (const std::string& libName); bool unloadAll (); void setAutoUnload ( bool enabled ); std::string lastError(); DECLARE_LOGGER; private : bool closeLib(const std::string libName); bool error(); std::string lastError_; }; trunk-2017.01a/lib/factory/Factorable.hpp000066400000000000000000000050071304022710500201540ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include "ClassFactory.hpp" #include #include //! macro for registering both class and its base #define REGISTER_CLASS_AND_BASE(cn,bcn) REGISTER_CLASS_NAME(cn); REGISTER_BASE_CLASS_NAME(bcn); #define REGISTER_CLASS_NAME(cn) \ public : virtual string getClassName() const { return #cn; }; // FIXME[1] - that macro below should go to another class! factorable has nothing to do with inheritance tree. #define REGISTER_BASE_CLASS_NAME(bcn) \ public : virtual string getBaseClassName(unsigned int i=0) const \ { \ string token; \ vector tokens; \ string str=#bcn; \ istringstream iss(str); \ while (!iss.eof()) \ { \ iss >> token; \ tokens.push_back(token); \ } \ if (i>=token.size()) \ return ""; \ else \ return tokens[i]; \ } \ public : virtual int getBaseClassNumber() \ { \ string token; \ vector tokens; \ string str=#bcn; \ istringstream iss(str); \ while (!iss.eof()) \ { \ iss >> token; \ tokens.push_back(token); \ } \ return tokens.size(); \ } class Factorable { public : Factorable() {} virtual ~Factorable() {} virtual string getBaseClassName(unsigned int i=0) const { return "";} // FIXME[1] virtual int getBaseClassNumber() { return 0;} // FIXME[1] REGISTER_CLASS_NAME(Factorable); // FIXME - virtual function to return version, long and short description, OR // maybe just a file with the same name as class with description inside // public : virtual std::string getVersion(); // FIXME[1] - we can make a class Plugin for all that extra stuff: // shortDescription(), longDescription(), baseClassName(), baseClassNumber() }; trunk-2017.01a/lib/multimethods/000077500000000000000000000000001304022710500164465ustar00rootroot00000000000000trunk-2017.01a/lib/multimethods/DynLibDispatcher.hpp000066400000000000000000000413731304022710500223570ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include #include #include // compat with former yade's local Loki #define TYPELIST_1 LOKI_TYPELIST_1 #define TYPELIST_2 LOKI_TYPELIST_2 #define TYPELIST_3 LOKI_TYPELIST_3 #define TYPELIST_4 LOKI_TYPELIST_4 #define TYPELIST_5 LOKI_TYPELIST_5 #define TYPELIST_7 LOKI_TYPELIST_7 #include #include #include #include struct DynLibDispatcher_Item2D { int ix1, ix2; std::string functorName; DynLibDispatcher_Item2D(int a, int b, std::string c):ix1(a),ix2(b),functorName(c){}; }; struct DynLibDispatcher_Item1D { int ix1; std::string functorName; DynLibDispatcher_Item1D(int a, std::string c):ix1(a), functorName(c){}; }; /// /// base classes involved in multiple dispatch must be derived from Indexable /// /// base template for all dispatchers /// template < class BaseClass, // a typelist with base classess involved in the dispatch (or single class, for 1D ) // FIXME: should use shared_ptr references, like this: DynLibDispatcher< TYPELIST_2( shared_ptr& , shared_ptr& ) , .... class Executor, // class which gives multivirtual function class ResultType, // type returned by multivirtual function class TList, // typelist of arguments passed to multivirtual function // WARNING: first arguments must be shared_ptr, for details see FunctorWrapper bool autoSymmetry=true /*true - the function called is always the same, only order of arguments is rearranged to make correct function call, only go() is called false - the function called is always different. arguments order is not rearranged go(), and goReverse() are called, respectively*/ > class DynLibDispatcher { // this template recursively defines a type for callBacks matrix, with required number of dimensions private: template struct Matrix { using ResultIterator = Loki::NullType; using ResultIteratorInt = Loki::NullType; }; template struct Matrix< Loki::Typelist< Head, Loki::NullType > > { using Result = vector< shared_ptr< Executor > >; using ResultInt = vector< int >; using ResultIterator = typename vector< shared_ptr< Executor > >::iterator; using ResultIteratorInt = vector< int >::iterator; }; template struct Matrix< Loki::Typelist< Head, Tail > > { // recursive typedef to get matrix of required dimensions using InsideType = typename Matrix< Tail >::Result; using InsideTypeInt = typename Matrix< Tail >::ResultInt; using Result = vector< InsideType >; using ResultInt = vector< InsideTypeInt >; using ResultIterator = typename vector< InsideType >::iterator; using ResultIteratorInt = typename vector< InsideTypeInt >::iterator; }; typedef typename Loki::TL::Append< Loki::NullType , BaseClass >::Result BaseClassList; typedef typename Loki::TL::TypeAtNonStrict::Result BaseClass1; // 1D typedef typename Loki::TL::TypeAtNonStrict::Result BaseClass2; // 2D typedef typename Matrix< BaseClassList >::ResultIterator Iterator2; // outer iterator 2D typedef typename Matrix< BaseClassList >::ResultIteratorInt IteratorInfo2; typedef typename Matrix< BaseClassList >::Result MatrixType; typedef typename Matrix< BaseClassList >::ResultInt MatrixIntType; MatrixType callBacks; // multidimensional matrix that stores functors ( 1D, 2D, 3D, 4D, ....) MatrixIntType callBacksInfo; // multidimensional matrix for extra information about functors in the matrix // currently used to remember if it is reversed functor public: DynLibDispatcher() { // FIXME - static_assert( typeid(BaseClass1) == typeid(Parm1) ); // 1D // FIXME - static_assert( typeid(BaseClass2) == typeid(Parm2) ); // 2D clearMatrix(); }; void clearMatrix() { callBacks.clear(); callBacksInfo.clear(); } shared_ptr getExecutor(shared_ptr& arg1){ int ix1; if(arg1->getClassIndex()<0) throw runtime_error("No functor for type "+arg1->getClassName()+" (index "+boost::lexical_cast(arg1->getClassIndex())+"), since the index is invalid (negative)."); if(locateMultivirtualFunctor1D(ix1,arg1)) return callBacks[ix1]; return shared_ptr(); } shared_ptr getExecutor(shared_ptr& arg1, shared_ptr& arg2){ if(arg1->getClassIndex()<0 || arg2->getClassIndex()<0) throw runtime_error("No functor for types "+arg1->getClassName()+" (index "+boost::lexical_cast(arg1->getClassIndex())+") + "+arg2->getClassName()+" (index "+boost::lexical_cast(arg2->getClassIndex())+"), since some of the indices is invalid (negative)."); int ix1,ix2; if(locateMultivirtualFunctor2D(ix1,ix2,arg1,arg2)) return callBacks[ix1][ix2]; return shared_ptr(); } shared_ptr getFunctor1D(shared_ptr& base1){ return getExecutor(base1); } /* Return pointer to the functor for two base classes given. Swap is true if the dispatch objects should be swapped before calling Executor::go. */ shared_ptr getFunctor2D(shared_ptr& base1, shared_ptr& base2, bool& swap){ int ix1, ix2; if(!locateMultivirtualFunctor2D(ix1,ix2,base1,base2)) return shared_ptr(); swap=(bool)(callBacksInfo[ix1][ix2]); return callBacks[ix1][ix2]; } /*! Return representation of the dispatch matrix as vector of int,string (i.e. index,functor name) */ vector dataDispatchMatrix1D(){ vector ret; for(size_t i=0; igetClassName())); } return ret; } /*! Return representation of the dispatch matrix as vector of int,int,string (i.e. index1,index2,functor name) */ vector dataDispatchMatrix2D(){ vector ret; for(size_t i=0; igetClassName())); } } } return ret; } /*! Dump 1d dispatch matrix to given stream. */ std::ostream& dumpDispatchMatrix1D(std::ostream& out, const string& prefix=""){ for(size_t i=0; i "<getClassName()< "<getClassName()< executor){ // create base class, to access its index. (we can't access static variable, because // the class might not exist in memory at all, and we have to load dynamic library, // so that a static variable is created and accessible) shared_ptr baseClass = YADE_PTR_CAST(ClassFactory::instance().createShared(baseClassName)); // this is a strange tweak without which it won't work. shared_ptr base = YADE_PTR_CAST(baseClass); assert(base); int& index = base->getClassIndex(); if(index == -1) std::cerr << "--------> Did you forget to call createIndex(); in constructor?\n"; assert (index != -1); int maxCurrentIndex = base->getMaxCurrentlyUsedClassIndex(); callBacks.resize( maxCurrentIndex+1 ); // make sure that there is a place for new Functor callBacks[index] = executor; }; public: void add2DEntry(string baseClassName1, string baseClassName2, shared_ptr executor){ shared_ptr baseClass1 = YADE_PTR_CAST(ClassFactory::instance().createShared(baseClassName1)); shared_ptr baseClass2 = YADE_PTR_CAST(ClassFactory::instance().createShared(baseClassName2)); shared_ptr base1 = YADE_PTR_CAST(baseClass1); shared_ptr base2 = YADE_PTR_CAST(baseClass2); assert(base1); assert(base2); int& index1 = base1->getClassIndex(); if(index1 == -1) std::cerr << "--------> Did you forget to call createIndex(); in constructor?\n"; assert (index1 != -1); int& index2 = base2->getClassIndex(); if(index2 == -1) std::cerr << "--------> Did you forget to call createIndex(); in constructor?\n"; assert(index2 != -1); if( typeid(BaseClass1) == typeid(BaseClass2) ) assert(base1->getMaxCurrentlyUsedClassIndex() == base2->getMaxCurrentlyUsedClassIndex()); int maxCurrentIndex1 = base1->getMaxCurrentlyUsedClassIndex(); int maxCurrentIndex2 = base2->getMaxCurrentlyUsedClassIndex(); callBacks.resize( maxCurrentIndex1+1 ); // resizing callBacks table callBacksInfo.resize( maxCurrentIndex1+1 ); for( Iterator2 ci = callBacks.begin() ; ci != callBacks.end() ; ++ci ) ci->resize(maxCurrentIndex2+1); for( IteratorInfo2 cii = callBacksInfo.begin() ; cii != callBacksInfo.end() ; ++cii ) cii->resize(maxCurrentIndex2+1); if( typeid(BaseClass1) == typeid(BaseClass2) ) // both base classes are the same { callBacks [index2][index1] = executor; callBacks [index1][index2] = executor; string order = baseClassName1 + " " + baseClassName2; string reverseOrder = baseClassName2 + " " + baseClassName1; if( autoSymmetry || executor->checkOrder() == order ) // if you want autoSymmetry, you don't have to DEFINE_FUNCTOR_ORDER_2D { callBacksInfo [index2][index1] = 1; // this is reversed call callBacksInfo [index1][index2] = 0; } else if( executor->checkOrder() == reverseOrder ) { callBacksInfo [index2][index1] = 0; callBacksInfo [index1][index2] = 1; // this is reversed call } else { throw std::runtime_error(("Multimethods: checkOrder: undefined dispatch order for "+executor->getClassName()).c_str()); } } else // classes are different, no symmetry possible { callBacks [index1][index2] = executor; callBacksInfo [index1][index2] = 0; } } bool locateMultivirtualFunctor1D(int& index, shared_ptr& base) { if(callBacks.empty()) return false; index = base->getClassIndex(); assert( index >= 0 && (unsigned int)( index ) < callBacks.size()); if(callBacks[index]) return true; int depth=1; int index_tmp = base->getBaseClassIndex(depth); while(1) if(index_tmp == -1) return false; else if(callBacks[index_tmp]) { // BEGIN FIXME - this should be a separate function to resize stuff //cerr << index << " " << index_tmp << endl; if( callBacksInfo.size() <= (unsigned int)index ) callBacksInfo.resize(index+1); if( callBacks.size() <= (unsigned int)index ) callBacks.resize(index+1); // END callBacksInfo[index] = callBacksInfo[index_tmp]; callBacks [index] = callBacks [index_tmp]; return true; } else index_tmp = base->getBaseClassIndex(++depth); return false; // FIXME - this line should be not needed } bool locateMultivirtualFunctor2D(int& index1, int& index2, shared_ptr& base1, shared_ptr& base2) { //#define _DISP_TRACE(msg) cerr<<"@DT@"<<__LINE__<<" "<getClassIndex(); index2 = base2->getClassIndex(); assert(index1>=0); assert(index2>=0); assert((unsigned int)(index1)getClassName()<<"="<getClassName()<<"="<getClassName()); return true; } int foundIx1,foundIx2; int maxDp1=-1, maxDp2=-1; for(int dist=1; ; dist++){ bool distTooBig=true; foundIx1=foundIx2=-1; // found no dispatch at this depth yet for(int dp1=0; dp1<=dist; dp1++){ int dp2=dist-dp1; if((maxDp1>=0 && dp1>maxDp1) || (maxDp2>=0 && dp2>maxDp2)) continue; _DISP_TRACE(" Trying indices with depths "<getClassName()); } } if(foundIx1!=-1) return true; if(distTooBig){ _DISP_TRACE("Undefined dispatch, dist="< ResultType operator() (shared_ptr& base, Args... args) { int index; if( locateMultivirtualFunctor1D(index,base) ) return (callBacks[index])->go(base, args...); else return ResultType(); } // calling multivirtual function, 2D, // symmetry handling in private struct private: template< bool useSymmetry, class BaseClassTrait1, class BaseClassTrait2, typename... Args> struct InvocationTraits { static ResultType doDispatch(shared_ptr& ex, shared_ptr base1, shared_ptr base2, Args... args) { return ex->goReverse (base1, base2, args...); } }; template< class BaseClassTrait, typename... Args> struct InvocationTraits< true , BaseClassTrait, BaseClassTrait, Args... > { static ResultType doDispatch( shared_ptr& ex , shared_ptr base1, shared_ptr base2, Args... args) { return ex->go (base2, base1, args...); } }; // calling multivirtual function, 2D, public interface public: template ResultType operator() (shared_ptr& base1, shared_ptr& base2, Args... args) { int index1, index2; if( locateMultivirtualFunctor2D(index1,index2,base1,base2) ) { if(callBacksInfo[index1][index2])// reversed { using CallTraits=InvocationTraits ; return CallTraits::doDispatch( callBacks[index1][index2] , base1, base2, args...); } else return (callBacks[index1][index2] )->go(base1, base2, args...); } else return ResultType(); } }; trunk-2017.01a/lib/multimethods/FunctorWrapper.hpp000066400000000000000000000151621304022710500221450ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include // compat with former yade's local Loki #define TYPELIST_1 LOKI_TYPELIST_1 #define TYPELIST_2 LOKI_TYPELIST_2 #define TYPELIST_3 LOKI_TYPELIST_3 #define TYPELIST_4 LOKI_TYPELIST_4 #define TYPELIST_5 LOKI_TYPELIST_5 #define TYPELIST_7 LOKI_TYPELIST_7 #include /////////////////////////////////////////////////////////////////////////////////////////////////// /// base template for classes that provide virtual functions for multiple dispatch, /// /// in other words for multivirtual function call /// /// /// /// This is a base template for all classes that will provide functions for multiple dispatch. /// /// To create a new category of virtual functions you must derive from this class, inside you will /// have provided virtual functions that you must overload to get multivirtual behaviour. /// /// Depending on the number of dimensions for which you need multiple dispatch you have to overload /// different virtual functions: /// /// for 1D, you overload function [*]: /// public: virtual ResultType go( ArgumentTypeList ); /// /// for 2D, you overload functions [*]: /// public: virtual ResultType go( ArgumentTypeList ); /// public: virtual ResultType goReverse( ArgumentTypeList ); /// /// function goReverse is called only when DynLibDispatcher has autoSymmetry set to false. /// otherwise DynLibDispatcher automatically reverses first two arguments, and calls go(), /// same applies for 3D. /// /// for 3D, you overload functions (not implemented now, but easy to write) [*]: /// public: virtual ResultType go( ArgumentTypeList ); /// public: virtual ResultType go012( ArgumentTypeList ); // forwards call to go() /// public: virtual ResultType go120( ArgumentTypeList ); /// public: virtual ResultType go201( ArgumentTypeList ); /// public: virtual ResultType go021( ArgumentTypeList ); /// public: virtual ResultType go210( ArgumentTypeList ); /// /// /// Template parameters: /// /// ResultType - is the type returned by multivirtual function /// /// ArgumentTypeList - is a TypeList of arguments accepted by multivirtual function, /// ATTENTION: /// - for 1D first type in this list must be of type shared_ptr /// this first argument acts like *this, in C++ virtual functions /// /// - for 2D first and second type in this list must be shared_ptr /// those argument act like *this1 and *this2 /// /// - for 3D first, second and third type in this list must be shared_ptr /// those argument act like *this1 , *this2 and *this3 /// /// /// /// [*] /// Note about virtual function arguents ArgumentTypeList - all functions take arguments by value /// only for fundametal types and pure pointers, all other types are passed by referece. For details look /// into Loki::TypeTraits::ParameterType. For example if you your class is: /// /// class ShapeDraw : public FunctorWrapper< std::string , TYPELIST_4(boost::shared_ptr,double,char,const std::string) > /// {} /// /// then virtual function to overload is: /// public: virtual std::string go(boost::shared_ptr&,double,char,const std::string& ); /// /// references were added where necessary, to optimize call speed. /// So pay attention when you overload this function. /// template < class ResultType, // type returned by multivirtual function class ArgumentTypeList // TypeList of arguments accepted by multivirtual function, > class FunctorWrapper //: public Serializable // FIXME functor shouldn't be serializable { private : typedef Loki::FunctorImpl Impl; typedef typename Impl::Parm1 Parm1; typedef typename Impl::Parm2 Parm2; typedef typename Impl::Parm3 Parm3; typedef typename Impl::Parm4 Parm4; typedef typename Impl::Parm5 Parm5; typedef typename Impl::Parm6 Parm6; typedef typename Impl::Parm7 Parm7; ResultType error(int n) { throw std::runtime_error(("Multimethods: bad virtual call (probably go/goReverse was not overridden with the same argument types; only fundamental types and pure pointers are passed by value, all other types (including shared_ptr<>) are passed by reference); types in the call were:\n" + string("1. ") + typeid(Parm1).name() + "\n" + "2. " + typeid(Parm2).name() + "\n" + "3. " + typeid(Parm3).name() + "\n" + "4. " + typeid(Parm4).name() + "\n" + "5. " + typeid(Parm5).name() + "\n" + "6. " + typeid(Parm6).name() + "\n" + "7. " + typeid(Parm7).name() + "\n" + "number of types used in the call: " + boost::lexical_cast(n) + "\n").c_str()); } public : FunctorWrapper () {}; virtual ~FunctorWrapper () {}; virtual string checkOrder() const { return ""; }; // in following functions a second throw was added - just to bypass compiler warnings - it will never be executed. virtual ResultType go ( Parm1) { return error(1); }; virtual ResultType go ( Parm1,Parm2) { return error(2); }; virtual ResultType go ( Parm1,Parm2,Parm3) { return error(3); }; virtual ResultType go ( Parm1,Parm2,Parm3,Parm4) { return error(4); }; virtual ResultType go ( Parm1,Parm2,Parm3,Parm4,Parm5) { return error(5); }; virtual ResultType go ( Parm1,Parm2,Parm3,Parm4,Parm5,Parm6) { return error(6); }; virtual ResultType go ( Parm1,Parm2,Parm3,Parm4,Parm5,Parm6,Parm7) { return error(7); }; virtual ResultType goReverse( Parm1) { return error(1); }; virtual ResultType goReverse( Parm1,Parm2) { return error(2); }; virtual ResultType goReverse( Parm1,Parm2,Parm3) { return error(3); }; virtual ResultType goReverse( Parm1,Parm2,Parm3,Parm4) { return error(4); }; virtual ResultType goReverse( Parm1,Parm2,Parm3,Parm4,Parm5) { return error(5); }; virtual ResultType goReverse( Parm1,Parm2,Parm3,Parm4,Parm5,Parm6) { return error(6); }; virtual ResultType goReverse( Parm1,Parm2,Parm3,Parm4,Parm5,Parm6,Parm7) { return error(7); }; }; #define DEFINE_FUNCTOR_ORDER_2D(class1,class2) \ public : virtual std::string checkOrder() const \ { \ return (string(#class1)+" "+string(#class2)); \ } \ trunk-2017.01a/lib/multimethods/Indexable.hpp000066400000000000000000000147001304022710500210540ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include /*! \brief Abstract interface for all Indexable class. An indexable class is a class that will be managed by a MultiMethodManager. The index the function getClassIndex() returns, corresponds to the index in the matrix where the class will be handled. */ #define _THROW_NOT_OVERRIDDEN throw std::logic_error(std::string("Derived class did not override ")+__PRETTY_FUNCTION__+", use REGISTER_INDEX_COUNTER and REGISTER_CLASS_INDEX.") class Indexable { protected : void createIndex() { int& index = getClassIndex(); if(index == -1) // assign new index { index = getMaxCurrentlyUsedClassIndex()+1; // so that other dispatchers will not fall in conflict with this index incrementMaxCurrentlyUsedClassIndex(); } } public : Indexable () {}; virtual ~Indexable () {}; /// Returns the id of the current class. This id is set by a multimethod manager virtual int& getClassIndex() { _THROW_NOT_OVERRIDDEN;}; virtual const int& getClassIndex() const { _THROW_NOT_OVERRIDDEN;}; virtual int& getBaseClassIndex(int ) { _THROW_NOT_OVERRIDDEN;}; virtual const int& getBaseClassIndex(int ) const { _THROW_NOT_OVERRIDDEN;}; virtual const int& getMaxCurrentlyUsedClassIndex() const { _THROW_NOT_OVERRIDDEN;}; virtual void incrementMaxCurrentlyUsedClassIndex() { _THROW_NOT_OVERRIDDEN;}; }; #undef _THROW_NOT_OVERRIDDEN // this macro is used by classes that are a dimension in multimethod matrix #define REGISTER_CLASS_INDEX(SomeClass,BaseClass) \ public: static int& getClassIndexStatic() { static int index = -1; return index; } \ public: virtual int& getClassIndex() { return getClassIndexStatic(); } \ public: virtual const int& getClassIndex() const { return getClassIndexStatic(); } \ public: virtual int& getBaseClassIndex(int depth) { \ static boost::scoped_ptr baseClass(new BaseClass); \ if(depth == 1) return baseClass->getClassIndex(); \ else return baseClass->getBaseClassIndex(--depth); \ } \ public: virtual const int& getBaseClassIndex(int depth) const { \ static boost::scoped_ptr baseClass(new BaseClass); \ if(depth == 1) return baseClass->getClassIndex(); \ else return baseClass->getBaseClassIndex(--depth); \ } // this macro is used by base class for classes that are a dimension in multimethod matrix // to keep track of maximum number of classes of their kin. Multimethod matrix can't // count this number (ie. as a size of the matrix), as there are many multimethod matrices #define REGISTER_INDEX_COUNTER(SomeClass) \ private: static int& getClassIndexStatic() { static int index = -1; return index; }\ public: virtual int& getClassIndex() { return getClassIndexStatic(); } \ public: virtual const int& getClassIndex() const { return getClassIndexStatic(); } \ public: virtual int& getBaseClassIndex(int) { throw std::logic_error("One of the following errors was detected:\n(1) Class " #SomeClass " called createIndex() in its ctor (but it shouldn't, being a top-level indexable; only use REGISTER_INDEX_COUNTER, but not createIndex()).\n(2) Some DerivedClass deriving from " #SomeClass " forgot to use REGISTER_CLASS_INDEX(DerivedClass," #SomeClass ").\nPlease fix that and come back again." ); } \ public: virtual const int& getBaseClassIndex(int) const { throw std::logic_error("One of the following errors was detected:\n(1) Class " #SomeClass " called createIndex() in its ctor (but it shouldn't, being a top-level indexable; only use REGISTER_INDEX_COUNTER, but not createIndex()).\n(2) Some DerivedClass deriving from " #SomeClass " forgot to use REGISTER_CLASS_INDEX(DerivedClass," #SomeClass ").\nPlease fix that and come back again." ); } \ private: static int& getMaxCurrentlyUsedIndexStatic() { static int maxCurrentlyUsedIndex = -1; return maxCurrentlyUsedIndex; } \ public: virtual const int& getMaxCurrentlyUsedClassIndex() const { \ SomeClass * Indexable##SomeClass = 0; \ Indexable##SomeClass = dynamic_cast(const_cast(this)); \ if (Indexable##SomeClass) { \ assert(Indexable##SomeClass); \ } \ return getMaxCurrentlyUsedIndexStatic(); \ } \ public: virtual void incrementMaxCurrentlyUsedClassIndex() { \ SomeClass * Indexable##SomeClass = 0; \ Indexable##SomeClass = dynamic_cast(this); \ if (Indexable##SomeClass) { \ assert(Indexable##SomeClass); \ } \ int& max = getMaxCurrentlyUsedIndexStatic(); \ max++; \ } \ // macro that should be passed in the 4th argument of YADE_CLASS_BASE_ATTR_PY in the top-level indexable #define YADE_PY_TOPINDEXABLE(className) .add_property("dispIndex",&Indexable_getClassIndex,"Return class index of this instance.").def("dispHierarchy",&Indexable_getClassIndices,(boost::python::arg("names")=true),"Return list of dispatch classes (from down upwards), starting with the class instance itself, top-level indexable at last. If names is true (default), return class names rather than numerical indices.") trunk-2017.01a/lib/opengl/000077500000000000000000000000001304022710500152145ustar00rootroot00000000000000trunk-2017.01a/lib/opengl/GLUtils.cpp000066400000000000000000000042341304022710500172460ustar00rootroot00000000000000#include"GLUtils.hpp" void GLUtils::Parallelepiped(const Vector3r& a, const Vector3r& b, const Vector3r& c){ glBegin(GL_LINE_STRIP); glVertex3v(b); glVertex3v(Vector3r(Vector3r::Zero())); glVertex3v(a); glVertex3v(Vector3r(a+b)); glVertex3v(Vector3r(a+b+c)); glVertex3v(Vector3r(b+c)); glVertex3v(b); glVertex3v(Vector3r(a+b)); glEnd(); glBegin(GL_LINE_STRIP); glVertex3v(Vector3r(b+c)); glVertex3v(c); glVertex3v(Vector3r(a+c)); glVertex3v(a); glEnd(); glBegin(GL_LINES); glVertex3v(Vector3r(Vector3r::Zero())); glVertex3v(c); glEnd(); glBegin(GL_LINES); glVertex3v(Vector3r(a+c)); glVertex3v(Vector3r(a+b+c)); glEnd(); } /**** code copied over from qglviewer ****/ /*! Draws a 3D arrow along the positive Z axis. \p length, \p radius and \p nbSubdivisions define its geometry. If \p radius is negative (default), it is set to 0.05 * \p length. Use drawArrow(const Vec& from, const Vec& to, float radius, int nbSubdivisions) or change the \c ModelView matrix to place the arrow in 3D. Uses current color and does not modify the OpenGL state. */ void GLUtils::QGLViewer::drawArrow(float length, float radius, int nbSubdivisions) { static GLUquadric* quadric = gluNewQuadric(); if (radius < 0.0) radius = 0.05 * length; const float head = 2.5*(radius / length) + 0.1; const float coneRadiusCoef = 4.0 - 5.0 * head; gluCylinder(quadric, radius, radius, length * (1.0 - head/coneRadiusCoef), nbSubdivisions, 1); glTranslatef(0.0, 0.0, length * (1.0 - head)); gluCylinder(quadric, coneRadiusCoef * radius, 0.0, head * length, nbSubdivisions, 1); glTranslatef(0.0, 0.0, -length * (1.0 - head)); } /*! Draws a 3D arrow between the 3D point \p from and the 3D point \p to, both defined in the current ModelView coordinates system. See drawArrow(float length, float radius, int nbSubdivisions) for details. */ void GLUtils::QGLViewer::drawArrow(const Vector3r& from, const Vector3r& to, float radius, int nbSubdivisions) { glPushMatrix(); glTranslatef(from[0],from[1],from[2]); Quaternionr q(Quaternionr().setFromTwoVectors(Vector3r(0,0,1),to-from)); glMultMatrix(q.toRotationMatrix().data()); drawArrow((to-from).norm(), radius, nbSubdivisions); glPopMatrix(); } trunk-2017.01a/lib/opengl/GLUtils.hpp000066400000000000000000000034561304022710500172600ustar00rootroot00000000000000// © 2008 Václav Šmilauer // // header-only utility functions for GL (moved over from extra/Shop.cpp) // #pragma once #include #include #include #include struct GLUtils{ // code copied from qglviewer struct QGLViewer{ static void drawArrow(float length=1.0f, float radius=-1.0f, int nbSubdivisions=12); static void drawArrow(const Vector3r& from, const Vector3r& to, float radius=-1.0f, int nbSubdivisions=12); }; // render wire of parallelepiped with sides given by vectors a,b,c; zero corner is at origin static void Parallelepiped(const Vector3r& a, const Vector3r& b, const Vector3r& c); static void GLDrawArrow(const Vector3r& from, const Vector3r& to, const Vector3r& color=Vector3r(1,1,1)){ glEnable(GL_LIGHTING); glColor3v(color); QGLViewer::drawArrow(from,to); } static void GLDrawLine(const Vector3r& from, const Vector3r& to, const Vector3r& color=Vector3r(1,1,1)){ glEnable(GL_LIGHTING); glColor3v(color); glBegin(GL_LINES); glVertex3v(from); glVertex3v(to); glEnd(); } static void GLDrawNum(const Real& n, const Vector3r& pos, const Vector3r& color=Vector3r(1,1,1), unsigned precision=3){ std::ostringstream oss; oss< // disable temporarily //#include #define STATIC_ASSERT(arg) #include #include struct OpenGLWrapper {}; // for ctags /// Primary Templates template< typename Type > inline void glRotate ( Type, Type, Type, Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glScale ( Type, Type, Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glScalev ( const Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glTranslate ( Type, Type, Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glTranslatev ( const Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glVertex2 ( Type, Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glVertex3 ( Type, Type, Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glVertex4 ( Type, Type, Type, Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glVertex2v ( const Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glVertex3v ( const Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glVertex4v ( const Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glNormal3 ( Type, Type, Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glNormal3v ( const Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glIndex ( Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glIndexv ( Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glColor3 ( Type, Type, Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glColor4 ( Type, Type, Type, Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glColor3v ( const Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glColor4v ( const Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glTexCoord1 ( Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glTexCoord2 ( Type, Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glTexCoord3 ( Type, Type, Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glTexCoord4 ( Type, Type, Type, Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glTexCoord1v ( const Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glTexCoord2v ( const Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glTexCoord3v ( const Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glTexCoord4v ( const Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glRasterPos2 ( Type, Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glRasterPos3 ( Type, Type, Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glRasterPos4 ( Type, Type, Type, Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glRasterPos2v ( const Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glRasterPos3v ( const Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glRasterPos4v ( const Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glRect ( Type, Type, Type, Type ) { STATIC_ASSERT(false); }; template< typename Type > inline void glMaterial ( GLenum face, GLenum pname, Type param ){ STATIC_ASSERT(false); }; template< typename Type > inline void glMaterialv ( GLenum face, GLenum pname, Type param ){ STATIC_ASSERT(false); }; template< typename Type > inline void glMultMatrix (const Type*){ STATIC_ASSERT(false); }; #define LDOUBL long double /// Template Specializations template< > inline void glMultMatrix(const double* m){glMultMatrixd(m); }; template< > inline void glMultMatrix(const LDOUBL* m){double mm[16]; for(int i=0;i<16;i++)mm[i]=(double)m[i]; glMultMatrixd(mm);}; template< > inline void glRotate< double > (double angle,double x,double y, double z ) { glRotated(angle,x,y,z); }; template< > inline void glRotate< LDOUBL > (LDOUBL angle, LDOUBL x, LDOUBL y, LDOUBL z ) { glRotated((double)angle,(double)x,(double)y,(double)z); }; template< > inline void glRotate< float > (float angle,float x,float y, float z ) { glRotatef(angle,x,y,z); }; template< > inline void glScale< double > ( double x,double y, double z ) { glScaled(x,y,z); }; template< > inline void glScale< LDOUBL > ( LDOUBL x,LDOUBL y, LDOUBL z ) { glScaled(x,y,z); }; template< > inline void glScale< float > ( float x,float y,float z ) { glScalef(x,y,z); }; template< > inline void glScalev< Vector3r > ( const Vector3r v ) { glScaled(v[0],v[1],v[2]);}; template< > inline void glTranslate< double > ( double x,double y, double z ) { glTranslated(x,y,z); }; template< > inline void glTranslate< LDOUBL > ( LDOUBL x, LDOUBL y, LDOUBL z ) { glTranslated(x,y,z); }; template< > inline void glTranslate< float > ( float x,float y,float z ) { glTranslatef(x,y,z); }; template< > inline void glTranslatev< Vector3r > ( const Vector3r v ) { glTranslated(v[0],v[1],v[2]);}; template< > inline void glVertex2< double > ( double x,double y ) { glVertex2d(x,y); }; template< > inline void glVertex2< LDOUBL > ( LDOUBL x, LDOUBL y ) { glVertex2d((double)x,(double)y); }; template< > inline void glVertex2< float > ( float x,float y ) { glVertex2f(x,y); }; template< > inline void glVertex2< int > ( int x,int y ) { glVertex2i(x,y); }; template< > inline void glVertex3< double > ( double x,double y, double z ) { glVertex3d(x,y,z); }; template< > inline void glVertex3< LDOUBL > ( LDOUBL x, LDOUBL y, LDOUBL z ) { glVertex3d((double)x,(double)y,(double)z); }; template< > inline void glVertex3< float > ( float x,float y,float z ) { glVertex3f(x,y,z); }; template< > inline void glVertex3< int > ( int x, int y, int z ) { glVertex3i(x,y,z); }; template< > inline void glVertex4< double > ( double x,double y,double z, double w ){ glVertex4d(x,y,z,w); }; template< > inline void glVertex4< LDOUBL > ( LDOUBL x, LDOUBL y, LDOUBL z, LDOUBL w ){ glVertex4d((double)x,(double)y,(double)z,(double)w); }; template< > inline void glVertex4< float > ( float x,float y,float z, float w ) { glVertex4f(x,y,z,w); }; template< > inline void glVertex4< int > ( int x,int y,int z, int w ) { glVertex4i(x,y,z,w); }; // :%s/\(void \)\(gl[A-Z,a-z,0-9]\+\)\(f\)( GLfloat \([a-z]\), GLfloat \([a-z]\), GLfloat \([a-z]\) );/template< > inline \1\2< float > ( float \4,float \5,float \6 ) { \2\3(\4,\5,\6); };/ template< > inline void glVertex2v< Vector3r > ( const Vector3r v ) { glVertex2dv((double*)&v); }; template< > inline void glVertex2v< Vector3i > ( const Vector3i v ) { glVertex2iv((int*)&v); }; template< > inline void glVertex3v< Vector3r > ( const Vector3r v ) { glVertex3dv((double*)&v); }; template< > inline void glVertex3v< Vector3i > ( const Vector3i v ) { glVertex3iv((int*)&v); }; template< > inline void glVertex4v< Vector3r > ( const Vector3r v ) { glVertex4dv((double*)&v); }; template< > inline void glVertex4v< Vector3i > ( const Vector3i v ) { glVertex4iv((int*)&v); }; template< > inline void glNormal3< double > (double nx,double ny,double nz ) { glNormal3d(nx,ny,nz); }; template< > inline void glNormal3< LDOUBL > ( LDOUBL nx, LDOUBL ny, LDOUBL nz ) { glNormal3d((double)nx,(double)ny,(double)nz); }; template< > inline void glNormal3< int > (int nx,int ny,int nz ) { glNormal3i(nx,ny,nz); }; template< > inline void glNormal3v< Vector3r > ( const Vector3r v ) { glNormal3dv((double*)&v); }; template< > inline void glNormal3v< Vector3i > ( const Vector3i v ) { glNormal3iv((int*)&v); }; template< > inline void glIndex< double > ( double c ) { glIndexd(c); }; template< > inline void glIndex< LDOUBL > ( LDOUBL c ) { glIndexd((double)c); }; template< > inline void glIndex< float > ( float c ) { glIndexf(c); }; template< > inline void glIndex< int > ( int c ) { glIndexi(c); }; template< > inline void glIndex< unsigned char > ( unsigned char c ) { glIndexub(c); }; template< > inline void glIndexv ( const Vector3r c) { glIndexdv((double*)&c); } template< > inline void glIndexv ( const Vector3i c) { glIndexiv((int*)&c); } template< > inline void glColor3< double > (double red,double green,double blue ) { glColor3d(red,green,blue); }; template< > inline void glColor3< LDOUBL > ( LDOUBL red, LDOUBL green, LDOUBL blue ) { glColor3d((double)red,(double)green,(double)blue); }; template< > inline void glColor3< float > (float red,float green,float blue ) { glColor3f(red,green,blue); }; template< > inline void glColor3< int > (int red,int green,int blue ) { glColor3i(red,green,blue); }; template< > inline void glColor4< double > (double red,double green,double blue, double alpha ) { glColor4d(red,green,blue,alpha); }; template< > inline void glColor4< LDOUBL > (LDOUBL red,LDOUBL green,LDOUBL blue, LDOUBL alpha ) { glColor4d((double)red,(double)green,(double)blue,(double)alpha); }; template< > inline void glColor4< float > (float red,float green,float blue, float alpha ) { glColor4f(red,green,blue,alpha); }; template< > inline void glColor4< int > (int red,int green,int blue, int alpha ) { glColor4i(red,green,blue,alpha); }; template< > inline void glColor3v< Vector3r > ( const Vector3r v ) { glColor3dv((double*)&v); }; template< > inline void glColor3v< Vector3i > ( const Vector3i v ) { glColor3iv((int*)&v); }; template< > inline void glColor4v< Vector3r > ( const Vector3r v ) { glColor4dv((double*)&v); }; template< > inline void glColor4v< Vector3i > ( const Vector3i v ) { glColor4iv((int*)&v); }; template< > inline void glTexCoord1< double > ( double s ) { glTexCoord1d(s); }; template< > inline void glTexCoord1< LDOUBL > ( LDOUBL s ) { glTexCoord1d((double)s); }; template< > inline void glTexCoord1< float > ( float s ) { glTexCoord1f(s); }; template< > inline void glTexCoord1< int > ( int s ) { glTexCoord1i(s); }; template< > inline void glTexCoord2< double > ( double s,double t ) { glTexCoord2d(s,t); }; template< > inline void glTexCoord2< LDOUBL > ( LDOUBL s,LDOUBL t ) { glTexCoord2d((double)s,(double)t); }; template< > inline void glTexCoord2< float > ( float s,float t ) { glTexCoord2f(s,t); }; template< > inline void glTexCoord2< int > ( int s,int t ) { glTexCoord2i(s,t); }; template< > inline void glTexCoord3< double > ( double s,double t, double r ) { glTexCoord3d(s,t,r); }; template< > inline void glTexCoord3< LDOUBL > ( LDOUBL s,LDOUBL t, LDOUBL r ) { glTexCoord3d((double)s,(double)t,(double)r); }; template< > inline void glTexCoord3< float > ( float s,float t,float r ) { glTexCoord3f(s,t,r); }; template< > inline void glTexCoord3< int > ( int s, int t, int r ) { glTexCoord3i(s,t,r); }; template< > inline void glTexCoord4< double > (double s,double t,double r, double q ) { glTexCoord4d(s,t,r,q); }; template< > inline void glTexCoord4< LDOUBL > (LDOUBL s,LDOUBL t,LDOUBL r, LDOUBL q ) { glTexCoord4d((double)s,(double)t,(double)r,(double)q); }; template< > inline void glTexCoord4< float > (float s,float t,float r, float q ) { glTexCoord4f(s,t,r,q); }; template< > inline void glTexCoord4< int > (int s,int t,int r, int q ) { glTexCoord4i(s,t,r,q); }; template< > inline void glTexCoord1v< Vector3r > ( const Vector3r v ) { glTexCoord1dv((double*)&v); }; template< > inline void glTexCoord1v< Vector3i > ( const Vector3i v ) { glTexCoord1iv((int*)&v); }; template< > inline void glTexCoord2v< Vector3r > ( const Vector3r v ) { glTexCoord2dv((double*)&v); }; template< > inline void glTexCoord2v< Vector3i > ( const Vector3i v ) { glTexCoord2iv((int*)&v); }; template< > inline void glTexCoord3v< Vector3r > ( const Vector3r v ) { glTexCoord3dv((double*)&v); }; template< > inline void glTexCoord3v< Vector3i > ( const Vector3i v ) { glTexCoord3iv((int*)&v); }; template< > inline void glTexCoord4v< Vector3r > ( const Vector3r v ) { glTexCoord4dv((double*)&v); }; template< > inline void glTexCoord4v< Vector3i > ( const Vector3i v ) { glTexCoord4iv((int*)&v); }; template< > inline void glRasterPos2< double > ( double x,double y ) { glRasterPos2d(x,y); }; template< > inline void glRasterPos2< LDOUBL > ( LDOUBL x,LDOUBL y ) { glRasterPos2d((double)x,(double)y); }; template< > inline void glRasterPos2< float > ( float x,float y ) { glRasterPos2f(x,y); }; template< > inline void glRasterPos2< int > ( int x,int y ) { glRasterPos2i(x,y); }; template< > inline void glRasterPos3< double > ( double x,double y, double z ) { glRasterPos3d(x,y,z); }; template< > inline void glRasterPos3< LDOUBL > ( LDOUBL x,LDOUBL y, LDOUBL z ) { glRasterPos3d((double)x,(double)y,(double)z); }; template< > inline void glRasterPos3< float > ( float x,float y,float z ) { glRasterPos3f(x,y,z); }; template< > inline void glRasterPos3< int > ( int x, int y, int z ) { glRasterPos3i(x,y,z); }; template< > inline void glRasterPos4< double > (double x,double y,double z, double w ) { glRasterPos4d(x,y,z,w); }; template< > inline void glRasterPos4< LDOUBL > (LDOUBL x,LDOUBL y,LDOUBL z, LDOUBL w ) { glRasterPos4d((double)x,(double)y,(double)z,(double)w); }; template< > inline void glRasterPos4< float > (float x,float y,float z, float w ) { glRasterPos4f(x,y,z,w); }; template< > inline void glRasterPos4< int > (int x,int y,int z, int w ) { glRasterPos4i(x,y,z,w); }; template< > inline void glRasterPos2v< Vector3r > ( const Vector3r v ) { glRasterPos2dv((double*)&v); }; template< > inline void glRasterPos2v< Vector3i > ( const Vector3i v ) { glRasterPos2iv((int*)&v); }; // :%s/\(void \)\(gl[A-Z,a-z,0-9]\+\)\(us\)\(v\)( const GLushort \*\(v\) );/template< > inline \1\2\4< Vector3 > ( const Vector3 \5 ) { \2\3\4(\5); };/ template< > inline void glRasterPos3v< Vector3r > ( const Vector3r v ) { glRasterPos3dv((double*)&v); }; template< > inline void glRasterPos3v< Vector3i > ( const Vector3i v ) { glRasterPos3iv((int*)&v); }; template< > inline void glRasterPos4v< Vector3r > ( const Vector3r v ) { glRasterPos4dv((double*)&v); }; template< > inline void glRasterPos4v< Vector3i > ( const Vector3i v ) { glRasterPos4iv((int*)&v); }; template< > inline void glRect< double > (double x1,double y1,double x2, double y2 ) { glRectd(x1,y1,x2,y2); }; template< > inline void glRect< LDOUBL > (LDOUBL x1,LDOUBL y1,LDOUBL x2, LDOUBL y2 ) { glRectd((double)x1,(double)y1,(double)x2,(double)y2); }; template< > inline void glRect< float > (float x1,float y1,float x2,float y2 ) { glRectf(x1,y1,x2,y2); }; template< > inline void glRect< int > (int x1,int y1,int x2, int y2 ) { glRecti(x1,y1,x2,y2); }; template< > inline void glMaterial< float > ( GLenum face, GLenum pname, float param ) { glMaterialf(face,pname,param); }; template< > inline void glMaterial< double > ( GLenum face, GLenum pname, double param ) { glMaterialf(face,pname,param); }; template< > inline void glMaterial< int > ( GLenum face, GLenum pname, int param ) { glMateriali(face,pname,param); }; template< > inline void glMaterialv< Vector3r > ( GLenum face, GLenum pname, const Vector3r params ) { const GLfloat _p[3]={(float) params[0], (float) params[1], (float) params[2]}; glMaterialfv(face,pname,_p); }; template< > inline void glMaterialv< Vector3i > ( GLenum face, GLenum pname, const Vector3i params ) { glMaterialiv(face,pname,(int*)¶ms); }; template< typename Type > inline void glOneWire(Type & t, unsigned int a, unsigned int b) { glVertex3v(t->v[a]); glVertex3v(t->v[b]); } template< typename Type > inline void glOneFace(Type & t, unsigned int a, unsigned int b, unsigned int c) { const Vector3r center = (t->v[0]+t->v[1]+t->v[2]+t->v[3])*.25; Vector3r n=(t->v[b]-t->v[a]).cross(t->v[c]-t->v[a]); n.normalize(); const Vector3r faceCenter=(t->v[a]+t->v[b]+t->v[c])/3.; if((faceCenter-center).dot(n)<0) n=-n; glNormal3v(n); glVertex3v(t->v[a]); glVertex3v(t->v[b]); glVertex3v(t->v[c]); } #undef LDOUBL trunk-2017.01a/lib/pyutil/000077500000000000000000000000001304022710500152565ustar00rootroot00000000000000trunk-2017.01a/lib/pyutil/README000066400000000000000000000001231304022710500161320ustar00rootroot00000000000000numpy_boost.cpp: http://code.google.com/p/numpy-boost/source/checkout (svn rev 9) trunk-2017.01a/lib/pyutil/doc_opts.hpp000066400000000000000000000004231304022710500176000ustar00rootroot00000000000000#pragma once // macro to set the same docstring generation options in all modules // disable_cpp_signatures apparently appeared after 1.35 or 1.34 #define YADE_SET_DOCSTRING_OPTS boost::python::docstring_options docopt; docopt.enable_all(); docopt.disable_cpp_signatures(); trunk-2017.01a/lib/pyutil/gil.cpp000066400000000000000000000001731304022710500165360ustar00rootroot00000000000000#include void pyRunString(const std::string& cmd){ gilLock lock; PyRun_SimpleString(cmd.c_str()); }; trunk-2017.01a/lib/pyutil/gil.hpp000066400000000000000000000006411304022710500165430ustar00rootroot00000000000000// 2009 © Václav Šmilauer #pragma once #include #include //! class (scoped lock) managing python's Global Interpreter Lock (gil) class gilLock{ PyGILState_STATE state; public: gilLock(){ state=PyGILState_Ensure(); } ~gilLock(){ PyGILState_Release(state); } }; //! run string as python command; locks & unlocks GIL automatically void pyRunString(const std::string& cmd); trunk-2017.01a/lib/pyutil/numpy_boost.hpp000066400000000000000000000172531304022710500203550ustar00rootroot00000000000000/* Copyright (c) 2012, Michael Droettboom All rights reserved. Licensed under the BSD license. Redistribution and use in source and binary forms, with or without modification, are permitted provided that the following conditions are met: * Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimer. * Redistributions in binary form must reproduce the above copyright notice, this list of conditions and the following disclaimer in the documentation and/or other materials provided with the distribution. * The names of its contributors may not be used to endorse or promote products derived from this software without specific prior written permission. THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE. */ #ifndef __NUMPY_BOOST_HPP__ #define __NUMPY_BOOST_HPP__ #include #include #include #include #include #include /* numpy_type_map Provides a mapping from C++ datatypes to Numpy type numbers. */ namespace detail { template class numpy_type_map { public: static const int typenum; }; template<> const int numpy_type_map::typenum = NPY_FLOAT; template<> const int numpy_type_map >::typenum = NPY_CFLOAT; template<> const int numpy_type_map::typenum = NPY_DOUBLE; template<> const int numpy_type_map >::typenum = NPY_CDOUBLE; template<> const int numpy_type_map::typenum = NPY_LONGDOUBLE; template<> const int numpy_type_map >::typenum = NPY_CLONGDOUBLE; template<> const int numpy_type_map::typenum = NPY_INT8; template<> const int numpy_type_map::typenum = NPY_UINT8; template<> const int numpy_type_map::typenum = NPY_INT16; template<> const int numpy_type_map::typenum = NPY_UINT16; template<> const int numpy_type_map::typenum = NPY_INT32; template<> const int numpy_type_map::typenum = NPY_UINT32; template<> const int numpy_type_map::typenum = NPY_INT64; template<> const int numpy_type_map::typenum = NPY_UINT64; } class python_exception : public std::exception { }; /* An array that acts like a boost::multi_array, but is backed by the memory of a Numpy array. Provides nice C++ interface to a Numpy array without any copying of the data. It may be constructed one of two ways: 1) With an existing Numpy array. The boost::multi_array will then have the data, dimensions and strides of the Numpy array. 2) With a list of dimensions, in which case a new contiguous Numpy array will be created and the new boost::array will point to it. */ template class numpy_boost : public boost::multi_array_ref { public: typedef numpy_boost self_type; typedef boost::multi_array_ref super; typedef typename super::size_type size_type; typedef T* TPtr; private: PyArrayObject* array; void init_from_array(PyArrayObject* a) throw() { /* Upon calling init_from_array, a should already have been incref'd for ownership by this object. */ /* Store a reference to the Numpy array so we can DECREF it in the destructor. */ array = a; /* Point the boost::array at the Numpy array data. We don't need to worry about free'ing this pointer, because it will always point to memory allocated as part of the data of a Numpy array. That memory is managed by Python reference counting. */ super::base_ = (TPtr)PyArray_DATA(a); /* Set the storage order. It would seem like we would want to choose C or Fortran ordering here based on the flags in the Numpy array. However, those flags are purely informational, the actually information about storage order is recorded in the strides. */ super::storage_ = boost::c_storage_order(); /* Copy the dimensions from the Numpy array to the boost::array. */ boost::detail::multi_array::copy_n(PyArray_DIMS(a), NDims, super::extent_list_.begin()); /* Copy the strides from the Numpy array to the boost::array. Numpy strides are in bytes. boost::array strides are in elements, so we need to divide. */ for (size_t i = 0; i < NDims; ++i) { super::stride_list_[i] = PyArray_STRIDE(a, i) / sizeof(T); } /* index_base_list_ stores the bases of the indices in each dimension. Since we want C-style and Numpy-style zero-based indexing, just fill it with zeros. */ std::fill_n(super::index_base_list_.begin(), NDims, 0); /* We don't want any additional offsets. If they exist, Numpy has already handled that for us when calculating the data pointer and strides. */ super::origin_offset_ = 0; super::directional_offset_ = 0; /* Calculate the number of elements. This has nothing to do with memory layout. */ super::num_elements_ = std::accumulate(super::extent_list_.begin(), super::extent_list_.end(), size_type(1), std::multiplies()); } public: /* Construct from an existing Numpy array */ numpy_boost(PyObject* obj) throw () : super(NULL, std::vector(NDims, 0)), array(NULL) { PyArrayObject* a; a = (PyArrayObject*)PyArray_FromObject( obj, detail::numpy_type_map::typenum, NDims, NDims); if (a == NULL) { throw boost::python::error_already_set(); } init_from_array(a); } /* Copy constructor */ numpy_boost(const self_type &other) throw() : super(NULL, std::vector(NDims, 0)), array(NULL) { Py_INCREF(other.array); init_from_array(other.array); } /* Construct a new array based on the given dimensions */ template explicit numpy_boost(const ExtentsList& extents) throw () : super(NULL, std::vector(NDims, 0)), array(NULL) { npy_intp shape[NDims]; PyArrayObject* a; boost::detail::multi_array::copy_n(extents, NDims, shape); a = (PyArrayObject*)PyArray_SimpleNew( NDims, shape, detail::numpy_type_map::typenum); if (a == NULL) { throw boost::python::error_already_set(); } init_from_array(a); } /* Destructor */ ~numpy_boost() { /* Dereference the numpy array. */ Py_XDECREF(array); } /* Assignment operator */ void operator=(const self_type &other) throw() { Py_INCREF(other.array); Py_DECREF(array); init_from_array(other.array); } /* Return the underlying Numpy array object. [Borrowed reference] */ PyObject* py_ptr() const throw() { return (PyObject*)array; } }; #endif trunk-2017.01a/lib/pyutil/raw_constructor.hpp000066400000000000000000000017701304022710500212320ustar00rootroot00000000000000#pragma once #include // many thanks to http://markmail.org/message/s4ksg6nfspw2wxwd namespace boost { namespace python { namespace detail { template struct raw_constructor_dispatcher { raw_constructor_dispatcher(F f): f(make_constructor(f)) {} PyObject* operator()(PyObject* args, PyObject* keywords) { borrowed_reference_t* ra = borrowed_reference(args); object a(ra); return incref(object(f(object(a[0]),object(a.slice(1,len(a))),keywords ? dict(borrowed_reference(keywords)) : dict())).ptr() ); } private: object f; }; } template object raw_constructor(F f, std::size_t min_args = 0) { return detail::make_raw_function( objects::py_function(detail::raw_constructor_dispatcher(f), mpl::vector2(), min_args+1, (std::numeric_limits::max)())); } } } trunk-2017.01a/lib/serialization/000077500000000000000000000000001304022710500166055ustar00rootroot00000000000000trunk-2017.01a/lib/serialization/ObjectIO.hpp000066400000000000000000000063111304022710500207550ustar00rootroot00000000000000// 2010 © Václav Šmilauer #pragma once #include #include #include #include #include #include #include #include namespace yade{ /* Utility template functions for (de)serializing objects using boost::serialization from/to streams or files. Includes boost::math::nonfinite_num_{put,get} for gracefully handling nan's and inf's. */ struct ObjectIO{ // tell whether given filename looks like XML static bool isXmlFilename(const std::string f){ return boost::algorithm::ends_with(f,".xml") || boost::algorithm::ends_with(f,".xml.bz2") || boost::algorithm::ends_with(f,".xml.gz"); } // save to given stream and archive format template static void save(std::ostream& ofs, const string& objectTag, T& object){ std::locale default_locale(std::locale::classic(), new boost::archive::codecvt_null); std::locale locale2(default_locale, new boost::math::nonfinite_num_put); ofs.imbue(locale2); oarchive oa(ofs,boost::archive::no_codecvt); oa << boost::serialization::make_nvp(objectTag.c_str(),object); ofs.flush(); } // load from given stream and archive format template static void load(std::istream& ifs, const string& objectTag, T& object){ std::locale default_locale(std::locale::classic(), new boost::archive::codecvt_null); std::locale locale2(default_locale, new boost::math::nonfinite_num_get); ifs.imbue(locale2); iarchive ia(ifs,boost::archive::no_codecvt); ia >> boost::serialization::make_nvp(objectTag.c_str(),object); } // save to given file, guessing compression and XML/binary from extension template static void save(const string fileName, const string& objectTag, T& object){ boost::iostreams::filtering_ostream out; if(boost::algorithm::ends_with(fileName,".bz2")) out.push(boost::iostreams::bzip2_compressor()); if(boost::algorithm::ends_with(fileName,".gz")) out.push(boost::iostreams::gzip_compressor()); out.push(boost::iostreams::file_sink(fileName)); if(!out.good()) throw std::runtime_error("Error opening file "+fileName+" for writing."); if(isXmlFilename(fileName)) save(out,objectTag,object); else save(out,objectTag,object); } // load from given file, guessing compression and XML/binary from extension template static void load(const string& fileName, const string& objectTag, T& object){ boost::iostreams::filtering_istream in; if(boost::algorithm::ends_with(fileName,".bz2")) in.push(boost::iostreams::bzip2_decompressor()); if(boost::algorithm::ends_with(fileName,".gz")) in.push(boost::iostreams::gzip_decompressor()); in.push(boost::iostreams::file_source(fileName)); if(!in.good()) throw std::runtime_error("Error opening file "+fileName+" for reading."); if(isXmlFilename(fileName)) load(in,objectTag,object); else load(in,objectTag,object); } }; } trunk-2017.01a/lib/serialization/Serializable.cpp000066400000000000000000000050031304022710500217150ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "Serializable.hpp" void Serializable::pyRegisterClass(boost::python::object _scope) { checkPyClassRegistersItself("Serializable"); boost::python::scope thisScope(_scope); boost::python::class_, boost::noncopyable >("Serializable") .def("__str__",&Serializable::pyStr).def("__repr__",&Serializable::pyStr) .def("dict",&Serializable::pyDict,"Return dictionary of attributes.") .def("updateAttrs",&Serializable::pyUpdateAttrs,"Update object attributes from given dictionary") /* boost::python pickling support, as per http://www.boost.org/doc/libs/1_42_0/libs/python/doc/v2/pickle.html */ .def("__getstate__",&Serializable::pyDict).def("__setstate__",&Serializable::pyUpdateAttrs) .add_property("__safe_for_unpickling__",&Serializable::getClassName,"just define the attr, return some bogus data") .add_property("__getstate_manages_dict__",&Serializable::getClassName,"just define the attr, return some bogus data") // constructor with dictionary of attributes .def("__init__",boost::python::raw_constructor(Serializable_ctor_kwAttrs)) // comparison operators .def(boost::python::self == boost::python::self) .def(boost::python::self != boost::python::self) ; } void Serializable::checkPyClassRegistersItself(const std::string& thisClassName) const { if(getClassName()!=thisClassName) throw std::logic_error(("Class "+getClassName()+" does not register with YADE_CLASS_BASE_DOC_ATTR*, would not be accessible from python.").c_str()); } void Serializable::pyUpdateAttrs(const boost::python::dict& d){ boost::python::list l=d.items(); size_t ll=boost::python::len(l); if(ll==0) return; for(size_t i=0; i(l[i]); string key=boost::python::extract(t[0]); pySetAttr(key,t[1]); } callPostLoad(); } trunk-2017.01a/lib/serialization/Serializable.hpp000066400000000000000000000527211304022710500217330ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include #include template void preLoad(T&){}; template void postLoad(T& obj){}; template void preSave(T&){}; template void postSave(T&){}; // attribute flags namespace yade{ namespace Attr{ // keep in sync with py/wrapper/yadeWrapper.cpp ! enum flags { noSave=1, readonly=2, triggerPostLoad=4, hidden=8, noResize=16 }; }; }; using namespace yade; // see: // https://bugs.launchpad.net/yade/+bug/539562 // http://www.boost.org/doc/libs/1_42_0/libs/python/doc/v2/faq.html#topythonconversionfailed // for reason why the original def_readwrite will not work: // #define _PYATTR_DEF(x,thisClass,z) .def_readwrite(BOOST_PP_STRINGIZE(BOOST_PP_TUPLE_ELEM(2,0,z)),&thisClass::BOOST_PP_TUPLE_ELEM(2,0,z),BOOST_PP_TUPLE_ELEM(2,1,z)) #define _PYATTR_DEF(x,thisClass,z) _DEF_READWRITE_CUSTOM(thisClass,z) // // return reference for vector and matrix types to allow things like // O.bodies.pos[1].state.vel[2]=0 // returning value would only change copy of velocity, without propagating back to the original // // see http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg03406.html // // note that for sequences (like vector<> etc), values are returned; but in case of // vector of shared_ptr's, things inside are still shared, so // O.engines[2].gravity=(0,0,9.33) will work // // OTOH got sequences of non-shared types, it sill (silently) fail: // f=Facet(); f.vertices[1][0]=4 // // see http://www.boost.org/doc/libs/1_42_0/libs/type_traits/doc/html/boost_typetraits/background.html // about how this works namespace yade{ // by default, do not return reference; return value instead template struct py_wrap_ref: public boost::false_type{}; // specialize for types that should be returned as references template<> struct py_wrap_ref: public boost::true_type{}; template<> struct py_wrap_ref: public boost::true_type{}; template<> struct py_wrap_ref: public boost::true_type{}; template<> struct py_wrap_ref: public boost::true_type{}; template<> struct py_wrap_ref: public boost::true_type{}; template<> struct py_wrap_ref: public boost::true_type{}; }; // ADL only works within the same namespace // this duplicate is for classes that are not in yade:: namespace (yet) template void make_setter_postLoad(C& instance, const T& val){ instance.*A=val; instance.callPostLoad(); } #define _DEF_READWRITE_BY_VALUE(thisClass,attr,doc)\ add_property(\ /*attr name*/ BOOST_PP_STRINGIZE(attr),\ /*read access*/ boost::python::make_getter(&thisClass::attr,boost::python::return_value_policy()),\ /*write access*/ boost::python::make_setter(&thisClass::attr,boost::python::return_value_policy()),\ /*docstring*/ doc) // not sure if this is correct: the getter works by value, the setter by reference (the default)...? #define _DEF_READWRITE_BY_VALUE_POSTLOAD(thisClass,attr,doc)\ add_property(\ /*attr name*/ BOOST_PP_STRINGIZE(attr),\ /*read access*/ boost::python::make_getter(&thisClass::attr,boost::python::return_value_policy()),\ /*write access*/ make_setter_postLoad,\ /*docstring*/ doc) #define _DEF_READONLY_BY_VALUE(thisClass,attr,doc)\ add_property(\ /*attr name*/ BOOST_PP_STRINGIZE(attr),\ /*read access*/ boost::python::make_getter(&thisClass::attr,boost::python::return_value_policy()),\ /*docstring*/ doc) /* Huh, add_static_property does not support doc argument (add_property does); if so, use add_property for now at least... */ #define _DEF_READWRITE_BY_VALUE_STATIC(thisClass,attr,doc)_DEF_READWRITE_BY_VALUE(thisClass,attr,doc) // the conditional yade::py_wrap_ref should be eliminated by compiler at compile-time, as it depends only on types, not their values // most of this could be written with templates, including flags (ints can be template args) #define _DEF_READWRITE_CUSTOM(thisClass,attr)\ if(!(_ATTR_FLG(attr) & yade::Attr::hidden)){\ bool _ro(_ATTR_FLG(attr) & Attr::readonly),\ _post(_ATTR_FLG(attr) & Attr::triggerPostLoad),\ _ref(yade::py_wrap_ref::value);\ std::string docStr(_ATTR_DOC(attr));\ docStr+=" :yattrflags:`"+boost::lexical_cast(_ATTR_FLG(attr))+"` "; \ \ if ( _ref && !_ro && !_post) _classObj.def_readwrite(_ATTR_NAM_STR(attr),&thisClass::_ATTR_NAM(attr),docStr.c_str()); \ else if ( _ref && !_ro && _post) _classObj.add_property(_ATTR_NAM_STR(attr),boost::python::make_getter(&thisClass::_ATTR_NAM(attr)),make_setter_postLoad,docStr.c_str()); \ else if ( _ref && _ro) _classObj.def_readonly(_ATTR_NAM_STR(attr),&thisClass::_ATTR_NAM(attr),docStr.c_str()); \ else if (!_ref && !_ro && !_post) _classObj._DEF_READWRITE_BY_VALUE(thisClass,_ATTR_NAM(attr),docStr.c_str()); \ else if (!_ref && !_ro && _post) _classObj._DEF_READWRITE_BY_VALUE_POSTLOAD(thisClass,_ATTR_NAM(attr),docStr.c_str()); \ else if (!_ref && _ro) _classObj._DEF_READONLY_BY_VALUE(thisClass,_ATTR_NAM(attr),docStr.c_str()); \ if(_ro && _post) std::cerr<<"WARN: " BOOST_PP_STRINGIZE(thisClass) "::" _ATTR_NAM_STR(attr) " with the yade::Attr::readonly flag also uselessly sets yade::Attr::triggerPostLoad."<(value); \ return; \ } #define _PYATTR_DEPREC_DEF(x,thisClass,z) \ .add_property(BOOST_PP_STRINGIZE(_DEPREC_OLDNAME(z)),\ &thisClass::BOOST_PP_CAT(_getDeprec_,_DEPREC_OLDNAME(z)),\ &thisClass::BOOST_PP_CAT(_setDeprec_,_DEPREC_OLDNAME(z)),\ "|ydeprecated| alias for :yref:`" BOOST_PP_STRINGIZE(_DEPREC_NEWNAME(z)) \ "<" BOOST_PP_STRINGIZE(thisClass) "." \ BOOST_PP_STRINGIZE(_DEPREC_NEWNAME(z)) ">` (" _DEPREC_COMMENT(z) ")") #define _PYHASKEY_ATTR_DEPREC(x,thisClass,z) \ if(key==BOOST_PP_STRINGIZE(_DEPREC_OLDNAME(z))) return true; /* accessors functions ussing warning */ #define _ACCESS_DEPREC(x,thisClass,z) /*getter*/ decltype(_DEPREC_NEWNAME(z)) BOOST_PP_CAT(_getDeprec_,_DEPREC_OLDNAME(z))(){_DEPREC_WARN(thisClass,z); return _DEPREC_NEWNAME(z); } /*setter*/ void BOOST_PP_CAT(_setDeprec_,_DEPREC_OLDNAME(z))(const decltype(_DEPREC_NEWNAME(z))& val){_DEPREC_WARN(thisClass,z); _DEPREC_NEWNAME(z)=val; } // loop bodies for attribute access #define _PYGET_ATTR(x,y,z) if(key==_ATTR_NAM_STR(z)) return boost::python::object(_ATTR_NAM(z)); #define _PYSET_ATTR(x,y,z) if(key==_ATTR_NAM_STR(z)) { _ATTR_NAM(z)=boost::python::extract(value); return; } #define _PYKEYS_ATTR(x,y,z) ret.append(_ATTR_NAM_STR(z)); #define _PYHASKEY_ATTR(x,y,z) if(key==_ATTR_NAM_STR(z)) return true; #define _PYDICT_ATTR(x,y,z) if(!(_ATTR_FLG(z) & yade::Attr::hidden)) ret[_ATTR_NAM_STR(z)]=boost::python::object(_ATTR_NAM(z)); #define _REGISTER_BOOST_ATTRIBUTES_REPEAT(x,y,z) if((_ATTR_FLG(z) & yade::Attr::noSave)==0) { ar & BOOST_SERIALIZATION_NVP(_ATTR_NAM(z)); } #define _REGISTER_BOOST_ATTRIBUTES(baseClass,attrs) \ friend class boost::serialization::access; \ private: template void serialize(ArchiveT & ar, unsigned int version){ \ ar & BOOST_SERIALIZATION_BASE_OBJECT_NVP(baseClass); \ /* with ADL, either the generic (empty) version above or baseClass::preLoad etc will be called (compile-time resolution) */ \ if(ArchiveT::is_loading::value) preLoad(*this); else preSave(*this); \ BOOST_PP_SEQ_FOR_EACH(_REGISTER_BOOST_ATTRIBUTES_REPEAT,~,attrs) \ if(ArchiveT::is_loading::value) postLoad(*this); else postSave(*this); \ } #define _REGISTER_ATTRIBUTES_DEPREC(thisClass,baseClass,attrs,deprec) _REGISTER_BOOST_ATTRIBUTES(baseClass,attrs) public: \ void pySetAttr(const std::string& key, const boost::python::object& value){BOOST_PP_SEQ_FOR_EACH(_PYSET_ATTR,~,attrs); BOOST_PP_SEQ_FOR_EACH(_PYSET_ATTR_DEPREC,thisClass,deprec); baseClass::pySetAttr(key,value); } \ /* list all attributes (except deprecated ones); could return boost::python::set instead*/ /* boost::python::list pyKeys() const { boost::python::list ret; BOOST_PP_SEQ_FOR_EACH(_PYKEYS_ATTR,~,attrs); ret.extend(baseClass::pyKeys()); return ret; } */ \ /* return dictionary of all acttributes and values; deprecated attributes omitted */ boost::python::dict pyDict() const { boost::python::dict ret; BOOST_PP_SEQ_FOR_EACH(_PYDICT_ATTR,~,attrs); ret.update(baseClass::pyDict()); return ret; } \ virtual void callPostLoad(void){ baseClass::callPostLoad(); postLoad(*this); } // print warning about deprecated attribute; thisClass is type name, not string #define _DEPREC_WARN(thisClass,deprec) std::cerr<<"WARN: "<,boost::python::bases,boost::noncopyable> _classObj(#thisClass,docString); _classObj.def("__init__",boost::python::raw_constructor(Serializable_ctor_kwAttrs)); BOOST_PP_SEQ_FOR_EACH(_PYATTR_DEF,thisClass,attrs); (void) _classObj BOOST_PP_SEQ_FOR_EACH(_PYATTR_DEPREC_DEF,thisClass,deprec); (void) _classObj extras ; } // use later: void must_use_both_YADE_CLASS_BASE_DOC_ATTRS_and_YADE_PLUGIN(); // #define YADE_CLASS_BASE_DOC_ATTRS_PY(thisClass,baseClass,docString,attrs,extras) YADE_CLASS_BASE_DOC_ATTRS_DEPREC_PY(thisClass,baseClass,docString,attrs,,extras) // return "type name;" (for declaration inside class body) #define _ATTR_DECL(x,y,z) _ATTR_TYP(z) _ATTR_NAM(z); // return name(default), (for initializers list); TRICKY: last one must not have the comma #define _ATTR_MAKE_INITIALIZER(x,maxIndex,i,z) BOOST_PP_TUPLE_ELEM(2,0,z)(BOOST_PP_TUPLE_ELEM(2,1,z)) BOOST_PP_COMMA_IF(BOOST_PP_NOT_EQUAL(maxIndex,i)) // attrDecl is (type,name,defaultValue,docString) #define _ATTR_MAKE_INIT_TUPLE(x,y,z) (( _ATTR_NAM(z),_ATTR_INI(z) )) #define _ATTR_NAME_ADD_DUMMY_FIELDS(x,y,z) ((/*type*/,z,/*default*/,/*flags*/,/*doc*/)) #define _STAT_NONSTAT_ATTR_PY(thisClass,attr,doc) _DEF_READWRITE_CUSTOM_STATIC(thisClass,attr,doc) /* _DEF_READWRITE_CUSTOM(thisClass,attr,doc) */ /* duplicate static and non-static attributes do not work (they apparently trigger to-python converter being added; for now, make then non-static, that's it. */ #define _STATATTR_PY(x,thisClass,z) _STAT_NONSTAT_ATTR_PY(thisClass,_ATTR_NAM(z),/*docstring*/ "|ystatic| :ydefault:`" _ATTR_INI_STR(z) "` :yattrtype:`" _ATTR_TYP_STR(z) "` " _ATTR_DOC(z)) #define _STATATTR_DECL(x,y,z) static _ATTR_TYP(z) _ATTR_NAM(z); #define _STATATTR_INITIALIZE(x,thisClass,z) thisClass::_ATTR_NAM(z)=_ATTR_INI(z); #define _STATATTR_MAKE_DOC(x,thisClass,z) ".. ystaticattr:: " BOOST_PP_STRINGIZE(thisClass) "." _ATTR_NAM_STR(z) "(=" _ATTR_INI_STR(z) ")" "\n\n\t" _ATTR_DOC(z) "\n\n" #define _STATCLASS_PY_REGISTER_CLASS(thisClass,baseClass,docString,attrs)\ virtual void pyRegisterClass(boost::python::object _scope) { checkPyClassRegistersItself(#thisClass); initSetStaticAttributesValue(); boost::python::scope thisScope(_scope); YADE_SET_DOCSTRING_OPTS; \ boost::python::class_,boost::python::bases,boost::noncopyable> _classObj(#thisClass,docString "\n\n" BOOST_PP_SEQ_FOR_EACH(_STATATTR_MAKE_DOC,thisClass,attrs) ); _classObj.def("__init__",boost::python::raw_constructor(Serializable_ctor_kwAttrs)); \ BOOST_PP_SEQ_FOR_EACH(_STATATTR_PY,thisClass,attrs); \ } #define _YADE_CLASS_PYCLASS_BASE_DOC_ATTRS_DEPREC_PY(thisClass,pyClassName,baseClass,docString,attrs,deprec,extras) \ _REGISTER_ATTRIBUTES_DEPREC(thisClass,baseClass,attrs,deprec) \ REGISTER_CLASS_AND_BASE(pyClassName,baseClass) \ /* accessors for deprecated attributes, with warnings */ BOOST_PP_SEQ_FOR_EACH(_ACCESS_DEPREC,thisClass,deprec) \ /* python class registration */ virtual void pyRegisterClass(boost::python::object _scope) { checkPyClassRegistersItself(#pyClassName); boost::python::scope thisScope(_scope); YADE_SET_DOCSTRING_OPTS; boost::python::class_,boost::python::bases,boost::noncopyable> _classObj(#pyClassName,docString); _classObj.def("__init__",boost::python::raw_constructor(Serializable_ctor_kwAttrs)); BOOST_PP_SEQ_FOR_EACH(_PYATTR_DEF,thisClass,attrs); (void) _classObj BOOST_PP_SEQ_FOR_EACH(_PYATTR_DEPREC_DEF,thisClass,deprec); (void) _classObj extras ; } /********************** USER MACROS START HERE ********************/ // attrs is (type,name,init-value,docstring) #define YADE_CLASS_BASE_DOC(klass,base,doc) YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(klass,base,doc,,,,) #define YADE_CLASS_BASE_DOC_ATTRS(klass,base,doc,attrs) YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(klass,base,doc,attrs,,,) #define YADE_CLASS_BASE_DOC_ATTRS_CTOR(klass,base,doc,attrs,ctor) YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(klass,base,doc,attrs,,ctor,) #define YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(klass,base,doc,attrs,ctor,py) YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(klass,base,doc,attrs,,ctor,py) #define YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(klass,base,doc,attrs,inits,ctor,py) YADE_CLASS_BASE_DOC_ATTRS_DEPREC_INIT_CTOR_PY(klass,base,doc,attrs,,inits,ctor,py) // the most general #define YADE_CLASS_BASE_DOC_ATTRS_DEPREC_INIT_CTOR_PY(thisClass,baseClass,docString,attrDecls,deprec,inits,ctor,extras) \ public: BOOST_PP_SEQ_FOR_EACH(_ATTR_DECL,~,attrDecls) /* attribute declarations */ \ thisClass() BOOST_PP_IF(BOOST_PP_SEQ_SIZE(inits attrDecls),:,) BOOST_PP_SEQ_FOR_EACH_I(_ATTR_MAKE_INITIALIZER,BOOST_PP_DEC(BOOST_PP_SEQ_SIZE(inits attrDecls)), inits BOOST_PP_SEQ_FOR_EACH(_ATTR_MAKE_INIT_TUPLE,~,attrDecls)) { ctor ; } /* ctor, with initialization of defaults */ \ _YADE_CLASS_BASE_DOC_ATTRS_DEPREC_PY(thisClass,baseClass,docString,BOOST_PP_SEQ_FOR_EACH(_ATTRS_EMBED_INI_TYP_IN_DOC,~,attrDecls),deprec,extras) // this one lets you give different class names in c++ and python, necessary for compatibility with c++ templates (else all instaces would have the same class name (ex. in FlowEngine.hpp) #define YADE_CLASS_PYCLASS_BASE_DOC_ATTRS_DEPREC_INIT_CTOR_PY(thisClass,pyClassName,baseClass,docString,attrDecls,deprec,inits,ctor,extras) \ public: BOOST_PP_SEQ_FOR_EACH(_ATTR_DECL,~,attrDecls) /* attribute declarations */ \ thisClass() BOOST_PP_IF(BOOST_PP_SEQ_SIZE(inits attrDecls),:,) BOOST_PP_SEQ_FOR_EACH_I(_ATTR_MAKE_INITIALIZER,BOOST_PP_DEC(BOOST_PP_SEQ_SIZE(inits attrDecls)), inits BOOST_PP_SEQ_FOR_EACH(_ATTR_MAKE_INIT_TUPLE,~,attrDecls)) { ctor ; } /* ctor, with initialization of defaults */ \ _YADE_CLASS_PYCLASS_BASE_DOC_ATTRS_DEPREC_PY(thisClass,pyClassName,baseClass,docString,BOOST_PP_SEQ_FOR_EACH(_ATTRS_EMBED_INI_TYP_IN_DOC,~,attrDecls),deprec,extras) #define REGISTER_SERIALIZABLE(name) REGISTER_FACTORABLE(name); BOOST_CLASS_EXPORT_KEY(name); // for static classes (Gl1 functors, for instance) #define YADE_CLASS_BASE_DOC_STATICATTRS(thisClass,baseClass,docString,attrs)\ public: BOOST_PP_SEQ_FOR_EACH(_STATATTR_DECL,~,attrs) /* attribute declarations */ \ /* no ctor */ \ REGISTER_CLASS_AND_BASE(thisClass,baseClass); \ _REGISTER_ATTRIBUTES_DEPREC(thisClass,baseClass,attrs,) \ /* called only at class registration, to set initial values; storage still has to be alocated in the cpp file! */ \ void initSetStaticAttributesValue(void){ BOOST_PP_SEQ_FOR_EACH(_STATATTR_INITIALIZE,thisClass,attrs); } \ _STATCLASS_PY_REGISTER_CLASS(thisClass,baseClass,docString,attrs) // used only in some exceptional cases, might disappear in the future #define REGISTER_ATTRIBUTES(baseClass,attrs) _REGISTER_ATTRIBUTES_DEPREC(_SOME_CLASS,baseClass,BOOST_PP_SEQ_FOR_EACH(_ATTR_NAME_ADD_DUMMY_FIELDS,~,attrs),) class Serializable: public Factorable { public: template void serialize(ArchiveT & ar, unsigned int version){ }; // lovely cast members like in eigen :-) template const DerivedT& cast() const { return *static_cast(this); } template DerivedT& cast(){ return *static_cast(this); } Serializable() {}; virtual ~Serializable() {}; // comparison of strong equality of 2 objects (by their address) bool operator==(const Serializable& other){ return this==&other; } bool operator!=(const Serializable& other){ return this!=&other; } void pyUpdateAttrs(const boost::python::dict& d); //static void pyUpdateAttrs(const shared_ptr&, const boost::python::dict& d); virtual void pySetAttr(const std::string& key, const boost::python::object& value){ PyErr_SetString(PyExc_AttributeError,(std::string("No such attribute: ")+key+".").c_str()); boost::python::throw_error_already_set(); }; //virtual boost::python::list pyKeys() const { return boost::python::list(); }; virtual boost::python::dict pyDict() const { return boost::python::dict(); } virtual void callPostLoad(void){ postLoad(*this); } // check whether the class registers itself or whether it calls virtual function of some base class; // that means that the class doesn't register itself properly virtual void checkPyClassRegistersItself(const std::string& thisClassName) const; // perform class registration; overridden in all classes virtual void pyRegisterClass(boost::python::object _scope); // perform any manipulation of arbitrary constructor arguments coming from python, manipulating them in-place; // the remainder is passed to the Serializable_ctor_kwAttrs of the respective class (note: args must be empty) virtual void pyHandleCustomCtorArgs(boost::python::tuple& args, boost::python::dict& kw){ return; } //! string representation of this object std::string pyStr() { return "<"+getClassName()+" instance at "+boost::lexical_cast(this)+">"; } REGISTER_CLASS_NAME(Serializable); REGISTER_BASE_CLASS_NAME(Factorable); }; // helper functions template shared_ptr Serializable_ctor_kwAttrs(boost::python::tuple& t, boost::python::dict& d){ shared_ptr instance; instance=shared_ptr(new T); instance->pyHandleCustomCtorArgs(t,d); // can change t and d in-place if(boost::python::len(t)>0) throw runtime_error("Zero (not "+boost::lexical_cast(boost::python::len(t))+") non-keyword constructor arguments required [in Serializable_ctor_kwAttrs; Serializable::pyHandleCustomCtorArgs might had changed it after your call]."); if(boost::python::len(d)>0){ instance->pyUpdateAttrs(d); instance->callPostLoad(); } return instance; } trunk-2017.01a/lib/smoothing/000077500000000000000000000000001304022710500157375ustar00rootroot00000000000000trunk-2017.01a/lib/smoothing/LinearInterpolate.hpp000066400000000000000000000022171304022710500220730ustar00rootroot00000000000000// 2008 © Václav Šmilauer #pragma once #include #include #include /* Linear interpolation function suitable only for sequential interpolation. * * Template parameter T must support: addition, subtraction, scalar multiplication. * * @param t "time" at which the interpolated variable should be evaluated. * @param tt "time" points at which values are given; must be increasing. * @param values values at "time" points specified by tt * @param pos holds lookup state * * @return value at "time" t; out of range: tt_last → value(t_last) */ template T linearInterpolate(const Real t, const std::vector& tt, const std::vector& values, size_t& pos){ assert(tt.size()==values.size()); if(t<=tt[0]){ pos=0; return values[0];} if(t>=*tt.rbegin()){ pos=tt.size()-2; return *values.rbegin();} pos=std::min(pos,tt.size()-2); while((tt[pos]>t) || (tt[pos+1]t) pos--; else pos++; } const Real& t0=tt[pos], t1=tt[pos+1]; const T& v0=values[pos], v1=values[pos+1]; return v0+(v1-v0)*((t-t0)/(t1-t0)); } trunk-2017.01a/lib/smoothing/WeightedAverage2d.hpp000066400000000000000000000262631304022710500217420ustar00rootroot00000000000000// © 2008 Václav Šmilauer #pragma once #include #include using std::vector; using std::string; template struct GridContainer{ private: Vector2r lo, hi; Vector2r cellSizes; Vector2i nCells; public: Vector2r getLo(){return lo;} Vector2r getHi(){return hi;} Vector2r getCellSize(){ return cellSizes; } vector > > grid; /* construct grid from lower left corner, upper right corner and number of cells in each direction */ GridContainer(Vector2r _lo, Vector2r _hi, Vector2i _nCells): lo(_lo), hi(_hi), nCells(_nCells){ cellSizes=Vector2r((hi[0]-lo[0])/nCells[0],(hi[1]-lo[1])/nCells[1]); grid.resize(nCells[0]); for(int i=0; i=nCells[0] || ret[1]<0 || ret[1]>=nCells[1]){ if(inGrid) *inGrid=false; else throw std::invalid_argument("Cell coordinates outside grid (xy="+boost::lexical_cast(xy[0])+","+boost::lexical_cast(xy[1])+", computed cell coordinates "+boost::lexical_cast(ret[0])+","+boost::lexical_cast(ret[1])+")."); } else {if(inGrid) *inGrid=true;} return ret; } Vector2r cell2xyMid(Vector2i cxy) const { return Vector2r(lo[0]+cellSizes[0]*(.5+cxy[0]),lo[1]+cellSizes[1]*(.5+cxy[1])); } const Vector2i& getSize() const{ return nCells;} // add new element to the right cell void add(const T& t, Vector2r xy){bool inGrid; Vector2i cxy=xy2cell(xy,&inGrid); if(!inGrid){ if(cxy[0]<0) cxy[0]=0; if(cxy[0]>=nCells[0]) cxy[0]=nCells[0]-1; if(cxy[1]<0) cxy[1]=0; if(cxy[1]>=nCells[1]) cxy[1]=nCells[1]-1; } grid[cxy[0]][cxy[1]].push_back(t);} /* Filters: return list of cells, based on some spatial criterion: rectangle, ellipse, circle (add more if you need that) */ vector rectangleFilter(Vector2r bbLo, Vector2r bbHi) const { vector ret; bool dummy; Vector2i cxymin=xy2cell(bbLo,&dummy), cxymax=xy2cell(bbHi,&dummy); for(int cx=cxymin[0]; cx<=cxymax[0]; cx++){ for(int cy=cxymin[1]; cy<=cxymax[1]; cy++){ if(cx>=0 && cx=0 && cy circleFilter(Vector2r xy, Real radius) const { return ellipseFilter(xy,Vector2r(radius,radius));} vector ellipseFilter(Vector2r xy0, Vector2r radii) const { vector rectangle=rectangleFilter(Vector2r(xy0[0]-radii[0],xy0[1]-radii[1]),Vector2r(xy0[0]+radii[0],xy0[1]+radii[1])); vector ret; bool inGrid; Vector2i cxy=xy2cell(xy0,&inGrid); FOREACH(Vector2i mid, rectangle){ // if we are in the cell where the middle is also, this cell passes the filter if(inGrid && mid[0]==cxy[0] && mid[1]==cxy[1]){ret.push_back(mid); continue;} Vector2r xyMid=cell2xyMid(mid); Vector2r xy(xyMid[0]-xy0[0],xyMid[1]-xy0[1]); // relative mid-cell coords // tricky: move the mid-cell to the corner (or aligned pt on edge) according to position WRT center if(mid[0]!=cxy[0]) xy.x()+=(mid[0] v){ vector > vvb; string ret; vvb.resize(nCells[0]); for(size_t i=0; i<(size_t)nCells[0]; i++) vvb[i].resize(nCells[1],false); FOREACH(Vector2i& vv, v) vvb[vv[0]][vv[1]]=true; for(int cy=nCells[1]-1; cy>=0; cy--){ ret+="|"; for(int cx=0; cx struct WeightedAverage{ const shared_ptr > grid; Real weightedSupportArea; // must be computed by derived class WeightedAverage(const shared_ptr >& _grid):grid(_grid){}; virtual Vector2r getPosition(const T&)=0; virtual Real getWeight(const Vector2r& refPt, const T&)=0; virtual Tvalue getValue(const T&)=0; virtual vector filterCells(const Vector2r& refPt)=0; Tvalue computeAverage(const Vector2r& refPt){ Real sumValues, sumWeights; sumValuesWeights(refPt,sumValues,sumWeights); return sumValues/sumWeights; } Tvalue computeAvgPerUnitArea(const Vector2r& refPt){ Real sumValues, sumWeights; sumValuesWeights(refPt,sumValues,sumWeights); return sumValues/weightedSupportArea; } void sumValuesWeights(const Vector2r& refPt, Real& sumValues, Real& sumWeights){ vector filtered=filterCells(refPt); sumValues=sumWeights=0; FOREACH(Vector2i cell, filtered){ FOREACH(const T& element, grid->grid[cell[0]][cell[1]]){ Real weight=getWeight(refPt,element); sumValues+=weight*getValue(element); sumWeights+=weight; } } } }; /* Class for doing template specialization of gaussian kernel average on SGDA_Scalar2d and for testing */ struct Scalar2d{ Vector2r pos; Real val; }; /* Symmetric Gaussian Distribution Average with scalar values */ struct SGDA_Scalar2d: public WeightedAverage { Real stDev, relThreshold; boost::math::normal_distribution distrib; SGDA_Scalar2d(const shared_ptr >& _grid, Real _stDev, Real _relThreshold=3): WeightedAverage(_grid), stDev(_stDev), relThreshold(_relThreshold), distrib(0,stDev) { // approximate probability density function between -stDev*relThreshold,stDev*relThreshold // it is enough to get Φ(-stDev*relThreshold) and subtract twice from 1 (symmetry) // http://en.wikipedia.org/wiki/Normal_distribution#Numerical_approximations_for_the_normal_CDF // using Abramowitz & Stegun approximation, which has error less that 7.5e-8 (fine for us) // FIXME: algorithm not correct, as it takes 1d quantile, while we would need PDF for symmetric 2d gaussian! Real clippedQuantile=boost::math::cdf(distrib,-stDev*relThreshold); Real area=M_PI*pow(relThreshold*stDev,2); // area of the support weightedSupportArea=(1-2*clippedQuantile)*area; } virtual Real getWeight(const Vector2r& meanPt, const Scalar2d& e){ Vector2r pos=getPosition(e); Real rSq=(meanPt-pos).squaredNorm(); //pow(meanPt[0]-pos[0],2)+pow(meanPt[1]-pos[1],2); if(rSq>pow(relThreshold*stDev,2)) return 0.; // discard points further than relThreshold*stDev, by default 3*stDev //return (1./(stDev*sqrt(2*M_PI)))*exp(-rSq/(2*stDev*stDev)); return boost::math::pdf(distrib,sqrt(rSq)); } vector filterCells(const Vector2r& refPt){return WeightedAverage::grid->circleFilter(refPt,stDev*relThreshold);} Real getValue(const Scalar2d& dp){return (Real)dp.val;} Vector2r getPosition(const Scalar2d& dp){return dp.pos;} }; /* simplified interface for python: * * ga=GaussAverage((0,0),(100,100),(10,10),5) * ga.add(53.444,(15.6,43.0)) * ... * ga.avg((10,10)) * ... * * */ class pyGaussAverage{ //struct Scalar2d{Vector2r pos; Real val;}; Vector2r tuple2vec2r(const boost::python::tuple& t){return Vector2r(boost::python::extract(t[0])(),boost::python::extract(t[1])());} Vector2i tuple2vec2i(const boost::python::tuple& t){return Vector2i(boost::python::extract(t[0])(),boost::python::extract(t[1])());} shared_ptr sgda; struct Poly2d{vector vertices; bool inclusive;}; vector clips; public: pyGaussAverage(boost::python::tuple lo, boost::python::tuple hi, boost::python::tuple nCells, Real stDev, Real relThreshold=3.){ shared_ptr > g(new GridContainer(tuple2vec2r(lo),tuple2vec2r(hi),tuple2vec2i(nCells))); sgda=shared_ptr(new SGDA_Scalar2d(g,stDev)); sgda->relThreshold=relThreshold; } bool pointInsidePolygon(const Vector2r&,const vector&); bool ptIsClipped(const Vector2r& pt){ FOREACH(const Poly2d& poly, clips){ bool inside=pointInsidePolygon(pt,poly.vertices); if((inside && !poly.inclusive) || (!inside && poly.inclusive)) return true; } return false; } bool addPt(Real val, boost::python::tuple pos){Scalar2d d; d.pos=tuple2vec2r(pos); if(ptIsClipped(d.pos)) return false; d.val=val; sgda->grid->add(d,d.pos); return true; } Real avg(Vector2r pt){ if(ptIsClipped(pt)) return std::numeric_limits::quiet_NaN(); return sgda->computeAverage(pt);} Real avgPerUnitArea(Vector2r pt){ if(ptIsClipped(pt)) return std::numeric_limits::quiet_NaN(); return sgda->computeAvgPerUnitArea(pt); } Real stDev_get(){return sgda->stDev;} void stDev_set(Real s){sgda->stDev=s;} Real relThreshold_get(){return sgda->relThreshold;} void relThreshold_set(Real rt){sgda->relThreshold=rt;} boost::python::tuple aabb_get(){return boost::python::make_tuple(sgda->grid->getLo(),sgda->grid->getHi());} boost::python::list clips_get(){ boost::python::list ret; FOREACH(const Poly2d& poly, clips){ boost::python::list vertices; FOREACH(const Vector2r& v, poly.vertices) vertices.append(boost::python::make_tuple(v[0],v[1])); ret.append(boost::python::make_tuple(vertices,poly.inclusive)); } return ret; } void clips_set(boost::python::list l){ /* [ ( [(x1,y1),(x2,y2),…], true), … ] */ clips.clear(); for(int i=0; i(l[i])(); boost::python::list coords=boost::python::extract(polyDesc[0]); Poly2d poly; poly.inclusive=boost::python::extract(polyDesc[1]); for(int j=0; j(coords[j]))); } clips.push_back(poly); } } boost::python::tuple data_get(){ boost::python::list x,y,val; const Vector2i& dim=sgda->grid->getSize(); for(int i=0; igrid->grid[i][j]){ x.append(element.pos[0]); y.append(element.pos[1]); val.append(element.val); } } } return boost::python::make_tuple(x,y,val); } Vector2i nCells_get(){ return sgda->grid->getSize(); } int cellNum(const Vector2i& cell){ return sgda->grid->grid[cell[0]][cell[1]].size(); } Real cellSum(const Vector2i& cell){ Real sum=0; FOREACH(const Scalar2d& v, sgda->grid->grid[cell[0]][cell[1]]) sum+=v.val; return sum; } Real cellAvg(const Vector2i& cell){ return cellSum(cell)/cellNum(cell); } Real cellArea(){ Vector2r sz=sgda->grid->getCellSize(); return sz[0]*sz[1]; } Vector2r cellDim(){ return sgda->grid->getCellSize(); } }; trunk-2017.01a/lib/triangulation/000077500000000000000000000000001304022710500166105ustar00rootroot00000000000000trunk-2017.01a/lib/triangulation/FlowBoundingSphere.hpp000066400000000000000000000203001304022710500230600ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2009 by Emanuele Catalano * * Copyright (C) 2009 by Bruno Chareyre * * Copyright (C) 2012 by Donia Marzougui * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef FLOW_ENGINE #pragma once #include "Network.hpp" #include "Timer.h" #include "basicVTKwritter.hpp" #include "Timer.h" typedef pair, vector > Constriction; namespace CGT { template class FlowBoundingSphere : public Network<_Tesselation> { public: typedef _Tesselation Tesselation; typedef Network _N; DECLARE_TESSELATION_TYPES(Network) //painfull, but we need that for templates inheritance... using _N::T; using _N::xMin; using _N::xMax; using _N::yMin; using _N::yMax; using _N::zMin; using _N::zMax; using _N::Rmoy; using _N::sectionArea; using _N::Height; using _N::vTotal; using _N::currentTes; using _N::debugOut; using _N::nOfSpheres; using _N::xMinId; using _N::xMaxId; using _N::yMinId; using _N::yMaxId; using _N::zMinId; using _N::zMaxId; using _N::boundsIds; using _N::cornerMin; using _N::cornerMax; using _N::VSolidTot; using _N::Vtotalissimo; using _N::vPoral; using _N::sSolidTot; using _N::vPoralPorosity; using _N::vTotalPorosity; using _N::boundaries; using _N::idOffset; using _N::vtkInfiniteVertices; using _N::vtkInfiniteCells; using _N::num_particles; using _N::boundingCells; using _N::facetVertices; using _N::facetNFictious; //same for functions using _N::defineFictiousCells; using _N::addBoundingPlanes; using _N::boundary; using _N::tesselation; using _N::surfaceSolidThroatInPore; virtual ~FlowBoundingSphere(); FlowBoundingSphere(); bool slipBoundary; double tolerance; double relax; double ks; //Hydraulic Conductivity bool clampKValues, meanKStat, distanceCorrection; bool OUTPUT_BOUDARIES_RADII; bool noCache;//flag for checking if cached values cell->unitForceVectors have been defined bool computedOnce;//flag for checking if current triangulation has been computed at least once bool pressureChanged;//are imposed pressures modified (on python side)? When it happens, we have to reApplyBoundaryConditions int errorCode; //Handling imposed pressures/fluxes on elements in the form of {point,value} pairs, IPCells contains the cell handles corresponding to point vector > imposedP; vector IPCells; vector > imposedF; vector IFCells; //Blocked cells, where pressure may be computed in undrained condition vector blockedCells; //Pointers to vectors used for user defined boundary pressure vector *pxpos, *ppval; void initNewTri () {noCache=true; /*isLinearSystemSet=false; areCellsOrdered=false;*/}//set flags after retriangulation bool permeabilityMap; bool computeAllCells;//exececute computeHydraulicRadius for all facets and all spheres (double cpu time but needed for now in order to define crossSections correctly) double KOptFactor; double minKdivKmean; double maxKdivKmean; int Iterations; bool rAverage; int walls_id[6]; #define parallel_forces #ifdef parallel_forces int ompThreads; vector< vector > perVertexUnitForce; vector< vector > perVertexPressure; #endif vector edgeSurfaces; vector > edgeIds; vector edgeNormalLubF; vector shearLubricationForces; vector shearLubricationTorques; vector pumpLubricationTorques; vector twistLubricationTorques; vector normalLubricationForce; vector shearLubricationBodyStress; vector normalLubricationBodyStress; vector deltaNormVel; vector deltaShearVel; vector normalV; vector surfaceDistance; vector onlySpheresInteractions; vector shearStressInteraction; vector normalStressInteraction; void Localize(); void computePermeability(); virtual void gaussSeidel (Real dt=0); virtual void resetNetwork(); virtual void resetLinearSystem();//reset both A and B in the linear system A*P=B, done typically after updating the mesh virtual void resetRHS() {};////reset only B in the linear system A*P=B, done typically after changing values of imposed pressures double kFactor; //permeability moltiplicator std::string key; //to give to consolidation files a name with iteration number // std::vector pressures; //for automatic write maximum pressures during consolidation bool tessBasedForce; //allow the force computation method to be chosen from FlowEngine Real minPermLength; //min branch length for Poiseuille double viscosity; double fluidBulkModulus; void displayStatistics(); void initializePressure ( double pZero ); bool reApplyBoundaryConditions (); void computeFacetForcesWithCache(bool onlyCache=false); void saveVtk (const char* folder); #ifdef XVIEW void dessineTriangulation ( Vue3D &Vue, RTriangulation &T ); void dessineShortTesselation ( Vue3D &Vue, Tesselation &Tes ); #endif double permeameter ( double PInf, double PSup, double Section, double DeltaY, const char *file ); double samplePermeability( double& xMin,double& xMax ,double& yMin,double& yMax,double& zMin,double& zMax); double computeHydraulicRadius (CellHandle cell, int j ); Real checkSphereFacetOverlap(const Sphere& v0, const Sphere& v1, const Sphere& v2); double dotProduct ( CVector x, CVector y ); double computeEffectiveRadius(CellHandle cell, int j); double computeEquivalentRadius(CellHandle cell, int j); //return the list of constriction values vector getConstrictions(); vector getConstrictionsFull(); CVector cellBarycenter(CellHandle& cell); void generateVoxelFile ( ); void computeEdgesSurfaces(); Vector3r computeViscousShearForce(const Vector3r& deltaV, const int& edge_id, const Real& Rh); Real computeNormalLubricationForce(const Real& deltaNormV, const Real& dist, const int& edge_id, const Real& eps, const Real& stiffness, const Real& dt, const Real& meanRad); Vector3r computeShearLubricationForce(const Vector3r& deltaShearV, const Real& dist, const int& edge_id, const Real& eps, const Real& centerDist, const Real& meanRad); Vector3r computePumpTorque(const Vector3r& deltaShearAngV, const Real& dist, const int& edge_id, const Real& eps, const Real& meanRad ); Vector3r computeTwistTorque(const Vector3r& deltaNormAngV, const Real& dist, const int& edge_id, const Real& eps, const Real& meanRad ); RTriangulation& buildTriangulation ( Real x, Real y, Real z, Real radius, unsigned const id ); bool isInsideSphere ( double& x, double& y, double& z ); void sliceField (const char *filename); void comsolField(); void interpolate ( Tesselation& Tes, Tesselation& NewTes ); virtual void averageRelativeCellVelocity(); void averageFluidVelocity(); void applySinusoidalPressure(RTriangulation& Tri, double amplitude, double averagePressure, double loadIntervals); void applyUserDefinedPressure(RTriangulation& Tri, vector& xpos, vector& pval); bool isOnSolid (double X, double Y, double Z); double getPorePressure (double X, double Y, double Z); void measurePressureProfile(double WallUpy, double WallDowny); double averageSlicePressure(double Y); double averagePressure(); int getCell (double X,double Y,double Z); double boundaryFlux(unsigned int boundaryId); void setBlocked(CellHandle& cell); vector averageFluidVelocityOnSphere(unsigned int Id_sph); //Solver? int useSolver;//(0 : GaussSeidel, 1:CHOLMOD) }; } //namespace CGT #include #ifdef LINSOLV #include "lib/triangulation/FlowBoundingSphereLinSolv.hpp" #endif /// _____ Template Implementation ____ // #include "lib/triangulation/FlowBoundingSphereLinSolv.ipp" #endif //FLOW_ENGINE trunk-2017.01a/lib/triangulation/FlowBoundingSphere.ipp000066400000000000000000001677631304022710500231120ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2009 by Emanuele Catalano * * Copyright (C) 2009 by Bruno Chareyre * * Copyright (C) 2012 by Donia Marzougui * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef FLOW_ENGINE // #define XVIEW #include "FlowBoundingSphere.hpp"//include after #define XVIEW #include #include #include #include #include "vector" #include #include #include #ifdef XVIEW // #include "Vue3D.h" //FIXME implicit dependencies will look for this class (out of tree) even ifndef XVIEW #endif #ifdef YADE_OPENMP #include // #define GS_OPEN_MP //It should never be defined if Yade is not using openmp #endif // #define USE_FAST_MATH 1 namespace CGT { typedef vector VectorR; //! Use this factor, or minLength, to reduce max permeability values (see usage below)) const double minLength = 0.01;//percentage of mean rad //! Factors including the effect of 1/2 symmetry in hydraulic radii const Real multSym1 = 1/pow(2,0.25); const Real multSym2 = 1/pow(4,0.25); #ifdef XVIEW Vue3D Vue1; #endif template FlowBoundingSphere::~FlowBoundingSphere() { } template FlowBoundingSphere::FlowBoundingSphere() { xMin = 1000.0, xMax = -10000.0, yMin = 1000.0, yMax = -10000.0, zMin = 1000.0, zMax = -10000.0; currentTes = 0; nOfSpheres = 0; sectionArea = 0, Height=0, vTotal=0; vtkInfiniteVertices=0, vtkInfiniteCells=0; viscosity = 1; fluidBulkModulus = 0; tessBasedForce = true; for (int i=0;i<6;i++) boundsIds[i] = 0; minPermLength=1e-6;// multiplier applied on throat radius to define a minimal throat length (escaping coincident points) slipBoundary = false;//no-slip/symmetry conditions on lateral boundaries tolerance = 1e-07; relax = 1.9; ks=0; distanceCorrection = true; clampKValues = true; meanKStat = true; KOptFactor=0; noCache=true; pressureChanged=false; computeAllCells=true;//might be turned false IF the code is reorganized (we can make a separate function to compute unitForceVectors outside compute_Permeability) AND it really matters for CPU time debugOut = true; rAverage = false; /** use the average between the effective radius (inscribed sphere in facet) and the equivalent (circle surface = facet fluid surface) **/ OUTPUT_BOUDARIES_RADII = false; rAverage = false; /** if true use the average between the effective radius (inscribed sphere in facet) and the equivalent (circle surface = facet fluid surface) **/ // areaR2Permeability=true; permeabilityMap = false; computedOnce=false; minKdivKmean=0.0001; maxKdivKmean=100.; ompThreads=1; errorCode=0; pxpos=ppval=NULL; } template void FlowBoundingSphere::resetNetwork() {T[currentTes].Clear();this->resetLinearSystem();} template void FlowBoundingSphere::resetLinearSystem() {noCache=true;} template void FlowBoundingSphere::averageRelativeCellVelocity() { if (noCache && T[!currentTes].Max_id()<=0) return; RTriangulation& Tri = T[noCache?(!currentTes):currentTes].Triangulation(); Point posAvFacet; int numCells = 0; double facetFlowRate = 0; FiniteCellsIterator cellEnd = Tri.finite_cells_end(); for ( FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if (cell->info().isGhost) continue; cell->info().averageVelocity() =CGAL::NULL_VECTOR; numCells++; Real totFlowRate = 0;//used to acount for influxes in elements where pressure is imposed for ( int i=0; i<4; i++ ) if (!Tri.is_infinite(cell->neighbor(i))){ CVector Surfk = cell->info()-cell->neighbor(i)->info(); Real area = sqrt ( Surfk.squared_length() ); Surfk = Surfk/area; CVector branch = cell->vertex ( facetVertices[i][0] )->point() - cell->info(); posAvFacet = (Point) cell->info() + ( branch*Surfk ) *Surfk; facetFlowRate = (cell->info().kNorm())[i] * (cell->info().shiftedP() - cell->neighbor (i)->info().shiftedP()); totFlowRate += facetFlowRate; cell->info().averageVelocity() = cell->info().averageVelocity() + (facetFlowRate) * ( posAvFacet-CGAL::ORIGIN ); } //This is the influx term if (cell->info().Pcondition) cell->info().averageVelocity() = cell->info().averageVelocity() - (totFlowRate)*((Point) cell->info()-CGAL::ORIGIN ); //now divide by volume cell->info().averageVelocity() = cell->info().averageVelocity() /std::abs(cell->info().volume()); } } template bool FlowBoundingSphere::isOnSolid (double X, double Y, double Z) { RTriangulation& Tri = T[currentTes].Triangulation(); FiniteCellsIterator cellEnd = Tri.finiteCellsEnd(); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++) { for (int i=0; i<4; i++){ double radius = sqrt(cell->vertex(i)->point().weight()); if (X < (cell->vertex(i)->point().x()+radius) && X > (cell->vertex(i)->point().x()-radius)){ if (Y < (cell->vertex(i)->point().y()+radius) && Y > (cell->vertex(i)->point().y()-radius)){ if (Z < (cell->vertex(i)->point().z()+radius) && Z > (cell->vertex(i)->point().z()-radius)){ return true;}}}}} return false; } template void FlowBoundingSphere::averageFluidVelocity() { if (noCache && T[!currentTes].Max_id()<=0) return; averageRelativeCellVelocity(); RTriangulation& Tri = T[noCache?(!currentTes):currentTes].Triangulation(); int numVertex = 0; FiniteVerticesIterator verticesEnd = Tri.finite_vertices_end(); for (FiniteVerticesIterator vIt = Tri.finite_vertices_begin(); vIt != verticesEnd; vIt++) { numVertex++;} vector volumes; vector velocityVolumes; velocityVolumes.resize(numVertex); volumes.resize(numVertex); for (FiniteVerticesIterator vIt = Tri.finite_vertices_begin(); vIt != verticesEnd; vIt++) { velocityVolumes[vIt->info().id()]=CGAL::NULL_VECTOR; volumes[vIt->info().id()]=0.f;} FiniteCellsIterator cellEnd = Tri.finiteCellsEnd(); for ( FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if (cell->info().fictious()==0){ for (int i=0;i<4;i++){ velocityVolumes[cell->vertex(i)->info().id()] = velocityVolumes[cell->vertex(i)->info().id()] + cell->info().averageVelocity()*std::abs(cell->info().volume()); volumes[cell->vertex(i)->info().id()] = volumes[cell->vertex(i)->info().id()] + std::abs(cell->info().volume());} }} std::ofstream fluid_vel ("Velocity", std::ios::out); double Rx = (xMax-xMin) /10; double Ry = (yMax-yMin) /12; double Rz = (zMax-zMin) /20; CellHandle cellula; CVector velocity = CGAL::NULL_VECTOR; int i=0; for(double X=xMin+Rx;Xvertex(y)->info().isFictious) {velocity = velocity + (velocityVolumes[cellula->vertex(y)->info().id()]/volumes[cellula->vertex(y)->info().id()]);i++;}} }velocity = velocity/i; fluid_vel << X << " " << Y << " " << velocity << endl; }} } template vector FlowBoundingSphere::averageFluidVelocityOnSphere(unsigned int Id_sph) { //FIXME: we are computing everything again for each other Id_sph... if (noCache && T[!currentTes].Max_id()<=0) return vector(3,0); averageRelativeCellVelocity(); RTriangulation& Tri = T[noCache?(!currentTes):currentTes].Triangulation(); Real volumes; CGT::CVector velocityVolumes; vector result; result.resize(3); velocityVolumes=CGAL::NULL_VECTOR; volumes=0.f; FiniteCellsIterator cellEnd = Tri.finite_cells_end(); for ( FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if (cell->info().fictious()==0){ for (unsigned int i=0;i<4;i++){ if (cell->vertex(i)->info().id()==Id_sph){ velocityVolumes = velocityVolumes + cell->info().averageVelocity()*std::abs(cell->info().volume()); volumes = volumes + std::abs(cell->info().volume());}}}} for (int i=0;i<3;i++) result[i] += velocityVolumes[i]/volumes; return result; } template double FlowBoundingSphere::getPorePressure (double X, double Y, double Z) { if (noCache && T[!currentTes].Max_id()<=0) return 0;//the engine never solved anything RTriangulation& Tri = T[noCache?(!currentTes):currentTes].Triangulation(); CellHandle cell = Tri.locate(Point(X,Y,Z)); return cell->info().p(); } template int FlowBoundingSphere::getCell (double X, double Y, double Z) { if (noCache && T[!currentTes].Max_id()<=0) {cout<<"Triangulation does not exist. Sorry."<info().id; } template void FlowBoundingSphere::measurePressureProfile(double WallUpy, double WallDowny) { if (noCache && T[!currentTes].Max_id()<=0) return;//the engine never solved anything RTriangulation& Tri = T[noCache?(!currentTes):currentTes].Triangulation(); CellHandle permeameter; std::ofstream capture ("Pressure_profile", std::ios::app); int intervals = 5; int captures = 6; double Rz = (zMax-zMin)/intervals; double Ry = (WallUpy-WallDowny)/captures; double X=(xMax+xMin)/2; double Y = WallDowny; double pressure = 0.f; int cell=0; for (int i=0; iinfo().p(); cell++; } Y += Ry; capture << pressure/cell << endl;} } template double FlowBoundingSphere::averageSlicePressure(double Y) { RTriangulation& Tri = T[currentTes].Triangulation(); double P_ave = 0.f; int n = 0; double Ry = (yMax-yMin)/30; double Rx = (xMax-xMin)/30; double Rz = (zMax-zMin)/30; for (double X=xMin; X<=xMax+Ry/10; X=X+Rx) { for (double Z=zMin; Z<=zMax+Ry/10; Z=Z+Rz) { P_ave+=Tri.locate(Point(X, Y, Z))->info().p(); n++; } } P_ave/=n; return P_ave; } template double FlowBoundingSphere::averagePressure() { RTriangulation& Tri = T[currentTes].Triangulation(); double P = 0.f, Ppond=0.f, Vpond=0.f; int n = 0; for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != Tri.finite_cells_end(); cell++) { P+=cell->info().p(); n++; Ppond+=cell->info().p()*std::abs(cell->info().volume()); Vpond+=std::abs(cell->info().volume());} P/=n; Ppond/=Vpond; return Ppond; } template void FlowBoundingSphere::computeFacetForcesWithCache(bool onlyCache) { RTriangulation& Tri = T[currentTes].Triangulation(); CVector nullVect(0,0,0); //reset forces if (!onlyCache) for (FiniteVerticesIterator v = Tri.finite_vertices_begin(); v != Tri.finite_vertices_end(); ++v) v->info().forces=nullVect; #ifdef parallel_forces if (noCache) { perVertexUnitForce.clear(); perVertexPressure.clear(); perVertexUnitForce.resize(T[currentTes].maxId+1); perVertexPressure.resize(T[currentTes].maxId+1);} #endif CellHandle neighbourCell; VertexHandle mirrorVertex; CVector tempVect; //FIXME : Ema, be carefull with this (noCache), it needs to be turned true after retriangulation if (noCache) {for (VCellIterator cellIt=T[currentTes].cellHandles.begin(); cellIt!=T[currentTes].cellHandles.end(); cellIt++){ CellHandle& cell = *cellIt; //reset cache for (int k=0;k<4;k++) cell->info().unitForceVectors[k]=nullVect; for (int j=0; j<4; j++) if (!Tri.is_infinite(cell->neighbor(j))) { neighbourCell = cell->neighbor(j); const CVector& Surfk = cell->info().facetSurfaces[j]; //FIXME : later compute that fluidSurf only once in hydraulicRadius, for now keep full surface not modified in cell->info for comparison with other forces schemes //The ratio void surface / facet surface //Area of the facet (i.e. the triangle) Real area = sqrt(Surfk.squared_length()); if (area<=0) cerr <<"AREA <= 0!!"<& crossSections = cell->info().facetSphereCrossSections; //This is the cross-sectional area of the throat CVector fluidSurfk = cell->info().facetSurfaces[j]*cell->info().facetFluidSurfacesRatio[j]; /// handle fictious vertex since we can get the projected surface easily here if (cell->vertex(j)->info().isFictious) { //projection of facet on the boundary Real projSurf=std::abs(Surfk[boundary(cell->vertex(j)->info().id()).coordinate]); tempVect=-projSurf*boundary(cell->vertex(j)->info().id()).normal; cell->vertex(j)->info().forces = cell->vertex(j)->info().forces+tempVect*cell->info().p(); //define the cached value for later use with cache*p cell->info().unitForceVectors[j]=cell->info().unitForceVectors[j]+ tempVect; } /// Apply weighted forces f_k=sqRad_k/sumSqRad*f CVector facetUnitForce = -fluidSurfk*cell->info().solidSurfaces[j][3]; CVector facetForce = cell->info().p()*facetUnitForce; for (int y=0; y<3;y++) { //1st the drag (viscous) force weighted by surface of spheres in the throat cell->vertex(facetVertices[j][y])->info().forces = cell->vertex(facetVertices[j][y])->info().forces + facetForce*cell->info().solidSurfaces[j][y]; //(add to cached value) cell->info().unitForceVectors[facetVertices[j][y]]=cell->info().unitForceVectors[facetVertices[j][y]]+facetUnitForce*cell->info().solidSurfaces[j][y]; //2nd the partial integral of pore pressure, which boils down to weighting by partial cross-sectional area //uncomment to get total force / comment to get only viscous forces (Bruno) if (!cell->vertex(facetVertices[j][y])->info().isFictious) { cell->vertex(facetVertices[j][y])->info().forces = cell->vertex(facetVertices[j][y])->info().forces -facetNormal*cell->info().p()*crossSections[j][y]; //add to cached value cell->info().unitForceVectors[facetVertices[j][y]]=cell->info().unitForceVectors[facetVertices[j][y]]-facetNormal*crossSections[j][y]; } } #ifdef parallel_forces perVertexUnitForce[cell->vertex(j)->info().id()].push_back(&(cell->info().unitForceVectors[j])); perVertexPressure[cell->vertex(j)->info().id()].push_back(&(cell->info().p())); #endif } } noCache=false;//cache should always be defined after execution of this function } if (onlyCache) return; // } else {//use cached values #ifndef parallel_forces for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++) { for (int yy=0;yy<4;yy++) cell->vertex(yy)->info().forces = cell->vertex(yy)->info().forces + cell->info().unitForceVectors[yy]*cell->info().p();} #else #pragma omp parallel for num_threads(ompThreads) for (int vn=0; vn<= T[currentTes].maxId; vn++) { if (T[currentTes].vertexHandles[vn]==NULL) continue; VertexHandle& v = T[currentTes].vertexHandles[vn]; const int& id = v->info().id(); CVector tf (0,0,0); int k=0; for (vector::iterator c = perVertexPressure[id].begin(); c != perVertexPressure[id].end(); c++) tf = tf + (*(perVertexUnitForce[id][k++]))*(**c); v->info().forces = tf; } #endif // } if (debugOut) { CVector totalForce = nullVect; for (FiniteVerticesIterator v = Tri.finite_vertices_begin(); v != Tri.finite_vertices_end(); ++v) { if (!v->info().isFictious) totalForce = totalForce + v->info().forces; else if (boundary(v->info().id()).flowCondition==1) totalForce = totalForce + v->info().forces; } cout << "totalForce = "<< totalForce << endl;} } template void FlowBoundingSphere::applySinusoidalPressure(RTriangulation& Tri, double amplitude, double averagePressure, double loadIntervals) { double step = 1/loadIntervals; VectorCell tmpCells; tmpCells.resize(10000); VCellIterator cellsIt = tmpCells.begin(); for (double alpha=0; alpha<1.001; alpha+=step) { VCellIterator cellsEnd = Tri.incident_cells(T[currentTes].vertexHandles[yMaxId],cellsIt); for (VCellIterator it = tmpCells.begin(); it != cellsEnd; it++) { if(!Tri.is_infinite(*it)){ Point& p1 = (*it)->info(); CellHandle& cell = *it; if (p1.x()info().p() = averagePressure+amplitude; else if (p1.x()>xMax) cell->info().p() = averagePressure-amplitude; else if (p1.x()>(xMin+alpha*(xMax-xMin)) && p1.x()<(xMin+(alpha+step)*(xMax-xMin))) cell->info().p() = averagePressure + (amplitude)*(cos(alpha*M_PI)); } } } } template void FlowBoundingSphere::applyUserDefinedPressure(RTriangulation& Tri, vector& xpos, vector& pval) { if (!(xpos.size() && xpos.size()==pval.size())) {cerr << "Wrong definition of boundary pressure, check input" <info(); CellHandle& cell = *it; if (p1.x()xlast) cerr<<"udef pressure: cell out of range"<info().p() = pval[intg]*(1-frac) + pval[intg+1]*frac; } } } template CVector FlowBoundingSphere::cellBarycenter(CellHandle& cell) { CVector center ( 0,0,0 ); for ( int k=0;k<4;k++ ) center= center + 0.25* (cell->vertex(k)->point()-CGAL::ORIGIN); return center; } template void FlowBoundingSphere::interpolate(Tesselation& Tes, Tesselation& NewTes) { CellHandle oldCell; RTriangulation& Tri = Tes.Triangulation(); for (typename VectorCell::iterator cellIt=NewTes.cellHandles.begin(); cellIt!=NewTes.cellHandles.end(); cellIt++){ CellHandle& newCell = *cellIt; if (newCell->info().Pcondition || newCell->info().isGhost) continue; CVector center ( 0,0,0 ); if (newCell->info().fictious()==0) for ( int k=0;k<4;k++ ) center= center + 0.25* (Tes.vertex(newCell->vertex(k)->info().id())->point()-CGAL::ORIGIN); else { Real boundPos=0; int coord=0; for ( int k=0;k<4;k++ ) if (!newCell->vertex (k)->info().isFictious) center= center+(1./(4.-newCell->info().fictious()))*(Tes.vertex(newCell->vertex(k)->info().id())->point()-CGAL::ORIGIN); for ( int k=0;k<4;k++ ) if (newCell->vertex (k)->info().isFictious) { coord=boundary (newCell->vertex(k)->info().id()).coordinate; boundPos=boundary (newCell->vertex(k)->info().id()).p[coord]; center=CVector(coord==0?boundPos:center[0],coord==1?boundPos:center[1],coord==2?boundPos:center[2]); } } oldCell = Tri.locate(Point(center[0],center[1],center[2])); newCell->info().getInfo(oldCell->info()); // newCell->info().p() = oldCell->info().shiftedP(); } // Tes.Clear();//Don't reset to avoid segfault when getting pressure in scripts just after interpolation } template Real FlowBoundingSphere::checkSphereFacetOverlap(const Sphere& v0, const Sphere& v1, const Sphere& v2) { //First, check that v0 projection fall between v1 and v2... Real dist=(v0-v1)*(v2-v1); if (dist<0) return 0; Real v1v2=(v2-v1).squared_length(); if (dist>v1v2) return 0; //... then, check distance Real m=(cross_product(v0-v1,v2-v1)).squared_length()/v1v2; if (m void FlowBoundingSphere::setBlocked(CellHandle& cell) { RTriangulation& Tri = T[currentTes].Triangulation(); if (cell->info().Pcondition) cell->info().p() = 0; else blockedCells.push_back(cell); for (int j=0; j<4; j++) { (cell->info().kNorm())[j]= 0; (cell->neighbor(j)->info().kNorm())[Tri.mirror_index(cell, j)]= 0;} } template void FlowBoundingSphere::computePermeability() { if (debugOut) cout << "----Computing_Permeability------" << endl; RTriangulation& Tri = T[currentTes].Triangulation(); VSolidTot = 0, Vtotalissimo = 0, vPoral = 0, sSolidTot = 0, vTotalPorosity=0, vPoralPorosity=0; FiniteCellsIterator cellEnd = Tri.finite_cells_end(); CellHandle neighbourCell; double k=0, distance = 0, radius = 0; int surfneg=0; int NEG=0, POS=0, pass=0; bool ref = Tri.finite_cells_begin()->info().isvisited; Real meanK=0, STDEV=0, meanRadius=0, meanDistance=0; Real infiniteK=1e10; for (VCellIterator cellIt=T[currentTes].cellHandles.begin(); cellIt!=T[currentTes].cellHandles.end(); cellIt++){ CellHandle& cell = *cellIt; if (cell->info().blocked) { setBlocked(cell); cell->info().isvisited = !ref;} Point& p1 = cell->info(); for (int j=0; j<4; j++) { neighbourCell = cell->neighbor(j); Point& p2 = neighbourCell->info(); if (!Tri.is_infinite(neighbourCell) && (neighbourCell->info().isvisited==ref || computeAllCells)) { //compute and store the area of sphere-facet intersections for later use VertexHandle W [3]; for (int kk=0; kk<3; kk++) { W[kk] = cell->vertex(facetVertices[j][kk]); } Sphere& v0 = W[0]->point(); Sphere& v1 = W[1]->point(); Sphere& v2 = W[2]->point(); cell->info().facetSphereCrossSections[j]=CVector( W[0]->info().isFictious ? 0 : 0.5*v0.weight()*acos((v1-v0)*(v2-v0)/sqrt((v1-v0).squared_length()*(v2-v0).squared_length())), W[1]->info().isFictious ? 0 : 0.5*v1.weight()*acos((v0-v1)*(v2-v1)/sqrt((v1-v0).squared_length()*(v2-v1).squared_length())), W[2]->info().isFictious ? 0 : 0.5*v2.weight()*acos((v0-v2)*(v1-v2)/sqrt((v1-v2).squared_length()*(v2-v0).squared_length()))); //FIXME: it should be possible to skip completely blocked cells, currently the problem is it segfault for undefined areas // if (cell->info().blocked) continue;//We don't need permeability for blocked cells, it will be set to zero anyway pass+=1; CVector l = p1 - p2; distance = sqrt(l.squared_length()); if (!rAverage) radius = 2* computeHydraulicRadius(cell, j); else radius = (computeEffectiveRadius(cell, j)+computeEquivalentRadius(cell,j))*0.5; if (radius<0) NEG++; else POS++; if (radius==0) { cout << "INS-INS PROBLEM!!!!!!!" << endl; } Real fluidArea=0; if (distance!=0) { if (minPermLength>0 && distanceCorrection) distance=max(minPermLength*radius,distance); const CVector& Surfk = cell->info().facetSurfaces[j]; Real area = sqrt(Surfk.squared_length()); const CVector& crossSections = cell->info().facetSphereCrossSections[j]; Real S0=0; S0=checkSphereFacetOverlap(v0,v1,v2); if (S0==0) S0=checkSphereFacetOverlap(v1,v2,v0); if (S0==0) S0=checkSphereFacetOverlap(v2,v0,v1); //take absolute value, since in rare cases the surface can be negative (overlaping spheres) fluidArea=std::abs(area-crossSections[0]-crossSections[1]-crossSections[2]+S0); cell->info().facetFluidSurfacesRatio[j]=fluidArea/area; // kFactor<0 means we replace Poiseuille by Darcy localy, yielding a particle size-independent bulk conductivity if (kFactor>0) cell->info().kNorm()[j]= kFactor*(fluidArea * pow(radius,2)) / (8*viscosity*distance); else cell->info().kNorm()[j]= -kFactor * area / distance; meanDistance += distance; meanRadius += radius; meanK += (cell->info().kNorm())[j]; if (!neighbourCell->info().isGhost) (neighbourCell->info().kNorm())[Tri.mirror_index(cell, j)]= (cell->info().kNorm())[j]; if (k<0 && debugOut) {surfneg+=1; cout<<"__ k<0 __"<info().id()<<" "<info().id()<<" "<info().id()<<" "<info().isGhost) (neighbourCell->info().kNorm())[Tri.mirror_index(cell, j)]= (cell->info().kNorm())[j]; } } cell->info().isvisited = !ref; } if (debugOut) cout<<"surfneg est "<0) globalK=kFactor*meanDistance*vPoral/(sSolidTot*8.*viscosity);//An approximate value of macroscopic permeability, for clamping local values below else globalK=meanK; if (debugOut) { cout << "PassCompK = " << pass << endl; cout << "meanK = " << meanK << endl; cout << "globalK = " << globalK << endl; cout << "maxKdivKmean*globalK = " << maxKdivKmean*globalK << endl; cout << "minKdivKmean*globalK = " << minKdivKmean*globalK << endl; cout << "meanTubesRadius = " << meanRadius << endl; cout << "meanDistance = " << meanDistance << endl; } ref = Tri.finite_cells_begin()->info().isvisited; pass=0; if (clampKValues) for (VCellIterator cellIt=T[currentTes].cellHandles.begin(); cellIt!=T[currentTes].cellHandles.end(); cellIt++){ CellHandle& cell = *cellIt; for (int j=0; j<4; j++) { neighbourCell = cell->neighbor(j); if (!Tri.is_infinite(neighbourCell) && neighbourCell->info().isvisited==ref) { pass++; (cell->info().kNorm())[j] = max(minKdivKmean*globalK ,min((cell->info().kNorm())[j], maxKdivKmean*globalK)); (neighbourCell->info().kNorm())[Tri.mirror_index(cell, j)]=(cell->info().kNorm())[j]; } } } if (debugOut) cout << "PassKcorrect = " << pass << endl; if (debugOut) cout << "POS = " << POS << " NEG = " << NEG << " pass = " << pass << endl; // A loop to compute the standard deviation of the local K distribution, and use it to include/exclude K values higher then (meanK +/- K_opt_factor*STDEV) if (meanKStat) { std::ofstream k_opt_file("k_stdev.txt" ,std::ios::out); ref = Tri.finite_cells_begin()->info().isvisited; pass=0; for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++) { for (int j=0; j<4; j++) { neighbourCell = cell->neighbor(j); if (!Tri.is_infinite(neighbourCell) && neighbourCell->info().isvisited==ref) { pass++; STDEV += pow(((cell->info().kNorm())[j]-meanK),2); } }cell->info().isvisited = !ref; } STDEV = sqrt(STDEV/pass); if (debugOut) cout << "PassSTDEV = " << pass << endl << "STATISTIC K" << endl; double k_min = 0, k_max = meanK + KOptFactor*STDEV; cout << "Kmoy = " << meanK << " Standard Deviation = " << STDEV << endl<< "kmin = " << k_min << " kmax = " << k_max << endl; ref = Tri.finite_cells_begin()->info().isvisited; pass=0; for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++) { for (int j=0; j<4; j++) { neighbourCell = cell->neighbor(j); if (!Tri.is_infinite(neighbourCell) && neighbourCell->info().isvisited==ref) { pass+=1; if ((cell->info().kNorm())[j]>k_max) { (cell->info().kNorm())[j]=k_max; (neighbourCell->info().kNorm())[Tri.mirror_index(cell, j)]= (cell->info().kNorm())[j]; } k_opt_file << KOptFactor << " " << (cell->info().kNorm())[j] << endl; } }cell->info().isvisited=!ref; } if (debugOut) cout << "PassKopt = " << pass << endl; } if (debugOut) { FiniteVerticesIterator verticesEnd = Tri.finite_vertices_end(); Real Vgrains = 0; int grains=0; for (FiniteVerticesIterator vIt = Tri.finite_vertices_begin(); vIt != verticesEnd; vIt++) { if (!vIt->info().isFictious && !vIt->info().isGhost) { grains +=1; Vgrains += 1.33333333 * M_PI * pow(vIt->point().weight(),1.5);}} cout< vector FlowBoundingSphere::getConstrictions() { RTriangulation& Tri = T[currentTes].Triangulation(); vector constrictions; for (FiniteFacetsIterator f_it=Tri.finite_facets_begin(); f_it != Tri.finite_facets_end();f_it++){ //in the periodic case, we skip facets with lowest id out of the base period if ( ((f_it->first->info().index <= f_it->first->neighbor(f_it->second)->info().index) && f_it->first->info().isGhost) || ((f_it->first->info().index >= f_it->first->neighbor(f_it->second)->info().index) && f_it->first->neighbor(f_it->second)->info().isGhost) || f_it->first->info().index == 0 || f_it->first->neighbor(f_it->second)->info().index == 0) continue; constrictions.push_back(computeEffectiveRadius(f_it->first, f_it->second)); } return constrictions; } template vector FlowBoundingSphere::getConstrictionsFull() { RTriangulation& Tri = T[currentTes].Triangulation(); vector constrictions; for (FiniteFacetsIterator f_it=Tri.finite_facets_begin(); f_it != Tri.finite_facets_end();f_it++){ //in the periodic case, we skip facets with lowest id out of the base period if ( ((f_it->first->info().index <= f_it->first->neighbor(f_it->second)->info().index) && f_it->first->info().isGhost) || ((f_it->first->info().index >= f_it->first->neighbor(f_it->second)->info().index) && f_it->first->neighbor(f_it->second)->info().isGhost) || f_it->first->info().index == 0 || f_it->first->neighbor(f_it->second)->info().index == 0) continue; vector rn; const CVector& normal = f_it->first->info().facetSurfaces[f_it->second]; if (!normal[0] && !normal[1] && !normal[2]) continue; rn.push_back(computeEffectiveRadius(f_it->first, f_it->second)); rn.push_back(normal[0]); rn.push_back(normal[1]); rn.push_back(normal[2]); Constriction cons (pair(f_it->first->info().id,f_it->first->neighbor(f_it->second)->info().id),rn); constrictions.push_back(cons); } return constrictions; } template double FlowBoundingSphere::computeEffectiveRadius(CellHandle cell, int j) { RTriangulation& Tri = T[currentTes].Triangulation(); if (Tri.is_infinite(cell->neighbor(j))) return 0; CVector B = cell->vertex(facetVertices[j][1])->point().point()-cell->vertex(facetVertices[j][0])->point().point(); CVector x = B/sqrt(B.squared_length()); CVector C = cell->vertex(facetVertices[j][2])->point().point()-cell->vertex(facetVertices[j][0])->point().point(); CVector z = CGAL::cross_product(x,C); CVector y = CGAL::cross_product(x,z); y = y/sqrt(y.squared_length()); double b1[2]; b1[0] = B*x; b1[1] = B*y; double c1[2]; c1[0] = C*x; c1[1] = C*y; double rA = sqrt(cell->vertex(facetVertices[j][0])->point().weight()); double rB = sqrt(cell->vertex(facetVertices[j][1])->point().weight()); double rC = sqrt(cell->vertex(facetVertices[j][2])->point().weight()); double A = ((pow(rA,2))*(1-c1[0]/b1[0])+((pow(rB,2)*c1[0])/b1[0])-pow(rC,2)+pow(c1[0],2)+pow(c1[1],2)-((pow(b1[0],2)+pow(b1[1],2))*c1[0]/b1[0]))/(2*c1[1]-2*b1[1]*c1[0]/b1[0]); double BB = (rA-rC-((rA-rB)*c1[0]/b1[0]))/(c1[1]-b1[1]*c1[0]/b1[0]); double CC = (pow(rA,2)-pow(rB,2)+pow(b1[0],2)+pow(b1[1],2))/(2*b1[0]); double D = (rA-rB)/b1[0]; double E = b1[1]/b1[0]; double F = pow(CC,2)+pow(E,2)*pow(A,2)-2*CC*E*A; double c = -F-pow(A,2)+pow(rA,2); double b = 2*rA-2*(D-BB*E)*(CC-E*A)-2*A*BB; double a = 1-pow((D-BB*E),2)-pow(BB,2); if ((pow(b,2)-4*a*c)<0){cout << "NEGATIVE DETERMINANT" << endl; } double reff = (-b+sqrt(pow(b,2)-4*a*c))/(2*a); if (reff<0) return 0;//happens very rarely, with bounding spheres most probably //if the facet involves one ore more bounding sphere, we return R with a minus sign if (cell->vertex(facetVertices[j][2])->info().isFictious || cell->vertex(facetVertices[j][1])->info().isFictious || cell->vertex(facetVertices[j][2])->info().isFictious) return -reff; else return reff; } template double FlowBoundingSphere::computeEquivalentRadius(CellHandle cell, int j) { Real fluidSurf = sqrt(cell->info().facetSurfaces[j].squared_length())*cell->info().facetFluidSurfacesRatio[j]; return sqrt(fluidSurf/M_PI); } template double FlowBoundingSphere::computeHydraulicRadius(CellHandle cell, int j) { RTriangulation& Tri = T[currentTes].Triangulation(); if (Tri.is_infinite(cell->neighbor(j))) return 0; double Vpore = this->volumePoreVoronoiFraction(cell, j); double Ssolid = this->surfaceSolidThroat(cell, j, slipBoundary, /*reuse the same facet data*/ true); //handle symmetry (tested ok) if (slipBoundary && facetNFictious>0) { //! Include a multiplier so that permeability will be K/2 or K/4 in symmetry conditions Real mult= facetNFictious==1 ? multSym1 : multSym2; return Vpore/Ssolid*mult;} return Vpore/Ssolid; } template void FlowBoundingSphere::initializePressure( double pZero ) { RTriangulation& Tri = T[currentTes].Triangulation(); FiniteCellsIterator cellEnd = Tri.finite_cells_end(); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++){ if (!cell->info().Pcondition) cell->info().p() = pZero; cell->info().dv()=0; } for (int bound=0; bound<6;bound++) { int& id = *boundsIds[bound]; boundingCells[bound].clear(); if (id<0) continue; Boundary& bi = boundary(id); if (!bi.flowCondition) { VectorCell tmpCells; tmpCells.resize(10000); VCellIterator cells_it = tmpCells.begin(); VCellIterator cells_end = Tri.incident_cells(T[currentTes].vertexHandles[id],cells_it); for (VCellIterator it = tmpCells.begin(); it != cells_end; it++){ (*it)->info().p() = bi.value;(*it)->info().Pcondition=true; boundingCells[bound].push_back(*it); } } } if (ppval && pxpos) applyUserDefinedPressure(Tri,*pxpos,*ppval); IPCells.clear(); for (unsigned int n=0; ninfo().Pcondition) cerr<<"Imposed pressure fall in a boundary condition."<info().p()=imposedP[n].second; cell->info().Pcondition=true;} pressureChanged=false; IFCells.clear(); for (unsigned int n=0; ninfo().Pcondition) cerr<<"Imposed flux fall in a pressure boundary condition."<info().Pcondition=false;} } template bool FlowBoundingSphere::reApplyBoundaryConditions() { if (!pressureChanged) return false; for (int bound=0; bound<6;bound++) { int& id = *boundsIds[bound]; if (id<0) continue; Boundary& bi = boundary(id); if (!bi.flowCondition) { for (VCellIterator it = boundingCells[bound].begin(); it != boundingCells[bound].end(); it++){ (*it)->info().p() = bi.value; (*it)->info().Pcondition=true; } } } if (ppval && pxpos) applyUserDefinedPressure(T[currentTes].Triangulation(),*pxpos,*ppval); for (unsigned int n=0; ninfo().p()=imposedP[n].second; IPCells[n]->info().Pcondition=true;} pressureChanged=false; return true; } template void FlowBoundingSphere::gaussSeidel(Real dt) { reApplyBoundaryConditions(); RTriangulation& Tri = T[currentTes].Triangulation(); int j = 0; double m, n, dp_max, p_max, sum_p, p_moy, dp, sum_dp; double compFlowFactor=0; vector previousP; previousP.resize(Tri.number_of_finite_cells()); const int num_threads=1; bool compressible= (fluidBulkModulus>0); #ifdef GS_OPEN_MP omp_set_num_threads(num_threads); #endif if(debugOut){ cout << "tolerance = " << tolerance << endl; cout << "relax = " << relax << endl;} vector t_sum_p, t_dp_max, t_sum_dp, t_p_max; t_sum_dp.resize(num_threads); t_dp_max.resize(num_threads); t_p_max.resize(num_threads); t_sum_p.resize(num_threads); FiniteCellsIterator cellEnd = Tri.finite_cells_end(); #ifdef GS_OPEN_MP vector cells_its; for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++) if ( !cell->info().Pcondition ) cells_its.push_back(cell); int numCells=cells_its.size(); cout<<"cells_its.size() "<info().Pcondition && !cell->info().blocked) { cell2++; #endif if (compressible && j==0) { previousP[bb]=cell->info().p(); } m=0, n=0; for (int j2=0; j2<4; j2++) { if (!Tri.is_infinite(cell->neighbor(j2))) { /// COMPRESSIBLE: if ( compressible ) { compFlowFactor = fluidBulkModulus*dt*cell->info().invVoidVolume(); m += compFlowFactor*(cell->info().kNorm())[j2] * cell->neighbor(j2)->info().p(); if (j==0) n +=compFlowFactor*(cell->info().kNorm())[j2]; } else { /// INCOMPRESSIBLE m += (cell->info().kNorm())[j2] * cell->neighbor(j2)->info().p(); if ( std::isinf(m) && j<10 ) cout << "(cell->info().kNorm())[j2] = " << (cell->info().kNorm())[j2] << " cell->neighbor(j2)->info().p() = " << cell->neighbor(j2)->info().p() << endl; if (j==0) n += (cell->info().kNorm())[j2]; } } } dp = cell->info().p(); if (n!=0 || j!=0) { if (j==0) { if (compressible) cell->info().invSumK=1/(1+n); else cell->info().invSumK=1/n; } if ( compressible ) { /// COMPRESSIBLE cell->info().p() = ( (previousP - compFlowFactor*cell->info().dv()) + m ) / n ; cell->info().p() = ( ((previousP[bb] - ((fluidBulkModulus*dt*cell->info().invVoidVolume())*(cell->info().dv()))) + m) * cell->info().invSumK - cell->info().p()) * relax + cell->info().p(); } else { /// INCOMPRESSIBLE cell->info().p() = - ( cell->info().dv() - m ) / ( n ) = ( -cell.info().dv() + m ) / n ; cell->info().p() = (- (cell->info().dv() - m) * cell->info().invSumK - cell->info().p()) * relax + cell->info().p(); } #ifdef GS_OPEN_MP #endif } dp -= cell->info().p(); #ifdef GS_OPEN_MP const int tn=omp_get_thread_num(); t_sum_dp[tn] += std::abs(dp); t_dp_max[tn]=max(t_dp_max[tn], std::abs(dp)); t_p_max[tn]= max(t_p_max[tn], std::abs(cell->info().p())); t_sum_p[tn]+= std::abs(cell->info().p()); #else dp_max = max(dp_max, std::abs(dp)); p_max = max(p_max, std::abs(cell->info().p())); sum_p += std::abs(cell->info().p()); sum_dp += std::abs(dp); #endif } } #ifdef GS_OPEN_MP for (int ii=0;ii tolerance /*&& j<4000*/ /*&& ( dp_max > tolerance )*//* &&*/ /*( j<50 )*/); #endif } if (debugOut) {cout << "pmax " << p_max << "; pmoy : " << p_moy << endl; cout << "iteration " << j <<"; erreur : " << dp_max/p_max << endl;} computedOnce=true; } template double FlowBoundingSphere::boundaryFlux(unsigned int boundaryId) { if (noCache && T[!currentTes].Max_id()<=0) return 0; bool tes = noCache?(!currentTes):currentTes; RTriangulation& Tri = T[tes].Triangulation(); double Q1=0; VectorCell tmpCells; tmpCells.resize(10000); VCellIterator cells_it = tmpCells.begin(); VCellIterator cell_up_end = Tri.incident_cells(T[tes].vertexHandles[boundaryId],cells_it); for (VCellIterator it = tmpCells.begin(); it != cell_up_end; it++) { const CellHandle& cell = *it; if (cell->info().isGhost) continue; Q1 -= cell->info().dv(); for (int j2=0; j2<4; j2++) Q1 += (cell->info().kNorm())[j2]* (cell->neighbor(j2)->info().shiftedP()-cell->info().shiftedP()); } return Q1; } template double FlowBoundingSphere::permeameter(double PInf, double PSup, double Section, double DeltaY, const char *file) { RTriangulation& Tri = T[currentTes].Triangulation(); std::ofstream kFile(file, std::ios::out); double Q2=0, Q1=0; int cellQ1=0, cellQ2=0; double p_out_max=-10000000, p_out_min=10000000, p_in_max=-100000000, p_in_min=10000000,p_out_moy=0, p_in_moy=0; VectorCell tmpCells; tmpCells.resize(10000); VCellIterator cells_it = tmpCells.begin(); VCellIterator cell_up_end = Tri.incident_cells(T[currentTes].vertexHandles[yMaxId],cells_it); for (VCellIterator it = tmpCells.begin(); it != cell_up_end; it++) { CellHandle& cell = *it; for (int j2=0; j2<4; j2++) { if (!cell->neighbor(j2)->info().Pcondition){ Q1 = Q1 + (cell->neighbor(j2)->info().kNorm())[Tri.mirror_index(cell, j2)]* (cell->neighbor(j2)->info().p()-cell->info().p()); cellQ1+=1; p_out_max = max(cell->neighbor(j2)->info().p(), p_out_max); p_out_min = min(cell->neighbor(j2)->info().p(), p_out_min); p_out_moy += cell->neighbor(j2)->info().p();} }} VectorCell tmpCells2; tmpCells2.resize(10000); VCellIterator cells_it2 = tmpCells2.begin(); VCellIterator cell_down_end = Tri.incident_cells(T[currentTes].vertexHandles[yMinId],cells_it2); for (VCellIterator it = tmpCells2.begin(); it != cell_down_end; it++) { CellHandle& cell = *it; for (int j2=0; j2<4; j2++){ if (!cell->neighbor(j2)->info().Pcondition){ Q2 = Q2 + (cell->neighbor(j2)->info().kNorm())[Tri.mirror_index(cell, j2)]* (cell->info().p()-cell->neighbor(j2)->info().p()); cellQ2+=1; p_in_max = max(cell->neighbor(j2)->info().p(), p_in_max); p_in_min = min(cell->neighbor(j2)->info().p(), p_in_min); p_in_moy += cell->neighbor(j2)->info().p();} }} double density = 1; double viscosity = viscosity; double gravity = 1; double Vdarcy = Q1/Section; double DeltaP = std::abs(PInf-PSup); double DeltaH = DeltaP/ (density*gravity); double k = viscosity*Vdarcy*DeltaY / DeltaP; /**m²**/ double Ks = k*(density*gravity)/viscosity; /**m/s**/ if (debugOut){ cout << "the maximum superior pressure is = " << p_out_max << " the min is = " << p_out_min << endl; cout << "the maximum inferior pressure is = " << p_in_max << " the min is = " << p_in_min << endl; cout << "superior average pressure is " << p_out_moy/cellQ1 << endl; cout << "inferior average pressure is " << p_in_moy/cellQ2 << endl; cout << "celle comunicanti in basso = " << cellQ2 << endl; cout << "celle comunicanti in alto = " << cellQ1 << endl; cout << "The incoming average flow rate is = " << Q2 << " m^3/s " << endl; cout << "The outgoing average flow rate is = " << Q1 << " m^3/s " << endl; cout << "The gradient of charge is = " << DeltaH/DeltaY << " [-]" << endl; cout << "Darcy's velocity is = " << Vdarcy << " m/s" < void FlowBoundingSphere::displayStatistics() { RTriangulation& Tri = T[currentTes].Triangulation(); int Zero =0, Inside=0, Fictious=0; FiniteCellsIterator cellEnd = Tri.finite_cells_end(); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++) { int zeros =0; for (int j=0; j!=4; j++) { if ((cell->info().kNorm())[j]==0) { zeros+=1; } } if (zeros==4) { Zero+=1; } if (!cell->info().fictious()) { Inside+=1; } else { Fictious+=1; } } int fict=0, real=0; for (FiniteVerticesIterator v = Tri.finite_vertices_begin(); v != Tri.finite_vertices_end(); ++v) { if (v->info().isFictious) fict+=1; else real+=1; } long Vertices = Tri.number_of_vertices(); long Cells = Tri.number_of_finite_cells(); long Facets = Tri.number_of_finite_facets(); if(debugOut) {cout << "zeros = " << Zero << endl; cout << "There are " << Vertices << " vertices, dont " << fict << " fictious et " << real << " reeeeeel" << std::endl; cout << "There are " << Cells << " cells " << std::endl; cout << "There are " << Facets << " facets " << std::endl; cout << "There are " << Inside << " cells INSIDE." << endl; cout << "There are " << Fictious << " cells FICTIOUS." << endl;} num_particles = real; } template void FlowBoundingSphere::saveVtk(const char* folder) { if (noCache && T[!currentTes].Max_id()<=0) {cout<<"Triangulation does not exist. Sorry."<info().isReal() && cell->vertex(0)->info().isReal() && cell->vertex(1)->info().isReal() && cell->vertex(2)->info().isReal() && cell->vertex(3)->info().isReal(); if (!isDrawable) vtkInfiniteCells+=1; } for (FiniteVerticesIterator v = Tri.finite_vertices_begin(); v != Tri.finite_vertices_end(); ++v) { if (!v->info().isReal()) vtkInfiniteVertices+=1; else if (firstReal==-1) firstReal=vtkInfiniteVertices;} basicVTKwritter vtkfile((unsigned int) Tri.number_of_vertices()-vtkInfiniteVertices, (unsigned int) Tri.number_of_finite_cells()-vtkInfiniteCells); vtkfile.open(filename,"test"); //!TEMPORARY FIX: //paraview needs zero-based vertex ids (from 0 ... numRealVertices) //in presence of clumps vertex ids are not zero-based anymore //to fix the vkt output vertex ids will be replaced by zero-based ones (CAUTION: output vertex ids != Yade vertex ids!) map vertexIdMap; int numVertices = 0; unsigned int minId = 1; vtkfile.begin_vertices(); double x,y,z; for (FiniteVerticesIterator v = Tri.finite_vertices_begin(); v != Tri.finite_vertices_end(); ++v) { if (v->info().isReal()) { x = (double)(v->point().point()[0]); y = (double)(v->point().point()[1]); z = (double)(v->point().point()[2]); vtkfile.write_point(x,y,z); vertexIdMap[v->info().id()-firstReal] = numVertices; minId = min(minId,v->info().id()-firstReal); numVertices += 1; } } vtkfile.end_vertices(); vtkfile.begin_cells(); int id0,id1,id2,id3; for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != Tri.finite_cells_end(); ++cell) { bool isDrawable = cell->info().isReal() && cell->vertex(0)->info().isReal() && cell->vertex(1)->info().isReal() && cell->vertex(2)->info().isReal() && cell->vertex(3)->info().isReal(); if (isDrawable) { id0 = cell->vertex(0)->info().id()-firstReal; id1 = cell->vertex(1)->info().id()-firstReal; id2 = cell->vertex(2)->info().id()-firstReal; id3 = cell->vertex(3)->info().id()-firstReal; if (minId != 0) vtkfile.write_cell(vertexIdMap[id0],vertexIdMap[id1],vertexIdMap[id2],vertexIdMap[id3]); else vtkfile.write_cell(id0, id1, id2, id3); } } vtkfile.end_cells(); if (permeabilityMap){ vtkfile.begin_data("Permeability",CELL_DATA,SCALARS,FLOAT); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != Tri.finite_cells_end(); ++cell) { bool isDrawable = cell->info().isReal() && cell->vertex(0)->info().isReal() && cell->vertex(1)->info().isReal() && cell->vertex(2)->info().isReal() && cell->vertex(3)->info().isReal(); if (isDrawable){vtkfile.write_data(cell->info().s);} } vtkfile.end_data();} else{ vtkfile.begin_data("Pressure",CELL_DATA,SCALARS,FLOAT); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != Tri.finite_cells_end(); ++cell) { bool isDrawable = cell->info().isReal() && cell->vertex(0)->info().isReal() && cell->vertex(1)->info().isReal() && cell->vertex(2)->info().isReal() && cell->vertex(3)->info().isReal(); if (isDrawable){vtkfile.write_data(cell->info().p());} } vtkfile.end_data();} if (1){ averageRelativeCellVelocity(); vtkfile.begin_data("Velocity",CELL_DATA,VECTORS,FLOAT); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != Tri.finite_cells_end(); ++cell) { bool isDrawable = cell->info().isReal() && cell->vertex(0)->info().isReal() && cell->vertex(1)->info().isReal() && cell->vertex(2)->info().isReal() && cell->vertex(3)->info().isReal(); if (isDrawable){vtkfile.write_data(cell->info().averageVelocity()[0],cell->info().averageVelocity()[1],cell->info().averageVelocity()[2]);} } vtkfile.end_data();} } #ifdef XVIEW template void FlowBoundingSphere::dessineTriangulation(Vue3D &Vue, RTriangulation &T) { double* Segments = NULL; long N_seg = newListeEdges(T, &Segments); Vue.Dessine_Segment(Segments, N_seg); deleteListeEdges(&Segments, N_seg); } template void FlowBoundingSphere::dessineShortTesselation(Vue3D &Vue, Tesselation &Tes) { if (!Tes.computed()) Tes.compute(); double* Segments = NULL; long N_seg = Tes.newListeShortEdges(&Segments); Vue.Dessine_Segment(Segments, N_seg); deleteListeEdges(&Segments, N_seg); } #endif template void FlowBoundingSphere::generateVoxelFile( ) { RTriangulation& Tri = T[currentTes].Triangulation(); double l = 1; int dx = 200; double eps = l/dx; std::ofstream voxelfile("MATRIX",std::ios::out); bool solid=false; for (double y=0; y<=l; y+=eps) { for (double z=0; z<=l; z+=eps) { for (double x=0; x<=l; x+=eps) { solid=false; for (FiniteVerticesIterator vIt = Tri.finite_vertices_begin(); vIt != Tri.finite_vertices_end(); vIt++) { double radius = sqrt(vIt->point().weight()); if ((sqrt(pow((x- (vIt->point()[0])),2) +pow((y- (vIt->point()[1])),2) +pow((z- (vIt->point()[2])),2))) <= radius) solid=true; } if (solid) voxelfile << 1; else voxelfile << 0; } voxelfile << endl; } } } template double FlowBoundingSphere::samplePermeability(double& xMin,double& xMax ,double& yMin,double& yMax,double& zMin,double& zMax/*, string key*/) { double Section = (xMax-xMin) * (zMax-zMin); double DeltaY = yMax-yMin; boundary(yMinId).flowCondition=0; boundary(yMaxId).flowCondition=0; boundary(yMinId).value=0; boundary(yMaxId).value=1; double pZero = std::abs((boundary(yMinId).value-boundary(yMaxId).value)/2); initializePressure( pZero ); gaussSeidel(); const char *kk = "Permeability"; return permeameter(boundary(yMinId).value, boundary(yMaxId).value, Section, DeltaY, kk); } template bool FlowBoundingSphere::isInsideSphere(double& x, double& y, double& z) { RTriangulation& Tri = T[currentTes].Triangulation(); for (FiniteVerticesIterator vIt = Tri.finite_vertices_begin(); vIt != Tri.finite_vertices_end(); vIt++) { double radius = vIt->point().weight(); if (pow((x- (vIt->point()[0])),2) +pow((y- (vIt->point()[1])),2) +pow((z- (vIt->point()[2])),2) <= radius) return true; } return false; } template void FlowBoundingSphere::sliceField(const char *filename) { /** Pressure field along one cutting plane **/ RTriangulation& Tri = T[noCache?(!currentTes):currentTes].Triangulation(); CellHandle permeameter; std::ofstream consFile(filename,std::ios::out); int intervals = 400; double Ry = (yMax-yMin) /intervals; double Rz = (zMax-zMin) /intervals; double X=0.5; for (double Y=min(yMax,yMin); Y<=max(yMax,yMin); Y=Y+std::abs(Ry)) { for (double Z=min(zMin,zMax); Z<=max(zMin,zMax); Z=Z+std::abs(Rz)) { permeameter = Tri.locate(Point(X, Y, Z)); consFile << permeameter->info().p() <<" "; } consFile << endl;} consFile << endl; consFile.close(); } template void FlowBoundingSphere::computeEdgesSurfaces() { RTriangulation& Tri = T[currentTes].Triangulation(); //first, copy interacting pairs and normal lub forces form prev. triangulation in a sorted structure for initializing the new lub. Forces vector > > lubPairs; lubPairs.resize(Tri.number_of_vertices()+1); for (unsigned int k=0; kid(),edgeIds[k].second->id())].push_back( pair (max(edgeIds[k].first->id(),edgeIds[k].second->id()),edgeNormalLubF[k])); //Now we reset the containers and initialize them edgeSurfaces.clear(); edgeIds.clear(); edgeNormalLubF.clear(); FiniteEdgesIterator ed_it; for ( FiniteEdgesIterator ed_it = Tri.finite_edges_begin(); ed_it!=Tri.finite_edges_end();ed_it++ ) { const VertexInfo& vi1=(ed_it->first)->vertex(ed_it->second)->info(); const VertexInfo& vi2=(ed_it->first)->vertex(ed_it->third)->info(); //We eliminate edges that would be periodic replications or involving two bounding objects, i.e. the min id must be non-ghost and non-fictious if (vi1.id()(&vi1,&vi2)); //For persistant edges, we must transfer the lub. force value from the older triangulation structure if (id1>id2) swap(id1,id2); unsigned int i=0; //Look for the pair (id1,id2) in lubPairs while (i Vector3r FlowBoundingSphere::computeViscousShearForce(const Vector3r& deltaV, const int& edge_id, const Real& Rh) { Vector3r tau = deltaV*viscosity/Rh; return tau * edgeSurfaces[edge_id]; } template Vector3r FlowBoundingSphere::computeShearLubricationForce(const Vector3r& deltaShearV, const Real& dist, const int& edge_id, const Real& eps, const Real& centerDist, const Real& meanRad ) { Real d = max(dist,0.) + 2.*eps*meanRad; Vector3r viscLubF = 0.5 * Mathr::PI * viscosity * (-2*meanRad + centerDist*log(centerDist/d)) * deltaShearV; return viscLubF; } template Vector3r FlowBoundingSphere::computePumpTorque(const Vector3r& deltaShearAngV, const Real& dist, const int& edge_id, const Real& eps, const Real& meanRad ) { Real d = max(dist,0.) + 2.*eps*meanRad; Vector3r viscPumpC = Mathr::PI * viscosity * pow(meanRad,3) *(3./20. * log(meanRad/d) + 63./500. * (d/meanRad) * log(meanRad/d)) * deltaShearAngV; return viscPumpC; } template Vector3r FlowBoundingSphere::computeTwistTorque(const Vector3r& deltaNormAngV, const Real& dist, const int& edge_id, const Real& eps, const Real& meanRad ) { Real d = max(dist,0.) + 2.*eps*meanRad; Vector3r twistC = Mathr::PI * viscosity * pow(meanRad,2) * d * log(meanRad/d) * deltaNormAngV; return twistC; } template Real FlowBoundingSphere::computeNormalLubricationForce(const Real& deltaNormV, const Real& dist, const int& edge_id, const Real& eps, const Real& stiffness, const Real& dt, const Real& meanRad) { //FIXME: here introduce elasticity Real d = max(dist,0.) + 2.*eps*meanRad;//account for grains roughness if (stiffness>0) { const Real k = stiffness*meanRad; Real prevForce = edgeNormalLubF[edge_id]; Real instantVisc = 1.5*Mathr::PI*pow(meanRad,2)*viscosity/(d-prevForce/k); Real normLubF = instantVisc*(deltaNormV + prevForce/(k*dt))/(1+instantVisc/(k*dt)); edgeNormalLubF[edge_id]=normLubF; return normLubF; } else { Real normLubF = (1.5*Mathr::PI*pow(meanRad,2)* viscosity* deltaNormV)/d; return normLubF; } } } //namespace CGT #endif //FLOW_ENGINE trunk-2017.01a/lib/triangulation/FlowBoundingSphereLinSolv.hpp000066400000000000000000000127451304022710500244050ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2010 by Bruno Chareyre * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef FLOW_ENGINE #pragma once #define EIGENSPARSE_LIB //comment this if CHOLMOD is not available // #define TAUCS_LIB //comment this if TAUCS lib is not available, it will disable PARDISO lib as well #ifdef EIGENSPARSE_LIB #include #include #include #endif #ifdef TAUCS_LIB #define TAUCS_CORE_DOUBLE #include //THIS ONE MUST ABSOLUTELY BE INCLUDED BEFORE TAUCS.H! #include #include extern "C" { #include "taucs.h" } #endif #include "FlowBoundingSphere.hpp" ///_____ Declaration ____ namespace CGT { template > class FlowBoundingSphereLinSolv : public FlowType { public: DECLARE_TESSELATION_TYPES(FlowType) typedef typename FlowType::Tesselation Tesselation; using FlowType::useSolver; using FlowType::T; using FlowType::currentTes; using FlowType::boundary; using FlowType::yMinId; using FlowType::yMaxId; using FlowType::debugOut; using FlowType::tolerance; using FlowType::relax; using FlowType::fluidBulkModulus; using FlowType::reApplyBoundaryConditions; using FlowType::pressureChanged; using FlowType::computedOnce; using FlowType::resetNetwork; using FlowType::tesselation; using FlowType::resetRHS; //! TAUCS DECs vector orderedCells; bool isLinearSystemSet; bool isFullLinearSystemGSSet; bool areCellsOrdered;//true when orderedCells is filled, turn it false after retriangulation bool updatedRHS; #ifdef EIGENSPARSE_LIB //Eigen's sparse matrix and solver Eigen::SparseMatrix A; typedef Eigen::Triplet ETriplet; std::vector tripletList;//The list of non-zero components in Eigen sparse matrix Eigen::CholmodDecomposition, Eigen::Lower > eSolver; bool factorizedEigenSolver; void exportMatrix(const char* filename) {ofstream f; f.open(filename); f<::InnerIterator it(A,k); it; ++it) f<< it.row()<<" "<< it.col()<<" "< T_an;//(size*5); vector T_jn;//(size+1); vector T_ia;//(size*5); vector T_f;//(size); // right-hand size vector object vector T_cells;//(size) int T_index; vector T_b; vector T_bv; vector T_x, P_x; vector bodv; vector xodv; int* perm; int* invperm; bool pardisoInitialized; //! END TAUCS DECs //! Pardiso int* ia; int* ja; double* a; int nnz; int mtype; /* Real symmetric positive def. matrix */ double* b; double* x;// the unknown vector to solve Ax=b int nrhs; /* Number of right hand sides. */ void *pt[64]; int iparm[64]; double dparm[64]; int maxfct, mnum, phase, error, msglvl, solver; int num_procs; char *var; int i; double ddum; /* Double dummy */ int idum; /* Integer dummy. */ //! end pardiso /// EXTERNAL_GS part vector > fullAvalues;//contains Kij's and 1/(sum Kij) in 5th value (for use in GuaussSeidel) vector > fullAcolumns;//contains columns numbers vector gsP;//a vector of pressures vector gsdV;//a vector of dV vector gsB;//a vector of dV public: virtual ~FlowBoundingSphereLinSolv(); FlowBoundingSphereLinSolv(); ///Linear system solve virtual int setLinearSystem(Real dt); void vectorizedGaussSeidel(Real dt); virtual int setLinearSystemFullGS(Real dt); int taucsSolveTest(); int taucsSolve(Real dt); int pardisoSolveTest(); int pardisoSolve(Real dt); int eigenSolve(Real dt); void copyGsToCells(); void copyCellsToGs(Real dt); void copyLinToCells(); void copyCellsToLin(Real dt); void swapFwd (double* v, int i); void swapFwd (int* v, int i); void sortV(int k1, int k2, int* is, double* ds); virtual void gaussSeidel (Real dt) { switch (useSolver) { case 0: vectorizedGaussSeidel(dt); break; case 1: taucsSolve(dt); break; case 2: pardisoSolve(dt); break; case 3: eigenSolve(dt); break; } computedOnce=true; } virtual void resetLinearSystem(); virtual void resetRHS() {updatedRHS=false;}; }; } //namespace CGT ///_____ Implementation ____ #include "FlowBoundingSphereLinSolv.ipp" #endif trunk-2017.01a/lib/triangulation/FlowBoundingSphereLinSolv.ipp000066400000000000000000001033551304022710500244040ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2010 by Bruno Chareyre * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef FLOW_ENGINE // #define XVIEW #include "FlowBoundingSphereLinSolv.hpp"//include after #define XVIEW #include "CGAL/constructions/constructions_on_weighted_points_cartesian_3.h" #include #include #include #include #include #include "vector" #include #include #include #ifdef XVIEW //#include "Vue3D.h" //FIXME implicit dependencies will look for this class (out of tree) even ifndef XVIEW #endif #ifdef YADE_OPENMP #include // #define GS_OPEN_MP //It should never be defined if Yade is not using openmp #endif // #define PARDISO //comment this if pardiso lib is not available #ifdef EIGENSPARSE_LIB extern "C" { void openblas_set_num_threads(int num_threads); } #endif namespace CGT { #ifdef PARDISO #ifdef AIX #define F77_FUNC(func) func #else #define F77_FUNC(func) func ## _ #endif /* PARDISO prototype. */ extern "C" int F77_FUNC(pardisoinit) (void *, int *, int *, int *, double *, int *); extern "C" int F77_FUNC(pardiso) (void *, int *, int *, int *, int *, int *, double *, int *, int *, int *, int *, int *, int *, double *, double *, int *, double *); #endif #ifdef XVIEW Vue3D Vue1; #endif template FlowBoundingSphereLinSolv<_Tesselation,FlowType>::~FlowBoundingSphereLinSolv() { #ifdef TAUCS_LIB if (Fccs) taucs_ccs_free(Fccs); #endif } template FlowBoundingSphereLinSolv<_Tesselation,FlowType>::FlowBoundingSphereLinSolv(): FlowType() { useSolver=0; isLinearSystemSet=0; isFullLinearSystemGSSet=0; areCellsOrdered=0;//true when orderedCells is filled, turn it false after retriangulation updatedRHS=false; ZERO=0; #ifdef TAUCS_LIB T_A = &SystemMatrix; F = NULL;//The taucs factor Fccs = NULL;//The taucs factor in CCS format #endif pardisoInitialized=false; pTimeInt=0;pTime1N=0;pTime2N=0; pTime1=0;pTime2=0; #ifdef EIGENSPARSE_LIB factorizedEigenSolver=false; numFactorizeThreads=1; numSolveThreads=1; #endif } template void FlowBoundingSphereLinSolv<_Tesselation,FlowType>::swapFwd (double* v, int i) {double temp = v[i]; v[i]=v[i+1]; v[i+1]=temp;} template void FlowBoundingSphereLinSolv<_Tesselation,FlowType>::swapFwd (int* v, int i) {double temp = v[i]; v[i]=v[i+1]; v[i+1]=temp;} //spatial sort traits to use with a pair of CGAL::sphere pointers and integer. //template // usage : spatial_sort(pointsPtrs.begin(),pointsPtrs.end(), RTraits_for_spatial_sort()/*, CGT::RTriangulation::Weighted_point*/); #include template struct CellTraits_for_spatial_sort : public Triangulation::Geom_traits { typedef typename Triangulation::Geom_traits Gt; typedef const typename Triangulation::Finite_cells_iterator Point_3; struct Less_x_3 {bool operator()(const Point_3& p,const Point_3& q) const { return typename Gt::Less_x_3()(p->info(),q->info());} }; struct Less_y_3 {bool operator()(const Point_3& p,const Point_3& q) const { return typename Gt::Less_y_3()(p->info(),q->info());} }; struct Less_z_3 {bool operator()(const Point_3& p,const Point_3& q) const { return typename Gt::Less_z_3()(p->info(),q->info());} }; Less_x_3 less_x_3_object() const {return Less_x_3();} Less_y_3 less_y_3_object() const {return Less_y_3();} Less_z_3 less_z_3_object() const {return Less_z_3();} }; template void FlowBoundingSphereLinSolv<_Tesselation,FlowType>::resetLinearSystem() { FlowType::resetLinearSystem(); isLinearSystemSet=false; isFullLinearSystemGSSet=false; areCellsOrdered=false; #ifdef TAUCS_LIB if (F) taucs_supernodal_factor_free(F); F=NULL; if (Fccs) taucs_ccs_free(Fccs); Fccs=NULL; #endif #ifdef EIGENSPARSE_LIB factorizedEigenSolver=false; #endif #ifdef PARDISO if (pardisoInitialized) { phase = -1; F77_FUNC(pardiso)(pt, &maxfct, &mnum, &mtype, &phase, &ncols, &ddum, NULL, NULL, &idum, &nrhs, iparm, &msglvl, &ddum, &ddum, &error, dparm); pardisoInitialized=false; } #endif } template int FlowBoundingSphereLinSolv<_Tesselation,FlowType>::setLinearSystem(Real dt) { RTriangulation& Tri = T[currentTes].Triangulation(); int n_cells=Tri.number_of_finite_cells(); vector clen; vector is; vector js; vector vs; if (!areCellsOrdered) { T_nnz=0; ncols=0; ///Ordered cells orderedCells.clear(); const FiniteCellsIterator cellEnd = Tri.finite_cells_end(); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++) { orderedCells.push_back(cell); cell->info().index=0; if (!cell->info().Pcondition && !cell->info().blocked) ++ncols;} // //Segfault on 14.10, and useless overall since SuiteSparse has preconditionners (including metis) // spatial_sort(orderedCells.begin(),orderedCells.end(), CellTraits_for_spatial_sort()); T_cells.clear(); T_index=0; isLinearSystemSet=false; areCellsOrdered=true; } if (!isLinearSystemSet) { #ifdef TAUCS_LIB if (Fccs) taucs_ccs_free(Fccs);//delete the old factor #endif int n = 3*(ncols+1);//number of non-zero in triangular matrix is.resize(n); js.resize(n); vs.resize(n); T_x.resize(ncols); T_b.resize(ncols); T_bv.resize(ncols); bodv.resize(ncols); xodv.resize(ncols); // gsB.resize(ncols+1); T_cells.resize(ncols+1); T_nnz=0;} for (int kk=0; kkinfo().Pcondition && !cell->info().blocked) { index=cell->info().index; if (index==0) { T_cells[++T_index]=cell; cell->info().index=index=T_index; } if (!isLinearSystemSet) { //Add diagonal term is[T_nnz] = index; js[T_nnz] = index; vs[T_nnz]=0; for (int j=0;j<4;j++) if (!cell->neighbor(j)->info().blocked) vs[T_nnz]+= (cell->info().kNorm())[j]; // vs[T_nnz] = (cell->info().kNorm())[0]+ (cell->info().kNorm())[1]+ (cell->info().kNorm())[2]+ (cell->info().kNorm())[3]; if (fluidBulkModulus>0) vs[T_nnz] += (1.f/(dt*fluidBulkModulus*cell->info().invVoidVolume())); ++T_nnz; } for (int j=0; j<4; j++) { neighbourCell = cell->neighbor(j); nIndex=neighbourCell->info().index; if (Tri.is_infinite(neighbourCell)) continue; if (!isLinearSystemSet && !(neighbourCell->info().Pcondition || neighbourCell->info().blocked)) { if (nIndex==0) { T_cells[++T_index]=neighbourCell; neighbourCell->info().index=nIndex=T_index; } else if (index > nIndex) { is[T_nnz] = index; js[T_nnz] = nIndex; vs[T_nnz] = - (cell->info().kNorm())[j]; T_nnz++; } } else if (neighbourCell->info().Pcondition && !neighbourCell->info().blocked) { //ADD TO b, FIXME : use updated volume change T_b[index-1]+=cell->info().kNorm()[j]*neighbourCell->info().p(); } } } } updatedRHS = true; if (!isLinearSystemSet) { if (useSolver==1 || useSolver==2){ #ifdef TAUCS_LIB clen.resize(ncols+1); T_jn.resize(ncols+1); T_A->colptr = &T_jn[0]; T_ia.resize(T_nnz); T_A->rowind = &T_ia[0]; T_A->flags = (TAUCS_DOUBLE | TAUCS_SYMMETRIC | TAUCS_LOWER); T_an.resize(T_nnz); T_A->values.d = &T_an[0]; T_A->n = ncols; T_A->m = ncols; int i,j,k; for (j=0; jcolptr[j]) = k; k += tmp; } clen[ncols] = (T_A->colptr[ncols]) = k; /* now read matrix into data structure */ for (k=0; ktaucs_values)[clen[j]] = vs[k]; (T_A->rowind)[clen[j]] = i; clen[j] ++; // cerr<<"i="<< i <<" j="<< j<<" v="<()); // double pZero=0; // if (yMinId>=0 and yMaxId>yMinId) pZero = abs((boundary(yMinId).value-boundary(yMaxId).value)/2); gsP.resize(ncols+1); // _gsP.resize(ncols+1); gsB.resize(ncols+1); T_b.resize(ncols+1); gsdV.resize(ncols+1); fullAcolumns.resize(ncols+1); fullAvalues.resize(ncols+1); T_cells.resize(ncols+1); for (int k=0; k<=ncols;k++) { fullAcolumns[k].resize(4); fullAvalues[k].resize(5); gsdV[k]=0; // gsP[k]=pZero; } // _gsP[0]= &ZERO; gsP[0]=0; areCellsOrdered=true; isFullLinearSystemGSSet=false; } for (int k=0; k<=ncols;k++) gsB[k]=0; ///we build the full matrix + RHS here, else only the RHS in the other loop if (!isFullLinearSystemGSSet) ///Ordered cells for (int i=0; iinfo().Pcondition && !cell->info().blocked) { if (cell->info().index==0) { T_cells[++T_index]=cell; cell->info().index=T_index; } gsP[cell->info().index]=cell->info().pression; //Add diagonal term double num = (cell->info().kNorm())[0]+ (cell->info().kNorm())[1]+ (cell->info().kNorm())[2]+ (cell->info().kNorm())[3]; if (fluidBulkModulus>0) num += (1.f/(dt*fluidBulkModulus*cell->info().invVoidVolume())); fullAvalues[cell->info().index][4] = 1.f/num; ++T_nnz; for (int j=0; j<4; j++) { CellHandle neighbourCell = cell->neighbor(j); if (Tri.is_infinite(neighbourCell)) { fullAvalues[cell->info().index][j] = 0; fullAcolumns[cell->info().index][j] = &gsP[0]; continue;} if (!neighbourCell->info().Pcondition) { if (neighbourCell->info().index==0) { T_cells[++T_index]=neighbourCell; neighbourCell->info().index=T_index; } ++T_nnz; fullAvalues[cell->info().index][j] = (cell->info().kNorm())[j]; fullAcolumns[cell->info().index][j] = &gsP[neighbourCell->info().index]; } else { fullAvalues[cell->info().index][j] = 0; fullAcolumns[cell->info().index][j] = &gsP[0]; gsB[cell->info().index]+=cell->info().kNorm()[j]*neighbourCell->info().p(); } } } } ///define only the new RHS, accouting for new imposed pressures else ///Ordered cells for (int i=0; iinfo().Pcondition && !cell->info().blocked) for (int j=0; j<4; j++) { CellHandle neighbourCell = cell->neighbor(j); if (!Tri.is_infinite(neighbourCell) && neighbourCell->info().Pcondition) gsB[cell->info().index]+=cell->info().kNorm()[j]*neighbourCell->info().p(); } } isFullLinearSystemGSSet=true; return ncols; } template void FlowBoundingSphereLinSolv<_Tesselation,FlowType>::vectorizedGaussSeidel(Real dt) { // cout<<"VectorizedGaussSeidel"< t_sum_p, t_dp_max, t_sum_dp, t_p_max; t_sum_dp.resize(num_threads); t_dp_max.resize(num_threads); t_p_max.resize(num_threads); t_sum_p.resize(num_threads); #endif int j2=-1; dp_max = 0; p_max = 0; p_moy=0; dp_moy=0; sum_p=0; sum_dp=0; do { if (++j2>=10) j2=0;//compute max/mean only each 10 iterations if (j2==0) { dp_max = 0; p_max = 0; p_moy=0; dp_moy=0; sum_p=0; sum_dp=0; #ifdef GS_OPEN_MP for (int ii=0;ii void FlowBoundingSphereLinSolv<_Tesselation,FlowType>::sortV(int k1, int k2, int* is, double* ds){ for (int k=k1; k=k1 && is[kk]>is[kk+1]) { swapFwd(is,kk); swapFwd(ds,kk); --kk;} } } template int FlowBoundingSphereLinSolv<_Tesselation,FlowType>::eigenSolve(Real dt) { #ifdef EIGENSPARSE_LIB if (!isLinearSystemSet || (isLinearSystemSet && reApplyBoundaryConditions()) || !updatedRHS) ncols = setLinearSystem(dt); copyCellsToLin(dt); //FIXME: we introduce new Eigen vectors, then we have to copy from/to c-arrays, can be optimized later Eigen::VectorXd eb(ncols); Eigen::VectorXd ex(ncols); for (int k=0; k0) { cerr << "something went wrong in Cholesky factorization, use LDLt as fallback this time" << eSolver.cholmod().status << endl; eSolver.setMode(Eigen::CholmodLDLt); eSolver.compute(A); } factorizedEigenSolver = true; } openblas_set_num_threads(numSolveThreads); ex = eSolver.solve(eb); for (int k=0; k int FlowBoundingSphereLinSolv<_Tesselation,FlowType>::taucsSolve(Real dt) { #ifdef TAUCS_LIB if (debugOut) cerr <LinSolver) : " << taucs_ctime()-t << endl; t = taucs_ctime(); //taucs_logfile("stdout");//! VERY USEFULL!!!!!!!!!!! (disable to exclude output time from taucs_ctime() measurments) taucs_double* x = &T_x[0];// the unknown vector to solve Ax=b taucs_double* bod = &bodv[0]; taucs_double* xod = &xodv[0]; if (Fccs==NULL) { if (debugOut) cerr << "_entering taucs_" << endl; // 1) Reordering taucs_ccs_order(T_A, &perm, &invperm, (char*)"metis"); if (debugOut) cerr << "_entering taucs_" << endl; taucs_ccs_matrix* Aod; if (debugOut) cerr << "_entering taucs_" << endl; Aod = taucs_ccs_permute_symmetrically(T_A, perm, invperm); if (debugOut) cerr << "Reordering : " << taucs_ctime()-t << endl; t = taucs_ctime(); // 2) Factoring F = taucs_ccs_factor_llt_mf(Aod); if (F==NULL) cerr<<"factorization failed"<Yade) : " << taucs_ctime()-t << endl; if (debugOut) cerr << "Total TAUCS time ................ : " << taucs_ctime()-t2 << endl; #else cerr<<"Flow engine not compiled with taucs, nothing computed if useSolver=1"< int FlowBoundingSphereLinSolv<_Tesselation,FlowType>::pardisoSolve(Real dt) { cerr <colptr; ja = T_A->rowind; a = T_A->values.d; if (debugOut) cerr<99) { cout <<"Pardiso..... "< int FlowBoundingSphereLinSolv<_Tesselation,FlowType>::pardisoSolveTest() { #ifndef PARDISO return 0; #else /* Matrix data. */ double t = taucs_ctime();//timer bool wasLSystemSet= isLinearSystemSet; int n = setLinearSystem(); // ncols=n;//for VectorizesGS cout<colptr; int* ja = T_A->rowind; double* a = T_A->values.d; if (!wasLSystemSet) for (int k=0; k int FlowBoundingSphereLinSolv<_Tesselation,FlowType>::taucsSolveTest() { #ifdef TAUCS_LIB cout < bodv(ncols); taucs_double* bod = &*bodv.begin(); vector xodv(ncols); taucs_double* xod = &*xodv.begin(); int* perm; int* invperm; taucs_ccs_matrix* Aod; t = taucs_ctime(); double t2 = taucs_ctime(); // 1) Reordering taucs_ccs_order(T_A, &perm, &invperm, "metis"); Aod = taucs_ccs_permute_symmetrically(T_A, perm, invperm); taucs_vec_permute(ncols, TAUCS_DOUBLE, &T_b[0], bod, perm); cout << "Reordering : " << taucs_ctime()-t << endl; t = taucs_ctime(); // 2) Factoring F = taucs_ccs_factor_llt_mf(Aod); //F = taucs_ccs_factor_llt_mf(T_A); cout << "Factoring : " << taucs_ctime()-t << endl; t = taucs_ctime(); // 3) Back substitution and reodering the solution back double t4 = taucs_ctime(); // for (int k=0;k<10;k++){ taucs_supernodal_solve_llt(F, xod, bod); // cout << "B3) Solving : " << taucs_ctime()-t << endl; t = taucs_ctime(); taucs_vec_ipermute(ncols, TAUCS_DOUBLE, xod, x, perm); // cout << "B4) Deordering : " << taucs_ctime()-t << endl; t = taucs_ctime(); // } double T4=taucs_ctime()-t4; cout << "Solving : " << T4 << endl; cout << "Low level reordered total time : " << taucs_ctime()-t2 << endl; t2 = taucs_ctime(); taucs_supernodal_factor_free(F); taucs_ccs_free(Aod); /// Using TAUCS inverse factoring // t = taucs_ctime(); t2 = taucs_ctime(); // F=taucs_ccs_factor_xxt(Aod); // cout << "C1_) inverse factoring (reordered) : " << taucs_ctime()-t << endl; t = taucs_ctime(); // taucs_ccs_solve_xxt (F,xod,bod);///REALLY TOO SLOW!! // cout << "C2) solve : " << taucs_ctime()-t << endl; t = taucs_ctime(); // taucs_vec_ipermute(ncols, TAUCS_DOUBLE, xod, x, perm); // cout << "C3) reordering : " << taucs_ctime()-t << endl; t = taucs_ctime(); // cout << "Inverse factoring total time : " << taucs_ctime()-t2 << endl; // taucs_linsolve(NULL, &F, 0, NULL, NULL, NULL, NULL); // taucs_ccs_free(Aod); // ofstream file("result.dat"); // if (!file.is_open()) cout << "problem opening file"; // for (unsigned i = 0; i < M ; i++) { // for (unsigned j = 0; j < L ; j++) file << i << " "<< j << " "<< x[index(i,j)] << endl; // file << endl << endl; // } // const FiniteCellsIterator cell_end = T[currentTes].Triangulation().finite_cells_end(); // if (debugOut) for (FiniteCellsIterator cell = T[currentTes].Triangulation().finite_cells_begin(); cell != cell_end; cell++) // { // // if (cell->info().index>0) { // cerr <<"ix "<< cell->info().index<<" "; // cerr <info().p()<<" "<info().index]<<" "<info().index-1)] <<" "<info().index-1)]<<" err="<<100*(cell->info().p()-x[max((unsigned int)0,cell->info().index-1)])/x[max((unsigned int)0,cell->info().index-1)]<<"%"<info().index==0) { // cerr <<"ix "<< cell->info().index<<" "; // cerr <info().p()<<" "<<"NaN"< #include "basicVTKwritter.hpp" //#include namespace CGT { int n_debug = 0; std::string _itoa(int i) { std::ostringstream buffer; buffer << i; return buffer.str(); } KinematicLocalisationAnalyser::KinematicLocalisationAnalyser() { sphere_discretisation = SPHERE_DISCRETISATION; linear_discretisation = LINEAR_DISCRETISATION; consecutive = false; bz2=true; TS1=new TriaxialState; TS0=new TriaxialState; } KinematicLocalisationAnalyser::~KinematicLocalisationAnalyser() { delete(TS1); delete(TS0); } KinematicLocalisationAnalyser::KinematicLocalisationAnalyser(const char* state_file1, bool usebz2) { sphere_discretisation = SPHERE_DISCRETISATION; linear_discretisation = LINEAR_DISCRETISATION; consecutive = false; bz2=true; TS1 = new(TriaxialState); TS0 = NULL; TS1->from_file(state_file1,/*use bz2?*/ bz2); } KinematicLocalisationAnalyser::KinematicLocalisationAnalyser(const char* state_file1, const char* state_file0, bool consecutive_files, bool usebz2) { consecutive = consecutive_files; bz2 = usebz2; sphere_discretisation = SPHERE_DISCRETISATION; linear_discretisation = LINEAR_DISCRETISATION; TS1 = new(TriaxialState); TS0 = new(TriaxialState); TS1->from_file(state_file1,/*use bz2?*/ bz2); TS0->from_file(state_file0,/*use bz2?*/ bz2); Delta_epsilon(3,3) = TS1->eps3 - TS0->eps3; Delta_epsilon(1,1) = TS1->eps1 - TS0->eps1; Delta_epsilon(2,2) = TS1->eps2 - TS0->eps2; } const vector& KinematicLocalisationAnalyser::computeParticlesDeformation(const char* state_file1, const char* state_file0, bool usebz2) { consecutive = false; bz2 = usebz2; TS1->from_file(state_file1,/*use bz2?*/ bz2); TS0->from_file(state_file0,/*use bz2?*/ bz2); //FIXME: redundant? Delta_epsilon(3,3) = TS1->eps3 - TS0->eps3; Delta_epsilon(1,1) = TS1->eps1 - TS0->eps1; Delta_epsilon(2,2) = TS1->eps2 - TS0->eps2; return computeParticlesDeformation(); } KinematicLocalisationAnalyser::KinematicLocalisationAnalyser(const char* base_name, int n0, int n1, bool usebz2) { file_number_1 = n1; file_number_0 = n0; base_file_name = string(base_name); consecutive = ((n1-n0)==1); bz2 = usebz2; sphere_discretisation = SPHERE_DISCRETISATION; linear_discretisation = LINEAR_DISCRETISATION; TS1 = new(TriaxialState); TS0 = new(TriaxialState); std::ostringstream file_name1, file_name0; file_name1 << (string)(base_file_name) << n1; file_name0 << (string)(base_file_name) << n0; TS1->from_file(file_name1.str().c_str(), bz2); TS0->from_file(file_name0.str().c_str(), bz2); Delta_epsilon(3,3) = TS1->eps3 - TS0->eps3; Delta_epsilon(1,1) = TS1->eps1 - TS0->eps1; Delta_epsilon(2,2) = TS1->eps2 - TS0->eps2; } void KinematicLocalisationAnalyser::SetBaseFileName(string name) { base_file_name = name; } bool KinematicLocalisationAnalyser::SetFileNumbers(int n0, int n1) { bool bf0 = false; bool bf1 = false; if (file_number_0 != n0) { if (file_number_1 != n0) { //file_name = base_file_name + n0; bf0 = TS0->from_file((base_file_name +_itoa(file_number_0)).c_str(), bz2); } else { delete(TS0); TS0 = TS1; bf0=true; TS1 = new(TriaxialState); //file_name = base_file_name + string(n1); bf1 = TS1->from_file((base_file_name + _itoa(file_number_1)).c_str(), bz2); } } else if (n1 != file_number_1) { //file_name = base_file_name + string(n1); bf0 = true; bf1 = TS1->from_file((base_file_name + _itoa(file_number_1)).c_str(), bz2);} file_number_1 = n1; file_number_0 = n0; consecutive = ((n1-n0) ==1); Delta_epsilon(3,3) = TS1->eps3 - TS0->eps3; Delta_epsilon(1,1) = TS1->eps1 - TS0->eps1; Delta_epsilon(2,2) = TS1->eps2 - TS0->eps2; return (bf0 && bf1); } void KinematicLocalisationAnalyser::SetConsecutive(bool t) { consecutive = t; } void KinematicLocalisationAnalyser::SetNO_ZERO_ID(bool t) { TS0->NO_ZERO_ID = t; TS1->NO_ZERO_ID = t; } void KinematicLocalisationAnalyser::SwitchStates(void) { TriaxialState* TStemp = TS0; TS0 = TS1; TS1 = TStemp; } vector& KinematicLocalisationAnalyser::Oriented_Filtered_edges(Real Nymin, Real Nymax, vector& filteredList) { RTriangulation& T = TS1->tesselation().Triangulation(); filteredList.clear(); Edge_iterator ed_end = T.edges_end(); for (Edge_iterator ed_it = T.edges_begin(); ed_it != ed_end; ++ed_it) { if (!T.is_infinite(*ed_it) && TS1->inside(T.segment(*ed_it).source()) && TS1->inside(T.segment(*ed_it).target())) { Segment s = T.segment(*ed_it); CVector v = s.to_vector(); Real ny = std::abs(v.y()/sqrt(s.squared_length())); if (Nymin < ny && ny <= Nymax) filteredList.push_back(ed_it); } } return filteredList; } bool KinematicLocalisationAnalyser::DefToFile(const char* state_file1, const char* state_file0, const char* output_file_name, bool usebz2) { consecutive = false; bz2 = usebz2; TS1->from_file(state_file1,/*use bz2?*/ bz2); TS0->from_file(state_file0,/*use bz2?*/ bz2); DefToFile(output_file_name); return 0; } bool KinematicLocalisationAnalyser::DefToFile(const char* output_file_name) { computeParticlesDeformation(); Tesselation& Tes = TS1->tesselation(); RTriangulation& Tri = Tes.Triangulation(); basicVTKwritter vtk(n_real_vertices, n_real_cells); vtk.open(output_file_name, "Output file generated by Yade's KinematicLocalisationAnalyser"); vtk.begin_vertices(); RTriangulation::Finite_vertices_iterator V_it = Tri.finite_vertices_begin(); bool beginWithFictious = V_it->info().isFictious; for (; V_it != Tri.finite_vertices_end(); ++V_it) if (!V_it->info().isFictious) vtk.file << V_it->point().point() << endl; vtk.end_vertices(); vtk.begin_cells(); Finite_cells_iterator cell = Tri.finite_cells_begin(); //FIXME : Preconditions : the fictious bounds are first in the list for (; cell != Tri.finite_cells_end(); ++cell) { if (!cell->info().isFictious) vtk.write_cell( cell->vertex(0)->info().id()- (beginWithFictious?n_fictious_vertices:0), cell->vertex(1)->info().id()- (beginWithFictious?n_fictious_vertices:0), cell->vertex(2)->info().id()- (beginWithFictious?n_fictious_vertices:0), cell->vertex(3)->info().id()- (beginWithFictious?n_fictious_vertices:0) ); } vtk.end_cells(); vtk.begin_data("Strain_matrix", POINT_DATA, TENSORS, FLOAT); V_it = Tri.finite_vertices_begin(); for (; V_it != Tri.finite_vertices_end(); ++V_it) { if (!V_it->info().isFictious) { Tenseur_sym3 epsilon(ParticleDeformation[V_it->info().id()]); vtk.file << ParticleDeformation[V_it->info().id()] << endl;} } vtk.end_data(); vtk.begin_data("Strain_deviator", POINT_DATA, SCALARS, FLOAT); V_it = Tri.finite_vertices_begin(); for (; V_it != Tri.finite_vertices_end(); ++V_it) { if (!V_it->info().isFictious) { Tenseur_sym3 epsilon(ParticleDeformation[V_it->info().id()]); vtk.write_data((float) epsilon.Deviatoric().Norme());} //vtk.write_data((float) epsilon.Deviatoric()(1,1)-epsilon.Deviatoric()(0,0));} } vtk.end_data(); return true; } bool KinematicLocalisationAnalyser::DistribsToFile(const char* output_file_name) { ofstream output_file(output_file_name); if (!output_file.is_open()) { cerr << "Error opening files"; return false;} output_file << "sym_grad_u_total_g (wrong averaged strain):"<< endl << Tenseur_sym3(grad_u_total_g) << endl; output_file << "Total volume = " << v_total << ", grad_u = " << endl << grad_u_total << endl << "sym_grad_u (true average strain): " << endl << Tenseur_sym3(grad_u_total) << endl; output_file << "Macro strain = " << Delta_epsilon << endl; ContactDistributionToFile(output_file); AllNeighborDistributionToFile(output_file); TS1->filter_distance = 2.0; ContactDistributionToFile(output_file); AllNeighborDistributionToFile(output_file); TS1->filter_distance = 4.0; ContactDistributionToFile(output_file); AllNeighborDistributionToFile(output_file); output_file << "Contact_fabric : "; output_file << (Tenseur_sym3) Contact_fabric(*TS1);// << endl; output_file << "Contact_anisotropy : " << Contact_anisotropy(*TS1) << endl << endl; output_file << "Neighbor_fabric : " << Neighbor_fabric(*TS1) << endl; output_file << "Neighbor_anisotropy : " << Neighbor_anisotropy(*TS1) << endl << endl; RTriangulation& T = TS1->tesselation().Triangulation(); Edge_iterator ed_end = T.edges_end(); vector edges; for (Edge_iterator ed_it = T.edges_begin(); ed_it != ed_end; ++ed_it) { if (!T.is_infinite(*ed_it)) { Segment s = T.segment(*ed_it); CVector v = s.to_vector(); Real xx = std::abs(v.z()/sqrt(s.squared_length())); if (xx>0.95) edges.push_back(ed_it); } } NormalDisplacementDistributionToFile(edges, output_file); edges.clear(); for (Edge_iterator ed_it = T.edges_begin(); ed_it != ed_end; ++ed_it) { if (!T.is_infinite(*ed_it)) { Segment s = T.segment(*ed_it); CVector v = s.to_vector(); Real xx = std::abs(v.z()/sqrt(s.squared_length())); if (xx<0.05) edges.push_back(ed_it); } } NormalDisplacementDistributionToFile(edges, output_file); edges.clear(); for (Edge_iterator ed_it = T.edges_begin(); ed_it != ed_end; ++ed_it) { if (!T.is_infinite(*ed_it)) { Segment s = T.segment(*ed_it); CVector v = s.to_vector(); Real xx = std::abs(v.z()/sqrt(s.squared_length())); if (xx>0.65 && xx<0.75) edges.push_back(ed_it); } } NormalDisplacementDistributionToFile(edges, output_file); output_file.close(); return true; } long KinematicLocalisationAnalyser::Filtered_contacts(TriaxialState& state) { long nc1 =0; TriaxialState::ContactIterator cend = state.contacts_end(); for (TriaxialState::ContactIterator cit = state.contacts_begin(); cit!=cend; ++cit) { if (state.inside((*cit)->grain1->sphere.point()) && state.inside((*cit)->grain2->sphere.point())) nc1 += 2; else if (state.inside((*cit)->grain1->sphere.point()) || state.inside((*cit)->grain2->sphere.point())) ++nc1;} return nc1; } long KinematicLocalisationAnalyser::Filtered_neighbors(TriaxialState& state) { long nv1=0; RTriangulation& T = state.tesselation().Triangulation(); Edge_iterator ed_end = T.edges_end(); for (Edge_iterator ed_it = T.edges_begin(); ed_it != ed_end; ++ed_it) { if (!T.is_infinite(*ed_it)) { Segment s(T.segment(*ed_it)); if (state.inside(s.source()) && state.inside(s.target())) nv1 += 2; else if (state.inside(s.source()) || state.inside(s.target())) ++nv1; } } return nv1; } long KinematicLocalisationAnalyser::Filtered_grains(TriaxialState& state) { long ng1 =0; TriaxialState::GrainIterator gend = state.grains_end(); for (TriaxialState::GrainIterator git = state.grains_begin(); git!=gend; ++git) { if (state.inside(git->sphere.point())) ++ng1; } return ng1; } Real KinematicLocalisationAnalyser::Filtered_volume(TriaxialState& state) { return 0; } Real KinematicLocalisationAnalyser::Contact_coordination(TriaxialState& state) { return Filtered_contacts(state) / Filtered_grains(state); } Real KinematicLocalisationAnalyser::Neighbor_coordination(TriaxialState& state) { return Filtered_neighbors(state) / Filtered_grains(state); } Tenseur_sym3 KinematicLocalisationAnalyser::Neighbor_fabric(TriaxialState& state) { RTriangulation& T = state.tesselation().Triangulation(); Edge_iterator ed_end = T.edges_end(); Tenseur_sym3 Tens; CVector v; Segment s; for (Edge_iterator ed_it = T.edges_begin(); ed_it != ed_end; ++ed_it) { if (!T.is_infinite(*ed_it)) { s = T.segment(*ed_it); if (state.inside(s.source()) && state.inside(s.target())) { v = T.segment(*ed_it).to_vector() * (1/sqrt(T.segment(*ed_it).squared_length())); for (int i=1; i<4; i++) for (int j=3; j>=i; j--) Tens(i,j) += 2*v[i-1]*v[j-1]; } else if (state.inside(s.source()) || state.inside(s.target())) { v = T.segment(*ed_it).to_vector() * (1/sqrt(T.segment(*ed_it).squared_length())); for (int i=1; i<4; i++) for (int j=3; j>=i; j--) Tens(i,j) += v[i-1]*v[j-1]; } } } Tens /= Filtered_neighbors(state); return Tens; } Tenseur_sym3 KinematicLocalisationAnalyser::Contact_fabric(TriaxialState& state) { Tenseur_sym3 Tens; CVector v; TriaxialState::ContactIterator cend = state.contacts_end(); for (TriaxialState::ContactIterator cit = state.contacts_begin(); cit!=cend; ++cit) { if (state.inside((*cit)->grain1->sphere.point()) && state.inside((*cit)->grain2->sphere.point())) { v = (*cit)->normal; for (int i=1; i<4; i++) for (int j=3; j>=i; j--) Tens(i,j) += 2*v[i-1]*v[j-1]; } else if (state.inside((*cit)->grain1->sphere.point()) || state.inside((*cit)->grain2->sphere.point())) { v = (*cit)->normal; for (int i=1; i<4; i++) for (int j=3; j>=i; j--) Tens(i,j) += v[i-1]*v[j-1];} } Tens /= Filtered_contacts(state); return Tens; } Real KinematicLocalisationAnalyser::Contact_anisotropy(TriaxialState& state) { Tenseur_sym3 tens(Contact_fabric(state)); return tens.Deviatoric().Norme()/tens.Trace(); } Real KinematicLocalisationAnalyser::Neighbor_anisotropy(TriaxialState& state) { Tenseur_sym3 tens(Neighbor_fabric(state)); return tens.Deviatoric().Norme()/tens.Trace(); } vector >& KinematicLocalisationAnalyser:: NormalDisplacementDistribution(vector& edges, vector > &row) { //cerr << "n_debug=" << n_debug++ << endl; /// DEBUG LINE /// row.clear(); row.resize(linear_discretisation+1); vector Un_values; Un_values.resize(edges.size()); Real UNmin(100000), UNmax(-100000); CVector branch, U; Real Un; Vertex_handle Vh1, Vh2; vector::iterator ed_end = edges.end(); long val_count = 0; //cerr << "n_debug=" << n_debug++ << endl; /// DEBUG LINE /// for (vector::iterator ed_it = edges.begin(); ed_it!=ed_end; ++ed_it) { Vh1= (*ed_it)->first->vertex((*ed_it)->second); Vh2= (*ed_it)->first->vertex((*ed_it)->third); branch = Vh1->point()- Vh2->point(); NORMALIZE(branch); if (consecutive) U = TS1->grain(Vh1->info().id()).translation - TS1->grain(Vh2->info().id()).translation; else { U = (TS1->grain(Vh1->info().id()).sphere.point() - TS0->grain(Vh1->info().id()).sphere.point()) - (TS1->grain(Vh2->info().id()).sphere.point() - TS0->grain(Vh2->info().id()).sphere.point()); } //Un = (U - (Delta_epsilon*branch))*branch; //Diff�rence par rapport � Un moyen Un = U*branch; UNmin = min(UNmin,Un); UNmax = max(UNmax,Un); Un_values[val_count++] = Un; //cerr << "Un=" << Un << " U=" << U << " branch=" << branch << endl; } //cerr << "n_debug=" << n_debug++ << endl; /// DEBUG LINE /// Real DUN = (UNmax-UNmin) /linear_discretisation; for (int i = 0; i <= linear_discretisation; ++i) { row[i].first = UNmin+ (i+0.5) *DUN; row[i].second = 0; } //cerr << "n_debug=" << n_debug++ << endl; /// DEBUG LINE /// val_count = val_count-1; //cerr << "nval=" << val_count << " reserved=" << edges.size() << endl; for (; val_count>=0; --val_count) { //cerr << "n_debug0=" << n_debug << endl; /// DEBUG LINE /// row[(int)((Un_values[val_count]-UNmin) /DUN)].second += 1; } //cerr << "DUN=" << DUN << " UNmin=" << UNmin << " UNmax=" << UNmax << endl; return row; //cerr << "n_debug=" << n_debug++ << endl; /// DEBUG LINE /// } ofstream& KinematicLocalisationAnalyser:: NormalDisplacementDistributionToFile(vector& edges, ofstream& output_file) { vector< pair > row; NormalDisplacementDistribution(edges, row); vector< pair >::iterator r_end = row.end(); //output part : output_file << "#Normal displacement distribution" << endl << "eps3=" << Delta_epsilon(3,3) << " eps2=" << Delta_epsilon(2,2) << " eps1=" << Delta_epsilon(1,1) << " number of neigbors: "<< edges.size() << endl << "Un_min=" << 1.5*row[0].first - 0.5*row[1].first << " Un_max=" << row[row.size()-1].first << endl; cout << "#Normal displacement distribution" << endl << "eps3=" << Delta_epsilon(3,3) << " eps2=" << Delta_epsilon(2,2) << " eps1=" << Delta_epsilon(1,1) << " number of neigbors: "<< edges.size() << endl << "Un_min=" << 1.5*row[0].first - 0.5*row[1].first << " Un_max=" << row[row.size()-1].first << endl; for (vector< pair >::iterator r_it = row.begin(); r_it != r_end; ++r_it) { output_file << r_it->first << " " << r_it->second << endl; cout << r_it->first << " " << r_it->second << endl; } output_file << endl; return output_file; } ofstream& KinematicLocalisationAnalyser:: ContactDistributionToFile(ofstream& output_file) { //cerr << "ContactDistributionToFile" << endl; vector< pair > row; row.resize(sphere_discretisation+1); Real DZ = 1.0/sphere_discretisation;//interval in term of cos(teta) long nc1=0; long nc2=0; long ng1=0; long ng2=0; //cerr << "ContactDistributionToFile05" << endl; TriaxialState::ContactIterator cend = (*TS1).contacts_end(); TriaxialState::GrainIterator gend = (*TS1).grains_end(); for (int i = 0; i <= sphere_discretisation; ++i) { row[i].first = (i+0.5) *DZ; row[i].second = 0; } for (TriaxialState::GrainIterator git = (*TS1).grains_begin(); git!=gend; ++git) { if ((*TS1).inside(git->sphere.point())) ++ng1; else ++ng2; } for (TriaxialState::ContactIterator cit = (*TS1).contacts_begin(); cit!=cend; ++cit) { if ((*TS1).inside((*cit)->grain1->sphere.point()) && (*TS1).inside((*cit)->grain2->sphere.point())) { row[(int)(std::abs((*cit)->normal.z()) /DZ)].second += 2; nc1 += 2; } else { if ((*TS1).inside((*cit)->grain1->sphere.point()) || (*TS1).inside((*cit)->grain2->sphere.point())) { row[(int)(std::abs((*cit)->normal.z()) /DZ)].second += 1; ++nc1; } //cerr << "(*cit)->normal.z(),DZ : " << (*cit)->normal.z() << " " << DZ << endl;} else ++nc2; } } //normalisation : Real normalize = 1.0/ (ng1*4*DZ*3.141592653); for (int i = 0; i <= sphere_discretisation; ++i) row[i].second *= normalize; //output part : output_file << "#Contacts distribution" << endl << "(filter dist. = " << (*TS1).filter_distance << ", "<< nc1 << " contacts, " << nc2 << " excluded contacts, for "<< ng1 <<"/"<< (ng1+ng2) << " grains)" << endl; output_file << "max_nz number_of_contacts" << endl; cerr << "#Contacts distribution (filter dist. = " << (*TS1).filter_distance << ", "<< nc1 << " contacts, " << nc2 << " excluded contacts, for "<< ng1 <<"/"<< (ng1+ng2) << " grains)" << endl; cerr << "mean_nz number_of_contacts" << endl; for (int i = 0; i <= sphere_discretisation; ++i) { output_file << row[i].first << " " << row[i].second << endl; cerr << row[i].first << " " << row[i].second << endl; } output_file << endl; return output_file; } ofstream& KinematicLocalisationAnalyser:: AllNeighborDistributionToFile(ofstream& output_file) { vector< pair > row; row.resize(sphere_discretisation); Real DZ = 1.0/sphere_discretisation; long nv1=0; long nv2=0; long nv3=0; long ng1=0; long ng2=0; for (int i = 0; i < sphere_discretisation; ++i) { row[i].first = (i+0.5) *DZ; row[i].second = 0; } TriaxialState::GrainIterator gend = (*TS1).grains_end(); for (TriaxialState::GrainIterator git = (*TS1).grains_begin(); git!=gend; ++git) { if ((*TS1).inside(git->sphere.point())) ++ng1; else ++ng2; } RTriangulation& T = (*TS1).tesselation().Triangulation(); Segment s; CVector v; for (Edge_iterator ed_it = T.edges_begin(); ed_it != T.edges_end(); ed_it++) { if (!T.is_infinite(*ed_it)) { s = T.segment(*ed_it); if ((*TS1).inside(s.source()) && (*TS1).inside(s.target())) { v = s.to_vector(); row[(int)(std::abs(v.z() /sqrt(s.squared_length())) /DZ)].second += 2; nv1 += 2; } else { if ((*TS1).inside(s.source()) || (*TS1).inside(s.target())) { v = s.to_vector(); row[(int)(std::abs(v.z() /sqrt(s.squared_length())) /DZ)].second += 1; ++nv1; } else ++nv2; } } else ++nv3; } Real normalize = 1.0/ (ng1*4*DZ*3.141592653); for (int i = 0; i < sphere_discretisation; ++i) row[i].second *= normalize; output_file << "#Neighbors distribution" << endl << "(filter dist. = " << (*TS1).filter_distance << ", "<< nv1 << " neighbors + " << nv2 << " excluded + " << nv3 << " infinite, for "<< ng1 <<"/"<< (ng1+ng2) << " grains)" << endl; output_file << "max_nz number_of_neighbors" << endl; cerr << "#Neighbors distribution" << endl << "(filter dist. = " << (*TS1).filter_distance << ", "<< nv1 << " neighbors + " << nv2 << " excluded + " << nv3 << " infinite, for "<< ng1 <<"/"<< (ng1+ng2) << " grains)" << endl; cerr << "mean_nz number_of_neighbors" << endl; for (int i = 0; i < sphere_discretisation; ++i) { output_file << row[i].first << " " << row[i].second << endl; cerr << row[i].first << " " << row[i].second << endl; } output_file << endl; return output_file; } void KinematicLocalisationAnalyser:: SetForceIncrements(void) //WARNING : This function will modify the contact lists : add virtual (lost)) contacts in state 1 and modify old_force and force in state 0, execute this function after all other force analysis functions if you want to avoid problems { //if (true) cerr << "SetForceIncrements"<< endl; // vector< pair > row; // row.resize ( sphere_discretisation ); // Real DZ = 1.0/sphere_discretisation; long Nc0 = TS0->contacts.size(); long Nc1 = TS1->contacts.size(); n_persistent = 0; n_new = 0; n_lost = 0; long lost_in_state0 = 0; for (int i = 0; i < Nc0; ++i) { TS0->contacts[i]->visited = false; if (TS0->contacts[i]->status == TriaxialState::Contact::LOST) ++lost_in_state0; } for (int i = 0; i < Nc1; ++i) TS1->contacts[i]->visited = false; //cerr << "Nc1 "<contacts[i]->status != TriaxialState::Contact::LOST) { // cerr << 2; for (int j = 0; j < Nc1; ++j) { if (TS0->contacts[i]->grain1->id == TS1->contacts[j]->grain1->id && TS0->contacts[i]->grain2->id == TS1->contacts[j]->grain2->id) { // This is a PERSISTENT contact (i.e. it is present in state 0 and 1) //TS0->contacts[i]->visited = true; TS1->contacts[j]->visited = true; //TS0->contacts[i]->status = TriaxialState::Contact::PERSISTENT; TS1->contacts[j]->status = TriaxialState::Contact::PERSISTENT; TS1->contacts[j]->old_fn = TS0->contacts[i]->fn; TS1->contacts[j]->old_fs = TS0->contacts[i]->fs; ++n_persistent; break; } else if (j+1==Nc1) { //This contact was not found in state 1, add it as a LOST contact // cerr << 3 << endl; TriaxialState::Contact* c = new TriaxialState::Contact; c->visited = true; c->status = TriaxialState::Contact::LOST; c->grain1 = TS0->contacts[i]->grain1; c->grain2 = TS0->contacts[i]->grain2; c->position = TS0->contacts[i]->position; c->normal = TS0->contacts[i]->normal; c->old_fn = TS0->contacts[i]->fn; c->fn = 0; c->old_fs = TS0->contacts[i]->fs; c->frictional_work = TS0->contacts[i]->frictional_work; c->fs = CGAL::NULL_VECTOR; TS1->contacts.push_back(c); ++Nc1; ++n_lost; break; } } } } //cerr << 4; for (int j = 0; j < Nc1; ++j) { //This contact was not visited, it is a NEW one //cerr << 5; if (!TS1->contacts[j]->visited /*&& TS1->contacts[j]->status != TriaxialState::Contact::LOST*/) { //cerr << 6; TS1->contacts[j]->status = TriaxialState::Contact::NEW; TS1->contacts[j]->old_fn = 0; TS1->contacts[j]->old_fs = CGAL::NULL_VECTOR; ++n_new; } } } void KinematicLocalisationAnalyser::SetDisplacementIncrements(void) { TriaxialState::GrainIterator gend = TS1->grains_end(); for (TriaxialState::GrainIterator git = TS1->grains_begin(); git!=gend; ++git) if (git->id >= 0) git->translation = TS1->grain(git->id).sphere.point() - TS0->grain(git->id).sphere.point(); consecutive = true; } ofstream& KinematicLocalisationAnalyser:: StrictNeighborDistributionToFile(ofstream& output_file) { return output_file; } CVector KinematicLocalisationAnalyser::Deplacement(Finite_cells_iterator cell, int facet) { CVector v(0.f, 0.f, 0.f); int id;// ident. de la particule CVector fixedPoint = 0.5*((TS0->box.base-CGAL::ORIGIN)+(TS0->box.sommet-CGAL::ORIGIN)); for (int i=0; i<4; i++) { // char msg [256]; if (i!=facet) { id = cell->vertex(i)->info().id(); CVector meanFieldDisp =CVector(TS0->grain(id).sphere.point().x(), TS0->grain(id).sphere.point().y(), TS0->grain(id).sphere.point().z())-fixedPoint; if (1){//fluctuations meanFieldDisp = CVector( meanFieldDisp[0]*Delta_epsilon(1,1), meanFieldDisp[1]*Delta_epsilon(2,2), meanFieldDisp[2]*Delta_epsilon(3,3)); } else meanFieldDisp=CVector(0,0,0); if (consecutive) v = v + TS1->grain(id).translation-meanFieldDisp; else v = v + (TS1->grain(id).sphere.point() - TS0->grain(id).sphere.point()-meanFieldDisp); } } v = v*0.333333333333; return v; } void KinematicLocalisationAnalyser::Grad_u(Finite_cells_iterator cell, int facet, CVector &V, Tenseur3& T) { CVector S = cross_product((cell->vertex(l_vertices[facet][1])->point()) - (cell->vertex(l_vertices[facet][0])->point()), (cell->vertex(l_vertices[facet][2])->point()) - (cell->vertex(l_vertices[facet][1])->point())) /2.f; Somme(T, V, S); } void KinematicLocalisationAnalyser::Grad_u(Finite_cells_iterator cell, Tenseur3& T, bool vol_divide)// Calcule le gradient de d�p. { T.reset(); CVector v; for (int facet=0; facet<4; facet++) { v = Deplacement(cell, facet); Grad_u(cell, facet, v, T); } if (vol_divide) T/= Tesselation::Volume(cell); } const vector& KinematicLocalisationAnalyser::computeParticlesDeformation(void) { Tesselation& Tes = TS1->tesselation(); RTriangulation& Tri = Tes.Triangulation(); Tenseur3 grad_u; Real v; v_total = 0; v_solid_total = 0; grad_u_total = NULL_TENSEUR3; v_total_g = 0; grad_u_total_g = NULL_TENSEUR3; Delta_epsilon(3,3) = TS1->eps3 - TS0->eps3; Delta_epsilon(1,1) = TS1->eps1 - TS0->eps1; Delta_epsilon(2,2) = TS1->eps2 - TS0->eps2; //compute Voronoi tesselation (i.e. voronoi center of each cell) if (!Tes.computed) Tes.compute(); if (ParticleDeformation.size() != (unsigned int)(Tes.Max_id() + 1)) { ParticleDeformation.clear(); ParticleDeformation.resize(Tes.Max_id() + 1); } //reset volumes and tensors of each particle n_real_vertices = 0; n_fictious_vertices=0; for (RTriangulation::Finite_vertices_iterator V_it=Tri.finite_vertices_begin(); V_it != Tri.finite_vertices_end(); V_it++) { //cerr << V_it->info().id() << endl; V_it->info().v() =0;//WARNING : this will erase previous values if some have been computed ParticleDeformation[V_it->info().id()]=NULL_TENSEUR3; if (!V_it->info().isFictious) ++n_real_vertices; else ++n_fictious_vertices; } Finite_cells_iterator cell = Tri.finite_cells_begin(); Finite_cells_iterator cell0 = Tri.finite_cells_end(); //compute grad_u and volumes of all cells in the triangulation, and assign them to each of the vertices ( volume*grad_u is added here rather than grad_u, the weighted average is computed later ) //define the number of non-fictious cells, i.e. not in contact with a boundary n_real_cells=0; for (; cell != cell0; cell++) { // calcule la norme du d�viateur dans chaque cellule cell->info().isFictious = (cell->vertex(0)->info().isFictious || cell->vertex(1)->info().isFictious || cell->vertex(2)->info().isFictious || cell->vertex(3)->info().isFictious); if (!cell->info().isFictious) { Grad_u(cell, grad_u, false); // false : don't divide by volume, here grad_u = volume of cell * average grad_u in cell, the final value is divided by the total volume later (see below) //cerr << "grad_u=" << grad_u << endl; v = Tri.tetrahedron(cell).volume(); grad_u_total += grad_u; v_total += v; ++n_real_cells; for (unsigned int index=0; index<4; index++) { cell->vertex(index)->info().v() += v; //WARNING2 : this will affect values which differ from the volumes of voronoi cells //cerr << "ParticleDeformation[cell->vertex (" << cell->vertex ( index )->info().id() << ")"<< endl; ParticleDeformation[cell->vertex(index)->info().id()] += grad_u; } } } //Do we delete volume and grad_u for particles on the border? // Tesselation::Vector_Vertex border_vertices; // Tes.Voisins(Tri.infinite_vertex(), border_vertices); // unsigned int l = border_vertices.size(); // for (unsigned int i=0; iinfo().v() =0; // // ParticleDeformation[border_vertices[i]->info().id()]=NULL_TENSEUR3; // } //Divide sum(v*grad_u) by sum(v) to get the average grad_u on each particle for (RTriangulation::Finite_vertices_iterator V_it = Tri.finite_vertices_begin(); V_it != Tri.finite_vertices_end(); V_it++) { v_total_g += V_it->info().v(); v_solid_total += 4.188790*pow(V_it->point().weight(),1.5);//4.18... = 4/3*PI; and here, weight is rad² grad_u_total_g += ParticleDeformation[V_it->info().id()]; if (V_it->info().v()) ParticleDeformation[V_it->info().id()]/=V_it->info().v(); } grad_u_total_g /= v_total_g; if(1){ cerr << "sym_grad_u_total_g (wrong averaged strain):"<< endl << Tenseur_sym3(grad_u_total_g) << endl; if (v_total) grad_u_total /= v_total; cerr << "Total volume = " << v_total << ", grad_u = " << endl << grad_u_total << endl << "sym_grad_u (true average strain): " << endl << Tenseur_sym3(grad_u_total) << endl; cerr << "Macro strain : "<< endl << Delta_epsilon << endl; } return ParticleDeformation; } Real KinematicLocalisationAnalyser::computeMacroPorosity(void) { return (1-v_solid_total/(TS1->haut*TS1->larg*TS1->prof)); } } // namespace CGT trunk-2017.01a/lib/triangulation/KinematicLocalisationAnalyser.hpp000066400000000000000000000133441304022710500252730ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ /*! \brief computes statistics of micro-variables assuming axi-symetry. */ #pragma once #include "TriaxialState.h" #include "Tenseur3.h" namespace CGT { using std::pair; using std::ofstream; #define SPHERE_DISCRETISATION 20; //number of "teta" intervals on the unit sphere #define LINEAR_DISCRETISATION 200; //number of intervals on segments like [UNmin,UNmax] // l_vertices : defines vertices for each facet // for facet k, the vertices indices are in column k const int l_vertices [4][3] = { {1, 2, 3}, {0, 3, 2}, {3, 0, 1}, {2, 1, 0} }; class KinematicLocalisationAnalyser { public: typedef TriaxialState::Tesselation Tesselation; typedef TriaxialState::RTriangulation RTriangulation; typedef RTriangulation::Vertex_handle Vertex_handle; typedef RTriangulation::Finite_cells_iterator Finite_cells_iterator; typedef RTriangulation::Cell_handle Cell_handle; typedef RTriangulation::Edge_iterator Edge_iterator; typedef vector< pair > RGrid1D; typedef vector > RGrid2D; typedef vector > > RGrid3D; KinematicLocalisationAnalyser(); KinematicLocalisationAnalyser ( const char* state_file1, bool usebz2 = true ); KinematicLocalisationAnalyser ( const char* state_file1, const char* state_file0, bool consecutive_files = true, bool usebz2 = true); KinematicLocalisationAnalyser ( const char* base_name, int file_number0, int file_number1, bool usebz2 = true); ~KinematicLocalisationAnalyser(); void SetBaseFileName (string name); bool SetFileNumbers (int n0, int n1); void SetConsecutive (bool); void SetNO_ZERO_ID (bool); void SwitchStates (void); bool DistribsToFile (const char* output_file_name); ///Write the averaged deformation on each grain in a file (vertices and cells lists included in the file), no need to call computeParticlesDeformation() bool DefToFile (const char* output_file_name = "deformations"); bool DefToFile (const char* state_file1, const char* state_file0, const char* output_file_name="deformation.vtk", bool usebz2=false); ///Save/Load states using bz2 compression bool bz2; ofstream& ContactDistributionToFile ( ofstream& output_file ); ofstream& AllNeighborDistributionToFile ( ofstream& output_file ); ofstream& StrictNeighborDistributionToFile ( ofstream& output_file ); ofstream& NormalDisplacementDistributionToFile ( vector& edges, ofstream& output_file ); long Filtered_contacts ( TriaxialState& state ); long Filtered_neighbors ( TriaxialState& state ); long Filtered_grains ( TriaxialState& state ); Real Filtered_volume ( TriaxialState& state ); Real Contact_coordination ( TriaxialState& state ); Real Neighbor_coordination ( TriaxialState& state ); Tenseur_sym3 Neighbor_fabric ( TriaxialState& state ); Tenseur_sym3 Contact_fabric ( TriaxialState& state ); Real Contact_anisotropy ( TriaxialState& state ); Real Neighbor_anisotropy ( TriaxialState& state ); void SetForceIncrements (void); void SetDisplacementIncrements (void); ///Add surface*displacement to T void Grad_u ( Finite_cells_iterator cell, int facet, CVector &V, Tenseur3& T ); ///compute grad_u in cell (by default, T= average grad_u in cell, if !vol_divide, T=grad_u*volume void Grad_u ( Finite_cells_iterator cell, Tenseur3& T, bool vol_divide=true ); /// compute grad_u for all particles, by summing grad_u of all adjaent cells using current states const vector& computeParticlesDeformation (void); /// Do everything in one step by giving some final (file1) and initial (file0) positions const vector& computeParticlesDeformation(const char* state_file1, const char* state_file0, bool usebz2 = true); ///compute porisity from cumulated spheres volumes and positions of boxes Real computeMacroPorosity (void ); CVector Deplacement ( Cell_handle cell ); //donne le d�placement d'un sommet de voronoi CVector Deplacement ( Finite_cells_iterator cell, int facet ); //mean displacement on a facet // Calcul du tenseur d'orientation des voisins //Tenseur_sym3 Orientation_voisins (Tesselation& Tes); //Set the list of edges of a given orientation (orientation defined via the z-coordinate of the normal) vector& Oriented_Filtered_edges (Real Nymin, Real Nymax, vector& filteredList); vector >& NormalDisplacementDistribution ( vector& edges, vector >& row ); //member data int sphere_discretisation; int linear_discretisation; Tenseur_sym3 Delta_epsilon; Tenseur3 grad_u_total; vector ParticleDeformation; Tenseur3 grad_u_total_g;//grad_u averaged on extended grain cells TriaxialState *TS1, *TS0; private: int file_number_1, file_number_0; string base_file_name; //Base name of state-files, complete name is (base_name+state_number). bool consecutive; //Are the two triax states consecutive? if "false" displacements are re-computed from the two source files; if "true" one file is enough. Real v_solid_total;//solid volume in the box Real v_total;//volume of the box Real v_total_g;//summed volumes of extended grain cells long n_persistent, n_new, n_lost, n_real_cells, n_real_vertices, n_fictious_vertices; }; } // namespace CGT trunk-2017.01a/lib/triangulation/Network.hpp000066400000000000000000000116731304022710500207620ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2010 by Emanuele Catalano * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef FLOW_ENGINE #pragma once #include "Tesselation.h" #include "Timer.h" #include "basicVTKwritter.hpp" /** Defines class Network. Which contains the geometrical representation of a pore network on the basis of regular triangulation (using CGAL lib) The class is the base of the pore-flow model. It has basic functions to compute quantities like void volumes and solid surfaces in the triangulation's elements. The same data structure is used with different template parameters for periodic and aperiodic boundary conditions. The network is bounded by infinite planes represented in the triangulation by very large spheres (so that their surface looks flat at the scale of the network). Two triangulations are in fact contained in the network, so that a simulation can switch between them and pass data from one to the other. Otherwise, some info would be lost when the problem is retriangulated. */ namespace CGT { /// Representation of a boundary condition along an axis aligned plane. struct Boundary { Point p;//position CVector normal;//orientation Vector3r velocity;//motion int coordinate;//the axis perpendicular to the boundary bool flowCondition;//flowCondition=0, pressure is imposed // flowCondition=1, flow is imposed Real value;// value of imposed pressure bool useMaxMin;// tells if this boundary was placed following the particles (using min/max of them) or with user defined position }; template class Network { public: DECLARE_TESSELATION_TYPES(Tesselation) //see Tesselation.h virtual ~Network(); Network(); Tesselation T [2]; bool currentTes; Tesselation& tesselation() {return T[currentTes];}; double xMin, xMax, yMin, yMax, zMin, zMax, Rmoy, sectionArea, Height, vTotal; bool debugOut; int nOfSpheres; int xMinId, xMaxId, yMinId, yMaxId, zMinId, zMaxId; int* boundsIds [6]; vector boundingCells [6]; Point cornerMin; Point cornerMax; Real VSolidTot, Vtotalissimo, vPoral, sSolidTot, vPoralPorosity, vTotalPorosity; Boundary boundaries [6]; Boundary& boundary (int b) {return boundaries[b-idOffset];} short idOffset; int vtkInfiniteVertices, vtkInfiniteCells, num_particles; void addBoundingPlanes(); void addBoundingPlane (CVector Normal, int id_wall); void addBoundingPlane (Real center[3], double thickness, CVector Normal, int id_wall ); void defineFictiousCells( ); int detectFacetFictiousVertices (CellHandle& cell, int& j); double volumeSolidPore (const CellHandle& cell); double volumeSingleFictiousPore(const VertexHandle& SV1, const VertexHandle& SV2, const VertexHandle& SV3, const Point& PV1, const Point& PV2, CVector& facetSurface); double volumeDoubleFictiousPore(const VertexHandle& SV1, const VertexHandle& SV2, const VertexHandle& SV3, const Point& PV1, const Point& PV2, CVector& facetSurface); double sphericalTriangleVolume(const Sphere& ST1, const Point& PT1, const Point& PT2, const Point& PT3); double fastSphericalTriangleArea(const Sphere& STA1, const Point& STA2, const Point& STA3, const Point& PTA1); Real fastSolidAngle(const Point& STA1, const Point& PTA1, const Point& PTA2, const Point& PTA3); double volumeDoubleFictiousPore(VertexHandle SV1, VertexHandle SV2, VertexHandle SV3, Point PV1); double volumeSingleFictiousPore(VertexHandle SV1, VertexHandle SV2, VertexHandle SV3, Point PV1); double volumePoreVoronoiFraction ( CellHandle& cell, int& j, bool reuseFacetData=false); double surfaceSolidThroat( CellHandle cell, int j, bool slipBoundary, bool reuseFacetData=false); double surfaceSolidThroatInPore( CellHandle cell, int j, bool slipBoundary, bool reuseFacetData=false);// returns the solid area in the throat, keeping only that part of the throat in cell double sphericalTriangleArea ( Sphere STA1, Sphere STA2, Sphere STA3, Point PTA1 ); CVector surfaceDoubleFictiousFacet(VertexHandle fSV1, VertexHandle fSV2, VertexHandle SV3); CVector surfaceSingleFictiousFacet(VertexHandle fSV1, VertexHandle SV2, VertexHandle SV3); double surfaceSolidDoubleFictiousFacet(VertexHandle SV1, VertexHandle SV2, VertexHandle SV3); double surfaceSolidFacet(Sphere ST1, Sphere ST2, Sphere ST3); void lineSolidPore(CellHandle cell, int j); double lineSolidFacet(Sphere ST1, Sphere ST2, Sphere ST3); int facetF1, facetF2, facetRe1, facetRe2, facetRe3; int facetNFictious; double FAR; static const double ONE_THIRD; static const int facetVertices [4][3]; static const int permut3 [3][3]; static const int permut4 [4][4]; }; } //namespaceCGT #include "Network.ipp" #endif //FLOW_ENGINE trunk-2017.01a/lib/triangulation/Network.ipp000066400000000000000000000714611304022710500207640ustar00rootroot00000000000000 #ifdef FLOW_ENGINE #include "CGAL/constructions/constructions_on_weighted_points_cartesian_3.h" #include #include #include #include #include "vector" #include #include #include #define FAST namespace CGT { using std::abs; // template const double Network::FAR = 50000; template const double Network::ONE_THIRD = 1.0/3.0; template const int Network::facetVertices [4][3] = {{1,2,3},{0,2,3},{0,1,3},{0,1,2}}; template const int Network::permut3 [3][3] = {{0,1,2},{1,2,0},{2,0,1}}; template const int Network::permut4 [4][4] = {{0,1,2,3},{1,2,3,0},{2,3,0,1},{3,0,1,2}}; template Network::~Network(){} template Network::Network(){ FAR = 50000; facetF1=facetF2=facetRe1=facetRe2=facetRe3=0; // F1=F2=Re1=Re2=0; } template int Network::detectFacetFictiousVertices (CellHandle& cell, int& j) { facetNFictious = 0; int nRealVtx=0; for (int kk=0; kk<3; kk++) { if (cell->vertex(facetVertices[j][kk])->info().isFictious) { if (facetNFictious==0) facetF1=kk; else facetF2=kk; facetNFictious +=1; } else { if (nRealVtx==0) facetRe1=kk; else if (nRealVtx==1) facetRe2=kk; else if (nRealVtx==2) facetRe3=kk; nRealVtx+=1;}} return facetNFictious; } template double Network::volumePoreVoronoiFraction (CellHandle& cell, int& j, bool reuseFacetData) { Point& p1 = cell->info(); Point& p2 = cell->neighbor(j)->info(); if (!reuseFacetData) facetNFictious = detectFacetFictiousVertices (cell,j); Sphere v [3]; VertexHandle W [3]; for (int kk=0; kk<3; kk++) {W[kk] = cell->vertex(facetVertices[j][kk]);v[kk] = cell->vertex(facetVertices[j][kk])->point();} switch (facetNFictious) { case (0) : { VertexHandle& SV1 = W[0]; VertexHandle& SV2 = W[1]; VertexHandle& SV3 = W[2]; cell->info().facetSurfaces[j]=0.5*CGAL::cross_product(SV1->point()-SV3->point(),SV2->point()-SV3->point()); if (cell->info().facetSurfaces[j][0]==0 && cell->info().facetSurfaces[j][1]==0 && cell->info().facetSurfaces[j][2]==0) cerr<<"NULL FACET SURF"<info().facetSurfaces[j]*(p2-p1) > 0) cell->info().facetSurfaces[j] = -1.0*cell->info().facetSurfaces[j]; Real Vtot = abs(ONE_THIRD*cell->info().facetSurfaces[j]*(p1-p2)); Vtotalissimo += Vtot; double Vsolid1=0, Vsolid2=0; for (int i=0;i<3;i++) { Vsolid1 += sphericalTriangleVolume(v[permut3[i][0]],v[permut3[i][1]],p1,p2); Vsolid2 += sphericalTriangleVolume(v[permut3[i][0]],v[permut3[i][2]],p1,p2);} VSolidTot += Vsolid1 + Vsolid2; vPoral += Vtot - (Vsolid1 + Vsolid2); bool border=false; for (int i=0;i<4;i++){ if (cell->neighbor(i)->info().fictious()!=0) border=true;} if (!border) {vPoralPorosity += Vtot - (Vsolid1 + Vsolid2); vTotalPorosity += Vtot;} /**Vpore**/ return Vtot - (Vsolid1 + Vsolid2); }; break; case (1) : {return volumeSingleFictiousPore(cell->vertex(facetVertices[j][facetF1]), cell->vertex(facetVertices[j][facetRe1]), cell->vertex(facetVertices[j][facetRe2]), p1,p2, cell->info().facetSurfaces[j]);}; break; case (2) : {return volumeDoubleFictiousPore(cell->vertex(facetVertices[j][facetF1]), cell->vertex(facetVertices[j][facetF2]), cell->vertex(facetVertices[j][facetRe1]), p1,p2, cell->info().facetSurfaces[j]);}; break; default : return 0;} } template double Network::volumeSolidPore (const CellHandle& cell) { double Vsolid=0; for (int i=0;i<4;i++) { if ( !cell->vertex(permut4[i][0])->info().isFictious ) Vsolid += sphericalTriangleVolume( cell->vertex(permut4[i][0])->point(), cell->vertex(permut4[i][1])->point(), cell->vertex(permut4[i][2])-> point(), cell->vertex(permut4[i][3])-> point()); } return Vsolid; } template double Network::volumeSingleFictiousPore(const VertexHandle& SV1, const VertexHandle& SV2, const VertexHandle& SV3, const Point& PV1, const Point& PV2, CVector& facetSurface) { double A [3], B[3]; Boundary &bi1 = boundary(SV1->info().id()); for (int m=0;m<3;m++) {A[m]= (SV2->point())[m];} for (int m=0;m<3;m++) {B[m]= (SV3->point())[m];} A[bi1.coordinate]=bi1.p[bi1.coordinate]; B[bi1.coordinate]=bi1.p[bi1.coordinate]; Point AA(A[0],A[1],A[2]); Point BB(B[0],B[1],B[2]); facetSurface = surfaceSingleFictiousFacet(SV1,SV2,SV3); if (facetSurface*(PV2-PV1) > 0) facetSurface = -1.0*facetSurface; Real Vtot=ONE_THIRD*abs(facetSurface*(PV1-PV2)); Vtotalissimo += Vtot; Sphere A1(AA, 0); Sphere B1(BB, 0); Sphere& SW2 = SV2->point(); Sphere& SW3 = SV3->point(); Real Vsolid1 = sphericalTriangleVolume(SW2, AA, PV1, PV2)+sphericalTriangleVolume(SW2, SW3, PV1, PV2); Real Vsolid2 = sphericalTriangleVolume(SW3, BB, PV1, PV2)+sphericalTriangleVolume(SW3, SW2, PV1, PV2); VSolidTot += Vsolid1 + Vsolid2; vPoral += Vtot - (Vsolid1 + Vsolid2); return (Vtot - (Vsolid1 + Vsolid2)); } template double Network::volumeDoubleFictiousPore(const VertexHandle& SV1, const VertexHandle& SV2, const VertexHandle& SV3, const Point& PV1, const Point& PV2, CVector& facetSurface) { double A [3], B[3]; Boundary &bi1 = boundary(SV1->info().id()); Boundary &bi2 = boundary(SV2->info().id()); for (int m=0;m<3;m++) {A[m]=B[m]= SV3->point()[m];} A[bi1.coordinate]=bi1.p[bi1.coordinate]; B[bi2.coordinate]=bi2.p[bi2.coordinate]; Point AA(A[0],A[1],A[2]); Point BB(B[0],B[1],B[2]); facetSurface = CGAL::cross_product(SV3->point()-AA,SV3->point()-BB); if (facetSurface*(PV2-PV1) > 0) facetSurface = -1.0*facetSurface; Real Vtot = abs(facetSurface*(PV1-PV2))*ONE_THIRD; Vtotalissimo += Vtot; Real Vsolid1 = sphericalTriangleVolume(SV3->point(), AA, PV1, PV2); Real Vsolid2 = sphericalTriangleVolume(SV3->point(), BB, PV1, PV2); vPoral += (Vtot - Vsolid1 - Vsolid2); VSolidTot += Vsolid1 + Vsolid2; return (Vtot - Vsolid1 - Vsolid2); } template double Network::sphericalTriangleVolume(const Sphere& ST1, const Point& PT1, const Point& PT2, const Point& PT3) { double rayon = sqrt(ST1.weight()); if (rayon == 0.0) return 0.0; return ((ONE_THIRD * rayon) * (fastSphericalTriangleArea(ST1, PT1, PT2, PT3))) ; } template double Network::fastSphericalTriangleArea(const Sphere& STA1, const Point& STA2, const Point& STA3, const Point& PTA1) { using namespace CGAL; double rayon2 = STA1.weight(); if (rayon2 == 0.0) return 0.0; return rayon2 * fastSolidAngle(STA1,STA2,STA3,PTA1); } template double Network::sphericalTriangleArea ( Sphere STA1, Sphere STA2, Sphere STA3, Point PTA1 ) { double rayon = STA1.weight(); if ( rayon == 0.0 ) return 0.0; CVector v12 = STA2.point() - STA1.point(); CVector v13 = STA3.point() - STA1.point(); CVector v14 = PTA1 - STA1.point(); double norme12 = ( v12.squared_length() ); double norme13 = ( v13.squared_length() ); double norme14 = ( v14.squared_length() ); double cosA = v12*v13 / sqrt ( ( norme13 * norme12 ) ); double cosB = v12*v14 / sqrt ( ( norme14 * norme12 ) ); double cosC = v14*v13 / sqrt ( ( norme13 * norme14 ) ); double A = acos ( cosA ); double B = acos ( cosB ); double C = acos ( cosC ); if ( A==0 || B==0 || C==0 ) return 0; double a = acos ( ( cosA - cosB * cosC ) / ( sin ( B ) * sin ( C ) ) ); double b = acos ( ( cosB - cosC * cosA ) / ( sin ( C ) * sin ( A ) ) ); double c = acos ( ( cosC - cosA * cosB ) / ( sin ( A ) * sin ( B ) ) ); double aire_triangle_spherique = rayon * ( a + b + c - M_PI ); return aire_triangle_spherique; } template Real Network::fastSolidAngle(const Point& STA1, const Point& PTA1, const Point& PTA2, const Point& PTA3) { //! This function needs to be fast because it is used heavily. Avoid using vector operations which require constructing vectors (~50% of cpu time in the non-fast version), and compute angle using the 3x faster formula of Oosterom and StrackeeVan Oosterom, A; Strackee, J (1983). "The Solid Angle of a Plane Triangle". IEEE Trans. Biom. Eng. BME-30 (2): 125-126. (or check http://en.wikipedia.org/wiki/Solid_angle) using namespace CGAL; double M[3][3]; M[0][0] = PTA1.x() - STA1.x(); M[0][1] = PTA2.x() - STA1.x(); M[0][2] = PTA3.x() - STA1.x(); M[1][0] = PTA1.y() - STA1.y(); M[1][1] = PTA2.y() - STA1.y(); M[1][2] = PTA3.y() - STA1.y(); M[2][0] = PTA1.z() - STA1.z(); M[2][1] = PTA2.z() - STA1.z(); M[2][2] = PTA3.z() - STA1.z(); double detM = M[0][0]* (M[1][1]*M[2][2]-M[2][1]*M[1][2]) + M[1][0]* (M[2][1]*M[0][2]-M[0][1]*M[2][2]) + M[2][0]* (M[0][1]*M[1][2]-M[1][1]*M[0][2]); double pv12N2 = pow(M[0][0],2) +pow(M[1][0],2) +pow(M[2][0],2); double pv13N2 = pow(M[0][1],2) +pow(M[1][1],2) +pow(M[2][1],2); double pv14N2 = pow(M[0][2],2) +pow(M[1][2],2) +pow(M[2][2],2); double pv12N = sqrt(pv12N2); double pv13N = sqrt(pv13N2); double pv14N = sqrt(pv14N2); double cp12 = (M[0][0]*M[0][1]+M[1][0]*M[1][1]+M[2][0]*M[2][1]); double cp13 = (M[0][0]*M[0][2]+M[1][0]*M[1][2]+M[2][0]*M[2][2]); double cp23 = (M[0][1]*M[0][2]+M[1][1]*M[1][2]+M[2][1]*M[2][2]); double ratio = detM/ (pv12N*pv13N*pv14N+cp12*pv14N+cp13*pv13N+cp23*pv12N); return abs(2*atan(ratio)); } template double Network::surfaceSolidThroat(CellHandle cell, int j, bool slipBoundary, bool reuseFacetData) { if (!reuseFacetData) facetNFictious=detectFacetFictiousVertices(cell,j); Point& p1 = cell->info(); Point& p2 = cell->neighbor(j)->info(); double Ssolid = 0; double Ssolid1= 0, Ssolid1n= 0, Ssolid2= 0, Ssolid2n= 0, Ssolid3= 0, Ssolid3n= 0; Sphere v [3]; VertexHandle W [3]; for (int kk=0; kk<3; kk++) { W[kk] = cell->vertex(facetVertices[j][kk]); v[kk] = cell->vertex(facetVertices[j][kk])->point();} switch (facetNFictious) { case (0) : { VertexHandle& SV1 = W[0]; VertexHandle& SV2 = W[1]; VertexHandle& SV3 = W[2]; Ssolid1 = fastSphericalTriangleArea(SV1->point(), SV2->point(), p1, p2); Ssolid1n = fastSphericalTriangleArea(SV1->point(), SV3->point(), p1, p2); cell->info().solidSurfaces[j][0]=Ssolid1+Ssolid1n; Ssolid2 = fastSphericalTriangleArea(SV2->point(),SV1->point(),p1, p2); Ssolid2n = fastSphericalTriangleArea(SV2->point(),SV3->point(),p1, p2); cell->info().solidSurfaces[j][1]=Ssolid2+Ssolid2n; Ssolid3 = fastSphericalTriangleArea(SV3->point(),SV2->point(),p1, p2); Ssolid3n = fastSphericalTriangleArea(SV3->point(),SV1->point(),p1, p2); cell->info().solidSurfaces[j][2]=Ssolid3+Ssolid3n; }; break; case (1) : { VertexHandle SV1 = cell->vertex(facetVertices[j][facetF1]); VertexHandle SV2 = cell->vertex(facetVertices[j][facetRe1]); VertexHandle SV3 = cell->vertex(facetVertices[j][facetRe2]); Boundary &bi1 = boundary(SV1->info().id()); Ssolid1 = 0; if (bi1.flowCondition && ! slipBoundary) { Ssolid1 = abs(0.5*CGAL::cross_product(p1-p2, SV2->point()-SV3->point())[bi1.coordinate]); cell->info().solidSurfaces[j][facetF1]=Ssolid1; } Ssolid2 = fastSphericalTriangleArea(SV2->point(),SV1->point(),p1, p2); Ssolid2n = fastSphericalTriangleArea(SV2->point(),SV3->point(),p1, p2); cell->info().solidSurfaces[j][facetRe1]=Ssolid2+Ssolid2n; Ssolid3 = fastSphericalTriangleArea(SV3->point(),SV2->point(),p1, p2); Ssolid3n = fastSphericalTriangleArea(SV3->point(),SV1->point(),p1, p2); cell->info().solidSurfaces[j][facetRe2]=Ssolid3+Ssolid3n; }; break; case (2) : { double A [3], B[3], C[3]; VertexHandle SV1 = cell->vertex(facetVertices[j][facetF1]); VertexHandle SV2 = cell->vertex(facetVertices[j][facetF2]); VertexHandle SV3 = cell->vertex(facetVertices[j][facetRe1]); Boundary &bi1 = boundary(SV1->info().id()); Boundary &bi2 = boundary(SV2->info().id()); for (int m=0;m<3;m++) { A[m]=B[m]=C[m]= (SV3->point())[m]; } A[bi1.coordinate]=bi1.p[bi1.coordinate]; B[bi2.coordinate]=bi2.p[bi2.coordinate]; C[bi1.coordinate]=bi1.p[bi1.coordinate]; C[bi2.coordinate]=bi2.p[bi2.coordinate]; Point AA(A[0],A[1],A[2]); Point BB(B[0],B[1],B[2]); Point CC(C[0],C[1],C[2]); Sphere A1(AA, 0); Sphere B1(BB, 0); Sphere C1(CC, 0); //FIXME : we are computing triangle area twice here, because its computed in volume_double_fictious already -> optimize Ssolid1 = fastSphericalTriangleArea(SV3->point(), AA, p1, p2); Ssolid1n = fastSphericalTriangleArea(SV3->point(), BB, p1, p2); cell->info().solidSurfaces[j][facetRe1]=Ssolid1+Ssolid1n; //area vector of triangle (p1,sphere,p2) CVector p1p2v1Surface = 0.5*CGAL::cross_product(p1-p2,SV3->point()-p2); if (bi1.flowCondition && ! slipBoundary) { //projection on boundary 1 Ssolid2 = abs(p1p2v1Surface[bi1.coordinate]); cell->info().solidSurfaces[j][facetF1]=Ssolid2; } else cell->info().solidSurfaces[j][facetF1]=0; if (bi2.flowCondition && ! slipBoundary) { //projection on boundary 2 Ssolid3 = abs(p1p2v1Surface[bi2.coordinate]); cell->info().solidSurfaces[j][facetF2]=Ssolid3; } else cell->info().solidSurfaces[j][facetF2]=0; }; break; } Ssolid = Ssolid1+Ssolid1n+Ssolid2+Ssolid2n+Ssolid3+Ssolid3n; if (Ssolid) cell->info().solidSurfaces[j][3]=1.0/Ssolid; else cell->info().solidSurfaces[j][3]=0; sSolidTot += Ssolid; return Ssolid; } template double Network::surfaceSolidThroatInPore(CellHandle cell, int j, bool slipBoundary, bool reuseFacetData) { if (!reuseFacetData) facetNFictious=detectFacetFictiousVertices(cell,j); Point& p1 = cell->info(); Point& p2 = cell->neighbor(j)->info(); double Ssolid1= 0, Ssolid2= 0, Ssolid3= 0; Sphere v [3]; VertexHandle W [3]; for (int kk=0; kk<3; kk++) { W[kk] = cell->vertex(facetVertices[j][kk]); v[kk] = cell->vertex(facetVertices[j][kk])->point();} switch (facetNFictious) { case (0) : { VertexHandle& SV1 = W[0]; VertexHandle& SV2 = W[1]; VertexHandle& SV3 = W[2]; Ssolid1 = fastSphericalTriangleArea(SV1->point(), SV2->point(), p1, SV3->point()); Ssolid2 = fastSphericalTriangleArea(SV2->point(),SV1->point(),p1, SV3->point()); Ssolid3 = fastSphericalTriangleArea(SV3->point(),SV2->point(),p1, SV1->point()); }; break; case (1) : { VertexHandle SV1 = cell->vertex(facetVertices[j][facetF1]); VertexHandle SV2 = cell->vertex(facetVertices[j][facetRe1]); VertexHandle SV3 = cell->vertex(facetVertices[j][facetRe2]); Boundary &bi1 = boundary(SV1->info().id()); Ssolid1 = 0; if (bi1.flowCondition && ! slipBoundary) Ssolid1 = abs(0.5*CGAL::cross_product(p1-SV2->point(), SV2->point()-SV3->point())[bi1.coordinate]); Ssolid2 = fastSphericalTriangleArea(SV2->point(),SV3->point(),p1, SV2->point()+bi1.normal); Ssolid3 = fastSphericalTriangleArea(SV3->point(),SV2->point(),p1, SV3->point()+bi1.normal); }; break; case (2) : { double A [3], B[3], C[3]; VertexHandle SV1 = cell->vertex(facetVertices[j][facetF1]); VertexHandle SV2 = cell->vertex(facetVertices[j][facetF2]); VertexHandle SV3 = cell->vertex(facetVertices[j][facetRe1]); Boundary &bi1 = boundary(SV1->info().id()); Boundary &bi2 = boundary(SV2->info().id()); for (int m=0;m<3;m++) {A[m]=B[m]=C[m]= (SV3->point())[m];} A[bi1.coordinate]=bi1.p[bi1.coordinate]; B[bi2.coordinate]=bi2.p[bi2.coordinate]; C[bi1.coordinate]=bi1.p[bi1.coordinate]; C[bi2.coordinate]=bi2.p[bi2.coordinate]; Point AA(A[0],A[1],A[2]); Point BB(B[0],B[1],B[2]); Point CC(C[0],C[1],C[2]); Sphere A1(AA, 0); Sphere B1(BB, 0); Sphere C1(CC, 0); //FIXME : we are computing triangle area twice here, because its computed in volume_double_fictious already -> optimize Ssolid1 = 0.5*(fastSphericalTriangleArea(SV3->point(), AA, p1, p2)+ fastSphericalTriangleArea(SV3->point(), BB, p1, p2)); CVector p1p2v1Surface = 0.5*CGAL::cross_product(p1-p2,SV3->point()-p2); if (bi1.flowCondition && ! slipBoundary) Ssolid2 = 0.5*abs(p1p2v1Surface[bi1.coordinate]); if (bi2.flowCondition && ! slipBoundary) Ssolid3 = 0.5*abs(p1p2v1Surface[bi2.coordinate]); }; break; } return Ssolid1+Ssolid2+Ssolid3; } template CVector Network::surfaceDoubleFictiousFacet(VertexHandle fSV1, VertexHandle fSV2, VertexHandle SV3) { //This function is correct only with axis-aligned boundaries const Boundary &bi1 = boundary(fSV1->info().id()); const Boundary &bi2 = boundary(fSV2->info().id()); double area=(bi1.p[bi1.coordinate]-SV3->point()[bi1.coordinate])*(bi2.p[bi2.coordinate]-SV3->point()[bi2.coordinate]); double surf [3] = {1,1,1}; surf[bi1.coordinate]=0; surf[bi2.coordinate]=0; return area*CVector(surf[0],surf[1],surf[2]); } template CVector Network::surfaceSingleFictiousFacet(VertexHandle fSV1, VertexHandle SV2, VertexHandle SV3) { //This function is correct only with axis-aligned boundaries const Boundary &bi1 = boundary(fSV1->info().id()); // const Boundary &bi2 = boundary ( fSV2->info().id() ); CVector mean_height = (bi1.p[bi1.coordinate]-0.5*(SV3->point()[bi1.coordinate]+SV2->point()[bi1.coordinate]))*bi1.normal; return CGAL::cross_product(mean_height,SV3->point()-SV2->point()); } template double Network::surfaceSolidDoubleFictiousFacet(VertexHandle SV1, VertexHandle SV2, VertexHandle SV3) { double A [3], B [3]; for (int m=0;m<3;m++) { A[m]=B[m]= (SV3->point())[m]; } const Boundary &bi1 = boundary(SV1->info().id()); const Boundary &bi2 = boundary(SV2->info().id()); A[bi1.coordinate]=bi1.p[bi1.coordinate]; B[bi2.coordinate]=bi2.p[bi2.coordinate]; double board1=0, board2=0, total_surface=0; for (int p=0;p<3;p++) { board1 += pow((SV3->point()[p]-A[p]),2); board2 += pow((SV3->point()[p]-B[p]),2); } total_surface = sqrt(board1 * board2); double solid_surface = surfaceSolidFacet(SV3->point(),SV2->point(),SV1->point()); return total_surface - solid_surface; } template double Network::surfaceSolidFacet(Sphere ST1, Sphere ST2, Sphere ST3) { double Area; double squared_radius = ST1.weight(); CVector v12 = ST2.point() - ST1.point(); CVector v13 = ST3.point() - ST1.point(); double norme12 = v12.squared_length(); double norme13 = v13.squared_length(); double cosA = v12*v13 / (sqrt(norme13 * norme12)); double A = acos(cosA); Area = (A/ (2*M_PI)) * (M_PI * squared_radius); return Area; } template void Network::addBoundingPlanes() { Tesselation& Tes = T[currentTes]; //FIXME: Id's order in boundsIds is done according to the enumerotation of boundaries from TXStressController.hpp, line 31. DON'T CHANGE IT! yMinId = Tes.Max_id() + 2; boundsIds[0]=&yMinId; yMaxId = Tes.Max_id() + 3; boundsIds[1]=&yMaxId; xMinId = Tes.Max_id() + 0; boundsIds[2]=&xMinId; xMaxId = Tes.Max_id() + 1; boundsIds[3]=&xMaxId; zMinId = Tes.Max_id() + 5; boundsIds[4]=&zMaxId; zMaxId = Tes.Max_id() + 6; boundsIds[5]=&zMinId; cornerMin = Point(xMin, yMin, zMin); cornerMax = Point(xMax, yMax, zMax); idOffset = Tes.Max_id() +1;//so that boundaries[vertex->id - offset] gives the ordered boundaries (also see function Boundary& boundary(int b)) addBoundingPlane (CVector(0,1,0) , yMinId); addBoundingPlane (CVector(0,-1,0) , yMaxId); addBoundingPlane (CVector(-1,0,0) , xMaxId); addBoundingPlane (CVector(1,0,0) , xMinId); addBoundingPlane (CVector(0,0,1) , zMinId); addBoundingPlane (CVector(0,0,-1) , zMaxId); // addBoundingPlanes(true); } template void Network::addBoundingPlane (CVector Normal, int id_wall) { // Tesselation& Tes = T[currentTes]; //FIXME: pre-condition: the normal is axis-aligned int Coordinate = abs(Normal[0])*0 + abs(Normal[1])*1 + abs(Normal[2])*2; double pivot = Normal[Coordinate]<0 ? cornerMax.x()*abs(Normal[0])+cornerMax.y()*abs(Normal[1])+cornerMax.z()*abs(Normal[2]) : cornerMin.x()*abs(Normal[0])+cornerMin.y()*abs(Normal[1])+cornerMin.z()*abs(Normal[2]); Real center [3] ={ 0.5*(cornerMin.x() +cornerMax.x())*(1-abs(Normal[0]))+pivot*abs(Normal[0]), 0.5*(cornerMax.y() +cornerMin.y())*(1-abs(Normal[1]))+pivot*abs(Normal[1]), 0.5*(cornerMax.z() +cornerMin.z())*(1-abs(Normal[2]))+pivot*abs(Normal[2])}; addBoundingPlane(center,0,Normal,id_wall); } template void Network::addBoundingPlane (Real center[3], double thickness, CVector Normal, int id_wall ) { Tesselation& Tes = T[currentTes]; int Coordinate = abs(Normal[0])*0 + abs(Normal[1])*1 + abs(Normal[2])*2; Tes.insert((center[0]+Normal[0]*thickness/2)*(1-abs(Normal[0])) + (center[0]+Normal[0]*thickness/2-Normal[0]*FAR*(cornerMax.y()-cornerMin.y()))*abs(Normal[0]), (center[1]+Normal[1]*thickness/2)*(1-abs(Normal[1])) + (center[1]+Normal[1]*thickness/2-Normal[1]*FAR*(cornerMax.y()-cornerMin.y()))*abs(Normal[1]), (center[2]+Normal[2]*thickness/2)*(1-abs(Normal[2])) + (center[2]+Normal[2]*thickness/2-Normal[2]*FAR*(cornerMax.y()-cornerMin.y()))*abs(Normal[2]), FAR*(cornerMax.y()-cornerMin.y()), id_wall, true); Point P (center[0],center[1],center[2]); boundaries[id_wall-idOffset].p = P; boundaries[id_wall-idOffset].normal = Normal; boundaries[id_wall-idOffset].coordinate = Coordinate; boundaries[id_wall-idOffset].flowCondition = 1; boundaries[id_wall-idOffset].value = 0; if(debugOut) cout << "A boundary -center/thick- has been created. ID = " << id_wall << " position = " << (center[0]+Normal[0]*thickness/2)*(1-abs(Normal[0])) + (center[0]+Normal[0]*thickness/2-Normal[0]*FAR*(cornerMax.y()-cornerMin.y()))*abs(Normal[0]) << " , " << (center[1]+Normal[1]*thickness/2)*(1-abs(Normal[1])) + (center[1]+Normal[1]*thickness/2-Normal[1]*FAR*(cornerMax.y()-cornerMin.y()))*abs(Normal[1]) << " , " << (center[2]+Normal[2]*thickness/2)*(1-abs(Normal[2])) + (center[2]+Normal[2]*thickness/2-Normal[2]*FAR*(cornerMax.y()-cornerMin.y()))*abs(Normal[2]) << ". Radius = " << FAR*(cornerMax.y()-cornerMin.y()) << endl; } template void Network::defineFictiousCells() { RTriangulation& Tri = T[currentTes].Triangulation(); FiniteCellsIterator cellEnd = Tri.finite_cells_end(); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++) { cell->info().fictious()=0;} for (int bound=0; bound<6;bound++) { int& id = *boundsIds[bound]; if (id<0) continue; VectorCell tmpCells; tmpCells.resize(10000); VCellIterator cells_it = tmpCells.begin(); VCellIterator cells_end = Tri.incident_cells(T[currentTes].vertexHandles[id],cells_it); for (VCellIterator it = tmpCells.begin(); it != cells_end; it++) { CellHandle& cell = *it; (cell->info().fictious())+=1; cell->info().isFictious=true; } } if(debugOut) cout << "Fictious cell defined" << endl; } // double Network::sphericalTriangleArea ( Sphere STA1, Sphere STA2, Sphere STA3, Point PTA1 ) // { // double rayon = STA1.weight(); // if ( rayon == 0.0 ) return 0.0; // // CVector v12 = STA2.point() - STA1.point(); // CVector v13 = STA3.point() - STA1.point(); // CVector v14 = PTA1 - STA1.point(); // // double norme12 = ( v12.squared_length() ); // double norme13 = ( v13.squared_length() ); // double norme14 = ( v14.squared_length() ); // // double cosA = v12*v13 / sqrt ( ( norme13 * norme12 ) ); // double cosB = v12*v14 / sqrt ( ( norme14 * norme12 ) ); // double cosC = v14*v13 / sqrt ( ( norme13 * norme14 ) ); // // double A = acos ( cosA ); // double B = acos ( cosB ); // double C = acos ( cosC ); // if ( A==0 || B==0 || C==0 ) return 0; // // double a = acos ( ( cosA - cosB * cosC ) / ( sin ( B ) * sin ( C ) ) ); // double b = acos ( ( cosB - cosC * cosA ) / ( sin ( C ) * sin ( A ) ) ); // double c = acos ( ( cosC - cosA * cosB ) / ( sin ( A ) * sin ( B ) ) ); // // double aire_triangle_spherique = rayon * ( a + b + c - M_PI ); // // return aire_triangle_spherique; // } template void Network::lineSolidPore(CellHandle cell, int j) { facetNFictious=detectFacetFictiousVertices(cell,j); double lSolid = 0; //total of solidLine[j][0], solidLine[j][1], solidLine[j][2]. Sphere v [3]; VertexHandle W [3]; for (int kk=0; kk<3; kk++) { W[kk] = cell->vertex(facetVertices[j][kk]); v[kk] = cell->vertex(facetVertices[j][kk])->point();} switch (facetNFictious) { case (0) : { VertexHandle& SV1 = W[0]; VertexHandle& SV2 = W[1]; VertexHandle& SV3 = W[2]; cell->info().solidLine[j][0]=lineSolidFacet(SV1->point(), SV2->point(), SV3->point()); cell->info().solidLine[j][1]=lineSolidFacet(SV2->point(), SV3->point(), SV1->point()); cell->info().solidLine[j][2]=lineSolidFacet(SV3->point(), SV1->point(), SV2->point()); }; break; case (1) : { VertexHandle SV1 = cell->vertex(facetVertices[j][facetRe1]); VertexHandle SV2 = cell->vertex(facetVertices[j][facetRe2]); VertexHandle SV3 = cell->vertex(facetVertices[j][facetF1]); cell->info().solidLine[j][facetRe1]=lineSolidFacet(SV1->point(), SV2->point(), SV3->point()); cell->info().solidLine[j][facetRe2]=lineSolidFacet(SV2->point(), SV1->point(), SV3->point()); Boundary &bi = boundary(SV3->info().id()); double A [3], B[3]; for (int m=0;m<3;m++) {A[m]=SV1->point()[m];B[m]= SV2->point()[m];} A[bi.coordinate]=bi.p[bi.coordinate]; B[bi.coordinate]=bi.p[bi.coordinate]; Point AA(A[0],A[1],A[2]); Point BB(B[0],B[1],B[2]); CVector AB= AA-BB; cell->info().solidLine[j][facetF1]=sqrt(AB.squared_length()); }; break; case (2) : { VertexHandle SV1 = cell->vertex(facetVertices[j][facetF1]); VertexHandle SV2 = cell->vertex(facetVertices[j][facetF2]); VertexHandle SV3 = cell->vertex(facetVertices[j][facetRe1]); cell->info().solidLine[j][facetRe1]=0.5*M_PI*sqrt(SV3->point().weight()); Boundary &bi1 = boundary(SV1->info().id()); Boundary &bi2 = boundary(SV2->info().id()); double d13 = bi1.p[bi1.coordinate] - (SV3->point())[bi1.coordinate]; double d23 = bi2.p[bi2.coordinate] - (SV3->point())[bi2.coordinate]; cell->info().solidLine[j][facetF1]= abs(d23); cell->info().solidLine[j][facetF2]= abs(d13); }; break; } lSolid = cell->info().solidLine[j][0] + cell->info().solidLine[j][1] + cell->info().solidLine[j][2]; if (lSolid) cell->info().solidLine[j][3]=1.0/lSolid; else cell->info().solidLine[j][3]=0; } template double Network::lineSolidFacet(Sphere ST1, Sphere ST2, Sphere ST3) { double line; double squaredRadius = ST1.weight(); CVector v12 = ST2.point() - ST1.point(); CVector v13 = ST3.point() - ST1.point(); double norme12 = v12.squared_length(); double norme13 = v13.squared_length(); double cosA = v12*v13 / (sqrt(norme13 * norme12)); line = acos(cosA) * sqrt(squaredRadius); return line; } } //namespace CGT #endif //FLOW_ENGINE trunk-2017.01a/lib/triangulation/PeriodicFlow.hpp000066400000000000000000000551411304022710500217150ustar00rootroot00000000000000#ifdef FLOW_ENGINE #pragma once #include //include after #define XVIEW // #include "Timer.h" // #include "PeriodicTesselation.h" // #include "basicVTKwritter.hpp" // #include "Timer.h" // #include "Network.hpp" // // #ifdef XVIEW // #include "Vue3D.h" //FIXME implicit dependencies will look for this class (out of tree) even ifndef XVIEW // #endif /* TODO: - remove computePermeability(), mostly a duplicate of the non-periodic version */ namespace CGT{ // typedef CGT::FlowBoundingSphere PeriodicFlowBoundingSphere; template class PeriodicFlow : public CGT::FlowBoundingSphere<_Tesselation> { public: typedef _Tesselation Tesselation; typedef Network _N; DECLARE_TESSELATION_TYPES(Network) typedef CGT::FlowBoundingSphere<_Tesselation> BaseFlowSolver; //painfull, but we need that for templates inheritance... using _N::T; using _N::xMin; using _N::xMax; using _N::yMin; using _N::yMax; using _N::zMin; using _N::zMax; using _N::Rmoy; using _N::sectionArea; using _N::Height; using _N::vTotal; using _N::currentTes; using _N::debugOut; using _N::nOfSpheres; using _N::xMinId; using _N::xMaxId; using _N::yMinId; using _N::yMaxId; using _N::zMinId; using _N::zMaxId; using _N::boundsIds; using _N::cornerMin; using _N::cornerMax; using _N::VSolidTot; using _N::Vtotalissimo; using _N::vPoral; using _N::sSolidTot; using _N::vPoralPorosity; using _N::vTotalPorosity; using _N::boundaries; using _N::idOffset; using _N::vtkInfiniteVertices; using _N::vtkInfiniteCells; using _N::num_particles; using _N::boundingCells; using _N::facetVertices; using _N::facetNFictious; using BaseFlowSolver::noCache; using BaseFlowSolver::rAverage; using BaseFlowSolver::distanceCorrection; using BaseFlowSolver::minPermLength; using BaseFlowSolver::checkSphereFacetOverlap; using BaseFlowSolver::viscosity; using BaseFlowSolver::kFactor; using BaseFlowSolver::permeabilityMap; using BaseFlowSolver::maxKdivKmean; using BaseFlowSolver::clampKValues; using BaseFlowSolver::KOptFactor; using BaseFlowSolver::meanKStat; using BaseFlowSolver::fluidBulkModulus; using BaseFlowSolver::relax; using BaseFlowSolver::tolerance; using BaseFlowSolver::minKdivKmean; using BaseFlowSolver::resetRHS; //same for functions using _N::defineFictiousCells; using _N::addBoundingPlanes; using _N::boundary; void interpolate(Tesselation& Tes, Tesselation& NewTes); void computeFacetForcesWithCache(bool onlyCache=false); void computePermeability(); void gaussSeidel(Real dt=0); void displayStatistics(); #ifdef EIGENSPARSE_LIB //Eigen's sparse matrix for forces computation // Eigen::SparseMatrix FIntegral; // Eigen::SparseMatrix PshiftsInts; // Eigen::SparseMatrix FRHS; // Eigen::VectorXd forces; #endif }; template void PeriodicFlow<_Tesselation>::interpolate(Tesselation& Tes, Tesselation& NewTes) { CellHandle oldCell; RTriangulation& Tri = Tes.Triangulation(); for (VCellIterator cellIt=NewTes.cellHandles.begin(); cellIt!=NewTes.cellHandles.end(); cellIt++){ CellHandle& newCell = *cellIt; if (newCell->info().Pcondition || newCell->info().isGhost) continue; CVector center ( 0,0,0 ); if (newCell->info().fictious()==0) for ( int k=0;k<4;k++ ) center= center + 0.25* (Tes.vertex(newCell->vertex(k)->info().id())->point()-CGAL::ORIGIN); else { Real boundPos=0; int coord=0; for ( int k=0;k<4;k++ ) { if (!newCell->vertex (k)->info().isFictious) center= center+0.3333333333*(Tes.vertex(newCell->vertex(k)->info().id())->point()-CGAL::ORIGIN); else { coord=boundary (newCell->vertex(k)->info().id()).coordinate; boundPos=boundary (newCell->vertex(k)->info().id()).p[coord]; } } center=CVector(coord==0?boundPos:center[0],coord==1?boundPos:center[1],coord==2?boundPos:center[2]); } oldCell = Tri.locate(Point(center[0],center[1],center[2])); //FIXME: should use getInfo newCell->info().p() = oldCell->info().shiftedP(); } // Tes.Clear();//Don't reset to avoid segfault when getting pressure in scripts just after interpolation } template void PeriodicFlow<_Tesselation>::computeFacetForcesWithCache(bool onlyCache) { RTriangulation& Tri = T[currentTes].Triangulation(); CVector nullVect(0,0,0); static vector oldForces; if (oldForces.size()<=Tri.number_of_vertices()) oldForces.resize(Tri.number_of_vertices()+1); //reset forces for (FiniteVerticesIterator v = Tri.finite_vertices_begin(); v != Tri.finite_vertices_end(); ++v) { if (noCache) {oldForces[v->info().id()]=nullVect; v->info().forces=nullVect;} else {oldForces[v->info().id()]=v->info().forces; v->info().forces=nullVect;} } CellHandle neighbourCell; VertexHandle mirrorVertex; CVector tempVect; //FIXME : Ema, be carefull with this (noCache), it needs to be turned true after retriangulation if (noCache) { for (VCellIterator cellIt=T[currentTes].cellHandles.begin(); cellIt!=T[currentTes].cellHandles.end(); cellIt++){ CellHandle& cell = *cellIt; for (int k=0;k<4;k++) cell->info().unitForceVectors[k]=nullVect; for (int j=0; j<4; j++) if (!Tri.is_infinite(cell->neighbor(j))) { // #ifdef EIGENSPARSE_LIB // if (!cell->info().Pcondition) ++nPCells; // #endif neighbourCell = cell->neighbor(j); const CVector& Surfk = cell->info().facetSurfaces[j]; //FIXME : later compute that fluidSurf only once in hydraulicRadius, for now keep full surface not modified in cell->info for comparison with other forces schemes //The ratio void surface / facet surface Real area = sqrt(Surfk.squared_length()); CVector facetNormal = Surfk/area; const std::vector& crossSections = cell->info().facetSphereCrossSections; CVector fluidSurfk = cell->info().facetSurfaces[j]*cell->info().facetFluidSurfacesRatio[j]; /// handle fictious vertex since we can get the projected surface easily here if (cell->vertex(j)->info().isFictious) { Real projSurf=abs(Surfk[boundary(cell->vertex(j)->info().id()).coordinate]); tempVect=-projSurf*boundary(cell->vertex(j)->info().id()).normal; //define the cached value for later use with cache*p cell->info().unitForceVectors[j]=cell->info().unitForceVectors[j]+ tempVect; } /// Apply weighted forces f_k=sqRad_k/sumSqRad*f CVector facetUnitForce = -fluidSurfk*cell->info().solidSurfaces[j][3]; for (int y=0; y<3;y++) { //add to cached value cell->info().unitForceVectors[facetVertices[j][y]]=cell->info().unitForceVectors[facetVertices[j][y]]+facetUnitForce*cell->info().solidSurfaces[j][y]; //uncomment to get total force / comment to get only viscous forces (Bruno) if (!cell->vertex(facetVertices[j][y])->info().isFictious) { //add to cached value cell->info().unitForceVectors[facetVertices[j][y]]=cell->info().unitForceVectors[facetVertices[j][y]]-facetNormal*crossSections[j][y]; } } } } noCache=false;//cache should always be defined after execution of this function if (onlyCache) return; }// end if(noCache) //use cached values //First define products that will be used below for all cells: Real pDeltas [3]; for (unsigned int k=0; k<3;k++) pDeltas[k]=CellInfo::hSize[k]*CellInfo::gradP; //Then compute the forces for (VCellIterator cellIt=T[currentTes].cellHandles.begin(); cellIt!=T[currentTes].cellHandles.end(); cellIt++){ const CellHandle& cell = *cellIt; for (int yy=0;yy<4;yy++) { VertexInfo& vhi = cell->vertex(yy)->info(); Real unshiftedP = cell->info().p(); //the pressure translated to a ghost cell adjacent to the non-ghost vertex unshiftedP -= pDeltas[0]*vhi.period[0] + pDeltas[1]*vhi.period[1] +pDeltas[2]*vhi.period[2]; T[currentTes].vertexHandles[vhi.id()]->info().forces=T[currentTes].vertexHandles[vhi.id()]->info().forces + cell->info().unitForceVectors[yy]*unshiftedP; } } if (debugOut) { CVector totalForce = nullVect; for (FiniteVerticesIterator v = Tri.finite_vertices_begin(); v != Tri.finite_vertices_end(); v++) { if (!v->info().isFictious /*&& !v->info().isGhost*/ ){ totalForce = totalForce + v->info().forces;} else /*if (!v->info().isGhost)*/{ if (boundary(v->info().id()).flowCondition==1) totalForce = totalForce + v->info().forces; } } cout << "totalForce = "<< totalForce << endl;} } template void PeriodicFlow<_Tesselation>::computePermeability() { if (debugOut) cout << "----Computing_Permeability (Periodic)------" << endl; RTriangulation& Tri = T[currentTes].Triangulation(); VSolidTot = 0, Vtotalissimo = 0, vPoral = 0, sSolidTot = 0, vTotalPorosity=0, vPoralPorosity=0; CellHandle neighbourCell; double k=0, distance = 0, radius = 0; int surfneg=0; int NEG=0, POS=0, pass=0; Real meanK=0, STDEV=0, meanRadius=0, meanDistance=0; Real infiniteK=1e3; double volume_sub_pore = 0.f; VectorCell& cellHandles= T[currentTes].cellHandles; for (VCellIterator cellIt=T[currentTes].cellHandles.begin(); cellIt!=T[currentTes].cellHandles.end(); cellIt++){ CellHandle& cell = *cellIt; Point& p1 = cell->info(); if (cell->info().blocked) { this->setBlocked(cell);} if (cell->info().isGhost) {cerr<<"skipping a ghost"<neighbor(j); Point& p2 = neighbourCell->info(); if (!Tri.is_infinite(neighbourCell) /*&& (neighbour_cell->info().isvisited==ref || computeAllCells)*/) { //compute and store the area of sphere-facet intersections for later use VertexHandle W [3]; for (int kk=0; kk<3; kk++) { W[kk] = cell->vertex(facetVertices[j][kk]); } Sphere& v0 = W[0]->point(); Sphere& v1 = W[1]->point(); Sphere& v2 = W[2]->point(); #ifdef USE_FAST_MATH //FIXME : code not compiling,, do the same as in "else" assert((W[permut3[jj][1]]->point()-W[permut3[jj][0]]->point())*(W[permut3[jj][2]]->point()-W[permut3[jj][0]]->point())>=0 && (W[permut3[jj][1]]->point()-W[permut3[jj][0]]->point())*(W[permut3[jj][2]]->point()-W[permut3[jj][0]]->point())<=1); for (int jj=0;jj<3;jj++) cell->info().facetSphereCrossSections[j][jj]=0.5*W[jj]->point().weight()*Wm3::FastInvCos1((W[permut3[jj][1]]->point()-W[permut3[jj][0]]->point())*(W[permut3[jj][2]]->point()-W[permut3[jj][0]]->point())); #else cell->info().facetSphereCrossSections[j]=CVector( W[0]->info().isFictious ? 0 : 0.5*v0.weight()*acos((v1-v0)*(v2-v0)/sqrt((v1-v0).squared_length()*(v2-v0).squared_length())), W[1]->info().isFictious ? 0 : 0.5*v1.weight()*acos((v0-v1)*(v2-v1)/sqrt((v1-v0).squared_length()*(v2-v1).squared_length())), W[2]->info().isFictious ? 0 : 0.5*v2.weight()*acos((v0-v2)*(v1-v2)/sqrt((v1-v2).squared_length()*(v2-v0).squared_length()))); #endif //FIXME: it should be possible to skip completely blocked cells, currently the problem is it segfault for undefined areas //if (cell->info().blocked) continue;//We don't need permeability for blocked cells, it will be set to zero anyway pass+=1; CVector l = p1 - p2; distance = sqrt(l.squared_length()); if (!rAverage) radius = 2* this->computeHydraulicRadius(cell, j); else radius = (this->computeEffectiveRadius(cell, j)+this->computeEquivalentRadius(cell,j))*0.5; if (radius<0) NEG++; else POS++; if (radius==0) { cout << "INS-INS PROBLEM!!!!!!!" << endl; } Real fluidArea=0; int test=0; if (distance!=0) { if (minPermLength>0 && distanceCorrection) distance=max(minPermLength*radius,distance); const CVector& Surfk = cell->info().facetSurfaces[j]; Real area = sqrt(Surfk.squared_length()); const CVector& crossSections = cell->info().facetSphereCrossSections[j]; Real S0=0; S0=checkSphereFacetOverlap(v0,v1,v2); if (S0==0) S0=checkSphereFacetOverlap(v1,v2,v0); if (S0==0) S0=checkSphereFacetOverlap(v2,v0,v1); //take absolute value, since in rare cases the surface can be negative (overlaping spheres) fluidArea=abs(area-crossSections[0]-crossSections[1]-crossSections[2]+S0); cell->info().facetFluidSurfacesRatio[j]=fluidArea/area; // kFactor<0 means we replace Poiseuille by Darcy localy, yielding a particle size-independent bulk conductivity if (kFactor>0) cell->info().kNorm()[j]= kFactor*(fluidArea * pow(radius,2)) / (8*viscosity*distance); else cell->info().kNorm()[j]= -kFactor * area / distance; meanDistance += distance; meanRadius += radius; meanK += (cell->info().kNorm())[j]; if (k<0 && debugOut) {surfneg+=1; cout<<"__ k<0 __"<info().id()<<" "<info().id()<<" "<info().id()<<" "<info().isGhost) (neighbourCell->info().kNorm())[Tri.mirror_index(cell, j)]= (cell->info().kNorm())[j]; //The following block is correct but not very usefull, since all values are clamped below with MIN and MAX, skip for now // else {//find the real neighbor connected to our cell through periodicity // CellHandle true_neighbour_cell = cellHandles[neighbour_cell->info().baseIndex]; // for (int ii=0;ii<4;ii++) // if (true_neighbour_cell->neighbor(ii)->info().index == cell->info().index){ // (true_neighbour_cell->info().kNorm())[ii]=(cell->info().kNorm())[j]; break; // } // } if(permeabilityMap){ CellHandle c = cell; cell->info().s = cell->info().s + k*distance/fluidArea*this->volumePoreVoronoiFraction (c,j); volume_sub_pore += this->volumePoreVoronoiFraction (c,j); } } } // cell->info().isvisited = !ref; if(permeabilityMap){ cell->info().s = cell->info().s/volume_sub_pore; volume_sub_pore = 0.f; } // } } if (debugOut) cout<<"surfneg est "<neighbor(j); if (!Tri.is_infinite(neighbourCell) /*&& neighbour_cell->info().isvisited==ref*/) { pass++; STDEV += pow(((cell->info().kNorm())[j]-meanK),2); } } } STDEV = sqrt(STDEV/pass); if (debugOut) cout << "PassSTDEV = " << pass << endl; cout << "STATISTIC K" << endl; double k_min = 0, k_max = meanK + KOptFactor*STDEV; cout << "Kmoy = " << meanK << " Standard Deviation = " << STDEV << endl; cout << "kmin = " << k_min << " kmax = " << k_max << endl; pass=0; for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++) { for (int j=0; j<4; j++) { neighbourCell = cell->neighbor(j); if (!Tri.is_infinite(neighbourCell) /*&& neighbour_cell->info().isvisited==ref*/) { pass+=1; if ((cell->info().kNorm())[j]>k_max) { (cell->info().kNorm())[j]=k_max; (neighbourCell->info().kNorm())[Tri.mirror_index(cell, j)]= (cell->info().kNorm())[j]; } k_opt_file << KOptFactor << " " << (cell->info().kNorm())[j] << endl; } } } if (debugOut) cout << "PassKopt = " << pass << endl; } if (debugOut) { FiniteVerticesIterator verticesEnd = Tri.finite_vertices_end(); Real Vgrains = 0; int grains=0; for (FiniteVerticesIterator vIt = Tri.finite_vertices_begin(); vIt != verticesEnd; vIt++) { if (!vIt->info().isFictious && !vIt->info().isGhost) { grains +=1; Vgrains += 1.33333333 * M_PI * pow(vIt->point().weight(),1.5); } } cout< void PeriodicFlow<_Tesselation>::gaussSeidel(Real dt) { RTriangulation& Tri = T[currentTes].Triangulation(); int j = 0; double m, n, dp_max, p_max, sum_p, dp, sum_dp; double compFlowFactor=0; vector previousP; previousP.resize(Tri.number_of_finite_cells()); const int num_threads=1; bool compressible= fluidBulkModulus>0; vector t_sum_p, t_dp_max, t_sum_dp, t_p_max; t_sum_dp.resize(num_threads); t_dp_max.resize(num_threads); t_p_max.resize(num_threads); t_sum_p.resize(num_threads); FiniteCellsIterator cellEnd = Tri.finite_cells_end(); do { int cell2=0; dp_max = 0; p_max = 0; sum_p=0; sum_dp=0; int bb=-1; for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++) { bb++; if ( !cell->info().Pcondition && !cell->info().isGhost) { cell2++; if (compressible && j==0) previousP[bb]=cell->info().shiftedP(); m=0, n=0; for (int j2=0; j2<4; j2++) { if (!Tri.is_infinite(cell->neighbor(j2))) { if ( compressible ) { compFlowFactor = fluidBulkModulus*dt*cell->info().invVoidVolume(); m += compFlowFactor*(cell->info().kNorm())[j2]*cell->neighbor(j2)->info().shiftedP(); if (j==0) n += compFlowFactor*(cell->info().kNorm())[j2]; } else { m += (cell->info().kNorm())[j2]*cell->neighbor(j2)->info().shiftedP(); if ( std::isinf(m) && j<10 ) cout << "(cell->info().kNorm())[j2] = " << (cell->info().kNorm())[j2] << " cell->neighbor(j2)->info().shiftedP() = " << cell->neighbor(j2)->info().shiftedP() << endl; if (j==0) n += (cell->info().kNorm())[j2]; } } } dp = cell->info().p(); if (n!=0 || j!=0) { if (j==0) { if (compressible) cell->info().invSumK=1/(1+n); else cell->info().invSumK=1/n; } if ( compressible ) { cell->info().setP( ( ((previousP[bb] - ((fluidBulkModulus*dt*cell->info().invVoidVolume())*(cell->info().dv()))) + m) * cell->info().invSumK - cell->info().shiftedP()) * relax + cell->info().shiftedP()); } else { cell->info().setP((-(cell->info().dv()-m)*cell->info().invSumK-cell->info().p())*relax+cell->info().shiftedP()); } } dp -= cell->info().p(); dp_max = max(dp_max, std::abs(dp)); p_max = max(p_max, std::abs(cell->info().shiftedP())); sum_p += cell->info().shiftedP(); sum_dp += std::abs(dp); } } j++; if (j>=40000) cerr<<"\r GS not converged after 40k iterations, break"; } while ((dp_max/p_max) > tolerance && j<40000 /*&& ( dp_max > tolerance )*//* &&*/ /*( j<50 )*/); int cel=0; double Pav=0; for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++) { cel++; Pav+=cell->info().shiftedP(); } Pav/=cel; } template void PeriodicFlow<_Tesselation>::displayStatistics() { RTriangulation& Tri = T[currentTes].Triangulation(); int Zero =0, Inside=0, Fictious=0, ghostC=0,realC=0, ghostV=0, realV=0; FiniteCellsIterator cellEnd = Tri.finite_cells_end(); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++) { int zeros =0; for (int j=0; j!=4; j++) if ((cell->info().kNorm())[j]==0) zeros+=1; if (zeros==4) Zero+=1; if (!cell->info().fictious()) Inside+=1; else Fictious+=1; if (cell->info().isGhost) ghostC+=1; else realC+=1; } int fict=0, real=0; for (FiniteVerticesIterator v = Tri.finite_vertices_begin(); v != Tri.finite_vertices_end(); ++v) { if (v->info().isFictious) fict+=1; else real+=1; } long Vertices = Tri.number_of_vertices(); long Cells = Tri.number_of_finite_cells(); long Facets = Tri.number_of_finite_facets(); if(debugOut) { cout << "zeros = " << Zero << endl; cout << "There are " << Vertices << " vertices, dont " << fict << " fictious et " << real << " reeeeeel" << std::endl; cout << "There are " << ghostV+realV << " vertices, dont " << ghostV << " ghost et " << realV << " reeeeeel" << std::endl; cout << "There are " << ghostC+realC << " cells, dont " << ghostC << " ghost et " << realC << " reeeeeel" << std::endl; cout << "There are " << Cells << " cells " << std::endl; cout << "There are " << Facets << " facets " << std::endl; cout << "There are " << Inside << " cells INSIDE." << endl; cout << "There are " << Fictious << " cells FICTIOUS." << endl; } vtkInfiniteVertices = fict; vtkInfiniteCells = Fictious; num_particles = real; } } //END NAMESPACE #ifdef LINSOLV #include "PeriodicFlowLinSolv.hpp" #endif #endif //FLOW_ENGINE trunk-2017.01a/lib/triangulation/PeriodicFlowLinSolv.hpp000066400000000000000000000070031304022710500232160ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2010 by Bruno Chareyre * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include "FlowBoundingSphere.hpp" #ifdef FLOW_ENGINE namespace CGT { template class PeriodicFlowLinSolv : public FlowBoundingSphereLinSolv<_Tesselation,PeriodicFlow<_Tesselation> > { public: typedef _Tesselation Tesselation; typedef Network _N; DECLARE_TESSELATION_TYPES(Network) typedef FlowBoundingSphereLinSolv<_Tesselation,PeriodicFlow<_Tesselation> > BaseFlowSolver; typedef typename BaseFlowSolver::ETriplet ETriplet; ///painfull, but we need that for templates inheritance... using _N::T; using _N::xMin; using _N::xMax; using _N::yMin; using _N::yMax; using _N::zMin; using _N::zMax; using _N::Rmoy; using _N::sectionArea; using _N::Height; using _N::vTotal; using _N::currentTes; using _N::debugOut; using _N::nOfSpheres; using _N::xMinId; using _N::xMaxId; using _N::yMinId; using _N::yMaxId; using _N::zMinId; using _N::zMaxId; using _N::boundsIds; using _N::cornerMin; using _N::cornerMax; using _N::VSolidTot; using _N::Vtotalissimo; using _N::vPoral; using _N::sSolidTot; using _N::vPoralPorosity; using _N::vTotalPorosity; using _N::boundaries; using _N::idOffset; using _N::vtkInfiniteVertices; using _N::vtkInfiniteCells; using _N::num_particles; using _N::boundingCells; using _N::facetVertices; using _N::facetNFictious; //same for functions using _N::defineFictiousCells; using _N::addBoundingPlanes; using _N::boundary; using BaseFlowSolver::noCache; using BaseFlowSolver::rAverage; using BaseFlowSolver::distanceCorrection; using BaseFlowSolver::minPermLength; using BaseFlowSolver::checkSphereFacetOverlap; using BaseFlowSolver::viscosity; using BaseFlowSolver::kFactor; using BaseFlowSolver::permeabilityMap; using BaseFlowSolver::maxKdivKmean; using BaseFlowSolver::clampKValues; using BaseFlowSolver::KOptFactor; using BaseFlowSolver::meanKStat; using BaseFlowSolver::fluidBulkModulus; using BaseFlowSolver::relax; using BaseFlowSolver::tolerance; using BaseFlowSolver::minKdivKmean; using BaseFlowSolver::resetRHS; /// More members from LinSolv variant using BaseFlowSolver::areCellsOrdered; using BaseFlowSolver::T_nnz; using BaseFlowSolver::ncols; using BaseFlowSolver::T_cells; using BaseFlowSolver::T_index; using BaseFlowSolver::orderedCells; using BaseFlowSolver::isLinearSystemSet; using BaseFlowSolver::T_x; using BaseFlowSolver::T_b; using BaseFlowSolver::T_bv; using BaseFlowSolver::bodv; using BaseFlowSolver::xodv; using BaseFlowSolver::errorCode; using BaseFlowSolver::useSolver; using BaseFlowSolver::tripletList; using BaseFlowSolver::A; using BaseFlowSolver::gsP; using BaseFlowSolver::gsB; using BaseFlowSolver::fullAcolumns; using BaseFlowSolver::fullAvalues; using BaseFlowSolver::isFullLinearSystemGSSet; using BaseFlowSolver::gsdV; vector indices;//redirection vector containing the rank of cell so that T_cells[indices[cell->info().index]]=cell virtual ~PeriodicFlowLinSolv(); PeriodicFlowLinSolv(); ///Linear system solve virtual int setLinearSystem(Real dt=0); virtual int setLinearSystemFullGS(Real dt=0); }; } //namespace CGTF #include "PeriodicFlowLinSolv.ipp" #endif //FLOW_ENGINE trunk-2017.01a/lib/triangulation/PeriodicFlowLinSolv.ipp000066400000000000000000000176331304022710500232310ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2010 by Bruno Chareyre * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef FLOW_ENGINE #include "CGAL/constructions/constructions_on_weighted_points_cartesian_3.h" #include #include #include #include #include #include "vector" #include #include #include #ifdef YADE_OPENMP #include #endif namespace CGT { #ifdef PARDISO #ifdef AIX #define F77_FUNC(func) func #else #define F77_FUNC(func) func ## _ #endif /* PARDISO prototype. */ extern "C" int F77_FUNC(pardisoinit) (void *, int *, int *, int *, double *, int *); extern "C" int F77_FUNC(pardiso) (void *, int *, int *, int *, int *, int *, double *, int *, int *, int *, int *, int *, int *, double *, double *, int *, double *); #endif template PeriodicFlowLinSolv<_Tesselation>::~PeriodicFlowLinSolv() { } template PeriodicFlowLinSolv<_Tesselation>::PeriodicFlowLinSolv(): BaseFlowSolver() {} template int PeriodicFlowLinSolv<_Tesselation>::setLinearSystem(Real dt) { //WARNING : boundary conditions (Pcondition, p values) must have been set for a correct definition of RTriangulation& Tri = T[currentTes].Triangulation(); vector clen; vector is; vector js; vector vs; if (!areCellsOrdered) { T_nnz=0; ncols=0; T_cells.clear(); T_index=0; unsigned int maxindex = 0; //FIXME: this is way too large since many cells will be ghosts T_cells.resize(Tri.number_of_finite_cells()+1); ///Ordered cells orderedCells.clear(); const FiniteCellsIterator cellEnd = Tri.finite_cells_end(); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++) { if (cell->info().Pcondition || cell->info().isGhost) continue; orderedCells.push_back(cell); // T_cells[++ncols]=cell; // indices[cell->info().index]=ncols; ++ncols; T_cells[cell->info().index]=cell; maxindex=max(maxindex,cell->info().index); } // spatial_sort(orderedCells.begin(),orderedCells.end(), CellTraits_for_spatial_sort());//FIXME: ordering will not work with the new "indices", which needs reordering to T_cells.resize(ncols+1); isLinearSystemSet=false; areCellsOrdered=true; } if (!isLinearSystemSet) { int n = 3*(ncols+1);//number of non-zero in triangular matrix is.resize(n); js.resize(n); vs.resize(n); T_x.resize(ncols); T_b.resize(ncols); T_bv.resize(ncols); bodv.resize(ncols); xodv.resize(ncols); T_cells.resize(ncols+1); T_nnz=0;} for (int kk=0; kkinfo().index; const CellInfo& cInfo = cell->info(); if (!isLinearSystemSet) { //Add diagonal term is[T_nnz] = index; js[T_nnz] = index; vs[T_nnz] = (cInfo.kNorm())[0]+ (cInfo.kNorm())[1]+ (cInfo.kNorm())[2]+ (cInfo.kNorm())[3]; if (vs[T_nnz]<0) cerr<<"!!!! WTF !!!"<0) vs[T_nnz] += (1.f/(dt*fluidBulkModulus*cInfo.invVoidVolume())); T_nnz++; } for (int j=0; j<4; j++) { neighbourCell = cell->neighbor(j); if (Tri.is_infinite(neighbourCell)) continue; CellInfo& nInfo = neighbourCell->info(); nIndex=nInfo.index; if (nIndex==index) { cerr<<"ERROR: nIndex==index, the cell is neighbour to itself"<< index<nIndex) { is[T_nnz] = index; js[T_nnz] = nIndex; vs[T_nnz] = - (cInfo.kNorm())[j]; if (vs[T_nnz]>0) cerr<<"!!!! WTF2 !!!"<0){ #ifdef EIGENSPARSE_LIB tripletList.clear(); tripletList.resize(T_nnz); for(int k=0;k0 not supported"< int PeriodicFlowLinSolv<_Tesselation>::setLinearSystemFullGS(Real dt) { //WARNING : boundary conditions (Pcondition, p values) must have been set for a correct definition RTriangulation& Tri = T[currentTes].Triangulation(); int n_cells=Tri.number_of_finite_cells(); if (!isFullLinearSystemGSSet){ T_cells.clear(); T_index=0;//FIXME : no need to clear if we don't re-triangulate T_nnz=0; ncols=0; const FiniteCellsIterator cellEnd = Tri.finite_cells_end(); orderedCells.clear(); T_cells.resize(n_cells+1); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++) { if (cell->info().Pcondition || cell->info().isGhost) continue; ++ncols; T_cells[cell->info().index]=cell; } // spatial_sort(orderedCells.begin(),orderedCells.end(), CellTraits_for_spatial_sort()); gsP.resize(ncols+1); gsB.resize(ncols+1); T_b.resize(ncols+1); gsdV.resize(ncols+1); fullAcolumns.resize(ncols+1); fullAvalues.resize(ncols+1); T_cells.resize(ncols+1); for (int k=0; k<=ncols;k++) { fullAcolumns[k].resize(4); fullAvalues[k].resize(5); gsdV[k]=0; } gsP[0]=0; areCellsOrdered=true; } for (int k=0; k<=ncols;k++) gsB[k]=0; if (!isFullLinearSystemGSSet){ ///Ordered cells for (int i=1; i<=ncols; i++) { CellHandle& cell = T_cells[i]; ///Non-ordered cells if (!cell->info().Pcondition && !cell->info().isGhost) { //Add diagonal term fullAvalues[cell->info().index][4] = 1.f/((cell->info().kNorm())[0]+ (cell->info().kNorm())[1]+ (cell->info().kNorm())[2]+ (cell->info().kNorm())[3] + (fluidBulkModulus>0? 1.f/(dt*fluidBulkModulus*cell->info().invVoidVolume()):0)); //DUMP T_nnz++; for (int j=0; j<4; j++) { CellHandle neighbourCell = cell->neighbor(j); const CellInfo& nInfo = neighbourCell->info(); CellInfo& cInfo = cell->info(); if (Tri.is_infinite(neighbourCell)) { fullAvalues[cInfo.index][j] = 0; //We point to the pressure of the adjacent cell. If the cell is ghost, then it has the index of the real one, and then the pointer is correct fullAcolumns[cInfo.index][j] = &gsP[0]; continue;} if (!nInfo.Pcondition) { ++T_nnz; fullAvalues[cInfo.index][j] = (cInfo.kNorm())[j]; fullAcolumns[cInfo.index][j] = &gsP[nInfo.index]; //DUMP //if the adjacent cell is ghost, we account for the pressure shift in the RHS if (nInfo.isGhost){ gsB[cInfo.index]+=cInfo.kNorm()[j]*nInfo.pShift(); } } else { fullAvalues[cInfo.index][j] = 0; fullAcolumns[cInfo.index][j] = &gsP[0]; gsB[cInfo.index]+=cInfo.kNorm()[j]*nInfo.shiftedP(); } } } } } else for (int i=1; i<=ncols; i++) { CellHandle& cell = T_cells[i]; ///Non-ordered cells if (!cell->info().Pcondition && !cell->info().isGhost) { for (int j=0; j<4; j++) { CellHandle neighbourCell = cell->neighbor(j); const CellInfo& nInfo = neighbourCell->info(); CellInfo& cInfo = cell->info(); if (!nInfo.Pcondition) { if (nInfo.isGhost) gsB[cInfo.index]+=cInfo.kNorm()[j]*nInfo.pShift(); } else gsB[cInfo.index]+=cInfo.kNorm()[j]*nInfo.shiftedP(); } } } isFullLinearSystemGSSet=true; return ncols; } } //namespace CGT #endif //FLOW_ENGINE trunk-2017.01a/lib/triangulation/RegularTriangulation.h000066400000000000000000000135701304022710500231310ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ //Define basic types from CGAL templates #pragma once #include #include #include #include #define ALPHASHAPES #ifdef ALPHASHAPES #include #include #include #endif #include #include #include #include #include #include //This include from yade let us use Eigen types #include const int facetVertices [4][3] = {{1,2,3},{0,2,3},{0,1,3},{0,1,2}}; namespace CGT { //Robust kernel typedef CGAL::Exact_predicates_inexact_constructions_kernel K; //A bit faster, but gives crash eventualy // typedef CGAL::Cartesian K; typedef CGAL::Regular_triangulation_euclidean_traits_3 Traits; typedef K::Point_3 Point; typedef Traits::Vector_3 CVector; typedef Traits::Segment_3 Segment; #ifndef NO_REAL_CHECK /** compilation inside yade: check that Real in yade is the same as Real we will define; otherwise it might make things go wrong badly (perhaps) **/ BOOST_STATIC_ASSERT(sizeof(Traits::RT)==sizeof(Real)); #endif typedef Traits::RT Real; //Dans cartesian, RT = FT typedef Traits::Weighted_point Sphere; typedef Traits::Plane_3 Plane; typedef Traits::Triangle_3 Triangle; typedef Traits::Tetrahedron_3 Tetrahedron; class SimpleCellInfo : public Point { public: //"id": unique identifier of each cell, independant of other numberings used in the fluid types. // Care to initialize it if you need it, there is no magic numbering to rely on unsigned int id; Real s; bool isFictious;//true if the cell has at least one fictious bounding sphere as a vertex SimpleCellInfo (void) {isFictious=false; s=0;} SimpleCellInfo& setPoint(const Point &p) { Point::operator= (p); return *this; } SimpleCellInfo& setScalar(const Real &scalar) { s=scalar; return *this; } inline Real x (void) {return Point::x();} inline Real y (void) {return Point::y();} inline Real z (void) {return Point::z();} inline Real& f (void) {return s;} //virtual function that will be defined for all classes, allowing shared function (e.g. for display of periodic and non-periodic with the unique function saveVTK) bool isReal (void) {return !isFictious;} }; class SimpleVertexInfo : public CVector { protected: Real s; unsigned int i; Real vol; public: bool isFictious; SimpleVertexInfo& setVector(const CVector &u) { CVector::operator= (u); return *this; } SimpleVertexInfo& setFloat(const float &scalar) { s=scalar; return *this; } SimpleVertexInfo& setId(const unsigned int &id) { i= id; return *this; } inline Real ux (void) {return CVector::x();} inline Real uy (void) {return CVector::y();} inline Real uz (void) {return CVector::z();} inline Real& f (void) {return s;} inline Real& v (void) {return vol;} inline const unsigned int& id (void) const {return i;} SimpleVertexInfo (void) {isFictious=false; s=0; i=0; vol=-1;} //virtual function that will be defined for all classes, allowing shared function (e.g. for display) bool isReal (void) {return !isFictious;} }; template class TriangulationTypes { public: typedef vertex_info Vertex_Info; typedef cell_info Cell_Info; typedef CGAL::Triangulation_vertex_base_with_info_3 Vb_info; typedef CGAL::Triangulation_cell_base_with_info_3 Cb_info; #ifdef ALPHASHAPES typedef CGAL::Alpha_shape_vertex_base_3 Vb; typedef CGAL::Alpha_shape_cell_base_3 Fb; typedef CGAL::Triangulation_data_structure_3 Tds; #else typedef CGAL::Triangulation_data_structure_3 Tds; #endif typedef CGAL::Triangulation_3 Triangulation; typedef CGAL::Regular_triangulation_3 RTriangulation; #ifdef ALPHASHAPES typedef CGAL::Alpha_shape_3 AlphaShape; #endif typedef typename RTriangulation::Vertex_iterator VertexIterator; typedef typename RTriangulation::Vertex_handle VertexHandle; typedef typename RTriangulation::Finite_vertices_iterator FiniteVerticesIterator; typedef typename RTriangulation::Cell_iterator CellIterator; typedef typename RTriangulation::Finite_cells_iterator FiniteCellsIterator; typedef typename RTriangulation::Cell_circulator CellCirculator; typedef typename RTriangulation::Cell_handle CellHandle; typedef typename RTriangulation::Facet Facet; typedef typename RTriangulation::Facet_iterator FacetIterator; typedef typename RTriangulation::Facet_circulator FacetCirculator; typedef typename RTriangulation::Finite_facets_iterator FiniteFacetsIterator; typedef typename RTriangulation::Locate_type LocateType; typedef typename RTriangulation::Edge_iterator EdgeIterator; typedef typename RTriangulation::Finite_edges_iterator FiniteEdgesIterator; }; typedef TriangulationTypes SimpleTriangulationTypes; } // namespace CGT trunk-2017.01a/lib/triangulation/Tenseur3.cpp000066400000000000000000000132341304022710500210270ustar00rootroot00000000000000#include "Tenseur3.h" #include "RegularTriangulation.h" namespace CGT { Real Tens::Norme2(void) { Real N=0; for (int i=1; i<=3; i++) for (int j=1; j<=3; j++) N+= pow(operator ()(i,j), 2); return N; } CVector operator* (Tens& tens, CVector& vect) { CVector result; result = CVector( tens(1,1)*vect.x()+ tens(1,2)*vect.y()+ tens(1,3)*vect.z(), tens(2,1)*vect.x()+ tens(2,2)*vect.y()+ tens(2,3)*vect.z(), tens(3,1)*vect.x()+ tens(3,2)*vect.y()+ tens(3,3)*vect.z() ); return result; } CVector& NormalizedCVector (CVector& vect) { vect = vect*(1.0/sqrt(pow(vect.x(),2)+pow(vect.y(),2)+pow(vect.z(),2))); return vect; } Tenseur3::Tenseur3(bool init) { if (init) for (int i=0; i<3; i++) for (int j=0; j<3; j++) T[i][j] = 0; } Tenseur3::~Tenseur3(void) { } Tenseur3::Tenseur3(const Tenseur3& source) { for (int i=0; i<3; i++) for (int j=0; j<3; j++) T[i][j] = source.T[i][j]; } Tenseur3::Tenseur3(Real a11, Real a12, Real a13, Real a21, Real a22, Real a23, Real a31, Real a32, Real a33) { T[0][0] = a11; T[0][1] = a12; T[0][2] = a13; T[1][0] = a21; T[1][1] = a22; T[1][2] = a23; T[2][0] = a31; T[2][1] = a32; T[2][2] = a33; } Tenseur3 &Tenseur3::operator=(const Tenseur3& source) { if (&source != this) for (int i=0; i<3; i++) for (int j=0; j<3; j++) T[i][j] = source.T[i][j]; return *this; } Tenseur3 &Tenseur3::operator/=(Real d) { if (d!=0) { d = 1.0/d; for (int i=0; i<3; i++) for (int j=0; j<3; j++) T[i][j] *= d; } return *this; } Tenseur3 & Tenseur3::operator +=(const Tenseur3 & source) { for (int i=0; i<3; i++) for (int j=0; j<3; j++) T[i][j] += source.T[i][j]; return *this; } /////////// Classe Tenseur_sym3 //////////// Tenseur_sym3::Tenseur_sym3(bool init) { if (init) { for (int i=0; i<6; i++) T[i] = 0; } } Tenseur_sym3::~Tenseur_sym3(void) { } Tenseur_sym3::Tenseur_sym3(const Tenseur_sym3& source) { for (int i=0; i<6; i++) { for (int i=0; i<6; i++) T[i] = source.T[i]; } } Tenseur_sym3::Tenseur_sym3(const Tenseur3& source) { for (int i=1; i<=3; i++) { T[i-1]=source(i,i); for (int j=3; j>i; j--) T[i+j] = (source(i,j)+source(j,i))*0.5; } } Tenseur_sym3::Tenseur_sym3(Real a11, Real a22, Real a33, Real a12, Real a13, Real a23) { T[0] = a11; T[1] = a22; T[2] = a33; T[3] = a12; T[4] = a13; T[5] = a23; } Tenseur_sym3 &Tenseur_sym3::operator=(const Tenseur_sym3& source) { if (&source != this) { for (int i=0; i<6; i++) T[i] = source.T[i]; } return *this; } Tenseur_sym3 &Tenseur_sym3::operator/=(Real d) { if (d!=0) { d=1.0/d; for (int i=0; i<6; i++) T[i]*= d;} return *this; } Real Tenseur_sym3::operator() (int i, int j) const { if (i==j) return T[i-1]; else return T[i+j]; } Real &Tenseur_sym3::operator() (int i, int j) { if (i==j) return T[i-1]; else return T[i+j]; } Tenseur_sym3 Tenseur_sym3::Deviatoric (void) const //retourne la partie d�viatoire { Tenseur_sym3 temp(*this); Real spheric = temp.Trace()/3; temp(1,1)-= spheric; temp(2,2)-= spheric; temp(3,3)-= spheric; return temp; } /////////// Classe Tenseur_anti3 //////////// Tenseur_anti3::Tenseur_anti3(bool init) { if (init) { for (int i=0; i<6; i++) T[i] = 0; } } Tenseur_anti3::~Tenseur_anti3(void) { } Tenseur_anti3::Tenseur_anti3(const Tenseur_anti3& source) { for (int i=0; i<6; i++) { for (int i=0; i<6; i++) T[i] = source.T[i]; } } Tenseur_anti3::Tenseur_anti3(const Tenseur3& source) { for (int i=1; i<=3; i++) { T[i-1]=0; for (int j=3; j>i; j--) T[i+j] = (source(i,j)-source(j,i))*0.5; } } Tenseur_anti3::Tenseur_anti3(Real a11, Real a22, Real a33, Real a12, Real a13, Real a23) { T[0] = a11; T[1] = a22; T[2] = a33; T[3] = a12; T[4] = a13; T[5] = a23; } Tenseur_anti3 &Tenseur_anti3::operator=(const Tenseur_anti3& source) { if (&source != this) { for (int i=0; i<6; i++) T[i] = source.T[i]; } return *this; } Tenseur_anti3 &Tenseur_anti3::operator/=(Real d) { if (d!=0) for (int i=0; i<6; i++) T[i]/= d; return *this; } Real Tenseur_anti3::operator() (int i, int j) const { if (i==j) return T[i-1]; else { if (i #include #include "RegularTriangulation.h" namespace CGT { using std::endl; using std::cout; using std::cerr; using std::string; #define NORMALIZE(vecteur) ((vecteur) = (vecteur)*(1.0/sqrt(pow((vecteur)[0],2)+pow((vecteur)[1],2)+pow((vecteur)[2],2)))) class Tens; class Tenseur3; class Tenseur_sym3; class Tenseur_anti3; CVector operator* ( Tens& tens, CVector& vect ); CVector& NormalizedCVector ( CVector& vect ); void Tenseur_produit ( CVector &v1, CVector &v2, Tenseur3 &result ); void Somme ( Tenseur3 &result, CVector &v1, CVector &v2 ); std::ostream& operator<< ( std::ostream& os,const Tenseur3& T ); std::ostream& operator<< ( std::ostream& os,const Tenseur_sym3& T ); std::ostream& operator<< ( std::ostream& os,const Tenseur_anti3& T ); class Tens { public: Tens ( void ) {} virtual ~Tens ( void ) {} virtual Real operator() ( int i, int j ) const {return 0;} Real Norme2 ( void ); Real Norme ( void ) {return sqrt ( Norme2() );} Real Trace ( void ) { return this->operator () ( 1,1 ) + this->operator () ( 2,2 ) + this->operator () ( 3,3 ); } }; class Tenseur3 : public Tens { private: Real T [3] [3]; public: Tenseur3 ( bool init = true );// Sp�cifier "false" pour �conomiser le temps d'initialisation du tableau virtual ~Tenseur3 ( void ); Tenseur3 ( const Tenseur3& source ); Tenseur3 ( Real a11, Real a12, Real a13, Real a21, Real a22, Real a23, Real a31, Real a32, Real a33 ); Tenseur3& operator= ( const Tenseur3& source ); Tenseur3& operator/= ( Real d ); Tenseur3& operator+= ( const Tenseur3& source ); Real operator() ( int i, int j ) const {return T[i-1][j-1];} Real &operator() ( int i, int j ) {return T[i-1][j-1];} virtual void reset ( void ) {for ( int i=0; i<3; i++ ) for ( int j=0; j<3; j++ ) T[i][j] = 0;} }; class Tenseur_sym3 : public Tens { private: Real T [6]; public: Tenseur_sym3 ( bool init = true );// Sp�cifier "false" pour �conomiser le temps d'initialisation du tableau ~Tenseur_sym3 ( void ); Tenseur_sym3 ( const Tenseur_sym3& source ); Tenseur_sym3 ( const Tenseur3& source ); Tenseur_sym3 ( Real a11, Real a22, Real a33, Real a12, Real a13, Real a23 ); Tenseur_sym3& operator= ( const Tenseur_sym3& source ); Tenseur_sym3& operator/= ( Real d ); Tenseur_sym3 Deviatoric ( void ) const; //retourne la partie d�viatoire Real operator() ( int i, int j ) const; Real &operator() ( int i, int j ); void reset ( void ) {for ( int i=0; i<6; i++ ) T[i] = 0;} }; class Tenseur_anti3 : public Tens { private: Real T [6]; public: Tenseur_anti3 ( bool init = true );// Sp�cifier "false" pour �conomiser le temps d'initialisation du tableau virtual ~Tenseur_anti3 ( void ); Tenseur_anti3 ( const Tenseur_anti3& source ); Tenseur_anti3 ( const Tenseur3& source ); Tenseur_anti3 ( Real a11, Real a22, Real a33, Real a12, Real a13, Real a23 ); Tenseur_anti3& operator= ( const Tenseur_anti3& source ); Tenseur_anti3& operator/= ( Real d ); Real operator() ( int i, int j ) const; //Real &operator() (int i, int j); //Supprim�e car pb. pour retourner une r�f�rence vers -T[i+j] void reset ( void ) {for ( int i=0; i<6; i++ ) T[i] = 0;} }; static const Tenseur3 NULL_TENSEUR3 ( 0,0,0,0,0,0,0,0,0 ); } trunk-2017.01a/lib/triangulation/Tesselation.h000066400000000000000000000170701304022710500212600ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include "RegularTriangulation.h" namespace CGT { //Since template inheritance does not automatically give access to the members of the base class, this macro can be used to declare all members at once. #define DECLARE_TESSELATION_TYPES(baseType)\ typedef typename baseType::RTriangulation RTriangulation;\ typedef typename baseType::AlphaShape AlphaShape;\ typedef typename baseType::VertexInfo VertexInfo;\ typedef typename baseType::CellInfo CellInfo;\ typedef typename baseType::VertexIterator VertexIterator;\ typedef typename baseType::VertexHandle VertexHandle;\ typedef typename baseType::FiniteVerticesIterator FiniteVerticesIterator;\ typedef typename baseType::CellIterator CellIterator;\ typedef typename baseType::FiniteCellsIterator FiniteCellsIterator;\ typedef typename baseType::CellCirculator CellCirculator;\ typedef typename baseType::CellHandle CellHandle;\ typedef typename baseType::Facet Facet;\ typedef typename baseType::FacetIterator FacetIterator;\ typedef typename baseType::FacetCirculator FacetCirculator;\ typedef typename baseType::FiniteFacetsIterator FiniteFacetsIterator;\ typedef typename baseType::LocateType LocateType;\ typedef typename baseType::EdgeIterator EdgeIterator;\ typedef typename baseType::FiniteEdgesIterator FiniteEdgesIterator;\ typedef typename baseType::VectorVertex VectorVertex;\ typedef typename baseType::VectorCell VectorCell;\ typedef typename baseType::ListPoint ListPoint;\ typedef typename baseType::VCellIterator VCellIterator; // Classe Tesselation, contient les fonctions permettant de calculer la Tessalisation // d'une RTriangulation et de stocker les centres dans chacune de ses cellules //TT is of model TriangulationTypes template class _Tesselation { public: typedef typename TT::RTriangulation RTriangulation; typedef typename TT::AlphaShape AlphaShape; typedef typename TT::Vertex_Info VertexInfo; typedef typename TT::Cell_Info CellInfo; typedef typename RTriangulation::Vertex_iterator VertexIterator; typedef typename RTriangulation::Vertex_handle VertexHandle; typedef typename RTriangulation::Finite_vertices_iterator FiniteVerticesIterator; typedef typename RTriangulation::Cell_iterator CellIterator; typedef typename RTriangulation::Finite_cells_iterator FiniteCellsIterator; typedef typename RTriangulation::Cell_circulator CellCirculator; typedef typename RTriangulation::Cell_handle CellHandle; typedef typename RTriangulation::Facet Facet; typedef typename RTriangulation::Facet_iterator FacetIterator; typedef typename RTriangulation::Facet_circulator FacetCirculator; typedef typename RTriangulation::Finite_facets_iterator FiniteFacetsIterator; typedef typename RTriangulation::Locate_type LocateType; typedef typename RTriangulation::Edge_iterator EdgeIterator; typedef typename RTriangulation::Finite_edges_iterator FiniteEdgesIterator; typedef std::vector VectorVertex; typedef std::vector VectorCell; typedef std::list ListPoint; typedef typename VectorCell::iterator VCellIterator; int maxId; protected: RTriangulation* Tri; RTriangulation* Tes; //=NULL or Tri depending on the constructor used. public: Real TotalFiniteVoronoiVolume; Real area; Real TotalInternalVoronoiVolume; Real TotalInternalVoronoiPorosity; VectorVertex vertexHandles;//This is a redirection vector to get vertex pointers by spheres id VectorCell cellHandles;//for speedup of global loops, iterating on this vector is faster than cellIterator++ bool redirected;//is vertexHandles filled with current vertex pointers? bool computed; _Tesselation(void); _Tesselation(RTriangulation &T);// : Tri(&T) { Calcule(); } ~_Tesselation(void); ///Insert a sphere VertexHandle insert(Real x, Real y, Real z, Real rad, unsigned int id, bool isFictious = false); /// move a spheres VertexHandle move (Real x, Real y, Real z, Real rad, unsigned int id); ///Fill a vector with vertexHandles[i] = handle of vertex with id=i for fast access bool redirect (void); ///Remove a sphere bool remove (unsigned int id); int Max_id (void) {return maxId;} void compute (); //Calcule le centres de Voronoi pour chaque cellule void Invalidate () {computed=false;} //Set the tesselation as "not computed" (computed=false), this will launch //tesselation internaly when using functions like computeVolumes()) // N.B : compute() must be executed before the functions below are used void Clear(void); static Point Dual (const CellHandle &cell); static Plane Dual (VertexHandle S1, VertexHandle S2); static Segment Dual (FiniteFacetsIterator &facet); //G�n�re le segment dual d'une facette finie static Real Volume (FiniteCellsIterator cell); inline void AssignPartialVolume (FiniteEdgesIterator& ed_it); double computeVFacetArea (FiniteEdgesIterator ed_it); void ResetVCellVolumes (void); void computeVolumes (void);//compute volume each voronoi cell void computePorosity (void);//compute volume and porosity of each voronoi cell inline Real& Volume (unsigned int id) { return vertexHandles[id]->info().v(); } inline const VertexHandle& vertex (unsigned int id) const { return vertexHandles[id]; } // FiniteCellsIterator finite_cells_begin(void);// {return Tri->finite_cells_begin();} // FiniteCellsIterator finiteCellsEnd(void);// {return Tri->finite_cells_end();} void voisins (VertexHandle v, VectorVertex& Output_vector);// {Tri->incident_vertices(v, back_inserter(Output_vector));} RTriangulation& Triangulation (void);// {return *Tri;} // bool computed (void) {return computed;} bool is_short ( FiniteFacetsIterator f_it ); inline bool is_internal ( FiniteFacetsIterator &facet );// long newListeEdges ( Real** Coordonnes ); //Genere la liste des segments de Voronoi long newListeShortEdges ( Real** Coordonnes ); //Genere la version tronquee (partie interieure) du graph de Voronoi long newListeShortEdges2 ( Real** Coordonnes ); long New_liste_adjacent_edges ( VertexHandle vertex0, Real** Coordonnes ); }; template class PeriodicTesselation : public Tesselation { public: DECLARE_TESSELATION_TYPES(Tesselation) using Tesselation::Tri; using Tesselation::vertexHandles; using Tesselation::maxId; using Tesselation::redirected; ///Insert a sphere, which can be a duplicate one from the base period if duplicateOfId>=0 VertexHandle insert(Real x, Real y, Real z, Real rad, unsigned int id, bool isFictious = false, int duplicateOfId=-1); ///Fill a vector with vertexHandles[i] = handle of vertex with id=i for fast access, contains only spheres from the base period bool redirect (void); }; } // namespace CGT #include "Tesselation.ipp" //Explicit instanciation typedef CGT::_Tesselation SimpleTesselation; trunk-2017.01a/lib/triangulation/Tesselation.ipp000066400000000000000000000246401304022710500216220ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ //FIXME: handle that a better way #define MAX_ID 200000 namespace CGT { using std::cerr; using std::cout; using std::endl; using std::max; using std::vector; using std::ifstream; template _Tesselation::_Tesselation ( void ) { Tri = new RTriangulation; Tes = Tri; computed=false; maxId = -1; TotalFiniteVoronoiVolume=0; area=0; TotalInternalVoronoiPorosity=0; TotalInternalVoronoiVolume=0; redirected = false; //FIXME : find a better way to avoid segfault when insert() is used before resizing this vector vertexHandles.resize(MAX_ID+1,NULL); } template _Tesselation::_Tesselation ( RTriangulation &T ) : Tri ( &T ), Tes ( &T ), computed ( false ) { std::cout << "Tesselation(RTriangulation &T)" << std::endl; compute(); } template _Tesselation::~_Tesselation ( void ) { if ( Tri ) Tri->~RTriangulation(); } template void _Tesselation::Clear ( void ) { Tri->clear(); redirected = false; vertexHandles.clear(); vertexHandles.resize(MAX_ID+1,NULL); maxId=0; } template typename _Tesselation::VertexHandle _Tesselation::insert ( Real x, Real y, Real z, Real rad, unsigned int id, bool isFictious ) { VertexHandle Vh; Vh = Tri->insert(Sphere(Point(x,y,z),pow(rad,2))); if ( Vh!=NULL ) { Vh->info().setId(id); Vh->info().isFictious = isFictious; assert (vertexHandles.size()>id); vertexHandles[id] = Vh; /*if ( !isFictious ) */maxId = std::max ( maxId, (int) id ); } else cout << id << " : Vh==NULL!!"<< " id=" << id << " Point=" << Point ( x,y,z ) << " rad=" << rad << endl; return Vh; } template typename _Tesselation::VertexHandle _Tesselation::move ( Real x, Real y, Real z, Real rad, unsigned int id ) { bool fictious = vertexHandles[id]->info().isFictious; VertexHandle Vh; Vh = Tri->move_point ( vertexHandles[id], Sphere ( Point ( x,y,z ),pow ( rad,2 ) ) ); if ( Vh!=NULL ) { vertexHandles[id] = Vh; Vh->info().setId(id); Vh->info().isFictious = fictious; } else cerr << "Vh==NULL" << " id=" << id << " Point=" << Point ( x,y,z ) << " rad=" << rad << endl; return Vh; } template bool _Tesselation::redirect ( void ) { if ( !redirected ) { //Set size of the redirection vector if ( (unsigned int)maxId+1 != vertexHandles.size() ) vertexHandles.resize ( maxId+1,NULL ); maxId = 0; FiniteVerticesIterator verticesEnd = Tri->finite_vertices_end (); for ( FiniteVerticesIterator vIt = Tri->finite_vertices_begin (); vIt != verticesEnd; vIt++ ) { vertexHandles[vIt->info().id()]= vIt; maxId = max(maxId, (int) vIt->info().id()); } if ( (unsigned int)maxId+1 != vertexHandles.size() ) vertexHandles.resize ( maxId+1 ); redirected = true; } else return false; return true; } template bool _Tesselation::remove ( unsigned int id ) { redirect(); Tri->remove ( vertexHandles[id] ); return true; } template void _Tesselation::voisins ( VertexHandle v, VectorVertex& Output_vector ) { Tri->incident_vertices ( v, back_inserter ( Output_vector ) ); } template typename _Tesselation::RTriangulation & _Tesselation::Triangulation ( void ) { return *Tri; } template Real _Tesselation::Volume ( FiniteCellsIterator cell ) { return ( Tetrahedron ( cell->vertex ( 0 )->point(), cell->vertex ( 1 )->point(), cell->vertex ( 2 )->point(), cell->vertex ( 3 )->point() ) ).volume(); } template Plane _Tesselation::Dual ( VertexHandle S1, VertexHandle S2 ) { Segment seg ( S1->point(), S2->point() ); Real r = 0.5* ( 1.0 + ( ( S1->point() ).weight() * ( S1->point() ).weight() - ( S2->point() ).weight() * ( S2->point() ).weight() ) /seg.squared_length() ); return Plan ( S1->point() + seg.to_vector() *r, seg.to_vector() ); } template Point _Tesselation::Dual ( const CellHandle &cell ) { return cell->info(); } template void _Tesselation::compute () { if (!redirected) redirect(); FiniteCellsIterator cellEnd = Tri->finite_cells_end(); for ( FiniteCellsIterator cell = Tri->finite_cells_begin(); cell != cellEnd; cell++ ) { const Sphere& S0 = cell->vertex ( 0 )->point(); const Sphere& S1 = cell->vertex ( 1 )->point(); const Sphere& S2 = cell->vertex ( 2 )->point(); const Sphere& S3 = cell->vertex ( 3 )->point(); Real x,y,z; CGAL::weighted_circumcenterC3 ( S0.point().x(), S0.point().y(), S0.point().z(), S0.weight(), S1.point().x(), S1.point().y(), S1.point().z(), S1.weight(), S2.point().x(), S2.point().y(), S2.point().z(), S2.weight(), S3.point().x(), S3.point().y(), S3.point().z(), S3.weight(), x, y, z ); cell->info().setPoint(Point(x,y,z)); } computed = true; // AlphaShape as (*Tri); // as.set_alpha(as.find_alpha_solid()); // cerr << "Alpha shape computed" < cells,cells2; // as.get_alpha_shape_cells(std::back_inserter(cells), // AlphaShape::EXTERIOR); // as.get_alpha_shape_cells(std::back_inserter(cells2), // AlphaShape::INTERIOR); // std::cerr<< "num exterior cells "<< cells.size() <<" vs. "< Segment _Tesselation::Dual ( FiniteFacetsIterator &f_it ) { return Segment ( f_it->first->info(), ( f_it->first->neighbor ( f_it->second ) )->info() ); } template double _Tesselation::computeVFacetArea ( FiniteEdgesIterator ed_it ) { CellCirculator cell0 = Tri->incident_cells ( *ed_it ); CellCirculator cell2 = cell0; if ( Tri->is_infinite ( cell2 ) ){ ++cell2; while ( Tri->is_infinite ( cell2 ) && cell2!=cell0 ) ++cell2; if ( cell2==cell0 ) return 0; } cell0=cell2++; CellCirculator cell1=cell2++; Real area = 0; while ( cell2!=cell0 ){ area+= sqrt(std::abs (( Triangle ( cell0->info(), cell1->info(), cell2->info() ) ).squared_area())) ; ++cell1; ++cell2; } return area; } template void _Tesselation::AssignPartialVolume ( FiniteEdgesIterator& ed_it ) { //EdgeIterator ed_it CellCirculator cell0=Tri->incident_cells ( *ed_it ); CellCirculator cell2=cell0; if ( Tri->is_infinite ( cell2 ) ) { ++cell2; while ( Tri->is_infinite ( cell2 ) && cell2!=cell0 ) ++cell2; if ( cell2==cell0 ) return; } cell0=cell2++; CellCirculator cell1=cell2++; bool isFictious1 = ( ed_it->first )->vertex ( ed_it->second )->info().isFictious; bool isFictious2 = ( ed_it->first )->vertex ( ed_it->third )->info().isFictious; Real r; while ( cell2!=cell0 ) { if ( !Tri->is_infinite ( cell1 ) && !Tri->is_infinite ( cell2 ) ) { if ( !isFictious1 ) { r = std::abs ( ( Tetrahedron ( ed_it->first->vertex ( ed_it->second )->point(), cell0->info(), cell1->info(), cell2->info() ) ).volume() ); ( ed_it->first )->vertex ( ed_it->second )->info().v() += r; TotalFiniteVoronoiVolume+=r; } if ( !isFictious2 ) { r = std::abs ( ( Tetrahedron ( ed_it->first->vertex ( ed_it->third )->point(), cell0->info(), cell1->info(), cell2->info() ) ).volume() ); ed_it->first->vertex ( ed_it->third )->info().v() +=r; TotalFiniteVoronoiVolume+=r; } } ++cell1; ++cell2; } } template void _Tesselation::ResetVCellVolumes ( void ) { for ( VertexIterator vIt = Tri->vertices_begin (); vIt != Tri->vertices_end (); vIt++ ) vIt->info().v() =0; TotalFiniteVoronoiVolume=0; TotalInternalVoronoiPorosity=0; } template void _Tesselation::computeVolumes ( void ) { if ( !computed ) compute(); ResetVCellVolumes(); for ( FiniteEdgesIterator ed_it=Tri->finite_edges_begin(); ed_it!=Tri->finite_edges_end();ed_it++ ) { AssignPartialVolume ( ed_it ); } //FIXME: find a way to compute a volume correctly for spheres of the boarders. } template void _Tesselation::computePorosity ( void ) //WARNING : This function will erase real volumes of cells { computeVolumes(); FiniteVerticesIterator verticesEnd = Tri->finite_vertices_end (); for ( FiniteVerticesIterator vIt = Tri->finite_vertices_begin (); vIt != verticesEnd; vIt++ ) { if ( vIt->info().v() && !vIt->info().isFictious ) { Real r = 4.188790 * std::pow ( ( vIt->point().weight() ),1.5 );// 4/3*PI*R³ = 4.188...*R³ TotalInternalVoronoiPorosity+=r; TotalInternalVoronoiVolume += vIt->info().v(); vIt->info().v() = ( vIt->info().v() - r ) / vIt->info().v(); } } TotalInternalVoronoiPorosity= ( TotalInternalVoronoiVolume-TotalInternalVoronoiPorosity ) /TotalInternalVoronoiVolume; } template bool _Tesselation::is_internal ( FiniteFacetsIterator &facet ) { return ( !Tri->is_infinite ( facet->first ) && !Tri->is_infinite ( facet->first->neighbor ( facet->second ) ) ); } template typename Tesselation::VertexHandle PeriodicTesselation::insert(Real x, Real y, Real z, Real rad, unsigned int id, bool isFictious, int duplicateOfId) { VertexHandle Vh; if (!Tri) cerr<<"!Tri!"<insert(Sphere(Point(x,y,z),pow(rad,2))); if ( Vh!=NULL ) { Vh->info() = id; Vh->info().isFictious = isFictious; if (duplicateOfId<0) { assert (vertexHandles.size()>id); vertexHandles[id] = Vh; maxId = std::max ( maxId, (int) id ); Vh->info().isGhost=0; } else Vh->info().isGhost=1; } else cerr << " : Vh==NULL!!" << " id=" << id << " Point=" << Point ( x,y,z ) << " rad=" << rad<<" fictious="< bool PeriodicTesselation::redirect ( void ) { if ( !redirected ) { //Set size of the redirection vector if ( (unsigned int)maxId+1 != vertexHandles.size() ) vertexHandles.resize ( maxId+1,NULL ); cout << "!redirected" << endl; maxId = 0; FiniteVerticesIterator verticesEnd = Tri->finite_vertices_end (); for ( FiniteVerticesIterator vIt = Tri->finite_vertices_begin (); vIt != verticesEnd; vIt++ ) { if (vIt->info().isGhost) continue; vertexHandles[vIt->info().id()]= vIt; maxId = max(maxId, (int) vIt->info().id()); } if ( (unsigned int)maxId+1 != vertexHandles.size() ) vertexHandles.resize ( maxId+1 ); redirected = true; } else return false; return true; } } //namespace CGT trunk-2017.01a/lib/triangulation/Timer.cpp000066400000000000000000000020761304022710500204010ustar00rootroot00000000000000#include #include "Timer.h" Real_timer::Real_timer() : T1(0), T2(0), elapsed(0.0), started(0.0), interv(0), running(true) { T1 = clock(); } // Member functions for Real_timer // =========================== void Real_timer::start() { //CGAL_precondition( ! running); //started = get_real_time(); T1=clock(); running = true; ++ interv; } void Real_timer::stop() { //CGAL_precondition( running); //double t = get_real_time(); //elapsed += (t - started); T2 = difftime(clock(), T1); started = 0.0; T1=0; running = false; } void Real_timer::reset() { interv = 0; elapsed = 0.0; T2=0; if (running) { //started = get_real_time(); T1=clock(); ++ interv; } else { started = 0.0; T1=0; } } double Real_timer::time() const { if (running) { clock_t T3 = clock(); return difftime(T3, T1); } return T2; } void Real_timer::top(string Texte) { clock_t T3 = clock(); double r = (double) (T3 - T1)/ CLOCKS_PER_SEC; std::cout << Texte << " .......... " << r << " s" << std::endl; reset(); } trunk-2017.01a/lib/triangulation/Timer.h000066400000000000000000000031171304022710500200430ustar00rootroot00000000000000#ifndef bru_REAL_TIMER_H #define bru_REAL_TIMER_H 1 #include #include using std::string; // SECTION: A Timer Measuring Real-Time // ======================================================================== // // DEFINITION // // A timer `t' of type Real_timer is an object with a state. It is either // running or it is stopped. The state is controlled with `t.start()' // and `t.stop()'. The timer counts the time elapsed since its creation // or last reset. It counts only the time where it is in the running // state. The time information is given in seconds. class Real_timer { private: clock_t T1; double T2; double elapsed; double started; int interv; bool running; static bool m_failed; double get_real_time() const; // in seconds double compute_precision() const; // in seconds public: Real_timer(); void start(); void stop (); void reset(); void top(std::string Texte); bool is_running() const { return running; } double time() const; int intervals() const { return interv; } double precision() const; // Returns timer precison. Computes it dynamically at first call. // Returns -1.0 if timer system call fails, which, for a proper coded // test towards precision leads to an immediate stop of an otherwise // infinite loop (fixed tolerance * total time >= precision). //double max() const { return DBL_MAX; } }; #endif // bru_REAL_TIMER_H // // EOF // trunk-2017.01a/lib/triangulation/TriaxialState.cpp000066400000000000000000000244421304022710500221000ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ /// The info types that will be used and the namespace in which the types will be defined (a unique namespace with different info types would give name conflicts) #include "TriaxialState.h" #include #include #include #include namespace CGT { TriaxialState::TriaxialState(void) : NO_ZERO_ID(false), filter_distance(-0.1), tesselated(false) {} TriaxialState::~TriaxialState(void) { ContactIterator last = contacts_end(); for (ContactIterator it=contacts_begin(); it!=last; ++it) { if (*it) delete *it;} } Real TriaxialState::find_parameter (const char* parameter_name, ifstream& file) { string buffer; Real value; file >> buffer; bool test = (buffer == string(parameter_name)); while (!test) { buffer.clear(); file >> buffer; test = ( buffer == string(parameter_name) || file.eof()); } if (!file.eof()) file >> value; else value = 0; // cout << string(parameter_name) << value << endl; return value; } Real TriaxialState::find_parameter (const char* parameter_name, boost::iostreams::filtering_istream& file) { string buffer; Real value; file >> buffer; bool test = (buffer == string(parameter_name)); while (!test) { buffer.clear(); file >> buffer; test = ( buffer == string(parameter_name) || file.eof()); } if (!file.eof()) file >> value; else value = 0; // cout << string(parameter_name) << value << endl; return value; } Real TriaxialState::find_parameter (const char* parameter_name, const char* filename) { ifstream statefile (filename); return find_parameter(parameter_name, statefile); } void TriaxialState::reset (void) { tesselated = false; Tes.Clear(); mean_radius=0; grains.clear(); ContactIterator contacts_end = contacts.end(); for (ContactIterator it=contacts.begin(); it!=contacts_end; ++it) delete *it; contacts.clear(); contacts.resize(0); box.base = Point(1.0e10, 1.0e10, 1.0e10); box.sommet = Point(-1.0e10, -1.0e10, -1.0e10); } TriaxialState::GrainIterator TriaxialState::grains_begin (void) { GrainIterator git = grains.begin(); if (NO_ZERO_ID) return ++git; else return git; } TriaxialState::ContactIterator TriaxialState::contacts_begin (void) { return contacts.begin(); } TriaxialState::GrainIterator TriaxialState::grains_end (void) { return grains.end(); } TriaxialState::ContactIterator TriaxialState::contacts_end (void) { return contacts.end(); } TriaxialState::Grain& TriaxialState::grain (unsigned int id) { return grains[id]; } TriaxialState::Tesselation& TriaxialState::Tesselate (void) { if (!tesselated) { Tes.Clear(); GrainIterator git = grains_begin(); GrainIterator last = grains_end(); Tes.vertexHandles.resize(grains.size()+ (NO_ZERO_ID ? 1 : 0)); for (; git!=last; ++git) { if (git->id != -1 /*&& git->isSphere*/) Tes.vertexHandles[git->id] = Tes.insert(git->sphere.x(), git->sphere.y(), git->sphere.z(), git->sphere.weight(),git->id,!git->isSphere); //vh->->info() = git->translation; FIXME : this could define displacements in the triangulation itself // cerr << "Tes.insert(git->sphere.x(), git->sphere.y(), git->sphere.z(), git->sphere.weight(), git->id);" << endl; } Tes.redirected = true;//vertexHandle has been filled here, no need to do it again tesselated = true; cerr << "Triangulated Grains : " << Tes.Triangulation().number_of_vertices() << endl; } return Tes; } TriaxialState::Tesselation& TriaxialState::tesselation (void) { return Tesselate(); } bool TriaxialState::inside(Real x, Real y, Real z) { return (x >= (box.base.x()+filter_distance*mean_radius) && x <= (box.sommet.x()-filter_distance*mean_radius) && y >= (box.base.y()+filter_distance*mean_radius) && y <= (box.sommet.y()-filter_distance*mean_radius) && z >= (box.base.z()+filter_distance*mean_radius) && z <= (box.sommet.z()-filter_distance*mean_radius) ); } bool TriaxialState::inside(CVector v) { return TriaxialState::inside(v.x(), v.y(), v.z()); } bool TriaxialState::inside(Point p) { return TriaxialState::inside(p.x(), p.y(), p.z()); } bool TriaxialState::from_file(const char* filename, bool bz2) { reset(); // // Don't use bzipped files // // cout << filename << endl; // ifstream Statefile(filename); // if (!Statefile.is_open()) { // cout << "Error opening files"; // return false; // } // // Use bzipped files boost::iostreams::filtering_istream Statefile; if (bz2) { Statefile.push(boost::iostreams::bzip2_decompressor()); Statefile.push(boost::iostreams::file_source(string(filename)+".bz2"));} else Statefile.push(boost::iostreams::file_source(string(filename))); if(!Statefile.good()) {cerr << "Error opening files"; return false;} long Idg; long Ns=0;//number of spheres (excluding fictious ones)) Statefile >> Ng; //Real x, y, z, rad; //coordonn�es/rayon //Real tx, ty, tz; Point pos(CGAL::ORIGIN); mean_radius=0; CVector trans, rot; Real rad; //coordonn�es/rayon bool isSphere; grains.resize(Ng+1); //cout << "Ngrains =" << Ng << endl; if (NO_ZERO_ID) { GrainIterator git= grains.begin(); git->id=0; git->sphere = Sphere(CGAL::ORIGIN, 0); git->translation = CGAL::NULL_VECTOR; git->rotation = CGAL::NULL_VECTOR; } long i= NO_ZERO_ID ? 1 : 0; for (; i <= Ng ; ++i) { Statefile >> Idg >> pos >> rad >> trans >> rot >> isSphere; grains[Idg].id = Idg; grains[Idg].sphere = Sphere(pos, rad); grains[Idg].translation = trans; grains[Idg].rotation = rot; grains[Idg].isSphere = isSphere; box.base = Point(min(box.base.x(), pos.x()-rad), min(box.base.y(), pos.y()-rad), min(box.base.z(), pos.z()-rad)); box.sommet = Point(max(box.sommet.x(), pos.x()+rad), max(box.sommet.y(), pos.y()+rad), max(box.sommet.z(), pos.z()+rad)); if (isSphere) {mean_radius += grains[Idg].sphere.weight(); ++Ns;} //cout << "Idg: "<< Idg << " sphere: " << grains[Idg].sphere << " trans: " << grains[Idg].translation << endl; } mean_radius /= Ns;//rayon moyen //cout << filename << " loaded : " << Ng << " grains with mean radius = " << mean_radius << endl; long id1, id2; int stat; CVector c_pos, normal, old_fs, fs; Real old_fn, fn, frictional_work; Statefile >> Nc; contacts.resize(Nc); for (long i=0 ; i < Nc ; ++i) { Contact* c = new Contact; Statefile >> id1 >> id2 >> normal >> c_pos >> old_fn >> old_fs >> fn >> fs >> frictional_work >> stat; normal = (grains[id2].sphere.point()-grains[id1].sphere.point()); normal = normal/sqrt(pow(normal.x(),2)+pow(normal.y(),2)+pow(normal.z(),2)); c->grain1 = &(grains[id1]); c->grain2 = &(grains[id2]); grains[id1].contacts.push_back(c); grains[id2].contacts.push_back(c); c->normal = normal; c->position = c_pos; c->old_fn = old_fn; c->old_fs = old_fs; c->fn = fn; c->fs = fs; c->frictional_work = frictional_work; c->status = (Contact::Status) stat; if (contacts[i]) delete contacts[i]; contacts[i] = c; } //cout << "c_pos=" << contacts[10]->position << " old_fn=" << contacts[10]->old_fn << " normal=" << contacts[10]->normal << endl; //rfric = find_parameter("rfric=", Statefile);// � remettre quand les fichiers n'auront plus l'espace de trop... Eyn = find_parameter("Eyn", Statefile); Eys = find_parameter("Eys", Statefile); wszzh = find_parameter("wszzh", Statefile); wsxxd = find_parameter("wsxxd", Statefile); wsyyfa = find_parameter("wsyyfa", Statefile); eps3 = find_parameter("eps3", Statefile); eps1 = find_parameter("eps1", Statefile); eps2 = find_parameter("eps2", Statefile); porom = find_parameter("porom", Statefile); haut = find_parameter("haut", Statefile); larg = find_parameter("larg", Statefile); prof = find_parameter("prof", Statefile); ratio_f = find_parameter("ratio_f", Statefile); vit = find_parameter("vit", Statefile); // //Don't use bzipped files // Statefile.close(); //cout << endl << "wszzh= " << wszzh << endl; /*GrainIterator grains_end = grains.end(); for (GrainIterator it=grains.begin(); it!=grains_end; ++it) { if (it==grains.begin()) ++it; Vue1.Dessine_Sphere(it->sphere.x(), it->sphere.y(), it->sphere.z(), it->sphere.weight(), 10); }*/ //Vue1.Affiche(); return true; } bool TriaxialState::to_file(const char* filename, bool bz2) { //string fname (filename); // use bzipped files boost::iostreams::filtering_ostream Statefile; //if(boost::algorithm::ends_with(filename,".bz2")) Statefile.push(iostreams::bzip2_compressor()); if (bz2) { Statefile.push(boost::iostreams::bzip2_compressor()); Statefile.push(boost::iostreams::file_sink(string(filename)+".bz2"));} else Statefile.push(boost::iostreams::file_sink(string(filename))); // Don't use bzipped files //ofstream Statefile (filename); //if (!Statefile.is_open()) { if(!Statefile.good()) { cerr << "Error opening files"; return false; } long Id_max = grains.size()-1; Statefile << Id_max << endl; for (long Idg=0 ; Idg <= Id_max ; ++Idg) { Statefile << grains[Idg].id << " " << grains[Idg].sphere.point() << " " << grains[Idg].sphere.weight() << " " << grains[Idg].translation << " " << grains[Idg].rotation << " "<grain1->id << " " << contacts[i]->grain2->id << " " << contacts[i]->normal << " " << contacts[i]->position << " " << contacts[i]->old_fn << " " << contacts[i]->old_fs << " " << contacts[i]->fn << " " << contacts[i]->fs << " " << contacts[i]->frictional_work << " " << contacts[i]->status << endl; } Statefile << "Eyn " << Eyn << " Eys " << Eys << " wszzh " << wszzh << " wsxxd " << wsxxd << " wsyyfa " << wsyyfa << " eps3 " << eps3 << " eps1 " << eps1 << " eps2 " << eps2 << " porom " << porom << " haut " << haut << " larg " << larg << " prof " << prof << " ratio_f " << ratio_f << " vit " << vit << endl; // //Don't use bzipped files // Statefile.close(); return true; } } // namespace CGT trunk-2017.01a/lib/triangulation/TriaxialState.h000066400000000000000000000061451304022710500215450ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ /** @author Bruno Chareyre */ #pragma once #include "Tesselation.h" #include #include /*! \class TriaxialState * \brief A storage class with ascii input/output for bodies, contacts, and macro-variables. Yade packings are first converted to this object type, before being processed in KinematicLocalisationAnalyser. * */ namespace CGT { using std::string; using std::min; class TriaxialState { public: typedef _Tesselation Tesselation; typedef Tesselation::RTriangulation RTriangulation; class Contact; class Grain; typedef struct {Point base; Point sommet;} Box; typedef vector VectorContact; typedef vector VectorGrain; typedef VectorContact::iterator ContactIterator; typedef VectorGrain::iterator GrainIterator; class Grain { public : int id; bool isSphere; Sphere sphere; CVector translation; CVector rotation; VectorContact contacts; Grain(void) {id=-1; isSphere=true;} }; class Contact { public : enum Status {NEW, PERSISTENT, LOST}; Grain* grain1; Grain* grain2; CVector position; CVector normal; Real fn; CVector fs; Real old_fn; CVector old_fs; Real frictional_work; bool visited; Status status; Contact(void) {visited=false; status=PERSISTENT;} }; TriaxialState(void); ~TriaxialState(void); bool from_file(const char* filename, bool bz2=false); bool to_file(const char* filename, bool bz2=false); bool inside(Real x, Real y, Real z); bool inside(CVector v); bool inside(Point p); static Real find_parameter (const char* parameter_name, const char* filename); static Real find_parameter (const char* parameter_name, boost::iostreams::filtering_istream& file); static Real find_parameter (const char* parameter_name, ifstream& file); void reset (void); GrainIterator grains_begin (void); ContactIterator contacts_begin (void); GrainIterator grains_end (void); ContactIterator contacts_end (void); Tesselation& tesselation (void); Grain& grain (unsigned int id); //Public member data : bool NO_ZERO_ID;//Is there a body with id=0? Real mean_radius; Box box; Real filter_distance; //distance de filtrage au voisinage des parois - normalis�e par le rayon moyen long Ng, Nc; Real rfric, Eyn, Eys, wszzh, wsxxd, wsyyfa, eps1, eps2, eps3, porom, haut, larg, prof, ratio_f, vit; VectorContact contacts; VectorGrain grains; private : Tesselation Tes; Tesselation& Tesselate (void); //Private member data : bool tesselated; }; } // namespace CGT trunk-2017.01a/lib/triangulation/basicVTKwritter.cpp000066400000000000000000000050541304022710500224070ustar00rootroot00000000000000#include "basicVTKwritter.hpp" bool basicVTKwritter::open(const char * filename, const char * comment) { file.open(filename,ios_base::out); if (!file) { cerr << "Cannot open file [" << filename << "]" << endl; return false; } // Header file << "# vtk DataFile Version 3.0" << endl; file << comment << endl; file << "ASCII" << endl; file << "DATASET UNSTRUCTURED_GRID" << endl; file << endl; return true; } bool basicVTKwritter::close() { file.close(); return true; } void basicVTKwritter::begin_vertices() { file << "POINTS " << nbVertices << " float" << endl; } void basicVTKwritter::begin_cells() { file << "CELLS " << nbCells << " " << 5*nbCells << endl; } void basicVTKwritter::write_point(float x, float y, float z) { file << x << " " << y << " " << z << endl; } // Note that identifiers must be defined with 0-offset void basicVTKwritter::write_cell(unsigned int id1, unsigned int id2, unsigned int id3, unsigned int id4) { file << "4 " << id1 << " " << id2 << " " << id3 << " " << id4 << endl; } void basicVTKwritter::end_vertices() { file << endl; } void basicVTKwritter::end_cells() { file << "CELL_TYPES " << nbCells << endl; for (unsigned int n = 0 ; n < nbCells ; ++n) { file << "10" << endl; } file << endl; } void basicVTKwritter::begin_data(const char * dataname, DataPosition pos, DataName name, DataType type) { switch(pos) { case POINT_DATA : if (!hasPointData) {file << "POINT_DATA " << nbVertices << endl; hasPointData=true;} break; case CELL_DATA : if (!hasCellData) {file << "CELL_DATA " << nbCells << endl; hasCellData=true;} break; } switch (name) { case SCALARS : file << "SCALARS " << dataname; break; case VECTORS : file << "VECTORS " << dataname; break; case TENSORS : file << "TENSORS " << dataname; break; } switch (type) { case INT : file << " int"; break; case FLOAT : file << " float"; break; } if (name == SCALARS) { file << " 1" << endl; file << "LOOKUP_TABLE default" << endl;} else file << endl; } void basicVTKwritter::write_data(float value) { file << value << endl; } void basicVTKwritter::write_data(float x, float y, float z) { file << x << " " << y << " " << z << endl; } void basicVTKwritter::write_data( float t11, float t12, float t13, float t21, float t22, float t23, float t31, float t32, float t33) { file << t11 << " " << t12 << " " << t13 << endl; file << t21 << " " << t22 << " " << t23 << endl; file << t31 << " " << t32 << " " << t33 << endl; file << endl; } void basicVTKwritter::end_data() { file << endl; } trunk-2017.01a/lib/triangulation/basicVTKwritter.hpp000066400000000000000000000022121304022710500224050ustar00rootroot00000000000000#pragma once #include #include enum DataPosition {POINT_DATA,CELL_DATA}; enum DataName {SCALARS,VECTORS,TENSORS}; enum DataType {INT,FLOAT}; using std::ios_base; using std::endl; using std::cout; using std::cerr; // Really simplistic struct for vtk file creation struct basicVTKwritter { std::ofstream file; unsigned int nbVertices, nbCells; bool hasPointData; bool hasCellData; basicVTKwritter(unsigned int nV, unsigned int nC) : nbVertices(nV),nbCells(nC),hasPointData(false),hasCellData(false) {} bool open(const char * filename, const char * comment); bool close(); void begin_vertices(); void write_point(float x, float y, float z); void end_vertices(); void begin_cells(); void write_cell(unsigned int id1, unsigned int id2, unsigned int id3, unsigned int id4); void end_cells(); void begin_data(const char * dataname, DataPosition pos, DataName name, DataType type); void write_data(float value); void write_data(float x, float y, float z); void write_data(float t11, float t12, float t13, float t21, float t22, float t23, float t31, float t32, float t33); void end_data(); }; trunk-2017.01a/pkg/000077500000000000000000000000001304022710500137435ustar00rootroot00000000000000trunk-2017.01a/pkg/common/000077500000000000000000000000001304022710500152335ustar00rootroot00000000000000trunk-2017.01a/pkg/common/Aabb.hpp000066400000000000000000000022101304022710500165640ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include /*! Representation of bound by min and max points. This class is redundant, since it has no data members; don't delete it, though, as Bound::{min,max} might move here one day. */ class Aabb : public Bound{ public : virtual ~Aabb() {}; YADE_CLASS_BASE_DOC_ATTRS_CTOR(Aabb,Bound,"Axis-aligned bounding box, for use with :yref:`InsertionSortCollider`. (This class is quasi-redundant since min,max are already contained in :yref:`Bound` itself. That might change at some point, though.)",/*attrs*/,/*ctor*/createIndex();); REGISTER_CLASS_INDEX(Aabb,Bound); }; REGISTER_SERIALIZABLE(Aabb); trunk-2017.01a/pkg/common/Bo1_Aabb.cpp000066400000000000000000000063041304022710500172700ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include YADE_PLUGIN((Bo1_Sphere_Aabb)(Bo1_Facet_Aabb)(Bo1_Box_Aabb)); void Bo1_Sphere_Aabb::go(const shared_ptr& cm, shared_ptr& bv, const Se3r& se3, const Body* b){ Sphere* sphere = static_cast(cm.get()); if(!bv){ bv=shared_ptr(new Aabb); } Aabb* aabb=static_cast(bv.get()); Vector3r halfSize = (aabbEnlargeFactor>0?aabbEnlargeFactor:1.)*Vector3r(sphere->radius,sphere->radius,sphere->radius); if(!scene->isPeriodic){ aabb->min=se3.position-halfSize; aabb->max=se3.position+halfSize; return; } // adjust box size along axes so that sphere doesn't stick out of the box even if sheared (i.e. parallelepiped) if(scene->cell->hasShear()) { Vector3r refHalfSize(halfSize); const Vector3r& cos=scene->cell->getCos(); for(int i=0; i<3; i++){ //cerr<<"cos["<min = scene->cell->unshearPt(se3.position)-halfSize; aabb->max = scene->cell->unshearPt(se3.position)+halfSize; } void Bo1_Facet_Aabb::go( const shared_ptr& cm , shared_ptr& bv , const Se3r& se3 , const Body* b) { if(!bv){ bv=shared_ptr(new Aabb); } Aabb* aabb=static_cast(bv.get()); Facet* facet = static_cast(cm.get()); const Vector3r& O = se3.position; Matrix3r facetAxisT=se3.orientation.toRotationMatrix(); const vector& vertices=facet->vertices; if(!scene->isPeriodic){ aabb->min=aabb->max = O + facetAxisT * vertices[0]; for (int i=1;i<3;++i) { Vector3r v = O + facetAxisT * vertices[i]; aabb->min = aabb->min.cwiseMin(v); aabb->max = aabb->max.cwiseMax(v); } } else { Real inf=std::numeric_limits::infinity(); aabb->min=Vector3r(inf,inf,inf); aabb->max=Vector3r(-inf,-inf,-inf); for(int i=0; i<3; i++){ Vector3r v=scene->cell->unshearPt(O+facetAxisT*vertices[i]); aabb->min=aabb->min.cwiseMin(v); aabb->max=aabb->max.cwiseMax(v); } } } void Bo1_Box_Aabb::go( const shared_ptr& cm, shared_ptr& bv, const Se3r& se3, const Body* b) { Box* box = static_cast(cm.get()); if(!bv){ bv=shared_ptr(new Aabb); } Aabb* aabb=static_cast(bv.get()); if(scene->isPeriodic && scene->cell->hasShear()) throw logic_error(__FILE__ "Boxes not (yet?) supported in sheared cell."); Matrix3r r=se3.orientation.toRotationMatrix(); Vector3r halfSize(Vector3r::Zero()); for( int i=0; i<3; ++i ) for( int j=0; j<3; ++j ) halfSize[i] += std::abs( r(i,j) * box->extents[j] ); aabb->min = se3.position-halfSize; aabb->max = se3.position+halfSize; } trunk-2017.01a/pkg/common/Bo1_Aabb.hpp000066400000000000000000000060771304022710500173040ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include #include class Bo1_Sphere_Aabb : public BoundFunctor { public : void go(const shared_ptr& cm, shared_ptr& bv, const Se3r&, const Body*); FUNCTOR1D(Sphere); YADE_CLASS_BASE_DOC_ATTRS(Bo1_Sphere_Aabb,BoundFunctor,"Functor creating :yref:`Aabb` from :yref:`Sphere`.", ((Real,aabbEnlargeFactor,((void)"deactivated",-1),,"Relative enlargement of the bounding box; deactivated if negative.\n\n.. note::\n\tThis attribute is used to create distant interaction, but is only meaningful with an :yref:`IGeomFunctor` which will not simply discard such interactions: :yref:`Ig2_Sphere_Sphere_ScGeom::interactionDetectionFactor` should have the same value as :yref:`aabbEnlargeFactor`.")) ); }; REGISTER_SERIALIZABLE(Bo1_Sphere_Aabb); /************************************************************************* * Copyright (C) 2008 by Sergei Dorofeenko * * sega@users.berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ class Bo1_Facet_Aabb : public BoundFunctor{ public: void go(const shared_ptr& cm, shared_ptr& bv, const Se3r& se3, const Body*); FUNCTOR1D(Facet); YADE_CLASS_BASE_DOC(Bo1_Facet_Aabb,BoundFunctor,"Creates/updates an :yref:`Aabb` of a :yref:`Facet`."); }; REGISTER_SERIALIZABLE(Bo1_Facet_Aabb); /************************************************************************* * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ class Box; class Bo1_Box_Aabb : public BoundFunctor{ public: void go(const shared_ptr& cm, shared_ptr& bv, const Se3r& se3, const Body*); FUNCTOR1D(Box); YADE_CLASS_BASE_DOC(Bo1_Box_Aabb,BoundFunctor,"Create/update an :yref:`Aabb` of a :yref:`Box`."); }; REGISTER_SERIALIZABLE(Bo1_Box_Aabb); trunk-2017.01a/pkg/common/BoundaryController.hpp000066400000000000000000000006751304022710500216030ustar00rootroot00000000000000#pragma once #include class BoundaryController: public GlobalEngine{ virtual void action() { { throw std::runtime_error("BoundaryController must not be used in simulations directly (BoundaryController::action called)."); } } YADE_CLASS_BASE_DOC(BoundaryController,GlobalEngine,"Base for engines controlling boundary conditions of simulations. Not to be used directly."); }; REGISTER_SERIALIZABLE(BoundaryController); trunk-2017.01a/pkg/common/Box.hpp000066400000000000000000000017001304022710500164720ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include class Box: public Shape{ public: Box(const Vector3r& _extents): extents(_extents){} virtual ~Box () {}; YADE_CLASS_BASE_DOC_ATTRS_CTOR(Box,Shape,"Box (cuboid) particle geometry. (Avoid using in new code, prefer :yref:`Facet` instead.", ((Vector3r,extents,,,"Half-size of the cuboid")), /* ctor */ createIndex(); ); REGISTER_CLASS_INDEX(Box,Shape); }; REGISTER_SERIALIZABLE(Box); trunk-2017.01a/pkg/common/Callbacks.hpp000066400000000000000000000040471304022710500176300ustar00rootroot00000000000000// 2010 © Václav Šmilauer #pragma once #include class Interaction; class Body; class Scene; class IntrCallback: public Serializable{ public: virtual ~IntrCallback() {}; // vtable typedef void(*FuncPtr)(IntrCallback*,Interaction*); // should be set at every step by InteractionLoop Scene* scene; /* At the beginning of each timestep, perform initialization and return pointer to the static member function that does the actual work. Returned value might be NULL, in which case the callback will be deactivated during that timestep. */ virtual FuncPtr stepInit(){ throw std::runtime_error("Called IntrCallback::stepInit() of the base class?"); } YADE_CLASS_BASE_DOC(IntrCallback,Serializable,"Abstract callback object which will be called for every (real) :yref:`Interaction` after the interaction has been processed by :yref:`InteractionLoop`.\n\nAt the beginning of the interaction loop, ``stepInit`` is called, initializing the object; it returns either ``NULL`` (to deactivate the callback during this time step) or pointer to function, which will then be passed (1) pointer to the callback object itself and (2) pointer to :yref:`Interaction`.\n\n.. note::\n\t(NOT YET DONE) This functionality is accessible from python by passing 4th argument to :yref:`InteractionLoop` constructor, or by appending the callback object to :yref:`InteractionLoop::callbacks`.\n"); }; REGISTER_SERIALIZABLE(IntrCallback); #ifdef YADE_BODY_CALLBACKS class BodyCallback: public Serializable{ public: virtual ~BodyCallback() {}; // vtable typedef void(*FuncPtr)(BodyCallback*,Body*); // set at every step, before stepInit() is called Scene* scene; virtual FuncPtr stepInit(){ throw std::runtime_error("Called BodyCallback::stepInit() of the base class?"); } YADE_CLASS_BASE_DOC(BodyCallback,Serializable,"Abstract callback object which will be called for every :yref:`Body` after being processed by :yref:`NewtonIntegrator`. See :yref:`IntrCallback` for details."); }; REGISTER_SERIALIZABLE(BodyCallback); #endif trunk-2017.01a/pkg/common/Collider.cpp000066400000000000000000000041571304022710500175030ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include YADE_PLUGIN((Collider)); int Collider::avoidSelfInteractionMask = 0 ; bool Collider::mayCollide(const Body* b1, const Body* b2){ return // might be called with deleted bodies, i.e. NULL pointers (b1!=NULL && b2!=NULL) && // only collide if at least one particle is standalone or they belong to different clumps (b1->isStandalone() || b2->isStandalone() || b1->clumpId!=b2->clumpId #ifdef YADE_SPH // If SPH-mode enabled, we do not skip interactions between clump-members // to get the correct calculation of density b->rho || true #endif ) && // do not collide clumps, since they are just containers, never interact !b1->isClump() && !b2->isClump() && // masks must have at least 1 bit in common b1->maskCompatible(b2->groupMask) && // avoid contact between particles having the same mask compatible with the avoidSelfInteractionMask. !( (b1->groupMask == b2->groupMask) && b1->maskCompatible(avoidSelfInteractionMask) ) ; } void Collider::pyHandleCustomCtorArgs(boost::python::tuple& t, boost::python::dict& d){ if(boost::python::len(t)==0) return; // nothing to do if(boost::python::len(t)!=1) throw invalid_argument(("Collider optionally takes exactly one list of BoundFunctor's as non-keyword argument for constructor ("+boost::lexical_cast(boost::python::len(t))+" non-keyword ards given instead)").c_str()); typedef std::vector > vecBound; vecBound vb=boost::python::extract(t[0])(); FOREACH(shared_ptr bf, vb) this->boundDispatcher->add(bf); t=boost::python::tuple(); // empty the args } trunk-2017.01a/pkg/common/Collider.hpp000066400000000000000000000053441304022710500175070ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include class Collider: public GlobalEngine { public: static int avoidSelfInteractionMask; /*! Probe the Bound on a bodies presense. Returns list of body ids with which there is potential overlap. */ virtual vector probeBoundingVolume(const Bound&){throw;} /*! Tell whether given bodies may interact, for other than spatial reasons. * * Concrete collider implementations should call this function if * the bodies are in potential interaction geometrically. */ static bool mayCollide(const Body*, const Body*); /*! Invalidate all persistent data (if the collider has any), forcing reinitialization at next run. The default implementation does nothing, colliders should override it if it is applicable. Currently used from Shop::flipCell, which changes cell information for bodies. */ virtual void invalidatePersistentData(){} // ctor with functors for the integrated BoundDispatcher virtual void pyHandleCustomCtorArgs(boost::python::tuple& t, boost::python::dict& d); int get_avoidSelfInteractionMask(){return avoidSelfInteractionMask;} void set_avoidSelfInteractionMask(const int &v){avoidSelfInteractionMask = v;} YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Collider,GlobalEngine,"Abstract class for finding spatial collisions between bodies. \n\n.. admonition:: Special constructor\n\n\tDerived colliders (unless they override ``pyHandleCustomCtorArgs``) can be given list of :yref:`BoundFunctors ` which is used to initialize the internal :yref:`boundDispatcher ` instance.", ((shared_ptr,boundDispatcher,new BoundDispatcher,Attr::readonly,":yref:`BoundDispatcher` object that is used for creating :yref:`bounds ` on collider's request as necessary.")), /*ctor*/, .add_property("avoidSelfInteractionMask",&Collider::get_avoidSelfInteractionMask,&Collider::set_avoidSelfInteractionMask,"This mask is used to avoid the interactions inside a group of particles. To do so, the particles must have the same mask and this mask have to be compatible with this one.") ); }; REGISTER_SERIALIZABLE(Collider); trunk-2017.01a/pkg/common/CylScGeom6D.hpp000066400000000000000000000076531304022710500177760ustar00rootroot00000000000000// 2011 © Bruno Chareyre // 2012 © Kneib Francois #pragma once #include class CylScGeom: public ScGeom { public: /// Emulate a sphere whose position is the projection of sphere's center on cylinder sphere, and with motion linearly interpolated between nodes State fictiousState; // shared_ptr duplicate; virtual ~CylScGeom () {}; YADE_CLASS_BASE_DOC_ATTRS_CTOR(CylScGeom,ScGeom,"Geometry of a cylinder-sphere contact.", ((bool,onNode,false,,"contact on node?")) ((int,isDuplicate,0,,"this flag is turned true (1) automatically if the contact is shared between two chained cylinders. A duplicated interaction will be skipped once by the constitutive law, so that only one contact at a time is effective. If isDuplicate=2, it means one of the two duplicates has no longer geometric interaction, and should be erased by the constitutive laws.")) ((int,trueInt,-1,,"Defines the body id of the cylinder where the contact is real, when :yref:`CylScGeom::isDuplicate`>0.")) ((Vector3r,start,Vector3r::Zero(),,"position of 1st node |yupdate|")) ((Vector3r,end,Vector3r::Zero(),,"position of 2nd node |yupdate|")) ((Body::id_t,id3,0,,"id of next chained cylinder |yupdate|")) ((Real,relPos,0,,"position of the contact on the cylinder (0: node-, 1:node+) |yupdate|")), createIndex(); /*ctor*/ ); REGISTER_CLASS_INDEX(CylScGeom,ScGeom); }; REGISTER_SERIALIZABLE(CylScGeom); class CylScGeom6D: public ScGeom6D { public: virtual ~CylScGeom6D() {}; void precomputeRotations(const State& rbp1, const State& rbp2, bool isNew, bool creep=false) { initRotations(rbp1,rbp2); } void initRotations(const State& rbp1, const State& rbp2){ initialOrientation1 = rbp1.ori; initialOrientation2 = rbp2.ori; twist=0; bending=Vector3r::Zero(); twistCreep=Quaternionr(1.0,0.0,0.0,0.0); } State fictiousState; YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(CylScGeom6D,ScGeom6D,"Class representing :yref:`geometry` of two :yref:`bodies` in contact. The contact has 6 DOFs (normal, 2×shear, twist, 2xbending) and uses :yref:`ScGeom` incremental algorithm for updating shear.", ((bool,onNode,false,,"contact on node?")) ((int,isDuplicate,0,,"this flag is turned true (1) automatically if the contact is shared between two chained cylinders. A duplicated interaction will be skipped once by the constitutive law, so that only one contact at a time is effective. If isDuplicate=2, it means one of the two duplicates has no longer geometric interaction, and should be erased by the constitutive laws.")) ((int,trueInt,-1,,"Defines the body id of the cylinder where the contact is real, when :yref:`CylScGeom::isDuplicate`>0.")) ((Vector3r,start,Vector3r::Zero(),,"position of 1st node |yupdate|")) ((Vector3r,end,Vector3r::Zero(),,"position of 2nd node |yupdate|")) ((Body::id_t,id3,0,,"id of next chained cylinder |yupdate|")) ((Real,relPos,0,,"position of the contact on the cylinder (0: node-, 1:node+) |yupdate|")), /* extra initializers */, /* ctor */ createIndex();, /* py */ ); REGISTER_CLASS_INDEX(CylScGeom6D,ScGeom6D); }; REGISTER_SERIALIZABLE(CylScGeom6D); trunk-2017.01a/pkg/common/Cylinder.cpp000066400000000000000000001203541304022710500175150ustar00rootroot00000000000000// 2011 © Bruno Chareyre // 2012 © Kneib Francois #include "Cylinder.hpp" #include #ifdef YADE_OPENGL #include #endif #include Cylinder::~Cylinder(){} ChainedCylinder::~ChainedCylinder(){} ChainedState::~ChainedState(){} // Ig2_Sphere_ChainedCylinder_CylScGeom::~Ig2_Sphere_ChainedCylinder_CylScGeom() {} // Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D::~Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D() {} YADE_PLUGIN((Cylinder)(ChainedCylinder)(ChainedState)(Ig2_Sphere_ChainedCylinder_CylScGeom)(Ig2_Sphere_ChainedCylinder_CylScGeom6D)(Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D)(Law2_CylScGeom6D_CohFrictPhys_CohesionMoment)(Law2_ChCylGeom6D_CohFrictPhys_CohesionMoment)(Law2_CylScGeom_FrictPhys_CundallStrack) #ifdef YADE_OPENGL (Gl1_Cylinder)(Gl1_ChainedCylinder) #endif (Bo1_Cylinder_Aabb)(Bo1_ChainedCylinder_Aabb) ); vector > ChainedState::chains; unsigned int ChainedState::currentChain=0; //!################## IG FUNCTORS ##################### //!Sphere-cylinder or cylinder-cylinder not implemented yet, see Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D and test/chained-cylinder-spring.py bool Ig2_Sphere_ChainedCylinder_CylScGeom::go( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { const State* sphereSt=YADE_CAST(&state1); const ChainedState* cylinderSt=YADE_CAST(&state2); ChainedCylinder *cylinder=YADE_CAST(cm2.get()); Sphere *sphere=YADE_CAST(cm1.get()); assert(sphereSt && cylinderSt && cylinder && sphere); bool isLast = (cylinderSt->chains[cylinderSt->chainNumber].size()==(cylinderSt->rank+1)); bool isNew = !c->geom; shared_ptr scm; if (!isNew) {scm=YADE_PTR_CAST(c->geom);} bool betweenTwoCylinders = false;//defines whether the sphere's center is moving between two cylinders who have an angle>180° Vector3r segment, branch, direction;//informations about the current cylinder Real length, dist; shared_ptr statePrev; Vector3r segmentPrev=Vector3r(0,0,0),directionPrev=Vector3r(0,0,0),branchPrev=Vector3r(0,0,0); Real lengthPrev=0,distPrev=0; if (cylinderSt->rank>0){//informations about the previous cylinder statePrev = YADE_PTR_CAST (Body::byId(cylinderSt->chains[cylinderSt->chainNumber][cylinderSt->rank-1],scene)->state); segmentPrev = cylinderSt->pos-statePrev->pos; lengthPrev = segmentPrev.norm(); directionPrev = segmentPrev/lengthPrev; branchPrev = sphereSt->pos-statePrev->pos; distPrev = directionPrev.dot(branchPrev); } //FIXME : definition of segment in next line breaks periodicity shared_ptr cylinderNext; branch = sphereSt->pos-cylinderSt->pos-shift2; if (isLast){//handle the last node with length=0 segment = Vector3r(0,0,0); length = 0; direction = Vector3r(0,1,0); dist = directionPrev.dot(branch); if (dist<0) { if (isNew) return false; else if (scm->isDuplicate) { scm->isDuplicate=2; scm->penetrationDepth=-1; return true; } } } else { cylinderNext = Body::byId(cylinderSt->chains[cylinderSt->chainNumber][cylinderSt->rank+1],scene); segment = cylinderNext->state->pos-cylinderSt->pos; length = segment.norm(); direction = segment/length; dist = direction.dot(branch); if(cylinderSt->rank>0){ if(distPrev>lengthPrev && dist<0){//the sphere is touching two cylinder who have an angle>180° betweenTwoCylinders = true; } } if (!betweenTwoCylinders && (cylinderSt->rank>0 or dist>0)) { if ( segment.dot(branch) >= segment.dot(segment) or dist<0) {//position after or before the cylinder //FIXME : scm->penetrationDepth=-1 is defined to workaround interactions never being erased when scm->isDuplicate=2 on the true interaction. if (isNew) return false; else if (scm->isDuplicate) { scm->isDuplicate=2; scm->penetrationDepth=-1; return true; } } } } //Check sphere-cylinder distance Vector3r projectedP = cylinderSt->pos+shift2 + direction*dist; branch = projectedP-sphereSt->pos; if(isLast || (cylinderSt->rank==0 && dist<0)){branch = cylinderSt->pos - sphereSt->pos;} if (branch.norm() > sphere->radius+cylinder->radius) { if (isNew) return false; else if (scm->isDuplicate){ scm->isDuplicate=2; scm->penetrationDepth=-1; return true; } } if (!isNew) scm->isDuplicate = false;//reset here at each step, and recompute below //if there is a contact with the previous element in the chain, consider this one a duplicate and push data to the new contact. Two interactions will share the same geometry and physics during a timestep. if (!betweenTwoCylinders && cylinderSt->rank>0 && dist<0) { if (!isNew) { const shared_ptr intr = scene->interactions->find(c->id1,cylinderSt->chains[cylinderSt->chainNumber][cylinderSt->rank-1]); if(!intr) {cout<<"Skipping contact because collider didn't found the previous cylinder"<geom = c->geom; intr->phys = c->phys; scm=YADE_PTR_CAST(c->geom); scm->isDuplicate = 2; scm->trueInt = cylinderSt->chains[cylinderSt->chainNumber][cylinderSt->rank-1]; isNew = false; return true; } else scm->isDuplicate=true; scm->trueInt = cylinderSt->chains[cylinderSt->chainNumber][cylinderSt->rank-1]; } //similarly, make sure there is no contact with the next element in the chain //else if (!isLast && dist>length) { if (!betweenTwoCylinders && !isLast && dist>=length) { if (!isNew) { const shared_ptr intr = scene->interactions->find(c->id1,cylinderSt->chains[cylinderSt->chainNumber][cylinderSt->rank+1]); if(!intr) {cout<<"Skipping contact because collider didn't found the next cylinder."<geom = c->geom; intr->phys = c->phys; scm=YADE_PTR_CAST(c->geom); scm->isDuplicate = 2; scm->trueInt = cylinderSt->chains[cylinderSt->chainNumber][cylinderSt->rank+1]; isNew = false; return true; } else scm->isDuplicate=true; scm->trueInt = cylinderSt->chains[cylinderSt->chainNumber][cylinderSt->rank+1]; } //We didn't find any special case, do normal geometry definition if (isNew) { scm=shared_ptr(new CylScGeom()); c->geom=scm;} scm->radius1=sphere->radius; scm->radius2=cylinder->radius; if (!isLast) scm->id3=cylinderSt->chains[cylinderSt->chainNumber][cylinderSt->rank+1]; scm->start=cylinderSt->pos+shift2; scm->end=scm->start+segment; //FIXME : there should be other checks without distanceFactor? if (dist<=0 || isLast) {//We have sphere-node contact Vector3r normal=(cylinderSt->pos+shift2)-sphereSt->pos; Real norm=normal.norm(); normal /=norm; scm->relPos=0; scm->onNode=true; scm->relPos=0; scm->penetrationDepth=sphere->radius+cylinder->radius-norm; scm->contactPoint=sphereSt->pos+(sphere->radius-0.5*scm->penetrationDepth)*normal; scm->precompute(state1,state2,scene,c,normal,isNew,shift2,true);//use sphere-sphere precompute (a node is a sphere) } else {//we have sphere-cylinder contact scm->onNode=false; scm->relPos=dist/length; Real norm=branch.norm(); Vector3r normal=branch/norm; scm->penetrationDepth= sphere->radius+cylinder->radius-norm; // define a virtual sphere at the projected center scm->fictiousState.pos = projectedP; scm->fictiousState.vel = (1-scm->relPos)*cylinderSt->vel + scm->relPos*cylinderNext->state->vel; scm->fictiousState.angVel = ((1-scm->relPos)*cylinderSt->angVel + scm->relPos*cylinderNext->state->angVel).dot(direction)*direction //twist part : interpolated + segment.cross(cylinderNext->state->vel - cylinderSt->vel);// non-twist part : defined from nodes velocities if (dist>length) { scm->penetrationDepth=sphere->radius+cylinder->radius-(cylinderSt->pos+segment-sphereSt->pos).norm(); //FIXME : handle contact jump on next element } scm->contactPoint = sphereSt->pos+normal*(sphere->radius-0.5*scm->penetrationDepth); scm->precompute(state1,scm->fictiousState,scene,c,branch/norm,isNew,shift2,true);//use sphere-sphere precompute (with a virtual sphere) } return true; } bool Ig2_Sphere_ChainedCylinder_CylScGeom::goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { cerr<<"Ig2_Sphere_ChainedCylinder_CylScGeom::goReverse"<swapOrder(); return go(cm2,cm1,state2,state1,-shift2,force,c); } bool Ig2_Sphere_ChainedCylinder_CylScGeom6D::go( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { const State* sphereSt=YADE_CAST(&state1); const ChainedState* cylinderSt=YADE_CAST(&state2); ChainedCylinder *cylinder=YADE_CAST(cm2.get()); Sphere *sphere=YADE_CAST(cm1.get()); assert(sphereSt && cylinderSt && cylinder && sphere); bool isLast = (cylinderSt->chains[cylinderSt->chainNumber].size()==(cylinderSt->rank+1)); bool isNew = !c->geom; shared_ptr scm; if (!isNew) {scm=YADE_PTR_CAST(c->geom);} bool betweenTwoCylinders = false;//defines whether the sphere's center is moving between two cylinders who have an angle>180° Vector3r segment, branch, direction;//informations about the current cylinder Real length, dist; shared_ptr statePrev; Vector3r segmentPrev=Vector3r(0,0,0),directionPrev=Vector3r(0,0,0),branchPrev=Vector3r(0,0,0); Real lengthPrev=0,distPrev=0; if (cylinderSt->rank>0){//informations about the previous cylinder statePrev = YADE_PTR_CAST (Body::byId(cylinderSt->chains[cylinderSt->chainNumber][cylinderSt->rank-1],scene)->state); segmentPrev = cylinderSt->pos-statePrev->pos; lengthPrev = segmentPrev.norm(); directionPrev = segmentPrev/lengthPrev; branchPrev = sphereSt->pos-statePrev->pos; distPrev = directionPrev.dot(branchPrev); } //FIXME : definition of segment in next line breaks periodicity shared_ptr cylinderNext; branch = sphereSt->pos-cylinderSt->pos-shift2; if (isLast){//handle the last node with length=0 segment = Vector3r(0,0,0); length = 0; direction = Vector3r(0,1,0); dist = directionPrev.dot(branch); if (dist<0) { if (isNew) return false; else if (scm->isDuplicate) { scm->isDuplicate=2; return true; } } } else { cylinderNext = Body::byId(cylinderSt->chains[cylinderSt->chainNumber][cylinderSt->rank+1],scene); segment = cylinderNext->state->pos-cylinderSt->pos; length = segment.norm(); direction = segment/length; dist = direction.dot(branch); if(cylinderSt->rank>0){ if(distPrev>lengthPrev && dist<0){//the sphere is touching two cylinder who have an angle>180° betweenTwoCylinders = true; } } if (!betweenTwoCylinders && (cylinderSt->rank>0 or dist>0)) { if ( segment.dot(branch) >= segment.dot(segment) or dist<0) {//position after or before the cylinder //FIXME : scm->penetrationDepth=-1 is defined to workaround interactions never being erased when scm->isDuplicate=2 on the true interaction. if (isNew) return false; else if (scm->isDuplicate) { scm->isDuplicate=2; return true; } } } } //Check sphere-cylinder distance Vector3r projectedP = cylinderSt->pos+shift2 + direction*dist; branch = projectedP-sphereSt->pos; if(isLast || (cylinderSt->rank==0 && dist<0)){branch = cylinderSt->pos - sphereSt->pos;} if (branch.norm() > sphere->radius+cylinder->radius) { if (isNew) return false; else if (scm->isDuplicate){ scm->isDuplicate=2; return true; } } if (!isNew) scm->isDuplicate = false;//reset here at each step, and recompute below //if there is a contact with the previous element in the chain, consider this one a duplicate and push data to the new contact. Two interactions will share the same geometry and physics during a timestep. if (!betweenTwoCylinders && cylinderSt->rank>0 && dist<0) { if (!isNew) { const shared_ptr intr = scene->interactions->find(c->id1,cylinderSt->chains[cylinderSt->chainNumber][cylinderSt->rank-1]); if(!intr) {cout<<"Skipping contact because collider didn't found the previous cylinder"<geom = c->geom; intr->phys = c->phys; scm=YADE_PTR_CAST(c->geom); scm->isDuplicate = 2; scm->trueInt = cylinderSt->chains[cylinderSt->chainNumber][cylinderSt->rank-1]; isNew = false; return true; } else scm->isDuplicate=true; scm->trueInt = cylinderSt->chains[cylinderSt->chainNumber][cylinderSt->rank-1]; } //similarly, make sure there is no contact with the next element in the chain //else if (!isLast && dist>length) { if (!betweenTwoCylinders && !isLast && dist>=length) { if (!isNew) { const shared_ptr intr = scene->interactions->find(c->id1,cylinderSt->chains[cylinderSt->chainNumber][cylinderSt->rank+1]); if(!intr) {cout<<"Skipping contact because collider didn't found the next cylinder."<geom = c->geom; intr->phys = c->phys; scm=YADE_PTR_CAST(c->geom); scm->isDuplicate = 2; scm->trueInt = cylinderSt->chains[cylinderSt->chainNumber][cylinderSt->rank+1]; isNew = false; return true; } else scm->isDuplicate=true; scm->trueInt = cylinderSt->chains[cylinderSt->chainNumber][cylinderSt->rank+1]; } //We didn't find any special case, do normal geometry definition if (isNew) { scm=shared_ptr(new CylScGeom6D()); c->geom=scm;} scm->radius1=sphere->radius; scm->radius2=cylinder->radius; if (!isLast && !scm->id3) scm->id3=cylinderSt->chains[cylinderSt->chainNumber][cylinderSt->rank+1]; scm->start=cylinderSt->pos+shift2; scm->end=scm->start+segment; //FIXME : there should be other checks without distanceFactor? if (dist<=0 || isLast) {//We have sphere-node contact Vector3r normal=(cylinderSt->pos+shift2)-sphereSt->pos; Real norm=normal.norm(); normal /=norm; scm->relPos=0; scm->onNode=true; scm->relPos=0; scm->penetrationDepth=sphere->radius+cylinder->radius-norm; scm->contactPoint=sphereSt->pos+(sphere->radius-0.5*scm->penetrationDepth)*normal; scm->precompute(state1,state2,scene,c,normal,isNew,shift2,true);//use sphere-sphere precompute (a node is a sphere) } else {//we have sphere-cylinder contact scm->onNode=false; scm->relPos=dist/length; Real norm=branch.norm(); Vector3r normal=branch/norm; scm->penetrationDepth= sphere->radius+cylinder->radius-norm; // define a virtual sphere at the projected center scm->fictiousState.pos = projectedP; scm->fictiousState.vel = (1-scm->relPos)*cylinderSt->vel + scm->relPos*cylinderNext->state->vel; scm->fictiousState.angVel = ((1-scm->relPos)*cylinderSt->angVel + scm->relPos*cylinderNext->state->angVel).dot(direction)*direction //twist part : interpolated + segment.cross(cylinderNext->state->vel - cylinderSt->vel);// non-twist part : defined from nodes velocities if (dist>length) { scm->penetrationDepth=sphere->radius+cylinder->radius-(cylinderSt->pos+segment-sphereSt->pos).norm(); //FIXME : handle contact jump on next element } scm->contactPoint = sphereSt->pos+normal*(sphere->radius-0.5*scm->penetrationDepth); scm->precompute(state1,scm->fictiousState,scene,c,branch/norm,isNew,shift2,true);//use sphere-sphere precompute (with a virtual sphere) } return true; } bool Ig2_Sphere_ChainedCylinder_CylScGeom6D::goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { return go(cm1,cm2,state2,state1,-shift2,force,c); } bool Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D::go( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { const ChainedState *pChain1, *pChain2; pChain1=YADE_CAST(&state1); pChain2=YADE_CAST(&state2); unsigned int sizeChain1=pChain1->chains[pChain1->chainNumber].size(); unsigned int sizeChain2=pChain2->chains[pChain2->chainNumber].size(); if (!pChain1 || !pChain2) { cerr <<"cast failed8567"<rank- (int) pChain1->rank == -1); const ChainedState& bchain1 = revert? *pChain2 : *YADE_CAST(&state1); const ChainedState& bchain2 = revert? *pChain1 : *pChain2; ChainedCylinder *bs1=static_cast(revert? cm2.get():cm1.get()); bool isLast = bchain1.chains[bchain1.chainNumber].size()==(bchain1.rank+1) || bchain2.chains[bchain2.chainNumber].size()==(bchain2.rank+1); bool isNew = !c->geom; if (pChain2->chainNumber!=pChain1->chainNumber) { shared_ptr scm; if(isLast){ return false; } shared_ptr cylinderNext1=Body::byId(pChain1->chains[pChain1->chainNumber][pChain1->rank+1],scene); shared_ptr cylinderNext2=Body::byId(pChain2->chains[pChain2->chainNumber][pChain2->rank+1],scene); //cout<id1<<" "<id2<pos, a=cylinderNext1->state->pos-A , B=pChain2->pos , b=cylinderNext2->state->pos-B; Vector3r N=a.cross(b); Vector3r normal; if(N.norm()>1e-14){ dist=std::abs(N.dot(B-A)/(N.norm())); //distance between the two LINES. //But we need to check that the intersection point is inside the two SEGMENTS ... //Projection of B to have a common plan between the two segments. Vector3r projB1=B+dist*(N/(N.norm())) , projB2=B-dist*(N/(N.norm())); Real distB1A=(projB1-A).norm() , distB2A=(projB2-A).norm() ; Vector3r projB=(distB1A<=distB2A)*projB1 + (distB1A>distB2A)*projB2; int b1=0, b2=1; //base vectors used to compute the segment intersection (if N is aligned with an axis, we can't use this axis) if(std::abs(N[1])<1e-14 && std::abs(N[2])<1e-14){b1=1;b2=2;} if(std::abs(N[0])<1e-14 && std::abs(N[2])<1e-14){b1=0;b2=2;} Real det=a[b1]*b[b2]-a[b2]*b[b1]; if(std::abs(det)>1e-14){ //Check if the two segments are intersected (using k and m) k = (b[b2]*(projB[b1]-A[b1])+b[b1]*(A[b2]-projB[b2]))/det; m = (a[b1]*(-projB[b2]+A[b2])+a[b2]*(projB[b1]-A[b1]))/det; if( k<0.0 || k>=1.0 || m<0.0 || m>=1.0 ) { //so they are not intersected dist=NaN; if(k>=1){k=1; if(!(pChain1->rank>=sizeChain1-2))insideCyl1=0; } if(k<0){k=0; if(!(pChain1->rank==0))insideCyl1=0; } if(m>=1){m=1; if(!(pChain2->rank>=sizeChain2-2))insideCyl2=0; } if(m<0){m=0; if(!(pChain2->rank==0))insideCyl2=0; } } } else cout<<"Error in Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D : det==0 !!!"<1 && pChain2->rank>=sizeChain2-2) || (h1<0 && pChain2->rank==0) || (h2>1 && pChain1->rank>=sizeChain1-2) || (h2<0 && pChain1->rank==0); if(edgeEdgeContact)colinearVectors=0; if( (0<=h1 and 1>h1) or (0<=h2 and 1>h2) or edgeEdgeContact){; //Do a perfectly flat contact } else return false;//Parallel lines but edge-edge contact } ChainedCylinder *cc1=static_cast(cm1.get()); ChainedCylinder *cc2=static_cast(cm2.get()); if(std::isnan(dist)){ //now if we didn't found a suitable distance because the segments don't cross each other, we try to find a sphere-cylinder distance. Vector3r pointsToCheck[4]={A,A+a,B,B+b}; Real resultDist=dist, resultProj=dist ; int whichCaseIsCloser=-1 ; for (int i=0;i<4;i++){ //loop on the 4 cylinder's extremities and look at the extremity-cylinder distance Vector3r S=pointsToCheck[i], C=(i<2)?B:A, vec=(i<2)?b:a; Vector3r CS=S-C; Real d=CS.dot(vec)/(vec.norm()); if(d<0.) resultDist=CS.norm(); else if(d>vec.norm()) resultDist=(C+vec-S).norm(); else resultDist=(CS.cross(vec)).norm()/(vec.norm()); if(dist>resultDist or std::isnan(dist)){dist=resultDist ; whichCaseIsCloser=i; resultProj=d;} } //we know which extremity may be in contact (i), so k and m are computed to generate the right fictiousStates. insideCyl1=1 ; insideCyl2=1; //FIXME:NATCHOS ! this should be reformulated if(whichCaseIsCloser==0 || whichCaseIsCloser==1){ k=whichCaseIsCloser==0?0:1; if(resultProj<=0){ m=0; if(!(pChain2->rank==0))insideCyl2=0;} else if(resultProj>b.norm()){ m=1; if(!(pChain2->rank>=sizeChain2-2))insideCyl2=0;} else m=resultProj/(b.norm()); if(isNew && whichCaseIsCloser==1 && !(pChain1->rank>=sizeChain1-2)) return false; } else{ m=whichCaseIsCloser==2?0:1; if(resultProj<=0){ k=0; if(!(pChain1->rank==0))insideCyl1=0;} else if(resultProj>a.norm()){ k=1; if(!(pChain1->rank>=sizeChain2-2))insideCyl1=0;} else k=resultProj/(a.norm()); if(isNew && whichCaseIsCloser==3 && !(pChain2->rank>=sizeChain2-2)) return false; } } if(isNew && dist>=cc1->radius + cc2->radius) return false; //if the contact had not yet occured, return false. //FIXME:the next line sometimes causes an error in the terminal, because instead of returning false here the contact should be correctly erased. if(insideCyl1==0 || insideCyl2==0) return false; //the contact may be duplicated ... else{ //else create the geometry. if(!isNew) scm=YADE_PTR_CAST(c->geom); else { scm=shared_ptr(new ChCylGeom6D()); c->geom=scm; } scm->relPos1=colinearVectors?0.5:k ; scm->relPos2=colinearVectors?0.5:m; scm->fictiousState1.pos=A + k*a; scm->fictiousState2.pos=B + m*b; scm->fictiousState1.vel = (1-k)*pChain1->vel + k*cylinderNext1->state->vel; scm->fictiousState2.vel = (1-m)*pChain2->vel + m*cylinderNext2->state->vel; Vector3r direction = a/(a.norm()); scm->fictiousState1.angVel = ((1-k)*pChain1->angVel + k*cylinderNext1->state->angVel).dot(direction)*direction //twist part : interpolated + a.cross(cylinderNext1->state->vel - pChain1->vel);// non-twist part : defined from nodes velocities direction = b/(b.norm()); scm->fictiousState2.angVel = ((1-m)*pChain2->angVel + m*cylinderNext2->state->angVel).dot(direction)*direction //twist part : interpolated + b.cross(cylinderNext2->state->vel - pChain2->vel);// non-twist part : defined from nodes velocities scm->contactPoint = 0.5*(scm->fictiousState1.pos+scm->fictiousState2.pos); normal= scm->fictiousState2.pos - scm->fictiousState1.pos; normal=normal/(normal.norm()); scm->penetrationDepth=cc1->radius+cc2->radius-dist; scm->radius1=cc1->radius; scm->radius2=cc2->radius; scm->precompute(scm->fictiousState1,scm->fictiousState2,scene,c,normal,isNew,shift2,true); return true; } } else if (bchain2.rank-bchain1.rank != 1) {/*cerr<<"Mutual contacts in same chain between not adjacent elements, not handled*/ return false;} else{ //contact between two Cylinders within the same chain. shared_ptr scm; if(!isNew) scm=YADE_PTR_CAST(c->geom); else { scm=shared_ptr(new ScGeom6D()); c->geom=scm; } Real length=(bchain2.pos-bchain1.pos).norm(); Vector3r segt =pChain2->pos-pChain1->pos; if(isNew) {/*scm->normal=scm->prevNormal=segt/length;*/bs1->initLength=length;} if (!halfLengthContacts){ scm->radius1=revert ? 0:bs1->initLength; scm->radius2=revert ? bs1->initLength:0; scm->contactPoint=bchain2.pos; } else { scm->radius1=scm->radius2=0.5*bs1->initLength; scm->contactPoint=0.5*(bchain2.pos+bchain1.pos); } scm->penetrationDepth=bs1->initLength-length; //bs1->segment used for fast BBs and projections + display bs1->segment= bchain2.pos-bchain1.pos; #ifdef YADE_OPENGL bs1->length=length; bs1->chainedOrientation.setFromTwoVectors(Vector3r::UnitZ(),bchain1.ori.conjugate()*segt); #endif scm->precompute(state1,state2,scene,c,segt/length,isNew,shift2,true); scm->precomputeRotations(state1,state2,isNew,false); //Set values that will be considered in Ip2 functor, geometry (precomputed) is really defined with values above scm->radius1 = scm->radius2 = bs1->initLength*0.5; return true; } } bool Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D::goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { return go(cm2,cm1,state2,state1,-shift2,force,c); } #ifdef YADE_OPENGL //!################## RENDERING ##################### bool Gl1_Cylinder::wire; bool Gl1_Cylinder::glutNormalize; int Gl1_Cylinder::glutSlices; int Gl1_Cylinder::glutStacks; int Gl1_Cylinder::glCylinderList=-1; void Gl1_Cylinder::out( Quaternionr q ) { AngleAxisr aa(q); std::cout << " axis: " << aa.axis()[0] << " " << aa.axis()[1] << " " << aa.axis()[2] << ", angle: " << aa.angle() << " | "; } void Gl1_Cylinder::go(const shared_ptr& cm, const shared_ptr& ,bool wire2, const GLViewInfo&) { Real r=(static_cast(cm.get()))->radius; Real length=(static_cast(cm.get()))->length; //glMaterialv(GL_FRONT, GL_AMBIENT_AND_DIFFUSE, Vector3f(cm->color[0],cm->color[1],cm->color[2])); glColor3v(cm->color); if(glutNormalize) glPushAttrib(GL_NORMALIZE); // glPushMatrix(); Quaternionr shift = (static_cast(cm.get()))->chainedOrientation; if (wire || wire2) drawCylinder(true, r,length,shift); else drawCylinder(false, r,length,shift); if(glutNormalize) glPopAttrib(); // glPopMatrix(); return; } void Gl1_ChainedCylinder::go(const shared_ptr& cm, const shared_ptr& state,bool wire2, const GLViewInfo&) { Real r=(static_cast(cm.get()))->radius; Real length=(static_cast(cm.get()))->length; Quaternionr shift;// = (static_cast(cm.get()))->chainedOrientation; shift.setFromTwoVectors(Vector3r::UnitZ(),state->ori.conjugate()*(static_cast(cm.get()))->segment); glColor3v(cm->color); if(glutNormalize) glPushAttrib(GL_NORMALIZE); if (wire || wire2) drawCylinder(true, r,length,shift); else drawCylinder(false, r,length,shift); if(glutNormalize) glPopAttrib(); return; } void Gl1_Cylinder::drawCylinder(bool wire, Real radius, Real length, const Quaternionr& shift) const { glPushMatrix(); GLUquadricObj *quadObj = gluNewQuadric(); gluQuadricDrawStyle(quadObj, (GLenum) (wire ? GLU_SILHOUETTE : GLU_FILL)); gluQuadricNormals(quadObj, (GLenum) GLU_SMOOTH); gluQuadricOrientation(quadObj, (GLenum) GLU_OUTSIDE); AngleAxisr aa(shift); glRotatef(aa.angle()*180.0/Mathr::PI,aa.axis()[0],aa.axis()[1],aa.axis()[2]); gluCylinder(quadObj, radius, radius, length, glutSlices,glutStacks); gluQuadricOrientation(quadObj, (GLenum) GLU_INSIDE); glutSolidSphere(radius,glutSlices,glutStacks); glTranslatef(0.0,0.0,length); glutSolidSphere(radius,glutSlices,glutStacks); // gluDisk(quadObj,0.0,radius,glutSlices,_loops); gluDeleteQuadric(quadObj); glPopMatrix(); } //!################## BOUNDS FUNCTOR ##################### #endif void Bo1_Cylinder_Aabb::go(const shared_ptr& cm, shared_ptr& bv, const Se3r& se3, const Body* b){ Cylinder* cylinder = static_cast(cm.get()); if(!bv){ bv=shared_ptr(new Aabb); } Aabb* aabb=static_cast(bv.get()); if(!scene->isPeriodic){ const Vector3r& O = se3.position; Vector3r O2 = se3.position+se3.orientation*cylinder->segment; aabb->min=aabb->max=O; for (int k=0;k<3;k++){ aabb->min[k]=min(aabb->min[k],min(O[k],O2[k])-cylinder->radius); aabb->max[k]=max(aabb->max[k],max(O[k],O2[k])+cylinder->radius); } return; } } void Bo1_ChainedCylinder_Aabb::go(const shared_ptr& cm, shared_ptr& bv, const Se3r& se3, const Body* b){ ChainedCylinder* cylinder = static_cast(cm.get()); if(!bv){ bv=shared_ptr(new Aabb); } Aabb* aabb=static_cast(bv.get()); if(!scene->isPeriodic){ const Vector3r& O = se3.position; Vector3r O2 = O+cylinder->segment; //cout<<"O="<isDuplicate==2) return false;} } Real& un=geom->penetrationDepth; phys->normalForce=phys->kn*std::max(un,(Real) 0)*geom->normal; Vector3r& shearForce = geom->rotate(phys->shearForce); const Vector3r& shearDisp = geom->shearIncrement(); shearForce -= phys->ks*shearDisp; Real maxFs = phys->normalForce.squaredNorm()*std::pow(phys->tangensOfFrictionAngle,2); if (!scene->trackEnergy){//Update force but don't compute energy terms (see below)) // PFC3d SlipModel, is using friction angle. CoulombCriterion if( shearForce.squaredNorm() > maxFs ){ Real ratio = sqrt(maxFs) / shearForce.norm(); shearForce *= ratio;} } else { //almost the same with additional Vector3r instanciated for energy tracing, duplicated block to make sure there is no cost for the instanciation of the vector when traceEnergy==false if(shearForce.squaredNorm() > maxFs){ Real ratio = sqrt(maxFs) / shearForce.norm(); Vector3r trialForce=shearForce;//store prev force for definition of plastic slip //define the plastic work input and increment the total plastic energy dissipated shearForce *= ratio; Real dissip=((1/phys->ks)*(trialForce-shearForce))/*plastic disp*/ .dot(shearForce)/*active force*/; if(dissip>0) scene->energy->add(dissip,"plastDissip",plastDissipIx,/*reset*/false); } // compute elastic energy as well scene->energy->add(0.5*(phys->normalForce.squaredNorm()/phys->kn+phys->shearForce.squaredNorm()/phys->ks),"elastPotential",elastPotentialIx,/*reset at every timestep*/true); } if (!scene->isPeriodic) { Vector3r force = -phys->normalForce-shearForce; scene->forces.addForce(id1,force); scene->forces.addTorque(id1,(geom->radius1-0.5*geom->penetrationDepth)* geom->normal.cross(force)); //FIXME : include moment due to axis-contact distance in forces on node Vector3r twist = (geom->radius2-0.5*geom->penetrationDepth)* geom->normal.cross(force); scene->forces.addForce(id2,(geom->relPos-1)*force); scene->forces.addTorque(id2,(1-geom->relPos)*twist); if (geom->relPos) { //else we are on node (or on last node - and id3 is junk) scene->forces.addForce(geom->id3,(-geom->relPos)*force); scene->forces.addTorque(geom->id3,geom->relPos*twist);} } // applyForceAtContactPoint(-phys->normalForce-shearForce, geom->contactPoint, id1, de1->se3.position, id2, de2->se3.position); else {//FIXME : periodicity not implemented here : Vector3r force = -phys->normalForce-shearForce; scene->forces.addForce(id1,force); scene->forces.addForce(id2,-force); scene->forces.addTorque(id1,(geom->radius1-0.5*geom->penetrationDepth)* geom->normal.cross(force)); scene->forces.addTorque(id2,(geom->radius2-0.5*geom->penetrationDepth)* geom->normal.cross(force)); } return true; } bool Law2_CylScGeom6D_CohFrictPhys_CohesionMoment::go(shared_ptr& ig, shared_ptr& ip, Interaction* contact) { int id1 = contact->getId1(), id2 = contact->getId2(); CylScGeom6D* geom= YADE_CAST(ig.get()); CohFrictPhys* currentContactPhysics = YADE_CAST(ip.get()); Vector3r& shearForce = currentContactPhysics->shearForce; //force tangentielle if (contact->isFresh(scene)) shearForce = Vector3r::Zero(); //contact nouveau => force tengentielle = 0,0,0 Real un = geom->penetrationDepth; //un : interpenetration Real Fn = currentContactPhysics->kn*(un-currentContactPhysics->unp); //Fn : force normale if (geom->isDuplicate) { if (id2!=geom->trueInt) { //cerr<<"skip duplicate "<isDuplicate==2) return false;} } if (currentContactPhysics->fragile && (-Fn)> currentContactPhysics->normalAdhesion) { // BREAK due to tension return false; } else { if ((-Fn)> currentContactPhysics->normalAdhesion) {//normal plasticity Fn=-currentContactPhysics->normalAdhesion; currentContactPhysics->unp = un+currentContactPhysics->normalAdhesion/currentContactPhysics->kn; if (currentContactPhysics->unpMax && currentContactPhysics->unpunpMax) return false; } currentContactPhysics->normalForce = Fn*geom->normal; Vector3r& shearForce = geom->rotate(currentContactPhysics->shearForce); const Vector3r& dus = geom->shearIncrement(); //Linear elasticity giving "trial" shear force shearForce -= currentContactPhysics->ks*dus; Real Fs = currentContactPhysics->shearForce.norm(); Real maxFs = currentContactPhysics->shearAdhesion; if (!currentContactPhysics->cohesionDisablesFriction || maxFs==0) maxFs += Fn*currentContactPhysics->tangensOfFrictionAngle; maxFs = std::max((Real) 0, maxFs); if (Fs > maxFs) {//Plasticity condition on shear force if (currentContactPhysics->fragile && !currentContactPhysics->cohesionBroken) { currentContactPhysics->SetBreakingState(); maxFs = max((Real) 0, Fn*currentContactPhysics->tangensOfFrictionAngle); } maxFs = maxFs / Fs; shearForce *= maxFs; if (Fn<0) currentContactPhysics->normalForce = Vector3r::Zero();//Vector3r::Zero() } Vector3r force = -currentContactPhysics->normalForce-shearForce; if (!scene->isPeriodic) { scene->forces.addForce(id1,force); scene->forces.addTorque(id1,(geom->radius1-0.5*geom->penetrationDepth)* geom->normal.cross(force)); //FIXME : include moment due to axis-contact distance in forces on node Vector3r twist = (geom->radius2-0.5*geom->penetrationDepth)* geom->normal.cross(force); scene->forces.addForce(id2,(geom->relPos-1)*force); scene->forces.addTorque(id2,(1-geom->relPos)*twist); if (geom->relPos) { //else we are on node (or on last node - and id3 is junk) scene->forces.addForce(geom->id3,(-geom->relPos)*force); scene->forces.addTorque(geom->id3,geom->relPos*twist);} } // applyForceAtContactPoint(-phys->normalForce-shearForce, geom->contactPoint, id1, de1->se3.position, id2, de2->se3.position); else {//FIXME : periodicity not implemented here : scene->forces.addForce(id1,force); scene->forces.addForce(id2,-force); scene->forces.addTorque(id1,(geom->radius1-0.5*geom->penetrationDepth)* geom->normal.cross(force)); scene->forces.addTorque(id2,(geom->radius2-0.5*geom->penetrationDepth)* geom->normal.cross(force)); } //applyForceAtContactPoint(-currentContactPhysics->normalForce-shearForce, geom->contactPoint, id1, de1->se3.position, id2, de2->se3.position); } return true; } bool Law2_ChCylGeom6D_CohFrictPhys_CohesionMoment::go(shared_ptr& ig, shared_ptr& ip, Interaction* contact){ int id1 = contact->getId1(), id2 = contact->getId2(); ChCylGeom6D* geom= YADE_CAST(ig.get()); CohFrictPhys* currentContactPhysics = YADE_CAST(ip.get()); /* shared_ptr state1 = YADE_PTR_CAST (Body::byId(id1,scene)->state); const shared_ptr intr = scene->interactions->find(id1,id2+1); if(!intr) {cout<<"Skipping contact because collider didn't found the next cylinder."<geom = c->geom; intr->phys = c->phys; */ Vector3r& shearForce = currentContactPhysics->shearForce; //force tangentielle if (contact->isFresh(scene)) shearForce = Vector3r::Zero(); //contact nouveau => force tengentielle = 0,0,0 Real un = geom->penetrationDepth; //un : interpenetration Real Fn = currentContactPhysics->kn*(un-currentContactPhysics->unp); //Fn : force normale if (currentContactPhysics->fragile && (-Fn)> currentContactPhysics->normalAdhesion) return false; // BREAK due to tension else { if ((-Fn)> currentContactPhysics->normalAdhesion) {//normal plasticity Fn=-currentContactPhysics->normalAdhesion; currentContactPhysics->unp = un+currentContactPhysics->normalAdhesion/currentContactPhysics->kn; if (currentContactPhysics->unpMax && currentContactPhysics->unpunpMax) return false; } currentContactPhysics->normalForce = Fn*geom->normal; Vector3r& shearForce = geom->rotate(currentContactPhysics->shearForce); const Vector3r& dus = geom->shearIncrement(); //Linear elasticity giving "trial" shear force shearForce -= currentContactPhysics->ks*dus; Real Fs = currentContactPhysics->shearForce.norm(); Real maxFs = currentContactPhysics->shearAdhesion; if (!currentContactPhysics->cohesionDisablesFriction || maxFs==0) maxFs += Fn*currentContactPhysics->tangensOfFrictionAngle; maxFs = std::max((Real) 0, maxFs); if (Fs > maxFs) {//Plasticity condition on shear force if (currentContactPhysics->fragile && !currentContactPhysics->cohesionBroken) { currentContactPhysics->SetBreakingState(); maxFs = max((Real) 0, Fn*currentContactPhysics->tangensOfFrictionAngle); } maxFs = maxFs / Fs; shearForce *= maxFs; if (Fn<0) currentContactPhysics->normalForce = Vector3r::Zero();//Vector3r::Zero() } Vector3r force = -currentContactPhysics->normalForce-shearForce; //cout<<"id1="<getId1()<<" id2="<getId2()<<" normalForce="<normalForce<<" shearForce="<isPeriodic) { Vector3r twist1 = (geom->radius1-0.5*geom->penetrationDepth)* geom->normal.cross(force); Vector3r twist2 = (geom->radius2-0.5*geom->penetrationDepth)* geom->normal.cross(force); scene->forces.addForce(id1,(1-geom->relPos1)*force); scene->forces.addTorque(id1,(1-geom->relPos1)*twist1); scene->forces.addForce(id2,-(1-geom->relPos2)*force); scene->forces.addTorque(id2,(1-geom->relPos2)*twist2); scene->forces.addForce(id1+1,geom->relPos1*force); scene->forces.addTorque(id1+1,geom->relPos1*twist1); scene->forces.addForce(id2+1,-geom->relPos2*force); scene->forces.addTorque(id2+1,geom->relPos2*twist2); } // applyForceAtContactPoint(-phys->normalForce-shearForce, geom->contactPoint, id1, de1->se3.position, id2, de2->se3.position); else {//FIXME : periodicity not implemented here : scene->forces.addForce(id1,force); scene->forces.addForce(id2,-force); scene->forces.addTorque(id1,(geom->radius1-0.5*geom->penetrationDepth)* geom->normal.cross(force)); scene->forces.addTorque(id2,(geom->radius2-0.5*geom->penetrationDepth)* geom->normal.cross(force)); } } return true; } trunk-2017.01a/pkg/common/Cylinder.hpp000066400000000000000000000477041304022710500175310ustar00rootroot00000000000000// 2011 © Bruno Chareyre // 2012 © Kneib Francois #pragma once #include #include #include #include #include #ifdef YADE_OPENGL #include #endif #include #include class Cylinder: public Sphere{ public: // Cylinder(Real _radius, Real _length): length(_length) { /*segment=Vector3r(0,0,1)*_length;*/ radius=_radius; createIndex(); } virtual ~Cylinder (); YADE_CLASS_BASE_DOC_ATTRS_CTOR(Cylinder,Sphere,"Geometry of a cylinder, as Minkowski sum of line and sphere.", // ((Real,radius,NaN,,"Radius [m]")) ((Real,length,NaN,,"Length [m]")) ((Vector3r,segment,Vector3r::Zero(),,"Length vector")), createIndex(); /*ctor*/ segment=Vector3r(0,0,1)*length; ); REGISTER_CLASS_INDEX(Cylinder,Sphere); }; REGISTER_SERIALIZABLE(Cylinder); class ChainedCylinder: public Cylinder{ public: // ChainedCylinder(Real _radius, Real _length);/*: Cylinder(_radius,_length){}*/ virtual ~ChainedCylinder (); //Keep pointers or copies of connected states? // ChainedState st1, st2; YADE_CLASS_BASE_DOC_ATTRS_CTOR(ChainedCylinder,Cylinder,"Geometry of a deformable chained cylinder, using geometry :yref:`Cylinder`.", ((Real,initLength,0,,"tensile-free length, used as reference for tensile strain")) ((Quaternionr,chainedOrientation,Quaternionr::Identity(),,"Deviation of node1 orientation from node-to-node vector")) ,createIndex();/*ctor*/ // state=shared_ptr(new ChainedState); ); REGISTER_CLASS_INDEX(ChainedCylinder,Cylinder); }; REGISTER_SERIALIZABLE(ChainedCylinder); class ChainedState: public State{ public: static vector > chains; static unsigned int currentChain; vector barContacts; vector nodeContacts; // shared_ptr statePrev; virtual ~ChainedState (); void addToChain(Body::id_t bodyId) { if (chains.size()<=currentChain) chains.resize(currentChain+1); chainNumber=currentChain; rank=chains[currentChain].size(); chains[currentChain].push_back(bodyId); bId=bodyId; // if (rank>0) statePrev = Body::byId(chains[chainNumber][rank-1],scene)->state; } void postLoad (ChainedState&){ if (bId<0) return;//state has not been chained yet if (chains.size()<=currentChain) chains.resize(currentChain+1); if (chains[currentChain].size()<=rank) chains[currentChain].resize(rank+1); chains[currentChain][rank]=bId; // if (rank>0) statePrev = Body::byId(chains[chainNumber][rank-1],scene)->state; } YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(ChainedState,State,"State of a chained bodies, containing information on connectivity in order to track contacts jumping over contiguous elements. Chains are 1D lists from which id of chained bodies are retrieved via :yref:`rank` and :yref:`chainNumber`.", ((unsigned int,rank,0,,"rank in the chain.")) ((unsigned int,chainNumber,0,,"chain id.")) ((int,bId,-1,,"id of the body containing - for postLoad operations only.")) , /* additional initializers */ /* ((pos,se3.position)) ((ori,se3.orientation)),*/ , /* ctor */ createIndex(); , /*py*/ // .def_readwrite("chains",&ChainedState::chains,"documentation") .def_readwrite("currentChain",&ChainedState::currentChain,"Current active chain (where newly created chained bodies will be appended).") .def("addToChain",&ChainedState::addToChain,(boost::python::arg("bodyId")),"Add body to current active chain") ); REGISTER_CLASS_INDEX(ChainedState,State); }; REGISTER_SERIALIZABLE(ChainedState); class Ig2_Sphere_ChainedCylinder_CylScGeom: public IGeomFunctor{ public: // virtual ~Ig2_Sphere_ChainedCylinder_CylScGeom (); virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); YADE_CLASS_BASE_DOC_ATTRS(Ig2_Sphere_ChainedCylinder_CylScGeom,IGeomFunctor,"Create/update a :yref:`ScGeom` instance representing intersection of two :yref:`Spheres`.", ((Real,interactionDetectionFactor,1,,"Enlarge both radii by this factor (if >1), to permit creation of distant interactions.")) ); FUNCTOR2D(Sphere,ChainedCylinder); DEFINE_FUNCTOR_ORDER_2D(Sphere,ChainedCylinder); }; REGISTER_SERIALIZABLE(Ig2_Sphere_ChainedCylinder_CylScGeom); class Ig2_Sphere_ChainedCylinder_CylScGeom6D: public Ig2_Sphere_ChainedCylinder_CylScGeom { public: virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); YADE_CLASS_BASE_DOC_ATTRS(Ig2_Sphere_ChainedCylinder_CylScGeom6D,Ig2_Sphere_ChainedCylinder_CylScGeom,"Create/update a :yref:`ScGeom6D` instance representing the geometry of a contact point between two :yref:`Spheres`, including relative rotations.", ((bool,updateRotations,false,,"Precompute relative rotations. Turning this false can speed up simulations when rotations are not needed in constitutive laws (e.g. when spheres are compressed without cohesion and moment in early stage of a triaxial test), but is not foolproof. Change this value only if you know what you are doing.")) ((bool,creep,false,,"Substract rotational creep from relative rotation. The rotational creep :yref:`ScGeom6D::twistCreep` is a quaternion and has to be updated inside a constitutive law, see for instance :yref:`Law2_ScGeom6D_CohFrictPhys_CohesionMoment`." )) ); FUNCTOR2D(Sphere,ChainedCylinder); // needed for the dispatcher, even if it is symmetric DEFINE_FUNCTOR_ORDER_2D(Sphere,ChainedCylinder); }; REGISTER_SERIALIZABLE(Ig2_Sphere_ChainedCylinder_CylScGeom6D); class Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D: public IGeomFunctor{ public: // virtual ~Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D () {}; virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); YADE_CLASS_BASE_DOC_ATTRS(Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D,IGeomFunctor,"Create/update a :yref:`ScGeom` instance representing connexion between :yref:`chained cylinders`.", ((Real,interactionDetectionFactor,1,,"Enlarge both radii by this factor (if >1), to permit creation of distant interactions.")) ((bool,halfLengthContacts,true,,"If True, Cylinders nodes interact like spheres of radius 0.5*length, else one node has size length while the other has size 0. The difference is mainly the locus of rotation definition.")) ); FUNCTOR2D(ChainedCylinder,ChainedCylinder); // needed for the dispatcher, even if it is symmetric DEFINE_FUNCTOR_ORDER_2D(ChainedCylinder,ChainedCylinder); }; REGISTER_SERIALIZABLE(Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D); #ifdef YADE_OPENGL class Gl1_Cylinder : public GlShapeFunctor{ private: static int glCylinderList; void subdivideTriangle(Vector3r& v1,Vector3r& v2,Vector3r& v3, int depth); void drawCylinder(bool wire, Real radius, Real length, const Quaternionr& shift=Quaternionr::Identity()) const; void initGlLists(void); public: virtual void go(const shared_ptr&, const shared_ptr&,bool,const GLViewInfo&); void out( Quaternionr q ); YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_Cylinder,GlShapeFunctor,"Renders :yref:`Cylinder` object", ((bool,wire,false,,"Only show wireframe (controlled by ``glutSlices`` and ``glutStacks``.")) ((bool,glutNormalize,true,,"Fix normals for non-wire rendering")) ((int,glutSlices,8,,"Number of sphere slices.")) ((int,glutStacks,4,,"Number of sphere stacks.")) ); RENDERS(Cylinder); friend class Gl1_ChainedCylinder; }; //!This doesn't work : the 1D dispatcher will pick Gl1_Cylinder to display ChainedCylinders, workaround : add shift to cylinders (should be a variable of chained cylinders only). class Gl1_ChainedCylinder : public Gl1_Cylinder{ public: virtual void go(const shared_ptr&, const shared_ptr& state, bool,const GLViewInfo&); YADE_CLASS_BASE_DOC(Gl1_ChainedCylinder,Gl1_Cylinder,"Renders :yref:`ChainedCylinder` object including a shift for compensating flexion." ); RENDERS(ChainedCylinder); }; /* class Gl1_ChainedCylinder : public GlShapeFunctor{ private: static int glCylinderList; void subdivideTriangle(Vector3r& v1,Vector3r& v2,Vector3r& v3, int depth); void drawCylinder(bool wire, Real radius, Real length, const Quaternionr& shift=Quaternionr::Identity()) const; void initGlLists(void); public: virtual void go(const shared_ptr&, const shared_ptr&,bool,const GLViewInfo&); YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_ChainedCylinder,GlShapeFunctor,"Renders :yref:`ChainedCylinder` object including a shift for compensating flexion.", ((bool,wire,false,,"Only show wireframe (controlled by ``glutSlices`` and ``glutStacks``.")) ((bool,glutNormalize,true,,"Fix normals for non-wire rendering")) ((int,glutSlices,8,,"Number of sphere slices.")) ((int,glutStacks,4,,"Number of sphere stacks.")) ); RENDERS(ChainedCylinder); };*/ #endif class Bo1_Cylinder_Aabb : public BoundFunctor { public : void go(const shared_ptr& cm, shared_ptr& bv, const Se3r&, const Body*); FUNCTOR1D(Cylinder); YADE_CLASS_BASE_DOC_ATTRS(Bo1_Cylinder_Aabb,BoundFunctor,"Functor creating :yref:`Aabb` from :yref:`Cylinder`.", ((Real,aabbEnlargeFactor,((void)"deactivated",-1),,"Relative enlargement of the bounding box; deactivated if negative.\n\n.. note::\n\tThis attribute is used to create distant interaction, but is only meaningful with an :yref:`IGeomFunctor` which will not simply discard such interactions: :yref:`Ig2_Cylinder_Cylinder_ScGeom::interactionDetectionFactor` should have the same value as :yref:`aabbEnlargeFactor`.")) ); }; REGISTER_SERIALIZABLE(Bo1_Cylinder_Aabb); class Bo1_ChainedCylinder_Aabb : public BoundFunctor { public : void go(const shared_ptr& cm, shared_ptr& bv, const Se3r&, const Body*); FUNCTOR1D(ChainedCylinder); YADE_CLASS_BASE_DOC_ATTRS(Bo1_ChainedCylinder_Aabb,BoundFunctor,"Functor creating :yref:`Aabb` from :yref:`ChainedCylinder`.", ((Real,aabbEnlargeFactor,((void)"deactivated",-1),,"Relative enlargement of the bounding box; deactivated if negative.\n\n.. note::\n\tThis attribute is used to create distant interaction, but is only meaningful with an :yref:`IGeomFunctor` which will not simply discard such interactions: :yref:`Ig2_Cylinder_Cylinder_ScGeom::interactionDetectionFactor` should have the same value as :yref:`aabbEnlargeFactor`.")) ); }; REGISTER_SERIALIZABLE(Bo1_ChainedCylinder_Aabb); class Law2_CylScGeom_FrictPhys_CundallStrack: public LawFunctor{ public: //OpenMPAccumulator plasticDissipation; virtual bool go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I); //Real elasticEnergy (); //Real getPlasticDissipation(); //void initPlasticDissipation(Real initVal=0); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Law2_CylScGeom_FrictPhys_CundallStrack,LawFunctor,"Law for linear compression, and Mohr-Coulomb plasticity surface without cohesion.\nThis law implements the classical linear elastic-plastic law from [CundallStrack1979]_ (see also [Pfc3dManual30]_). The normal force is (with the convention of positive tensile forces) $F_n=\\min(k_n u_n, 0)$. The shear force is $F_s=k_s u_s$, the plasticity condition defines the maximum value of the shear force : $F_s^{\\max}=F_n\\tan(\\phi)$, with $\\phi$ the friction angle.\n\n.. note::\n This law uses :yref:`ScGeom`.\n\n.. note::\n This law is well tested in the context of triaxial simulation, and has been used for a number of published results (see e.g. [Scholtes2009b]_ and other papers from the same authors). It is generalised by :yref:`Law2_ScGeom6D_CohFrictPhys_CohesionMoment`, which adds cohesion and moments at contact.", ((bool,neverErase,false,,"Keep interactions even if particles go away from each other (only in case another constitutive law is in the scene, e.g. :yref:`Law2_ScGeom_CapillaryPhys_Capillarity`)")) ((bool,traceEnergy,false,Attr::hidden,"Define the total energy dissipated in plastic slips at all contacts.")) ((int,plastDissipIx,-1,(Attr::hidden|Attr::noSave),"Index for plastic dissipation (with O.trackEnergy)")) ((int,elastPotentialIx,-1,(Attr::hidden|Attr::noSave),"Index for elastic potential energy (with O.trackEnergy)")) ,, //.def("elasticEnergy",&Law2_ScGeom_FrictPhys_CundallStrack::elasticEnergy,"Compute and return the total elastic energy in all \"FrictPhys\" contacts") //.def("plasticDissipation",&Law2_ScGeom_FrictPhys_CundallStrack::getPlasticDissipation,"Total energy dissipated in plastic slips at all FrictPhys contacts. Computed only if :yref:`Law2_ScGeom_FrictPhys_CundallStrack::traceEnergy` is true.") //.def("initPlasticDissipation",&Law2_ScGeom_FrictPhys_CundallStrack::initPlasticDissipation,"Initialize cummulated plastic dissipation to a value (0 by default).") ); FUNCTOR2D(CylScGeom,FrictPhys); }; REGISTER_SERIALIZABLE(Law2_CylScGeom_FrictPhys_CundallStrack); class Law2_CylScGeom6D_CohFrictPhys_CohesionMoment: public LawFunctor { public: //OpenMPAccumulator plasticDissipation; virtual bool go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I); //Real elasticEnergy (); //Real getPlasticDissipation(); //void initPlasticDissipation(Real initVal=0); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Law2_CylScGeom6D_CohFrictPhys_CohesionMoment,LawFunctor,"This law generalises :yref:`Law2_CylScGeom_FrictPhys_CundallStrack` by adding cohesion and moments at contact.", ((bool,neverErase,false,,"Keep interactions even if particles go away from each other (only in case another constitutive law is in the scene, e.g. :yref:`Law2_ScGeom_CapillaryPhys_Capillarity`)")) ((bool,traceEnergy,false,Attr::hidden,"Define the total energy dissipated in plastic slips at all contacts.")) ((int,plastDissipIx,-1,(Attr::hidden|Attr::noSave),"Index for plastic dissipation (with O.trackEnergy)")) ((int,elastPotentialIx,-1,(Attr::hidden|Attr::noSave),"Index for elastic potential energy (with O.trackEnergy)")) ((bool,always_use_moment_law,false,,"If true, use bending/twisting moments at all contacts. If false, compute moments only for cohesive contacts.")) ((bool,shear_creep,false,,"activate creep on the shear force, using :yref:`CohesiveFrictionalContactLaw::creep_viscosity`.")) ((bool,twist_creep,false,,"activate creep on the twisting moment, using :yref:`CohesiveFrictionalContactLaw::creep_viscosity`.")) ((bool,useIncrementalForm,false,,"use the incremental formulation to compute bending and twisting moments. Creep on the twisting moment is not included in such a case.")) ((Real,creep_viscosity,1,,"creep viscosity [Pa.s/m]. probably should be moved to Ip2_CohFrictMat_CohFrictMat_CohFrictPhys...")) ,, ); FUNCTOR2D(CylScGeom6D,CohFrictPhys); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_CylScGeom6D_CohFrictPhys_CohesionMoment); class Law2_ChCylGeom6D_CohFrictPhys_CohesionMoment: public LawFunctor { public: //OpenMPAccumulator plasticDissipation; virtual bool go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Law2_ChCylGeom6D_CohFrictPhys_CohesionMoment,LawFunctor,"Law for linear compression, and Mohr-Coulomb plasticity surface without cohesion.\nThis law implements the classical linear elastic-plastic law from [CundallStrack1979]_ (see also [Pfc3dManual30]_). The normal force is (with the convention of positive tensile forces) $F_n=\\min(k_n u_n, 0)$. The shear force is $F_s=k_s u_s$, the plasticity condition defines the maximum value of the shear force : $F_s^{\\max}=F_n\\tan(\\phi)$, with $\\phi$ the friction angle.\n\n.. note::\n This law is well tested in the context of triaxial simulation, and has been used for a number of published results (see e.g. [Scholtes2009b]_ and other papers from the same authors). It is generalised by :yref:`Law2_ScGeom6D_CohFrictPhys_CohesionMoment`, which adds cohesion and moments at contact.", ((bool,neverErase,false,,"Keep interactions even if particles go away from each other (only in case another constitutive law is in the scene, e.g. :yref:`Law2_ScGeom_CapillaryPhys_Capillarity`)")) ((bool,traceEnergy,false,Attr::hidden,"Define the total energy dissipated in plastic slips at all contacts.")) ((int,plastDissipIx,-1,(Attr::hidden|Attr::noSave),"Index for plastic dissipation (with O.trackEnergy)")) ((int,elastPotentialIx,-1,(Attr::hidden|Attr::noSave),"Index for elastic potential energy (with O.trackEnergy)")) ((bool,always_use_moment_law,false,,"If true, use bending/twisting moments at all contacts. If false, compute moments only for cohesive contacts.")) ((bool,shear_creep,false,,"activate creep on the shear force, using :yref:`CohesiveFrictionalContactLaw::creep_viscosity`.")) ((bool,twist_creep,false,,"activate creep on the twisting moment, using :yref:`CohesiveFrictionalContactLaw::creep_viscosity`.")) ((bool,useIncrementalForm,false,,"use the incremental formulation to compute bending and twisting moments. Creep on the twisting moment is not included in such a case.")) ((Real,creep_viscosity,1,,"creep viscosity [Pa.s/m]. probably should be moved to Ip2_CohFrictMat_CohFrictMat_CohFrictPhys...")) ,, ); FUNCTOR2D(ChCylGeom6D,CohFrictPhys); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_ChCylGeom6D_CohFrictPhys_CohesionMoment); // Keep this : Cylinders and ChainedCylinders will have different centers maybe. // class Bo1_ChainedCylinder_Aabb : public Bo1_Cylinder_Aabb // { // public : // void go(const shared_ptr& cm, shared_ptr& bv, const Se3r&, const Body*); // FUNCTOR1D(ChainedCylinder); // YADE_CLASS_BASE_DOC_ATTRS(Bo1_ChainedCylinder_Aabb,Bo1_Cylinder_Aabb,"Functor creating :yref:`Aabb` from :yref:`Cylinder`.", // ((Real,aabbEnlargeFactor,((void)"deactivated",-1),,"Relative enlargement of the bounding box; deactivated if negative.\n\n.. note::\n\tThis attribute is used to create distant interaction, but is only meaningful with an :yref:`IGeomFunctor` which will not simply discard such interactions: :yref:`Ig2_Cylinder_Cylinder_Dem3DofGeom::distFactor` / :yref:`Ig2_Cylinder_Cylinder_ScGeom::interactionDetectionFactor` should have the same value as :yref:`aabbEnlargeFactor`.")) // ); // }; #ifdef YADE_OPENGL REGISTER_SERIALIZABLE(Gl1_Cylinder); REGISTER_SERIALIZABLE(Gl1_ChainedCylinder); #endif trunk-2017.01a/pkg/common/Dispatching.cpp000066400000000000000000000200441304022710500201740ustar00rootroot00000000000000#include YADE_PLUGIN((BoundFunctor)(IGeomFunctor)(IPhysFunctor)(LawFunctor)(BoundDispatcher)(IGeomDispatcher)(IPhysDispatcher)(LawDispatcher)); BoundFunctor::~BoundFunctor(){}; IGeomFunctor::~IGeomFunctor(){}; IPhysFunctor::~IPhysFunctor(){}; LawFunctor::~LawFunctor(){}; /******************************************************************** BoundDispatcher *********************************************************************/ CREATE_LOGGER(BoundDispatcher); void BoundDispatcher::action() { updateScenePtr(); shared_ptr& bodies = scene->bodies; const long numBodies=(long)bodies->size(); #ifdef YADE_OPENMP #pragma omp parallel for num_threads(ompThreads>0 ? min(ompThreads,omp_get_max_threads()) : omp_get_max_threads()) #endif for(int id=0; idexists(id)) continue; // don't delete this check - Janek const shared_ptr& b=(*bodies)[id]; processBody(b); } } void BoundDispatcher::processBody(const shared_ptr& b) { shared_ptr& shape=b->shape; if(!b->isBounded() || !shape) return; if(b->bound) { Real& sweepLength = b->bound->sweepLength; if (targetInterv>=0) { Vector3r disp = b->state->pos-b->bound->refPos; Real dist = max(std::abs(disp[0]),max(std::abs(disp[1]),std::abs(disp[2]))); if (dist){ Real newLength = dist*targetInterv/(scene->iter-b->bound->lastUpdateIter); newLength = max(0.9*sweepLength,newLength);//don't decrease size too fast to prevent time consuming oscillations sweepLength=max(minSweepDistFactor*sweepDist,min(newLength,sweepDist));} else sweepLength=0; } else sweepLength=sweepDist; } #ifdef BV_FUNCTOR_CACHE if(!shape->boundFunctor){ shape->boundFunctor=this->getFunctor1D(shape); if(!shape->boundFunctor) return; } shape->boundFunctor->go(shape,b->bound,b->state->se3,b.get()); #else operator()(shape,b->bound,b->state->se3,b.get()); #endif if(!b->bound) return; // the functor did not create new bound b->bound->refPos=b->state->pos; b->bound->lastUpdateIter=scene->iter; const Real& sweepLength = b->bound->sweepLength; if(sweepLength>0){ Aabb* aabb=YADE_CAST(b->bound.get()); aabb->min-=Vector3r(sweepLength,sweepLength,sweepLength); aabb->max+=Vector3r(sweepLength,sweepLength,sweepLength); } } /******************************************************************** IGeomDispatcher *********************************************************************/ CREATE_LOGGER(IGeomDispatcher); shared_ptr IGeomDispatcher::explicitAction(const shared_ptr& b1, const shared_ptr& b2, bool force){ scene=Omega::instance().getScene().get(); // to make sure if called from outside of the loop Vector3i cellDist=Vector3i::Zero(); if(scene->isPeriodic) { for(int i=0; i<3; i++) cellDist[i]=-(int)((b2->state->pos[i]-b1->state->pos[i])/scene->cell->getSize()[i]+.5); } Vector3r shift2=scene->cell->hSize*cellDist.cast(); updateScenePtr(); if(force){ assert(b1->shape && b2->shape); shared_ptr I(new Interaction(b1->getId(),b2->getId())); I->cellDist=cellDist; // FIXME: this code is more or less duplicated from InteractionLoop :-( bool swap=false; I->functorCache.geom=getFunctor2D(b1->shape,b2->shape,swap); if(!I->functorCache.geom) throw invalid_argument("IGeomDispatcher::explicitAction could not dispatch for given types ("+b1->shape->getClassName()+","+b2->shape->getClassName()+")."); if(swap){I->swapOrder();} const shared_ptr& b1=Body::byId(I->getId1(),scene); const shared_ptr& b2=Body::byId(I->getId2(),scene); bool succ=I->functorCache.geom->go(b1->shape,b2->shape,*b1->state,*b2->state,shift2,/*force*/true,I); if(!succ) throw logic_error("Functor "+I->functorCache.geom->getClassName()+"::go returned false, even if asked to force IGeom creation. Please report bug."); return I; } else { shared_ptr I(new Interaction(b1->getId(),b2->getId())); I->cellDist=cellDist; b1->shape && b2->shape && I->functorCache.geom->go(b1->shape,b2->shape,*b1->state,*b2->state,shift2,/*force*/true,I); return I; } } void IGeomDispatcher::action(){ updateScenePtr(); shared_ptr& bodies = scene->bodies; const bool isPeriodic(scene->isPeriodic); Matrix3r cellHsize; if(isPeriodic) cellHsize=scene->cell->hSize; bool removeUnseenIntrs=(scene->interactions->iterColliderLastRun>=0 && scene->interactions->iterColliderLastRun==scene->iter); #ifdef YADE_OPENMP const long size=scene->interactions->size(); #pragma omp parallel for for(long i=0; i& I=(*scene->interactions)[i]; #else FOREACH(const shared_ptr& I, *scene->interactions){ #endif if(removeUnseenIntrs && !I->isReal() && I->iterLastSeeniter) { scene->interactions->requestErase(I); continue; } const shared_ptr& b1=(*bodies)[I->getId1()]; const shared_ptr& b2=(*bodies)[I->getId2()]; if(!b1 || !b2){ LOG_DEBUG("Body #"<<(b1?I->getId2():I->getId1())<<" vanished, erasing intr #"<getId1()<<"+#"<getId2()<<"!"); scene->interactions->requestErase(I); continue; } bool wasReal=I->isReal(); if (!b1->shape || !b2->shape) { assert(!wasReal); continue; } // some bodies do not have shape bool geomCreated; //const bool forceFalse=false; if(!isPeriodic){ geomCreated=I->functorCache.geom->go(b1->shape,b2->shape, *b1->state, *b2->state, Vector3r::Zero(), /*force*/false, I); } else{ Vector3r shift2=cellHsize*I->cellDist.cast(); geomCreated=I->functorCache.geom->go(b1->shape,b2->shape,*b1->state,*b2->state,shift2,/*force*/false,I); } // reset && erase interaction that existed but now has no geometry anymore if(wasReal && !geomCreated){ scene->interactions->requestErase(I); } } } /******************************************************************** IPhysDispatcher *********************************************************************/ void IPhysDispatcher::explicitAction(shared_ptr& pp1, shared_ptr& pp2, shared_ptr& I){ updateScenePtr(); if(!I->geom) throw invalid_argument(string(__FILE__)+": explicitAction received interaction without geom."); if(!I->functorCache.phys){ bool dummy; I->functorCache.phys=getFunctor2D(pp1,pp2,dummy); if(!I->functorCache.phys) throw invalid_argument("IPhysDispatcher::explicitAction did not find a suitable dispatch for types "+pp1->getClassName()+" and "+pp2->getClassName()); I->functorCache.phys->go(pp1,pp2,I); } } void IPhysDispatcher::action() { updateScenePtr(); shared_ptr& bodies = scene->bodies; #ifdef YADE_OPENMP const long size=scene->interactions->size(); #pragma omp parallel for for(long i=0; i& interaction=(*scene->interactions)[i]; #else FOREACH(const shared_ptr& interaction, *scene->interactions){ #endif if(interaction->geom){ shared_ptr& b1 = (*bodies)[interaction->getId1()]; shared_ptr& b2 = (*bodies)[interaction->getId2()]; bool hadPhys=(interaction->phys.get() != 0); operator()(b1->material, b2->material, interaction); assert(interaction->phys); if(!hadPhys) interaction->iterMadeReal=scene->iter; } } } /******************************************************************** LawDispatcher *********************************************************************/ CREATE_LOGGER(LawDispatcher); void LawDispatcher::action(){ updateScenePtr(); #ifdef YADE_OPENMP const long size=scene->interactions->size(); #pragma omp parallel for for(long i=0; i& I=(*scene->interactions)[i]; #else FOREACH(shared_ptr I, *scene->interactions){ #endif if(I->isReal()){ assert(I->geom); assert(I->phys); operator()(I->geom,I->phys,I.get()); if(!I->isReal() && I->isFresh(scene)) LOG_ERROR("Law functor deleted interaction that was just created. Please report bug: either this message is spurious, or the functor (or something else) is buggy."); } } } trunk-2017.01a/pkg/common/Dispatching.hpp000066400000000000000000000120451304022710500202030ustar00rootroot00000000000000#pragma once #include #include #include #include #include #include #include #include #include #include #include /******** functors *********************/ class BoundFunctor: public Functor1D< /*dispatch types*/ Shape, /*return type*/ void , /*argument types*/ TYPELIST_4(const shared_ptr&, shared_ptr&, const Se3r&, const Body*) >{ public: virtual ~BoundFunctor(); YADE_CLASS_BASE_DOC(BoundFunctor,Functor,"Functor for creating/updating :yref:`Body::bound`."); }; REGISTER_SERIALIZABLE(BoundFunctor); class IGeomFunctor: public Functor2D< /*dispatch types*/ Shape,Shape, /*return type*/ bool, /*argument types*/ TYPELIST_7(const shared_ptr&, const shared_ptr&, const State&, const State&, const Vector3r&, const bool&, const shared_ptr&) >{ public: virtual ~IGeomFunctor(); // called before every step once, from InteractionLoop (used to set Scene::flags & Scene::LOCAL_COORDS) virtual void preStep(){}; YADE_CLASS_BASE_DOC(IGeomFunctor,Functor,"Functor for creating/updating :yref:`Interaction::geom` objects."); }; REGISTER_SERIALIZABLE(IGeomFunctor); class IPhysFunctor: public Functor2D< /*dispatch types*/ Material, Material, /*retrun type*/ void, /*argument types*/ TYPELIST_3(const shared_ptr&, const shared_ptr&, const shared_ptr&) >{ public: virtual ~IPhysFunctor(); YADE_CLASS_BASE_DOC(IPhysFunctor,Functor,"Functor for creating/updating :yref:`Interaction::phys` objects."); }; REGISTER_SERIALIZABLE(IPhysFunctor); class LawFunctor: public Functor2D< /*dispatch types*/ IGeom,IPhys, /*return type*/ bool, /*argument types*/ TYPELIST_3(shared_ptr&, shared_ptr&, Interaction*) >{ public: virtual ~LawFunctor(); /*! Convenience functions to get forces/torques quickly. */ void addForce (const Body::id_t id, const Vector3r& f,Scene* rb){rb->forces.addForce (id,f);} void addTorque(const Body::id_t id, const Vector3r& t,Scene* rb){rb->forces.addTorque(id,t);} /*! Convenience function to apply force and torque from one force at contact point. Not sure if this is the right place for it. */ void applyForceAtContactPoint(const Vector3r& force, const Vector3r& contactPoint, const Body::id_t id1, const Vector3r& pos1, const Body::id_t id2, const Vector3r& pos2){ addForce(id1, force,scene); addTorque(id1, (contactPoint-pos1).cross(force),scene); addForce(id2,-force,scene); addTorque(id2,-(contactPoint-pos2).cross(force),scene); } YADE_CLASS_BASE_DOC(LawFunctor,Functor,"Functor for applying constitutive laws on :yref:`interactions`."); }; REGISTER_SERIALIZABLE(LawFunctor); /******** dispatchers *********************/ class BoundDispatcher: public Dispatcher1D< /* functor type*/ BoundFunctor >{ public: virtual void action(); virtual bool isActivated(){ return activated; } void processBody(const shared_ptr&); DECLARE_LOGGER; YADE_DISPATCHER1D_FUNCTOR_DOC_ATTRS_CTOR_PY(BoundDispatcher,BoundFunctor,/*optional doc*/, /*additional attrs*/ ((bool,activated,true,,"Whether the engine is activated (only should be changed by the collider)")) ((Real,sweepDist,0,,"Distance by which enlarge all bounding boxes, to prevent collider from being run at every step (only should be changed by the collider).")) ((Real,minSweepDistFactor,0.2,,"Minimal distance by which enlarge all bounding boxes; superseeds computed value of sweepDist when lower that (minSweepDistFactor x sweepDist). Updated by the collider. |yupdate|.")) ((Real,updatingDispFactor,-1,,"see :yref:`InsertionSortCollider::updatingDispFactor` |yupdate|")) ((Real,targetInterv,-1,,"see :yref:`InsertionSortCollider::targetInterv` |yupdate|")) ,/*ctor*/,/*py*/ ); }; REGISTER_SERIALIZABLE(BoundDispatcher); class IGeomDispatcher: public Dispatcher2D< /* functor type*/ IGeomFunctor, /* autosymmetry*/ false >{ bool alreadyWarnedNoCollider; public: virtual void action(); shared_ptr explicitAction(const shared_ptr& b1, const shared_ptr& b2, bool force); YADE_DISPATCHER2D_FUNCTOR_DOC_ATTRS_CTOR_PY(IGeomDispatcher,IGeomFunctor,/* doc is optional*/,/*attrs*/,/*ctor*/alreadyWarnedNoCollider=false;,/*py*/); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(IGeomDispatcher); class IPhysDispatcher: public Dispatcher2D< /*functor type*/ IPhysFunctor >{ public: virtual void action(); void explicitAction(shared_ptr& pp1, shared_ptr& pp2, shared_ptr& i); YADE_DISPATCHER2D_FUNCTOR_DOC_ATTRS_CTOR_PY(IPhysDispatcher,IPhysFunctor,/*doc is optional*/,/*attrs*/,/*ctor*/,/*py*/); }; REGISTER_SERIALIZABLE(IPhysDispatcher); class LawDispatcher: public Dispatcher2D< /*functor type*/ LawFunctor, /*autosymmetry*/ false >{ public: virtual void action(); YADE_DISPATCHER2D_FUNCTOR_DOC_ATTRS_CTOR_PY(LawDispatcher,LawFunctor,/*doc is optional*/,/*attrs*/,/*ctor*/,/*py*/); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(LawDispatcher); trunk-2017.01a/pkg/common/ElastMat.hpp000066400000000000000000000024111304022710500174540ustar00rootroot00000000000000// 2009 © Václav Šmilauer #pragma once #include /*! Elastic material */ class ElastMat: public Material{ public: virtual ~ElastMat() {}; YADE_CLASS_BASE_DOC_ATTRS_CTOR(ElastMat,Material,"Purely elastic material. The material parameters may have different meanings depending on the :yref:`IPhysFunctor` used : true Young and Poisson in :yref:`Ip2_FrictMat_FrictMat_MindlinPhys`, or contact stiffnesses in :yref:`Ip2_FrictMat_FrictMat_FrictPhys`.", ((Real,young,1e9,,"elastic modulus [Pa]. It has different meanings depending on the Ip functor.")) ((Real,poisson,.25,,"Poisson's ratio or the ratio between shear and normal stiffness [-]. It has different meanings depending on the Ip functor. ")), /*ctor*/ createIndex(); ); REGISTER_CLASS_INDEX(ElastMat,Material); }; REGISTER_SERIALIZABLE(ElastMat); /*! Granular material */ class FrictMat: public ElastMat{ public: virtual ~FrictMat() {}; YADE_CLASS_BASE_DOC_ATTRS_CTOR(FrictMat,ElastMat,"Elastic material with contact friction. See also :yref:`ElastMat`.", ((Real,frictionAngle,.5,,"Contact friction angle (in radians). Hint : use 'radians(degreesValue)' in python scripts.")), createIndex(); ); REGISTER_CLASS_INDEX(FrictMat,ElastMat); }; REGISTER_SERIALIZABLE(FrictMat); trunk-2017.01a/pkg/common/Facet.cpp000066400000000000000000000033001304022710500167550ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2008 by Sergei Dorofeenko * * sega@users.berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "Facet.hpp" CREATE_LOGGER(Facet); Facet::~Facet() { } void Facet::postLoad(Facet&) { // if this fails, it means someone did vertices push_back, but they are resized to 3 at Facet initialization already // in the future, a fixed-size array should be used instead of vector for vertices // this is prevented by yade::serialization now IIRC if(vertices.size()!=3){ throw runtime_error(("Facet must have exactly 3 vertices (not "+boost::lexical_cast(vertices.size())+")").c_str()); } if(std::isnan(vertices[0][0])) return; // not initialized, nothing to do Vector3r e[3] = {vertices[1]-vertices[0] ,vertices[2]-vertices[1] ,vertices[0]-vertices[2]}; #define CHECK_EDGE(i) if(e[i].squaredNorm()==0){LOG_FATAL("Facet has coincident vertices "< #include // define this to have topology information about facets enabled; // it is necessary for FacetTopologyAnalyzer // #define FACET_TOPO class Facet : public Shape { public: virtual ~Facet(); // Postprocessed attributes /// Facet's normal //Vector3r nf; /// Normals of edges Vector3r ne[3]; /// Inscribing cirle radius Real icr; /// Length of the vertice vectors Real vl[3]; /// Unit vertice vectors Vector3r vu[3]; void postLoad(Facet&); void setVertices(const Vector3r& v0, const Vector3r& v1, const Vector3r& v2) { vertices[0]=v0; vertices[1]=v1; vertices[2]=v2; postLoad(*this); } YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Facet,Shape,"Facet (triangular particle) geometry.", ((vector,vertices,vector(3,Vector3r(NaN,NaN,NaN)),(Attr::triggerPostLoad | Attr::noResize),"Vertex positions in local coordinates.")) ((Vector3r,normal,Vector3r(NaN,NaN,NaN),(Attr::readonly | Attr::noSave),"Facet's normal (in local coordinate system)")) ((Real,area,NaN,(Attr::readonly | Attr::noSave),"Facet's area")) #ifdef FACET_TOPO ((vector,edgeAdjIds,vector(3,Body::ID_NONE),,"Facet id's that are adjacent to respective edges [experimental]")) ((vector,edgeAdjHalfAngle,vector(3,0),,"half angle between normals of this facet and the adjacent facet [experimental]")) #endif , /* ctor */ createIndex();, .def("setVertices",&Facet::setVertices,"TODO") ); DECLARE_LOGGER; REGISTER_CLASS_INDEX(Facet,Shape); }; REGISTER_SERIALIZABLE(Facet); trunk-2017.01a/pkg/common/FieldApplier.hpp000066400000000000000000000010431304022710500203020ustar00rootroot00000000000000#pragma once #include #include class FieldApplier: public GlobalEngine{ virtual void action() { throw std::runtime_error("FieldApplier must not be used in simulations directly (FieldApplier::action called)."); } YADE_CLASS_BASE_DOC_ATTRS(FieldApplier,GlobalEngine,"Base for engines applying force files on particles. Not to be used directly.", ((int,fieldWorkIx,-1,(Attr::hidden|Attr::noSave),"Index for the work done by this field, if tracking energies.")) ); }; REGISTER_SERIALIZABLE(FieldApplier); trunk-2017.01a/pkg/common/ForceEngine.cpp000066400000000000000000000446671304022710500201440ustar00rootroot00000000000000// 2004 © Janek Kozicki // 2009 © Václav Šmilauer // 2014 © Raphael Maurin #include"ForceEngine.hpp" #include #include #include #include #include #include #include #include #include YADE_PLUGIN((ForceEngine)(InterpolatingDirectedForceEngine)(RadialForceEngine)(DragEngine)(LinearDragEngine)(HydroForceEngine)); void ForceEngine::action(){ FOREACH(Body::id_t id, ids){ if (!(scene->bodies->exists(id))) continue; scene->forces.addForce(id,force); } } void InterpolatingDirectedForceEngine::action(){ Real virtTime=wrap ? Shop::periodicWrap(scene->time,*times.begin(),*times.rbegin()) : scene->time; direction.normalize(); force=linearInterpolate(virtTime,times,magnitudes,_pos)*direction; ForceEngine::action(); } void RadialForceEngine::postLoad(RadialForceEngine&){ axisDir.normalize(); } void RadialForceEngine::action(){ FOREACH(Body::id_t id, ids){ if (!(scene->bodies->exists(id))) continue; const Vector3r& pos=Body::byId(id,scene)->state->pos; Vector3r radial=(pos - (axisPt+axisDir * /* t */ ((pos-axisPt).dot(axisDir)))).normalized(); if(radial.squaredNorm()==0) continue; scene->forces.addForce(id,fNorm*radial); } } void DragEngine::action(){ FOREACH(Body::id_t id, ids){ Body* b=Body::byId(id,scene).get(); if (!b) continue; if (!(scene->bodies->exists(id))) continue; const Sphere* sphere = dynamic_cast(b->shape.get()); if (sphere){ Real A = sphere->radius*sphere->radius*Mathr::PI; //Crossection of the sphere Vector3r velSphTemp = b->state->vel; Vector3r dragForce = Vector3r::Zero(); if (velSphTemp != Vector3r::Zero()) { dragForce = -0.5*Rho*A*Cd*velSphTemp.squaredNorm()*velSphTemp.normalized(); } scene->forces.addForce(id,dragForce); } } } void LinearDragEngine::action(){ FOREACH(Body::id_t id, ids){ Body* b=Body::byId(id,scene).get(); if (!b) continue; if (!(scene->bodies->exists(id))) continue; const Sphere* sphere = dynamic_cast(b->shape.get()); if (sphere){ Vector3r velSphTemp = b->state->vel; Vector3r dragForce = Vector3r::Zero(); Real b = 6*Mathr::PI*nu*sphere->radius; if (velSphTemp != Vector3r::Zero()) { dragForce = -b*velSphTemp; } scene->forces.addForce(id,dragForce); } } } void HydroForceEngine::action(){ /* Application of hydrodynamical forces */ if (activateAverage==true) averageProfile(); //Calculate the average solid profiles FOREACH(Body::id_t id, ids){ Body* b=Body::byId(id,scene).get(); if (!b) continue; if (!(scene->bodies->exists(id))) continue; const Sphere* sphere = dynamic_cast(b->shape.get()); if (sphere){ Vector3r posSphere = b->state->pos;//position vector of the sphere int p = floor((posSphere[2]-zRef)/deltaZ); //cell number in which the particle is if ((p=0)) { Vector3r liftForce = Vector3r::Zero(); Vector3r dragForce = Vector3r::Zero(); Vector3r vRel = Vector3r(vxFluid[p]+vFluctX[id],vFluctY[id],vFluctZ[id]) - b->state->vel;//fluid-particle relative velocity //Drag force calculation if (vRel.norm()!=0.0) { dragForce = 0.5*densFluid*Mathr::PI*pow(sphere->radius,2.0)*(0.44*vRel.norm()+24.4*viscoDyn/(densFluid*sphere->radius*2))*pow(1-phiPart[p],-expoRZ)*vRel; } //lift force calculation due to difference of fluid pressure between top and bottom of the particle int intRadius = floor(sphere->radius/deltaZ); if ((p+intRadius0)&&(lift==true)) { Real vRelTop = vxFluid[p+intRadius] - b->state->vel[0]; // relative velocity of the fluid wrt the particle at the top of the particle Real vRelBottom = vxFluid[p-intRadius] - b->state->vel[0]; // same at the bottom liftForce[2] = 0.5*densFluid*Mathr::PI*pow(sphere->radius,2.0)*Cl*(vRelTop*vRelTop-vRelBottom*vRelBottom); } //buoyant weight force calculation Vector3r buoyantForce = -4.0/3.0*Mathr::PI*pow(sphere->radius,3.0)*densFluid*gravity; //add the hydro forces to the particle scene->forces.addForce(id,dragForce+liftForce+buoyantForce); } } } } void HydroForceEngine::averageProfile(){ //Initialization int minZ; int maxZ; int numLayer; Real deltaCenter; Real zInf; Real zSup; Real volPart; Vector3r uRel = Vector3r::Zero(); Vector3r fDrag = Vector3r::Zero(); int nMax = nCell; vector velAverageX(nMax,0.0); vector velAverageY(nMax,0.0); vector velAverageZ(nMax,0.0); vector phiAverage(nMax,0.0); vector dragAverage(nMax,0.0); vector phiAverage1(nMax,0.0); vector dragAverage1(nMax,0.0); vector velAverageX1(nMax,0.0); vector velAverageY1(nMax,0.0); vector velAverageZ1(nMax,0.0); vector phiAverage2(nMax,0.0); vector dragAverage2(nMax,0.0); vector velAverageX2(nMax,0.0); vector velAverageY2(nMax,0.0); vector velAverageZ2(nMax,0.0); //Loop over the particles FOREACH(const shared_ptr& b, *Omega::instance().getScene()->bodies){ shared_ptr s=YADE_PTR_DYN_CAST(b->shape); if(!s) continue; const Real zPos = b->state->pos[2]-zRef; int Np = floor(zPos/deltaZ); //Define the layer number with 0 corresponding to zRef. Let the z position wrt to zero, that way all z altitude are positive. (otherwise problem with volPart evaluation) if ((b->state->blockedDOFs==State::DOF_ALL)&&(zPos > s->radius)) continue;// to remove contribution from the fixed particles on the sidewalls. // Relative fluid/particle velocity using also the associated fluid vel. fluct. if ((Np>=0)&&(Npid], vFluctY[b->id],vFluctZ[b->id]) - b->state->vel; // Drag force with a Dallavalle formulation (drag coef.) and Richardson-Zaki Correction (hindrance effect) fDrag = 0.5*Mathr::PI*pow(s->radius,2.0)*densFluid*(0.44*uRel.norm()+24.4*viscoDyn/(densFluid*2.0*s->radius))*pow((1-phiPart[Np]),-expoRZ)*uRel; } else fDrag = Vector3r::Zero(); minZ= floor((zPos-s->radius)/deltaZ); maxZ= floor((zPos+s->radius)/deltaZ); deltaCenter = zPos - Np*deltaZ; // Loop over the cell in which the particle is contained numLayer = minZ; while (numLayer<=maxZ){ if ((numLayer>=0)&&(numLayerradius) zInf = -s->radius; if (zSup>s->radius) zSup = s->radius; //Analytical formulation of the volume of a slice of sphere volPart = Mathr::PI*pow(s->radius,2)*(zSup - zInf +(pow(zInf,3)-pow(zSup,3))/(3*pow(s->radius,2))); phiAverage[numLayer]+=volPart; velAverageX[numLayer]+=volPart*b->state->vel[0]; velAverageY[numLayer]+=volPart*b->state->vel[1]; velAverageZ[numLayer]+=volPart*b->state->vel[2]; dragAverage[numLayer]+=volPart*fDrag[0]; if (twoSize==true){ if (s->radius==radiusPart1){ phiAverage1[numLayer]+=volPart; dragAverage1[numLayer]+=volPart*fDrag[0]; velAverageX1[numLayer]+=volPart*b->state->vel[0]; velAverageY1[numLayer]+=volPart*b->state->vel[1]; velAverageZ1[numLayer]+=volPart*b->state->vel[2]; } if (s->radius==radiusPart2){ phiAverage2[numLayer]+=volPart; dragAverage2[numLayer]+=volPart*fDrag[0]; velAverageX2[numLayer]+=volPart*b->state->vel[0]; velAverageY2[numLayer]+=volPart*b->state->vel[1]; velAverageZ2[numLayer]+=volPart*b->state->vel[2]; } } } numLayer+=1; } } //Normalized the weighted velocity by the volume of particles contained inside the cell for(int n=0;nbodies->size()){ size=scene->bodies->size(); vFluctX.resize(size); vFluctY.resize(size); vFluctZ.resize(size); } /* reset stored values to zero */ memset(& vFluctX[0],0,size); memset(& vFluctY[0],0,size); memset(& vFluctZ[0],0,size); /* Create a random number generator rnd() with a gaussian distribution of mean 0 and stdev 1.0 */ /* see http://www.boost.org/doc/libs/1_55_0/doc/html/boost_random/reference.html and the chapter 7 of Numerical Recipes in C, second edition (1992) for more details */ static boost::minstd_rand0 randGen((int)TimingInfo::getNow(true)); static boost::normal_distribution dist(0.0, 1.0); static boost::variate_generator > rnd(randGen,dist); double rand1 = 0.0; double rand2 = 0.0; double rand3 = 0.0; /* Attribute a fluid velocity fluctuation to each body above the bed elevation */ FOREACH(Body::id_t id, ids){ Body* b=Body::byId(id,scene).get(); if (!b) continue; if (!(scene->bodies->exists(id))) continue; const Sphere* sphere = dynamic_cast(b->shape.get()); if (sphere){ Vector3r posSphere = b->state->pos;//position vector of the sphere int p = floor((posSphere[2]-zRef)/deltaZ); //cell number in which the particle is // If the particle is inside the water and above the bed elevation, so inside the turbulent flow, evaluate a turbulent fluid velocity fluctuation which will be used to apply the drag. // The fluctuation magnitude is linked to the value of the Reynolds stress tensor at the given position, a kind of local friction velocity ustar // The fluctuations along wall-normal and streamwise directions are correlated in order to be consistent with the formulation of the Reynolds stress tensor and to recover the result // that the magnitude of the fluctuation along streamwise = 2*along wall normal if ((pbedElevation)) { // Remove the particles outside of the flow and inside the granular bed, they are not submitted to turbulent fluctuations. Real uStar2 = simplifiedReynoldStresses[p]; if (uStar2>0.0){ Real uStar = sqrt(uStar2); rand1 = rnd(); rand2 = rnd(); rand3 = -rand1 + rnd();// x and z fluctuation are correlated as measured by Nezu 1977 and as expected from the formulation of the Reynolds stress tensor. vFluctZ[id] = rand1*uStar; vFluctY[id] = rand2*uStar; vFluctX[id] = rand3*uStar; } } else{ vFluctZ[id] = 0.0; vFluctY[id] = 0.0; vFluctX[id] = 0.0; } } } } /* Alternative Velocity fluctuation model, same as turbulentFluctuation model but with a time step associated with the fluctuation generation depending on z */ /* Should be executed in the python script at a period dtFluct corresponding to the smallest value of the fluctTime vector */ /* Should be initialized before running HydroForceEngine */ void HydroForceEngine::turbulentFluctuationBIS(){ int idPartMax = vFluctX.size(); double rand1 = 0.0; double rand2 = 0.0; double rand3 = 0.0; /* Create a random number generator rnd() with a gaussian distribution of mean 0 and stdev 1.0 */ /* see http://www.boost.org/doc/libs/1_55_0/doc/html/boost_random/reference.html and the chapter 7 of Numerical Recipes in C, second edition (1992) for more details */ static boost::minstd_rand0 randGen((int)TimingInfo::getNow(true)); static boost::normal_distribution dist(0.0, 1.0); static boost::variate_generator > rnd(randGen,dist); //Loop on the particles for(int idPart=0;idPartbodies->exists(idPart))) continue; const Sphere* sphere = dynamic_cast(b->shape.get()); Real uStar = 0.0; if (sphere){ Vector3r posSphere = b->state->pos;//position vector of the sphere int p = floor((posSphere[2]-zRef)/deltaZ); //cell number in which the particle is if (simplifiedReynoldStresses[p]>0.0) uStar = sqrt(simplifiedReynoldStresses[p]); // Remove the particles outside of the flow and inside the granular bed, they are not submitted to turbulent fluctuations. if ((pbedElevation)) { rand1 = rnd(); rand2 = rnd(); rand3 = -rand1 + rnd(); // x and z fluctuation are correlated as measured by Nezu 1977 and as expected from the formulation of the Reynolds stress tensor. vFluctZ[idPart] = rand1*uStar; vFluctY[idPart] = rand2*uStar; vFluctX[idPart] = rand3*uStar; // Limit the value to avoid the application of fluctuations in the viscous sublayer const Real zPos = max(b->state->pos[2]-zRef-bedElevation,11.6*viscoDyn/densFluid/uStar); // Time of application of the fluctuation as a function of depth from kepsilon model if (uStar>0.0) fluctTime[idPart]=min(0.33*0.41*zPos/uStar,10.); } else{ vFluctZ[idPart] = 0.0; vFluctY[idPart] = 0.0; vFluctX[idPart] = 0.0; fluctTime[idPart] = 0.0; } } } } } /* Velocity fluctuation determination. To execute at a given period*/ /* Should be initialized before running HydroForceEngine */ void HydroForceEngine::turbulentFluctuationFluidizedBed(){ /* check size */ size_t size=vFluctX.size(); if(sizebodies->size()){ size=scene->bodies->size(); vFluctX.resize(size); vFluctY.resize(size); vFluctZ.resize(size); } /* reset stored values to zero */ memset(& vFluctX[0],0,size); memset(& vFluctY[0],0,size); memset(& vFluctZ[0],0,size); /* Create a random number generator rnd() with a gaussian distribution of mean 0 and stdev 1.0 */ /* see http://www.boost.org/doc/libs/1_55_0/doc/html/boost_random/reference.html and the chapter 7 of Numerical Recipes in C, second edition (1992) for more details */ static boost::minstd_rand0 randGen((int)TimingInfo::getNow(true)); static boost::normal_distribution dist(0.0, 1.0); static boost::variate_generator > rnd(randGen,dist); double rand1 = 0.0; double rand2 = 0.0; double rand3 = 0.0; /* Attribute a fluid velocity fluctuation to each body above the bed elevation */ FOREACH(Body::id_t id, ids){ Body* b=Body::byId(id,scene).get(); if (!b) continue; if (!(scene->bodies->exists(id))) continue; const Sphere* sphere = dynamic_cast(b->shape.get()); if (sphere){ Vector3r posSphere = b->state->pos;//position vector of the sphere int p = floor((posSphere[2]-zRef)/deltaZ); //cell number in which the particle is // If the particle is inside the water and above the bed elevation, so inside the turbulent flow, evaluate a turbulent fluid velocity fluctuation which will be used to apply the drag. // The fluctuation magnitude is linked to the value of the Reynolds stress tensor at the given position, a kind of local friction velocity ustar if ((p0.)) { // Remove the particles outside of the flow Real uStar2 = simplifiedReynoldStresses[p]; if (uStar2>0.0){ Real uStar = sqrt(uStar2); rand1 = rnd(); rand2 = rnd(); rand3 = rnd(); vFluctZ[id] = rand1*uStar; vFluctY[id] = rand2*uStar; vFluctX[id] = rand3*uStar; } } else{ vFluctZ[id] = 0.0; vFluctY[id] = 0.0; vFluctX[id] = 0.0; } } } } trunk-2017.01a/pkg/common/ForceEngine.hpp000066400000000000000000000375731304022710500201470ustar00rootroot00000000000000// 2004 © Janek Kozicki // 2009 © Václav Šmilauer // 2014 © Raphael Maurin #pragma once #include class ForceEngine: public PartialEngine{ public: virtual void action(); YADE_CLASS_BASE_DOC_ATTRS(ForceEngine,PartialEngine,"Apply contact force on some particles at each step.", ((Vector3r,force,Vector3r::Zero(),,"Force to apply.")) ); }; REGISTER_SERIALIZABLE(ForceEngine); /* Engine for applying force of varying magnitude but constant direction * on subscribed bodies. times and magnitudes must have the same length, * direction (normalized automatically) gives the orientation. * * As usual with interpolating engines: the first magnitude is used before the first * time point, last magnitude is used after the last time point. Wrap specifies whether * time wraps around the last time point to the first time point. */ class InterpolatingDirectedForceEngine: public ForceEngine{ size_t _pos; public: virtual void action(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(InterpolatingDirectedForceEngine,ForceEngine,"Engine for applying force of varying magnitude but constant direction on subscribed bodies. times and magnitudes must have the same length, direction (normalized automatically) gives the orientation. \n\n\ \ As usual with interpolating engines: the first magnitude is used before the first time point, last magnitude is used after the last time point. Wrap specifies whether time wraps around the last time point to the first time point.", ((vector,times,,,"Time readings [s]")) ((vector,magnitudes,,,"Force magnitudes readings [N]")) ((Vector3r,direction,Vector3r::UnitX(),,"Contact force direction (normalized automatically)")) ((bool,wrap,false,,"wrap to the beginning of the sequence if beyond the last time point")), /*ctor*/ _pos=0 ); }; REGISTER_SERIALIZABLE(InterpolatingDirectedForceEngine); struct RadialForceEngine: public PartialEngine{ virtual void action(); virtual void postLoad(RadialForceEngine&); YADE_CLASS_BASE_DOC_ATTRS(RadialForceEngine,PartialEngine,"Apply force of given magnitude directed away from spatial axis.", ((Vector3r,axisPt,Vector3r::Zero(),,"Point on axis")) ((Vector3r,axisDir,Vector3r::UnitX(),Attr::triggerPostLoad,"Axis direction (normalized automatically)")) ((Real,fNorm,0,,"Applied force magnitude")) ); }; REGISTER_SERIALIZABLE(RadialForceEngine); class DragEngine: public PartialEngine{ public: virtual void action(); YADE_CLASS_BASE_DOC_ATTRS(DragEngine,PartialEngine,"Apply `drag force `__ on some particles at each step, decelerating them proportionally to their linear velocities. The applied force reads\n\n.. math:: F_{d}=-\\frac{\\vec{v}}{|\\vec{v}|}\\frac{1}{2}\\rho|\\vec{v}|^2 C_d A\n\nwhere $\\rho$ is the medium density (:yref:`density`), $v$ is particle's velocity, $A$ is particle projected area (disc), $C_d$ is the drag coefficient (0.47 for :yref:`Sphere`), \n\n.. note:: Drag force is only applied to spherical particles, listed in ids.", ((Real,Rho,1.225,,"Density of the medium (fluid or air), by default - the density of the air.")) ((Real,Cd,0.47,,"Drag coefficient `_.")) ); }; REGISTER_SERIALIZABLE(DragEngine); class LinearDragEngine: public PartialEngine{ public: virtual void action(); YADE_CLASS_BASE_DOC_ATTRS(LinearDragEngine,PartialEngine,"Apply `viscous resistance or linear drag `__ on some particles at each step, decelerating them proportionally to their linear velocities. The applied force reads\n\n.. math:: F_{d}=-b{\\vec{v}} \n\nwhere $b$ is the linear drag, $\\vec{v}$ is particle's velocity. \n\n.. math:: b=6\\pi\\nu r \n\nwhere $\\nu$ is the medium viscosity, $r$ is the `Stokes radius `__ of the particle (but in this case we accept it equal to sphere radius for simplification), \n\n.. note:: linear drag is only applied to spherical particles, listed in ids.", ((Real,nu,0.001,,"Viscosity of the medium.")) ); }; REGISTER_SERIALIZABLE(LinearDragEngine); class HydroForceEngine: public PartialEngine{ public: void averageProfile(); void turbulentFluctuation(); void turbulentFluctuationBIS(); void turbulentFluctuationFluidizedBed(); public: virtual void action(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(HydroForceEngine,PartialEngine,"Apply drag and lift due to a fluid flow vector (1D) to each sphere + the buoyant weight.\n The applied drag force reads\n\n $F_{d}=\\frac{1}{2} C_d A\\rho^f|\\vec{v_f - v}| \\vec{v_f - v}$ \n\n where $\\rho$ is the medium density (:yref:`densFluid`), $v$ is particle's velocity, $v_f$ is the velocity of the fluid at the particle center(:yref:`vxFluid`), $A$ is particle projected area (disc), $C_d$ is the drag coefficient. The formulation of the drag coefficient depends on the local particle reynolds number and the solid volume fraction. The formulation of the drag is [Dallavalle1948]_ [RevilBaudard2013]_ with a correction of Richardson-Zaki [Richardson1954]_ to take into account the hindrance effect. This law is classical in sediment transport. It is possible to activate a fluctuation of the drag force for each particle which account for the turbulent fluctuation of the fluid velocity (:yref:`velFluct`). The model implemented for the turbulent velocity fluctuation is a simple discrete random walk which takes as input the Reynolds stress tensor $R^f_{xz}$ as a function of the depth, and allows to recover the main property of the fluctuations by imposing $ (z) = (z)/\\rho^f$. It requires as input $(z)/\\rho^f$ called :yref:`simplifiedReynoldStresses` in the code. \n The formulation of the lift is taken from [Wiberg1985]_ and is such that : \n\n $F_{L}=\\frac{1}{2} C_L A\\rho^f((v_f - v)^2_{top} - (v_f - v)^2_{bottom})$ \n\n Where the subscript top and bottom means evaluated at the top (respectively the bottom) of the sphere considered. This formulation of the lift account for the difference of pressure at the top and the bottom of the particle inside a turbulent shear flow. As this formulation is controversial when approaching the threshold of motion [Schmeeckle2007]_ it is possible to desactivate it with the variable :yref:`lift`.\n The buoyancy is taken into account through the buoyant weight : \n\n $F_{buoyancy}= - \\rho^f V^p g$ \n\n, where g is the gravity vector along the vertical, and $V^p$ is the volume of the particle. This engine also evaluate the average particle velocity, solid volume fraction and drag force depth profiles, through the function averageProfile. This is done as the solid volume fraction depth profile is required for the drag calculation, and as the three are required for the independent fluid resolution.", ((Real,densFluid,1000,,"Density of the fluid, by default - density of water")) ((Real,viscoDyn,1e-3,,"Dynamic viscosity of the fluid, by default - viscosity of water")) ((Real,zRef,,,"Position of the reference point which correspond to the first value of the fluid velocity, i.e. to the ground.")) ((Real,deltaZ,,,"Height of the discretization cell.")) ((Real,expoRZ,3.1,,"Value of the Richardson-Zaki exponent, for the drag correction due to hindrance")) ((bool,lift,false,,"Option to activate or not the evaluation of the lift")) ((Real,Cl,0.2,,"Value of the lift coefficient taken from [Wiberg1985]_")) ((Real,vCell,,,"Volume of averaging cell")) ((int,nCell,,,"Number of cell in the depth")) ((Vector3r,gravity,Vector3r(0,0,-9.81),,"Gravity vector (may depend on the slope).")) ((vector,vxFluid,,,"Discretized streamwise fluid velocity depth profile")) ((vector,phiPart,,,"Discretized solid volume fraction depth profile. Can be taken as input parameter, or evaluated directly inside the engine, calling from python the averageProfile() function, or puting :yref:`activateAverage` to True.")) ((vector,vxPart,,,"Discretized streamwise solid velocity depth profile. Can be taken as input parameter, or evaluated directly inside the engine, calling from python the averageProfile() function, or puting :yref:`activateAverage` to True.")) ((vector,vyPart,,,"Discretized spanwise solid velocity depth profile. No role in the engine, output parameter. For practical reason, it can be evaluated directly inside the engine, calling from python the averageProfile() method of the engine, or puting :yref:`activateAverage` to True.")) ((vector,vzPart,,,"Discretized normal solid velocity depth profile. No role in the engine, output parameter. For practical reason, it can be evaluated directly inside the engine, calling from python the averageProfile() method of the engine, or puting :yref:`activateAverage` to True.")) ((vector,averageDrag,,,"Discretized average drag depth profile. No role in the engine, output parameter. For practical reason, it can be evaluated directly inside the engine, calling from python the averageProfile() method of the engine, or puting :yref:`activateAverage` to True.")) ((bool,twoSize,false,,"Option to activate when considering two particle size in the simulation. When activated evaluate the average solid volume fraction and drag force for the two type of particles of diameter diameterPart1 and diameterPart2 independently.")) ((Real,radiusPart1,0.,,"Radius of the particles of type 1. Useful only when :yref:`twoSize` is set to True.")) ((Real,radiusPart2,0.,,"Radius of the particles of type 2. Useful only when :yref:`twoSize` is set to True.")) ((vector,phiPart1,,,"Discretized solid volume fraction depth profile of particles of type 1. Evaluated when :yref:`twoSize` is set to True.")) ((vector,phiPart2,,,"Discretized solid volume fraction depth profile of particles of type 2. Evaluated when :yref:`twoSize` is set to True.")) ((vector,averageDrag1,,,"Discretized average drag depth profile of particles of type 1. Evaluated when :yref:`twoSize` is set to True.")) ((vector,averageDrag2,,,"Discretized average drag depth profile of particles of type 2. Evaluated when :yref:`twoSize` is set to True.")) ((vector,vxPart1,,,"Discretized solid streamwise velocity depth profile of particles of type 1. Evaluated when :yref:`twoSize` is set to True.")) ((vector,vxPart2,,,"Discretized solid streamwise velocity depth profile of particles of type 2. Evaluated when :yref:`twoSize` is set to True.")) ((vector,vyPart1,,,"Discretized solid spanwise velocity depth profile of particles of type 1. Evaluated when :yref:`twoSize` is set to True.")) ((vector,vyPart2,,,"Discretized solid spanwise velocity depth profile of particles of type 2. Evaluated when :yref:`twoSize` is set to True.")) ((vector,vzPart1,,,"Discretized solid wall-normal velocity depth profile of particles of type 1. Evaluated when :yref:`twoSize` is set to True.")) ((vector,vzPart2,,,"Discretized solid wall-normal velocity depth profile of particles of type 2. Evaluated when :yref:`twoSize` is set to True.")) ((bool,activateAverage,false,,"If true, activate the calculation of the average depth profiles of drag, solid volume fraction, and solid velocity for the application of the force (phiPart in hindrance function) and to use in python for the coupling with the fluid.")) ((bool,velFluct,false,,"If true, activate the determination of turbulent fluid velocity fluctuation for the next time step only at the position of each particle, using a simple discrete random walk (DRW) model based on the Reynolds stresses profile (:yref:`simplifiedReynoldStresses`)")) ((vector,vFluctX,,,"Vector associating a streamwise fluid velocity fluctuation to each particle. Fluctuation calculated in the C++ code from the discrete random walk model")) ((vector,vFluctY,,,"Vector associating a spanwise fluid velocity fluctuation to each particle. Fluctuation calculated in the C++ code from the discrete random walk model")) ((vector,vFluctZ,,,"Vector associating a normal fluid velocity fluctuation to each particle. Fluctuation calculated in the C++ code from the discrete random walk model")) ((vector,simplifiedReynoldStresses,,,"Vector of size equal to :yref:`nCell` containing the Reynolds stresses divided by the fluid density in function of the depth. simplifiedReynoldStresses(z) $= (z)^2$")) ((Real,bedElevation,,,"Elevation of the bed above which the fluid flow is turbulent and the particles undergo turbulent velocity fluctuation.")) ((vector,fluctTime,,,"Vector containing the time of life of the fluctuations associated to each particles.")) ((Real,dtFluct,,,"Execution time step of the turbulent fluctuation model.")) ,/*ctor*/ ,/*py*/ .def("averageProfile",&HydroForceEngine::averageProfile,"Compute and store the particle velocity (:yref:`vxPart`, :yref:`vyPart`, :yref:`vzPart`) and solid volume fraction (:yref:`phiPart`) depth profile. For each defined cell z, the k component of the average particle velocity reads: \n\n $^z= \\sum_p V^p v_k^p/\\sum_p V^p$,\n\n where the sum is made over the particles contained in the cell, $v_k^p$ is the k component of the velocity associated to particle p, and $V^p$ is the part of the volume of the particle p contained inside the cell. This definition allows to smooth the averaging, and is equivalent to taking into account the center of the particles only when there is a lot of particles in each cell. As for the solid volume fraction, it is evaluated in the same way: for each defined cell z, it reads: \n\n $<\\phi>^z= \\frac{1}{V_{cell}}\\sum_p V^p$, where $V_{cell}$ is the volume of the cell considered, and $V^p$ is the volume of particle p contained in cell z.\n This function gives depth profiles of average velocity and solid volume fraction, returning the average quantities in each cell of height dz, from the reference horizontal plane at elevation :yref:`zRef` (input parameter) until the plane of elevation :yref:`zRef` plus :yref:`nCell` times :yref:`deltaZ` (input parameters). When the option :yref:`twoSize` is set to True, evaluate in addition the average drag (:yref:`averageDrag1` and :yref:`averageDrag2`) and solid volume fraction (:yref:`phiPart1` and :yref:`phiPart2`) depth profiles considering only the particles of radius respectively :yref:`radiusPart1` and :yref:`radiusPart2` in the averaging.") .def("turbulentFluctuation",&HydroForceEngine::turbulentFluctuation,"Apply turbulent fluctuation to the problem.") .def("turbulentFluctuationBIS",&HydroForceEngine::turbulentFluctuationBIS,"Apply turbulent fluctuation to the problem with an alternative formulation.") .def("turbulentFluctuationFluidizedBed",&HydroForceEngine::turbulentFluctuationFluidizedBed,"Apply turbulent fluctuation to the problem with another alternative formulation.") ); }; REGISTER_SERIALIZABLE(HydroForceEngine); trunk-2017.01a/pkg/common/ForceResetter.hpp000066400000000000000000000010751304022710500205230ustar00rootroot00000000000000#pragma once #include #include class Scene; class ForceResetter: public GlobalEngine{ public: virtual void action() { scene->forces.reset(scene->iter); if(scene->trackEnergy) scene->energy->resetResettables(); } YADE_CLASS_BASE_DOC(ForceResetter,GlobalEngine,"Reset all forces stored in Scene::forces (``O.forces`` in python). Typically, this is the first engine to be run at every step. In addition, reset those energies that should be reset, if energy tracing is enabled."); }; REGISTER_SERIALIZABLE(ForceResetter); trunk-2017.01a/pkg/common/GLDrawFunctors.hpp000066400000000000000000000043131304022710500206110ustar00rootroot00000000000000// © 2004 Olivier Galizzi // © 2006 Janek Kozicki #pragma once #include #include #include #include #include #include #include #include #include #include #define RENDERS(name) public: virtual string renders() const { return #name;}; FUNCTOR1D(name); struct GLViewInfo{ GLViewInfo(): sceneCenter(Vector3r::Zero()), sceneRadius(1.){} Vector3r sceneCenter; Real sceneRadius; }; class OpenGLRenderer; #define GL_FUNCTOR(Klass,typelist,renderedType) class Klass: public Functor1D{public:\ virtual ~Klass(){};\ virtual string renders() const { throw std::runtime_error(#Klass ": unregistered gldraw class.\n"); };\ virtual void initgl(){/*WARNING: it must deal with static members, because it is called from another instance!*/};\ YADE_CLASS_BASE_DOC(Klass,Functor,"Abstract functor for rendering :yref:`" #renderedType "` objects."); \ }; REGISTER_SERIALIZABLE(Klass); #define GL_DISPATCHER(Klass,Functor) class Klass: public Dispatcher1D{public:\ YADE_DISPATCHER1D_FUNCTOR_DOC_ATTRS_CTOR_PY(Klass,Functor,/*optional doc*/,/*attrs*/,/*ctor*/,/*py*/); \ }; REGISTER_SERIALIZABLE(Klass); GL_FUNCTOR(GlBoundFunctor,TYPELIST_2(const shared_ptr&, Scene*),Bound); GL_FUNCTOR(GlShapeFunctor,TYPELIST_4(const shared_ptr&, const shared_ptr&,bool,const GLViewInfo&),Shape); GL_FUNCTOR(GlIGeomFunctor,TYPELIST_5(const shared_ptr&, const shared_ptr&, const shared_ptr&, const shared_ptr&, bool),IGeom); GL_FUNCTOR(GlIPhysFunctor,TYPELIST_5(const shared_ptr&, const shared_ptr&, const shared_ptr&, const shared_ptr&, bool),IPhys); GL_FUNCTOR(GlStateFunctor,TYPELIST_1(const shared_ptr&),State); GL_DISPATCHER(GlBoundDispatcher,GlBoundFunctor); GL_DISPATCHER(GlShapeDispatcher,GlShapeFunctor); GL_DISPATCHER(GlIGeomDispatcher,GlIGeomFunctor); GL_DISPATCHER(GlIPhysDispatcher,GlIPhysFunctor); GL_DISPATCHER(GlStateDispatcher,GlStateFunctor); #undef GL_FUNCTOR #undef GL_DISPATCHER trunk-2017.01a/pkg/common/Gl1_NormPhys.cpp000066400000000000000000000071471304022710500202320ustar00rootroot00000000000000#ifdef YADE_OPENGL #include #include #include #include #include #include YADE_PLUGIN((Gl1_NormPhys)); GLUquadric* Gl1_NormPhys::gluQuadric=NULL; Real Gl1_NormPhys::maxFn; Real Gl1_NormPhys::refRadius; Real Gl1_NormPhys::maxRadius; int Gl1_NormPhys::signFilter; int Gl1_NormPhys::slices; int Gl1_NormPhys::stacks; Real Gl1_NormPhys::maxWeakFn; int Gl1_NormPhys::weakFilter; Real Gl1_NormPhys::weakScale; void Gl1_NormPhys::go(const shared_ptr& ip, const shared_ptr& i, const shared_ptr& b1, const shared_ptr& b2, bool wireFrame){ if(!gluQuadric){ gluQuadric=gluNewQuadric(); if(!gluQuadric) throw runtime_error("Gl1_NormPhys::go unable to allocate new GLUquadric object (out of memory?)."); } NormPhys* np=static_cast(ip.get()); shared_ptr ig(i->geom); if(!ig) return; // changed meanwhile? GenericSpheresContact* geom=YADE_CAST(ig.get()); //if(!geom) cerr<<"Gl1_NormPhys: IGeom is not a GenericSpheresContact, but a "<getClassName()<normalForce.dot(geom->normal); if((signFilter>0 && fnNorm<0) || (signFilter<0 && fnNorm>0)) return; int fnSign=fnNorm>0?1:-1; fnNorm=std::abs(fnNorm); Real radiusScale=1.; // weak/strong fabric, only used if maxWeakFn is set if(!std::isnan(maxWeakFn)){ if(fnNorm*fnSign0) return; radiusScale=weakScale; } else { // strong fabric if(weakFilter<0) return; } } maxFn=max(fnNorm,maxFn); Real realMaxRadius; if(maxRadius<0){ if(geom->refR1>0) refRadius=min(geom->refR1,refRadius); if(geom->refR2>0) refRadius=min(geom->refR2,refRadius); realMaxRadius=refRadius; } else realMaxRadius=maxRadius; Real radius=radiusScale*realMaxRadius*(fnNorm/maxFn); // use logarithmic scale here? Vector3r color=Shop::scalarOnColorScale(fnNorm*fnSign,-maxFn,maxFn); # if 0 // get endpoints from body positions Vector3r p1=b1->state->pos, p2=b2->state->pos; Vector3r relPos; if(scene->isPeriodic){ relPos=p2+scene->cell->Hsize*i->cellDist.cast()-p1; p1=scene->cell->wrapShearedPt(p1); p2=p1+relPos; } else { relPos=p2-p1; } Real dist=relPos.norm(); #else // get endpoints from geom // max(r,0) handles r<0 which is the case for "radius" of the facet Vector3r cp=scene->isPeriodic? scene->cell->wrapShearedPt(geom->contactPoint) : geom->contactPoint; Vector3r p1=cp-max(geom->refR1,(Real)0.)*geom->normal; Vector3r p2=cp+max(geom->refR2,(Real)0.)*geom->normal; const Vector3r& dispScale=scene->renderer ? scene->renderer->dispScale : Vector3r::Ones(); if(dispScale!=Vector3r::Ones()){ // move p1 and p2 by the same amounts as particles themselves would be moved p1+=dispScale.cwiseProduct(Vector3r(b1->state->pos-b1->state->refPos)); p2+=dispScale.cwiseProduct(Vector3r(b2->state->pos-b2->state->refPos)); } Vector3r relPos=p2-p1; Real dist=relPos.norm(); //max(geom->refR1,0.)+max(geom->refR2,0.); #endif glDisable(GL_CULL_FACE); glPushMatrix(); glTranslatef(p1[0],p1[1],p1[2]); Quaternionr q(Quaternionr().setFromTwoVectors(Vector3r(0,0,1),relPos/dist /* normalized */)); // using Transform with OpenGL: http://eigen.tuxfamily.org/dox/TutorialGeometry.html //glMultMatrixd(Eigen::Affine3d(q).data()); glMultMatrix(Eigen::Transform(q).data()); glColor3v(color); gluCylinder(gluQuadric,radius,radius,dist,slices,stacks); glPopMatrix(); } #endif /* YADE_OPENGL */ trunk-2017.01a/pkg/common/Gl1_NormPhys.hpp000066400000000000000000000050471304022710500202340ustar00rootroot00000000000000#pragma once #include #include #include #include #include class Gl1_NormPhys: public GlIPhysFunctor{ static GLUquadric* gluQuadric; // needed for gluCylinder, initialized by ::go if no initialized yet public: virtual void go(const shared_ptr&,const shared_ptr&,const shared_ptr&,const shared_ptr&,bool wireFrame); YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_NormPhys,GlIPhysFunctor,"Renders :yref:`NormPhys` objects as cylinders of which diameter and color depends on :yref:`NormPhys.normalForce` magnitude.", // changed doc maxDiameter -> maxRadius ((Real,maxFn,0,,"Value of :yref:`NormPhys.normalForce` corresponding to :yref:`maxDiameter`. This value will be increased (but *not decreased* ) automatically.")) ((Real,maxFn,0,,"Value of :yref:`NormPhys.normalForce` corresponding to :yref:`maxRadius`. This value will be increased (but *not decreased* ) automatically.")) ((int,signFilter,0,,"If non-zero, only display contacts with negative (-1) or positive (+1) normal forces; if zero, all contacts will be displayed.")) ((Real,refRadius,std::numeric_limits::infinity(),,"Reference (minimum) particle radius; used only if :yref:`maxRadius` is negative. This value will be decreased (but *not increased* ) automatically. |yupdate|")) ((Real,maxRadius,-1,,"Cylinder radius corresponding to the maximum normal force. If negative, auto-updated :yref:`refRadius` will be used instead.")) ((int,slices,6,,"Number of sphere slices; (see `glutCylinder reference `_)")) // FIXME: the link does not exist ((int,stacks,1,,"Number of sphere stacks; (see `glutCylinder reference `_)")) // strong/weak fabric attributes ((Real,maxWeakFn,NaN,,"Value that divides contacts by their normal force into the 'weak fabric' and 'strong fabric'. This value is set as side-effect by :yref:`utils.fabricTensor`.")) ((int,weakFilter,0,,"If non-zero, only display contacts belonging to the 'weak' (-1) or 'strong' (+1) fabric.")) ((Real,weakScale,1.,,"If :yref:`maxWeakFn` is set, scale radius of the weak fabric by this amount (usually smaller than 1). If zero, 1 pixel line is displayed. Colors are not affected by this value.")) ); RENDERS(NormPhys); }; REGISTER_SERIALIZABLE(Gl1_NormPhys); trunk-2017.01a/pkg/common/Gl1_PFacet.cpp000066400000000000000000000032451304022710500176100ustar00rootroot00000000000000#ifdef YADE_OPENGL #include #include // bool Gl1_PFacet::normals=false; bool Gl1_PFacet::wire=true; void Gl1_PFacet::go(const shared_ptr& cm, const shared_ptr& ,bool wire2,const GLViewInfo&) { PFacet* Pfacet = static_cast(cm.get()); vector vertices; vertices.push_back(Pfacet->node1->state->pos); vertices.push_back(Pfacet->node2->state->pos); vertices.push_back(Pfacet->node3->state->pos); Vector3r pos=Pfacet->node1->state->pos; vertices[0]=vertices[0]-pos; vertices[1]=vertices[1]-pos; vertices[2]=vertices[2]-pos; vector verticesF1 = vertices; Vector3r normal=(vertices[1]-vertices[0]).cross(vertices[2]-vertices[1]); normal.normalize(); verticesF1[0]=vertices[0] + normal*Pfacet->radius; verticesF1[1]=vertices[1] + normal*Pfacet->radius; verticesF1[2]=vertices[2] + normal*Pfacet->radius; vector verticesF2 = vertices; verticesF2[0] = vertices[0] - normal*Pfacet->radius; verticesF2[1] = vertices[1] - normal*Pfacet->radius; verticesF2[2] = vertices[2] - normal*Pfacet->radius; if(!wire2||!wire){ glDisable(GL_CULL_FACE); glColor3v(cm->color); glBegin(GL_TRIANGLES); glNormal3v(normal); // this makes every triangle different WRT the light direction; important! glVertex3v(verticesF1[0]); glVertex3v(verticesF1[1]); glVertex3v(verticesF1[2]); glEnd(); glBegin(GL_TRIANGLES); glNormal3v(Pfacet->normal); // this makes every triangle different WRT the light direction; important! glVertex3v(verticesF2[2]); glVertex3v(verticesF2[1]); glVertex3v(verticesF2[0]); glEnd(); } } YADE_PLUGIN((Gl1_PFacet)); #endiftrunk-2017.01a/pkg/common/Gl1_PFacet.hpp000066400000000000000000000010651304022710500176130ustar00rootroot00000000000000#pragma once #include #include #include #include #ifdef YADE_OPENGL class Gl1_PFacet : public GlShapeFunctor { public: virtual void go(const shared_ptr&, const shared_ptr&,bool,const GLViewInfo&); RENDERS(PFacet); YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_PFacet,GlShapeFunctor,"Renders :yref:`Facet` object", ((bool,wire,false,,"Only show wireframe (controlled by ``glutSlices`` and ``glutStacks``.")) ); }; REGISTER_SERIALIZABLE(Gl1_PFacet); #endif trunk-2017.01a/pkg/common/Gl1_PotentialBlock.cpp000077500000000000000000001222651304022710500213670ustar00rootroot00000000000000/* CWBoon 2016 */ #ifdef YADE_POTENTIAL_BLOCKS #include "Gl1_PotentialBlock.hpp" //#include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include //#include #include #include #include #include #include #include #include #include #include #include #include #include #include //#include #include #include #include #if 0 void Gl1_PotentialBlock::calcMinMax(const shared_ptr& cm) { PotentialBlock* pp = static_cast(cm.get()); int planeNo = pp->d.size(); Real maxD = pp->d[0]; for (int i=0; id[i] > maxD) { maxD = pp->d[i]; } } Real R = pp->R; Real r = pp->r; Real maxTip = R; //std::max(maxD + r, R); min =-1.1*pp->minAabb; // 1.5*Vector3r(-maxTip,-maxTip,-maxTip); max = 1.1*pp->maxAabb; //-1.0*min; float dx = (max[0]-min[0])/((float)(sizeX)); float dy = (max[1]-min[1])/((float)(sizeY)); float dz = (max[2]-min[2])/((float)(sizeZ)); isoStep=Vector3r(dx,dy,dz); } void Gl1_PotentialBlock::generateScalarField(const shared_ptr& cm) { for(int i=0;i Gl1_PotentialBlock::SF; int Gl1_PotentialBlock::sizeX, Gl1_PotentialBlock::sizeY, Gl1_PotentialBlock::sizeZ; bool Gl1_PotentialBlock::store; bool Gl1_PotentialBlock::initialized; void Gl1_PotentialBlock::clearMemory(){ SF.clear(); } void Gl1_PotentialBlock::go( const shared_ptr& cm, const shared_ptr& state ,bool wire2, const GLViewInfo&){ PotentialBlock* pp = static_cast(cm.get()); int shapeId = pp->id; if(store == false){ if(SF.size()>0){SF.clear(); initialized = false; } return; } if(initialized == false ){ FOREACH(const shared_ptr& b, *scene->bodies){ if (!b) continue; const shared_ptr& cmbody=b->shape; calcMinMax(cmbody); mc.init(sizeX,sizeY,sizeZ,min,max); mc.resizeScalarField(scalarField,sizeX,sizeY,sizeZ); SF.push_back(scalarF()); generateScalarField(cmbody); mc.computeTriangulation(scalarField,0.0); SF[b->id].triangles = mc.getTriangles(); SF[b->id].normals = mc.getNormals(); SF[b->id].nbTriangles = mc.getNbTriangles(); for(int i=0; icolor[0],cm->color[1],cm->color[2])); glColor3v(cm->color); vector& triangles = SF[shapeId].triangles; //mc.getTriangles(); int nbTriangles = SF[shapeId].nbTriangles; // //mc.getNbTriangles(); vector& normals = SF[shapeId].normals; //mc.getNormals(); glDisable(GL_CULL_FACE); glEnable(GL_LIGHTING); // 2D glEnable(GL_NORMALIZE); glBegin(GL_TRIANGLES); for(int i=0;i<3*nbTriangles;++i) { glNormal3v(normals[i]); glVertex3v(triangles[i]); glNormal3v(normals[++i]); glVertex3v(triangles[i]); glNormal3v(normals[++i]); glVertex3v(triangles[i]); } glEnd(); return; } double Gl1_PotentialBlock::evaluateF(const shared_ptr& cm, double x, double y, double z){ PotentialBlock* pp = static_cast(cm.get()); Real k = pp->k; Real r = pp->r; Real R = pp->R; int planeNo = pp->a.size(); vectora; vectorb; vectorc; vectord; vectorp; Real pSum3 = 0.0; for (int i=0; ia[i]); b.push_back(pp->b[i]); c.push_back(pp->c[i]); d.push_back(pp->d[i]); Real plane = a[i]*x + b[i]*y + c[i]*z - d[i]; if (planep; double pSum2 = 0.0; if(clump==false){ Eigen::Vector3d xori(x[0],x[1],x[2]); Eigen::Vector3d xlocal = rotationMatrix*xori; xlocal[0] = rotationMatrix(0,0)*x[0] + rotationMatrix(0,1)*x[1] + rotationMatrix(0,2)*x[2]; xlocal[1] = rotationMatrix(1,0)*x[0] + rotationMatrix(1,1)*x[1] + rotationMatrix(1,2)*x[2]; xlocal[2] = rotationMatrix(2,0)*x[0] + rotationMatrix(2,1)*x[1] + rotationMatrix(2,2)*x[2]; //std::cout<<"rotationMatrix: "< pbPos = vtkSmartPointer::New(); vtkSmartPointer appendFilter = vtkSmartPointer::New(); vtkSmartPointer appendFilterID = vtkSmartPointer::New(); //vtkSmartPointer transformFilter = vtkSmartPointer::New(); //vtkSmartPointer transform = vtkSmartPointer::New(); // interactions ############################################### vtkSmartPointer intrBodyPos = vtkSmartPointer::New(); vtkSmartPointer intrCells = vtkSmartPointer::New(); vtkSmartPointer intrForceN = vtkSmartPointer::New(); intrForceN->SetNumberOfComponents(3); intrForceN->SetName("forceN"); vtkSmartPointer intrAbsForceT = vtkSmartPointer::New(); intrAbsForceT->SetNumberOfComponents(1); intrAbsForceT->SetName("absForceT"); // interactions ############################################### // interaction contact point ############################################### vtkSmartPointer pbContactPoint = vtkSmartPointer::New(); vtkSmartPointer pbCellsContact = vtkSmartPointer::New(); vtkSmartPointer pbNormalForce = vtkSmartPointer::New(); pbNormalForce->SetNumberOfComponents(3); pbNormalForce->SetName("normalForce"); //Linear velocity in Vector3 form vtkSmartPointer pbShearForce = vtkSmartPointer::New(); pbShearForce->SetNumberOfComponents(3); pbShearForce->SetName("shearForce"); //Angular velocity in Vector3 form vtkSmartPointer pbTotalForce = vtkSmartPointer::New(); pbTotalForce->SetNumberOfComponents(3); pbTotalForce->SetName("totalForce"); vtkSmartPointer pbTotalStress = vtkSmartPointer::New(); pbTotalStress->SetNumberOfComponents(3); pbTotalStress->SetName("totalStress"); vtkSmartPointer pbMobilizedShear = vtkSmartPointer::New(); pbMobilizedShear->SetNumberOfComponents(1); pbMobilizedShear->SetName("mobilizedShear"); // interactions contact point############################################### // velocity ################################################### vtkSmartPointer pbCells = vtkSmartPointer::New(); vtkSmartPointer pbLinVelVec = vtkSmartPointer::New(); pbLinVelVec->SetNumberOfComponents(3); pbLinVelVec->SetName("linVelVec"); //Linear velocity in Vector3 form vtkSmartPointer pbLinVelLen = vtkSmartPointer::New(); pbLinVelLen->SetNumberOfComponents(1); pbLinVelLen->SetName("linVelLen"); //Length (magnitude) of linear velocity vtkSmartPointer pbAngVelVec = vtkSmartPointer::New(); pbAngVelVec->SetNumberOfComponents(3); pbAngVelVec->SetName("angVelVec"); //Angular velocity in Vector3 form vtkSmartPointer pbAngVelLen = vtkSmartPointer::New(); pbAngVelLen->SetNumberOfComponents(1); pbAngVelLen->SetName("angVelLen"); //Length (magnitude) of angular velocity vtkSmartPointer pbDisplacementVec = vtkSmartPointer::New(); pbDisplacementVec->SetNumberOfComponents(3); pbDisplacementVec->SetName("Displacement"); //Linear velocity in Vector3 form // velocity #################################################### // bodyId ############################################################## //#if 0 vtkSmartPointer pbPosID = vtkSmartPointer::New(); vtkSmartPointer pbIdCells = vtkSmartPointer::New(); vtkSmartPointer blockId = vtkSmartPointer::New(); blockId->SetNumberOfComponents(1); blockId->SetName("id"); // bodyId ############################################################## //#endif int countID = 0; vtkSmartPointer textArray2[scene->bodies->size()]; vtkSmartPointer txtMapper[scene->bodies->size()]; vtkSmartPointer extrude[scene->bodies->size()]; vtkSmartPointer textActor[scene->bodies->size()]; FOREACH(const shared_ptr& b, *scene->bodies){ if (!b) continue; if (b->isClumpMember() == true ) continue; //const PotentialBlock* pb=dynamic_cast(b->shape.get()); //if(!pb) continue; if(REC_ID==true){ //#if 0 blockId->InsertNextValue(b->getId()); vtkIdType pid[1]; Vector3r pos(b->state->pos); pid[0] = pbPosID->InsertNextPoint(pos[0], pos[1], pos[2]); pbIdCells->InsertNextCell(1,pid); //#endif /* ################# Display id VTK extrusion vector ############## */ #if 0 textArray2[countID]= vtkVectorText::New(); //#if 0 int bid = b->id; std::string testString = boost::lexical_cast(bid); const char * testChar = testString.c_str(); textArray2[countID]->SetText(testChar); extrude[countID] = vtkLinearExtrusionFilter::New(); extrude[countID]->SetInputConnection( textArray2[countID]->GetOutputPort()); extrude[countID]->SetExtrusionTypeToNormalExtrusion(); extrude[countID]->SetVector(0, 0, 1.0 ); extrude[countID]->SetScaleFactor (1.0); #if 0 txtMapper[countID] = vtkPolyDataMapper::New(); txtMapper[countID]->SetInputConnection( extrude[countID]->GetOutputPort()); textActor[countID] = vtkActor::New(); textActor[countID]->SetMapper(txtMapper[countID]); textActor[countID]->RotateX(-90); textActor[countID]->SetPosition(b->state->pos[0], b->state->pos[1], b->state->pos[2]); double contactPtSize = 5.0; textActor[countID]->SetScale(3.0*contactPtSize); textActor[countID]->GetProperty()->SetColor(0.0,0.0,0.0); #endif //#if 0 //txtMapper[countID] = vtkPolyDataMapper::New(); //txtMapper[countID]->SetInputConnection( extrude[count]->GetOutputPort()); //appendFilterID->AddInputConnection(extrude[countID]-> GetOutputPort()); //vtkSmartPointer polydata = vtkSmartPointer::New(); //polydata->DeepCopy(extrude[countID]-> GetOutput()); Vector3r centre (b->state->pos[0], b->state->pos[1], b->state->pos[2]); vtkSmartPointer transformFilter = vtkSmartPointer::New(); transformFilter->SetInput( extrude[countID]-> GetOutput() ); vtkSmartPointer transform = vtkSmartPointer::New(); transformFilter->SetTransform( transform ); transform->PostMultiply(); transform->Translate (centre[0], centre[1],centre[2]); //#endif appendFilterID->AddInputConnection(transformFilter-> GetOutputPort()); //polydata->DeleteCells(); #endif countID++; } //vtkSmartPointer function = ImpFunc::New(); vtkSmartPointer boolFunction = vtkSmartPointer::New(); vtkSmartPointer* functionBool; int ImplicitBoolNo = 0; double xmin = 0.0; double xmax = 0.0; double ymin = 0.0; double ymax = 0.0; double zmin = 0.0; double zmax =0.0; Vector3r particleColour (0,0,0); if(b->isClump() == false && b->isClumpMember() == false){ const PotentialBlock* pb=dynamic_cast(b->shape.get()); if (pb->isLining==true){continue;} function->a = pb->a; function->b = pb->b; function->c = pb->c; function->d = pb->d; function->R = pb->R; function->r = pb->r; function->k = pb->k; Eigen::Matrix3d directionCos = b->state->ori.conjugate().toRotationMatrix(); int count = 0; function->clump = false; for (int i=0; i<3; i++){ for (int j=0; j<3; j++){ //function->rotationMatrix[count] = directionCos(j,i); function->rotationMatrix(i,j) = directionCos(j,i); count++; } } xmin = -pb->halfSize.x(); xmax = pb->halfSize.x(); ymin = -pb->halfSize.y(); ymax = pb->halfSize.y(); zmin = -pb->halfSize.z(); zmax = pb->halfSize.z(); particleColour = pb->color; }else if(b->isClump() == true){ //const Clump* clump = dynamic_cast(b->shape.get()); const shared_ptr clump(YADE_PTR_CAST(b->shape)); bool firstBound = true; //vtkSmartPointer functionBool [clump->ids.size()]; functionBool = new vtkSmartPointer [clump->ids.size()]; ImplicitBoolNo = clump->ids.size(); for (int i=0; iids.size();i++){ const shared_ptr clumpMember = Body::byId(clump->ids[i],scene); const PotentialBlock* pbShape =dynamic_cast(clumpMember->shape.get()); functionBool[i] = vtkSmartPointer::New(); functionBool[i]->R = pbShape->R; functionBool[i]->r = pbShape->r; functionBool[i]->k = pbShape->k; functionBool[i]->clump=true; functionBool[i]->clumpMemberCentreX = clumpMember->state->pos.x()-b->state->pos.x(); functionBool[i]->clumpMemberCentreY = clumpMember->state->pos.y()-b->state->pos.y(); functionBool[i]->clumpMemberCentreZ = clumpMember->state->pos.z()-b->state->pos.z(); Eigen::Matrix3d directionCos = clumpMember->state->ori.conjugate().toRotationMatrix(); for (int j=0; ja.size();j++){ Vector3r plane = directionCos.transpose()*Vector3r(pbShape->a[j], pbShape->b[j], pbShape->c[j]); double d = pbShape->d[j]; //-1.0*(plane.x()*(b->state->pos.x()-clumpMember->state->pos.x() ) + plane.y()*(b->state->pos.y()-clumpMember->state->pos.y() ) + plane.z()*(b->state->pos.z()-clumpMember->state->pos.z() ) - pbShape->d[j]); functionBool[i]->a.push_back(plane.x() ); functionBool[i]->b.push_back(plane.y() ); functionBool[i]->c.push_back(plane.z() ); functionBool[i]->d.push_back(d ); } const Aabb* aabb = static_cast(clumpMember->bound.get()); if (firstBound == true){ xmin = aabb->min.x(); xmax = aabb->max.x(); ymin = aabb->min.y(); ymax = aabb->max.y(); zmin = aabb->min.z(); zmax = aabb->max.z(); firstBound = false; particleColour = pbShape->color; }else{ xmin=std::min(xmin,aabb->min.x() ); xmax=std::max(xmax,aabb->max.x() ); ymin=std::min(ymin,aabb->min.y() ); ymax=std::max(ymax,aabb->max.y() ); zmin=std::min(zmin,aabb->min.z() ); zmax=std::max(zmax,aabb->max.z() ); } boolFunction->AddFunction(functionBool[i]); } xmin = xmin - b->state->pos.x(); xmax = xmax - b->state->pos.x(); ymin = ymin - b->state->pos.y(); ymax = ymax - b->state->pos.y(); zmin = zmin - b->state->pos.z(); zmax = zmax - b->state->pos.z(); boolFunction->SetOperationTypeToUnion(); } vtkSmartPointer sample = vtkSampleFunction::New(); if(b->isClump() == false && b->isClumpMember() == false){ sample->SetImplicitFunction(function); }else if(b->isClump()==true){ sample->SetImplicitFunction(boolFunction); boolFunction->SetOperationTypeToUnion(); } //double xmin = -value; double xmax = value; double ymin = -value; double ymax=value; double zmin=-value; double zmax=value; //double xmin = -std::max(pb->minAabb.x(),pb->maxAabb.x()); double xmax = -xmin; double ymin = -std::max(pb->minAabb.y(),pb->maxAabb.y()); double ymax=-ymin; double zmin=-std::max(pb->minAabb.z(),pb->maxAabb.z()); double zmax=-zmin; if (twoDimension == true){ if(sampleY < 2){ ymin = 0.0; ymax = 0.0; }else if(sampleZ < 2){ zmin = 0.0; zmax = 0.0; } } sample->SetModelBounds(xmin, xmax, ymin, ymax, zmin, zmax); //sample->SetModelBounds(pb->minAabb.x(), pb->maxAabb.x(), pb->minAabb.y(), pb->maxAabb.y(), pb->minAabb.z(), pb->maxAabb.z()); int sampleXno = sampleX; int sampleYno = sampleY; int sampleZno = sampleZ; if(fabs(xmax-xmin)/static_cast(sampleX) > maxDimension) { sampleXno = static_cast(fabs(xmax-xmin)/maxDimension); } if(fabs(ymax-ymin)/static_cast(sampleY) > maxDimension) { sampleYno = static_cast(fabs(ymax-ymin)/maxDimension); } if(fabs(zmax-zmin)/static_cast(sampleZ) > maxDimension) { sampleZno = static_cast(fabs(zmax-zmin)/maxDimension); } if (twoDimension == true){ if(sampleY < 2){ sampleYno = 1; }else if(sampleZ < 2){ sampleZno = 1; } } sample->SetSampleDimensions(sampleXno,sampleYno,sampleZno); sample->ComputeNormalsOff(); //sample->Update(); vtkSmartPointer contours = vtkContourFilter::New(); contours->SetInputConnection(sample->GetOutputPort()); contours->SetNumberOfContours(1); contours->SetValue(0,0.0); vtkSmartPointer polydata = vtkSmartPointer::New(); contours->Update(); polydata->DeepCopy(contours->GetOutput()); //polydata->Update(); vtkSmartPointer pbColors = vtkSmartPointer::New(); pbColors->SetName("pbColors"); pbColors->SetNumberOfComponents(3); Vector3r color = particleColour; //Vector3r(0,100,0); if (b->isDynamic() == false){ color = Vector3r(157,157,157); } unsigned char c[3]; //c = {color[0],color[1],color[2]}; c[0]=color[0]; c[1]=color[1]; c[2]=color[2]; int nbCells=polydata->GetNumberOfPoints(); for (int i=0;iInsertNextTupleValue(c); } polydata->GetPointData()->SetScalars(pbColors); //polydata->Update(); Vector3r centre (b->state->pos[0], b->state->pos[1], b->state->pos[2]); Quaternionr orientation= b->state->ori; orientation.normalize(); AngleAxisr aa(orientation); Vector3r axis = aa.axis(); /* axis.normalize(); */ double angle = aa.angle()/3.14159*180.0; double xAxis = axis[0]; double yAxis = axis[1]; double zAxis = axis[2]; vtkSmartPointer transformFilter = vtkSmartPointer::New(); transformFilter->SetInputData( polydata ); vtkSmartPointer transform = vtkSmartPointer::New(); transformFilter->SetTransform( transform ); transform->PostMultiply(); transform->Translate (centre[0], centre[1],centre[2]); //transform->RotateWXYZ(angle,xAxis, yAxis, zAxis); //transformFilter->Update(); appendFilter->AddInputConnection(transformFilter-> GetOutputPort()); // ################## velocity #################### if(REC_VELOCITY == true){ vtkIdType pid[1]; Vector3r pos(b->state->pos); pid[0] = pbPos->InsertNextPoint(pos[0], pos[1], pos[2]); pbCells->InsertNextCell(1,pid); const Vector3r& vel = b->state->vel; float v[3]; //v = { vel[0],vel[1],vel[2] }; v[0]=vel[0]; v[1]=vel[1]; v[2]=vel[2]; pbLinVelVec->InsertNextTupleValue(v); pbLinVelLen->InsertNextValue(vel.norm()); const Vector3r& angVel = b->state->angVel; float av[3]; //av = { angVel[0],angVel[1],angVel[2] }; av[0]=angVel[0]; av[1]=angVel[1]; av[2]=angVel[2]; pbAngVelVec->InsertNextTupleValue(av); pbAngVelLen->InsertNextValue(angVel.norm()); //if(b->state->refPos.squaredNorm()>0.001){ //if initialized Vector3r displacement = pos- b->state->refPos; float disp[3]; disp[0]=displacement[0]; disp[1]=displacement[1]; disp[2]=displacement[2]; pbDisplacementVec->InsertNextTupleValue(disp); //} } // ################ velocity ########################### polydata->DeleteCells(); sample->Delete(); contours->Delete(); //function->Delete(); //#if 0 if(b->isClump()==true){ //boolFunction->Delete(); for(int i=0; i < ImplicitBoolNo; i++){ functionBool[i]->Delete(); } //boolFunction = NULL; } //#endif sample = NULL; contours = NULL; } if(REC_VELOCITY == true){ vtkSmartPointer pbUg = vtkSmartPointer::New(); pbUg->SetPoints(pbPos); pbUg->SetCells(VTK_VERTEX, pbCells); pbUg->GetPointData()->AddArray(pbLinVelVec); pbUg->GetPointData()->AddArray(pbAngVelVec); pbUg->GetPointData()->AddArray(pbLinVelLen); pbUg->GetPointData()->AddArray(pbAngVelLen); pbUg->GetPointData()->AddArray(pbDisplacementVec); vtkSmartPointer writerA = vtkSmartPointer::New(); writerA->SetDataModeToAscii(); string fv=fileName+"vel."+std::to_string(scene->iter)+".vtu"; writerA->SetFileName(fv.c_str()); writerA->SetInputData(pbUg); writerA->Write(); //writerA->Delete(); //pbUg->Delete(); } //###################### bodyId ############################### if(REC_ID == true){ #if 0 vtkSmartPointer writerA = vtkXMLPolyDataWriter::New(); writerA->SetDataModeToAscii(); string fn=fileName+"-Id."+std::to_string(scene->iter)+".vtp"; writerA->SetFileName(fn.c_str()); writerA->SetInputConnection(appendFilterID->GetOutputPort());//(extrude->GetOutputPort()); writerA->Write(); writerA->Delete(); #endif //#if 0 vtkSmartPointer pbUg = vtkSmartPointer::New(); pbUg->SetPoints(pbPosID); pbUg->SetCells(VTK_VERTEX, pbIdCells); pbUg->GetPointData()->AddArray(blockId); vtkSmartPointer writerA = vtkSmartPointer::New(); writerA->SetDataModeToAscii(); string fv=fileName+"Id."+std::to_string(scene->iter)+".vtu"; writerA->SetFileName(fv.c_str()); writerA->SetInputData(pbUg); writerA->Write(); //writerA->Delete(); //pbUg->Delete(); //#endif } #if 0 if(REC_ID== true){ int counter =0; FOREACH(const shared_ptr& b, *scene->bodies){ if (!b) {continue;} if (b->isClumpMember()==true) {continue;} textArray2[counter]->Delete(); //txtMapper[count]->Delete(); extrude[counter]->Delete(); counter++; } } #endif // ################## contact point #################### if(REC_INTERACTION == true){ int count = 0; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) { continue; } const KnKsPBPhys* phys = YADE_CAST(I->phys.get()); const ScGeom* geom = YADE_CAST(I->geom.get()); vtkIdType pid[1]; Vector3r pos(geom->contactPoint); pid[0] = pbContactPoint->InsertNextPoint(pos[0], pos[1], pos[2]); pbCellsContact->InsertNextCell(1,pid); //intrBodyPos->InsertNextPoint(geom->contactPoint[0],geom->contactPoint[1],geom->contactPoint[2]); // gives _signed_ scalar of normal force, following the convention used in the respective constitutive law float fn[3]={phys->normalForce[0],phys->normalForce[1], phys->normalForce[2]}; float fs[3]={phys->shearForce[0], phys->shearForce[1], phys->shearForce[2]}; float totalForce[3] = {fn[0]+fs[0], fn[1]+fs[1], fn[2]+fs[2]}; float totalStress[3] = {0.0,0.0,0.0}; //{totalForce[0]/phys->contactArea, totalForce[1]/phys->contactArea, totalForce[2]/phys->contactArea}; float mobilizedShear = phys->mobilizedShear; pbTotalForce->InsertNextTupleValue(totalForce); pbMobilizedShear->InsertNextValue(mobilizedShear); pbNormalForce->InsertNextTupleValue(fn); pbShearForce->InsertNextTupleValue(fs); pbTotalStress->InsertNextTupleValue(totalStress); count++; } if(count>0){ vtkSmartPointer pbUgCP = vtkSmartPointer::New(); pbUgCP->SetPoints(pbContactPoint); pbUgCP->SetCells(VTK_VERTEX, pbCellsContact); pbUgCP->GetPointData()->AddArray(pbNormalForce); pbUgCP->GetPointData()->AddArray(pbShearForce); pbUgCP->GetPointData()->AddArray(pbTotalForce); pbUgCP->GetPointData()->AddArray(pbMobilizedShear); pbUgCP->GetPointData()->AddArray(pbTotalStress); vtkSmartPointer writerB = vtkSmartPointer::New(); writerB->SetDataModeToAscii(); string fcontact=fileName+"contactPoint."+std::to_string(scene->iter)+".vtu"; writerB->SetFileName(fcontact.c_str()); writerB->SetInputData(pbUgCP); writerB->Write(); //writerB->Delete(); //pbUgCP->Delete(); } } // ################ contact point ########################### vtkSmartPointer writer = vtkXMLPolyDataWriter::New(); writer->SetDataModeToAscii(); string fn=fileName+"-pb."+std::to_string(scene->iter)+".vtp"; writer->SetFileName(fn.c_str()); writer->SetInputConnection(appendFilter->GetOutputPort()); writer->Write(); writer->Delete(); //intrBodyPos->Delete(); //intrForceN->Delete(); //intrAbsForceT->Delete(); //pbContactPoint->Delete(); //pbCellsContact->Delete(); //pbNormalForce->Delete(); //pbShearForce->Delete(); //pbCells->Delete(); //pbLinVelVec->Delete(); //pbLinVelLen->Delete(); //pbAngVelVec->Delete(); //pbAngVelLen->Delete(); } void PotentialBlockVTKRecorder::action(){ if(fileName.size()==0) return; vtkSmartPointer pbPos = vtkSmartPointer::New(); vtkSmartPointer appendFilter = vtkSmartPointer::New(); vtkSmartPointer appendFilterID = vtkSmartPointer::New(); //vtkSmartPointer transformFilter = vtkSmartPointer::New(); //vtkSmartPointer transform = vtkSmartPointer::New(); // interactions ############################################### vtkSmartPointer intrBodyPos = vtkSmartPointer::New(); vtkSmartPointer intrCells = vtkSmartPointer::New(); vtkSmartPointer intrForceN = vtkSmartPointer::New(); intrForceN->SetNumberOfComponents(3); intrForceN->SetName("forceN"); vtkSmartPointer intrAbsForceT = vtkSmartPointer::New(); intrAbsForceT->SetNumberOfComponents(1); intrAbsForceT->SetName("absForceT"); // interactions ############################################### // interaction contact point ############################################### vtkSmartPointer pbContactPoint = vtkSmartPointer::New(); vtkSmartPointer pbCellsContact = vtkSmartPointer::New(); vtkSmartPointer pbNormalForce = vtkSmartPointer::New(); pbNormalForce->SetNumberOfComponents(3); pbNormalForce->SetName("normalForce"); //Linear velocity in Vector3 form vtkSmartPointer pbShearForce = vtkSmartPointer::New(); pbShearForce->SetNumberOfComponents(3); pbShearForce->SetName("shearForce"); //Angular velocity in Vector3 form // interactions contact point############################################### // velocity ################################################### vtkSmartPointer pbCells = vtkSmartPointer::New(); vtkSmartPointer pbLinVelVec = vtkSmartPointer::New(); pbLinVelVec->SetNumberOfComponents(3); pbLinVelVec->SetName("linVelVec"); //Linear velocity in Vector3 form vtkSmartPointer pbLinVelLen = vtkSmartPointer::New(); pbLinVelLen->SetNumberOfComponents(1); pbLinVelLen->SetName("linVelLen"); //Length (magnitude) of linear velocity vtkSmartPointer pbAngVelVec = vtkSmartPointer::New(); pbAngVelVec->SetNumberOfComponents(3); pbAngVelVec->SetName("angVelVec"); //Angular velocity in Vector3 form vtkSmartPointer pbAngVelLen = vtkSmartPointer::New(); pbAngVelLen->SetNumberOfComponents(1); pbAngVelLen->SetName("angVelLen"); //Length (magnitude) of angular velocity // velocity #################################################### // bodyId ############################################################## //#if 0 vtkSmartPointer pbPosID = vtkSmartPointer::New(); vtkSmartPointer pbIdCells = vtkSmartPointer::New(); vtkSmartPointer blockId = vtkSmartPointer::New(); blockId->SetNumberOfComponents(1); blockId->SetName("id"); // bodyId ############################################################## //#endif int countID = 0; vtkSmartPointer textArray2[scene->bodies->size()]; vtkSmartPointer txtMapper[scene->bodies->size()]; vtkSmartPointer extrude[scene->bodies->size()]; vtkSmartPointer textActor[scene->bodies->size()]; FOREACH(const shared_ptr& b, *scene->bodies){ if (!b) continue; if (b->isClump() == true) continue; const PotentialBlock* pb=dynamic_cast(b->shape.get()); if(!pb) continue; if(REC_ID==true){ //#if 0 blockId->InsertNextValue(b->getId()); vtkIdType pid[1]; Vector3r pos(b->state->pos); pid[0] = pbPosID->InsertNextPoint(pos[0], pos[1], pos[2]); pbIdCells->InsertNextCell(1,pid); //#endif countID++; } //vtkSmartPointer function = ImpFuncPB::New(); function->a = pb->a; function->b = pb->b; function->c = pb->c; function->d = pb->d; function->R = pb->R; function->r = pb->r; function->k = pb->k; Eigen::Matrix3d directionCos = b->state->ori.conjugate().toRotationMatrix(); int count = 0; for (int i=0; i<3; i++){ for (int j=0; j<3; j++){ //function->rotationMatrix[count] = directionCos(j,i); function->rotationMatrix(i,j) = directionCos(j,i); count++; } } vtkSmartPointer sample = vtkSampleFunction::New(); sample->SetImplicitFunction(function); double value = 1.05*pb->R; double xmin = -pb->halfSize.x(); double xmax = pb->halfSize.x(); double ymin = -pb->halfSize.y(); double ymax=pb->halfSize.y(); double zmin=-pb->halfSize.z(); double zmax=pb->halfSize.z(); //double xmin = -value; double xmax = value; double ymin = -value; double ymax=value; double zmin=-value; double zmax=value; //double xmin = -std::max(pb->minAabb.x(),pb->maxAabb.x()); double xmax = -xmin; double ymin = -std::max(pb->minAabb.y(),pb->maxAabb.y()); double ymax=-ymin; double zmin=-std::max(pb->minAabb.z(),pb->maxAabb.z()); double zmax=-zmin; if(twoDimension==true){ ymax = 0.0; ymin = 0.0; } sample->SetModelBounds(xmin, xmax, ymin, ymax, zmin, zmax); //sample->SetModelBounds(pb->minAabb.x(), pb->maxAabb.x(), pb->minAabb.y(), pb->maxAabb.y(), pb->minAabb.z(), pb->maxAabb.z()); int sampleXno = sampleX; int sampleYno = sampleY; int sampleZno = sampleZ; if(fabs(xmax-xmin)/static_cast(sampleX) > maxDimension) { sampleXno = static_cast(fabs(xmax-xmin)/maxDimension); } if(fabs(ymax-ymin)/static_cast(sampleY) > maxDimension) { sampleYno = static_cast(fabs(ymax-ymin)/maxDimension); } if(fabs(zmax-zmin)/static_cast(sampleZ) > maxDimension) { sampleZno = static_cast(fabs(zmax-zmin)/maxDimension); } if(twoDimension==true){sampleYno=1;} sample->SetSampleDimensions(sampleXno,sampleYno,sampleZno); sample->ComputeNormalsOff(); //sample->Update(); vtkSmartPointer contours = vtkContourFilter::New(); contours->SetInputConnection(sample->GetOutputPort()); contours->SetNumberOfContours(1); contours->SetValue(0,0.0); vtkSmartPointer polydata = vtkSmartPointer::New(); contours->Update(); polydata->DeepCopy(contours->GetOutput()); //polydata->Update(); vtkSmartPointer pbColors = vtkSmartPointer::New(); pbColors->SetName("pbColors"); pbColors->SetNumberOfComponents(3); Vector3r color = pb->color; //Vector3r(0,100,0); //if (b->isDynamic() == false){ color = Vector3r(157,157,157); } color = Vector3r(157,157,157); unsigned char c[3]; //c = {color[0],color[1],color[2]}; c[0]=color[0]; c[1]=color[1]; c[2]=color[2]; int nbCells=polydata->GetNumberOfPoints(); for (int i=0;iInsertNextTupleValue(c); } polydata->GetPointData()->SetScalars(pbColors); //polydata->Update(); Vector3r centre (b->state->pos[0], b->state->pos[1], b->state->pos[2]); Quaternionr orientation= b->state->ori; orientation.normalize(); AngleAxisr aa(orientation); Vector3r axis = aa.axis(); /* axis.normalize(); */ double angle = aa.angle()/3.14159*180.0; double xAxis = axis[0]; double yAxis = axis[1]; double zAxis = axis[2]; vtkSmartPointer transformFilter = vtkSmartPointer::New(); transformFilter->SetInputData( polydata ); vtkSmartPointer transform = vtkSmartPointer::New(); transformFilter->SetTransform( transform ); transform->PostMultiply(); transform->Translate (centre[0], centre[1],centre[2]); //transform->RotateWXYZ(angle,xAxis, yAxis, zAxis); //transformFilter->Update(); appendFilter->AddInputConnection(transformFilter-> GetOutputPort()); // ################## velocity #################### if(REC_VELOCITY == true){ vtkIdType pid[1]; Vector3r pos(b->state->pos); pid[0] = pbPos->InsertNextPoint(pos[0], pos[1], pos[2]); pbCells->InsertNextCell(1,pid); const Vector3r& vel = b->state->vel; float v[3]; //v = { vel[0],vel[1],vel[2] }; v[0]=vel[0]; v[1]=vel[1]; v[2]=vel[2]; pbLinVelVec->InsertNextTupleValue(v); pbLinVelLen->InsertNextValue(vel.norm()); const Vector3r& angVel = b->state->angVel; float av[3]; //av = { angVel[0],angVel[1],angVel[2] }; av[0]=angVel[0]; av[1]=angVel[1]; av[2]=angVel[2]; pbAngVelVec->InsertNextTupleValue(av); pbAngVelLen->InsertNextValue(angVel.norm()); } // ################ velocity ########################### polydata->DeleteCells(); sample->Delete(); contours->Delete(); //function->Delete(); sample = NULL; contours = NULL; } if(REC_VELOCITY == true){ vtkSmartPointer pbUg = vtkSmartPointer::New(); pbUg->SetPoints(pbPos); pbUg->SetCells(VTK_VERTEX, pbCells); pbUg->GetPointData()->AddArray(pbLinVelVec); pbUg->GetPointData()->AddArray(pbAngVelVec); pbUg->GetPointData()->AddArray(pbLinVelLen); pbUg->GetPointData()->AddArray(pbAngVelLen); vtkSmartPointer writerA = vtkSmartPointer::New(); writerA->SetDataModeToAscii(); string fv=fileName+"vel."+std::to_string(scene->iter)+".vtu"; writerA->SetFileName(fv.c_str()); writerA->SetInputData(pbUg); writerA->Write(); //writerA->Delete(); //pbUg->Delete(); } //###################### bodyId ############################### if(REC_ID == true){ #if 0 vtkSmartPointer writerA = vtkXMLPolyDataWriter::New(); writerA->SetDataModeToAscii(); string fn=fileName+"-Id."+std::to_string(scene->iter)+".vtp"; writerA->SetFileName(fn.c_str()); writerA->SetInputConnection(appendFilterID->GetOutputPort());//(extrude->GetOutputPort()); writerA->Write(); writerA->Delete(); #endif //#if 0 vtkSmartPointer pbUg = vtkSmartPointer::New(); pbUg->SetPoints(pbPosID); pbUg->SetCells(VTK_VERTEX, pbIdCells); pbUg->GetPointData()->AddArray(blockId); vtkSmartPointer writerA = vtkSmartPointer::New(); writerA->SetDataModeToAscii(); string fv=fileName+"Id."+std::to_string(scene->iter)+".vtu"; writerA->SetFileName(fv.c_str()); writerA->SetInputData(pbUg); writerA->Write(); //writerA->Delete(); //pbUg->Delete(); //#endif } //#if 0 // ################## contact point #################### if(REC_INTERACTION == true){ int count = 0; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) { continue; } const KnKsPBPhys* phys = YADE_CAST(I->phys.get()); const ScGeom* geom = YADE_CAST(I->geom.get()); vtkIdType pid[1]; Vector3r pos(geom->contactPoint); pid[0] = pbContactPoint->InsertNextPoint(pos[0], pos[1], pos[2]); pbCellsContact->InsertNextCell(1,pid); //intrBodyPos->InsertNextPoint(geom->contactPoint[0],geom->contactPoint[1],geom->contactPoint[2]); // gives _signed_ scalar of normal force, following the convention used in the respective constitutive law float fn[3]={phys->normalForce[0],phys->normalForce[1], phys->normalForce[2]}; float fs[3]={phys->shearForce[0], phys->shearForce[1], phys->shearForce[2]}; pbNormalForce->InsertNextTupleValue(fn); pbShearForce->InsertNextTupleValue(fs); count++; } if(count>0){ vtkSmartPointer pbUgCP = vtkSmartPointer::New(); pbUgCP->SetPoints(pbContactPoint); pbUgCP->SetCells(VTK_VERTEX, pbCellsContact); pbUgCP->GetPointData()->AddArray(pbNormalForce); pbUgCP->GetPointData()->AddArray(pbShearForce); vtkSmartPointer writerB = vtkSmartPointer::New(); writerB->SetDataModeToAscii(); string fcontact=fileName+"contactPoint."+std::to_string(scene->iter)+".vtu"; writerB->SetFileName(fcontact.c_str()); writerB->SetInputData(pbUgCP); writerB->Write(); //writerB->Delete(); //pbUgCP->Delete(); } } //#endif // ################ contact point ########################### vtkSmartPointer writer = vtkXMLPolyDataWriter::New(); writer->SetDataModeToAscii(); string fn=fileName+"-pb."+std::to_string(scene->iter)+".vtp"; writer->SetFileName(fn.c_str()); writer->SetInputConnection(appendFilter->GetOutputPort()); writer->Write(); writer->Delete(); //intrBodyPos->Delete(); //intrForceN->Delete(); //intrAbsForceT->Delete(); //pbContactPoint->Delete(); //pbCellsContact->Delete(); //pbNormalForce->Delete(); //pbShearForce->Delete(); //pbCells->Delete(); //pbLinVelVec->Delete(); //pbLinVelLen->Delete(); //pbAngVelVec->Delete(); //pbAngVelLen->Delete(); } YADE_PLUGIN(/*(Gl1_PotentialBlock)*/(PotentialBlockVTKRecorder)(PotentialBlockVTKRecorderTunnel)); //YADE_REQUIRE_FEATURE(OPENGL) #endif // YADE_POTENTIAL_BLOCKS trunk-2017.01a/pkg/common/Gl1_PotentialBlock.hpp000077500000000000000000000131011304022710500213600ustar00rootroot00000000000000/* CWBoon 2016 */ #ifdef YADE_POTENTIAL_BLOCKS #pragma once #include #include #include //#include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include class ImpFuncPB : public vtkImplicitFunction { public: vtkTypeMacro(ImpFuncPB,vtkImplicitFunction); //void PrintSelf(ostream& os, vtkIndent indent); // Description // Create a new function static ImpFuncPB * New(void); vectora; vectorb; vectorc; vectord; double k; double r; double R; Eigen::Matrix3d rotationMatrix; bool clump; double clumpMemberCentreX; double clumpMemberCentreY; double clumpMemberCentreZ; // Description // Evaluate function double FunctionValue(double x[3]); double EvaluateFunction(double x[3]){ //return this->vtkImplicitFunction::EvaluateFunction(x); return FunctionValue(x); }; double EvaluateFunction(double x, double y, double z) { return this->vtkImplicitFunction::EvaluateFunction(x, y, z); }; // Description // Evaluate gradient for function void EvaluateGradient(double x[3], double n[3]){ }; // If you need to set parameters, add methods here protected: ImpFuncPB(); ~ImpFuncPB(); ImpFuncPB(const ImpFuncPB&) {} void operator=(const ImpFuncPB&) {} // Add parameters/members here if you need }; #if 0 class Gl1_PotentialBlock : public GlShapeFunctor { private : MarchingCube mc; Vector3r min,max; vector > > scalarField,weights; void generateScalarField(const shared_ptr& cm); void calcMinMax(const shared_ptr& cm); float oldIsoValue,oldIsoSec,oldIsoThick; Vector3r isoStep; public : struct Leaf{ Vector3r centre; Leaf(Vector3r pos){centre = pos;} Leaf(){centre = Vector3r(0,0,0);} }; struct scalarF{ vector > > scalarField2; vector triangles; vector normals; int nbTriangles; }; virtual void go(const shared_ptr&, const shared_ptr&,bool,const GLViewInfo&); double evaluateF(const shared_ptr& cm, double x, double y, double z); static vector SF ; void clearMemory(); RENDERS(PotentialBlock); //YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_PotentialBlock,GlShapeFunctor,"Renders :yref:`Sphere` object", //(( vector, SF ," ")) //); YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_PotentialBlock,GlShapeFunctor,"Renders :yref:`Sphere` object", ((int,sizeX,80,,"Number of divisions in the x direction for triangulation")) ((int,sizeY,80,,"Number of divisions in the x direction for triangulation")) ((int,sizeZ,80,,"Number of divisions in the y direction for triangulation")) ((bool,store,false,,"Number of divisions in the z direction for triangulation")) ((bool,initialized,false,,"Number of divisions in the z direction for triangulation")) ); }; REGISTER_SERIALIZABLE(Gl1_PotentialBlock); #endif class PotentialBlockVTKRecorder: public PeriodicEngine{ public: vtkSmartPointer function; virtual void action(void); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(PotentialBlockVTKRecorder,PeriodicEngine,"Engine recording potential blocks as surfaces into files with given periodicity.", ((string,fileName,,,"File prefix to save to")) ((int,sampleX,30,,"size of contact point")) ((int,sampleY,30,,"size of contact point")) ((int,sampleZ,30,,"size of contact point")) ((double,maxDimension,30,,"size of contact point")) ((bool,twoDimension,false,,"size of contact point")) ((bool,REC_INTERACTION,false,,"contact point and forces")) ((bool,REC_COLORS,false,,"colors")) ((bool,REC_VELOCITY,false,,"velocity")) ((bool,REC_ID,true,,"id")) , function = ImpFuncPB::New(); , ); }; REGISTER_SERIALIZABLE(PotentialBlockVTKRecorder); class PotentialBlockVTKRecorderTunnel: public PeriodicEngine{ public: vtkSmartPointer function; virtual void action(void); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(PotentialBlockVTKRecorderTunnel,PeriodicEngine,"Engine recording potential blocks as surfaces into files with given periodicity.", ((string,fileName,,,"File prefix to save to")) ((int,sampleX,30,,"size of contact point")) ((int,sampleY,30,,"size of contact point")) ((int,sampleZ,30,,"size of contact point")) ((double,maxDimension,30,,"size of contact point")) ((bool,twoDimension,false,,"size of contact point")) ((bool,REC_INTERACTION,false,,"contact point and forces")) ((bool,REC_COLORS,false,,"colors")) ((bool,REC_VELOCITY,false,,"velocity")) ((bool,REC_ID,true,,"id")) , function = ImpFuncPB::New(); , ); }; REGISTER_SERIALIZABLE(PotentialBlockVTKRecorderTunnel); #endif // YADE_POTENTIAL_BLOCKS trunk-2017.01a/pkg/common/Gl1_PotentialParticle.cpp000066400000000000000000000471321304022710500220740ustar00rootroot00000000000000/*CWBoon 2015 */ #ifdef YADE_POTENTIAL_PARTICLES #include "Gl1_PotentialParticle.hpp" //#include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include //#include #include #include #include #ifdef YADE_OPENGL void Gl1_PotentialParticle::calcMinMax(const PotentialParticle& pp) { int planeNo = pp.d.size(); Real maxD = pp.d[0]; for (int i=0; i maxD) { maxD = pp.d[i]; } } min = -aabbEnlargeFactor*pp.minAabb; max = aabbEnlargeFactor*pp.maxAabb; Real dx = (max[0]-min[0])/((Real)(sizeX-1)); Real dy = (max[1]-min[1])/((Real)(sizeY-1)); Real dz = (max[2]-min[2])/((Real)(sizeZ-1)); isoStep=Vector3r(dx,dy,dz); } void Gl1_PotentialParticle::generateScalarField(const PotentialParticle& pp) { for(int i=0; i Gl1_PotentialParticle::SF; int Gl1_PotentialParticle::sizeX, Gl1_PotentialParticle::sizeY, Gl1_PotentialParticle::sizeZ; Real Gl1_PotentialParticle::aabbEnlargeFactor; bool Gl1_PotentialParticle::store; bool Gl1_PotentialParticle::initialized; void Gl1_PotentialParticle::go( const shared_ptr& cm, const shared_ptr& state ,bool wire2, const GLViewInfo&) { PotentialParticle* pp = static_cast(cm.get()); int shapeId = pp->id; if(store == false) { if(SF.size()>0) { SF.clear(); initialized = false; } } if(initialized == false ) { FOREACH(const shared_ptr& b, *scene->bodies) { if (!b) continue; PotentialParticle* cmbody = dynamic_cast(b->shape.get()); if (!cmbody) continue; calcMinMax(*cmbody); mc.init(sizeX,sizeY,sizeZ,min,max); mc.resizeScalarField(scalarField,sizeX,sizeY,sizeZ); SF.push_back(scalarF()); generateScalarField(*cmbody); mc.computeTriangulation(scalarField,0.0); SF[b->id].triangles = mc.getTriangles(); SF[b->id].normals = mc.getNormals(); SF[b->id].nbTriangles = mc.getNbTriangles(); for(unsigned int i=0; icolor[0],cm->color[1],cm->color[2])); glColor3v(cm->color); const vector& triangles = SF[shapeId].triangles; //mc.getTriangles(); int nbTriangles = SF[shapeId].nbTriangles; // //mc.getNbTriangles(); const vector& normals = SF[shapeId].normals; //mc.getNormals(); glDisable(GL_CULL_FACE); glEnable(GL_LIGHTING); // 2D glEnable(GL_NORMALIZE); glBegin(GL_TRIANGLES); for(int i=0; i<3*nbTriangles; ++i) { glNormal3v(normals[i]); glVertex3v(triangles[i]); glNormal3v(normals[++i]); glVertex3v(triangles[i]); glNormal3v(normals[++i]); glVertex3v(triangles[i]); } glEnd(); return; } Real Gl1_PotentialParticle::evaluateF(const PotentialParticle& pp, Real x, Real y, Real z) { Real k = pp.k; Real r = pp.r; Real R = pp.R; int planeNo = pp.a.size(); vectora; vectorb; vectorc; vectord; vectorp; Real pSum3 = 0.0; for (int i=0; ip; Real pSum2 = 0.0; if (!clump) { Eigen::Vector3d xori(x[0],x[1],x[2]); Eigen::Vector3d xlocal = rotationMatrix*xori; xlocal[0] = rotationMatrix(0,0)*x[0] + rotationMatrix(0,1)*x[1] + rotationMatrix(0,2)*x[2]; xlocal[1] = rotationMatrix(1,0)*x[0] + rotationMatrix(1,1)*x[1] + rotationMatrix(1,2)*x[2]; xlocal[2] = rotationMatrix(2,0)*x[0] + rotationMatrix(2,1)*x[1] + rotationMatrix(2,2)*x[2]; //std::cout<<"rotationMatrix: "< pbPos = vtkSmartPointer::New(); vtkSmartPointer appendFilter = vtkSmartPointer::New(); vtkSmartPointer appendFilterID = vtkSmartPointer::New(); //vtkSmartPointer transformFilter = vtkSmartPointer::New(); //vtkSmartPointer transform = vtkSmartPointer::New(); // interactions ############################################### vtkSmartPointer intrBodyPos = vtkSmartPointer::New(); vtkSmartPointer intrCells = vtkSmartPointer::New(); vtkSmartPointer intrForceN = vtkSmartPointer::New(); intrForceN->SetNumberOfComponents(3); intrForceN->SetName("forceN"); vtkSmartPointer intrAbsForceT = vtkSmartPointer::New(); intrAbsForceT->SetNumberOfComponents(1); intrAbsForceT->SetName("absForceT"); // interactions ############################################### // interaction contact point ############################################### vtkSmartPointer pbContactPoint = vtkSmartPointer::New(); vtkSmartPointer pbCellsContact = vtkSmartPointer::New(); vtkSmartPointer pbNormalForce = vtkSmartPointer::New(); pbNormalForce->SetNumberOfComponents(3); pbNormalForce->SetName("normalForce"); //Linear velocity in Vector3 form vtkSmartPointer pbShearForce = vtkSmartPointer::New(); pbShearForce->SetNumberOfComponents(3); pbShearForce->SetName("shearForce"); //Angular velocity in Vector3 form // interactions contact point############################################### // velocity ################################################### vtkSmartPointer pbCells = vtkSmartPointer::New(); vtkSmartPointer pbLinVelVec = vtkSmartPointer::New(); pbLinVelVec->SetNumberOfComponents(3); pbLinVelVec->SetName("linVelVec"); //Linear velocity in Vector3 form vtkSmartPointer pbLinVelLen = vtkSmartPointer::New(); pbLinVelLen->SetNumberOfComponents(1); pbLinVelLen->SetName("linVelLen"); //Length (magnitude) of linear velocity vtkSmartPointer pbAngVelVec = vtkSmartPointer::New(); pbAngVelVec->SetNumberOfComponents(3); pbAngVelVec->SetName("angVelVec"); //Angular velocity in Vector3 form vtkSmartPointer pbAngVelLen = vtkSmartPointer::New(); pbAngVelLen->SetNumberOfComponents(1); pbAngVelLen->SetName("angVelLen"); //Length (magnitude) of angular velocity // velocity #################################################### // bodyId ############################################################## vtkSmartPointer pbPosID = vtkSmartPointer::New(); vtkSmartPointer pbIdCells = vtkSmartPointer::New(); vtkSmartPointer blockId = vtkSmartPointer::New(); blockId->SetNumberOfComponents(1); blockId->SetName("id"); // bodyId ############################################################## int countID = 0; vtkSmartPointer textArray2[scene->bodies->size()]; vtkSmartPointer txtMapper[scene->bodies->size()]; vtkSmartPointer extrude[scene->bodies->size()]; vtkSmartPointer textActor[scene->bodies->size()]; FOREACH(const shared_ptr& b, *scene->bodies) { if (!b) continue; if (b->isClump() == true) continue; const PotentialParticle* pb=dynamic_cast(b->shape.get()); if(!pb) continue; if(REC_ID==true) { blockId->InsertNextValue(b->getId()); vtkIdType pid[1]; Vector3r pos(b->state->pos); pid[0] = pbPosID->InsertNextPoint(pos[0], pos[1], pos[2]); pbIdCells->InsertNextCell(1,pid); countID++; } //vtkSmartPointer function = ImpFunc::New(); function->a = pb->a; function->b = pb->b; function->c = pb->c; function->d = pb->d; function->R = pb->R; function->r = pb->r; function->k = pb->k; Eigen::Matrix3d directionCos = b->state->ori.conjugate().toRotationMatrix(); int count = 0; for (int i=0; i<3; i++) { for (int j=0; j<3; j++) { //function->rotationMatrix[count] = directionCos(j,i); function->rotationMatrix(i,j) = directionCos(j,i); count++; } } vtkSmartPointer sample = vtkSampleFunction::New(); sample->SetImplicitFunction(function); Real xmin = -std::max(pb->minAabb.x(),pb->maxAabb.x()); Real xmax = -xmin; Real ymin = -std::max(pb->minAabb.y(),pb->maxAabb.y()); Real ymax=-ymin; Real zmin=-std::max(pb->minAabb.z(),pb->maxAabb.z()); Real zmax=-zmin; if(twoDimension==true) { ymax = 0.0; ymin = 0.0; } sample->SetModelBounds(xmin, xmax, ymin, ymax, zmin, zmax); //sample->SetModelBounds(pb->minAabb.x(), pb->maxAabb.x(), pb->minAabb.y(), pb->maxAabb.y(), pb->minAabb.z(), pb->maxAabb.z()); int sampleXno = sampleX; int sampleYno = sampleY; int sampleZno = sampleZ; if(fabs(xmax-xmin)/static_cast(sampleX) > maxDimension) { sampleXno = static_cast(fabs(xmax-xmin)/maxDimension); } if(fabs(ymax-ymin)/static_cast(sampleY) > maxDimension) { sampleYno = static_cast(fabs(ymax-ymin)/maxDimension); } if(fabs(zmax-zmin)/static_cast(sampleZ) > maxDimension) { sampleZno = static_cast(fabs(zmax-zmin)/maxDimension); } if(twoDimension==true) { sampleYno=1; } sample->SetSampleDimensions(sampleXno,sampleYno,sampleZno); sample->ComputeNormalsOff(); //sample->Update(); vtkSmartPointer contours = vtkContourFilter::New(); #ifdef YADE_VTK6 contours->SetInputData(sample->GetOutput()); #else contours->SetInput(sample->GetOutput()); #endif contours->SetNumberOfContours(1); contours->SetValue(0,0.0); vtkSmartPointer polydata = vtkSmartPointer::New(); contours->Update(); polydata->DeepCopy(contours->GetOutput()); //polydata->Update(); vtkSmartPointer pbColors = vtkSmartPointer::New(); pbColors->SetName("pbColors"); pbColors->SetNumberOfComponents(3); Vector3r color = pb->color; //Vector3r(0,100,0); if (b->isDynamic() == false) { color = Vector3r(157,157,157); } unsigned char c[3]; //c = {color[0],color[1],color[2]}; c[0]=color[0]; c[1]=color[1]; c[2]=color[2]; int nbCells=polydata->GetNumberOfPoints(); for (int i=0; iInsertNextTupleValue(c); } polydata->GetPointData()->SetScalars(pbColors); //polydata->Update(); Vector3r centre (b->state->pos[0], b->state->pos[1], b->state->pos[2]); Quaternionr orientation= b->state->ori; orientation.normalize(); AngleAxisr aa(orientation); //Vector3r axis = aa.axis(); vtkSmartPointer transformFilter = vtkSmartPointer::New(); #ifdef YADE_VTK6 transformFilter->SetInputData( polydata ); #else transformFilter->SetInput( polydata ); #endif vtkSmartPointer transform = vtkSmartPointer::New(); transformFilter->SetTransform( transform ); transform->PostMultiply(); transform->Translate (centre[0], centre[1],centre[2]); //transform->RotateWXYZ(angle,xAxis, yAxis, zAxis); //transformFilter->Update(); appendFilter->AddInputConnection(transformFilter-> GetOutputPort()); // ################## velocity #################### if(REC_VELOCITY == true) { vtkIdType pid[1]; Vector3r pos(b->state->pos); pid[0] = pbPos->InsertNextPoint(pos[0], pos[1], pos[2]); pbCells->InsertNextCell(1,pid); const Vector3r& vel = b->state->vel; float v[3]; //v = { vel[0],vel[1],vel[2] }; v[0]=vel[0]; v[1]=vel[1]; v[2]=vel[2]; pbLinVelVec->InsertNextTupleValue(v); pbLinVelLen->InsertNextValue(vel.norm()); const Vector3r& angVel = b->state->angVel; float av[3]; //av = { angVel[0],angVel[1],angVel[2] }; av[0]=angVel[0]; av[1]=angVel[1]; av[2]=angVel[2]; pbAngVelVec->InsertNextTupleValue(av); pbAngVelLen->InsertNextValue(angVel.norm()); } // ################ velocity ########################### polydata->DeleteCells(); sample->Delete(); contours->Delete(); //function->Delete(); sample = NULL; contours = NULL; } if(REC_VELOCITY == true) { vtkSmartPointer pbUg = vtkSmartPointer::New(); pbUg->SetPoints(pbPos); pbUg->SetCells(VTK_VERTEX, pbCells); pbUg->GetPointData()->AddArray(pbLinVelVec); pbUg->GetPointData()->AddArray(pbAngVelVec); pbUg->GetPointData()->AddArray(pbLinVelLen); pbUg->GetPointData()->AddArray(pbAngVelLen); vtkSmartPointer writerA = vtkSmartPointer::New(); writerA->SetDataModeToAscii(); string fv=fileName+"vel."+std::to_string(scene->iter)+".vtu"; writerA->SetFileName(fv.c_str()); #ifdef YADE_VTK6 writerA->SetInputData(pbUg); #else writerA->SetInput(pbUg); #endif writerA->Write(); //writerA->Delete(); //pbUg->Delete(); } //###################### bodyId ############################### if(REC_ID == true) { vtkSmartPointer pbUg = vtkSmartPointer::New(); pbUg->SetPoints(pbPosID); pbUg->SetCells(VTK_VERTEX, pbIdCells); pbUg->GetPointData()->AddArray(blockId); vtkSmartPointer writerA = vtkSmartPointer::New(); writerA->SetDataModeToAscii(); string fv=fileName+"Id."+std::to_string(scene->iter)+".vtu"; writerA->SetFileName(fv.c_str()); #ifdef YADE_VTK6 writerA->SetInputData(pbUg); #else writerA->SetInput(pbUg); #endif writerA->Write(); //writerA->Delete(); //pbUg->Delete(); } // ################## contact point #################### if(REC_INTERACTION == true) { int count = 0; FOREACH(const shared_ptr& I, *scene->interactions) { if(!I->isReal()) { continue; } const KnKsPhys* phys = YADE_CAST(I->phys.get()); const ScGeom* geom = YADE_CAST(I->geom.get()); vtkIdType pid[1]; Vector3r pos(geom->contactPoint); pid[0] = pbContactPoint->InsertNextPoint(pos[0], pos[1], pos[2]); pbCellsContact->InsertNextCell(1,pid); //intrBodyPos->InsertNextPoint(geom->contactPoint[0],geom->contactPoint[1],geom->contactPoint[2]); // gives _signed_ scalar of normal force, following the convention used in the respective constitutive law float fn[3]= {(float)phys->normalForce[0], (float)phys->normalForce[1], (float)phys->normalForce[2]}; float fs[3]= {(float)phys->shearForce[0], (float)phys->shearForce[1], (float)phys->shearForce[2]}; pbNormalForce->InsertNextTupleValue(fn); pbShearForce->InsertNextTupleValue(fs); count++; } if(count>0) { vtkSmartPointer pbUgCP = vtkSmartPointer::New(); pbUgCP->SetPoints(pbContactPoint); pbUgCP->SetCells(VTK_VERTEX, pbCellsContact); pbUgCP->GetPointData()->AddArray(pbNormalForce); pbUgCP->GetPointData()->AddArray(pbShearForce); vtkSmartPointer writerB = vtkSmartPointer::New(); writerB->SetDataModeToAscii(); string fcontact=fileName+"contactPoint."+std::to_string(scene->iter)+".vtu"; writerB->SetFileName(fcontact.c_str()); #ifdef YADE_VTK6 writerB->SetInputData(pbUgCP); #else writerB->SetInput(pbUgCP); #endif writerB->Write(); //writerB->Delete(); //pbUgCP->Delete(); } } // ################ contact point ########################### vtkSmartPointer writer = vtkXMLPolyDataWriter::New(); writer->SetDataModeToAscii(); string fn=fileName+"-pb."+std::to_string(scene->iter)+".vtp"; writer->SetFileName(fn.c_str()); writer->SetInputConnection(appendFilter->GetOutputPort()); writer->Write(); writer->Delete(); //intrBodyPos->Delete(); //intrForceN->Delete(); //intrAbsForceT->Delete(); //pbContactPoint->Delete(); //pbCellsContact->Delete(); //pbNormalForce->Delete(); //pbShearForce->Delete(); //pbCells->Delete(); //pbLinVelVec->Delete(); //pbLinVelLen->Delete(); //pbAngVelVec->Delete(); //pbAngVelLen->Delete(); } YADE_PLUGIN((Gl1_PotentialParticle)(PotentialParticleVTKRecorder)); //YADE_REQUIRE_FEATURE(OPENGL) #endif // YADE_POTENTIAL_PARTICLES trunk-2017.01a/pkg/common/Gl1_PotentialParticle.hpp000066400000000000000000000113701304022710500220740ustar00rootroot00000000000000/*CWBoon 2015 */ #pragma once #ifdef YADE_POTENTIAL_PARTICLES #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include class ImpFunc : public vtkImplicitFunction { public: vtkTypeMacro(ImpFunc,vtkImplicitFunction); //void PrintSelf(ostream& os, vtkIndent indent); // Description // Create a new function static ImpFunc * New(void); vectora; vectorb; vectorc; vectord; Real k; Real r; Real R; Eigen::Matrix3d rotationMatrix; bool clump; Real clumpMemberCentreX; Real clumpMemberCentreY; Real clumpMemberCentreZ; // Description // Evaluate function Real FunctionValue(Real x[3]); Real EvaluateFunction(Real x[3]) { //return this->vtkImplicitFunction::EvaluateFunction(x); return FunctionValue(x); }; Real EvaluateFunction(Real x, Real y, Real z) { return this->vtkImplicitFunction::EvaluateFunction(x, y, z); }; // Description // Evaluate gradient for function void EvaluateGradient(Real x[3], Real n[3]) { }; // If you need to set parameters, add methods here protected: ImpFunc(); ~ImpFunc(); ImpFunc(const ImpFunc&) {} void operator=(const ImpFunc&) {} // Add parameters/members here if you need }; #ifdef YADE_OPENGL class Gl1_PotentialParticle : public GlShapeFunctor { private : MarchingCube mc; Vector3r min,max; vector > > scalarField,weights; void generateScalarField(const PotentialParticle& pp); void calcMinMax(const PotentialParticle& pp); Real oldIsoValue,oldIsoSec,oldIsoThick; Vector3r isoStep; struct Leaf { Vector3r centre; Leaf(Vector3r pos) { centre = pos; } Leaf() { centre = Vector3r(0,0,0); } }; struct scalarF { vector > > scalarField2; vector triangles; vector normals; int nbTriangles; }; Real evaluateF(const PotentialParticle& pp, Real x, Real y, Real z); static vector SF ; public : virtual void go(const shared_ptr&, const shared_ptr&,bool,const GLViewInfo&); YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_PotentialParticle,GlShapeFunctor,"Renders :yref:`PotentialParticle` object", ((int,sizeX,10,,"Number of divisions in the x direction for triangulation")) ((int,sizeY,10,,"Number of divisions in the y direction for triangulation")) ((int,sizeZ,10,,"Number of divisions in the z direction for triangulation")) ((bool,store,false,,"store computed triangulation or not")) ((bool,initialized,false,,"if triangulation is initialized")) ((Real,aabbEnlargeFactor,1.3,,"some factor for displaying algorithm, try different value if you have problems with displaying")) ); RENDERS(PotentialParticle); }; REGISTER_SERIALIZABLE(Gl1_PotentialParticle); #endif // YADE_OPENGL class PotentialParticleVTKRecorder: public PeriodicEngine { public: vtkSmartPointer function; virtual void action(void); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(PotentialParticleVTKRecorder,PeriodicEngine,"Engine recording potential blocks as surfaces into files with given periodicity.", ((string,fileName,,,"File prefix to save to")) ((int,sampleX,30,,"Number of divisions in the x direction for triangulation")) ((int,sampleY,30,,"Number of divisions in the y direction for triangulation")) ((int,sampleZ,30,,"Number of divisions in the z direction for triangulation")) ((Real,maxDimension,30,,"max dimension")) ((bool,twoDimension,false,,"2D or not")) ((bool,REC_INTERACTION,false,,"contact point and forces")) ((bool,REC_COLORS,false,,"colors")) ((bool,REC_VELOCITY,false,,"velocity")) ((bool,REC_ID,true,,"id")) , function = ImpFunc::New(); , ); }; REGISTER_SERIALIZABLE(PotentialParticleVTKRecorder); #endif // YADE_POTENTIAL_PARTICLES trunk-2017.01a/pkg/common/Gl1_Primitives.cpp000066400000000000000000000217441304022710500206050ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * * * Copyright (C) 2008 by Sergei Dorofeenko * * sega@users.berlios.de * * * * © 2008 Václav Šmilauer * * * * © 2008 Bruno Chareyre * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef YADE_OPENGL #include "Gl1_Primitives.hpp" #include #include YADE_PLUGIN((Gl1_Aabb)(Gl1_Box)(Gl1_Facet)); YADE_PLUGIN((GlBoundFunctor)(GlShapeFunctor)(GlIGeomFunctor)(GlIPhysFunctor)(GlStateFunctor) (GlBoundDispatcher)(GlShapeDispatcher)(GlIGeomDispatcher)(GlIPhysDispatcher) (GlStateDispatcher)); void Gl1_Aabb::go(const shared_ptr& bv, Scene* scene){ Aabb* aabb = static_cast(bv.get()); glColor3v(bv->color); if(!scene->isPeriodic){ glTranslatev(Vector3r(.5*(aabb->min+aabb->max))); glScalev(Vector3r(aabb->max-aabb->min)); } else { glTranslatev(Vector3r(scene->cell->shearPt(scene->cell->wrapPt(.5*(aabb->min+aabb->max))))); glMultMatrixd(scene->cell->getGlShearTrsfMatrix()); glScalev(Vector3r(aabb->max-aabb->min)); } glutWireCube(1); } void Gl1_Box::go(const shared_ptr& cg, const shared_ptr&,bool wire,const GLViewInfo&) { glColor3v(cg->color); Vector3r &extents = (static_cast(cg.get()))->extents; glScalef(2*extents[0],2*extents[1],2*extents[2]); if (wire) glutWireCube(1); else glutSolidCube(1); } bool Gl1_Facet::normals=false; void Gl1_Facet::go(const shared_ptr& cm, const shared_ptr& ,bool wire,const GLViewInfo&) { Facet* facet = static_cast(cm.get()); const vector& vertices = facet->vertices; const Vector3r* ne = facet->ne; const Real& icr = facet->icr; if(cm->wire || wire){ // facet glBegin(GL_LINE_LOOP); glColor3v(normals ? Vector3r(1,0,0): cm->color); glVertex3v(vertices[0]); glVertex3v(vertices[1]); glVertex3v(vertices[2]); glEnd(); if(!normals) return; // facet's normal glBegin(GL_LINES); glColor3(0.0,0.0,1.0); glVertex3(0.0,0.0,0.0); glVertex3v(facet->normal); glEnd(); // normal of edges glColor3(0.0,0.0,1.0); glBegin(GL_LINES); glVertex3(0.0,0.0,0.0); glVertex3v(Vector3r(icr*ne[0])); glVertex3(0.0,0.0,0.0); glVertex3v(Vector3r(icr*ne[1])); glVertex3(0.0,0.0,0.0); glVertex3v(Vector3r(icr*ne[2])); glEnd(); } else { glDisable(GL_CULL_FACE); Vector3r normal=(facet->vertices[1]-facet->vertices[0]).cross(facet->vertices[2]-facet->vertices[1]); normal.normalize(); glColor3v(cm->color); glBegin(GL_TRIANGLES); glNormal3v(normal); // this makes every triangle different WRT the light direction; important! glVertex3v(facet->vertices[0]); glVertex3v(facet->vertices[1]); glVertex3v(facet->vertices[2]); glEnd(); } } // Spheres========================================== bool Gl1_Sphere::wire; bool Gl1_Sphere::stripes; int Gl1_Sphere::glutSlices; int Gl1_Sphere::glutStacks; Real Gl1_Sphere::quality; bool Gl1_Sphere::localSpecView; bool Gl1_Sphere::circleView; Real Gl1_Sphere::circleRelThickness; vector Gl1_Sphere::vertices, Gl1_Sphere::faces; int Gl1_Sphere::glStripedSphereList=-1; int Gl1_Sphere::glGlutSphereList=-1; Real Gl1_Sphere::prevQuality=0; string Gl1_Sphere::prevDisplayMode=""; char Gl1_Sphere::circleAllowedRotationAxis; char Gl1_Sphere::prevCircleAllowedRotationAxis='z'; void Gl1_Sphere::go(const shared_ptr& cm, const shared_ptr& ,bool wire2, const GLViewInfo&) { glClearDepth(1.0f); glEnable(GL_NORMALIZE); Real r=(static_cast(cm.get()))->radius; glColor3v(cm->color); if (circleView) { bool somethingChanged = (std::abs(quality-prevQuality)>0.001 || prevDisplayMode!="torus" || prevCircleAllowedRotationAxis!=circleAllowedRotationAxis); if (somethingChanged) { prevCircleAllowedRotationAxis=circleAllowedRotationAxis; prevDisplayMode="torus"; glDeleteLists(glGlutSphereList,1); glGlutSphereList = glGenLists(1); glNewList(glGlutSphereList,GL_COMPILE); glEnable(GL_LIGHTING); glShadeModel(GL_SMOOTH); switch (tolower(circleAllowedRotationAxis)) { //rotate the torus according to the axis from which we want to look at it. case 'z':break; //Initial torus axis is z, nothing to do case 'x':glRotatef(90,0,1,0);break; case 'y':glRotatef(90,1,0,0);break; default:cerr<<"Error in Gl1_Sphere::go, circleAllowedRotationAxis should be \"x\", \"y\" or \"z\"."<0.001 || glIsList(glStripedSphereList)!=GL_TRUE || prevDisplayMode!="sphere"); if (somethingChanged) {initStripedGlList(); initGlutGlList(); prevQuality=quality;prevDisplayMode="sphere";} glScalef(r,r,r); if(stripes) glCallList(glStripedSphereList); else glCallList(glGlutSphereList); } return; } YADE_PLUGIN((Gl1_Sphere)); void Gl1_Sphere::subdivideTriangle(Vector3r& v1,Vector3r& v2,Vector3r& v3, int depth){ Vector3r v; //Change color only at the appropriate level, i.e. 8 times in total, since we draw 8 mono-color sectors one after another if (depth==int(quality) || quality<=0){ v = (v1+v2+v3)/3.0; GLfloat matEmit[4]; if (v[1]*v[0]*v[2]>0){ matEmit[0] = 0.3; matEmit[1] = 0.3; matEmit[2] = 0.3; matEmit[3] = 1.f; }else{ matEmit[0] = 0.15; matEmit[1] = 0.15; matEmit[2] = 0.15; matEmit[3] = 0.2; } glMaterialfv(GL_FRONT, GL_EMISSION, matEmit); } if (depth==1){//Then display 4 triangles Vector3r v12 = v1+v2; Vector3r v23 = v2+v3; Vector3r v31 = v3+v1; v12.normalize(); v23.normalize(); v31.normalize(); //Use TRIANGLE_STRIP for faster display of adjacent facets glBegin(GL_TRIANGLE_STRIP); glNormal3v(v1); glVertex3v(v1); glNormal3v(v31); glVertex3v(v31); glNormal3v(v12); glVertex3v(v12); glNormal3v(v23); glVertex3v(v23); glNormal3v(v2); glVertex3v(v2); glEnd(); //terminate with this triangle left behind glBegin(GL_TRIANGLES); glNormal3v(v3); glVertex3v(v3); glNormal3v(v23); glVertex3v(v23); glNormal3v(v31); glVertex3v(v31); glEnd(); return; } Vector3r v12 = v1+v2; Vector3r v23 = v2+v3; Vector3r v31 = v3+v1; v12.normalize(); v23.normalize(); v31.normalize(); subdivideTriangle(v1,v12,v31,depth-1); subdivideTriangle(v2,v23,v12,depth-1); subdivideTriangle(v3,v31,v23,depth-1); subdivideTriangle(v12,v23,v31,depth-1); } void Gl1_Sphere::initStripedGlList() { if (!vertices.size()){//Fill vectors with vertices and facets //Define 6 points for +/- coordinates vertices.push_back(Vector3r(-1,0,0));//0 vertices.push_back(Vector3r(1,0,0));//1 vertices.push_back(Vector3r(0,-1,0));//2 vertices.push_back(Vector3r(0,1,0));//3 vertices.push_back(Vector3r(0,0,-1));//4 vertices.push_back(Vector3r(0,0,1));//5 //Define 8 sectors of the sphere faces.push_back(Vector3r(3,4,1)); faces.push_back(Vector3r(3,0,4)); faces.push_back(Vector3r(3,5,0)); faces.push_back(Vector3r(3,1,5)); faces.push_back(Vector3r(2,1,4)); faces.push_back(Vector3r(2,4,0)); faces.push_back(Vector3r(2,0,5)); faces.push_back(Vector3r(2,5,1)); } //Generate the list. Only once for each qtView, or more if quality is modified. glDeleteLists(glStripedSphereList,1); glStripedSphereList = glGenLists(1); glNewList(glStripedSphereList,GL_COMPILE); glEnable(GL_LIGHTING); glShadeModel(GL_SMOOTH); // render the sphere now for (int i=0;i<8;i++) subdivideTriangle(vertices[(unsigned int)faces[i][0]],vertices[(unsigned int)faces[i][1]],vertices[(unsigned int)faces[i][2]],1+ (int) quality); glEndList(); } void Gl1_Sphere::initGlutGlList(){ //Generate the "no-stripes" display list, each time quality is modified glDeleteLists(glGlutSphereList,1); glGlutSphereList = glGenLists(1); glNewList(glGlutSphereList,GL_COMPILE); glEnable(GL_LIGHTING); glShadeModel(GL_SMOOTH); glutSolidSphere(1.0,max(quality*glutSlices,(Real)2.),max(quality*glutStacks,(Real)3.)); glEndList(); } #endif /* YADE_OPENGL */ trunk-2017.01a/pkg/common/Gl1_Primitives.hpp000066400000000000000000000122421304022710500206030ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * * * Copyright (C) 2008 by Sergei Dorofeenko * * sega@users.berlios.de * * * * © 2008 Václav Šmilauer * * * * © 2008 Bruno Chareyre * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include #include class Gl1_Aabb: public GlBoundFunctor{ public: virtual void go(const shared_ptr&, Scene*); RENDERS(Aabb); YADE_CLASS_BASE_DOC(Gl1_Aabb,GlBoundFunctor,"Render Axis-aligned bounding box (:yref:`Aabb`)."); }; REGISTER_SERIALIZABLE(Gl1_Aabb); class Gl1_Box : public GlShapeFunctor{ public : virtual void go(const shared_ptr&, const shared_ptr&,bool,const GLViewInfo&); RENDERS(Box); YADE_CLASS_BASE_DOC(Gl1_Box,GlShapeFunctor,"Renders :yref:`Box` object"); }; REGISTER_SERIALIZABLE(Gl1_Box); class Gl1_Facet : public GlShapeFunctor { public: virtual void go(const shared_ptr&, const shared_ptr&,bool,const GLViewInfo&); RENDERS(Facet); YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_Facet,GlShapeFunctor,"Renders :yref:`Facet` object", ((bool,normals,false,,"In wire mode, render normals of facets and edges; facet's :yref:`colors` are disregarded in that case.")) ); }; REGISTER_SERIALIZABLE(Gl1_Facet); class Gl1_Sphere : public GlShapeFunctor{ private: // for stripes static vector vertices, faces; static int glStripedSphereList; static int glGlutSphereList; void subdivideTriangle(Vector3r& v1,Vector3r& v2,Vector3r& v3, int depth); //Generate GlList for GLUT sphere void initGlutGlList(); //Generate GlList for sliced spheres void initStripedGlList(); //for regenerating glutSphere or glutTorus list if needed static Real prevQuality; //for regenerating glutSphere or glutTorus list if needed static string prevDisplayMode; //for regenerating glutTorus list if needed static char prevCircleAllowedRotationAxis; public: virtual void go(const shared_ptr&, const shared_ptr&,bool,const GLViewInfo&); YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_Sphere,GlShapeFunctor,"Renders :yref:`Sphere` object", ((Real,quality,1.0,,"Change discretization level of spheres. quality>1 for better image quality, at the price of more cpu/gpu usage, 0`_)")) ((int,glutStacks,6,(Attr::noSave | Attr::readonly),"Base number of sphere stacks, multiplied by :yref:`Gl1_Sphere::quality` before use; not used with ``stripes`` (see `glut{Solid,Wire}Sphere reference `_)")) ((bool,circleView,false,,"For 2D simulations : display tori instead of spheres, so they will appear like circles if the viewer is looking in the right direction. In this case, remember to disable perspective by pressing \"t\"-key in the viewer.")) ((Real,circleRelThickness,0.2,,"If :yref:`Gl1_Sphere::circleView` is enabled, this is the torus diameter relative to the sphere radius (i.e. the circle relative thickness).")) ((char,circleAllowedRotationAxis,'z',,"If :yref:`Gl1_Sphere::circleView` is enabled, this is the only axis ('x', 'y' or 'z') along which rotation is allowed for the 2D simulation. It allows right orientation of the tori to appear like circles in the viewer. For example, if circleAllowedRotationAxis='x' is set, blockedDOFs=\"YZ\" should also be set for all your particles.")) ); RENDERS(Sphere); }; REGISTER_SERIALIZABLE(Gl1_Sphere); trunk-2017.01a/pkg/common/GravityEngines.cpp000066400000000000000000000076371304022710500207120ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include #include #include #include #include YADE_PLUGIN((GravityEngine)(CentralGravityEngine)(AxialGravityEngine)(HdapsGravityEngine)); CREATE_LOGGER(GravityEngine); void GravityEngine::action(){ if (warnOnce) {warnOnce=false; LOG_WARN("GravityEngine is deprecated, consider using Newton::gravity instead (unless gravitational energy has to be tracked - not implemented with the newton attribute).")} const bool trackEnergy(scene->trackEnergy); const Real dt(scene->dt); YADE_PARALLEL_FOREACH_BODY_BEGIN(const shared_ptr& b, scene->bodies){ // skip clumps, only apply forces on their constituents if(b->isClump()) continue; if(mask!=0 && !b->maskCompatible(mask)) continue; scene->forces.addForce(b->getId(),gravity*b->state->mass); // work done by gravity is "negative", since the energy appears in the system from outside if(trackEnergy) scene->energy->add(-gravity.dot(b->state->vel)*b->state->mass*dt,"gravWork",fieldWorkIx,/*non-incremental*/false); } YADE_PARALLEL_FOREACH_BODY_END(); } void CentralGravityEngine::action(){ const Vector3r& centralPos=Body::byId(centralBody)->state->pos; FOREACH(const shared_ptr& b, *scene->bodies){ if(b->isClump() || b->getId()==centralBody) continue; // skip clumps and central body if(mask!=0 && !b->maskCompatible(mask)) continue; Real F=accel*b->state->mass; Vector3r toCenter=centralPos-b->state->pos; toCenter.normalize(); scene->forces.addForce(b->getId(),F*toCenter); if(reciprocal) scene->forces.addForce(centralBody,-F*toCenter); } } void AxialGravityEngine::action(){ FOREACH(const shared_ptr&b, *scene->bodies){ if(!b || b->isClump()) continue; if(mask!=0 && !b->maskCompatible(mask)) continue; /* http://mathworld.wolfram.com/Point-LineDistance3-Dimensional.html */ const Vector3r& x0=b->state->pos; const Vector3r& x1=axisPoint; const Vector3r x2=axisPoint+axisDirection; Vector3r closestAxisPoint=x1+(x2-x1) * /* t */ (-(x1-x0).dot(x2-x1))/((x2-x1).squaredNorm()); Vector3r toAxis=closestAxisPoint-x0; toAxis.normalize(); if(toAxis.squaredNorm()==0) continue; scene->forces.addForce(b->getId(),acceleration*b->state->mass*toAxis); } } Vector2i HdapsGravityEngine::readSysfsFile(const string& name){ char buf[256]; ifstream f(name.c_str()); if(!f.is_open()) throw std::runtime_error(("HdapsGravityEngine: unable to open file "+name).c_str()); f.read(buf,256);f.close(); const boost::regex re("\\(([0-9+-]+),([0-9+-]+)\\).*"); boost::cmatch matches; if(!boost::regex_match(buf,matches,re)) throw std::runtime_error(("HdapsGravityEngine: error parsing data from "+name).c_str()); //cerr<(matches[1]),boost::lexical_cast(matches[2])); } void HdapsGravityEngine::action(){ if(!calibrated) { calibrate=readSysfsFile(hdapsDir+"/calibrate"); calibrated=true; } Real now=PeriodicEngine::getClock(); if(now-lastReading>1e-3*msecUpdate){ Vector2i a=readSysfsFile(hdapsDir+"/position"); lastReading=now; a-=calibrate; if(std::abs(a[0]-accel[0])>updateThreshold) accel[0]=a[0]; if(std::abs(a[1]-accel[1])>updateThreshold) accel[1]=a[1]; Quaternionr trsf(AngleAxisr(.5*accel[0]*M_PI/180.,-Vector3r::UnitY())*AngleAxisr(.5*accel[1]*M_PI/180.,-Vector3r::UnitX())); gravity=trsf*zeroGravity; } GravityEngine::action(); } trunk-2017.01a/pkg/common/GravityEngines.hpp000066400000000000000000000077731304022710500207200ustar00rootroot00000000000000// 2004 © Janek Kozicki // 2007,2008 © Václav Šmilauer #pragma once #include #include #include /*! Homogeneous gravity field; applies gravity×mass force on all bodies. */ class GravityEngine: public FieldApplier{ public: virtual void action(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(GravityEngine,FieldApplier,"Engine applying constant acceleration to all bodies. DEPRECATED, use :yref:`Newton::gravity` unless you need energy tracking or selective gravity application using groupMask).", ((Vector3r,gravity,Vector3r::Zero(),,"Acceleration [kgms⁻²]")) ((int,gravPotIx,-1,(Attr::noSave|Attr::hidden),"Index for gravPot energy")) ((int,mask,0,,"If mask defined, only bodies with corresponding groupMask will be affected by this engine. If 0, all bodies will be affected.")) ((bool,warnOnce,true,,"For deprecation warning once.")) ,/*ctor*/,/*py*/ ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(GravityEngine); /*! Engine attracting all bodies towards a central body (doesn't depend on distance); * * @todo This code has not been yet tested at all. */ class CentralGravityEngine: public FieldApplier { public: virtual void action(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(CentralGravityEngine,FieldApplier,"Engine applying acceleration to all bodies, towards a central body.", ((Body::id_t,centralBody,Body::ID_NONE,,"The :yref:`body` towards which all other bodies are attracted.")) ((Real,accel,0,,"Acceleration magnitude [kgms⁻²]")) ((bool,reciprocal,false,,"If true, acceleration will be applied on the central body as well.")) ((int,mask,0,,"If mask defined, only bodies with corresponding groupMask will be affected by this engine. If 0, all bodies will be affected.")) ,, ); }; REGISTER_SERIALIZABLE(CentralGravityEngine); /*! Apply acceleration (independent of distance) directed towards an axis. * */ class AxialGravityEngine: public FieldApplier { public: virtual void action(); YADE_CLASS_BASE_DOC_ATTRS(AxialGravityEngine,FieldApplier,"Apply acceleration (independent of distance) directed towards an axis.", ((Vector3r,axisPoint,Vector3r::Zero(),,"Point through which the axis is passing.")) ((Vector3r,axisDirection,Vector3r::UnitX(),,"direction of the gravity axis (will be normalized automatically)")) ((Real,acceleration,0,,"Acceleration magnitude [kgms⁻²]")) ((int,mask,0,,"If mask defined, only bodies with corresponding groupMask will be affected by this engine. If 0, all bodies will be affected.")) ); }; REGISTER_SERIALIZABLE(AxialGravityEngine); class HdapsGravityEngine: public GravityEngine{ public: Vector2i readSysfsFile(const std::string& name); virtual void action(); YADE_CLASS_BASE_DOC_ATTRS(HdapsGravityEngine,GravityEngine,"Read accelerometer in Thinkpad laptops (`HDAPS `__ and accordingly set gravity within the simulation. This code draws from `hdaps-gl `__ . See :ysrc:`scripts/test/hdaps.py` for an example.", ((string,hdapsDir,"/sys/devices/platform/hdaps",,"Hdaps directory; contains ``position`` (with accelerometer readings) and ``calibration`` (zero acceleration).")) ((Real,msecUpdate,50,,"How often to update the reading.")) ((int,updateThreshold,4,,"Minimum difference of reading from the file before updating gravity, to avoid jitter.")) ((Real,lastReading,-1,(Attr::hidden|Attr::noSave),"Time of the last reading.")) ((Vector2i,accel,Vector2i::Zero(),(Attr::noSave|Attr::readonly),"reading from the sysfs file")) ((Vector2i,calibrate,Vector2i::Zero(),,"Zero position; if NaN, will be read from the *hdapsDir* / calibrate.")) ((bool,calibrated,false,,"Whether *calibrate* was already updated. Do not set to ``True`` by hand unless you also give a meaningful value for *calibrate*.")) ((Vector3r,zeroGravity,Vector3r(0,0,-1),,"Gravity if the accelerometer is in flat (zero) position.")) ); }; REGISTER_SERIALIZABLE(HdapsGravityEngine); trunk-2017.01a/pkg/common/Grid.cpp000066400000000000000000000751321304022710500166340ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2012 by François Kneib francois.kneib@gmail.com * * Copyright (C) 2012 by Bruno Chareyre bruno.chareyre@hmg.inpg.fr * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "Grid.hpp" //!################## SHAPES ##################### GridNode::~GridNode(){} YADE_PLUGIN((GridNode)); GridConnection::~GridConnection(){} YADE_PLUGIN((GridConnection)); GridNodeGeom6D::~GridNodeGeom6D(){} YADE_PLUGIN((GridNodeGeom6D)); ScGridCoGeom::~ScGridCoGeom(){} YADE_PLUGIN((ScGridCoGeom)); GridCoGridCoGeom::~GridCoGridCoGeom(){} YADE_PLUGIN((GridCoGridCoGeom)); void GridNode::addConnection(shared_ptr GC){ ConnList.push_back(GC); } Vector3r GridConnection::getSegment(){ if (!periodic) return node2->state->pos - node1->state->pos; //else const Scene* scene=Omega::instance().getScene().get(); return node2->state->pos + scene->cell->hSize*cellDist.cast() - node1->state->pos; } Real GridConnection::getLength(){ return getSegment().norm(); } void GridNode::addPFacet(shared_ptr PF){ pfacetList.push_back(PF); } void GridConnection::addPFacet(shared_ptr PF){ pfacetList.push_back(PF); } PFacet::~PFacet(){} YADE_PLUGIN((PFacet)); //!################## IGeom Functors ##################### //! O-O bool Ig2_GridNode_GridNode_GridNodeGeom6D::go( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { //GridConnection* GC = static_cast(cm.get()); bool isNew = !c->geom; GridNode* GN[2]={static_cast(cm1.get()),static_cast(cm2.get())}; if (Ig2_Sphere_Sphere_ScGeom::go(cm1,cm2,state1,state2,shift2,force,c)){//the 3 DOFS from ScGeom are updated here if (isNew) {//generate a 6DOF interaction from the 3DOF one generated by Ig2_Sphere_Sphere_ScGeom shared_ptr sc (new GridNodeGeom6D()); *(YADE_PTR_CAST(sc)) = *(YADE_PTR_CAST(c->geom)); c->geom=sc; } if (updateRotations) YADE_PTR_CAST(c->geom)->precomputeRotations(state1,state2,isNew,creep); if(YADE_PTR_CAST(c->geom)->connectionBody){ //test this because the connectionBody may not have been yet initialized. YADE_PTR_CAST(c->geom)->connectionBody->state->pos=state1.pos; for (unsigned int j=0; j<2; j++){ for (unsigned int i=0; i< GN[j]->pfacetList.size() ;i++){ PFacet* Pfacet = YADE_CAST(GN[j]->pfacetList[i]->shape.get()); if(c->id1==Pfacet->node1->getId()) GN[j]->pfacetList[i]->state->pos=state1.pos; } } } return true; } else return false; } bool Ig2_GridNode_GridNode_GridNodeGeom6D::goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { return go(cm1,cm2,state2,state1,-shift2,force,c); } YADE_PLUGIN((Ig2_GridNode_GridNode_GridNodeGeom6D)); //! \\// bool Ig2_GridConnection_GridConnection_GridCoGridCoGeom::go( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { /*FIXME : /!\ Note that this geometry doesn't take care of any unwished duplicated contact or shear force following. /!\*/ GridConnection* conn1 = YADE_CAST(cm1.get()); GridConnection* conn2 = YADE_CAST(cm2.get()); State* stNode11 = conn1->node1->state.get(); State* stNode12 = conn1->node2->state.get(); State* stNode21 = conn2->node1->state.get(); State* stNode22 = conn2->node2->state.get(); if(conn1->node1==conn2->node1 || conn1->node1==conn2->node2 || conn1->node2==conn2->node1 || conn1->node2==conn2->node2){ //Two connections share at least one node, so they are contiguous => they must not interact. return false; } //There could be a contact between to connections. Check this now. bool isNew = !c->geom; Real k,m; Vector3r A=stNode11->pos, a=stNode12->pos-A; //"A" is an extremity of conn1, "a" is the connection's segment. Vector3r B=stNode21->pos, b=stNode22->pos-B; //"B" is an extremity of conn2, "b" is the connection's segment. B+=shift2;//periodicity. /* NOW STARTS THE OLD VERSION. IT SHOULD BE REMOVED LATER. Vector3r N=a.cross(b); //"N" is orthogonal to "a" and "b". It means that "N" describes the common plan between a and b. if(N.norm()>1e-14){ //If "a" and "b" are colinear, "N==0" and this is a special case. Real dist=N.dot(B-A)/(N.norm()); //here "dist" is oriented, so it's sign depends on the orientation of "N" against "AB". Vector3r pB=B-dist*(N/(N.norm())); //"pB" is the projection of the point "B" in the plane defined by his normal vector "N". //Now we have pB, so we will compute the intersection of two segments into a plane. int b0, b1; //2 base vectors used to compute the segment intersection. For more accuracy and to avoid det==0, don't choose the axis where N is max. if(std::abs(N[0])1e-14){ //Now compute k and m, who are the parameters (relative position on the connections) of the intersection on conn1 ("A" and "a") and conn2 ("B" and "b") respectively. k = (b[b1]*(pB[b0]-A[b0])+b[b0]*(A[b1]-pB[b1]))/det; m = (a[b0]*(-pB[b1]+A[b1])+a[b1]*(pB[b0]-A[b0]))/det; //This is a little bit tricky : if we haven't 0radius + conn2->radius - (A+k*a - (B+m*b)).norm(); shared_ptr scm; if(isNew){ if(penetrationDepth<0)return false; scm=shared_ptr(new GridCoGridCoGeom()); c->geom=scm; } else scm=YADE_PTR_CAST(c->geom); //k and m are used to compute almost everything... //Fictious states (spheres) are generated at k or m of each connection, they will handle the contact. scm->relPos1=k ; scm->relPos2=m; scm->fictiousState1.pos=A + k*a ; scm->fictiousState2.pos=B + m*b; scm->radius1 = conn1->radius ; scm->radius2 = conn2->radius; scm->fictiousState1.vel = (1-k)*stNode11->vel + k*stNode12->vel; scm->fictiousState2.vel = (1-m)*stNode21->vel + m*stNode22->vel; Vector3r direction = a/(a.norm()); scm->fictiousState1.angVel = ((1-k)*stNode11->angVel + k*stNode12->angVel).dot(direction)*direction //twist part : interpolated + a.cross(stNode12->vel - stNode11->vel);// non-twist part : defined from nodes velocities direction = b/(b.norm()); scm->fictiousState2.angVel = ((1-m)*stNode21->angVel + m*stNode22->angVel).dot(direction)*direction //twist part : interpolated + b.cross(stNode22->vel - stNode21->vel);// non-twist part : defined from nodes velocities Vector3r normal= scm->fictiousState2.pos - scm->fictiousState1.pos; normal/=normal.norm(); scm->contactPoint = scm->fictiousState1.pos + (scm->radius1-0.5*penetrationDepth)*normal; scm->penetrationDepth=penetrationDepth; scm->precompute(scm->fictiousState1,scm->fictiousState2,scene,c,normal,isNew,shift2,true); return true; } bool Ig2_GridConnection_GridConnection_GridCoGridCoGeom::goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { return go(cm1,cm2,state2,state1,-shift2,force,c); } YADE_PLUGIN((Ig2_GridConnection_GridConnection_GridCoGridCoGeom)); //! O/ bool Ig2_Sphere_GridConnection_ScGridCoGeom::go( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { // Useful variables : const State* sphereSt = YADE_CAST(&state1); Sphere* sphere = YADE_CAST(cm1.get()); GridConnection* gridCo = YADE_CAST(cm2.get()); GridNode* gridNo1 = YADE_CAST(gridCo->node1->shape.get()); GridNode* gridNo2 = YADE_CAST(gridCo->node2->shape.get()); State* gridNo1St = YADE_CAST(gridCo->node1->state.get()); State* gridNo2St = YADE_CAST(gridCo->node2->state.get()); bool isNew = !c->geom; shared_ptr scm; if (!isNew) scm = YADE_PTR_CAST(c->geom); else {scm = shared_ptr(new ScGridCoGeom());} Vector3r segt = gridCo->getSegment(); Real len = gridCo->getLength(); Vector3r spherePos = sphereSt->pos - shift2; Vector3r branch = spherePos - gridNo1St->pos; Vector3r branchN = spherePos - gridNo2St->pos; for(int i=0;i<3;i++){ if(std::abs(branch[i])<1e-14) branch[i]=0.0; if(std::abs(branchN[i])<1e-14) branchN[i]=0.0; } Real relPos = branch.dot(segt)/(len*len); if(scm->isDuplicate==2 && scm->trueInt!=c->id2)return true; //the contact will be deleted into the Law, no need to compute here. scm->isDuplicate=0; scm->trueInt=-1; /* The 4 conditions below are used to avoid double contact between a sphere and two cylinders, and to follow contact properties when the sphere is sliding along different consecutive GridConnections. If none of these conditions are satisfied, the classic contact will be done at the bottom of the Ig2. Else the contact may be copied (if sliding), deleted (if just copied and/or duplicated) and the return statement may be used to abort the Ig2. The first and the second conditions detect if a sphere's projections is outside the connection. So the contact : - have to be created if the projection is outside all neighbours and not already created. - have to be ignored if the projection is inside at least one neighbour. - if the contact is sliding out to another connection (detected via isNew), mark it as duplicated (it will be ignored by the law and imported (copied) by the new contact). The third and the fourth conditions detect if a sphere's projections is inside the connection. So if the contact is new and : - is before the middle of the connection, we search an old contact that may have slided from one of the previous connections. If we find one, we import it here. - is after the middle of the connection, we search an old contact that may have slided from one of the following connections. If we find one, we import it here. */ if(relPos<=0){ // if the sphere projection is BEFORE the segment ... if(gridNo1->ConnList.size()>1){// if the node is not an extremity of the Grid (only one connection) for(int unsigned i=0;iConnList.size();i++){ // ... loop on all the Connections of the same Node ... GridConnection* GC = (GridConnection*)gridNo1->ConnList[i]->shape.get(); if(GC==gridCo)continue;// self comparison. Vector3r segtCandidate1 = GC->node1->state->pos - gridNo1St->pos; // (be sure of the direction of segtPrev to compare relPosPrev.) Vector3r segtCandidate2 = GC->node2->state->pos - gridNo1St->pos; Vector3r segtPrev = segtCandidate1.norm()>segtCandidate2.norm() ? segtCandidate1:segtCandidate2; for(int j=0;j<3;j++){ if(std::abs(segtPrev[j])<1e-14) segtPrev[j]=0.0; } Real relPosPrev = (branch.dot(segtPrev))/(segtPrev.norm()*segtPrev.norm()); // ... and check whether the sphere projection is before the neighbours connections too. if(relPosPrev<=0){ //if the sphere projection is outside both the current Connection AND this neighbouring connection, then create the interaction if the neighbour did not already do it before. const shared_ptr intr = scene->interactions->find(c->id1,gridNo1->ConnList[i]->getId()); if(intr && intr->isReal()){ shared_ptr intrGeom=YADE_PTR_CAST(intr->geom); if(!(intrGeom->isDuplicate==1)){ //skip contact. if (isNew) return false; else {scm->isDuplicate=1;/*cout<<"Declare "<id1<<"-"<id2<<" as duplicated."<id1<<"-"<id2<<" may be copied and will be deleted now."<isDuplicate=1; scm->trueInt=-1; return true; } } } } } //Exactly the same but in the case the sphere projection is AFTER the segment. else if(relPos>=1){ if(gridNo2->ConnList.size()>1){ for(int unsigned i=0;iConnList.size();i++){ GridConnection* GC = (GridConnection*)gridNo2->ConnList[i]->shape.get(); if(GC==gridCo)continue;// self comparison. Vector3r segtCandidate1 = GC->node1->state->pos - gridNo2St->pos; Vector3r segtCandidate2 = GC->node2->state->pos - gridNo2St->pos; Vector3r segtNext = segtCandidate1.norm()>segtCandidate2.norm() ? segtCandidate1:segtCandidate2; for(int j=0;j<3;j++){ if(std::abs(segtNext[j])<1e-14) segtNext[j]=0.0; } Real relPosNext = (branchN.dot(segtNext))/(segtNext.norm()*segtNext.norm()); if(relPosNext<=0){ //if the sphere projection is outside both the current Connection AND this neighbouring connection, then create the interaction if the neighbour did not already do it before. const shared_ptr intr = scene->interactions->find(c->id1,gridNo2->ConnList[i]->getId()); if(intr && intr->isReal()){ shared_ptr intrGeom=YADE_PTR_CAST(intr->geom); if(!(intrGeom->isDuplicate==1)){ if (isNew) return false; else {scm->isDuplicate=1;/*cout<<"Declare "<id1<<"-"<id2<<" as duplicated."<id1<<"-"<id2<<" may be copied and will be deleted now."<isDuplicate=1 ; scm->trueInt=-1 ; return true; } } } } } else if (relPos<=0.5){ if(gridNo1->ConnList.size()>1){// if the node is not an extremity of the Grid (only one connection) for(int unsigned i=0;iConnList.size();i++){ // ... loop on all the Connections of the same Node ... GridConnection* GC = (GridConnection*)gridNo1->ConnList[i]->shape.get(); if(GC==gridCo)continue;// self comparison. Vector3r segtCandidate1 = GC->node1->state->pos - gridNo1St->pos; // (be sure of the direction of segtPrev to compare relPosPrev.) Vector3r segtCandidate2 = GC->node2->state->pos - gridNo1St->pos; Vector3r segtPrev = segtCandidate1.norm()>segtCandidate2.norm() ? segtCandidate1:segtCandidate2; for(int j=0;j<3;j++){ if(std::abs(segtPrev[j])<1e-14) segtPrev[j]=0.0; } Real relPosPrev = (branch.dot(segtPrev))/(segtPrev.norm()*segtPrev.norm()); if(relPosPrev<=0){ //the sphere projection is inside the current Connection and outide this neighbour connection. const shared_ptr intr = scene->interactions->find(c->id1,gridNo1->ConnList[i]->getId()); if( intr && intr->isReal() ){// if an ineraction exist between the sphere and the previous connection, import parameters. scm=YADE_PTR_CAST(intr->geom); if(isNew){ // cout<<"Copying contact geom and phys from "<id1<<"-"<id2<<" to here ("<id1<<"-"<id2<<")"<geom=scm; c->phys=intr->phys; c->iterMadeReal=intr->iterMadeReal; } scm->trueInt=c->id2; scm->isDuplicate=2; //command the old contact deletion. isNew=0; break; } } } } } else if (relPos>0.5){ if(gridNo2->ConnList.size()>1){ for(int unsigned i=0;iConnList.size();i++){ GridConnection* GC = (GridConnection*)gridNo2->ConnList[i]->shape.get(); if(GC==gridCo)continue;// self comparison. Vector3r segtCandidate1 = GC->node1->state->pos - gridNo2St->pos; Vector3r segtCandidate2 = GC->node2->state->pos - gridNo2St->pos; Vector3r segtNext = segtCandidate1.norm()>segtCandidate2.norm() ? segtCandidate1:segtCandidate2; for(int j=0;j<3;j++){ if(std::abs(segtNext[j])<1e-14) segtNext[j]=0.0; } Real relPosNext = (branchN.dot(segtNext))/(segtNext.norm()*segtNext.norm()); if(relPosNext<=0){ //the sphere projection is inside the current Connection and outide this neighbour connection. const shared_ptr intr = scene->interactions->find(c->id1,gridNo2->ConnList[i]->getId()); if( intr && intr->isReal() ){// if an ineraction exist between the sphere and the previous connection, import parameters. scm=YADE_PTR_CAST(intr->geom); if(isNew){ // cout<<"Copying contact geom and phys from "<id1<<"-"<id2<<" to here ("<id1<<"-"<id2<<")"<geom=scm; c->phys=intr->phys; c->iterMadeReal=intr->iterMadeReal; } scm->trueInt=c->id2; scm->isDuplicate=2; //command the old contact deletion. isNew=0; break; } } } } } relPos=relPos<0?0:relPos; //min value of relPos : 0 relPos=relPos>1?1:relPos; //max value of relPos : 1 Vector3r fictiousPos=gridNo1St->pos+relPos*segt; Vector3r branchF = fictiousPos - spherePos; Real dist = branchF.norm(); if(isNew && (dist > (sphere->radius + gridCo->radius))) return false; // Create the geometry : if(isNew) c->geom=scm; scm->radius1=sphere->radius; scm->radius2=gridCo->radius; scm->id3=gridCo->node1->getId(); scm->id4=gridCo->node2->getId(); scm->relPos=relPos; Vector3r normal=branchF/dist; scm->penetrationDepth = sphere->radius+gridCo->radius-dist; scm->fictiousState.pos = fictiousPos; scm->contactPoint = spherePos + normal*(scm->radius1 - 0.5*scm->penetrationDepth); scm->fictiousState.vel = (1-relPos)*gridNo1St->vel + relPos*gridNo2St->vel; scm->fictiousState.angVel = ((1-relPos)*gridNo1St->angVel + relPos*gridNo2St->angVel).dot(segt/len)*segt/len //twist part : interpolated + segt.cross(gridNo2St->vel - gridNo1St->vel);// non-twist part : defined from nodes velocities scm->precompute(state1,scm->fictiousState,scene,c,normal,isNew,shift2,true);//use sphere-sphere precompute (with a virtual sphere) return true; } bool Ig2_Sphere_GridConnection_ScGridCoGeom::goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { c->swapOrder(); return go(cm2,cm1,state2,state1,-shift2,force,c); } YADE_PLUGIN((Ig2_Sphere_GridConnection_ScGridCoGeom)); //!################## Laws ##################### //! O/ bool Law2_ScGridCoGeom_FrictPhys_CundallStrack::go(shared_ptr& ig, shared_ptr& ip, Interaction* contact){ int id1 = contact->getId1(), id2 = contact->getId2(); ScGridCoGeom* geom= static_cast(ig.get()); FrictPhys* phys = static_cast(ip.get()); if(geom->penetrationDepth <0){ if (neverErase) { phys->shearForce = Vector3r::Zero(); phys->normalForce = Vector3r::Zero();} else return false;} if (geom->isDuplicate) { if (id2!=geom->trueInt) { //cerr<<"skip duplicate "<isDuplicate==2) return false; return true; } } Real& un=geom->penetrationDepth; phys->normalForce=phys->kn*std::max(un,(Real) 0)*geom->normal; // std::cout<< "phys->shearForce1= "<shearForce<rotate(phys->shearForce); // std::cout<< "phys->shearForce2= "<shearForce<<", geom->shearIncrement()= "<shearIncrement()<<", phys->ks= "<ks<shearIncrement(); shearForce -= phys->ks*shearDisp; Real maxFs = phys->normalForce.squaredNorm()*std::pow(phys->tangensOfFrictionAngle,2); // std::cout<< "shearForce3= "<normalForce="<normalForce<trackEnergy){//Update force but don't compute energy terms (see below)) // PFC3d SlipModel, is using friction angle. CoulombCriterion if( shearForce.squaredNorm() > maxFs ){ Real ratio = sqrt(maxFs) / shearForce.norm(); shearForce *= ratio;} } else { //almost the same with additional Vector3r instanciated for energy tracing, duplicated block to make sure there is no cost for the instanciation of the vector when traceEnergy==false if(shearForce.squaredNorm() > maxFs){ Real ratio = sqrt(maxFs) / shearForce.norm(); Vector3r trialForce=shearForce;//store prev force for definition of plastic slip //define the plastic work input and increment the total plastic energy dissipated shearForce *= ratio; Real dissip=((1/phys->ks)*(trialForce-shearForce))/*plastic disp*/ .dot(shearForce)/*active force*/; if(dissip>0) scene->energy->add(dissip,"plastDissip",plastDissipIx,/*reset*/false); } // compute elastic energy as well scene->energy->add(0.5*(phys->normalForce.squaredNorm()/phys->kn+phys->shearForce.squaredNorm()/phys->ks),"elastPotential",elastPotentialIx,/*reset at every timestep*/true); } Vector3r force = -phys->normalForce-shearForce; // std::cout<< "id1= "<isDuplicate==2) return false; return true; } } Vector3r& shearForce = phys->shearForce; if (contact->isFresh(scene) && geom->isDuplicate!=2) shearForce = Vector3r::Zero(); Real un = geom->penetrationDepth; Real Fn = phys->kn*(un-phys->unp); if (phys->fragile && (-Fn)> phys->normalAdhesion) { // BREAK due to tension return false; } else { if ((-Fn)> phys->normalAdhesion) {//normal plasticity Fn=-phys->normalAdhesion; phys->unp = un+phys->normalAdhesion/phys->kn; if (phys->unpMax && phys->unpunpMax) return false; } phys->normalForce = Fn*geom->normal; Vector3r& shearForce = geom->rotate(phys->shearForce); const Vector3r& dus = geom->shearIncrement(); //Linear elasticity giving "trial" shear force shearForce -= phys->ks*dus; Real Fs = phys->shearForce.norm(); Real maxFs = phys->shearAdhesion; if (!phys->cohesionDisablesFriction || maxFs==0) maxFs += Fn*phys->tangensOfFrictionAngle; maxFs = std::max((Real) 0, maxFs); if (Fs > maxFs) {//Plasticity condition on shear force if (phys->fragile && !phys->cohesionBroken) { phys->SetBreakingState(); maxFs = max((Real) 0, Fn*phys->tangensOfFrictionAngle); } maxFs = maxFs / Fs; Vector3r trialForce=shearForce; shearForce *= maxFs; if (scene->trackEnergy){ Real dissip=((1/phys->ks)*(trialForce-shearForce))/*plastic disp*/ .dot(shearForce)/*active force*/; if(dissip>0) scene->energy->add(dissip,"plastDissip",plastDissipIx,/*reset*/false);} if (Fn<0) phys->normalForce = Vector3r::Zero();//Vector3r::Zero() } Vector3r force = -phys->normalForce-shearForce; scene->forces.addForce(id1,force); scene->forces.addTorque(id1,(geom->radius1-0.5*geom->penetrationDepth)* geom->normal.cross(force)); Vector3r twist = (geom->radius2-0.5*geom->penetrationDepth)* geom->normal.cross(force); scene->forces.addForce(geom->id3,(geom->relPos-1)*force); scene->forces.addTorque(geom->id3,(1-geom->relPos)*twist); scene->forces.addForce(geom->id4,(-geom->relPos)*force); scene->forces.addTorque(geom->id4,geom->relPos*twist); return true; } } YADE_PLUGIN((Law2_ScGridCoGeom_CohFrictPhys_CundallStrack)); bool Law2_GridCoGridCoGeom_FrictPhys_CundallStrack::go(shared_ptr& ig, shared_ptr& ip, Interaction* contact){ int id1 = contact->getId1(), id2 = contact->getId2(); id_t id11 = (static_cast((&Body::byId(id1)->shape)->get()))->node1->getId(); id_t id12 = (static_cast((&Body::byId(id1)->shape)->get()))->node2->getId(); id_t id21 = (static_cast((&Body::byId(id2)->shape)->get()))->node1->getId(); id_t id22 = (static_cast((&Body::byId(id2)->shape)->get()))->node2->getId(); GridCoGridCoGeom* geom= static_cast(ig.get()); FrictPhys* phys = static_cast(ip.get()); if(geom->penetrationDepth <0){ if (neverErase) { phys->shearForce = Vector3r::Zero(); phys->normalForce = Vector3r::Zero();} else return false;} Real& un=geom->penetrationDepth; phys->normalForce=phys->kn*std::max(un,(Real) 0)*geom->normal; Vector3r& shearForce = geom->rotate(phys->shearForce); const Vector3r& shearDisp = geom->shearIncrement(); shearForce -= phys->ks*shearDisp; Real maxFs = phys->normalForce.squaredNorm()*std::pow(phys->tangensOfFrictionAngle,2); if (!scene->trackEnergy && !traceEnergy){//Update force but don't compute energy terms (see below)) // PFC3d SlipModel, is using friction angle. CoulombCriterion if( shearForce.squaredNorm() > maxFs ){ Real ratio = sqrt(maxFs) / shearForce.norm(); shearForce *= ratio;} } else { //almost the same with additional Vector3r instatinated for energy tracing, //duplicated block to make sure there is no cost for the instanciation of the vector when traceEnergy==false if(shearForce.squaredNorm() > maxFs){ Real ratio = sqrt(maxFs) / shearForce.norm(); Vector3r trialForce=shearForce;//store prev force for definition of plastic slip //define the plastic work input and increment the total plastic energy dissipated shearForce *= ratio; Real dissip=((1/phys->ks)*(trialForce-shearForce))/*plastic disp*/ .dot(shearForce)/*active force*/; if (traceEnergy) plasticDissipation += dissip; else if(dissip>0) scene->energy->add(dissip,"plastDissip",plastDissipIx,/*reset*/false); } // compute elastic energy as well scene->energy->add(0.5*(phys->normalForce.squaredNorm()/phys->kn+phys->shearForce.squaredNorm()/phys->ks),"elastPotential",elastPotentialIx,/*reset at every timestep*/true); } Vector3r force = -phys->normalForce-shearForce; Vector3r torque1 = (geom->radius1-0.5*geom->penetrationDepth)* geom->normal.cross(force); Vector3r torque2 = (geom->radius2-0.5*geom->penetrationDepth)* geom->normal.cross(force); scene->forces.addForce(id11,(1-geom->relPos1)*force); scene->forces.addForce(id12,geom->relPos1*force); scene->forces.addForce(id21,-(1-geom->relPos2)*force); scene->forces.addForce(id22,-geom->relPos2*force); scene->forces.addTorque(id11,(1-geom->relPos1)*torque1); scene->forces.addTorque(id12,geom->relPos1*torque1); scene->forces.addTorque(id21,(1-geom->relPos2)*torque2); scene->forces.addTorque(id22,geom->relPos2*torque2); return true; } YADE_PLUGIN((Law2_GridCoGridCoGeom_FrictPhys_CundallStrack)); //!################## Bounds ##################### void Bo1_GridConnection_Aabb::go(const shared_ptr& cm, shared_ptr& bv, const Se3r& se3, const Body* b){ GridConnection* GC = static_cast(cm.get()); if(!bv){ bv=shared_ptr(new Aabb); } Aabb* aabb=static_cast(bv.get()); Vector3r O = YADE_CAST(GC->node1->state.get())->pos; Vector3r O2 = YADE_CAST(GC->node2->state.get())->pos; if(!scene->isPeriodic){ for (int k=0;k<3;k++){ aabb->min[k]=min(O[k],O2[k])-GC->radius; aabb->max[k]=max(O[k],O2[k])+GC->radius; } return; } else{ O = scene->cell->unshearPt(O); O2 = scene->cell->unshearPt(O2); O2 = O2 + scene->cell->hSize*GC->cellDist.cast(); for (int k=0;k<3;k++){ aabb->min[k]=min(O[k],O2[k])-GC->radius; aabb->max[k]=max(O[k],O2[k])+GC->radius; } } } YADE_PLUGIN((Bo1_GridConnection_Aabb)); trunk-2017.01a/pkg/common/Grid.hpp000066400000000000000000000404351304022710500166370ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2012 by François Kneib francois.kneib@gmail.com * * Copyright (C) 2012 by Bruno Chareyre bruno.chareyre@hmg.inpg.fr * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ /* TABLE OF CONTENT, and the minimum you need to understand. - 2 new shapes for grids : GridNode (vertices) and GridConnection (edges) - 2 new contact geometries : * GridNodeGeom6D to handle GridNode-GridNode contacts (the internal behaviour of the grid) * ScGridCoGeom to handle Sphere-GridConnection contacts (the interaction between the grid and an external sphere) Note : the Sphere-Grid contacts are always handled by the GridConnections, but the forces are applied on the related GridNodes. Note : there is no contact between two GridConnections, they must be linked with GridNodes. - The 2 related Ig2 : * Ig2_GridNode_GridNode_GridNodeGeom6D (doing almost the same than Ig2_Sphere_Sphere_ScGeom6D) * Ig2_Sphere_GridConnection_ScGridCoGeom (the biggest part of the code, it handles contact detection and history when a sphere is sliding on the grid over consecutive GridConnections) - The Law2_ScGridCoGeom_FrictPhys_CundallStrack who handles the elastic frictional Sphere-GridConnection contact. The GridNode-GridNode law is Law2_ScGeom6D_CohFrictPhys_CohesionMoment by inheritance. */ #pragma once #include "Sphere.hpp" #include #include #include #include #include #include #include #ifdef YADE_OPENGL #include #endif //!################## SHAPES ##################### class GridConnection: public Sphere{ public: virtual ~GridConnection(); Real getLength(); Vector3r getSegment(); void addPFacet(shared_ptr PF); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(GridConnection,Sphere,"GridConnection shape (see [Effeindzourou2016]_, [Bourrier2013]_). Component of a grid designed to link two :yref:`GridNodes`. It is highly recommended to use :yref:`yade.gridpfacet.gridConnection` to generate correct :yref:`GridConnections`.", ((shared_ptr , node1 , ,,"First :yref:`Body` the GridConnection is connected to.")) ((shared_ptr , node2 , ,,"Second :yref:`Body` the GridConnection is connected to.")) ((bool, periodic, false,,"true if two nodes from different periods are connected.")) ((vector >,pfacetList,,,"List of :yref:`PFacet` the GridConnection is connected to.")) ((Vector3i , cellDist , Vector3i(0,0,0),,"Distance of bodies in cell size units, if using periodic boundary conditions. Note that periodic boundary conditions for GridConnections have not yet been fully implemented.")), createIndex();, /*ctor*/ /*py*/ .def("addPFacet",&GridConnection::addPFacet,(boost::python::arg("Body")),"Add a PFacet to the GridConnection.") ); REGISTER_CLASS_INDEX(GridConnection,Sphere); }; REGISTER_SERIALIZABLE(GridConnection); class GridNode: public Sphere{ public: virtual ~GridNode(); void addConnection(shared_ptr GC); void addPFacet(shared_ptr PF); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(GridNode,Sphere,"GridNode shape, component of a grid.\nTo create a Grid, place the nodes first, they will define the spacial discretisation of it. It is highly recommended to use :yref:`yade.gridpfacet.gridNode` to generate correct :yref:`GridNodes`. Note that the GridNodes should only be in an Interaction with other GridNodes. The Sphere-Grid contact is only handled by the :yref:`GridConnections`.", ((vector >,pfacetList,,,"List of :yref:`PFacets` the GridConnection is connected to.")) ((vector >,ConnList,,,"List of :yref:`GridConnections` the GridNode is connected to.")), /*ctor*/ createIndex();, /*py*/ .def("addConnection",&GridNode::addConnection,(boost::python::arg("Body")),"Add a GridConnection to the GridNode.") .def("addPFacet",&GridNode::addPFacet,(boost::python::arg("Body")),"Add a PFacet to the GridNode.") ); REGISTER_CLASS_INDEX(GridNode,Sphere); }; REGISTER_SERIALIZABLE(GridNode); //!################## PFacet SHAPE ##################### class PFacet : public Shape { public: virtual ~PFacet(); /// Normals of edges Vector3r ne[3]; /// Inscribing cirle radius Real icr; /// Length of the vertice vectors Real vl[3]; /// Unit vertice vectors Vector3r vu[3]; YADE_CLASS_BASE_DOC_ATTRS_CTOR(PFacet,Shape,"PFacet (particle facet) geometry (see [Effeindzourou2016]_, [Effeindzourou2015a]_). It is highly recommended to use the helper functions in :yref:`yade.gridpfacet` (e.g., gridpfacet.pfacetCreator1-4) to generate correct :yref:`PFacet` elements.", ((shared_ptr , node1 , ,,"First :yref:`Body` the Pfacet is connected to.")) ((shared_ptr , node2 , ,,"Second :yref:`Body` the Pfacet is connected to.")) ((shared_ptr , node3 , ,,"third :yref:`Body` the Pfacet is connected to.")) ((shared_ptr , conn1 , ,,"First :yref:`Body` the Pfacet is connected to.")) ((shared_ptr , conn2 , ,,"Second :yref:`Body` the Pfacet is connected to.")) ((shared_ptr , conn3 , ,,"third :yref:`Body` the Pfacet is connected to.")) ((Vector3r,normal,Vector3r(NaN,NaN,NaN),(Attr::readonly | Attr::noSave),"PFacet's normal (in local coordinate system)")) ((Real,radius,-1,,"PFacet's radius")) ((Real,area,NaN,(Attr::readonly | Attr::noSave),"PFacet's area")) ((Vector3i , cellDist , Vector3i(0,0,0),,"Distance of bodies in cell size units, if using periodic boundary conditions. Note that periodic boundary conditions for PFacets have not yet been fully implemented.")) , /* ctor */ createIndex(); ); DECLARE_LOGGER; REGISTER_CLASS_INDEX(PFacet,Shape); }; REGISTER_SERIALIZABLE(PFacet); //!################## Contact Geometry ##################### //! O-O class GridNodeGeom6D: public ScGeom6D { public: virtual ~GridNodeGeom6D(); YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(GridNodeGeom6D,ScGeom6D,"Geometry of a :yref:`GridNode`-:yref:`GridNode` contact. Inherits almost everything from :yref:`ScGeom6D`.", ((shared_ptr, connectionBody,,,"Reference to the :yref:`GridNode` :yref:`Body` who is linking the two :yref:`GridNodes`.")), /* extra initializers */, /* ctor */ createIndex();, /* py */ ); REGISTER_CLASS_INDEX(GridNodeGeom6D,ScGeom6D); }; REGISTER_SERIALIZABLE(GridNodeGeom6D); //! O/ class ScGridCoGeom: public ScGeom6D { public: /// Emulate a sphere whose position is the projection of sphere's center on cylinder sphere, and with motion linearly interpolated between nodes State fictiousState; virtual ~ScGridCoGeom (); YADE_CLASS_BASE_DOC_ATTRS_CTOR(ScGridCoGeom,ScGeom6D,"Geometry of a :yref:`GridConnection`-:yref:`Sphere` contact.", ((int,isDuplicate,0,,"this flag is turned true (1) automatically if the contact is shared between two Connections. A duplicated interaction will be skipped once by the constitutive law, so that only one contact at a time is effective. If isDuplicate=2, it means one of the two duplicates has no longer geometric interaction, and should be erased by the constitutive laws.")) ((int,trueInt,-1,,"Defines the body id of the :yref:`GridConnection` where the contact is real, when :yref:`ScGridCoGeom::isDuplicate`>0.")) ((int,id3,0,,"id of the first :yref:`GridNode`. |yupdate|")) ((int,id4,0,,"id of the second :yref:`GridNode`. |yupdate|")) ((int,id5,-1,,"id of the third :yref:`GridNode`. |yupdate|")) ((Vector3r,weight,Vector3r(0,0,0),,"barycentric coordinates of the projection point |yupdate|")) ((Real,relPos,0,,"position of the contact on the connection (0: node-, 1:node+) |yupdate|")), createIndex(); /*ctor*/ ); REGISTER_CLASS_INDEX(ScGridCoGeom,ScGeom6D); }; REGISTER_SERIALIZABLE(ScGridCoGeom); //! -|- class GridCoGridCoGeom: public ScGeom { public: /// Emulate a sphere whose position is the projection of sphere's center on cylinder sphere, and with motion linearly interpolated between nodes State fictiousState1,fictiousState2; virtual ~GridCoGridCoGeom (); YADE_CLASS_BASE_DOC_ATTRS_CTOR(GridCoGridCoGeom,ScGeom,"Geometry of a :yref:`GridConnection`-:yref:`GridConnection` contact.", ((Real,relPos1,0,,"position of the contact on the first connection (0: node-, 1:node+) |yupdate|")) ((Real,relPos2,0,,"position of the contact on the first connection (0: node-, 1:node+) |yupdate|")), createIndex(); /*ctor*/ ); REGISTER_CLASS_INDEX(ScGridCoGeom,ScGeom); }; REGISTER_SERIALIZABLE(GridCoGridCoGeom); //!################## IGeom Functors ##################### //! O-O class Ig2_GridNode_GridNode_GridNodeGeom6D: public Ig2_Sphere_Sphere_ScGeom{ public: virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); YADE_CLASS_BASE_DOC_ATTRS(Ig2_GridNode_GridNode_GridNodeGeom6D,Ig2_Sphere_Sphere_ScGeom,"Create/update a :yref:`GridNodeGeom6D` instance representing the geometry of a contact point between two :yref:`GridNode`, including relative rotations.", ((bool,updateRotations,true,,"Precompute relative rotations. Turning this false can speed up simulations when rotations are not needed in constitutive laws (e.g. when spheres are compressed without cohesion and moment in early stage of a triaxial test), but is not foolproof. Change this value only if you know what you are doing.")) ((bool,creep,false,,"Substract rotational creep from relative rotation. The rotational creep :yref:`ScGeom6D::twistCreep` is a quaternion and has to be updated inside a constitutive law, see for instance :yref:`Law2_ScGeom6D_CohFrictPhys_CohesionMoment`.")) ); FUNCTOR2D(GridNode,GridNode); // needed for the dispatcher, even if it is symmetric DEFINE_FUNCTOR_ORDER_2D(GridNode,GridNode); }; REGISTER_SERIALIZABLE(Ig2_GridNode_GridNode_GridNodeGeom6D); //! -/- class Ig2_GridConnection_GridConnection_GridCoGridCoGeom: public IGeomFunctor{ public: virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); YADE_CLASS_BASE_DOC_ATTRS(Ig2_GridConnection_GridConnection_GridCoGridCoGeom,IGeomFunctor,"Create/update a :yref:`GridCoGridCoGeom` instance representing the geometry of a contact point between two :yref:`GridConnection` , including relative rotations.", ); FUNCTOR2D(GridConnection,GridConnection); DEFINE_FUNCTOR_ORDER_2D(GridConnection,GridConnection); }; REGISTER_SERIALIZABLE(Ig2_GridConnection_GridConnection_GridCoGridCoGeom); //! O/ class Ig2_Sphere_GridConnection_ScGridCoGeom: public IGeomFunctor{ public: virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); YADE_CLASS_BASE_DOC_ATTRS(Ig2_Sphere_GridConnection_ScGridCoGeom,IGeomFunctor,"Create/update a :yref:`ScGridCoGeom6D` instance representing the geometry of a contact point between a :yref:`GricConnection` and a :yref:`Sphere` including relative rotations.", ((Real,interactionDetectionFactor,1,,"Enlarge both radii by this factor (if >1), to permit creation of distant interactions.")) ); FUNCTOR2D(Sphere,GridConnection); DEFINE_FUNCTOR_ORDER_2D(Sphere,GridConnection); }; REGISTER_SERIALIZABLE(Ig2_Sphere_GridConnection_ScGridCoGeom); //!################## Laws ##################### //! O/ class Law2_ScGridCoGeom_FrictPhys_CundallStrack: public LawFunctor{ public: virtual bool go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Law2_ScGridCoGeom_FrictPhys_CundallStrack,LawFunctor,"Law between a frictional :yref:`GridConnection` and a frictional :yref:`Sphere`. Almost the same than :yref:`Law2_ScGeom_FrictPhys_CundallStrack`, but the force is divided and applied on the two :yref:`GridNodes` only.", ((bool,neverErase,false,,"Keep interactions even if particles go away from each other (only in case another constitutive law is in the scene, e.g. :yref:`Law2_ScGeom_CapillaryPhys_Capillarity`)")) ((int,plastDissipIx,-1,(Attr::hidden|Attr::noSave),"Index for plastic dissipation (with O.trackEnergy)")) ((int,elastPotentialIx,-1,(Attr::hidden|Attr::noSave),"Index for elastic potential energy (with O.trackEnergy)")) ,, ); FUNCTOR2D(ScGridCoGeom,FrictPhys); }; REGISTER_SERIALIZABLE(Law2_ScGridCoGeom_FrictPhys_CundallStrack); class Law2_ScGridCoGeom_CohFrictPhys_CundallStrack: public LawFunctor{ public: virtual bool go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Law2_ScGridCoGeom_CohFrictPhys_CundallStrack,LawFunctor,"Law between a cohesive frictional :yref:`GridConnection` and a cohesive frictional :yref:`Sphere`. Almost the same than :yref:`Law2_ScGeom6D_CohFrictPhys_CohesionMoment`, but THE ROTATIONAL MOMENTS ARE NOT COMPUTED.", ((bool,neverErase,false,,"Keep interactions even if particles go away from each other (only in case another constitutive law is in the scene, e.g. :yref:`Law2_ScGeom_CapillaryPhys_Capillarity`)")) ((int,plastDissipIx,-1,(Attr::hidden|Attr::noSave),"Index for plastic dissipation (with O.trackEnergy)")) ,, ); FUNCTOR2D(ScGridCoGeom,CohFrictPhys); }; REGISTER_SERIALIZABLE(Law2_ScGridCoGeom_CohFrictPhys_CundallStrack); //! -/- class Law2_GridCoGridCoGeom_FrictPhys_CundallStrack: public Law2_ScGeom_FrictPhys_CundallStrack{ public: virtual bool go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I); YADE_CLASS_BASE_DOC_ATTRS(Law2_GridCoGridCoGeom_FrictPhys_CundallStrack,Law2_ScGeom_FrictPhys_CundallStrack,"Frictional elastic contact law between two :yref:`gridConnection` . See :yref:`Law2_ScGeom_FrictPhys_CundallStrack` for more details.", /*ATTRS*/ ); FUNCTOR2D(GridCoGridCoGeom,FrictPhys); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_GridCoGridCoGeom_FrictPhys_CundallStrack); //!################## Bounds ##################### class Bo1_GridConnection_Aabb : public BoundFunctor { public : void go(const shared_ptr& cm, shared_ptr& bv, const Se3r&, const Body*); FUNCTOR1D(GridConnection); YADE_CLASS_BASE_DOC_ATTRS(Bo1_GridConnection_Aabb,BoundFunctor,"Functor creating :yref:`Aabb` from a :yref:`GridConnection`.", ((Real,aabbEnlargeFactor,((void)"deactivated",-1),,"Relative enlargement of the bounding box; deactivated if negative.")) ); }; REGISTER_SERIALIZABLE(Bo1_GridConnection_Aabb); //!################## Rendering ##################### #ifdef YADE_OPENGL class Gl1_GridConnection : public GlShapeFunctor{ private: //static int glCylinderList; //void subdivideTriangle(Vector3r& v1,Vector3r& v2,Vector3r& v3, int depth); void drawCylinder(bool wire, Real radius, Real length, const Quaternionr& shift=Quaternionr::Identity()); //void initGlLists(void); public: virtual void go(const shared_ptr&, const shared_ptr&,bool,const GLViewInfo&); void out( Quaternionr q ); YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_GridConnection,GlShapeFunctor,"Renders :yref:`Cylinder` object", ((bool,wire,false,,"Only show wireframe (controlled by ``glutSlices`` and ``glutStacks``.")) ((bool,glutNormalize,true,,"Fix normals for non-wire rendering")) ((int,glutSlices,8,,"Number of cylinder slices.")) ((int,glutStacks,4,,"Number of cylinder stacks.")) ); RENDERS(GridConnection); }; REGISTER_SERIALIZABLE(Gl1_GridConnection); #endif trunk-2017.01a/pkg/common/Grid_GUI.cpp000066400000000000000000000053571304022710500173420ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2012 by François Kneib francois.kneib@gmail.com * * Copyright (C) 2012 by Bruno Chareyre bruno.chareyre@hmg.inpg.fr * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "Grid.hpp" #ifdef YADE_OPENGL #include //!################## Rendering ##################### bool Gl1_GridConnection::wire; bool Gl1_GridConnection::glutNormalize; int Gl1_GridConnection::glutSlices; int Gl1_GridConnection::glutStacks; void Gl1_GridConnection::out( Quaternionr q ) { AngleAxisr aa(q); std::cout << " axis: " << aa.axis()[0] << " " << aa.axis()[1] << " " << aa.axis()[2] << ", angle: " << aa.angle() << " | "; } void Gl1_GridConnection::go(const shared_ptr& cm, const shared_ptr& st ,bool wire2, const GLViewInfo&) { GridConnection *GC=static_cast(cm.get()); Real r=GC->radius; Real length=GC->getLength(); const shared_ptr intr = scene->interactions->find((int)GC->node1->getId(),(int)GC->node2->getId()); Vector3r segt = GC->node2->state->pos - GC->node1->state->pos; if (scene->isPeriodic && intr) segt+=scene->cell->intrShiftPos(intr->cellDist); //glMaterialv(GL_FRONT, GL_AMBIENT_AND_DIFFUSE, Vector3f(cm->color[0],cm->color[1],cm->color[2])); glColor3v(cm->color); if(glutNormalize) glPushAttrib(GL_NORMALIZE); // glPushMatrix(); Quaternionr shift; shift.setFromTwoVectors(Vector3r::UnitZ(),segt); if(intr){drawCylinder(wire || wire2, r,length,shift);} // if (intr && scene->isPeriodic) { glTranslatef(-segt[0],-segt[1],-segt[2]); drawCylinder(wire || wire2, r,length,-shift);} if(glutNormalize) glPopAttrib(); // glPopMatrix(); return; } void Gl1_GridConnection::drawCylinder(bool wire, Real radius, Real length, const Quaternionr& shift) { glPushMatrix(); GLUquadricObj *quadObj = gluNewQuadric(); gluQuadricDrawStyle(quadObj, (GLenum) (wire ? GLU_SILHOUETTE : GLU_FILL)); gluQuadricNormals(quadObj, (GLenum) GLU_SMOOTH); gluQuadricOrientation(quadObj, (GLenum) GLU_OUTSIDE); AngleAxisr aa(shift); glRotatef(aa.angle()*180.0/Mathr::PI,aa.axis()[0],aa.axis()[1],aa.axis()[2]); gluCylinder(quadObj, radius, radius, length, glutSlices,glutStacks); gluQuadricOrientation(quadObj, (GLenum) GLU_INSIDE); //glutSolidSphere(radius,glutSlices,glutStacks); glTranslatef(0.0,0.0,length); //glutSolidSphere(radius,glutSlices,glutStacks); // gluDisk(quadObj,0.0,radius,glutSlices,_loops); gluDeleteQuadric(quadObj); glPopMatrix(); } YADE_PLUGIN((Gl1_GridConnection)); #endif trunk-2017.01a/pkg/common/InsertionSortCollider.cpp000066400000000000000000000621521304022710500222450ustar00rootroot00000000000000// 2009 © Václav Šmilauer // 2013 © Bruno Chareyre #include"InsertionSortCollider.hpp" #include #include #include #include #include #include #include #ifdef YADE_OPENMP #include #endif YADE_PLUGIN((InsertionSortCollider)) CREATE_LOGGER(InsertionSortCollider); // called by the insertion sort if 2 bodies swapped their bounds in such a way that a new overlap may appear void InsertionSortCollider::handleBoundInversion(Body::id_t id1, Body::id_t id2, InteractionContainer* interactions, Scene*){ assert(!periodic); assert(id1!=id2); if (spatialOverlap(id1,id2) && Collider::mayCollide(Body::byId(id1,scene).get(),Body::byId(id2,scene).get()) && !interactions->found(id1,id2)) interactions->insert(shared_ptr(new Interaction(id1,id2))); } void InsertionSortCollider::insertionSort(VecBounds& v, InteractionContainer* interactions, Scene*, bool doCollide){ assert(!periodic); assert(v.size==(long)v.vec.size()); for(long i=1; i=0 && v[j]>viInit){ v[j+1]=v[j]; // no collisions without bounding boxes // also, do not collide body with itself; it sometimes happens for facets aligned perpendicular to an axis, for reasons that are not very clear // see https://bugs.launchpad.net/yade/+bug/669095 // skip bounds with same isMin flags, since inversion doesn't imply anything in that case if(isMin && !v[j].flags.isMin && doCollide && viInitBB && v[j].flags.hasBB && (viInit.id!=v[j].id)) { /*if (isMin)*/ handleBoundInversion(viInit.id,v[j].id,interactions,scene); // else handleBoundSplit(viInit.id,v[j].id,interactions,scene); } j--; } v[j+1]=viInit; } } //Periodic version, only for non-periodic case at the moment (feel free to implement for the periodic case...) void InsertionSortCollider::insertionSortParallel(VecBounds& v, InteractionContainer* interactions, Scene*, bool doCollide){ #ifdef YADE_OPENMP assert(!periodic); assert(v.size==(long)v.vec.size()); if (ompThreads<=1) return insertionSort(v,interactions, scene, doCollide); Real chunksVerlet = 4*verletDist;//is 2* the theoretical requirement? if (chunksVerlet<=0) {LOG_ERROR("Parallel insertion sort needs verletDist>0");} ///chunks defines subsets of the bounds lists, we make sure they are not too small wrt. verlet dist. std::vector chunks; unsigned nChunks = ompThreads; unsigned chunkSize = unsigned(v.size/nChunks)+1; for(unsigned n=0; n1){ bool changeChunks=false; for(unsigned n=1; n(v[chunks[n]].coord-v[chunks[n-1]].coord)) changeChunks=true; if (!changeChunks) break; nChunks--; chunkSize = unsigned(v.size/nChunks)+1; chunks.clear(); for(unsigned n=0; n > > newInteractions; newInteractions.resize(ompThreads,std::vector >()); for (int kk=0; kk0 ? min(ompThreads,omp_get_max_threads()) : omp_get_max_threads()) for (unsigned k=0; k=chunks[k] && v[j]>viInit){ v[j+1]=v[j]; if(isMin && !v[j].flags.isMin && doCollide && viInitBB && v[j].flags.hasBB && (viInit.id!=v[j].id)) { const Body::id_t& id1 = v[j].id; const Body::id_t& id2 = viInit.id; if (spatialOverlap(id1,id2) && Collider::mayCollide(Body::byId(id1,scene).get(),Body::byId(id2,scene).get()) && !interactions->found(id1,id2)) newInteractions[threadNum].push_back(std::pair(v[j].id,viInit.id)); } j--; } v[j+1]=viInit; } } ///In the second sort, the chunks are connected consistently. ///If sorting requires to move a bound past half-chunk, the algorithm is not thread safe, /// if it happens we run the 1-thread sort at the end bool parallelFailed=false; #pragma omp parallel for schedule(dynamic,1) num_threads(ompThreads>0 ? min(ompThreads,omp_get_max_threads()) : omp_get_max_threads()) for (unsigned k=1; k=halfChunkStart && viInitfound(id1,id2)) newInteractions[threadNum].push_back(std::pair(v[j].id,viInit.id));} j--; } v[j+1]=viInit; if (j=halfChunkEnd) parallelFailed=true; } /// Now insert interactions sequentially for (int n=0;nfound(newInteractions[n][k].first,newInteractions[n][k].second))*/ //Not needed, already checked above interactions->insert(shared_ptr(new Interaction(newInteractions[n][k].first,newInteractions[n][k].second))); /// If some bounds traversed more than a half-chunk, we complete colliding with the sequential sort if (parallelFailed) return insertionSort(v,interactions, scene, doCollide); #endif } vector InsertionSortCollider::probeBoundingVolume(const Bound& bv){ if(periodic){ throw invalid_argument("InsertionSortCollider::probeBoundingVolume: handling periodic boundary not implemented."); } vector ret; for( vector::iterator it=BB[0].vec.begin(),et=BB[0].vec.end(); it < et; ++it) { if (it->coord > bv.max[0]) break; if (!it->flags.isMin || !it->flags.hasBB) continue; int offset = 3*it->id; const shared_ptr& b=Body::byId(it->id,scene); if(!b || !b->bound) continue; const Real& sweepLength = b->bound->sweepLength; Vector3r disp = b->state->pos - b->bound->refPos; if (!(maxima[offset]-sweepLength+disp[0] < bv.min[0] || minima[offset]+sweepLength+disp[0] > bv.max[0] || minima[offset+1]+sweepLength+disp[1] > bv.max[1] || maxima[offset+1]-sweepLength+disp[1] < bv.min[1] || minima[offset+2]+sweepLength+disp[2] > bv.max[2] || maxima[offset+2]-sweepLength+disp[2] < bv.min[2] )) { ret.push_back(it->id); } } return ret; } // STRIDE bool InsertionSortCollider::isActivated(){ // activated if number of bodies changes (hence need to refresh collision information) // or the time of scheduled run already came, or we were never scheduled yet if(!strideActive) return true; if(!newton) return true; if(fastestBodyMaxDist<0){fastestBodyMaxDist=0; return true;} fastestBodyMaxDist=newton->maxVelocitySq; if(fastestBodyMaxDist>=1 || fastestBodyMaxDist==0) return true; if((size_t)BB[0].size!=2*scene->bodies->size()) return true; if(scene->interactions->dirty) return true; if(scene->doSort) { scene->doSort=false; return true; } return false; } void InsertionSortCollider::action(){ #ifdef ISC_TIMING timingDeltas->start(); #endif long nBodies=(long)scene->bodies->size(); InteractionContainer* interactions=scene->interactions.get(); scene->interactions->iterColliderLastRun=-1; #ifdef YADE_OPENMP if (ompThreads<=0) ompThreads = omp_get_max_threads(); #endif // periodicity changed, force reinit if(scene->isPeriodic != periodic){ for(int i=0; i<3; i++) BB[i].vec.clear(); periodic=scene->isPeriodic; } // pre-conditions // adjust storage size bool doInitSort=false; if (doSort) { doInitSort=true; doSort=false; } if(BB[0].size!=2*nBodies){ long BBsize=BB[0].size; LOG_DEBUG("Resize bounds containers from "<200 || BBsize==0) doInitSort=true; assert((BBsize%2)==0); for(int i=0; i<3; i++){ BB[i].vec.reserve(2*nBodies); // add lower and upper bounds; coord is not important, will be updated from bb shortly for(long id=BBsize/2; idbodies->size()); //Increase the size of force container. scene->forces.addMaxId(2*scene->bodies->size()); // update periodicity assert(BB[0].axis==0); assert(BB[1].axis==1); assert(BB[2].axis==2); if(periodic) for(int i=0; i<3; i++) BB[i].updatePeriodicity(scene); if(verletDist<0){ Real minR=std::numeric_limits::infinity(); FOREACH(const shared_ptr& b, *scene->bodies){ if(!b || !b->shape) continue; Sphere* s=dynamic_cast(b->shape.get()); if(!s) continue; minR=min(s->radius,minR); } if (std::isinf(minR)) LOG_ERROR("verletDist is set to 0 because no spheres were found. It will result in suboptimal performances, consider setting a positive verletDist in your script."); // if no spheres, disable stride verletDist=std::isinf(minR) ? 0 : std::abs(verletDist)*minR; } // if interactions are dirty, force reinitialization if(scene->interactions->dirty){ doInitSort=true; scene->interactions->dirty=false; } // update bounds via boundDispatcher boundDispatcher->scene=scene; boundDispatcher->sweepDist=verletDist; boundDispatcher->minSweepDistFactor=minSweepDistFactor; boundDispatcher->targetInterv=targetInterv; boundDispatcher->updatingDispFactor=updatingDispFactor; boundDispatcher->action(); ISC_CHECKPOINT("boundDispatcher"); // STRIDE if(verletDist>0){ // get NewtonIntegrator, to ask for the maximum velocity value if(!newton){ FOREACH(shared_ptr& e, scene->engines){ newton=YADE_PTR_DYN_CAST(e); if(newton) break; } if(!newton){ throw runtime_error("InsertionSortCollider.verletDist>0, but unable to locate NewtonIntegrator within O.engines."); } } } // STRIDE // get us ready for strides, if they were deactivated if(!strideActive && verletDist>0 && newton->maxVelocitySq>=0) strideActive=true; if(strideActive){ assert(verletDist>0); assert(strideActive); assert(newton->maxVelocitySq>=0); newton->updatingDispFactor=updatingDispFactor; } else boundDispatcher->sweepDist=0; ISC_CHECKPOINT("bound"); // copy bounds along given axis into our arrays #pragma omp parallel for schedule(guided) num_threads(ompThreads>0 ? min(ompThreads,omp_get_max_threads()) : omp_get_max_threads()) for(long i=0; i<2*nBodies; i++){ // const long cacheIter = scene->iter; for(int j=0; j<3; j++){ VecBounds& BBj=BB[j]; Bounds& BBji = BBj[i]; const Body::id_t id=BBji.id; const shared_ptr& b=Body::byId(id,scene); if(b){ const shared_ptr& bv=b->bound; // coordinate is min/max if has bounding volume, otherwise both are the position. Add periodic shift so that we are inside the cell // watch out for the parentheses around ?: within ?: (there was unwanted conversion of the Reals to bools!) BBji.coord=((BBji.flags.hasBB=((bool)bv)) ? (BBji.flags.isMin ? bv->min[j] : bv->max[j]) : (b->state->pos[j])) - (periodic ? BBj.cellDim*BBji.period : 0.); // if initializing periodic, shift coords & record the period into BBj[i].period if(doInitSort && periodic) BBji.coord=cellWrap(BBji.coord,0,BBj.cellDim,BBji.period); // for each body, copy its minima and maxima, for quick checks of overlaps later //bounds have been all updated when j==0, we can safely copy them here when j==1 if (BBji.flags.isMin && j==1 &&bv) { memcpy(&minima[3*id],&bv->min,3*sizeof(Real)); memcpy(&maxima[3*id],&bv->max,3*sizeof(Real)); } } else { BBj[i].flags.hasBB=false; /* for vanished body, keep the coordinate as-is, to minimize inversions. */ } } } ISC_CHECKPOINT("copy"); // remove interactions which have disconnected bounds and are not real (will run parallel if YADE_OPENMP) interactions->conditionalyEraseNonReal(*this,scene); ISC_CHECKPOINT("erase"); // sort // the regular case if(!doInitSort && !sortThenCollide){ /* each inversion in insertionSort calls may add interaction */ //1000 bodies is heuristic minimum above which parallel sort is called if(!periodic) for(int i=0; i<3; i++) { #ifdef YADE_OPENMP if (ompThreads<=1 || nBodies<1000) insertionSort(BB[i],interactions,scene); else insertionSortParallel(BB[i],interactions,scene);} #else insertionSort(BB[i],interactions,scene);} #endif else for(int i=0; i<3; i++) insertionSortPeri(BB[i],interactions,scene); } // create initial interactions (much slower) else { if(doInitSort){ // the initial sort is in independent in 3 dimensions, may be run in parallel; it seems that there is no time gain running in parallel, though // important to reset loInx for periodic simulation (!!) // #pragma omp parallel for schedule(dynamic,1) num_threads(min(ompThreads,3)) for(int i=0; i<3; i++) { BB[i].loIdx=0; std::sort(BB[i].vec.begin(),BB[i].vec.end()); } numReinit++; } else { // sortThenCollide if(!periodic) for(int i=0; i<3; i++) insertionSort(BB[i],interactions,scene,false); else for(int i=0; i<3; i++) insertionSortPeri(BB[i],interactions,scene,false); } // traverse the container along requested axis assert(sortAxis==0 || sortAxis==1 || sortAxis==2); VecBounds& V=BB[sortAxis]; // go through potential aabb collisions, create interactions as necessary if(!periodic){ #ifdef YADE_OPENMP std::vector > > newInts; newInts.resize(ompThreads,std::vector >()); for (int kk=0; kk(iid,jid)); #else if (!interactions->found(iid,jid)) interactions->insert(shared_ptr(new Interaction(iid,jid))); #endif } } } //go through newly created candidates sequentially, duplicates coming from different threads may exist so we check existence with found() #ifdef YADE_OPENMP for (int n=0;nfound(newInts[n][k].first,newInts[n][k].second)) interactions->insert(shared_ptr(new Interaction(newInts[n][k].first,newInts[n][k].second))); #endif } else { // periodic case: see comments above for(long i=0; i<2*nBodies; i++){ if(!(V[i].flags.isMin && V[i].flags.hasBB)) continue; const Body::id_t& iid=V[i].id; long cnt=0; // we might wrap over the periodic boundary here; that's why the condition is different from the aperiodic case for(long j=V.norm(i+1); V[j].id!=iid; j=V.norm(j+1)){ const Body::id_t& jid=V[j].id; if(!(V[j].flags.isMin && V[j].flags.hasBB)) continue; handleBoundInversionPeri(iid,jid,interactions,scene); if(cnt++>2*(long)nBodies){ LOG_FATAL("Uninterrupted loop in the initial sort?"); throw std::logic_error("loop??"); } } } } } ISC_CHECKPOINT("sort&collide"); } // return floating value wrapped between x0 and x1 and saving period number to period Real InsertionSortCollider::cellWrap(const Real x, const Real x0, const Real x1, int& period){ Real xNorm=(x-x0)/(x1-x0); period=(int)floor(xNorm); // some people say this is very slow; probably optimized by gcc, however (google suggests) return x0+(xNorm-period)*(x1-x0); } // return coordinate wrapped to 0…x1, relative to x0; don't care about period Real InsertionSortCollider::cellWrapRel(const Real x, const Real x0, const Real x1){ Real xNorm=(x-x0)/(x1-x0); return (xNorm-floor(xNorm))*(x1-x0); } void InsertionSortCollider::insertionSortPeri(VecBounds& v, InteractionContainer* interactions, Scene*, bool doCollide){ assert(periodic); long &loIdx=v.loIdx; const long &size=v.size; for(long _i=0; _ivi.coord + /* wrap for elt just below split */ (v.norm(j+1)==loIdx ? v.cellDim : 0)){ long j1=v.norm(j+1); // OK, now if many bodies move at the same pace through the cell and at one point, there is inversion, // this can happen without any side-effects if (false && v[j].coord>2*v.cellDim){ // this condition is not strictly necessary, but the loop of insertionSort would have to run more times. // Since size of particle is required to be < .5*cellDim, this would mean simulation explosion anyway LOG_FATAL("Body #"<found(id1,id2)){ shared_ptr newI=shared_ptr(new Interaction(id1,id2)); newI->cellDist=periods; interactions->insert(newI); } } /* Performance hint ================ Since this function is called (most the time) from insertionSort, we actually already know what is the overlap status in that one dimension, including periodicity information; both values could be passed down as a parameters, avoiding 1 of 3 loops here. We do some floats math here, so the speedup could noticeable; doesn't concertn the non-periodic variant, where it is only plain comparisons taking place. In the same way, handleBoundInversion is passed only id1 and id2, but again insertionSort already knows in which sense the inversion happens; if the boundaries get apart (min getting up over max), it wouldn't have to check for overlap at all, for instance. */ //! return true if bodies bb overlap in all 3 dimensions bool InsertionSortCollider::spatialOverlapPeri(Body::id_t id1, Body::id_t id2,Scene* scene, Vector3i& periods) const { assert(periodic); assert(id1!=id2); // programming error, or weird bodies (too large?) for(int axis=0; axis<3; axis++){ Real dim=scene->cell->getSize()[axis]; // LOG_DEBUG("dim["<= mn2)) return false;} } return true; } boost::python::tuple InsertionSortCollider::dumpBounds(){ boost::python::list bl[3]; // 3 bound lists, inserted into the tuple at the end for(int axis=0; axis<3; axis++){ VecBounds& V=BB[axis]; if(periodic){ for(long i=0; iisPeriodic); assert(axis>=0 && axis <=2); cellDim=scene->cell->getSize()[axis]; } trunk-2017.01a/pkg/common/InsertionSortCollider.hpp000066400000000000000000000334071304022710500222530ustar00rootroot00000000000000// 2009 © Václav Šmilauer // 2013 © Bruno Chareyre #pragma once #include #include class InteractionContainer; /*! Periodic collider notes. Architecture ============ Values from bounding boxes are added information about period in which they are. Their container (VecBounds) holds position of where the space wraps. The sorting algorithm is changed in such way that periods are changed when body crosses cell boundary. Interaction::cellDist holds information about relative cell coordinates of the 2nd body relative to the 1st one. Dispatchers (IGeomDispatcher and InteractionLoop) use this information to pass modified position of the 2nd body to IGeomFunctors. Since properly behaving IGeomFunctor's and LawFunctor's do not take positions directly from Body::state, the interaction is computed with the periodic positions. Positions of bodies (in the sense of Body::state) and their natural bboxes are not wrapped to the periodic cell, they can be anywhere (but not "too far" in the sense of int overflow). Since Interaction::cellDists holds cell coordinates, it is possible to change the cell boundaries at runtime. This should make it easy to implement some stress control on the top. Clumps do not interfere with periodicity in any way. Rendering --------- OpenGLRenderer renders Shape at all periodic positions that touch the periodic cell (i.e. Bounds crosses its boundary). It seems to affect body selection somehow, but that is perhaps not related at all. Periodicity control =================== c++: Scene::isPeriodic, Scene::cellSize python: O.periodicCell=((0,0,0),(10,10,10) # activates periodic boundary O.periodicCell=() # deactivates periodic boundary Requirements ============ * By default, no body can have Aabb larger than about .499*cellSize. Exception is thrown if that is false. Large bodies are accepted if allowBiggerThanPeriod (experimental) * Constitutive law must not get body positions from Body::state directly. If it does, it uses Interaction::cellDist to compute periodic position. * No body can get further away than MAXINT periods. It will do horrible things if there is overflow. Not checked at the moment. * Body cannot move over distance > cellSize in one step. Since body size is limited as well, that would mean simulation explosion. Exception is thrown if the movement is upwards. If downwards, it is not handled at all. Possible performance improvements & bugs ======================================== * PeriodicInsertionSortCollider::{cellWrap,cellWrapRel} OpenGLRenderer::{wrapCell,wrapCellPt} Shop::PeriodicWrap are all very similar functions. They should be put into separate header and included from all those places. */ // #define this macro to enable timing within this engine // #define ISC_TIMING #ifdef ISC_TIMING #define ISC_CHECKPOINT(cpt) timingDeltas->checkpoint(cpt) #else #define ISC_CHECKPOINT(cpt) #endif class NewtonIntegrator; class Integrator; class GeneralIntegratorInsertionSortCollider;// Forward decleration of child to decleare it as friend class InsertionSortCollider: public Collider{ friend class GeneralIntegratorInsertionSortCollider; //! struct for storing bounds of bodies struct Bounds{ //! coordinate along the given sortAxis Real coord; //! id of the body this bound belongs to Body::id_t id; //! periodic cell coordinate int period; //! is it the minimum (true) or maximum (false) bound? struct {bool hasBB:true, isMin:true;} flags; Bounds(Real coord_, Body::id_t id_, bool isMin): coord(coord_), id(id_), period(0){ flags.isMin=isMin; } bool operator<(const Bounds& b) const { /* handle special case of zero-width bodies, which could otherwise get min/max swapped in the unstable std::sort */ if(id==b.id && coord==b.coord) return flags.isMin; return coord(const Bounds& b) const { if(id==b.id && coord==b.coord) return !flags.isMin; return coord>b.coord; } }; // we need this to find out about current maxVelocitySq shared_ptr newton; // if False, no type of striding is used // if True, then either verletDist XOR nBins is set bool strideActive; struct VecBounds{ // axis set in the ctor int axis; std::vector vec; Real cellDim; // cache vector size(), update at every step in action() long size; // index of the lowest coordinate element, before which the container wraps long loIdx; Bounds& operator[](long idx){ assert(idx=0); return vec[idx]; } const Bounds& operator[](long idx) const { assert(idx=0); return vec[idx]; } // update number of bodies, periodic properties and size from Scene void updatePeriodicity(Scene* ); // normalize given index to the right range (wraps around) long norm(long i) const { if(i<0) i+=size; long ret=i%size; assert(ret>=0 && ret maxima, minima; //! Whether the Scene was periodic (to detect the change, which shouldn't happen, but shouldn't crash us either) bool periodic; // return python representation of the BB struct, as ([...],[...],[...]). boost::python::tuple dumpBounds(); /*! sorting routine; insertion sort is very fast for strongly pre-sorted lists, which is our case http://en.wikipedia.org/wiki/Insertion_sort has the algorithm and other details */ void insertionSort(VecBounds& v,InteractionContainer*,Scene*,bool doCollide=true); void insertionSortParallel(VecBounds& v,InteractionContainer*,Scene*,bool doCollide=true); void handleBoundInversion(Body::id_t,Body::id_t,InteractionContainer*,Scene*); // periodic variants void insertionSortPeri(VecBounds& v,InteractionContainer*,Scene*,bool doCollide=true); void handleBoundInversionPeri(Body::id_t,Body::id_t,InteractionContainer*,Scene*); void handleBoundSplit(Body::id_t,Body::id_t,InteractionContainer*,Scene*); bool spatialOverlapPeri(Body::id_t,Body::id_t,Scene*,Vector3i&) const; inline bool spatialOverlap(const Body::id_t& id1, const Body::id_t& id2) const { assert(!periodic); return (minima[3*id1+0]<=maxima[3*id2+0]) && (maxima[3*id1+0]>=minima[3*id2+0]) && (minima[3*id1+1]<=maxima[3*id2+1]) && (maxima[3*id1+1]>=minima[3*id2+1]) && (minima[3*id1+2]<=maxima[3*id2+2]) && (maxima[3*id1+2]>=minima[3*id2+2]); } static Real cellWrap(const Real, const Real, const Real, int&); static Real cellWrapRel(const Real, const Real, const Real); public: //! Predicate called from loop within InteractionContainer::erasePending bool shouldBeErased(Body::id_t id1, Body::id_t id2, Scene* rb) const { if(!periodic) return !spatialOverlap(id1,id2); else { Vector3i periods; return !spatialOverlapPeri(id1,id2,rb,periods); } } virtual bool isActivated(); // force reinitialization at next run virtual void invalidatePersistentData(){ for(int i=0; i<3; i++){ BB[i].vec.clear(); BB[i].size=0; }} vector probeBoundingVolume(const Bound&); virtual void action(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(InsertionSortCollider,Collider,"\ Collider with O(n log(n)) complexity, using :yref:`Aabb` for bounds.\ \n\n\ At the initial step, Bodies' bounds (along :yref:`sortAxis`) are first std::sort'ed along this (sortAxis) axis, then collided. The initial sort has :math:`O(n^2)` complexity, see `Colliders' performance `_ for some information (There are scripts in examples/collider-perf for measurements). \ \n\n \ Insertion sort is used for sorting the bound list that is already pre-sorted from last iteration, where each inversion calls checkOverlap which then handles either overlap (by creating interaction if necessary) or its absence (by deleting interaction if it is only potential). \ \n\n \ Bodies without bounding volume (such as clumps) are handled gracefully and never collide. Deleted bodies are handled gracefully as well.\ \n\n \ This collider handles periodic boundary conditions. There are some limitations, notably:\ \n\n \ #. No body can have Aabb larger than cell's half size in that respective dimension. You get exception if it does and gets in interaction. One way to explicitly by-pass this restriction is offered by ``allowBiggerThanPeriod``, which can be turned on to insert a floor in the form of a very large box for instance (see examples/periodicSandPile.py). \ \n\n \ #. No body can travel more than cell's distance in one step; this would mean that the simulation is numerically exploding, and it is only detected in some cases.\ \n\n \ **Stride** can be used to avoid running collider at every step by enlarging the particle's bounds, tracking their displacements and only re-run if they might have gone out of that bounds (see `Verlet list `_ for brief description and background) . This requires cooperation from :yref:`NewtonIntegrator` as well as :yref:`BoundDispatcher`, which will be found among engines automatically (exception is thrown if they are not found).\ \n\n \ If you wish to use strides, set ``verletDist`` (length by which bounds will be enlarged in all directions) to some value, e.g. 0.05 × typical particle radius. This parameter expresses the tradeoff between many potential interactions (running collider rarely, but with longer exact interaction resolution phase) and few potential interactions (running collider more frequently, but with less exact resolutions of interactions); it depends mainly on packing density and particle radius distribution.\ \n\n \ If ``targetInterv`` is >1, not all particles will have their bound enlarged by ``verletDist``; instead, they will have bounds increased by a length in order to trigger a new colliding after ``targetInterv`` iteration, assuming they move at almost constant velocity. Ideally in this method, all particles would reach their bounds at the sime iteration. This is of course not the case as soon as velocities fluctuate in time. :yref:`Bound::sweepLength` is tuned on the basis of the displacement recorded between the last two runs of the collider. In this situation, ``verletDist`` defines the maximum sweep length.\ ", ((int,sortAxis,0,,"Axis for the initial contact detection.")) ((bool,allowBiggerThanPeriod,false,,"If true, tests on bodies sizes will be disabled, and the simulation will run normaly even if bodies larger than period are found. It can be useful when the periodic problem include e.g. a floor modelized with wall/box/facet.\nBe sure you know what you are doing if you touch this flag. The result is undefined if one large body moves out of the (0,0,0) period.")) ((bool,sortThenCollide,false,,"Separate sorting and colliding phase; it is MUCH slower, but all interactions are processed at every step; this effectively makes the collider non-persistent, not remembering last state. (The default behavior relies on the fact that inversions during insertion sort are overlaps of bounding boxes that just started/ceased to exist, and only processes those; this makes the collider much more efficient.)")) ((int,targetInterv,50,,"(experimental) Target number of iterations between bound update, used to define a smaller sweep distance for slower grains if >0, else always use 1*verletDist. Useful in simulations with strong velocity contrasts between slow bodies and fast bodies.")) ((Real,updatingDispFactor,-1,,"(experimental) Displacement factor used to trigger bound update: the bound is updated only if updatingDispFactor*disp>sweepDist when >0, else all bounds are updated.")) ((Real,verletDist,((void)"Automatically initialized",-.5),,"Length by which to enlarge particle bounds, to avoid running collider at every step. Stride disabled if zero. Negative value will trigger automatic computation, so that the real value will be *verletDist* × minimum spherical particle radius; if there are no spherical particles, it will be disabled. The actual length added to one bound can be only a fraction of verletDist when :yref:`InsertionSortCollider::targetInterv` is > 0.")) ((Real,minSweepDistFactor,0.1,,"Minimal distance by which enlarge all bounding boxes; superseeds computed value of verletDist when lower that (minSweepDistFactor x verletDist).")) ((Real,fastestBodyMaxDist,-1,,"Normalized maximum displacement of the fastest body since last run; if >= 1, we could get out of bboxes and will trigger full run. |yupdate|")) ((int,numReinit,0,Attr::readonly,"Cummulative number of bound array re-initialization.")) ((Real,useless,,,"for compatibility of scripts defining the old collider's attributes - see deprecated attributes")) ((bool,doSort,false,,"Do forced resorting of interactions.")) , /* ctor */ #ifdef ISC_TIMING timingDeltas=shared_ptr(new TimingDeltas); #endif for(int i=0; i<3; i++) BB[i].axis=i; periodic=false; strideActive=false; , /* py */ .def_readonly("strideActive",&InsertionSortCollider::strideActive,"Whether striding is active (read-only; for debugging). |yupdate|") .def_readonly("periodic",&InsertionSortCollider::periodic,"Whether the collider is in periodic mode (read-only; for debugging) |yupdate|") .def("dumpBounds",&InsertionSortCollider::dumpBounds,"Return representation of the internal sort data. The format is ``([...],[...],[...])`` for 3 axes, where each ``...`` is a list of entries (bounds). The entry is a tuple with the fllowing items:\n\n* coordinate (float)\n* body id (int), but negated for negative bounds\n* period numer (int), if the collider is in the periodic regime.") ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(InsertionSortCollider); trunk-2017.01a/pkg/common/InteractionLoop.cpp000066400000000000000000000152031304022710500210510ustar00rootroot00000000000000#include"InteractionLoop.hpp" YADE_PLUGIN((InteractionLoop)); CREATE_LOGGER(InteractionLoop); void InteractionLoop::pyHandleCustomCtorArgs(boost::python::tuple& t, boost::python::dict& d){ if(boost::python::len(t)==0) return; // nothing to do if(boost::python::len(t)!=3) throw invalid_argument("Exactly 3 lists of functors must be given"); // parse custom arguments (3 lists) and do in-place modification of args using vecGeom = std::vector >; using vecPhys = std::vector >; using vecLaw = std::vector >; vecGeom vg=boost::python::extract(t[0])(); vecPhys vp=boost::python::extract(t[1])(); vecLaw vl=boost::python::extract(t[2])(); for(const auto gf : vg) this->geomDispatcher->add(gf); for(const auto pf : vp) this->physDispatcher->add(pf); for(const auto cf : vl) this->lawDispatcher->add(cf); t=boost::python::tuple(); // empty the args; not sure if this is OK, as there is some refcounting in raw_constructor code } void InteractionLoop::action(){ // update Scene* of the dispatchers lawDispatcher->scene=scene; physDispatcher->scene=scene; geomDispatcher->scene=scene; // ask dispatchers to update Scene* of their functors geomDispatcher->updateScenePtr(); physDispatcher->updateScenePtr(); lawDispatcher->updateScenePtr(); /* initialize callbacks; they return pointer (used only in this timestep) to the function to be called returning NULL deactivates the callback in this timestep */ // pair of callback object and pointer to the function to be called vector callbackPtrs; for (const auto cb : callbacks){ cb->scene=scene; callbackPtrs.push_back(cb->stepInit()); } assert(callbackPtrs.size()==callbacks.size()); const size_t callbacksSize=callbacks.size(); // cache transformed cell size Matrix3r cellHsize = Matrix3r::Zero(); if(scene->isPeriodic) { cellHsize=scene->cell->hSize; } // force removal of interactions that were not encountered by the collider // (only for some kinds of colliders; see comment for InteractionContainer::iterColliderLastRun) const bool removeUnseenIntrs=(scene->interactions->iterColliderLastRun>=0 && scene->interactions->iterColliderLastRun==scene->iter); #ifdef YADE_OPENMP const long size=scene->interactions->size(); #pragma omp parallel for schedule(guided) num_threads(ompThreads>0 ? min(ompThreads,omp_get_max_threads()) : omp_get_max_threads()) for(long i=0; i& I=(*scene->interactions)[i]; #else for (const auto & I : *scene->interactions){ #endif if(removeUnseenIntrs && !I->isReal() && I->iterLastSeeniter) { eraseAfterLoop(I->getId1(),I->getId2()); continue; } const shared_ptr& b1_=Body::byId(I->getId1(),scene); const shared_ptr& b2_=Body::byId(I->getId2(),scene); if(!b1_ || !b2_){ LOG_DEBUG("Body #"<<(b1_?I->getId2():I->getId1())<<" vanished, erasing intr #"<getId1()<<"+#"<getId2()<<"!"); scene->interactions->requestErase(I); continue; } // Skip interaction with clumps if (b1_->isClump() || b2_->isClump()) { continue; } // we know there is no geometry functor already, take the short path if(!I->functorCache.geomExists) { assert(!I->isReal()); continue; } // no interaction geometry for either of bodies; no interaction possible if(!b1_->shape || !b2_->shape) { assert(!I->isReal()); continue; } bool swap=false; // IGeomDispatcher if(!I->functorCache.geom){ I->functorCache.geom=geomDispatcher->getFunctor2D(b1_->shape,b2_->shape,swap); // returns NULL ptr if no functor exists; remember that and shortcut if(!I->functorCache.geom) { I->functorCache.geomExists=false; continue; } } // arguments for the geom functor are in the reverse order (dispatcher would normally call goReverse). // we don't remember the fact that is reverse, so we swap bodies within the interaction // and can call go in all cases if(swap){I->swapOrder();} // body pointers must be updated, in case we swapped const shared_ptr& b1=swap?b2_:b1_; const shared_ptr& b2=swap?b1_:b2_; assert(I->functorCache.geom); bool wasReal=I->isReal(); bool geomCreated; if(!scene->isPeriodic){ geomCreated=I->functorCache.geom->go(b1->shape,b2->shape, *b1->state, *b2->state, Vector3r::Zero(), /*force*/false, I); } else { // handle periodicity Vector3r shift2=cellHsize*I->cellDist.cast(); // in sheared cell, apply shear on the mutual position as well geomCreated=I->functorCache.geom->go(b1->shape,b2->shape,*b1->state,*b2->state,shift2,/*force*/false,I); } if(!geomCreated){ if(wasReal) LOG_WARN("IGeomFunctor returned false on existing interaction!"); if(wasReal) scene->interactions->requestErase(I); // fully created interaction without geometry is reset and perhaps erased in the next step continue; // in any case don't care about this one anymore } // IPhysDispatcher if(!I->functorCache.phys){ I->functorCache.phys=physDispatcher->getFunctor2D(b1->material,b2->material,swap); assert(!swap); // InteractionPhysicsEngineUnits are symmetric } if(!I->functorCache.phys){ throw std::runtime_error("Undefined or ambiguous IPhys dispatch for types "+b1->material->getClassName()+" and "+b2->material->getClassName()+"."); } I->functorCache.phys->go(b1->material,b2->material,I); assert(I->phys); if(!wasReal) I->iterMadeReal=scene->iter; // mark the interaction as created right now // LawDispatcher // populating constLaw cache must be done after geom and physics dispatchers have been called, since otherwise the interaction // would not have geom and phys yet. if(!I->functorCache.constLaw){ I->functorCache.constLaw=lawDispatcher->getFunctor2D(I->geom,I->phys,swap); if(!I->functorCache.constLaw){ LOG_FATAL("None of given Law2 functors can handle interaction #"<getId1()<<"+"<getId2()<<", types geom:"<geom->getClassName()<<"="<geom->getClassIndex()<<" and phys:"<phys->getClassName()<<"="<phys->getClassIndex()<<" (LawDispatcher::getFunctor2D returned empty functor)"); exit(1); } assert(!swap); // reverse call would make no sense, as the arguments are of different types } assert(I->functorCache.constLaw); //If the functor return false, the interaction is reset if (!I->functorCache.constLaw->go(I->geom,I->phys,I.get())) scene->interactions->requestErase(I); // process callbacks for this interaction if(!I->isReal()) continue; // it is possible that Law2_ functor called requestErase, hence this check for(size_t i=0; i #pragma once #include #include #include #ifdef USE_TIMING_DELTAS #define TIMING_DELTAS_CHECKPOINT(cpt) timingDeltas->checkpoint(cpt) #define TIMING_DELTAS_START() timingDeltas->start() #else #define TIMING_DELTAS_CHECKPOINT(cpt) #define TIMING_DELTAS_START() #endif class InteractionLoop: public GlobalEngine { bool alreadyWarnedNoCollider; using idPair = std::pair; // store interactions that should be deleted after loop in action, not later #ifdef YADE_OPENMP std::vector > eraseAfterLoopIds; void eraseAfterLoop(Body::id_t id1,Body::id_t id2){ eraseAfterLoopIds[omp_get_thread_num()].push_back(idPair(id1,id2)); } #else list eraseAfterLoopIds; void eraseAfterLoop(Body::id_t id1,Body::id_t id2){ eraseAfterLoopIds.push_back(idPair(id1,id2)); } #endif public: virtual void pyHandleCustomCtorArgs(boost::python::tuple& t, boost::python::dict& d); virtual void action(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(InteractionLoop,GlobalEngine,"Unified dispatcher for handling interaction loop at every step, for parallel performance reasons.\n\n.. admonition:: Special constructor\n\n\tConstructs from 3 lists of :yref:`Ig2`, :yref:`Ip2`, :yref:`Law` functors respectively; they will be passed to interal dispatchers, which you might retrieve.", ((shared_ptr,geomDispatcher,new IGeomDispatcher,Attr::readonly,":yref:`IGeomDispatcher` object that is used for dispatch.")) ((shared_ptr,physDispatcher,new IPhysDispatcher,Attr::readonly,":yref:`IPhysDispatcher` object used for dispatch.")) ((shared_ptr,lawDispatcher,new LawDispatcher,Attr::readonly,":yref:`LawDispatcher` object used for dispatch.")) ((vector >,callbacks,,,":yref:`Callbacks` which will be called for every :yref:`Interaction`, if activated.")) ((bool, eraseIntsInLoop, false,,"Defines if the interaction loop should erase pending interactions, else the collider takes care of that alone (depends on what collider is used).")) , /*ctor*/ alreadyWarnedNoCollider=false; #ifdef YADE_OPENMP eraseAfterLoopIds.resize(omp_get_max_threads()); #endif , /*py*/ ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(InteractionLoop); trunk-2017.01a/pkg/common/KinematicEngines.cpp000066400000000000000000000147461304022710500211700ustar00rootroot00000000000000 #include #include #include #include YADE_PLUGIN((KinematicEngine)(CombinedKinematicEngine)(TranslationEngine)(HarmonicMotionEngine)(RotationEngine)(HelixEngine)(InterpolatingHelixEngine)(HarmonicRotationEngine)(ServoPIDController)(BicyclePedalEngine)); CREATE_LOGGER(KinematicEngine); void KinematicEngine::action(){ if (ids.size()>0) { FOREACH(Body::id_t id,ids){ assert(id<(Body::id_t)scene->bodies->size()); Body* b=Body::byId(id,scene).get(); if(b) b->state->vel=b->state->angVel=Vector3r::Zero(); } apply(ids); } else { LOG_WARN("The list of ids is empty! Can't move any body."); } } void CombinedKinematicEngine::action(){ if (ids.size()>0) { // reset first FOREACH(Body::id_t id,ids){ assert(id<(Body::id_t)scene->bodies->size()); Body* b=Body::byId(id,scene).get(); if(b) b->state->vel=b->state->angVel=Vector3r::Zero(); } // apply one engine after another FOREACH(const shared_ptr& e, comb){ if (e->dead) continue; e->scene=scene; e->apply(ids); } } else { LOG_WARN("The list of ids is empty! Can't move any body."); } } const shared_ptr CombinedKinematicEngine::fromTwo(const shared_ptr& first, const shared_ptr& second){ shared_ptr ret(new CombinedKinematicEngine); ret->ids=first->ids; ret->comb.push_back(first); ret->comb.push_back(second); return ret; } void TranslationEngine::apply(const vector& ids){ if (ids.size()>0) { #ifdef YADE_OPENMP const long size=ids.size(); #pragma omp parallel for schedule(static) for(long i=0; ibodies->size()); Body* b=Body::byId(id,scene).get(); if(!b) continue; b->state->vel+=velocity*translationAxis; } } else { LOG_WARN("The list of ids is empty! Can't move any body."); } } void HarmonicMotionEngine::apply(const vector& ids){ if (ids.size()>0) { Vector3r w = f*2.0*Mathr::PI; //Angular frequency Vector3r velocity = (((w*scene->time + fi).array().sin())*(-1.0)); velocity = velocity.cwiseProduct(A); velocity = velocity.cwiseProduct(w); FOREACH(Body::id_t id,ids){ assert(id<(Body::id_t)scene->bodies->size()); Body* b=Body::byId(id,scene).get(); if(!b) continue; b->state->vel+=velocity; } } else { LOG_WARN("The list of ids is empty! Can't move any body."); } } void InterpolatingHelixEngine::apply(const vector& ids){ Real virtTime=wrap ? Shop::periodicWrap(scene->time,*times.begin(),*times.rbegin()) : scene->time; angularVelocity=linearInterpolate(virtTime,times,angularVelocities,_pos); linearVelocity=angularVelocity*slope; HelixEngine::apply(ids); } void HelixEngine::apply(const vector& ids){ if (ids.size()>0) { const Real& dt=scene->dt; angleTurned+=angularVelocity*dt; shared_ptr bodies = scene->bodies; FOREACH(Body::id_t id,ids){ assert(id<(Body::id_t)bodies->size()); Body* b=Body::byId(id,scene).get(); if(!b) continue; b->state->vel+=linearVelocity*rotationAxis; } rotateAroundZero=true; RotationEngine::apply(ids); } else { LOG_WARN("The list of ids is empty! Can't move any body."); } } void RotationEngine::apply(const vector& ids){ if (ids.size()>0) { #ifdef YADE_OPENMP const long size=ids.size(); #pragma omp parallel for schedule(static) for(long i=0; ibodies->size()); Body* b=Body::byId(id,scene).get(); if(!b) continue; b->state->angVel+=rotationAxis*angularVelocity; if(rotateAroundZero){ const Vector3r l=b->state->pos-zeroPoint; Quaternionr q(AngleAxisr(angularVelocity*scene->dt,rotationAxis)); Vector3r newPos=q*l+zeroPoint; b->state->vel+=Vector3r(newPos-b->state->pos)/scene->dt; } } } else { LOG_WARN("The list of ids is empty! Can't move any body."); } } void HarmonicRotationEngine::apply(const vector& ids){ const Real& time=scene->time; Real w = f*2.0*Mathr::PI; //Angular frequency angularVelocity = -1.0*A*w*sin(w*time + fi); RotationEngine::apply(ids); } void ServoPIDController::apply(const vector& ids){ if (iterPrevStart < 0 or ((scene->iter-iterPrevStart)>=iterPeriod)) { Vector3r tmpForce = Vector3r::Zero(); if (ids.size()>0) { FOREACH(Body::id_t id,ids){ assert(id<(Body::id_t)scene->bodies->size()); tmpForce += scene->forces.getForce(id); } } else { LOG_WARN("The list of ids is empty!"); } axis.normalize(); tmpForce = tmpForce.cwiseProduct(axis); // Take into account given axis errorCur = tmpForce.norm() - target; // Find error const Real pTerm = errorCur*kP; // Calculate proportional term iTerm += errorCur*kI; // Calculate integral term const Real dTerm = (errorCur-errorPrev)*kD; // Calculate derivative term errorPrev = errorCur; // Save the current value of the error curVel = (pTerm + iTerm + dTerm); // Calculate current velocity if (std::abs(curVel) > std::abs(maxVelocity)) { curVel*=std::abs(maxVelocity)/std::abs(curVel); } iterPrevStart = scene->iter; current = tmpForce; } translationAxis = axis; velocity = curVel; TranslationEngine::apply(ids); } void BicyclePedalEngine::apply(const vector& ids){ if (ids.size()>0) { Quaternionr qRotateZVec(Quaternionr().setFromTwoVectors(Vector3r(0,0,1), rotationAxis)); Vector3r newPos = Vector3r(cos(fi + angularVelocity*scene->dt)*radius, sin(fi + angularVelocity*scene->dt)*radius, 0.0); Vector3r oldPos = Vector3r(cos(fi)*radius, sin(fi)*radius, 0.0); Vector3r newVel = (oldPos - newPos)/scene->dt; fi += angularVelocity*scene->dt; newVel = qRotateZVec*newVel; #ifdef YADE_OPENMP const long size=ids.size(); #pragma omp parallel for schedule(static) for(long i=0; ibodies->size()); Body* b=Body::byId(id,scene).get(); if(!b) continue; b->state->vel+=newVel; } } else { LOG_WARN("The list of ids is empty! Can't move any body."); } } trunk-2017.01a/pkg/common/KinematicEngines.hpp000066400000000000000000000204201304022710500211570ustar00rootroot00000000000000 #pragma once #include #include struct KinematicEngine; struct CombinedKinematicEngine: public PartialEngine{ virtual void action(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(CombinedKinematicEngine,PartialEngine,"Engine for applying combined displacements on pre-defined bodies. Constructed using ``+`` operator on regular :yref:`KinematicEngines`. The ``ids`` operated on are those of the first engine in the combination (assigned automatically).", ((vector >,comb,,,"Kinematic engines that will be combined by this one, run in the order given.")) , /* ctor */ , /* py */ .def("__add__",&CombinedKinematicEngine::appendOne) ); // exposed as operator + in python static const shared_ptr appendOne(const shared_ptr& self, const shared_ptr& other){ self->comb.push_back(other); return self; } static const shared_ptr fromTwo(const shared_ptr& first, const shared_ptr& second); }; REGISTER_SERIALIZABLE(CombinedKinematicEngine); struct KinematicEngine: public PartialEngine{ virtual void action(); virtual void apply(const vector& ids){ LOG_ERROR("KinematicEngine::apply called, derived class ("<` and :yref:`angular velocity` of all subscribed bodies is reset before the ``apply`` method is called, it should therefore only increment those quantities.", /* attrs*/, /* ctor */, /* py */ .def("__add__",&CombinedKinematicEngine::fromTwo) ) DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(KinematicEngine); struct TranslationEngine: public KinematicEngine{ virtual void apply(const vector& ids); void postLoad(TranslationEngine&){ translationAxis.normalize(); } YADE_CLASS_BASE_DOC_ATTRS(TranslationEngine,KinematicEngine,"Engine applying translation motion (by setting linear velocity) to subscribed bodies.", ((Real,velocity,,,"Scalar value of the imposed velocity [m/s]. Imposed vector velocity is :yref:`velocity` * :yref:`axis`")) ((Vector3r,translationAxis,,Attr::triggerPostLoad,"Direction of imposed translation [Vector3]")) ); }; REGISTER_SERIALIZABLE(TranslationEngine); struct HarmonicMotionEngine: public KinematicEngine{ virtual void apply(const vector& ids); YADE_CLASS_BASE_DOC_ATTRS(HarmonicMotionEngine,KinematicEngine,"This engine implements the harmonic oscillation of bodies. http://en.wikipedia.org/wiki/Simple_harmonic_motion#Dynamics_of_simple_harmonic_motion", ((Vector3r,A,Vector3r::Zero(),,"Amplitude [m]")) ((Vector3r,f,Vector3r::Zero(),,"Frequency [hertz]")) ((Vector3r,fi,Vector3r(Mathr::PI/2.0, Mathr::PI/2.0, Mathr::PI/2.0),,"Initial phase [radians]. By default, the body oscillates around initial position.")) ); }; REGISTER_SERIALIZABLE(HarmonicMotionEngine); struct RotationEngine: public KinematicEngine{ virtual void apply(const vector& ids); void postLoad(RotationEngine&){ rotationAxis.normalize(); } YADE_CLASS_BASE_DOC_ATTRS(RotationEngine,KinematicEngine,"Engine applying rotation (by setting angular velocity) to subscribed bodies. If :yref:`rotateAroundZero` is set, then each body is also displaced around :yref:`zeroPoint`.", ((Real,angularVelocity,0,,"Angular velocity. [rad/s]")) ((Vector3r,rotationAxis,Vector3r::UnitX(),Attr::triggerPostLoad,"Axis of rotation (direction); will be normalized automatically.")) ((bool,rotateAroundZero,false,,"If True, bodies will not rotate around their centroids, but rather around ``zeroPoint``.")) ((Vector3r,zeroPoint,Vector3r::Zero(),,"Point around which bodies will rotate if ``rotateAroundZero`` is True")) ); }; REGISTER_SERIALIZABLE(RotationEngine); struct HelixEngine:public RotationEngine{ virtual void apply(const vector& ids); YADE_CLASS_BASE_DOC_ATTRS(HelixEngine,RotationEngine,"Engine applying both rotation and translation, along the same axis, whence the name HelixEngine", ((Real,linearVelocity,0,,"Linear velocity [m/s]")) ((Real,angleTurned,0,,"How much have we turned so far. |yupdate| [rad]")) ); }; REGISTER_SERIALIZABLE(HelixEngine); struct InterpolatingHelixEngine: public HelixEngine{ virtual void apply(const vector& ids); YADE_CLASS_BASE_DOC_ATTRS(InterpolatingHelixEngine,HelixEngine,"Engine applying spiral motion, finding current angular velocity by linearly interpolating in times and velocities and translation by using slope parameter. \n\n The interpolation assumes the margin value before the first time point and last value after the last time point. If wrap is specified, time will wrap around the last times value to the first one (note that no interpolation between last and first values is done).", ((vector,times,,,"List of time points at which velocities are given; must be increasing [s]")) ((vector,angularVelocities,,,"List of angular velocities; manadatorily of same length as times. [rad/s]")) ((bool,wrap,false,,"Wrap t if t>times_n, i.e. t_wrapped=t-N*(times_n-times_0)")) ((Real,slope,0,,"Axial translation per radian turn (can be negative) [m/rad]")) ((size_t,_pos,0,(Attr::hidden),"holder of interpolation state, should not be touched by user")) ); }; REGISTER_SERIALIZABLE(InterpolatingHelixEngine); struct HarmonicRotationEngine: public RotationEngine{ virtual void apply(const vector& ids); YADE_CLASS_BASE_DOC_ATTRS(HarmonicRotationEngine,RotationEngine,"This engine implements the harmonic-rotation oscillation of bodies. http://en.wikipedia.org/wiki/Simple_harmonic_motion#Dynamics_of_simple_harmonic_motion ; please, set dynamic=False for bodies, droven by this engine, otherwise amplitude will be 2x more, than awaited.", ((Real,A,0,,"Amplitude [rad]")) ((Real,f,0,,"Frequency [hertz]")) ((Real,fi,Mathr::PI/2.0,,"Initial phase [radians]. By default, the body oscillates around initial position.")) ); }; REGISTER_SERIALIZABLE(HarmonicRotationEngine); struct ServoPIDController: public TranslationEngine{ virtual void apply(const vector& ids); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(ServoPIDController,TranslationEngine,"PIDController servo-engine for applying prescribed force on bodies. http://en.wikipedia.org/wiki/PID_controller", ((Real,maxVelocity,0.0,,"Velocity [m/s]")) ((Vector3r,axis,Vector3r::Zero(),,"Unit vector along which apply the velocity [-]")) ((Real,target,0.0,,"Target value for the controller [N]")) ((Vector3r,current,Vector3r::Zero(),,"Current value for the controller [N]")) ((Real,kP,0.0,,"Proportional gain/coefficient for the PID-controller [-]")) ((Real,kI,0.0,,"Integral gain/coefficient for the PID-controller [-]")) ((Real,kD,0.0,,"Derivative gain/coefficient for the PID-controller [-]")) ((Real,iTerm,0.0,,"Integral term [N]")) ((Real,curVel,0.0,,"Current applied velocity [m/s]")) ((Real,errorCur,0.0,,"Current error [N]")) ((Real,errorPrev,0.0,,"Previous error [N]")) ((long,iterPeriod,100.0,,"Periodicity criterion of velocity correlation [-]")) ((long,iterPrevStart,-1.0,,"Previous iteration of velocity correlation [-]")) /* attrs*/, /* ctor */, /* py */ ) DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(ServoPIDController); struct BicyclePedalEngine: public KinematicEngine{ virtual void apply(const vector& ids); void postLoad(BicyclePedalEngine&){ rotationAxis.normalize(); } YADE_CLASS_BASE_DOC_ATTRS(BicyclePedalEngine,KinematicEngine,"Engine applying the linear motion of ``bicycle pedal`` e.g. moving points around the axis without rotation", ((Real,angularVelocity,0,,"Angular velocity. [rad/s]")) ((Vector3r,rotationAxis,Vector3r::UnitX(),Attr::triggerPostLoad,"Axis of rotation (direction); will be normalized automatically.")) ((Real,radius,-1.0,,"Rotation radius. [m]")) ((Real,fi,Mathr::PI/2.0,,"Initial phase [radians]")) ); }; REGISTER_SERIALIZABLE(BicyclePedalEngine); trunk-2017.01a/pkg/common/MatchMaker.cpp000066400000000000000000000033661304022710500177630ustar00rootroot00000000000000// 2010 © Václav Šmilauer #include YADE_PLUGIN((MatchMaker)); Real MatchMaker::operator()(int id1, int id2, Real val1, Real val2) const { const int minId = std::min(id1, id2); const int maxId = std::max(id1, id2); const auto foundMatchItem = matchSet.find (std::make_pair(minId, maxId)); if ( foundMatchItem != matchSet.end() ) { return foundMatchItem->second; } else { if(fbNeedsValues && (std::isnan(val1) || std::isnan(val2))) { throw std::invalid_argument("MatchMaker: no match for ("+boost::lexical_cast(id1)+ ","+boost::lexical_cast(id2)+"), and values required for algo computation '"+ algo+"' not specified."); } return computeFallback(val1,val2); } } void MatchMaker::postLoad(MatchMaker&){ if(algo=="val") { fbPtr=&MatchMaker::fbVal; fbNeedsValues=false; } else if(algo=="zero"){ fbPtr=&MatchMaker::fbZero;fbNeedsValues=false; } else if(algo=="avg") { fbPtr=&MatchMaker::fbAvg; fbNeedsValues=true; } else if(algo=="min") { fbPtr=&MatchMaker::fbMin; fbNeedsValues=true; } else if(algo=="max") { fbPtr=&MatchMaker::fbMax; fbNeedsValues=true; } else if(algo=="harmAvg") { fbPtr=&MatchMaker::fbHarmAvg; fbNeedsValues=true; } else throw std::invalid_argument("MatchMaker:: algo '"+algo+"' not recognized (possible values: val, avg, min, max, harmAvg)."); // Fill matchSet with values for a fast coefficient search for (const auto & m : matches) { const int minId = std::min((int)m[0], (int)m[1]); const int maxId = std::max((int)m[0], (int)m[1]); const auto idPair = std::make_pair(minId, maxId); matchSet.insert(std::make_pair(idPair, m[2])); } } Real MatchMaker::computeFallback(Real v1, Real v2) const { return (this->*MatchMaker::fbPtr)(v1,v2); } trunk-2017.01a/pkg/common/MatchMaker.hpp000066400000000000000000000074761304022710500177760ustar00rootroot00000000000000// 2010 © Václav Šmilauer #pragma once #include #include namespace py = boost::python; /* Future optimizations, in postLoad: 1. Use matches to update lookup table/hash for faster matching, instead of traversing matches every time 2. Use algo to update fbPtr, instead of string-comparison of algo every time */ class MatchMaker: public Serializable { Real fbZero(Real v1, Real v2) const{ return 0.; } Real fbAvg(Real v1, Real v2) const{ return (v1+v2)/2.; } Real fbMin(Real v1, Real v2) const{ return min(v1,v2); } Real fbMax(Real v1, Real v2) const{ return max(v1,v2); } Real fbHarmAvg(Real v1, Real v2) const { return 2*v1*v2/(v1+v2); } Real fbVal(Real v1, Real v2) const { return val; } Real (MatchMaker::*fbPtr)(Real,Real) const; // whether the current fbPtr function needs valid input values in order to give meaningful result. // must be kept in sync with fbPtr, which is done in postLoad bool fbNeedsValues; // unordered set for a fast coefficient search boost::unordered_map, Real> matchSet; public: virtual ~MatchMaker() {}; MatchMaker(std::string _algo): algo(_algo){ postLoad(*this); } MatchMaker(Real _val): algo("val"), val(_val){ postLoad(*this); } Real computeFallback(Real val1, Real val2) const ; void postLoad(MatchMaker&); // return value looking up matches for id1+id2 (the order is arbitrary) // if no match is found, use val1,val2 and algo strategy to compute new value. // if no match is found and val1 or val2 are not given, throw exception Real operator()(const int id1, const int id2, const Real val1=NaN, const Real val2=NaN) const; YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(MatchMaker,Serializable,"Class matching pair of ids to return pre-defined (for a pair of ids defined in :yref:`matches`) or derived value (computed using :yref:`algo`) of a scalar parameter. It can be called (``id1``, ``id2``, ``val1=NaN``, ``val2=NaN``) in both python and c++. \n\n.. note:: There is a :ref:`converter ` from python number defined for this class, which creates a new :yref:`MatchMaker` returning the value of that number; instead of giving the object instance therefore, you can only pass the number value and it will be converted automatically.", ((std::vector,matches,,Attr::readonly,"Array of ``(id1,id2,value)`` items; queries matching ``id1`` + ``id2`` or ``id2`` + ``id1`` will return ``value``")) ((std::string,algo,"avg",Attr::triggerPostLoad,"Alogorithm used to compute value when no match for ids is found. Possible values are\n\n* 'avg' (arithmetic average)\n* 'min' (minimum value)\n* 'max' (maximum value)\n* 'harmAvg' (harmonic average)\n\nThe following algo algorithms do *not* require meaningful input values in order to work:\n\n* 'val' (return value specified by :yref:`val`)\n* 'zero' (always return 0.)\n\n")) ((Real,val,NaN,,"Constant value returned if there is no match and :yref:`algo` is ``val``")) , fbPtr=&MatchMaker::fbAvg; fbNeedsValues=true; /* keep in sync with the algo value for algo */ , /*py*/ .def("__call__",&MatchMaker::operator(),(py::arg("id1"),py::arg("id2"),py::arg("val1")=NaN,py::arg("val2")=NaN),"Ask the instance for scalar value for given pair *id1*,*id2* (the order is irrelevant). Optionally, *val1*, *val2* can be given so that if there is no :yref:`match`, return value can be computed using given :yref:`algo`. If there is no match and *val1*, *val2* are not given, an exception is raised.") .def("computeFallback",&MatchMaker::computeFallback,(py::arg("val1"),py::arg("val2")),"Compute algo value for *val1* and *val2*, using algorithm specified by :yref:`algo`.") ); }; REGISTER_SERIALIZABLE(MatchMaker); trunk-2017.01a/pkg/common/NormShearPhys.hpp000066400000000000000000000023471304022710500205140ustar00rootroot00000000000000// © 2007 Janek Kozicki // © 2008 Václav Šmilauer #pragma once #include class NormPhys:public IPhys { public: virtual ~NormPhys() {}; virtual Vector3r getRotStiffness() {return Vector3r::Zero();} YADE_CLASS_BASE_DOC_ATTRS_CTOR(NormPhys,IPhys,"Abstract class for interactions that have normal stiffness.", ((Real,kn,0,,"Normal stiffness")) ((Vector3r,normalForce,Vector3r::Zero(),,"Normal force after previous step (in global coordinates), as sustained by particle #2 (from particle #1).")), createIndex(); ); REGISTER_CLASS_INDEX(NormPhys,IPhys); }; REGISTER_SERIALIZABLE(NormPhys); class NormShearPhys: public NormPhys{ public: virtual ~NormShearPhys() {}; YADE_CLASS_BASE_DOC_ATTRS_CTOR(NormShearPhys,NormPhys, "Abstract class for interactions that have shear stiffnesses, in addition to normal stiffness. This class is used in the PFC3d-style stiffness timestepper.", ((Real,ks,0,,"Shear stiffness")) ((Vector3r,shearForce,Vector3r::Zero(),,"Shear force after previous step (in global coordinates), as sustained by particle #2 (from particle #1).")), createIndex(); ); REGISTER_CLASS_INDEX(NormShearPhys,NormPhys); }; REGISTER_SERIALIZABLE(NormShearPhys); trunk-2017.01a/pkg/common/OpenGLRenderer.cpp000066400000000000000000000416151304022710500205610ustar00rootroot00000000000000// © 2004 Olivier Galizzi // © 2008 Václav Šmilauer #ifdef YADE_OPENGL #include "OpenGLRenderer.hpp" #include #include #include #include #include #include #include #include YADE_PLUGIN((OpenGLRenderer)(GlExtraDrawer)); CREATE_LOGGER(OpenGLRenderer); void GlExtraDrawer::render(){ throw runtime_error("GlExtraDrawer::render called from class "+getClassName()+". (did you forget to override it in the derived class?)"); } bool OpenGLRenderer::initDone=false; const int OpenGLRenderer::numClipPlanes; OpenGLRenderer::~OpenGLRenderer(){} void OpenGLRenderer::init(){ typedef std::pair strDldPair; // necessary as FOREACH, being macro, cannot have the "," inside the argument (preprocessor does not parse templates) FOREACH(const strDldPair& item, Omega::instance().getDynlibsDescriptor()){ // if (Omega::instance().isInheritingFrom_recursive(item.first,"GlStateFunctor")) stateFunctorNames.push_back(item.first); if (Omega::instance().isInheritingFrom_recursive(item.first,"GlBoundFunctor")) boundFunctorNames.push_back(item.first); if (Omega::instance().isInheritingFrom_recursive(item.first,"GlShapeFunctor")) shapeFunctorNames.push_back(item.first); if (Omega::instance().isInheritingFrom_recursive(item.first,"GlIGeomFunctor")) geomFunctorNames.push_back(item.first); if (Omega::instance().isInheritingFrom_recursive(item.first,"GlIPhysFunctor")) physFunctorNames.push_back(item.first); } initgl(); // creates functor objects in the proper sense clipPlaneNormals.resize(numClipPlanes); static bool glutInitDone=false; if(!glutInitDone){ glutInit(&Omega::instance().origArgc,Omega::instance().origArgv); /* transparent spheres (still not working): glutInitDisplayMode(GLUT_DOUBLE | GLUT_RGBA | GLUT_DEPTH | GLUT_MULTISAMPLE | GLUT_ALPHA); glEnable(GL_BLEND); glBlendFunc(GL_SRC_ALPHA, GL_ONE); */ glutInitDone=true; } initDone=true; } void OpenGLRenderer::setBodiesRefSe3(){ LOG_DEBUG("(re)initializing reference positions and orientations."); FOREACH(const shared_ptr& b, *scene->bodies) if(b && b->state) { b->state->refPos=b->state->pos; b->state->refOri=b->state->ori; } scene->cell->refHSize=scene->cell->hSize; } template void OpenGLRenderer::setupDispatcher(const vector & names, DispatcherT & dispatcher) { dispatcher.clearMatrix(); for(const auto & s : names) { shared_ptr f(boost::static_pointer_cast(ClassFactory::instance().createShared(s))); f->initgl(); dispatcher.add(f); } } void OpenGLRenderer::initgl(){ LOG_DEBUG("(re)initializing GL for gldraw methods.\n"); setupDispatcher (boundFunctorNames, boundDispatcher); setupDispatcher (shapeFunctorNames, shapeDispatcher); setupDispatcher (geomFunctorNames, geomDispatcher); setupDispatcher (physFunctorNames, physDispatcher); } bool OpenGLRenderer::pointClipped(const Vector3r& p){ if(numClipPlanes<1) return false; for(int i=0;ibodies->size()!=bodyDisp.size()) { bodyDisp.resize(scene->bodies->size()); for (unsigned k=0; kbodies->size(); k++) bodyDisp[k].hidden=0;} bool scaleRotations=(rotScale!=1.0); bool scaleDisplacements=(dispScale!=Vector3r::Ones()); FOREACH(const shared_ptr& b, *scene->bodies){ if(!b || !b->state) continue; size_t id=b->getId(); const Vector3r& pos=b->state->pos; const Vector3r& refPos=b->state->refPos; const Quaternionr& ori=b->state->ori; const Quaternionr& refOri=b->state->refOri; Vector3r cellPos=(!scene->isPeriodic ? pos : scene->cell->wrapShearedPt(pos)); // inside the cell if periodic, same as pos otherwise bodyDisp[id].isDisplayed=!pointClipped(cellPos); // if no scaling and no periodic, return quickly if(!(scaleDisplacements||scaleRotations||scene->isPeriodic)){ bodyDisp[id].pos=pos; bodyDisp[id].ori=ori; continue; } // apply scaling bodyDisp[id].pos=cellPos; // point of reference (inside the cell for periodic) if(scaleDisplacements) bodyDisp[id].pos+=dispScale.cwiseProduct(Vector3r(pos-refPos)); // add scaled translation to the point of reference if(!scaleRotations) bodyDisp[id].ori=ori; else{ Quaternionr relRot=refOri.conjugate()*ori; AngleAxisr aa(relRot); aa.angle()*=rotScale; bodyDisp[id].ori=refOri*Quaternionr(aa); } } } // draw periodic cell, if active void OpenGLRenderer::drawPeriodicCell(){ if(!scene->isPeriodic) return; glColor3v(cellColor); glPushMatrix(); // Vector3r size=scene->cell->getSize(); const Matrix3r& hSize=scene->cell->hSize; if(dispScale!=Vector3r::Ones()){ const Matrix3r& refHSize(scene->cell->refHSize); Matrix3r scaledHSize; for(int i=0; i<3; i++) scaledHSize.col(i)=refHSize.col(i)+dispScale.cwiseProduct(Vector3r(hSize.col(i)-refHSize.col(i))); GLUtils::Parallelepiped(scaledHSize.col(0),scaledHSize.col(1),scaledHSize.col(2)); } else { GLUtils::Parallelepiped(hSize.col(0),hSize.col(1),hSize.col(2)); } glPopMatrix(); } void OpenGLRenderer::resetSpecularEmission(){ glMateriali(GL_FRONT, GL_SHININESS, 80); const GLfloat glutMatSpecular[4]={0.3,0.3,0.3,0.5}; const GLfloat glutMatEmit[4]={0.2,0.2,0.2,1.0}; glMaterialfv(GL_FRONT,GL_SPECULAR,glutMatSpecular); glMaterialfv(GL_FRONT,GL_EMISSION,glutMatEmit); } void OpenGLRenderer::render(const shared_ptr& _scene,Body::id_t selection){ gilLock lockgil; if(!initDone) init(); assert(initDone); selId = selection; scene=_scene; // assign scene inside functors boundDispatcher.updateScenePtr(); geomDispatcher.updateScenePtr(); physDispatcher.updateScenePtr(); shapeDispatcher.updateScenePtr(); // stateDispatcher.updateScenePtr(); // just to make sure, since it is not initialized by default if(!scene->bound) scene->bound=shared_ptr(new Aabb); // recompute emissive light colors for highlighted bodies Real now=TimingInfo::getNow(/*even if timing is disabled*/true)*1e-9; highlightEmission0[0]=highlightEmission0[1]=highlightEmission0[2]=.8*normSquare(now,1); highlightEmission1[0]=highlightEmission1[1]=highlightEmission0[2]=.5*normSaw(now,2); // clipping assert(clipPlaneNormals.size()==(size_t)numClipPlanes); for(size_t i=0;i<(size_t)numClipPlanes; i++){ // someone could have modified those from python and truncate the vectors; fill those here in that case if(i==clipPlaneSe3.size()) clipPlaneSe3.push_back(Se3r(Vector3r::Zero(),Quaternionr::Identity())); if(i==clipPlaneActive.size()) clipPlaneActive.push_back(false); if(i==clipPlaneNormals.size()) clipPlaneNormals.push_back(Vector3r::UnitX()); // end filling stuff modified from python if(clipPlaneActive[i]) clipPlaneNormals[i]=clipPlaneSe3[i].orientation*Vector3r(0,0,1); /* glBegin(GL_LINES);glVertex3v(clipPlaneSe3[i].position);glVertex3v(clipPlaneSe3[i].position+clipPlaneNormals[i]);glEnd(); */ } // set displayed Se3 of body (scaling) and isDisplayed (clipping) setBodiesDispInfo(); glClearColor(bgColor[0],bgColor[1],bgColor[2],1.0); // set light sources glLightModelf(GL_LIGHT_MODEL_TWO_SIDE,1); // important: do lighting calculations on both sides of polygons const GLfloat pos[4] = {(float) lightPos[0], (float) lightPos[1], (float) lightPos[2],1.0}; const GLfloat ambientColor[4]={0.2,0.2,0.2,1.0}; const GLfloat specularColor[4]={1,1,1,1.f}; const GLfloat diffuseLight[4] = { (float) lightColor[0], (float) lightColor[1], (float) lightColor[2], 1.0f }; glLightfv(GL_LIGHT0, GL_POSITION,pos); glLightfv(GL_LIGHT0, GL_SPECULAR, specularColor); glLightfv(GL_LIGHT0, GL_AMBIENT, ambientColor); glLightfv(GL_LIGHT0, GL_DIFFUSE, diffuseLight); if (light1) glEnable(GL_LIGHT0); else glDisable(GL_LIGHT0); const GLfloat pos2[4] = {(float) light2Pos[0], (float) light2Pos[1], (float) light2Pos[2],1.0}; const GLfloat ambientColor2[4]={0.0,0.0,0.0,1.0}; const GLfloat specularColor2[4]={1,1,0.6,1.f}; const GLfloat diffuseLight2[4] = { (float) light2Color[0], (float) light2Color[1], (float) light2Color[2], 1.0f }; glLightfv(GL_LIGHT1, GL_POSITION,pos2); glLightfv(GL_LIGHT1, GL_SPECULAR, specularColor2); glLightfv(GL_LIGHT1, GL_AMBIENT, ambientColor2); glLightfv(GL_LIGHT1, GL_DIFFUSE, diffuseLight2); if (light2) glEnable(GL_LIGHT1); else glDisable(GL_LIGHT1); glEnable(GL_LIGHTING); glEnable(GL_CULL_FACE); // http://www.sjbaker.org/steve/omniv/opengl_lighting.html glColorMaterial(GL_FRONT,GL_AMBIENT_AND_DIFFUSE); glEnable(GL_COLOR_MATERIAL); //Shared material settings resetSpecularEmission(); drawPeriodicCell(); if (dof || id) renderDOF_ID(); if (bound) renderBound(); if (shape) renderShape(); if (intrAllWire) renderAllInteractionsWire(); if (intrGeom) renderIGeom(); if (intrPhys) renderIPhys(); FOREACH(const shared_ptr d, extraDrawers){ if(d->dead) continue; glPushMatrix(); d->scene=scene.get(); d->render(); glPopMatrix(); } } void OpenGLRenderer::renderAllInteractionsWire(){ FOREACH(const shared_ptr& i, *scene->interactions){ if(!i->functorCache.geomExists) continue; glColor3v(i->isReal()? Vector3r(0,1,0) : Vector3r(.5,0,1)); Vector3r p1=Body::byId(i->getId1(),scene)->state->pos; const Vector3r& size=scene->cell->getSize(); Vector3r shift2(i->cellDist[0]*size[0],i->cellDist[1]*size[1],i->cellDist[2]*size[2]); // in sheared cell, apply shear on the mutual position as well shift2=scene->cell->shearPt(shift2); Vector3r rel=Body::byId(i->getId2(),scene)->state->pos+shift2-p1; if(scene->isPeriodic) p1=scene->cell->wrapShearedPt(p1); glBegin(GL_LINES); glVertex3v(p1);glVertex3v(Vector3r(p1+rel));glEnd(); } } void OpenGLRenderer::renderDOF_ID(){ const GLfloat ambientColorSelected[4]={10.0,0.0,0.0,1.0}; const GLfloat ambientColorUnselected[4]={0.5,0.5,0.5,1.0}; FOREACH(const shared_ptr b, *scene->bodies){ if(!b) continue; if(b->shape && ((b->getGroupMask() & mask) || b->getGroupMask()==0)){ if(!id && b->state->blockedDOFs==0) continue; if(selId==b->getId()){glLightModelfv(GL_LIGHT_MODEL_AMBIENT,ambientColorSelected);} { // write text glColor3f(1.0-bgColor[0],1.0-bgColor[1],1.0-bgColor[2]); unsigned d = b->state->blockedDOFs; std::string sDof = std::string()+(((d&State::DOF_X )!=0)?"x":"")+(((d&State::DOF_Y )!=0)?"y":" ")+(((d&State::DOF_Z )!=0)?"z":"")+(((d&State::DOF_RX)!=0)?"X":"")+(((d&State::DOF_RY)!=0)?"Y":"")+(((d&State::DOF_RZ)!=0)?"Z":""); std::string sId = boost::lexical_cast(b->getId()); std::string str; if(dof && id) sId += " "; if(id) str += sId; if(dof) str += sDof; const Vector3r& h(selId==b->getId() ? highlightEmission0 : Vector3r(1,1,1)); glColor3v(h); GLUtils::GLDrawText(str,bodyDisp[b->id].pos,h); } if(selId == b->getId()){glLightModelfv(GL_LIGHT_MODEL_AMBIENT,ambientColorUnselected);} } } } void OpenGLRenderer::renderIGeom(){ geomDispatcher.scene=scene.get(); geomDispatcher.updateScenePtr(); { boost::mutex::scoped_lock lock(scene->interactions->drawloopmutex); FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->geom) continue; // avoid refcount manipulations if the interaction is not real anyway shared_ptr ig(I->geom); // keep reference so that ig does not disappear suddenly while being rendered if(!ig) continue; const shared_ptr& b1=Body::byId(I->getId1(),scene), b2=Body::byId(I->getId2(),scene); if(!(bodyDisp[I->getId1()].isDisplayed||bodyDisp[I->getId2()].isDisplayed)) continue; glPushMatrix(); geomDispatcher(ig,I,b1,b2,intrWire); glPopMatrix(); } } } void OpenGLRenderer::renderIPhys(){ physDispatcher.scene=scene.get(); physDispatcher.updateScenePtr(); { boost::mutex::scoped_lock lock(scene->interactions->drawloopmutex); FOREACH(const shared_ptr& I, *scene->interactions){ shared_ptr ip(I->phys); if(!ip) continue; const shared_ptr& b1=Body::byId(I->getId1(),scene), b2=Body::byId(I->getId2(),scene); Body::id_t id1=I->getId1(), id2=I->getId2(); if(!(bodyDisp[id1].isDisplayed||bodyDisp[id2].isDisplayed)) continue; glPushMatrix(); physDispatcher(ip,I,b1,b2,intrWire); glPopMatrix(); } } } void OpenGLRenderer::renderBound(){ boundDispatcher.scene=scene.get(); boundDispatcher.updateScenePtr(); FOREACH(const shared_ptr& b, *scene->bodies){ if(!b || !b->bound) continue; if(!bodyDisp[b->getId()].isDisplayed or bodyDisp[b->getId()].hidden) continue; if(b->bound && ((b->getGroupMask()&mask) || b->getGroupMask()==0)){ glPushMatrix(); boundDispatcher(b->bound,scene.get()); glPopMatrix(); } } // since we remove the functor as Scene doesn't inherit from Body anymore, hardcore the rendering routine here // for periodic scene, renderPeriodicCell is called separately if(!scene->isPeriodic){ if(!scene->bound) scene->updateBound(); glColor3v(Vector3r(0,1,0)); Vector3r size=scene->bound->max-scene->bound->min; Vector3r center=.5*(scene->bound->min+scene->bound->max); glPushMatrix(); glTranslatev(center); glScalev(size); glutWireCube(1); glPopMatrix(); } } // this function is called for both rendering as well as // in the selection mode // nice reading on OpenGL selection // http://glprogramming.com/red/chapter13.html void OpenGLRenderer::renderShape(){ shapeDispatcher.scene=scene.get(); shapeDispatcher.updateScenePtr(); // instead of const shared_ptr&, get proper shared_ptr; // Less efficient in terms of performance, since memory has to be written (not measured, though), // but it is still better than crashes if the body gets deleted meanwile. FOREACH(shared_ptr b, *scene->bodies){ if(!b || !b->shape) continue; if(!(bodyDisp[b->getId()].isDisplayed and !bodyDisp[b->getId()].hidden)) continue; Vector3r pos=bodyDisp[b->getId()].pos; Quaternionr ori=bodyDisp[b->getId()].ori; if(!b->shape || !((b->getGroupMask()&mask) || b->getGroupMask()==0)) continue; // ignored in non-selection mode, use it always glPushName(b->id); bool highlight=(b->id==selId || (b->clumpId>=0 && b->clumpId==selId) || b->shape->highlight); glPushMatrix(); AngleAxisr aa(ori); glTranslatef(pos[0],pos[1],pos[2]); glRotatef(aa.angle()*Mathr::RAD_TO_DEG,aa.axis()[0],aa.axis()[1],aa.axis()[2]); if(highlight){ // set hightlight // different color for body highlighted by selection and by the shape attribute const Vector3r& h((selId==b->id||(b->clumpId>=0 && selId==b->clumpId)) ? highlightEmission0 : highlightEmission1); glMaterialv(GL_FRONT_AND_BACK,GL_EMISSION,h); glMaterialv(GL_FRONT_AND_BACK,GL_SPECULAR,h); shapeDispatcher(b->shape,b->state,wire || b->shape->wire,viewInfo); // reset highlight resetSpecularEmission(); } else { // no highlight; in case previous functor fiddled with glMaterial resetSpecularEmission(); shapeDispatcher(b->shape,b->state,wire || b->shape->wire,viewInfo); } glPopMatrix(); if(highlight){ if(!b->bound || wire || b->shape->wire) GLUtils::GLDrawInt(b->getId(),pos); else { // move the label towards the camera by the bounding box so that it is not hidden inside the body const Vector3r& mn=b->bound->min; const Vector3r& mx=b->bound->max; const Vector3r& p=pos; Vector3r ext(viewDirection[0]>0?p[0]-mn[0]:p[0]-mx[0],viewDirection[1]>0?p[1]-mn[1]:p[1]-mx[1],viewDirection[2]>0?p[2]-mn[2]:p[2]-mx[2]); // signed extents towards the camera Vector3r dr=-1.01*(viewDirection.dot(ext)*viewDirection); GLUtils::GLDrawInt(b->getId(),pos+dr,Vector3r::Ones()); } } // if the body goes over the cell margin, draw it in positions where the bbox overlaps with the cell in wire // precondition: pos is inside the cell. if(b->bound && scene->isPeriodic && ghosts){ const Vector3r& cellSize(scene->cell->getSize()); pos=scene->cell->unshearPt(pos); // remove the shear component // traverse all periodic cells around the body, to see if any of them touches Vector3r halfSize=b->bound->max-b->bound->min; halfSize*=.5; Vector3r pmin,pmax; Vector3i i; for(i[0]=-1; i[0]<=1; i[0]++) for(i[1]=-1;i[1]<=1; i[1]++) for(i[2]=-1; i[2]<=1; i[2]++){ if(i[0]==0 && i[1]==0 && i[2]==0) continue; // middle; already rendered above Vector3r pos2=pos+Vector3r(cellSize[0]*i[0],cellSize[1]*i[1],cellSize[2]*i[2]); // shift, but without shear! pmin=pos2-halfSize; pmax=pos2+halfSize; if(pmin[0]<=cellSize[0] && pmax[0]>=0 && pmin[1]<=cellSize[1] && pmax[1]>=0 && pmin[2]<=cellSize[2] && pmax[2]>=0) { Vector3r pt=scene->cell->shearPt(pos2); if(pointClipped(pt)) continue; glLoadName(b->id); glPushMatrix(); glTranslatev(pt); glRotatef(aa.angle()*Mathr::RAD_TO_DEG,aa.axis()[0],aa.axis()[1],aa.axis()[2]); shapeDispatcher(b->shape,b->state,/*wire*/ true, viewInfo); glPopMatrix(); } } } glPopName(); } } #endif /* YADE_OPENGL */ trunk-2017.01a/pkg/common/OpenGLRenderer.hpp000066400000000000000000000137631304022710500205710ustar00rootroot00000000000000// © 2004 Olivier Galizzi // © 2008 Václav Šmilauer #pragma once #include #include #include #include struct GlExtraDrawer: public Serializable{ Scene* scene; virtual void render(); YADE_CLASS_BASE_DOC_ATTRS(GlExtraDrawer,Serializable,"Performing arbitrary OpenGL drawing commands; called from :yref:`OpenGLRenderer` (see :yref:`OpenGLRenderer.extraDrawers`) once regular rendering routines will have finished.\n\nThis class itself does not render anything, derived classes should override the *render* method.", ((bool,dead,false,,"Deactivate the object (on error/exception).")) ); }; REGISTER_SERIALIZABLE(GlExtraDrawer); class OpenGLRenderer : public Serializable { public: static const int numClipPlanes=3; bool pointClipped(const Vector3r& p); vector clipPlaneNormals; void setBodiesDispInfo(); static bool initDone; Vector3r viewDirection; // updated from GLViewer regularly GLViewInfo viewInfo; // update from GLView regularly Vector3r highlightEmission0; Vector3r highlightEmission1; // normalized saw signal with given periodicity, with values ∈ 〈0,1〉 */ Real normSaw(Real t, Real period){ Real xi=(t-period*((int)(t/period)))/period; /* normalized value, (0-1〉 */ return (xi<.5?2*xi:2-2*xi); } Real normSquare(Real t, Real period){ Real xi=(t-period*((int)(t/period)))/period; /* normalized value, (0-1〉 */ return (xi<.5?0:1); } void drawPeriodicCell(); void setBodiesRefSe3(); struct BodyDisp{ Vector3r pos; Quaternionr ori; bool isDisplayed; bool hidden; }; //! display data for individual bodies vector bodyDisp; void hide(Body::id_t id) {if ((unsigned int) id // stateFunctorNames, boundFunctorNames, shapeFunctorNames, geomFunctorNames, physFunctorNames; DECLARE_LOGGER; public : // updated after every call to render shared_ptr scene; void init(); void initgl(); void render(const shared_ptr& scene, Body::id_t selection=Body::id_t(-1)); void pyRender(){render(Omega::instance().getScene());} void renderDOF_ID(); void renderIPhys(); void renderIGeom(); void renderBound(); // called also to render selectable entitites; void renderShape(); void renderAllInteractionsWire(); template void setupDispatcher(const vector & names, DispatcherT & dispatcher); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(OpenGLRenderer,Serializable,"Class responsible for rendering scene on OpenGL devices.", ((Vector3r,dispScale,((void)"disable scaling",Vector3r::Ones()),,"Artificially enlarge (scale) dispalcements from bodies' :yref:`reference positions` by this relative amount, so that they become better visible (independently in 3 dimensions). Disbled if (1,1,1).")) ((Real,rotScale,((void)"disable scaling",1.),,"Artificially enlarge (scale) rotations of bodies relative to their :yref:`reference orientation`, so the they are better visible.")) ((Vector3r,lightPos,Vector3r(75,130,0),,"Position of OpenGL light source in the scene.")) ((Vector3r,light2Pos,Vector3r(-130,75,30),,"Position of secondary OpenGL light source in the scene.")) ((Vector3r,lightColor,Vector3r(0.6,0.6,0.6),,"Per-color intensity of primary light (RGB).")) ((Vector3r,light2Color,Vector3r(0.5,0.5,0.1),,"Per-color intensity of secondary light (RGB).")) ((Vector3r,cellColor,Vector3r(1,1,0),,"Color of the periodic cell (RGB).")) ((Vector3r,bgColor,Vector3r(.2,.2,.2),,"Color of the background canvas (RGB)")) ((bool,wire,false,,"Render all bodies with wire only (faster)")) ((bool,light1,true,,"Turn light 1 on.")) ((bool,light2,true,,"Turn light 2 on.")) ((bool,dof,false,,"Show which degrees of freedom are blocked for each body")) ((bool,id,false,,"Show body id's")) ((bool,bound,false,,"Render body :yref:`Bound`")) ((bool,shape,true,,"Render body :yref:`Shape`")) ((bool,intrWire,false,,"If rendering interactions, use only wires to represent them.")) ((bool,intrGeom,false,,"Render :yref:`Interaction::geom` objects.")) ((bool,intrPhys,false,,"Render :yref:`Interaction::phys` objects")) ((bool,ghosts,true,,"Render objects crossing periodic cell edges by cloning them in multiple places (periodic simulations only).")) ((int,mask,((void)"draw everything",~0),,"Bitmask for showing only bodies where ((mask & :yref:`Body::mask`)!=0)")) ((Body::id_t,selId,Body::ID_NONE,,"Id of particle that was selected by the user.")) ((vector,clipPlaneSe3,vector(numClipPlanes,Se3r(Vector3r::Zero(),Quaternionr::Identity())),,"Position and orientation of clipping planes")) ((vector,clipPlaneActive,vector(numClipPlanes,false),,"Activate/deactivate respective clipping planes")) ((vector >,extraDrawers,,,"Additional rendering components (:yref:`GlExtraDrawer`).")) ((bool,intrAllWire,false,,"Draw wire for all interactions, blue for potential and green for real ones (mostly for debugging)")), /*ctor*/, /*py*/ .def("setRefSe3",&OpenGLRenderer::setBodiesRefSe3,"Make current positions and orientation reference for scaleDisplacements and scaleRotations.") .def("render",&OpenGLRenderer::pyRender,"Render the scene in the current OpenGL context.") .def("hideBody",&OpenGLRenderer::hide,(boost::python::arg("id")),"Hide body from id (see :yref:`OpenGLRenderer::showBody`)") .def("showBody",&OpenGLRenderer::show,(boost::python::arg("id")),"Make body visible (see :yref:`OpenGLRenderer::hideBody`)") ); }; REGISTER_SERIALIZABLE(OpenGLRenderer); trunk-2017.01a/pkg/common/PFacet.cpp000066400000000000000000001050041304022710500171010ustar00rootroot00000000000000/***************************************************************************** * Copyright (C) 2015 by Anna Effeindzourou anna.effeindzourou@gmail.com * * Copyright (C) 2015 by Bruno Chareyre bruno.chareyre@hmg.inpg.fr * * Copyright (C) 2015 by Klaus Thoeni klaus.thoeni@gmail.com * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * ******************************************************************************/ #include "PFacet.hpp" #ifdef YADE_OPENGL #include #endif //!################## IGeom Functors ##################### // Function used in order to calculate the projection of the sphere on the PFacet element. The function returns if the the porjection is on the inside the triangle and the barycentric coordinates of the projection P on PFacet the element. boost::tuple Ig2_Sphere_PFacet_ScGridCoGeom::projection( const shared_ptr& cm2, const State& state1) { const State* sphereSt = YADE_CAST(&state1); PFacet* Pfacet = YADE_CAST(cm2.get()); vector vertices; vertices.push_back(Pfacet->node1->state->pos); vertices.push_back(Pfacet->node2->state->pos); vertices.push_back(Pfacet->node3->state->pos); Vector3r center=vertices[0]+((vertices[2]-vertices[0])*(vertices[1]-vertices[0]).norm()+(vertices[1]-vertices[0])*(vertices[2]-vertices[0]).norm())/((vertices[1]-vertices[0]).norm()+(vertices[2]-vertices[1]).norm()+(vertices[0]-vertices[2]).norm()); Vector3r e[3] = {vertices[1]-vertices[0] ,vertices[2]-vertices[1] ,vertices[0]-vertices[2]}; Vector3r normal = e[0].cross(e[1])/((e[0].cross(e[1])).norm()); // Vector3r centerS=sphereSt->pos+shift2;//FIXME: periodicity? const Vector3r& centerS=sphereSt->pos; Vector3r cl=centerS-center; Real dist=normal.dot(cl); if (dist<0) {normal=-normal; dist=-dist;} Vector3r P =center+(cl - dist*normal); Vector3r v0 = vertices[1] - vertices[0]; Vector3r v1 = vertices[2] - vertices[0]; Vector3r v2 = P - vertices[0]; // Compute dot products Real dot00 = v0.dot(v0); Real dot01 = v0.dot(v1); Real dot02 = v0.dot(v2); Real dot11 = v1.dot(v1); Real dot12 = v1.dot(v2); // Compute the barycentric coordinates of the projection P Real invDenom = 1 / (dot00 * dot11 - dot01 * dot01); Real p1 = (dot11 * dot02 - dot01 * dot12) * invDenom; Real p2 = (dot00 * dot12 - dot01 * dot02) * invDenom; Real p3 = 1-p1-p2; // Check if P is in triangle bool isintriangle= (p1 > 0) && (p2 > 0) && (p1 + p2 < 1); return boost::make_tuple(P,isintriangle,p1,p2,p3); } bool Ig2_Sphere_PFacet_ScGridCoGeom::go( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { TIMING_DELTAS_START(); Sphere* sphere = YADE_CAST(cm1.get()); PFacet* Pfacet = YADE_CAST(cm2.get()); const State* sphereSt = YADE_CAST(&state1); Real sphereRadius = sphere->radius; Real PFacetradius=Pfacet->radius; vector vertices; vertices.push_back(Pfacet->node1->state->pos); vertices.push_back(Pfacet->node2->state->pos); vertices.push_back(Pfacet->node3->state->pos); Vector3r center=vertices[0]+((vertices[2]-vertices[0])*(vertices[1]-vertices[0]).norm()+(vertices[1]-vertices[0])*(vertices[2]-vertices[0]).norm())/((vertices[1]-vertices[0]).norm()+(vertices[2]-vertices[1]).norm()+(vertices[0]-vertices[2]).norm()); Vector3r e[3] = {vertices[1]-vertices[0] ,vertices[2]-vertices[1] ,vertices[0]-vertices[2]}; Vector3r normal = e[0].cross(e[1])/((e[0].cross(e[1])).norm()); // Vector3r centerS=sphereSt->pos+shift2;//FIXME: periodicity? const Vector3r& centerS=sphereSt->pos; Vector3r cl=centerS-center; Real dist=normal.dot(cl); shared_ptr scm; bool isNew = !(c->geom); if (c->geom) scm = YADE_PTR_CAST(c->geom); else scm = shared_ptr(new ScGridCoGeom()); if(scm->isDuplicate==2 && scm->trueInt!=c->id2)return true; //the contact will be deleted into the Law, no need to compute here. scm->isDuplicate=0; scm->trueInt=-1; if (std::abs(dist)>(PFacetradius+sphereRadius) && !c->isReal() && !force) { // no contact, but only if there was no previous contact; ortherwise, the constitutive law is responsible for setting Interaction::isReal=false TIMING_DELTAS_CHECKPOINT("Ig2_Sphere_PFacet_ScGridCoGeom"); return false; } if (dist<0) {normal=-normal; dist=-dist;} boost::tuple projectionres = projection(cm2, state1); Vector3r P = boost::get<0>(projectionres); bool isintriangle = boost::get<1>(projectionres); Real p1 = boost::get<2>(projectionres); Real p2 = boost::get<3>(projectionres); Real p3 = boost::get<4>(projectionres); shared_ptr GridList[3]={Pfacet->conn1,Pfacet->conn2,Pfacet->conn3}; // Check if the projection of the contact point is inside the triangle bool isconn1=((p1 > 0) && (p2 <= 0) && (p1 + p2 < 1))||((p1 > 0) && (p2 <= 0) && (p1 + p2 >= 1)); bool isconn2=((p1 > 0) && (p2 > 0) && (p1 + p2 >= 1))||((p1 <= 0) && (p2 > 0) && (p1 + p2 >= 1)); bool isconn3=((p1 <= 0) && (p2 > 0) && (p1 + p2 < 1))||((p1 <= 0) && (p2 <= 0) && (p1 + p2 < 1)); Real penetrationDepth=0; int connnum=-1; GridNode* GridNodeList[3]={ YADE_CAST(Pfacet->node1->shape.get()), YADE_CAST(Pfacet->node2->shape.get()),YADE_CAST(Pfacet->node3->shape.get())}; // If the contact projection is in the triangle, a search for an old contact is performed to export the information regarding the contact (phys) if (isintriangle){ if(isNew){ for (int unsigned i=0; i<3;i++){ for(int unsigned j=0;jpfacetList.size();j++){ if(GridNodeList[i]->pfacetList[j]->getId()!=c->id2){ boost::tuple projectionPrev = projection(GridNodeList[i]->pfacetList[j]->shape,state1); bool isintrianglePrev = boost::get<1>(projectionPrev); if(!isintrianglePrev){ //if(!isintrianglePrev) const shared_ptr intr = scene->interactions->find(c->id1,GridNodeList[i]->pfacetList[j]->getId()); if( intr && intr->isReal() ){// if an interaction exist between the sphere and the previous pfacet, import parameters. // cout<<"Copying contact with pfacet geom and phys from "<id1<<"-"<id2<<" to here ("<id1<<"-"<id2<<")"<(intr->geom); c->geom=scm; c->phys=intr->phys; c->iterMadeReal=intr->iterMadeReal;// iteration from the time when the contact became real scm->trueInt=c->id2; scm->isDuplicate=2; //command the old contact deletion. isNew=0; break; } } } } } } } else{ // identification of the cylinder possibly in contact with the sphere if (isconn1) connnum=0; if (isconn2) connnum=1; if (isconn3) connnum=2; // check if the identified cylinder previously is in contact with the sphere if (connnum!=-1){ //verify if there is a contact between the a neighbouring PFacet, avoid double contacts for (int unsigned i=0; i<3;i++){ for(int unsigned j=0;jpfacetList.size();j++){ if(GridNodeList[i]->pfacetList[j]->getId()!=c->id2){ boost::tuple projectionPrev = projection(GridNodeList[i]->pfacetList[j]->shape,state1); bool isintrianglePrev = boost::get<1>(projectionPrev); if(isintrianglePrev){ const shared_ptr intr = scene->interactions->find(c->id1,GridNodeList[i]->pfacetList[j]->getId()); if( intr && intr->isReal() ){// if an interaction exist between the sphere and the previous pfacet, import parameters. if (isNew){ return false;} else { scm->isDuplicate=1 ; scm->trueInt=-1 ; return true; } } } } } } //SPhere-cylinder contact const State* sphereSt = YADE_CAST(&state1); GridConnection* gridCo = YADE_CAST(GridList[connnum]->shape.get()); GridNode* gridNo1 = YADE_CAST(gridCo->node1->shape.get()); GridNode* gridNo2 = YADE_CAST(gridCo->node2->shape.get()); State* gridNo1St = YADE_CAST(gridCo->node1->state.get()); State* gridNo2St = YADE_CAST(gridCo->node2->state.get()); Vector3r segt = gridCo->getSegment(); Real len = gridCo->getLength(); Vector3r spherePos = sphereSt->pos; Vector3r branch = spherePos - gridNo1St->pos; Vector3r branchN = spherePos - gridNo2St->pos; for(int i=0;i<3;i++){ if(std::abs(branch[i])<1e-14) branch[i]=0.0; if(std::abs(branchN[i])<1e-14) branchN[i]=0.0; } Real relPos = branch.dot(segt)/(len*len); bool SGr=true; if(relPos<=0){ // if the sphere projection is BEFORE the segment ... if(gridNo1->ConnList.size()>1){// if the node is not an extremity of the Grid (only one connection) for(int unsigned i=0;iConnList.size();i++){ // ... loop on all the Connections of the same Node ... GridConnection* GC = (GridConnection*)gridNo1->ConnList[i]->shape.get(); if(GC==gridCo)continue;// self comparison. Vector3r segtCandidate1 = GC->node1->state->pos - gridNo1St->pos; // (be sure of the direction of segtPrev to compare relPosPrev.) Vector3r segtCandidate2 = GC->node2->state->pos - gridNo1St->pos; Vector3r segtPrev = segtCandidate1.norm()>segtCandidate2.norm() ? segtCandidate1:segtCandidate2; for(int j=0;j<3;j++){ if(std::abs(segtPrev[j])<1e-14) segtPrev[j]=0.0; } Real relPosPrev = (branch.dot(segtPrev))/(segtPrev.norm()*segtPrev.norm()); // ... and check whether the sphere projection is before the neighbours connections too. if(relPosPrev<=0){//if the sphere projection is outside both the current Connection AND this neighbouring connection, then create the interaction if the neighbour did not already do it before. for(int unsigned j=0;jpfacetList.size();j++){ if(GC->pfacetList[j]->getId()!=c->id2){ const shared_ptr intr = scene->interactions->find(c->id1,GC->pfacetList[j]->getId()); if(intr && intr->isReal()){ shared_ptr intrGeom=YADE_PTR_CAST(intr->geom); if(!(intrGeom->isDuplicate==1)){ //skip contact. if (isNew) {SGr=false;} else {scm->isDuplicate=1;}/*cout<<"Declare "<id1<<"-"<id2<<" as duplicated."<id1<<"-"<id2<<" HAVE to be copied and deleted NOW."<isDuplicate=1; scm->trueInt=-1; //trueInt id de l'objet avec lequel il y a un contact -1 = rien faire return true; } } } } } //Exactly the same but in the case the sphere projection is AFTER the segment. else if(relPos>=1){ if(gridNo2->ConnList.size()>1){ for(int unsigned i=0;iConnList.size();i++){ GridConnection* GC = (GridConnection*)gridNo2->ConnList[i]->shape.get(); if(GC==gridCo)continue;// self comparison. Vector3r segtCandidate1 = GC->node1->state->pos - gridNo2St->pos; Vector3r segtCandidate2 = GC->node2->state->pos - gridNo2St->pos; Vector3r segtNext = segtCandidate1.norm()>segtCandidate2.norm() ? segtCandidate1:segtCandidate2; for(int j=0;j<3;j++){ if(std::abs(segtNext[j])<1e-14) segtNext[j]=0.0; } Real relPosNext = (branchN.dot(segtNext))/(segtNext.norm()*segtNext.norm()); if(relPosNext<=0){ //if the sphere projection is outside both the current Connection AND this neighbouring connection, then create the interaction if the neighbour did not already do it before. for(int unsigned j=0;jpfacetList.size();j++){ if(GC->pfacetList[j]->getId()!=c->id2){ const shared_ptr intr = scene->interactions->find(c->id1,GC->pfacetList[j]->getId()); if(intr && intr->isReal()){ shared_ptr intrGeom=YADE_PTR_CAST(intr->geom); if(!(intrGeom->isDuplicate==1)){ if (isNew) SGr=false; else scm->isDuplicate=1;/*cout<<"Declare "<id1<<"-"<id2<<" as duplicated."<id1<<"-"<id2<<" HAVE to be copied and deleted NOW."<isDuplicate=1 ; scm->trueInt=-1 ; return true; } } } } } else if (relPos<=0.5){ if(gridNo1->ConnList.size()>1){// if the node is not an extremity of the Grid (only one connection) for(int unsigned i=0;iConnList.size();i++){ // ... loop on all the Connections of the same Node ... GridConnection* GC = (GridConnection*)gridNo1->ConnList[i]->shape.get(); if(GC==gridCo)continue;// self comparison. Vector3r segtCandidate1 = GC->node1->state->pos - gridNo1St->pos; // (be sure of the direction of segtPrev to compare relPosPrev.) Vector3r segtCandidate2 = GC->node2->state->pos - gridNo1St->pos; Vector3r segtPrev = segtCandidate1.norm()>segtCandidate2.norm() ? segtCandidate1:segtCandidate2; for(int j=0;j<3;j++){ if(std::abs(segtPrev[j])<1e-14) segtPrev[j]=0.0; } Real relPosPrev = (branch.dot(segtPrev))/(segtPrev.norm()*segtPrev.norm()); if(relPosPrev<=0){ //the sphere projection is inside the current Connection and outide this neighbour connection. for(int unsigned j=0;jpfacetList.size();j++){ if(GC->pfacetList[j]->getId()!=c->id2){ const shared_ptr intr = scene->interactions->find(c->id1,GC->pfacetList[j]->getId()); if( intr && intr->isReal() ){// if an ineraction exist between the sphere and the previous connection, import parameters. // cout<<"1Copying contact geom and phys from "<id1<<"-"<id2<<" to here ("<id1<<"-"<id2<<")"<(intr->geom); if(isNew){ c->geom=scm; c->phys=intr->phys; c->iterMadeReal=intr->iterMadeReal; } scm->trueInt=c->id2; scm->isDuplicate=2; //command the old contact deletion. isNew=0; break; } } } } } } } else if (relPos>0.5){ if(gridNo2->ConnList.size()>1){ for(int unsigned i=0;iConnList.size();i++){ GridConnection* GC = (GridConnection*)gridNo2->ConnList[i]->shape.get(); if(GC==gridCo)continue;// self comparison. Vector3r segtCandidate1 = GC->node1->state->pos - gridNo2St->pos; Vector3r segtCandidate2 = GC->node2->state->pos - gridNo2St->pos; Vector3r segtNext = segtCandidate1.norm()>segtCandidate2.norm() ? segtCandidate1:segtCandidate2; for(int j=0;j<3;j++){ if(std::abs(segtNext[j])<1e-14) segtNext[j]=0.0; } Real relPosNext = (branchN.dot(segtNext))/(segtNext.norm()*segtNext.norm()); if(relPosNext<=0){ //the sphere projection is inside the current Connection and outside this neighbour connection. for(int unsigned j=0;jpfacetList.size();j++){ if(GC->pfacetList[j]->getId()!=c->id2){ const shared_ptr intr = scene->interactions->find(c->id1,GC->pfacetList[j]->getId()); if( intr && intr->isReal() ){// if an ineraction exist between the sphere and the previous connection, import parameters. scm=YADE_PTR_CAST(intr->geom); if(isNew){ c->geom=scm; c->phys=intr->phys; c->iterMadeReal=intr->iterMadeReal; } scm->trueInt=c->id2; scm->isDuplicate=2; //command the old contact deletion. break; } } } } } } } if(SGr){ relPos=relPos<0?0:relPos; //min value of relPos : 0 relPos=relPos>1?1:relPos; //max value of relPos : 1 Vector3r fictiousPos=gridNo1St->pos+relPos*segt; Vector3r branchF = fictiousPos - spherePos; Real dist = branchF.norm(); bool SG= !(isNew && (dist > (sphere->radius + gridCo->radius))); if(SG){ // Create the geometry : if(isNew) c->geom=scm; scm->radius1=sphere->radius; scm->radius2=gridCo->radius; scm->id3=gridCo->node1->getId(); scm->id4=gridCo->node2->getId(); scm->relPos=relPos; Vector3r normal=branchF/dist; scm->penetrationDepth = sphere->radius+gridCo->radius-dist; scm->fictiousState.pos = fictiousPos; scm->contactPoint = spherePos + normal*(scm->radius1 - 0.5*scm->penetrationDepth); scm->fictiousState.vel = (1-relPos)*gridNo1St->vel + relPos*gridNo2St->vel; scm->fictiousState.angVel = ((1-relPos)*gridNo1St->angVel + relPos*gridNo2St->angVel).dot(segt/len)*segt/len //twist part : interpolated + segt.cross(gridNo2St->vel - gridNo1St->vel);// non-twist part : defined from nodes velocities scm->precompute(state1,scm->fictiousState,scene,c,normal,isNew,shift2,true);//use sphere-sphere precompute (with a virtual sphere) return true; } } } else{//taking into account the shadow zone for (int unsigned i=0; i<3;i++){ for(int unsigned j=0;jpfacetList.size();j++){ if(GridNodeList[i]->pfacetList[j]->getId()!=c->id2){ boost::tuple projectionPrev = projection(GridNodeList[i]->pfacetList[j]->shape,state1); bool isintrianglePrev = boost::get<1>(projectionPrev); if(!isintrianglePrev){ //if the sphere projection is outside both the current PFacet AND this neighbouring PFacet, then create the interaction if the neighbour did not already do it before. const shared_ptr intr = scene->interactions->find(c->id1,GridNodeList[i]->pfacetList[j]->getId()); if(intr && intr->isReal()){ shared_ptr intrGeom=YADE_PTR_CAST(intr->geom); if(!(intrGeom->isDuplicate==1)){ //skip contact. if (isNew) { return false;} else { scm->isDuplicate=1; }/*cout<<"Declare "<id1<<"-"<id2<<" as duplicated."<id1<<"-"<id2<<" HAVE to be copied and deleted NOW."<isDuplicate=1; //scm->isDuplicate=1; scm->trueInt=-1; //trueInt id de l'objet avec lequel il y a un contact -1 = rien faire return true; } } } } } } } if(isintriangle){ penetrationDepth = sphereRadius + PFacetradius - std::abs(dist); normal.normalize(); if (penetrationDepth>0 || c->isReal() ){ if(isNew) c->geom=scm; scm->radius1=sphereRadius; scm->radius2=PFacetradius; scm->id3=Pfacet->node1->getId(); scm->id4=Pfacet->node2->getId(); scm->id5=Pfacet->node3->getId(); scm->weight[0]=p1; scm->weight[1]=p2; scm->weight[2]=p3; scm->penetrationDepth = penetrationDepth; scm->fictiousState.pos = P; scm->contactPoint = centerS - (PFacetradius-0.5*penetrationDepth)*normal; scm->fictiousState.vel = (p1*Pfacet->node1->state->vel + p2*Pfacet->node2->state->vel +p3*Pfacet->node3->state->vel); scm->fictiousState.angVel = (p1*Pfacet->node1->state->angVel + p2*Pfacet->node2->state->angVel+ p3*Pfacet->node3->state->angVel); scm->precompute(state1,scm->fictiousState,scene,c,-normal,isNew,shift2,true);//use sphere-sphere precompute (with a virtual sphere) TIMING_DELTAS_CHECKPOINT("Ig2_Sphere_PFacet_ScGridCoGeom"); return true; } } TIMING_DELTAS_CHECKPOINT("Ig2_Sphere_PFacet_ScGridCoGeom"); return false; } bool Ig2_Sphere_PFacet_ScGridCoGeom::goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { c->swapOrder(); return go(cm2,cm1,state2,state1,-shift2,force,c); } YADE_PLUGIN((Ig2_Sphere_PFacet_ScGridCoGeom)); bool Ig2_GridConnection_PFacet_ScGeom::go( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { GridConnection* gridCo = YADE_CAST(cm1.get()); PFacet* Pfacet = YADE_CAST(cm2.get()); if(gridCo->node1==Pfacet->node1 || gridCo->node1==Pfacet->node2|| gridCo->node1==Pfacet->node3 || gridCo->node2==Pfacet->node1 || gridCo->node2==Pfacet->node2|| gridCo->node2==Pfacet->node3){return false;} Body::id_t idNode1=gridCo->node1->getId(); Body::id_t idNode2=gridCo->node2->getId(); Body::id_t ids2[3]={Pfacet->conn1->getId(),Pfacet->conn2->getId(),Pfacet->conn3->getId()}; Body::id_t id1=c->id1; Body::id_t id2=c->id2; if (!scene->interactions->found(idNode1,id2)){ shared_ptr scm1 (new Interaction(idNode1,id2)); scene->interactions->insert(scm1); } if (!scene->interactions->found(idNode2,id2)){ shared_ptr scm2 (new Interaction(idNode2,id2)); scene->interactions->insert(scm2); } for (int i=0; i<3; i++){ int entier=i; ostringstream oss; string chaine = "scm"; oss << chaine << entier; string chaine1=oss.str(); if (!scene->interactions->found(id1,ids2[i])){ shared_ptr chaine1 (new Interaction(id1,ids2[i])); scene->interactions->insert(chaine1); } } return(false); } bool Ig2_GridConnection_PFacet_ScGeom::goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { return go(cm1,cm2,state2,state1,-shift2,force,c); } YADE_PLUGIN((Ig2_GridConnection_PFacet_ScGeom)); bool Ig2_PFacet_PFacet_ScGeom::go( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { PFacet* Pfacet1 = YADE_CAST(cm1.get()); PFacet* Pfacet2 = YADE_CAST(cm2.get()); Body::id_t id1=c->id1; Body::id_t id2=c->id2; if(Pfacet1->node1==Pfacet2->node1 || Pfacet1->node1==Pfacet2->node2|| Pfacet1->node1==Pfacet2->node3 || Pfacet1->node2==Pfacet2->node1 || Pfacet1->node2==Pfacet2->node2|| Pfacet1->node2==Pfacet2->node3 || Pfacet1->node3==Pfacet2->node1 || Pfacet1->node3==Pfacet2->node2|| Pfacet1->node3==Pfacet2->node3 ){ return false;} boost::tuple p1 = Ig2_Sphere_PFacet_ScGridCoGeom::projection(cm1,* Pfacet2->node1->state); boost::tuple p2 = Ig2_Sphere_PFacet_ScGridCoGeom::projection(cm1,* Pfacet2->node2->state); boost::tuple p3 = Ig2_Sphere_PFacet_ScGridCoGeom::projection(cm1,* Pfacet2->node3->state); boost::tuple p4 = Ig2_Sphere_PFacet_ScGridCoGeom::projection(cm2,* Pfacet1->node1->state); boost::tuple p5 = Ig2_Sphere_PFacet_ScGridCoGeom::projection(cm2,* Pfacet1->node2->state); boost::tuple p6 = Ig2_Sphere_PFacet_ScGridCoGeom::projection(cm2,* Pfacet1->node3->state); bool isintriangle1 = boost::get<1>(p1); bool isintriangle2 = boost::get<1>(p2); bool isintriangle3 = boost::get<1>(p3); bool isintriangle4 = boost::get<1>(p4); bool isintriangle5 = boost::get<1>(p5); bool isintriangle6 = boost::get<1>(p6); bool istriangleNodes2P1 = (isintriangle1==true) && (isintriangle2==true) && (isintriangle3==true); bool istriangleNodes1P2 = (isintriangle4==true) && (isintriangle5==true) && (isintriangle6==true); if(istriangleNodes1P2 ){ Body::id_t idNode11=Pfacet1->node1->getId(); Body::id_t idNode12=Pfacet1->node2->getId(); Body::id_t idNode13=Pfacet1->node3->getId(); if (!scene->interactions->found(idNode11,id2)){ shared_ptr scm1 (new Interaction(idNode11,id2)); scene->interactions->insert(scm1); } if (!scene->interactions->found(idNode12,id2)){ shared_ptr scm2 (new Interaction(idNode12,id2)); scene->interactions->insert(scm2); } if (!scene->interactions->found(idNode13,id2)){ shared_ptr scm3 (new Interaction(idNode13,id2)); scene->interactions->insert(scm3); } } else if(istriangleNodes2P1 ){ Body::id_t idNode21=Pfacet2->node1->getId(); Body::id_t idNode22=Pfacet2->node2->getId(); Body::id_t idNode23=Pfacet2->node3->getId(); if (!scene->interactions->found(idNode21,id1)){ shared_ptr scm1 (new Interaction(idNode21,id1)); scene->interactions->insert(scm1); } if (!scene->interactions->found(idNode22,id1)){ shared_ptr scm2 (new Interaction(idNode22,id1)); scene->interactions->insert(scm2); } if (!scene->interactions->found(idNode23,id1)){ shared_ptr scm3 (new Interaction(idNode23,id1)); scene->interactions->insert(scm3); } } else{ vector vertices1={Pfacet1->node1->state->pos,Pfacet1->node2->state->pos,Pfacet1->node3->state->pos}; vector vertices2={Pfacet2->node1->state->pos,Pfacet2->node2->state->pos,Pfacet2->node3->state->pos}; GridConnection* gridCo1P1 = (GridConnection*) Pfacet1->conn1->shape.get(); GridConnection* gridCo2P1 = (GridConnection*) Pfacet1->conn2->shape.get(); GridConnection* gridCo3P1 = (GridConnection*) Pfacet1->conn3->shape.get(); GridConnection* gridCo1P2 = (GridConnection*) Pfacet2->conn1->shape.get(); GridConnection* gridCo2P2 = (GridConnection*) Pfacet2->conn2->shape.get(); GridConnection* gridCo3P2 = (GridConnection*) Pfacet2->conn3->shape.get(); State* gridNo1StgridCo1P1 = YADE_CAST(gridCo1P1->node1->state.get()); State* gridNo2StgridCo1P1 = YADE_CAST(gridCo1P1->node2->state.get()); State* gridNo1StgridCo2P1 = YADE_CAST(gridCo2P1->node1->state.get()); State* gridNo2StgridCo2P1 = YADE_CAST(gridCo2P1->node2->state.get()); State* gridNo1StgridCo3P1 = YADE_CAST(gridCo3P1->node1->state.get()); State* gridNo2StgridCo3P1 = YADE_CAST(gridCo3P1->node2->state.get()); State* gridNo1StgridCo1P2 = YADE_CAST(gridCo1P2->node1->state.get()); State* gridNo2StgridCo1P2 = YADE_CAST(gridCo1P2->node2->state.get()); State* gridNo1StgridCo2P2 = YADE_CAST(gridCo2P2->node1->state.get()); State* gridNo2StgridCo2P2 = YADE_CAST(gridCo2P2->node2->state.get()); State* gridNo1StgridCo3P2 = YADE_CAST(gridCo3P2->node1->state.get()); State* gridNo2StgridCo3P2 = YADE_CAST(gridCo3P2->node2->state.get()); Vector3r seg11=(gridNo1StgridCo1P1->pos - gridNo2StgridCo1P1->pos)/(gridNo1StgridCo1P1->pos - gridNo2StgridCo1P1->pos).norm(); Vector3r seg12=(gridNo1StgridCo2P1->pos - gridNo2StgridCo2P1->pos)/(gridNo1StgridCo2P1->pos - gridNo2StgridCo2P1->pos).norm() ; Vector3r seg13=(gridNo1StgridCo3P1->pos - gridNo2StgridCo3P1->pos)/(gridNo1StgridCo3P1->pos - gridNo2StgridCo3P1->pos).norm(); Vector3r seg21=(gridNo1StgridCo1P2->pos - gridNo2StgridCo1P2->pos)/(gridNo1StgridCo1P2->pos - gridNo2StgridCo1P2->pos).norm(); Vector3r seg22=(gridNo1StgridCo2P2->pos - gridNo2StgridCo2P2->pos)/(gridNo1StgridCo2P2->pos - gridNo2StgridCo2P2->pos).norm(); Vector3r seg23=(gridNo1StgridCo3P2->pos - gridNo2StgridCo3P2->pos)/(gridNo1StgridCo3P2->pos - gridNo2StgridCo3P2->pos).norm(); Real normal1seg21seg11= seg21.dot(seg11); Real normal1seg21seg12= seg21.dot(seg12); Real normal1seg21seg13= seg21.dot(seg13); Real normal1seg22seg11= seg22.dot(seg11); Real normal1seg22seg12= seg22.dot(seg12); Real normal1seg22seg13= seg22.dot(seg13); Real normal1seg23seg11= seg23.dot(seg11); Real normal1seg23seg12= seg23.dot(seg12); Real normal1seg23seg13= seg23.dot(seg13); Body::id_t ids1[3]={Pfacet1->conn1->getId(),Pfacet1->conn2->getId(),Pfacet1->conn3->getId()}; Body::id_t ids2[3]={Pfacet2->conn1->getId(),Pfacet2->conn2->getId(),Pfacet2->conn3->getId()}; Body::id_t c1 =-1; Body::id_t c2 =-1; if(std::abs(normal1seg21seg11)==1){c1=ids2[0];c2=ids1[0];} if(std::abs(normal1seg21seg12)==1){c1=ids2[0];c2=ids1[1];} if(std::abs(normal1seg21seg13)==1){c1=ids2[0];c2=ids1[2];} if(std::abs(normal1seg22seg11)==1){c1=ids2[1];c2=ids1[0];} if(std::abs(normal1seg22seg12)==1){c1=ids2[1];c2=ids1[1];} if(std::abs(normal1seg22seg13)==1){c1=ids2[1];c2=ids1[2];} if(std::abs(normal1seg23seg11)==1){c1=ids2[2];c2=ids1[0];} if(std::abs(normal1seg23seg12)==1){c1=ids2[2];c2=ids1[1];} if(std::abs(normal1seg23seg13)==1){c1=ids2[2];c2=ids1[2];} if( (isintriangle1==false) && (isintriangle2==false) && (isintriangle3==false) && (isintriangle4==false) && (isintriangle5==false) && (isintriangle6==false)){ if((c1!=-1)and (c2!=-1) and(Body::byId(c1)->getGroupMask()!=0)and(Body::byId(c2)->getGroupMask()!=0)){ ostringstream oss; string chaine = "scm"; if (!scene->interactions->found(c1,c2)){ shared_ptr chaine (new Interaction(c1,c2)); scene->interactions->insert(chaine); } } else{ for (int i=0; i<3; i++){ for (int j=0; j<3; j++){ int entier = j+i*3; ostringstream oss; string chaine = "scm"; oss << chaine << entier; string chaine1=oss.str(); if (!scene->interactions->found(ids1[i],ids2[j])){ if((Body::byId(ids1[i])->getGroupMask()!=0)and(Body::byId(ids2[j])->getGroupMask()!=0)){ shared_ptr chaine1 (new Interaction(ids1[i],ids2[j])); scene->interactions->insert(chaine1); } } } } } } else{ Body::id_t idNode11=Pfacet1->node1->getId(); Body::id_t idNode12=Pfacet1->node2->getId(); Body::id_t idNode13=Pfacet1->node3->getId(); if (!scene->interactions->found(idNode11,id2)){ shared_ptr scm1 (new Interaction(idNode11,id2)); scene->interactions->insert(scm1); } if (!scene->interactions->found(idNode12,id2)){ shared_ptr scm2 (new Interaction(idNode12,id2)); scene->interactions->insert(scm2); } if (!scene->interactions->found(idNode13,id2)){ shared_ptr scm3 (new Interaction(idNode13,id2)); scene->interactions->insert(scm3); } Body::id_t idNode21=Pfacet2->node1->getId(); Body::id_t idNode22=Pfacet2->node2->getId(); Body::id_t idNode23=Pfacet2->node3->getId(); if (!scene->interactions->found(idNode21,id1)){ shared_ptr scm1 (new Interaction(idNode21,id1)); scene->interactions->insert(scm1); } if (!scene->interactions->found(idNode22,id1)){ shared_ptr scm2 (new Interaction(idNode22,id1)); scene->interactions->insert(scm2); } if (!scene->interactions->found(idNode23,id1)){ shared_ptr scm3 (new Interaction(idNode23,id1)); scene->interactions->insert(scm3); } Body::id_t ids1[3]={Pfacet1->conn1->getId(),Pfacet1->conn2->getId(),Pfacet1->conn3->getId()}; Body::id_t ids2[3]={Pfacet2->conn1->getId(),Pfacet2->conn2->getId(),Pfacet2->conn3->getId()}; for (int i=0; i<3; i++){ for (int j=0; j<3; j++){ int entier = j+i*3; ostringstream oss; string chaine = "scm"; oss << chaine << entier; string chaine1=oss.str(); if (!scene->interactions->found(ids1[i],ids2[j])){ if((Body::byId(ids1[i])->getGroupMask()!=0)and(Body::byId(ids2[j])->getGroupMask()!=0)){ shared_ptr chaine1 (new Interaction(ids1[i],ids2[j])); scene->interactions->insert(chaine1); } } } } } } return(false); } bool Ig2_PFacet_PFacet_ScGeom::goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { return go(cm1,cm2,state2,state1,-shift2,force,c); } YADE_PLUGIN((Ig2_PFacet_PFacet_ScGeom)); /********* Wall + Sphere **********/ bool Ig2_Wall_PFacet_ScGeom::go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c){ PFacet* Pfacet = YADE_CAST(cm2.get()); Body::id_t idNode1=Pfacet->node1->getId(); Body::id_t idNode2=Pfacet->node2->getId(); Body::id_t idNode3=Pfacet->node3->getId(); Body::id_t id1=c->id1; if (!scene->interactions->found(id1,idNode1)){ shared_ptr scm1 (new Interaction(id1,idNode1)); scene->interactions->insert(scm1); } if (!scene->interactions->found(id1,idNode2)){ shared_ptr scm2 (new Interaction(id1,idNode2)); scene->interactions->insert(scm2); } if (!scene->interactions->found(id1,idNode3)){ shared_ptr scm3 (new Interaction(id1,idNode3)); scene->interactions->insert(scm3); } return(false); } YADE_PLUGIN((Ig2_Wall_PFacet_ScGeom)); //!################## Bounds ##################### void Bo1_PFacet_Aabb::go(const shared_ptr& cm, shared_ptr& bv, const Se3r& se3, const Body* b) { PFacet* Pfacet = YADE_CAST(cm.get()); if(!bv){ bv=shared_ptr(new Aabb); } Aabb* aabb=static_cast(bv.get()); Vector3r O = Pfacet->node1->state->pos; Vector3r O2 =Pfacet->node2->state->pos; Vector3r O3 =Pfacet->node3->state->pos; if(!scene->isPeriodic){ for (int k=0;k<3;k++){ aabb->min[k] = min(min(O[k],O2[k]),O3[k]) - Pfacet->radius; aabb->max[k] = max(max(O[k],O2[k]),O3[k]) + Pfacet->radius; } return; } else{ O = scene->cell->unshearPt(O); O2 = scene->cell->unshearPt(O2); O3= scene->cell->unshearPt(O3); Vector3r T=scene->cell->hSize*Pfacet->cellDist.cast(); O = O + T; O2 = O2 + T; O3 = O3 + T; for (int k=0;k<3;k++){ aabb->min[k] = min(min(O[k],O2[k]),O3[k]) - Pfacet->radius; aabb->max[k] = max(max(O[k],O2[k]),O3[k]) + Pfacet->radius; } } } YADE_PLUGIN((Bo1_PFacet_Aabb)); trunk-2017.01a/pkg/common/PFacet.hpp000066400000000000000000000145601304022710500171140ustar00rootroot00000000000000/***************************************************************************** * Copyright (C) 2015 by Anna Effeindzourou anna.effeindzourou@gmail.com * * Copyright (C) 2015 by Bruno Chareyre bruno.chareyre@hmg.inpg.fr * * Copyright (C) 2015 by Klaus Thoeni klaus.thoeni@gmail.com * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * ******************************************************************************/ #pragma once #include #include #include #include #include #include #include #include #include #include #include #include #ifdef YADE_OPENGL #include #endif //!################## IGeom Functors ################## //! O/ class Ig2_Sphere_PFacet_ScGridCoGeom: public Ig2_Sphere_GridConnection_ScGridCoGeom{ public : boost::tuple projection( const shared_ptr& cm2, const State& state1); virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); YADE_CLASS_BASE_DOC_ATTRS(Ig2_Sphere_PFacet_ScGridCoGeom,Ig2_Sphere_GridConnection_ScGridCoGeom,"Create/update a :yref:`ScPFaceCoGeom` instance representing intersection of :yref:`Facet` and :yref:`Sphere`.", ((Real,shrinkFactor,((void)"no shrinking",0),,"The radius of the inscribed circle of the facet is decreased by the value of the sphere's radius multipled by *shrinkFactor*. From the definition of contact point on the surface made of facets, the given surface is not continuous and becomes in effect surface covered with triangular tiles, with gap between the separate tiles equal to the sphere's radius multiplied by 2×*shrinkFactor*. If zero, no shrinking is done.")) ); DECLARE_LOGGER; FUNCTOR2D(Sphere,PFacet); DEFINE_FUNCTOR_ORDER_2D(Sphere,PFacet); }; REGISTER_SERIALIZABLE(Ig2_Sphere_PFacet_ScGridCoGeom); class Ig2_GridConnection_PFacet_ScGeom: public Ig2_Sphere_GridConnection_ScGridCoGeom{ public : virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); YADE_CLASS_BASE_DOC_ATTRS(Ig2_GridConnection_PFacet_ScGeom,Ig2_Sphere_GridConnection_ScGridCoGeom,"Create/update a :yref:`ScGeom` instance representing intersection of :yref:`Facet` and :yref:`GridConnection`.", ((Real,shrinkFactor,((void)"no shrinking",0),,"The radius of the inscribed circle of the facet is decreased by the value of the sphere's radius multipled by *shrinkFactor*. From the definition of contact point on the surface made of facets, the given surface is not continuous and becomes in effect surface covered with triangular tiles, with gap between the separate tiles equal to the sphere's radius multiplied by 2×*shrinkFactor*. If zero, no shrinking is done.")) ); DECLARE_LOGGER; FUNCTOR2D(GridConnection,PFacet); DEFINE_FUNCTOR_ORDER_2D(GridConnection,PFacet); }; REGISTER_SERIALIZABLE(Ig2_GridConnection_PFacet_ScGeom); //! O/ class Ig2_PFacet_PFacet_ScGeom: public Ig2_Sphere_PFacet_ScGridCoGeom{ public : virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); YADE_CLASS_BASE_DOC_ATTRS(Ig2_PFacet_PFacet_ScGeom,Ig2_Sphere_PFacet_ScGridCoGeom,"Create/update a :yref:`ScGridCoGeom` instance representing intersection of :yref:`Facet` and :yref:`Sphere`.", ((Real,shrinkFactor,((void)"no shrinking",0),,"The radius of the inscribed circle of the facet is decreased by the value of the sphere's radius multipled by *shrinkFactor*. From the definition of contact point on the surface made of facets, the given surface is not continuous and becomes in effect surface covered with triangular tiles, with gap between the separate tiles equal to the sphere's radius multiplied by 2×*shrinkFactor*. If zero, no shrinking is done.")) ); DECLARE_LOGGER; FUNCTOR2D(PFacet,PFacet); DEFINE_FUNCTOR_ORDER_2D(PFacet,PFacet); }; REGISTER_SERIALIZABLE(Ig2_PFacet_PFacet_ScGeom); /********* Wall + Sphere **********/ class Ig2_Wall_PFacet_ScGeom: public Ig2_Wall_Sphere_ScGeom{ public: virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); YADE_CLASS_BASE_DOC_ATTRS(Ig2_Wall_PFacet_ScGeom,Ig2_Wall_Sphere_ScGeom,"Create/update a :yref:`ScGeom` instance representing intersection of :yref:`Wall` and :yref:`PFacet`.", ); FUNCTOR2D(Wall,PFacet); DEFINE_FUNCTOR_ORDER_2D(Wall,PFacet); }; REGISTER_SERIALIZABLE(Ig2_Wall_PFacet_ScGeom); //!################## Bounds ##################### class Bo1_PFacet_Aabb : public BoundFunctor { public : void go(const shared_ptr& cm, shared_ptr& bv, const Se3r&, const Body*); FUNCTOR1D(PFacet); YADE_CLASS_BASE_DOC_ATTRS(Bo1_PFacet_Aabb,BoundFunctor,"Functor creating :yref:`Aabb` from a :yref:`PFacet`.", ((Real,aabbEnlargeFactor,((void)"deactivated",-1),,"Relative enlargement of the bounding box; deactivated if negative.")) ); }; REGISTER_SERIALIZABLE(Bo1_PFacet_Aabb); trunk-2017.01a/pkg/common/ParallelEngine.cpp000066400000000000000000000037661304022710500206350ustar00rootroot00000000000000#include YADE_PLUGIN((ParallelEngine)); #ifdef YADE_OPENMP #include #endif //! ParallelEngine's pseudo-ctor (factory), taking nested lists of slave engines (might be moved to real ctor perhaps) shared_ptr ParallelEngine_ctor_list(const boost::python::list& slaves){ shared_ptr instance(new ParallelEngine); instance->slaves_set(slaves); return instance; } void ParallelEngine::action(){ // openMP warns if the iteration variable is unsigned... const int size=(int)slaves.size(); #ifdef YADE_OPENMP //nested parallel regions are disabled by default on some platforms, we enable them since some of the subengine may be also parallel omp_set_nested(1); #pragma omp parallel for num_threads(ompThreads) #endif for(int i=0; i& e, slaves[i]) { //cerr<<"["<getClassName()<<"]"; e->scene=scene; if(!e->dead && e->isActivated()) e->action(); } } } void ParallelEngine::slaves_set(const boost::python::list& slaves2){ int len=boost::python::len(slaves2); slaves.clear(); for(int i=0; i > > serialGroup(slaves2[i]); if (serialGroup.check()){ slaves.push_back(serialGroup()); continue; } boost::python::extract > serialAlone(slaves2[i]); if (serialAlone.check()){ vector > aloneWrap; aloneWrap.push_back(serialAlone()); slaves.push_back(aloneWrap); continue; } PyErr_SetString(PyExc_TypeError,"List elements must be either\n (a) sequences of engines to be executed one after another\n(b) alone engines."); boost::python::throw_error_already_set(); } } boost::python::list ParallelEngine::slaves_get(){ boost::python::list ret; FOREACH(vector >& grp, slaves){ if(grp.size()==1) ret.append(boost::python::object(grp[0])); else ret.append(boost::python::object(grp)); } return ret; } trunk-2017.01a/pkg/common/ParallelEngine.hpp000066400000000000000000000020521304022710500206250ustar00rootroot00000000000000#pragma once #include class ParallelEngine; shared_ptr ParallelEngine_ctor_list(const boost::python::list& slaves); class ParallelEngine: public Engine { public: typedef vector > > slaveContainer; virtual void action(); virtual bool isActivated(){return true;} // py access boost::python::list slaves_get(); void slaves_set(const boost::python::list& slaves); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(ParallelEngine,Engine,"Engine for running other Engine in parallel.", ((slaveContainer,slaves,,,"[will be overridden]")) , /*ctor*/ ompThreads=2; , /*py*/ .def("__init__",boost::python::make_constructor(ParallelEngine_ctor_list),"Construct from (possibly nested) list of slaves.") .add_property("slaves",&ParallelEngine::slaves_get,&ParallelEngine::slaves_set,"List of lists of Engines; each top-level group will be run in parallel with other groups, while Engines inside each group will be run sequentially, in given order."); ); }; REGISTER_SERIALIZABLE(ParallelEngine); trunk-2017.01a/pkg/common/PeriodicEngines.hpp000066400000000000000000000076041304022710500210220ustar00rootroot00000000000000// 2008, 2009 © Václav Šmilauer #pragma once #include #include #include #include class PeriodicEngine: public GlobalEngine { public: static Real getClock(){ timeval tp; gettimeofday(&tp,NULL); return tp.tv_sec+tp.tv_usec/1e6; } virtual ~PeriodicEngine() {}; // vtable virtual bool isActivated(){ const Real& virtNow=scene->time; Real realNow=getClock(); const long& iterNow=scene->iter; if((firstIterRun > 0) && (nDone==0)) { if((firstIterRun > 0) && (firstIterRun == iterNow)) { realLast=realNow; virtLast=virtNow; iterLast=iterNow; nDone++; return true; } return false; } if (iterNow0 && virtNow-virtLast>=virtPeriod) || (realPeriod>0 && realNow-realLast>=realPeriod) || (iterPeriod>0 && iterNow-iterLast>=iterPeriod))){ realLast=realNow; virtLast=virtNow; iterLast=iterNow; nDone++; return true; } if(nDone==0){ realLast=realNow; virtLast=virtNow; iterLast=iterNow; nDone++; if(initRun) return true; return false; } return false; } YADE_CLASS_BASE_DOC_ATTRS_CTOR(PeriodicEngine,GlobalEngine, "Run Engine::action with given fixed periodicity real time (=wall clock time, computation time), \ virtual time (simulation time), iteration number), by setting any of those criteria \ (virtPeriod, realPeriod, iterPeriod) to a positive value. They are all negative (inactive)\ by default.\n\n\ \ The number of times this engine is activated can be limited by setting nDo>0. If the number of activations \ will have been already reached, no action will be called even if an active period has elapsed. \n\n\ \ If initRun is set (false by default), the engine will run when called for the first time; otherwise it will only \ start counting period (realLast etc interal variables) from that point, but without actually running, and will run \ only once a period has elapsed since the initial run. \n\n\ \ This class should not be used directly; rather, derive your own engine which you want to be run periodically. \n\n\ \ Derived engines should override Engine::action(), which will be called periodically. If the derived Engine \ overrides also Engine::isActivated, it should also take in account return value from PeriodicEngine::isActivated, \ since otherwise the periodicity will not be functional. \n\n\ \ Example with :yref:`PyRunner`, which derives from PeriodicEngine; likely to be encountered in python scripts:: \n\n\ \ PyRunner(realPeriod=5,iterPeriod=10000,command='print O.iter') \n\n\ \ will print iteration number every 10000 iterations or every 5 seconds of wall clock time, whiever comes first since it was \ last run.", ((Real,virtPeriod,((void)"deactivated",0),,"Periodicity criterion using virtual (simulation) time (deactivated if <= 0)")) ((Real,realPeriod,((void)"deactivated",0),,"Periodicity criterion using real (wall clock, computation, human) time (deactivated if <=0)")) ((long,iterPeriod,((void)"deactivated",0),,"Periodicity criterion using step number (deactivated if <= 0)")) ((long,nDo,((void)"deactivated",-1),,"Limit number of executions by this number (deactivated if negative)")) ((bool,initRun,false,,"Run the first time we are called as well.")) ((long,firstIterRun,0,,"Sets the step number, at each an engine should be executed for the first time (disabled by default).")) ((Real,virtLast,0,,"Tracks virtual time of last run |yupdate|.")) ((Real,realLast,0,,"Tracks real time of last run |yupdate|.")) ((long,iterLast,0,,"Tracks step number of last run |yupdate|.")) ((long,nDone,0,,"Track number of executions (cummulative) |yupdate|.")), /* this will be put inside the ctor */ realLast=getClock(); ); }; REGISTER_SERIALIZABLE(PeriodicEngine); trunk-2017.01a/pkg/common/PersistentTriangulationCollider.cpp000066400000000000000000000077111304022710500243240ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2009 by Bruno Chareyre * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef YADE_CGAL #include"PersistentTriangulationCollider.hpp" #include #include #include #include #include // PersistentTriangulationCollider::PersistentTriangulationCollider() : Collider() // { // haveDistantTransient=false; // isTriangulated = false; // Tes = new ( TesselationWrapper ); // // nbObjects=0; // xBounds.clear(); // yBounds.clear(); // zBounds.clear(); // minima.clear(); // maxima.clear(); // } PersistentTriangulationCollider::~PersistentTriangulationCollider() { delete Tes; } void PersistentTriangulationCollider::action () { // update bounds boundDispatcher->scene=scene; boundDispatcher->action(); shared_ptr bodies=scene->bodies; bool triangulationIteration = false; //BEGIN VORONOI TESSELATION if ( !isTriangulated || scene->iter % 50 == 0 ) { //TesselationWrapper Tes; Tes->clear(); FOREACH(const shared_ptr& b, *scene->bodies){ if(!b || !b->isDynamic()) continue; //means "is it a sphere (not a wall)" const Sphere* s = YADE_CAST(b->shape.get()); Tes->insert ( b->state->pos[0],b->state->pos[1],b->state->pos[2], s->radius, b->getId() ); } Tes->addBoundingPlanes(); isTriangulated = true; triangulationIteration = true; //} // else // { // //if (scene->iter % 100 == 0) { // if (1) { // Tes->RemoveBoundingPlanes(); // BodyContainer::iterator bi = bodies->begin(); // BodyContainer::iterator biEnd = bodies->end(); // for ( ; bi!=biEnd ; ++bi ) // { // if ( ( *bi )->isDynamic() ) // {//means "is it a sphere (not a wall)" // const Sphere* s = YADE_CAST ( ( *bi )->shape.get() ); // const RigidBodyParameters* p = YADE_CAST ( ( *bi )->physicalParameters.get() ); // Tes->move ( p->se3.position[0],p->se3.position[1],p->se3.position[2], s->radius, ( *bi )->getId() ); // // else { // // const Box* s = YADE_CAST((*bi)->shape.get()); // // const RigidBodyParameters* p = YADE_CAST((*bi)->physicalParameters.get()); // // Tes.move(p->se3.position[0],p->se3.position[1],p->se3.position[2], s->radius, (*bi)->getId()); // // } // } // } // Tes->AddBoundingPlanes(); // } } //ENDOF VORONOI TESSELATION interactions = scene->interactions; if ( triangulationIteration ) { std::pair interaction_pair; unsigned int& id1 = interaction_pair.first; unsigned int& id2 = interaction_pair.second; unsigned int numberOfInteractions = Tes->NumberOfFacets(true); for ( unsigned int i=0; inextFacet ( interaction_pair ); // look if the pair (id1,id2) already exists in the overleppingBB collection const shared_ptr& interaction=interactions->find ( Body::id_t ( id1 ),Body::id_t ( id2 ) ); bool found= ( interaction!=0 );//Bruno's Hack // inserts the pair p=(id1,id2) if the two Aabb overlaps and if p does not exists in the overlappingBB if ( !found ) { interactions->insert ( Body::id_t ( id1 ),Body::id_t ( id2 ) ); //cerr << "inserted " << id1 << "-" << id2<iter will be deleted by InteractionLoop, if the collider was run at that step as well interaction->iterLastSeen=scene->iter; // removes the pair p=(id1,id2) if the two Aabb do not overlapp any more and if p already exists in the overlappingBB } } } YADE_PLUGIN((PersistentTriangulationCollider)); #endif /* YADE_CGAL */ trunk-2017.01a/pkg/common/PersistentTriangulationCollider.hpp000066400000000000000000000041241304022710500243240ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include /*! \brief Collision detection engine based on regular triangulation. This engine is using CGAL library (see http://www.cgal.org/) It is still experimental. Uncoment lines in sconscript file to compile it and just change the name of the collider in an existing xml and it will (should) work. Also needed : uncommenting lines in core/Interaction.cpp and core/Interaction.hpp (see NOTE:TriangulationCollider */ class TesselationWrapper; class PersistentTriangulationCollider : public Collider { private : TesselationWrapper* Tes; public : virtual ~PersistentTriangulationCollider(); /// return a list "interactions" of pairs of Body which bounding spheres are overlapping void action(); //! this flag is used to check if the packing has been triangulated bool isTriangulated; shared_ptr interactions; YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY( PersistentTriangulationCollider,Collider,"Collision detection engine based on regular triangulation. Handles spheres and flat boundaries (considered as infinite-sized bounding spheres).", ((bool,haveDistantTransient,false,,"Keep distant interactions? If True, don't delete interactions once bodies don't overlap anymore; constitutive laws will be responsible for requesting deletion. If False, delete as soon as there is no object penetration.")) , isTriangulated = false; Tes = new (TesselationWrapper); ,); }; REGISTER_SERIALIZABLE(PersistentTriangulationCollider); trunk-2017.01a/pkg/common/PyRunner.hpp000066400000000000000000000013021304022710500175220ustar00rootroot00000000000000// 2008 © Václav Šmilauer #pragma once #include #include #include #include class PyRunner: public PeriodicEngine { public : /* virtual bool isActivated: not overridden, PeriodicEngine handles that */ virtual void action(){ if(command.size()>0) pyRunString(command); } YADE_CLASS_BASE_DOC_ATTRS(PyRunner,PeriodicEngine, "Execute a python command periodically, with defined (and adjustable) periodicity. See :yref:`PeriodicEngine` documentation for details.", ((string,command,"",,"Command to be run by python interpreter. Not run if empty.")) ); }; REGISTER_SERIALIZABLE(PyRunner); trunk-2017.01a/pkg/common/Recorder.hpp000066400000000000000000000026531304022710500175170ustar00rootroot00000000000000// 2009 © Václav Šmilauer #pragma once #include class Recorder: public PeriodicEngine{ void openAndCheck() { assert(!out.is_open()); std::string fileTemp = file; if (addIterNum) fileTemp+="-" + boost::lexical_cast(scene->iter); if(fileTemp.empty()) throw ios_base::failure(__FILE__ ": Empty filename."); out.open(fileTemp.c_str(), truncate ? fstream::trunc : fstream::app); if(!out.good()) throw ios_base::failure(__FILE__ ": I/O error opening file `"+fileTemp+"'."); } protected: //! stream object that derived engines should write to std::ofstream out; public: virtual ~Recorder() {}; virtual bool isActivated(){ if(PeriodicEngine::isActivated()){ if(!out.is_open()) openAndCheck(); return true; } return false; } YADE_CLASS_BASE_DOC_ATTRS(Recorder,PeriodicEngine,"Engine periodically storing some data to (one) external file. In addition PeriodicEngine, it handles opening the file as needed. See :yref:`PeriodicEngine` for controlling periodicity.", ((std::string,file,,,"Name of file to save to; must not be empty.")) ((bool,truncate,false,,"Whether to delete current file contents, if any, when opening (false by default)")) ((bool,addIterNum,false,,"Adds an iteration number to the file name, when the file was created. Useful for creating new files at each call (false by default)")) ); }; REGISTER_SERIALIZABLE(Recorder); trunk-2017.01a/pkg/common/ResetRandomPosition.cpp000066400000000000000000000107421304022710500217130ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2009 by Sergei Dorofeenko * * sega@users.berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef pi #undef pi #endif #include #include #include #include #include #include //#include #include"ResetRandomPosition.hpp" YADE_PLUGIN((ResetRandomPosition)); CREATE_LOGGER(ResetRandomPosition); boost::variate_generator > ResetRandomPosition::randomUnit(boost::mt19937(),boost::uniform_real<>(0,1)); boost::variate_generator > ResetRandomPosition::randomSymmetricUnit(boost::mt19937(),boost::uniform_real<>(-1,1)); void ResetRandomPosition::action() { if (first_run) { FOREACH(shared_ptr eng, scene->engines) { bI=dynamic_cast(eng.get()); if (bI) break; } if (!bI) { LOG_FATAL("Can't find Collider." ); return; } iGME=dynamic_cast(scene->engineByName("IGeomDispatcher").get()); if (!iGME) { InteractionLoop* iDsp=dynamic_cast(scene->engineByName("InteractionLoop").get()); if (!iDsp) { LOG_FATAL("Can't find nor IGeomDispatcher nor InteractionLoop." ); return; } iGME=dynamic_cast(iDsp->geomDispatcher.get()); if (!iGME) { LOG_FATAL("Can't find IGeomDispatcher." ); return; } } first_run=false; randomFacet= shared_ptr(new RandomInt(boost::minstd_rand(),boost::uniform_int<>(0,factoryFacets.size()-1))); } shiftedBodies.clear(); FOREACH(int id, subscribedBodies) { shared_ptr b = Body::byId(id); State* rb = b->state.get(); Vector3r& position = rb->se3.position; if ( (position-point).dot(normal) < 0 ) { Vector3r backup_pos = position; bool is_overlap; for (int attempt=0; attempt(b->shape.get())->radius; Bound bv; bv.min = Vector3r(position[0]-r, position[1]-r, position[2]-r); bv.max = Vector3r(position[0]+r, position[1]+r, position[2]+r); is_overlap=false; // Test overlap with already shifted bodies FOREACH(shared_ptr sb, shiftedBodies) { if (iGME->explicitAction(b,sb,/*force*/false)->geom) { is_overlap=true; break; } } if (is_overlap) continue; // new attempt // Test overlap with other bodies vector probedBodies=bI->probeBoundingVolume(bv); FOREACH(Body::id_t id, probedBodies){ if (iGME->explicitAction(b,Body::byId(id),/*force*/false)->geom){ is_overlap=true; break; } } if (is_overlap) continue; // new attempt break; } if (is_overlap) { LOG_WARN("Can't placing sphere during " << maxAttempts << " attempts."); position=backup_pos; return; } rb->vel = Vector3r(// velocity[0]+velocityRange[0]*randomSymmetricUnit(), velocity[1]+velocityRange[1]*randomSymmetricUnit(), velocity[2]+velocityRange[2]*randomSymmetricUnit()); rb->angVel = Vector3r(// angularVelocity[0]+angularVelocityRange[0]*randomSymmetricUnit(), angularVelocity[1]+angularVelocityRange[1]*randomSymmetricUnit(), angularVelocity[2]+angularVelocityRange[2]*randomSymmetricUnit()); shiftedBodies.push_back(b); } } // next sphere } Vector3r ResetRandomPosition::generatePositionOnSurface() { Body::id_t facetId = factoryFacets[(*randomFacet)()]; Real t1 = randomUnit(); Real t2 = randomUnit()*(1-t1); shared_ptr facet = Body::byId(facetId); Facet* ifacet = static_cast(facet->shape.get()); return t1*(ifacet->vertices[1]-ifacet->vertices[0])+t2*(ifacet->vertices[2]-ifacet->vertices[0])+ifacet->vertices[0]+facet->state->se3.position; } Vector3r ResetRandomPosition::generatePositionInVolume() { Vector3r p1 = generatePositionOnSurface(); Vector3r p2 = generatePositionOnSurface(); Real t = randomUnit(); return p1+t*(p2-p1); } trunk-2017.01a/pkg/common/ResetRandomPosition.hpp000066400000000000000000000062511304022710500217200ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2009 by Sergei Dorofeenko * * sega@users.berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include #include #include /// @brief Produces spheres over the course of a simulation. class ResetRandomPosition : public PeriodicEngine { public: /// @brief Create one sphere per call. virtual void action(); private: /// @brief Pointer to Collider. /// It is necessary in order to probe the bounding volume for new sphere. Collider* bI; /// @brief Pointer to IGeomDispatcher. /// It is necessary in order to detect a real overlap with other bodies. IGeomDispatcher* iGME; std::vector > shiftedBodies; bool first_run; //bool generateNewPosition(const shared_ptr& b, Vector3r& new_position); Vector3r generatePositionOnSurface(); Vector3r generatePositionInVolume(); typedef boost::variate_generator > RandomInt; shared_ptr randomFacet; static boost::variate_generator > randomUnit; static boost::variate_generator > randomSymmetricUnit; DECLARE_LOGGER; YADE_CLASS_BASE_DOC_ATTRS_CTOR(ResetRandomPosition,PeriodicEngine,"Creates spheres during simulation, placing them at random positions. Every time called, one new sphere will be created and inserted in the simulation.", ((vector,factoryFacets,,,"The geometry of the section where spheres will be placed; they will be placed on facets or in volume between them depending on *volumeSection* flag.")) ((std::vector,subscribedBodies,,,"Affected bodies.")) ((Vector3r,point,Vector3r::Zero(),,"??")) ((Vector3r,normal,Vector3r(0,1,0),,"??")) ((bool,volumeSection,((void)"define factory by facets.",false),,"Create new spheres inside factory volume rather than on its surface.")) ((int,maxAttempts,20,,"Max attempts to place sphere. If placing the sphere in certain random position would cause an overlap with any other physical body in the model, SpheresFactory will try to find another position.")) ((Vector3r,velocity,Vector3r::Zero(),,"Mean velocity of spheres.")) ((Vector3r,velocityRange,Vector3r::Zero(),,"Half size of a velocities distribution interval. New sphere will have random velocity within the range velocity±velocityRange.")) ((Vector3r,angularVelocity,Vector3r::Zero(),,"Mean angularVelocity of spheres.")) ((Vector3r,angularVelocityRange,Vector3r::Zero(),,"Half size of a angularVelocity distribution interval. New sphere will have random angularVelocity within the range angularVelocity±angularVelocityRange.")), first_run=true; ); }; REGISTER_SERIALIZABLE(ResetRandomPosition); trunk-2017.01a/pkg/common/SPHEngine.cpp000066400000000000000000000217021304022710500175210ustar00rootroot00000000000000#ifdef YADE_SPH #include"SPHEngine.hpp" #include #include #include #include #include void SPHEngine::action(){ { YADE_PARALLEL_FOREACH_BODY_BEGIN(const shared_ptr& b, scene->bodies){ if(mask>0 && (b->groupMask & mask)==0) continue; this->calculateSPHRho(b); b->state->press=std::max(0.0, k*(b->state->rho - b->state->rho0)); } YADE_PARALLEL_FOREACH_BODY_END(); } } void SPHEngine::calculateSPHRho(const shared_ptr& b) { if (b->state->rho0<0) { b->state->rho0 = rho0; } if (not b->isClump()) { Real rho = 0; // Pointer to kernel function KernelFunction kernelFunctionCurDensity = returnKernelFunction (KernFunctionDensity, Norm); // Calculate rho for every particle for(Body::MapId2IntrT::iterator it=b->intrs.begin(),end=b->intrs.end(); it!=end; ++it) { const shared_ptr b2 = Body::byId((*it).first,scene); Sphere* s=dynamic_cast(b->shape.get()); if(!s) continue; if (((*it).second)->geom and ((*it).second)->phys) { const ScGeom geom = *(YADE_PTR_CAST(((*it).second)->geom)); const ViscElPhys phys=*(YADE_PTR_CAST(((*it).second)->phys)); Real Mass = b2->state->mass; if (Mass == 0) Mass = b->state->mass; const Real SmoothDist = (b2->state->pos - b->state->pos).norm(); // [Monaghan1992], (2.7) (3.8) rho += b2->state->mass*kernelFunctionCurDensity(SmoothDist, h); } } // Self mass contribution rho += b->state->mass*kernelFunctionCurDensity(0.0, h); b->state->rho = rho; } } Real smoothkernelLucy(const double & r, const double & h) { if (r<=h && h>0) { // Lucy Kernel function, [Lucy1977] (27) const Real r_h = r / h; return 105./(16.*M_PI*h*h*h) * (1. + 3. * r_h) * std::pow((1. - r_h), 3); } else { return 0; } } Real smoothkernelLucyGrad(const double & r, const double & h) { if (r<=h && h>0) { // 1st derivative of Lucy Kernel function, [Lucy1977] (27) return 105./(16.*M_PI*h*h*h) * (-12. * r) * std::pow((h - r), 2) / ( h * h * h * h ); } else { return 0; } } Real smoothkernelLucyLapl(const double & r, const double & h) { if (r<=h && h>0) { // 2nd derivative of Lucy Kernel function, [Lucy1977] (27) return 105./(16.*M_PI*h*h*h) * (-12.) / (h * h * h * h) * (h * h - 2. * r * h + 3. * r * r); } else { return 0; } } //========================================================================= Real smoothkernelBSpline1(const double & r, const double & h) { // BSpline Kernel function, [Monaghan1985] (21) if (r<=2.0*h && h>0) { const Real coefA = 3. / (2. * M_PI * h * h * h); const Real r_h = r / h; if (r<=h) { return coefA * (2. /3. - r_h * r_h + 1. / 2. * r_h * r_h * r_h); } else { return coefA / 6. * std::pow((2. - r_h), 3); } } else { return 0; } } Real smoothkernelBSpline1Grad(const double & r, const double & h) { // 1st derivative of BSpline Kernel function, [Monaghan1985] (21) if (r<=2.*h && h>0) { const Real coefA = 3. / (2. * M_PI * h * h * h); const Real r_h = r / h; if (r<=h) { return coefA * ( -r_h ) * (2. - 3. / 2. * r_h); } else { return coefA * (-1. / 2.) * std::pow((2. - r_h), 2); } } else { return 0; } } Real smoothkernelBSpline1Lapl(const double & r, const double & h) { // 2nd derivative of BSpline Kernel function, [Monaghan1985] (21) if (r<=2.0*h && h>0) { const Real coefA = 3. / (2. * M_PI * h * h * h); const Real r_h = r / h; if (r<=h) { return coefA * (-2. + 3. * r_h); } else { return coefA * (2. - r_h); } } else { return 0; } } //========================================================================= Real smoothkernelBSpline2(const double & r, const double & h) { // BSpline Kernel function, [Monaghan1985] (22) if (r<=2.0*h && h>0) { const Real coefA = 3. / (4. * M_PI * h * h * h); const Real r_h = r / h; if (r<=h) { return coefA * (10. /3. - 7. * r_h * r_h + 4 * r_h * r_h * r_h); } else { return coefA * std::pow((2. - r_h), 2)*((5. - 4. * r_h) / 3.); } } else { return 0; } } Real smoothkernelBSpline2Grad(const double & r, const double & h) { // 1st derivative of BSpline Kernel function, [Monaghan1985] (22) if (r<=2.0*h && h>0) { const Real coefA = 3. / (4. * M_PI * h * h * h); const Real r_h = r / h; if (r<=h) { return coefA * (-2.) / (h * h) * ( 7. * r - 6. * r * r_h); } else { return coefA * 2. / h * (-6. + 7. * r_h - 2. * std::pow(r_h, 2) ); } } else { return 0; } } Real smoothkernelBSpline2Lapl(const double & r, const double & h) { // 2nd derivative of BSpline Kernel function, [Monaghan1985] (22) if (r<=2.0*h && h>0) { const Real coefA = 3. / (4. * M_PI * h * h * h); const Real r_h = r / h; if (r<=h) { return coefA * (-2.) / (h * h) * ( 7. - 12. * r_h); } else { return coefA * 2. / (h * h) * ( 7. - 4. * r_h); } } else { return 0; } } //========================================================================= KernelFunction returnKernelFunction(const int a, const typeKernFunctions typeF) { return returnKernelFunction(a, a, typeF); } KernelFunction returnKernelFunction(const int a, const int b, const typeKernFunctions typeF) { if (a != b) { throw runtime_error("Kernel types should be equal!"); } if (a==Lucy) { if (typeF==Norm) { return smoothkernelLucy; } else if (typeF==Grad) { return smoothkernelLucyGrad; } else if (typeF==Lapl) { return smoothkernelLucyLapl; } else { KERNELFUNCDESCR } } else if (a==BSpline1) { if (typeF==Norm) { return smoothkernelBSpline1; } else if (typeF==Grad) { return smoothkernelBSpline1Grad; } else if (typeF==Lapl) { return smoothkernelBSpline1Lapl; } else { KERNELFUNCDESCR } } else if (a==BSpline2) { if (typeF==Norm) { return smoothkernelBSpline2; } else if (typeF==Grad) { return smoothkernelBSpline2Grad; } else if (typeF==Lapl) { return smoothkernelBSpline2Lapl; } else { KERNELFUNCDESCR } } else { KERNELFUNCDESCR } } bool computeForceSPH(shared_ptr& _geom, shared_ptr& _phys, Interaction* I, Vector3r & force) { const ScGeom& geom=*static_cast(_geom.get()); Scene* scene=Omega::instance().getScene().get(); ViscElPhys& phys=*static_cast(_phys.get()); const int id1 = I->getId1(); const int id2 = I->getId2(); const BodyContainer& bodies = *scene->bodies; if (bodies[id1]->isClumpMember() and bodies[id2]->isClumpMember() and bodies[id1]->clumpId==bodies[id2]->clumpId) { //If 2 bodies belong to the same clump, do not calculate forces force = Vector3r::Zero(); return true; } ////////////////////////////////////////////////////////////////// // Copy-paste // Handle periodicity. const Vector3r shift2 = scene->isPeriodic ? scene->cell->intrShiftPos(I->cellDist): Vector3r::Zero(); const Vector3r shiftVel = scene->isPeriodic ? scene->cell->intrShiftVel(I->cellDist): Vector3r::Zero(); const State& de1 = *static_cast(bodies[id1]->state.get()); const State& de2 = *static_cast(bodies[id2]->state.get()); const Vector3r c1x = (geom.contactPoint - de1.pos); const Vector3r c2x = (geom.contactPoint - de2.pos - shift2); const Vector3r relativeVelocity = (de1.vel+de1.angVel.cross(c1x)) - (de2.vel+de2.angVel.cross(c2x)) + shiftVel; const Real normalVelocity = geom.normal.dot(relativeVelocity); // Copy-paste ////////////////////////////////////////////////////////////////// const Real Mass1 = bodies[id1]->state->mass; const Real Mass2 = bodies[id2]->state->mass; const Real Rho1 = bodies[id1]->state->rho; const Real Rho2 = bodies[id2]->state->rho; const Vector3r xixj = de2.pos - de1.pos; if ( phys.kernelFunctionCurrentPressure(xixj.norm(), phys.h)) { Real fpressure = 0.0; if (Rho1!=0.0 and Rho2!=0.0) { // from [Monaghan1992], (3.3), multiply by Mass2, because we need a force, not du/dt fpressure = - Mass1 * Mass2 * ( bodies[id1]->state->press/(Rho1*Rho1) + bodies[id2]->state->press/(Rho2*Rho2) ) * phys.kernelFunctionCurrentPressure(xixj.norm(), phys.h); } Vector3r fvisc = Vector3r::Zero(); if (Rho1!=0.0 and Rho2!=0.0) { // from [Morris1997], (22), multiply by Mass2, because we need a force, not du/dt fvisc = phys.mu * Mass1 * Mass2 * (-normalVelocity*geom.normal)/(Rho1*Rho2) * 1 / (xixj.norm()) * phys.kernelFunctionCurrentPressure(xixj.norm(), phys.h); //phys.kernelFunctionCurrentVisco(xixj.norm(), phys.h); } force = fpressure*geom.normal + fvisc; return true; } else { return false; } } YADE_PLUGIN((SPHEngine)); #endif trunk-2017.01a/pkg/common/SPHEngine.hpp000066400000000000000000000045411304022710500175300ustar00rootroot00000000000000#ifdef YADE_SPH #pragma once #include #include typedef Real (* KernelFunction)(const double & r, const double & h); enum KernFunctions {Lucy=1,BSpline1=2,BSpline2=3}; #define KERNELFUNCDESCR throw runtime_error("Type of kernel function undefined! The following kernel functions are available: Lucy=1 ([Lucy1977]_ (27)), BSpline1=2 ([Monaghan1985]_ (21)), BSpline2=3 ([Monaghan1985]_ (22))."); enum typeKernFunctions {Norm, Grad, Lapl}; class SPHEngine: public PartialEngine{ public: void calculateSPHRho(const shared_ptr& b); virtual void action(); YADE_CLASS_BASE_DOC_ATTRS(SPHEngine,PartialEngine,"Apply given torque (momentum) value at every subscribed particle, at every step. ", ((int, mask,-1,, "Bitmask for SPH-particles.")) ((Real,k,-1,, "Gas constant for SPH-interactions (only for SPH-model). See Mueller [Mueller2003]_ .")) // [Mueller2003], (11) ((Real,rho0,-1,, "Rest density. See Mueller [Mueller2003]_ .")) // [Mueller2003], (1) ((Real,h,-1,, "Core radius. See Mueller [Mueller2003]_ .")) // [Mueller2003], (1) ((int,KernFunctionDensity, Lucy,, "Kernel function for density calculation (by default - Lucy). The following kernel functions are available: Lucy=1 ([Lucy1977]_ (27)), BSpline1=2 ([Monaghan1985]_ (21)), BSpline2=3 ([Monaghan1985]_ (22)).")) ); }; REGISTER_SERIALIZABLE(SPHEngine); Real smoothkernelLucy(const double & r, const double & h); Real smoothkernelLucyGrad(const double & r, const double & h); Real smoothkernelLucyLapl(const double & r, const double & h); Real smoothkernelBSpline1(const double & r, const double & h); Real smoothkernelBSpline1Grad(const double & r, const double & h); Real smoothkernelBSpline1Lapl(const double & r, const double & h); Real smoothkernelBSpline2(const double & r, const double & h); Real smoothkernelBSpline2Grad(const double & r, const double & h); Real smoothkernelBSpline2Lapl(const double & r, const double & h); KernelFunction returnKernelFunction(const int a, const int b, const typeKernFunctions typeF); KernelFunction returnKernelFunction(const int a, const typeKernFunctions typeF); bool computeForceSPH(shared_ptr& _geom, shared_ptr& _phys, Interaction* I, Vector3r & force); #endif trunk-2017.01a/pkg/common/SpatialQuickSortCollider.cpp000066400000000000000000000046661304022710500226730ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2008 by Sergei Dorofeenko * * sega@users.berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "SpatialQuickSortCollider.hpp" #include #include #include #include YADE_PLUGIN((SpatialQuickSortCollider)); void SpatialQuickSortCollider::action() { if(scene->isPeriodic){ throw runtime_error("SpatialQuickSortCollider doesn't handle periodic boundaries."); } // update bounds boundDispatcher->scene=scene; boundDispatcher->action(); const shared_ptr& bodies = scene->bodies; // This collider traverses all interactions at every step, therefore all interactions // that were requested for erase might be erased here and will be recreated if necessary. scene->interactions->eraseNonReal(); size_t nbElements=bodies->size(); if (nbElements!=rank.size()) { size_t n = rank.size(); rank.resize(nbElements); for (; n(new AABBBound); } Vector3r min,max; int i=0; FOREACH(const shared_ptr& b, *bodies){ if(!b->bound) continue; min = b->bound->min; max = b->bound->max; rank[i]->id = b->getId(); rank[i]->min = min; rank[i]->max = max; i++; } const shared_ptr& interactions=scene->interactions; scene->interactions->iterColliderLastRun=scene->iter; sort(rank.begin(), rank.end(), xBoundComparator()); // sorting along X int id,id2; size_t j; shared_ptr interaction; for(int i=0,e=nbElements-1; iid; min = rank[i]->min; max = rank[i]->max; j=i; while(++jmin[0] > max[0]) break; if ( rank[j]->min[1] < max[1] && rank[j]->max[1] > min[1] && rank[j]->min[2] < max[2] && rank[j]->max[2] > min[2]) { id2=rank[j]->id; if ( (interaction = interactions->find(Body::id_t(id),Body::id_t(id2))) == 0) { interaction = shared_ptr(new Interaction(id,id2) ); interactions->insert(interaction); } interaction->iterLastSeen=scene->iter; } } } } trunk-2017.01a/pkg/common/SpatialQuickSortCollider.hpp000066400000000000000000000026461304022710500226740ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2008 by Sergei Dorofeenko * * sega@users.berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include class SpatialQuickSortCollider : public Collider { protected: struct AABBBound { Vector3r min,max; int id; }; class xBoundComparator { public: bool operator() (shared_ptr b1, shared_ptr b2) { return b1->min[0] < b2->min[0]; } }; vector > rank; public: virtual void action(); YADE_CLASS_BASE_DOC(SpatialQuickSortCollider,Collider,"Collider using quicksort along axes at each step, using :yref:`Aabb` bounds. \n\n Its performance is lower than that of :yref:`InsertionSortCollider` (see `Colliders' performance `_), but the algorithm is simple enought to make it good for checking other collider's correctness."); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(SpatialQuickSortCollider); trunk-2017.01a/pkg/common/Sphere.hpp000066400000000000000000000010751304022710500171750ustar00rootroot00000000000000#pragma once #include // HACK to work around https://bugs.launchpad.net/yade/+bug/528509 // see comments there for explanation namespace yade{ class Sphere: public Shape{ public: Sphere(Real _radius): radius(_radius){ createIndex(); } virtual ~Sphere () {}; YADE_CLASS_BASE_DOC_ATTRS_CTOR(Sphere,Shape,"Geometry of spherical particle.", ((Real,radius,NaN,,"Radius [m]")), createIndex(); /*ctor*/ ); REGISTER_CLASS_INDEX(Sphere,Shape); }; } // necessary using namespace yade; // must be outside yade namespace REGISTER_SERIALIZABLE(Sphere); trunk-2017.01a/pkg/common/StepDisplacer.hpp000066400000000000000000000032311304022710500205050ustar00rootroot00000000000000// 2008 © Václav Šmilauer #pragma once #include #include #include class StepDisplacer: public PartialEngine { public: virtual void action() { FOREACH(Body::id_t id, ids){ const shared_ptr& b=Body::byId(id,scene); if(setVelocities){ const Real& dt=scene->dt; b->state->vel=mov/dt; AngleAxisr aa(rot); aa.axis().normalize(); b->state->angVel=aa.axis()*aa.angle()/dt; LOG_DEBUG("Angular velocity set to "<` is supposed to be used, so that, thanks to this Engine, the bodies will have the prescribed jump over one iteration (dt).")) ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(StepDisplacer); trunk-2017.01a/pkg/common/TorqueEngine.hpp000066400000000000000000000020351304022710500203510ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2008 by Janek Kozicki * * cosurgi@berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include class TorqueEngine: public PartialEngine{ public: virtual void action() { FOREACH(const Body::id_t id, ids){ // check that body really exists? scene->forces.addTorque(id,moment); } } YADE_CLASS_BASE_DOC_ATTRS(TorqueEngine,PartialEngine,"Apply given torque (momentum) value at every subscribed particle, at every step.", ((Vector3r,moment,Vector3r::Zero(),,"Torque value to be applied.")) ); }; REGISTER_SERIALIZABLE(TorqueEngine); trunk-2017.01a/pkg/common/Wall.cpp000066400000000000000000000040021304022710500166320ustar00rootroot00000000000000// © 2009 Václav Šmilauer #include #include YADE_PLUGIN((Wall)(Bo1_Wall_Aabb) #ifdef YADE_OPENGL (Gl1_Wall) #endif ); Wall::~Wall(){} // vtable void Bo1_Wall_Aabb::go(const shared_ptr& cm, shared_ptr& bv, const Se3r& se3, const Body* b){ Wall* wall=static_cast(cm.get()); if(!bv){ bv=shared_ptr(new Aabb); } Aabb* aabb=static_cast(bv.get()); if(scene->isPeriodic && scene->cell->hasShear()) throw logic_error(__FILE__ "Walls not supported in sheared cell."); const Real& inf=std::numeric_limits::infinity(); aabb->min=Vector3r(-inf,-inf,-inf); aabb->min[wall->axis]=se3.position[wall->axis]; aabb->max=Vector3r( inf, inf, inf); aabb->max[wall->axis]=se3.position[wall->axis]; } #ifdef YADE_OPENGL #include int Gl1_Wall::div=20; void Gl1_Wall::go(const shared_ptr& cm, const shared_ptr& pp, bool, const GLViewInfo& glinfo){ Wall* wall=static_cast(cm.get()); int ax0=wall->axis,ax1=(wall->axis+1)%3,ax2=(wall->axis+2)%3; Vector3r a1,b1,a2,b2; // beginnings (a) and endings (b) of lines in both senses (0,1) // compensate for our position, since the functor is called with transformation to the wall se3 already, but we really want to be centered in the middle of the scene Real mn1=glinfo.sceneCenter[ax1]-glinfo.sceneRadius-pp->se3.position[ax1]; Real mn2=glinfo.sceneCenter[ax2]-glinfo.sceneRadius-pp->se3.position[ax2]; Real step=2*glinfo.sceneRadius/div; //cerr<<"center "<& cm, shared_ptr& bv, const Se3r& se3, const Body*); FUNCTOR1D(Wall); YADE_CLASS_BASE_DOC(Bo1_Wall_Aabb,BoundFunctor,"Creates/updates an :yref:`Aabb` of a :yref:`Wall`"); }; REGISTER_SERIALIZABLE(Bo1_Wall_Aabb); #ifdef YADE_OPENGL #include class Gl1_Wall: public GlShapeFunctor{ public: virtual void go(const shared_ptr&, const shared_ptr&,bool,const GLViewInfo&); RENDERS(Wall); YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_Wall,GlShapeFunctor,"Renders :yref:`Wall` object", ((int,div,20,,"Number of divisions of the wall inside visible scene part.")) ); }; REGISTER_SERIALIZABLE(Gl1_Wall); #endif trunk-2017.01a/pkg/common/ZECollider.cpp000066400000000000000000000105271304022710500177400ustar00rootroot00000000000000// 2011 © Bruno Chareyre #ifdef YADE_CGAL #include"ZECollider.hpp" #include #include #include #include #include #include #include YADE_PLUGIN((ZECollider)) CREATE_LOGGER(ZECollider); InteractionContainer* ZECollider::interactions = NULL; Scene* ZECollider::sscene = NULL; void ZECollider::handleOverlap(const CGBox& a, const CGBox& b){ const Body::id_t& id1=a.handle()->id; const Body::id_t& id2=b.handle()->id; //existing interaction? if (interactions->found(id1,id2)) return; //if it doesn't exist and bounds overlap, create a virtual interaction else if (Collider::mayCollide(Body::byId(id1,sscene).get(),Body::byId(id2,sscene).get())) interactions->insert(shared_ptr(new Interaction(id1,id2))); } // STRIDE bool ZECollider::isActivated(){ // activated if number of bodies changes (hence need to refresh collision information) // or the time of scheduled run already came, or we were never scheduled yet if(!strideActive) return true; if(!newton) return true; if(fastestBodyMaxDist<0){fastestBodyMaxDist=0; return true;} fastestBodyMaxDist=newton->maxVelocitySq; if(fastestBodyMaxDist>=1 || fastestBodyMaxDist==0) return true; if(scene->interactions->dirty) return true; return false; } void ZECollider::action(){ #ifdef ISC_TIMING timingDeltas->start(); #endif interactions=scene->interactions.get(); sscene = scene; scene->interactions->iterColliderLastRun=-1; // periodicity changed, force reinit if(scene->isPeriodic != periodic){ // for(int i=0; i<3; i++) BB[i].vec.clear(); periodic=scene->isPeriodic; } if(verletDist<0){ Real minR=std::numeric_limits::infinity(); FOREACH(const shared_ptr& b, *scene->bodies){ if(!b || !b->shape) continue; Sphere* s=dynamic_cast(b->shape.get()); if(!s) continue; minR=min(s->radius,minR); } // if no spheres, disable stride verletDist=std::isinf(minR) ? 0 : std::abs(verletDist)*minR; } // update bounds via boundDispatcher boundDispatcher->scene=scene; boundDispatcher->sweepDist=verletDist; boundDispatcher->targetInterv=targetInterv; boundDispatcher->updatingDispFactor=updatingDispFactor; boundDispatcher->action(); // if interactions are dirty, force reinitialization if(scene->interactions->dirty){ // doInitSort=true; scene->interactions->dirty=false; } // STRIDE if(verletDist>0){ // get NewtonIntegrator, to ask for the maximum velocity value if(!newton){ FOREACH(shared_ptr& e, scene->engines){ newton=YADE_PTR_DYN_CAST(e); if(newton) break; } if(!newton){ throw runtime_error("ZECollider.verletDist>0, but unable to locate NewtonIntegrator within O.engines."); } } } ISC_CHECKPOINT("init"); // STRIDE // get us ready for strides, if they were deactivated if(!strideActive && verletDist>0 && newton->maxVelocitySq>=0){ // maxVelocitySq is a really computed value strideActive=true; } if(strideActive){ assert(verletDist>0); assert(strideActive); assert(newton->maxVelocitySq>=0); newton->updatingDispFactor=updatingDispFactor; } else { /* !strideActive */ boundDispatcher->sweepDist=0; } ISC_CHECKPOINT("bound"); // // erase virtuals the lazy way // // FIXME: suboptimal since some of them will re-created just below, needs smarter erase by checking overlaps // interactions->eraseNonReal(); // ISC_CHECKPOINT("eraseNonReal"); // copy bounds into our arrays // std::vector boxesIdx; // boxesIdx.resize(scene->bodies.size()); boxes.clear(); FOREACH(shared_ptr& b, *scene->bodies){ if(b){ shared_ptr& bv=b->bound; if(bv) { boxes.push_back(CGBox(CGBbox(bv->min[0],bv->min[1],bv->min[2],bv->max[0],bv->max[1],bv->max[2]),b)); // boxesIdx[b->id] } } } ISC_CHECKPOINT("copy"); // erase virtuals the lazy way // FIXME: suboptimal since some of them will re-created just below, needs smarter erase by checking overlaps // interactions->conditionalyEraseNonReal(*this,scene); interactions->eraseNonReal(); ISC_CHECKPOINT("conditionalyEraseNonReal"); // collide CGAL::box_self_intersection_d( boxes.begin(), boxes.end(), handleOverlap); ISC_CHECKPOINT("collide"); } #endif trunk-2017.01a/pkg/common/ZECollider.hpp000066400000000000000000000117021304022710500177410ustar00rootroot00000000000000// 2011 © Bruno Chareyre #pragma once #include #include class InteractionContainer; // #define this macro to enable timing within this engine #define ISC_TIMING #ifdef ISC_TIMING #define ISC_CHECKPOINT(cpt) timingDeltas->checkpoint(cpt) #else #define ISC_CHECKPOINT(cpt) #endif class NewtonIntegrator; #include #include #include #include #include #include #include #include #include #include typedef CGAL::Bbox_3 CGBbox; // typedef CGAL::Box_intersection_d::Box_with_handle_d > CGBox; typedef CGAL::Box_intersection_d::Box_with_handle_d > CGBox_noId; class CGBox: public CGBox_noId { public: Body::id_t bid; CGBox(CGBbox box, shared_ptr& body): CGBox_noId(box, body) {} }; // class CGBox; class ZECollider: public Collider{ //! struct for storing bounds of bodies std::vector boxes; // we need this to find out about current maxVelocitySq shared_ptr newton; // if False, no type of striding is used // if True, then either verletDist XOR nBins is set bool strideActive; bool periodic; private: static InteractionContainer* interactions; static Scene* sscene; static void handleOverlap(const CGBox& a, const CGBox& b); //FIXME: this will not work if bodies are not numbered from 0 to N with increment 1 inline bool spatialOverlap(const Body::id_t& id1, const Body::id_t& id2) const { assert(!scene->isPeriodic); assert(boxes.size()); const CGBox& b1 = boxes[id1]; const CGBox& b2 = boxes[id2]; return (b1.min_coord(0)<=b2.max_coord(0)) && (b1.max_coord(0)>=b2.min_coord(0)) && (b1.min_coord(1)<=b2.max_coord(1)) && (b1.max_coord(1)>=b2.min_coord(1)) && (b1.min_coord(2)<=b2.max_coord(2)) && (b1.max_coord(2)>=b2.min_coord(2)); } public: //! Predicate called from loop within InteractionContainer::conditionalyEraseNonReal() bool shouldBeErased(Body::id_t id1, Body::id_t id2, Scene* rb) const {return !spatialOverlap(id1,id2);} virtual bool isActivated(); // force reinitialization at next run virtual void invalidatePersistentData(){} // vector probeBoundingVolume(const Bound&); virtual void action(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(ZECollider,Collider,"\ Collider with O(n log(n)) complexity, using a CGAL algorithm from Zomorodian and Edelsbrunner [Kettner2011]_ (http://www.cgal.org/Manual/beta/doc_html/cgal_manual/Box_intersection_d/Chapter_main.html)", ((int,sortAxis,0,,"Axis for the initial contact detection.")) ((bool,sortThenCollide,false,,"Separate sorting and colliding phase; it is MUCH slower, but all interactions are processed at every step; this effectively makes the collider non-persistent, not remembering last state. (The default behavior relies on the fact that inversions during insertion sort are overlaps of bounding boxes that just started/ceased to exist, and only processes those; this makes the collider much more efficient.)")) // ((bool,oriVerlet,true,,"Compare Verlet distance with displacement instead of velocity (only used if nBins<=0)")) ((int,targetInterv,30,,"(experimental) Target number of iterations between bound update, used to define a smaller sweep distance for slower grains if >0, else always use 1*verletDist. Useful in simulations with strong velocity contrasts between slow bodies and fast bodies.")) ((Real,updatingDispFactor,-1,,"(experimental) Displacement factor used to trigger bound update: the bound is updated only if updatingDispFactor*disp>sweepDist when >0, else all bounds are updated.")) ((Real,verletDist,((void)"Automatically initialized",-.15),,"Length by which to enlarge particle bounds, to avoid running collider at every step. Stride disabled if zero. Negative value will trigger automatic computation, so that the real value will be *verletDist* × minimum spherical particle radius; if there are no spherical particles, it will be disabled.")) ((Real,fastestBodyMaxDist,-1,,"Maximum displacement of the fastest body since last run; if >= verletDist, we could get out of bboxes and will trigger full run. DEPRECATED, was only used without bins. |yupdate|")) ((int,numReinit,0,Attr::readonly,"Cummulative number of bound array re-initialization.")), /* ctor */ #ifdef ISC_TIMING timingDeltas=shared_ptr(new TimingDeltas); #endif periodic=false; strideActive=false; , /* py */ .def_readonly("strideActive",&ZECollider::strideActive,"Whether striding is active (read-only; for debugging). |yupdate|") .def_readonly("periodic",&ZECollider::periodic,"Whether the collider is in periodic mode (read-only; for debugging) |yupdate|") ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(ZECollider); trunk-2017.01a/pkg/common/common.cpp000066400000000000000000000020541304022710500172300ustar00rootroot00000000000000// ======================================================= // Some plugins from removed CPP-fiels #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include YADE_PLUGIN((IntrCallback) #ifdef YADE_BODY_CALLBACK (BodyCallback) #endif ); YADE_PLUGIN((ForceResetter)(TorqueEngine)(FieldApplier)(BoundaryController) (NormPhys)(NormShearPhys)(Recorder)(CylScGeom6D)(CylScGeom)(Box) (StepDisplacer)(GenericSpheresContact) (PeriodicEngine)(Sphere)(Aabb)(ElastMat)(FrictMat)(PyRunner) ); trunk-2017.01a/pkg/dem/000077500000000000000000000000001304022710500145105ustar00rootroot00000000000000trunk-2017.01a/pkg/dem/BlockGen.cpp000077500000000000000000003432141304022710500167120ustar00rootroot00000000000000/*CWBoon 2016 */ /* Please cite: */ /* CW Boon, GT Houlsby, S Utili (2015). A new rock slicing method based on linear programming. Computers and Geotechnics 65, 12-29. */ /* The numerical library is changed from CPLEX to CLP because subscription to the academic initiative is required to use CPLEX for free */ #ifdef YADE_POTENTIAL_BLOCKS #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include // random #include #include #include #include #include //#include #include "BlockGen.hpp" #include #include #include /* IpOpt */ #include #include CREATE_LOGGER(BlockGen); YADE_PLUGIN((BlockGen)); //using namespace boost; //using namespace std; BlockGen::~BlockGen () {} std::ofstream BlockGen::output("BlockGenFindExtreme.txt", fstream::trunc); bool BlockGen::generate(string& message) { scene = shared_ptr(new Scene); shared_ptr body; positionRootBody(scene); createActors(scene); /* Create domain: start with one big block */ vector blk; Vector3r firstBlockCentre(0,0,0); firstBlockCentre.x() = 0.0; //0.5*(boundarySizeXmax + boundarySizeXmin); firstBlockCentre.y() = 0.0; //0.5*(boundarySizeYmax + boundarySizeYmin); firstBlockCentre.z() = 0.0; //0.5*(boundarySizeZmax + boundarySizeZmin); blk.push_back(Block(firstBlockCentre,kForPP, rForPP, RForPP)); Real xmin = fabs(firstBlockCentre.x() - boundarySizeXmin); Real xmax = fabs(-firstBlockCentre.x() + boundarySizeXmax); Real ymin = fabs(firstBlockCentre.y() - boundarySizeYmin); Real ymax = fabs(-firstBlockCentre.y() + boundarySizeYmax); Real zmin = fabs(firstBlockCentre.z() - boundarySizeZmin); Real zmax = fabs(-firstBlockCentre.z() + boundarySizeZmax); blk[0].a.push_back(1.0); blk[0].a.push_back(-1.0); blk[0].a.push_back(0.0); blk[0].a.push_back(0.0); blk[0].a.push_back(0.0); blk[0].a.push_back(0.0); blk[0].b.push_back(0.0); blk[0].b.push_back(0.0); blk[0].b.push_back(1.0); blk[0].b.push_back(-1.0); blk[0].b.push_back(0.0); blk[0].b.push_back(0.0); blk[0].c.push_back(0.0); blk[0].c.push_back(0.0); blk[0].c.push_back(0.0); blk[0].c.push_back(0.0); blk[0].c.push_back(1.0); blk[0].c.push_back(-1.0); blk[0].d.push_back(xmax); blk[0].d.push_back(xmin); blk[0].d.push_back(ymax); blk[0].d.push_back(ymin); blk[0].d.push_back(zmax); blk[0].d.push_back(zmin); blk[0].redundant.push_back(false); blk[0].redundant.push_back(false); blk[0].redundant.push_back(false); blk[0].redundant.push_back(false); blk[0].redundant.push_back(false); blk[0].redundant.push_back(false); blk[0].JRC.push_back(15.0);blk[0].JRC.push_back(15.0);blk[0].JRC.push_back(15.0);blk[0].JRC.push_back(15.0);blk[0].JRC.push_back(15.0);blk[0].JRC.push_back(15.0); blk[0].JCS.push_back(pow(10,6));blk[0].JCS.push_back(pow(10,6));blk[0].JCS.push_back(pow(10,6));blk[0].JCS.push_back(pow(10,6));blk[0].JCS.push_back(pow(10,6));blk[0].JCS.push_back(pow(10,6)); blk[0].sigmaC.push_back(pow(10,6));blk[0].sigmaC.push_back(pow(10,6));blk[0].sigmaC.push_back(pow(10,6));blk[0].sigmaC.push_back(pow(10,6));blk[0].sigmaC.push_back(pow(10,6));blk[0].sigmaC.push_back(pow(10,6)); blk[0].phi_r.push_back(40.0);blk[0].phi_r.push_back(40.0);blk[0].phi_r.push_back(40.0);blk[0].phi_r.push_back(40.0);blk[0].phi_r.push_back(40.0);blk[0].phi_r.push_back(40.0); blk[0].phi_b.push_back(40.0);blk[0].phi_b.push_back(40.0);blk[0].phi_b.push_back(40.0);blk[0].phi_b.push_back(40.0);blk[0].phi_b.push_back(40.0);blk[0].phi_b.push_back(40.0); blk[0].asperity.push_back(5.0);blk[0].asperity.push_back(5.0);blk[0].asperity.push_back(5.0);blk[0].asperity.push_back(5.0);blk[0].asperity.push_back(5.0);blk[0].asperity.push_back(5.0); blk[0].cohesion.push_back(0.0);blk[0].cohesion.push_back(0.0);blk[0].cohesion.push_back(0.0);blk[0].cohesion.push_back(0.0);blk[0].cohesion.push_back(0.0);blk[0].cohesion.push_back(0.0); blk[0].tension.push_back(0.0);blk[0].tension.push_back(0.0);blk[0].tension.push_back(0.0);blk[0].tension.push_back(0.0);blk[0].tension.push_back(0.0);blk[0].tension.push_back(0.0); blk[0].isBoundaryPlane.push_back(false);blk[0].isBoundaryPlane.push_back(false);blk[0].isBoundaryPlane.push_back(false);blk[0].isBoundaryPlane.push_back(false);blk[0].isBoundaryPlane.push_back(false);blk[0].isBoundaryPlane.push_back(false); blk[0].lambda0.push_back(0.0);blk[0].lambda0.push_back(0.0);blk[0].lambda0.push_back(0.0);blk[0].lambda0.push_back(0.0);blk[0].lambda0.push_back(0.0);blk[0].lambda0.push_back(0.0); blk[0].heatCapacity.push_back(0.0);blk[0].heatCapacity.push_back(0.0);blk[0].heatCapacity.push_back(0.0);blk[0].heatCapacity.push_back(0.0);blk[0].heatCapacity.push_back(0.0);blk[0].heatCapacity.push_back(0.0); blk[0].hwater.push_back(-1.0);blk[0].hwater.push_back(-1.0);blk[0].hwater.push_back(-1.0);blk[0].hwater.push_back(-1.0);blk[0].hwater.push_back(-1.0);blk[0].hwater.push_back(-1.0); blk[0].intactRock.push_back(false);blk[0].intactRock.push_back(false);blk[0].intactRock.push_back(false);blk[0].intactRock.push_back(false);blk[0].intactRock.push_back(false);blk[0].intactRock.push_back(false); blk[0].jointType.push_back(0); blk[0].jointType.push_back(0); blk[0].jointType.push_back(0); blk[0].jointType.push_back(0); blk[0].jointType.push_back(0); blk[0].jointType.push_back(0); /* List of Discontinuities */ vector joint; /* Read boundary size */ Real boundarySize = max(max(fabs(boundarySizeXmax-boundarySizeXmin),fabs(boundarySizeYmax-boundarySizeYmin)),fabs(boundarySizeZmax-boundarySizeZmin)); Real dip = 0.0;Real dipdir = 0.0; /*Python input for discontinuities */ for(unsigned int i=0; i 180.0){ dipdirN = dipdir - 180.0; }else{ dipdirN = dipdir + 180.0; } Real dipRad = dipN/180.0*PI; Real dipdirRad = dipdirN/180.0*PI; Real a = cos(dipdirRad)*cos(dipRad); Real b = sin(dipdirRad)*cos(dipRad); Real c = sin(dipRad); Real l = sqrt(a*a + b*b +c*c); joint.push_back(Discontinuity(globalOrigin)); int i = joint.size()-1; jointNo=i; joint[i].a = a/l; joint[i].b = b/l; joint[i].c = c/l; joint[i].d = 0.0; planeNormal = Vector3r(a/l,b/l,c/l); //std::cout<<"planeNormal: "< 180.0){ dipdirN = dipdir - 180.0; }else{ dipdirN = dipdir + 180.0; } Real dipRad = dipN/180.0*PI; Real dipdirRad = dipdirN/180.0*PI; Real a = cos(dipdirRad)*cos(dipRad); Real b = sin(dipdirRad)*cos(dipRad); Real c = sin(dipRad); Real l = sqrt(a*a + b*b +c*c); joint.push_back(Discontinuity(globalOrigin)); int i = joint.size()-1; jointNo=i; joint[i].a = a/l; joint[i].b = b/l; joint[i].c = c/l; joint[i].d = 0.0; planeNormal = Vector3r(a/l,b/l,c/l); //std::cout<<"planeNormal: "< 180.0){ dipdirN = dipdir - 180.0; }else{ dipdirN = dipdir + 180.0; } Real dipRad = dipN/180.0*PI; Real dipdirRad = dipdirN/180.0*PI; a = cos(dipdirRad)*cos(dipRad); b = sin(dipdirRad)*cos(dipRad); c = sin(dipRad); l = sqrt(a*a + b*b +c*c); planeNormal = Vector3r(a/l,b/l,c/l); //save for later //std::cout<<"planeNormal1: "<(j); joint[i].phi_b = phi_b; joint[i].phi_r = phi_r; joint[i].JRC = JRC; joint[i].JCS = JCS; joint[i].asperity = asperity; joint[i].sigmaC = sigmaC; joint[i].cohesion = cohesion; joint[i].tension = tension; joint.push_back(Discontinuity(firstBlockCentre)); i = joint.size()-1; joint[i].a = -a/l; joint[i].b = -b/l; joint[i].c = -c/l; joint[i].d =spacing*static_cast(j); joint[i].phi_b = phi_b; joint[i].phi_r = phi_r; joint[i].JRC = JRC; joint[i].JCS = JCS; joint[i].asperity = asperity; joint[i].sigmaC = sigmaC; joint[i].cohesion = cohesion; joint[i].tension = tension; } count = 0; } } } if(jointProbabilistic){ /* Read csv file for info on discontinuities */ const char *filenameChar = filenameProbabilistic.c_str(); ifstream file ( filenameChar ); // declare file stream: http://www.cplusplus.com/reference/iostream/ifstream/ string value; /* skip first line */ getline ( file, value); int count = 0; int linecount = 0; Real dip = 0.0;Real dipdir = 0.0; Vector3r jointCentre(0,0,0); const double PI = std::atan(1.0)*4; int boundaryNo = 0; int boundaryCount = 0; int abdCount=0; Vector3r planeNormal(0,0,0); int jointNo = 0; double persistenceA=0; double persistenceB=0; double spacing = 0; boost::normal_distribution<> nd(0.0, 1.0); boost::variate_generator > generator(boost::mt19937(time(0)),nd); while ( file.good() ) { //std::cout<<"reading file, count"< 180.0){ dipdirN = dipdir - 180.0; }else{ dipdirN = dipdir + 180.0; } if(probabilisticOrientation == true && dip < 120.0 && dip > 60.0 ){ double perturb = gen_normal_3(generator); dipN = dipN + perturb; std::cout<<"perturb: "<(valueDouble); } if(count == 17){count = 0; /* to include comments */ if(intactRockDegradation==true){ joint[jointNo].intactRock = true; } } } } if(slopeFace){ /* Read csv file for info on discontinuities */ const char *filenameChar = filenameSlopeFace.c_str(); ifstream file ( filenameChar ); // declare file stream: http://www.cplusplus.com/reference/iostream/ifstream/ string value; /* skip first line */ getline ( file, value); int count = 0; Vector3r jointCentre(0,0,0); const double PI = std::atan(1.0)*4; Vector3r planeNormal(0,0,0); int jointNo = 0; while ( file.good() ) { count ++; getline ( file, value, ';' ); // read a string until next comma: http://www.cplusplus.com/reference/string/getline/ //std::cout<<"count: "< 180.0){ dipdirN = dipdir - 180.0; }else{ dipdirN = dipdir + 180.0; } Real dipRad = dipN/180.0*PI; Real dipdirRad = dipdirN/180.0*PI; Real a = cos(dipdirRad)*cos(dipRad); Real b = sin(dipdirRad)*cos(dipRad); Real c = sin(dipRad); Real l = sqrt(a*a + b*b +c*c); joint.push_back(Discontinuity(globalOrigin)); int i = joint.size()-1; jointNo=i; joint[i].a = a/l; joint[i].b = b/l; joint[i].c = c/l; joint[i].d = 0.0; planeNormal = Vector3r(a/l,b/l,c/l); //std::cout<<"planeNormal: "< twoRadiiDist ){subMemberIter++; continue;} /* std::cout<<"centroidDist: "< maxd){maxd= fabs(blkA.d[h]);} } if(converge== false){ blkA.tooSmall = true; bool inside = checkCentroid(blkA,blkA.centre); std::cout<<"blki inside: "< maxd){maxd=fabs( blkB.d[h]);} } if(converge== false){ blkB.tooSmall = true; bool inside = checkCentroid(blkB,blkB.centre); std::cout<<"blkNo inside: "<0.0){ blkA.isBoundary = true; }else{ blkB.isBoundary = true; } } double RblkA = 0.0; Vector3r tempCentreA(0,0,0); double RblkB = 0.0; Vector3r tempCentreB(0,0,0); /* Prune blocks that are too small or too elongated */ bool tooSmall = false; if(joint[j].throughGoing == false){ double conditioningFactor = 1.0; Real minX = 0.0; Real minY = 0.0; Real minZ = 0.0; Real maxX = 0.0; Real maxY = 0.0; Real maxZ = 0.0; Discontinuity plane=Discontinuity(Vector3r(0,0,0)); plane.a=directionA.x(); //1.0; plane.b=directionA.y(); //0.0; plane.c=directionA.z(); //0.0; plane.d=1.2*boundarySizeXmax; Vector3r falseVertex (0.0,0.0,0.0); if (contactBoundaryLPCLP(plane, blkA,falseVertex) ){ minX = directionA.dot(falseVertex); //falseVertex.x(); }else{tooSmall=true;} tempCentreA = tempCentreA + falseVertex; plane=Discontinuity(Vector3r(0,0,0)); plane.a=directionB.x(); //0.0; plane.b=directionB.y(); //1.0; plane.c=directionB.z(); //0.0; plane.d=1.2*boundarySizeYmax; if (contactBoundaryLPCLP(plane, blkA,falseVertex) ){ minY = directionB.dot(falseVertex); //falseVertex.y(); }else{tooSmall=true;} tempCentreA = tempCentreA + falseVertex; plane=Discontinuity(Vector3r(0,0,0)); plane.a=directionC.x(); //0.0; plane.b=directionC.y(); //0.0; plane.c=directionC.z(); //1.0; plane.d=1.2*boundarySizeZmax; if (contactBoundaryLPCLP(plane, blkA,falseVertex) ){ minZ = directionC.dot(falseVertex); //falseVertex.z(); }else{tooSmall=true;} tempCentreA = tempCentreA + falseVertex; plane=Discontinuity(Vector3r(0,0,0)); plane.a=-directionA.x(); //-1.0; plane.b=-directionA.y(); //0.0; plane.c=-directionA.z(); //0.0; plane.d=1.2*boundarySizeXmin; if (contactBoundaryLPCLP(plane, blkA,falseVertex) ){ maxX = directionA.dot(falseVertex); //falseVertex.x(); }else{tooSmall=true;} tempCentreA = tempCentreA + falseVertex; plane=Discontinuity(Vector3r(0,0,0)); plane.a=-directionB.x(); //0.0; plane.b=-directionB.y(); //-1.0; plane.c=-directionB.z(); //0.0; plane.d=1.2*boundarySizeYmin; if (contactBoundaryLPCLP(plane, blkA,falseVertex) ){ maxY = directionB.dot(falseVertex); //falseVertex.y(); }else{tooSmall=true;} tempCentreA = tempCentreA + falseVertex; plane=Discontinuity(Vector3r(0,0,0)); plane.a=-directionC.x(); // 0.0; plane.b=-directionC.y(); //0.0; plane.c=-directionC.z(); //-1.0; plane.d=1.2*boundarySizeZmin; if (contactBoundaryLPCLP(plane,blkA,falseVertex) ){ maxZ = directionC.dot(falseVertex); //falseVertex.z(); }else{tooSmall=true;} tempCentreA = tempCentreA + falseVertex; Real maxXoverall = fabs(maxX-minX); Real maxYoverall = fabs(maxY-minY); Real maxZoverall = fabs(maxZ-minZ); tempCentreA = 1.0/6.0*tempCentreA; Vector3r tempA(0,0,0); double chebyshevRa = inscribedSphereCLP(blkA, tempA, twoDimension); tempCentreA = tempA; //std::cout<<"chebyshevRa: "< maxRatio || maxYoverall/(2.0*chebyshevRa) > maxRatio || maxZoverall/(2.0*chebyshevRa) > maxRatio){ tooSmall = true; } plane=Discontinuity(Vector3r(0,0,0)); plane.a=directionA.x(); //1.0; plane.b=directionA.y(); //0.0; plane.c=directionA.z(); //0.0; plane.d=1.2*boundarySizeXmax; if (contactBoundaryLPCLP(plane, blkB,falseVertex) ){ minX = directionA.dot(falseVertex); //falseVertex.x(); }else{tooSmall=true;} tempCentreB = tempCentreB + falseVertex; plane=Discontinuity(Vector3r(0,0,0)); plane.a=directionB.x(); //0.0; plane.b=directionB.y(); //1.0; plane.c=directionB.z(); //0.0; plane.d=1.2*boundarySizeYmax; if (contactBoundaryLPCLP(plane, blkB,falseVertex) ){ minY = directionB.dot(falseVertex); //falseVertex.y(); }else{tooSmall=true;} tempCentreB = tempCentreB + falseVertex; plane=Discontinuity(Vector3r(0,0,0)); plane.a=directionC.x(); //0.0; plane.b=directionC.y(); //0.0; plane.c=directionC.z(); //1.0; plane.d=1.2*boundarySizeZmax; if (contactBoundaryLPCLP(plane, blkB,falseVertex) ){ minZ = directionC.dot(falseVertex); //falseVertex.z(); }else{tooSmall=true;} tempCentreB = tempCentreB + falseVertex; plane=Discontinuity(Vector3r(0,0,0)); plane.a=-directionA.x(); //-1.0; plane.b=-directionA.y(); //0.0; plane.c=-directionA.z(); //0.0; plane.d=1.2*boundarySizeXmin; if (contactBoundaryLPCLP(plane, blkB,falseVertex) ){ maxX = directionA.dot(falseVertex); //falseVertex.x(); }else{tooSmall=true;} tempCentreB = tempCentreB + falseVertex; plane=Discontinuity(Vector3r(0,0,0)); plane.a=-directionB.x(); //0.0; plane.b=-directionB.y(); //-1.0; plane.c=-directionB.z(); //0.0; plane.d=1.2*boundarySizeYmin; if (contactBoundaryLPCLP(plane, blkB,falseVertex) ){ maxY = directionB.dot(falseVertex); //falseVertex.y(); }else{tooSmall=true;} tempCentreB = tempCentreB + falseVertex; plane=Discontinuity(Vector3r(0,0,0)); plane.a=-directionC.x(); //0.0; plane.b=-directionC.y(); //0.0; plane.c=-directionC.z(); //-1.0; plane.d=1.2*boundarySizeZmin; if (contactBoundaryLPCLP(plane,blkB,falseVertex) ){ maxZ = directionC.dot(falseVertex); //falseVertex.z(); }else{tooSmall=true;} tempCentreB = tempCentreB + falseVertex; maxXoverall = fabs(maxX-minX); maxYoverall = fabs(maxY-minY); maxZoverall = fabs(maxZ-minZ); tempCentreB = 1.0/6.0*tempCentreB; Vector3r tempB(0,0,0); double chebyshevRb = inscribedSphereCLP(blkB, tempB, twoDimension); tempCentreB = tempB; //std::cout<<"chebyshevRb: "< maxRatio || maxYoverall/(2.0*chebyshevRb) > maxRatio || maxZoverall/(2.0*chebyshevRb) > maxRatio){ tooSmall = true; } } if(tooSmall== false){ #if 0 /* Identify redundant planes */ for(int k=0; k0){ blk[i].subMembers.push_back(Block(blkB.centre,kForPP,rForPP,RForPP )); int subMemberCount = blk[i].subMembers.size()-1; blk[i].subMembers[subMemberIter] = blkA; blk[i].subMembers[subMemberCount] = blkB; blk[i].subMembers[subMemberIter].R = RblkA; blk[i].subMembers[subMemberCount].R = RblkB; blk[i].subMembers[subMemberIter].tempCentre = tempCentreA; blk[i].subMembers[subMemberCount].tempCentre = tempCentreB; }else{ blk[i].subMembers.push_back(Block(blkA.centre,kForPP,rForPP,RForPP )); blk[i].subMembers.push_back(Block(blkB.centre,kForPP,rForPP,RForPP )); int subMemberCount = blk[i].subMembers.size()-2; blk[i].subMembers[subMemberCount] = blkA; blk[i].subMembers[subMemberCount+1] = blkB; blk[i].subMembers[subMemberCount].R = RblkA; blk[i].subMembers[subMemberCount+1].R = RblkB; blk[i].subMembers[subMemberCount].tempCentre = tempCentreA; blk[i].subMembers[subMemberCount+1].tempCentre = tempCentreB; } }else{ blk.push_back(Block(blkB.centre,kForPP,rForPP,RForPP )); blk[blkNo] = blkB; blk[i] = blkA; blk[blkNo].R = RblkB; blk[i].R=RblkA; blk[blkNo].tempCentre = tempCentreB; blk[i].tempCentre = tempCentreA; } } }/* outer if-braces for detected */ subMemberIter++; }while(subMemberIter0){ for(int j=0; j maxd){maxd= fabs(blk[i].subMembers[j].d[h]);} } if(converge== false){ blk[i].subMembers[j].tooSmall = true; bool inside = checkCentroid(blk[i].subMembers[j],blk[i].subMembers[j].centre); std::cout<<"blki inside: "< maxd){maxd= fabs(blk[i].d[h]);} } if(converge== false){ blk[i].tooSmall = true; bool inside = checkCentroid(blk[i],blk[i].centre); std::cout<<"blki inside: "<0){ //#if 0 shared_ptr clumpBody=shared_ptr(new Body()); shared_ptr clump=shared_ptr(new Clump()); clumpBody->shape=clump; clumpBody->setDynamic(true); clumpBody->setBounded(false); // Body::id_t clumpId=scene->bodies->insert(clumpBody); // std::cout<<"clumpId: "< memberId; int clumpMemberCount = 0; for(int j=0; jbodies->insert(body); Body::id_t lastId=(Body::id_t)scene->bodies->insert(body); /* new */ memberId.push_back(lastId); //Clump::add(clumpBody, /* body*/ Body::byId(lastId,scene) ); //clump->ids.push_back(lastId); clumpMemberCount++; } //std::cout<<"Generating progress.... sub-block no: "< 1){ Body::id_t clumpId=scene->bodies->insert(clumpBody); //std::cout<<"ok 1"<ids.push_back(memberId[j]); //std::cout<<"ok 3"<bodies->insert(body); } } } scene->dt=defaultDt; //globalStiffnessTimeStepper->defaultDt=0.000001; //defaultDt; //scene->updateBound(); //scene->bound->min = Vector3r(5,5,5); //scene->bound->max = -1.0*Vector3r(5,5,5); std::cout<<"complete "<& body, struct Block block, int number ){ //std::cout<<"createBlockBegin"<(new Body); shared_ptr aabb(new Aabb); shared_ptr pBlock(new PotentialBlock); pBlock->minAabbRotated = 1.02*min; pBlock->maxAabbRotated = 1.02*max; body->setDynamic(true); Real volume = 0.0; Real Ixx = 0.0; Real Iyy = 0.0; Real Izz = 0.0; Real Ixy = 0.0; Real Ixz = 0.0; Real Iyz = 0.0; Vector3r boundingDist = Vector3r(fabs(max[0]+min[0]),fabs(max[1]+min[1]),fabs(max[2]+min[2])); //std::cout<<"beforeInertia"<state->mass = blockVol*density; //blockVol pBlock->volume = blockVol; char jobz = 'V'; char uplo = 'L'; int N=3; double A[9]; int lda=3; double eigenValues[3]; double work[15]; int lwork = 15; int info = 0; A[0] = Ixx; A[1]=Ixy; A[2]=Ixz; A[3]=Ixy; A[4]= Iyy; A[5]=Iyz; A[6]=Ixz; A[7]=Iyz; A[8]=Izz; dsyev_(&jobz, &uplo, &N, &A[0], &lda, &eigenValues[0], &work[0], &lwork, &info); Vector3r eigenVec1 (A[0],A[1],A[2]); eigenVec1.normalize(); Vector3r eigenVec2 (A[3],A[4],A[5]); eigenVec2.normalize(); Vector3r eigenVec3 (A[6],A[7],A[8]); eigenVec3.normalize(); Eigen::Matrix3d lapackEigenVec; lapackEigenVec(0,0) = eigenVec1[0]; lapackEigenVec(0,1) = eigenVec2[0]; lapackEigenVec(0,2)=eigenVec3[0]; lapackEigenVec(1,0) = eigenVec1[1]; lapackEigenVec(1,1) = eigenVec2[1]; lapackEigenVec(1,2)=eigenVec3[1]; lapackEigenVec(2,0) = eigenVec1[2]; lapackEigenVec(2,1) = eigenVec2[2]; lapackEigenVec(2,2)=eigenVec3[2]; /* make sure diagonals are positive */ if(lapackEigenVec(0,0)<0.0){ lapackEigenVec(0,0) = -lapackEigenVec(0,0); lapackEigenVec(1,0) = -lapackEigenVec(1,0); lapackEigenVec(2,0) = -lapackEigenVec(2,0); } if(lapackEigenVec(1,1)<0.0){ lapackEigenVec(0,1) = -lapackEigenVec(0,1); lapackEigenVec(1,1) = -lapackEigenVec(1,1); lapackEigenVec(2,1) = -lapackEigenVec(2,1); } if(lapackEigenVec(2,2)<0.0){ lapackEigenVec(0,2) = -lapackEigenVec(0,2); lapackEigenVec(1,2) = -lapackEigenVec(1,2); lapackEigenVec(2,2) = -lapackEigenVec(2,2); } Eigen::Matrix3d lapackEigenVal = Eigen::Matrix3d::Zero(); lapackEigenVal(0,0) = eigenValues[0]; lapackEigenVal(1,1) = eigenValues[1]; lapackEigenVal(2,2) = eigenValues[2]; //std::cout<<"Ixx: "<state->inertia= inertiaFactor*Vector3r(lapackEigenVal(0,0)*density,lapackEigenVal(1,1)*density,lapackEigenVal(2,2)*density); }else{ double maxInertia = std::max(std::max(std::max(lapackEigenVal(0,0),lapackEigenVal(1,1)),lapackEigenVal(2,2)),2.0/5.0*body->state->mass/density*minSize*minSize); body->state->inertia= inertiaFactor*Vector3r(maxInertia*density,maxInertia*density,maxInertia*density); } body->state->pos=block.centre; body->state->ori = q.conjugate(); shared_ptr mat(new FrictMat); mat->frictionAngle = frictionDeg * Mathr::PI/180.0; aabb->color = Vector3r(0,1,0); //std::cout<<"afterInertia"<a.push_back(plane.x()); block.a[i] = plane.x(); pBlock->b.push_back(plane.y()); block.b[i] = plane.y(); pBlock->c.push_back(plane.z()); block.c[i] = plane.z(); pBlock->d.push_back( block.d[i] /* newd */); pBlock->addPlaneStruct(); //#if 0 tempA(i,0) = block.a[i]; tempA(i,1) = block.b[i]; tempA(i,2) = block.c[i]; tempD(i,0) = block.d[i] + block.r; //#endif pBlock->JRC.push_back(block.JRC[i]); pBlock->JCS.push_back(block.JCS[i]); pBlock->sigmaC.push_back(block.sigmaC[i]); pBlock->phi_r.push_back(block.phi_r[i]); pBlock->phi_b.push_back(block.phi_b[i]); pBlock->asperity.push_back(block.asperity[i]); pBlock->cohesion.push_back(block.cohesion[i]); pBlock->tension.push_back(block.tension[i]); pBlock->isBoundaryPlane.push_back(block.isBoundaryPlane[i]); pBlock->lambda0.push_back(block.lambda0[i]); pBlock->heatCapacity.push_back(block.heatCapacity[i]); pBlock->hwater.push_back(block.hwater[i]); pBlock->intactRock.push_back(block.intactRock[i]); pBlock->jointType.push_back(block.jointType[i]); if(i>10000){std::cout<<"i: "<Amatrix =tempA; pBlock->Dmatrix = tempD; //std::cout<<"blockgen, A: "<Amatrix<<", D: "<Dmatrix<oriAabb = body->state->ori; pBlock->r = block.r;// + initialOverlap; pBlock->k = block.k; pBlock->AabbMinMax=true; pBlock->minAabb = 1.02*min; pBlock->maxAabb = 1.02*max; pBlock->R = std::max(max.norm(),min.norm()); //findExtreme(block); //block.R; //tempMax.norm(); // //if(min.norm()/max.norm() <0.125 || min.norm()/max.norm() > 8.0){return false;} pBlock->id =number; pBlock->color = Vector3r(Mathr::UnitRandom(),Mathr::UnitRandom(),Mathr::UnitRandom()); //std::max(std::max(maxXoverall, maxYoverall),maxZoverall) ; // if(block.isBoundary == true){ pBlock->color = Vector3r(0,100,0); body->setDynamic(false); } pBlock->isBoundary = block.isBoundary; body->bound = aabb; body->material = mat; //if (exactRotation == false){ // double sphereInertia = 2.0/5.0*body->state->mass*pBlock->R*pBlock->R; // body->state->inertia= inertiaFactor*Vector3r(sphereInertia,sphereInertia,sphereInertia); //} //#if 0 //std::cout<<"beforeVertices"<a[i],pBlock->b[i], pBlock->c[i]); Vector3r plane2 = Vector3r(pBlock->a[j],pBlock->b[j], pBlock->c[j]); Vector3r plane3 = Vector3r(pBlock->a[k],pBlock->b[k], pBlock->c[k]); Vector3r centre = body->state->pos; double d1 = pBlock->d[i]+pBlock->r; double d2 = pBlock->d[j]+pBlock->r; double d3 = pBlock->d[k]+pBlock->r; D[0]=d1; D[1]=d2; D[2]=d3; Ax[0]=plane1.x(); Ax[3]=plane1.y(); Ax[6]=plane1.z(); Aplanes(0,0)= Ax[0]; Aplanes(0,1) = Ax[3]; Aplanes(0,2) = Ax[6]; Ax[1]=plane2.x(); Ax[4]=plane2.y(); Ax[7]=plane2.z(); Aplanes(1,0) = Ax[1]; Aplanes(1,1) = Ax[4];Aplanes(1,2) = Ax[7]; Ax[2]=plane3.x(); Ax[5]=plane3.y(); Ax[8]=plane3.z(); Aplanes(2,0) = Ax[2]; Aplanes(2,1) = Ax[5];Aplanes(2,2) = Ax[8]; bool parallel = false; if (fabs(plane1.dot(plane2))<1.0002 && fabs(plane1.dot(plane2))>0.9998){parallel = true;} if (fabs(plane1.dot(plane3))<1.0002 && fabs(plane1.dot(plane3))>0.9998){parallel = true;} if (fabs(plane2.dot(plane3))<1.0002 && fabs(plane2.dot(plane3))>0.9998){parallel = true;} double det = Aplanes.determinant(); if(fabs(det)>pow(10,-15) ){ int ipiv[3]; int bColNo=1; int info=0; /* LU */ int three =3; dgesv_( &three, &bColNo, Ax, &three, ipiv, D, &three, &info); if (info!=0){ //std::cout<<"linear algebra error"<a[i]*vertex.x() + pBlock->b[i]*vertex.y() + pBlock->c[i]*vertex.z() - pBlock->d[i]- pBlock->r; if (plane>pow(10,-3)){inside = false;} } if (inside == true){ //std::cout<<"vertex: "<verticesCD.push_back(vertex); int vertexID = pBlock->verticesCD.size()-1; pBlock->addVertexStruct(); pBlock->vertexStruct[vertexID].planeID.push_back(i); /*Note that the planeIDs are arranged from small to large! */ pBlock->vertexStruct[vertexID].planeID.push_back(j); /* planeIDs are arranged in the same sequence as [a,b,c] and d */ pBlock->vertexStruct[vertexID].planeID.push_back(k); /* vertices store information on planeIDs */ /*Planes */ pBlock->planeStruct[i].vertexID.push_back(vertexID); /* planes store information on vertexIDs */ pBlock->planeStruct[j].vertexID.push_back(vertexID); pBlock->planeStruct[k].vertexID.push_back(vertexID); } } } } } } //#endif #if 0 int vertexNo = pBlock->verticesCD.size(); int edgeCount=0; for (int i=0; ivertexStruct[i].planeID[0]; int v2a = pBlock->vertexStruct[i].planeID[1]; int v3a = pBlock->vertexStruct[i].planeID[2]; int v1b = pBlock->vertexStruct[j].planeID[0]; int v2b = pBlock->vertexStruct[j].planeID[1]; int v3b = pBlock->vertexStruct[j].planeID[2]; if( (v1a != v1b && v2a == v2b && v3a == v3b) || (v1a == v1b && v2a != v2b && v3a == v3b) || (v1a == v1b && v2a == v2b && v3a != v3b) ){ double length = ( pBlock->verticesCD[i] - pBlock->verticesCD[j] ).norm(); if(lengthaddEdgeStruct(); pBlock->edgeStruct[edgeCount].vertexID.push_back(i); /* edges store information on vertexIDs */ pBlock->edgeStruct[edgeCount].vertexID.push_back(j); pBlock->vertexStruct[i].edgeID.push_back(edgeCount); /* vertices store information on edgeIDs */ pBlock->vertexStruct[j].edgeID.push_back(edgeCount); edgeCount++; } } } #endif body->setAspherical(true); body->shape = pBlock; //std::cout<<"BLOCKGEN pBlock->verticesCD.size() "<verticesCD.size()<<", pBlock->vertexStruct.size(): "<vertexStruct.size()<& scene){ shared_ptr interactionGeometryDispatcher(new IGeomDispatcher); shared_ptr cd(new Ig2_PB_PB_ScGeom); cd-> stepAngle=calAreaStep; cd->twoDimension = twoDimension; interactionGeometryDispatcher->add(cd); shared_ptr interactionPhysicsDispatcher(new IPhysDispatcher); shared_ptr ss(new Ip2_FrictMat_FrictMat_KnKsPBPhys); ss->Knormal = Kn; ss->Kshear = Ks; ss->kn_i = Kn; ss->ks_i = Ks; ss->viscousDamping = viscousDamping; ss->useOverlapVol = useOverlapVol; ss->useFaceProperties = useFaceProperties; ss->unitWidth2D = unitWidth2D; ss->calJointLength = calJointLength; ss->twoDimension = twoDimension; ss->brittleLength = brittleLength; ss->u_peak = peakDisplacement; ss->maxClosure = maxClosure; interactionPhysicsDispatcher->add(ss); //shared_ptr gravityCondition(new GravityEngine); //gravityCondition->gravity = gravity; if (useGlobalStiffnessTimeStepper){ globalStiffnessTimeStepper=shared_ptr(new GlobalStiffnessTimeStepper); globalStiffnessTimeStepper->timeStepUpdateInterval = timeStepUpdateInterval; globalStiffnessTimeStepper->defaultDt = defaultDt; } scene->engines.clear(); scene->engines.push_back(shared_ptr(new ForceResetter)); shared_ptr collider(new InsertionSortCollider); collider->verletDist = 0.1*minSize; collider->boundDispatcher->add(new PotentialBlock2AABB); scene->engines.push_back(collider); shared_ptr ids(new InteractionLoop); ids->geomDispatcher=interactionGeometryDispatcher; ids->physDispatcher=interactionPhysicsDispatcher; ids->lawDispatcher=shared_ptr(new LawDispatcher); shared_ptr see(new Law2_SCG_KnKsPBPhys_KnKsPBLaw); see->traceEnergy = traceEnergy; see->Talesnick = Talesnick; see->neverErase = neverErase; ids->lawDispatcher->add(see); scene->engines.push_back(ids); //scene->engines.push_back(globalStiffnessTimeStepper); //scene->engines.push_back(gravityCondition); shared_ptr newton(new NewtonIntegrator); newton->damping=dampingMomentum; newton->gravity= gravity; //Vector3r(0,0,9.81); // FIXME: // newton->damping3DEC=damp3DEC; newton->exactAsphericalRot=exactRotation; scene->engines.push_back(newton); //scene->initializers.clear(); } Real BlockGen::evaluateFNoSphere(struct Block block, Vector3r presentTrial){ Real x = presentTrial[0]-block.centre[0]; Real y = presentTrial[1]-block.centre[1]; Real z = presentTrial[2]-block.centre[2]; int planeNo = block.a.size(); vectora; vectorb; vectorc; vectord; vectorp; Real pSum2 = 0.0; for (int i=0; i vertices; Vector3r pointInside = Vector3r(0,0,0); double totalVolume=0; int planeNo = block.a.size(); double D[3]; double Ax[9]; Eigen::Matrix3d Aplanes; Vector3r centroid(0,0,0); for (int i=0; i0.9998){parallel = true;} if (fabs(plane1.dot(plane3))<1.0002 && fabs(plane1.dot(plane3))>0.9998){parallel = true;} if (fabs(plane2.dot(plane3))<1.0002 && fabs(plane2.dot(plane3))>0.9998){parallel = true;} double det = Aplanes.determinant(); if(fabs(det)>pow(10,-15) ){ //if (parallel == false){ int ipiv[3]; int bColNo=1; int info=0; /* LU */ int three =3; dgesv_( &three, &bColNo, Ax, &three, ipiv, D, &three, &info); if (info!=0){ //std::cout<<"linear algebra error"<pow(10,-3)){inside = false;} } if (inside == true){ vertices.push_back(vertex); } } } } } } vector verticesOnPlane; vector oriVerticesOnPlane; for (int j=0; j0){ verticesOnPlane.clear(); oriVerticesOnPlane.clear(); } for (int i=0; i orderedVerticesOnPlane; vector oriOrderedVerticesOnPlane; int h = 0; int k = 1; int m =2; Vector3r pt1 = verticesOnPlane[h]; Vector3r pt2 = verticesOnPlane[k]; Vector3r pt3 = verticesOnPlane[m]; orderedVerticesOnPlane.push_back(pt1); oriOrderedVerticesOnPlane.push_back(oriVerticesOnPlane[0]); int counter = 1; while(counter(orderedVerticesOnPlane.size()); oriBaseOnPolygon = oriBaseOnPolygon/static_cast(oriOrderedVerticesOnPlane.size()); int lastEntry = orderedVerticesOnPlane.size(); vertexOnPlane(lastEntry,0)=orderedVerticesOnPlane[0].x(); vertexOnPlane(lastEntry,1)=orderedVerticesOnPlane[0].y(); //vertexOnPlane(lastEntry,2)=orderedVerticesOnPlane[0].z(); //std::cout<<"vertexOnPlane0: "< vertices; Vector3r pointInside = Vector3r(0,0,0); double totalVolume=0; int planeNo = block.a.size(); double D[3]; double Ax[9]; Eigen::Matrix3d Aplanes; Vector3r centroid(0,0,0); for (int i=0; i0.9998){parallel = true;} if (fabs(plane1.dot(plane3))<1.0002 && fabs(plane1.dot(plane3))>0.9998){parallel = true;} if (fabs(plane2.dot(plane3))<1.0002 && fabs(plane2.dot(plane3))>0.9998){parallel = true;} double det = Aplanes.determinant(); if(fabs(det)>pow(10,-15) ){ //if (parallel == false){ int ipiv[3]; int bColNo=1; int info=0; /* LU */ int three =3; dgesv_( &three, &bColNo, Ax, &three, ipiv, D, &three, &info); if (info!=0){ //std::cout<<"linear algebra error"<pow(10,-3)){inside = false;} } if (inside == true){ vertices.push_back(vertex); } } } } } } vector verticesOnPlane; vector oriVerticesOnPlane; for (int j=0; j0){ verticesOnPlane.clear(); oriVerticesOnPlane.clear(); } for (int i=0; i orderedVerticesOnPlane; vector oriOrderedVerticesOnPlane; int h = 0; int k = 1; int m =2; Vector3r pt1 = verticesOnPlane[h]; Vector3r pt2 = verticesOnPlane[k]; Vector3r pt3 = verticesOnPlane[m]; orderedVerticesOnPlane.push_back(pt1); oriOrderedVerticesOnPlane.push_back(oriVerticesOnPlane[0]); int counter = 1; while(counter(orderedVerticesOnPlane.size()); oriBaseOnPolygon = oriBaseOnPolygon/static_cast(oriOrderedVerticesOnPlane.size()); int lastEntry = orderedVerticesOnPlane.size(); vertexOnPlane(lastEntry,0)=orderedVerticesOnPlane[0].x(); vertexOnPlane(lastEntry,1)=orderedVerticesOnPlane[0].y(); //vertexOnPlane(lastEntry,2)=orderedVerticesOnPlane[0].z(); //std::cout<<"vertexOnPlane0: "<-pow(10,-12) || convergeSuccess !=0 ){ // delete & model2; return false; }else{ //delete & model2; return true; } } bool BlockGen::contactBoundaryLPCLP(struct Discontinuity joint, struct Block block, Vector3r& touchingPt){ if(block.tooSmall == true){return false;} Vector3r solution(0,0,0); /* Parameters for particles A and B */ int planeNoA = block.a.size(); /* Variables to keep things neat */ int NUMCON = planeNoA /*block inequality */; int NUMVAR = 3/*3D */; double s = 0.0; double xlocalA=0; double ylocalA = 0; double zlocalA = 0; Vector3r localA (0,0,0); Vector3r xGlobalA (0,0,0); /* LINEAR CONSTRAINTS */ ClpSimplex model2; model2.setOptimizationDirection(1); // Create space for 3 columns and 10000 rows int numberRows = NUMCON; int numberColumns = NUMVAR; model2.resize(0, numberColumns); // Columns - objective was packed model2.setObjectiveCoefficient(0, joint.a); model2.setObjectiveCoefficient(1, joint.b); model2.setObjectiveCoefficient(2, joint.c); model2.setColumnLower(0, -COIN_DBL_MAX); model2.setColumnLower(1, -COIN_DBL_MAX); model2.setColumnLower(2, -COIN_DBL_MAX); model2.setColumnUpper(0, COIN_DBL_MAX); model2.setColumnUpper(1, COIN_DBL_MAX); model2.setColumnUpper(2, COIN_DBL_MAX); double rowLower[numberRows]; double rowUpper[numberRows]; // Rows for(int i=0; iassignMatrix(true, numberRows, numberColumns, numberElements,&aval[0], &asub[0], &aptrb[0], &columnCount[0]); model2.setLogLevel(0); matrix->assignMatrix(true, numberRows, numberColumns, numberElements,elements, rows, starts, lengths); ClpPackedMatrix * clpMatrix = new ClpPackedMatrix(matrix); model2.replaceMatrix(clpMatrix, true); } model2.primal(); // model2.writeMps("contactBoundary.mps"); // Print column solution int numberColumns = model2.numberColumns(); // Alternatively getColSolution() double * columnPrimal = model2.primalColumnSolution(); xGlobalA = Vector3r(columnPrimal[0],columnPrimal[1],columnPrimal[2]); touchingPt = xGlobalA; int convergeSuccess = model2.status(); if(convergeSuccess==3 || convergeSuccess==4 ){ //delete & model2; return false; }else{ //delete & model2; return true; } return true; } bool BlockGen::checkRedundancyLPCLP(struct Discontinuity joint, struct Block block, Vector3r& touchingPt){ if(block.tooSmall == true){return false;} Vector3r solution(0,0,0); /* Parameters for particles A and B */ int planeNoA = block.a.size(); /* Variables to keep things neat */ int NUMCON = planeNoA /*block inequality */; int NUMVAR = 3/*3D */; double s = 0.0; double xlocalA=0; double ylocalA = 0; double zlocalA = 0; Vector3r localA (0,0,0); Vector3r xGlobalA (0,0,0); ClpSimplex model2; { model2.setOptimizationDirection(1); // Create space for 3 columns and 10000 rows int numberRows = NUMCON; int numberColumns = NUMVAR; // This is fully dense - but would not normally be so int numberElements = numberRows * numberColumns; // Arrays will be set to default values model2.resize(numberRows, numberColumns); double * elements = new double [numberElements]; CoinBigIndex * starts = new CoinBigIndex [numberColumns+1]; int * rows = new int [numberElements];; int * lengths = new int[numberColumns]; // Now fill in - totally unsafe but .... double * columnLower = model2.columnLower(); double * columnUpper = model2.columnUpper(); double * objective = model2.objective(); double * rowLower = model2.rowLower(); double * rowUpper = model2.rowUpper(); // Columns - objective was packed objective[0] = -joint.a; objective[1] = -joint.b; objective[2] = -joint.c; for (int k = 0; k < numberColumns; k++){ columnLower[k]= -COIN_DBL_MAX; columnUpper[k] = COIN_DBL_MAX; } // Rows for(int i=0; iassignMatrix(true, numberRows, numberColumns, numberElements,&aval[0], &asub[0], &aptrb[0], &columnCount[0]); model2.setLogLevel(0); matrix->assignMatrix(true, numberRows, numberColumns, numberElements,elements, rows, starts, lengths); ClpPackedMatrix * clpMatrix = new ClpPackedMatrix(matrix); model2.replaceMatrix(clpMatrix, true); } model2.scaling(0); model2.dual(); // model2.writeMps("redundancy.mps"); // Print column solution int numberColumns = model2.numberColumns(); // Alternatively getColSolution() double * columnPrimal = model2.primalColumnSolution(); xGlobalA = Vector3r(columnPrimal[0],columnPrimal[1],columnPrimal[2]); touchingPt = xGlobalA; Real f = touchingPt.x()*joint.a + touchingPt.y()*joint.b + touchingPt.z()*joint.c - joint.d-block.r; if(fabs(f)>pow(10,-3) ){ //delete & model2; return false; }else{ //delete & model2; return true; } } double BlockGen::inscribedSphereCLP(struct Block block, Vector3r& initialPoint, bool twoDimension){ /* minimise s */ /* s.t. Ax - s <= d*/ bool converge = true; /* Parameters for particles A and B */ double s = 0.0; /* get value of x[3] after optimization */ int planeNoA = block.a.size(); vector plane2Dno; if (twoDimension == true){ for (int i=0; i0.99 ){ plane2Dno.push_back(i); //std::cout<<"2d: "<& scene) { } #endif // YADE_POTENTIAL_BLOCKS trunk-2017.01a/pkg/dem/BlockGen.hpp000077500000000000000000000235331304022710500167160ustar00rootroot00000000000000/*CWBoon 2016 */ /* Please cite: */ /* CW Boon, GT Houlsby, S Utili (2015). A new rock slicing method based on linear programming. Computers and Geotechnics 65, 12-29. */ /* The numerical library is changed from CPLEX to CLP because subscription to the academic initiative is required to use CPLEX for free */ #ifdef YADE_POTENTIAL_BLOCKS #pragma once #include #include #include #include #include #include #include #include #include #include #include #include #include class GlobalStiffnessTimeStepper; class BlockGen : public FileGenerator { private : void createActors(shared_ptr& scene); void positionRootBody(shared_ptr& scene); shared_ptr globalStiffnessTimeStepper; protected: std::ofstream output2; std::string myfile; std::string Key; static std::ofstream output; public : ~BlockGen (); bool generate(string&); template double gen_normal_3(T &generator){ return generator();} struct Discontinuity{ Vector3r centre; Discontinuity(Vector3r pos){centre = pos; persistence = false; phi_b = 30.0; phi_r= 30.0; JRC=15; JCS = pow(10,6); asperity = 5; sigmaC = JCS;isBoundary= false;sliceBoundaries=false; lambda0=0.0; heatCapacity=0.0;hwater=-1.0;intactRock=false; throughGoing = false; constructionJoints=false;jointType=0;} Real a; Real b; Real c; Real d; Real a_p; Real b_p; Real c_p; Real d_p; bool persistence; bool isBoundary; bool sliceBoundaries; bool constructionJoints; vector persistence_a; vector persistence_b; vector persistence_c; vector persistence_d; /* Joint properties */ double phi_b; double phi_r; double JRC; double JCS; double asperity; double sigmaC; double cohesion; double tension; double lambda0; double heatCapacity; double hwater; bool intactRock; bool throughGoing; int jointType; }; struct Planes{ vector vertexID; }; struct Block{ Vector3r tempCentre; Vector3r centre; Block(Vector3r pos, Real kPP, Real rPP, Real RPP){centre = pos; k=kPP; r=rPP; R=RPP; tooSmall=false;isBoundary=false;tempCentre=pos;} vector a; vector b; vector c; vector d; vector redundant; vector isBoundaryPlane; bool isBoundary; vector subMembers; vector falseVertex; vector node; Real gridVol; Real r; Real R; Real k; bool tooSmall; /* Joint properties */ vector phi_b; vector phi_r; vector JRC; vector JCS; vector asperity; vector sigmaC; vector cohesion; vector tension; vector lambda0; vector heatCapacity; vector hwater; vector intactRock; vector jointType; vector planes; }; double getSignedArea(const Vector3r pt1,const Vector3r pt2, const Vector3r pt3); double getDet(const Eigen::MatrixXd A); double getCentroidTetrahedron(const Eigen::MatrixXd A); bool createBlock(shared_ptr& body, struct BlockGen::Block block, int no); bool contactDetection(struct BlockGen::Discontinuity joint, struct BlockGen::Block block, Vector3r& touchingPt); bool contactDetectionLPCLP(struct BlockGen::Discontinuity joint, struct BlockGen::Block block, Vector3r& touchingPt); bool contactDetectionLPCLPglobal(struct BlockGen::Discontinuity joint, struct BlockGen::Block block, Vector3r& touchingPt); bool checkRedundancyLPCLP(struct BlockGen::Discontinuity joint, struct BlockGen::Block block, Vector3r& touchingPt); bool startingPointFeasibility(struct BlockGen::Block block, Vector3r& initialPoint); double inscribedSphereCLP(struct BlockGen::Block block, Vector3r& initialPoint, bool twoDimension); bool contactBoundaryLPCLP(struct BlockGen::Discontinuity joint, struct BlockGen::Block block, Vector3r& touchingPt); bool contactBoundaryLPCLPslack(struct BlockGen::Discontinuity joint, struct BlockGen::Block block, Vector3r& touchingPt); void calculateInertia(struct Block block, Real& Ixx, Real& Iyy, Real& Izz,Real& Ixy, Real& Ixz, Real& Iyz); Vector3r calCentroid(struct Block block, double & blockVol); bool checkCentroid(struct Block block, Vector3r presentTrial); Real evaluateFNoSphere(struct Block block, Vector3r presentTrial); YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY( BlockGen,FileGenerator,"Prepare a scene for triaxial tests. See full documentation at http://yade-dem.org/wiki/TriaxialTest." , /* public */ ((Real,dampingMomentum,0.2,,"Coefficient of Cundal-Non-Viscous damping (applied on on the 3 components of torques)")) ((Real, maxClosure, 0.0002, ,"vmi")) ((Real, peakDisplacement, 0.02, ,"vmi")) ((double, brittleLength, 2.0, ,"brittle rock")) ((Real,damp3DEC,0.8,,"Coefficient of Cundal-Non-Viscous damping (applied on on the 3 components of torques)")) ((Real,unitWidth2D,1.0,,"out of plane distance")) ((Real,density,2600,,"density of blocks")) ((Real,Kn,pow(10,-5),,"density of blocks")) ((Real,Ks,pow(10,-5),,"density of blocks")) ((Real,frictionDeg,18.0,,"friction angle [°]")) ((Vector3r,globalOrigin,Vector3r(0.0,0.0,0.0),,"friction angle [°]")) ((Real,inertiaFactor,1.0,,"to avoid wobbling")) ((Real,rForPP,0.1,,"r")) ((Real,kForPP,0.01,,"k")) ((Real,RForPP,3.5,,"R")) ((int,numberOfGrids,1,,"R")) ((bool,probabilisticOrientation,false,,"use random number generator")) ((bool,Talesnick,false,,"R")) ((bool,neverErase,false,,"erase non interacting contacts")) ((bool,calJointLength,false,,"whether to calculate jointLength")) ((bool,twoDimension,false,,"whether it is 2D")) ((Real,shrinkFactor,1.0,,"ratio to shrink r")) ((Real,viscousDamping,0.8,,"viscous damping")) ((bool, intactRockDegradation, false, ,"brittle rock")) ((Real,initialOverlap,0.0,,"initial overlap between blocks")) ((Vector3r,gravity,Vector3r(0.0,-9.81,0.0),,"gravity")) ((Real,defaultDt,-1,,"Max time-step. Used as initial value if defined. Latter adjusted by the time stepper.")) ((int,timeStepUpdateInterval,50,,"interval for :yref:`GlobalStiffnessTimeStepper`")) ((bool,traceEnergy,true,,"friction angle [°]")) ((bool,exactRotation,true,,"friction angle [°]")) ((Real,minSize,50.0,,"length X of domain")) ((Real,maxRatio,3.0,,"length X of domain")) ((Real,boundarySizeXmax,1.0,,"length X of domain")) ((Real,boundarySizeYmax,1.0,,"length Y of domain")) ((Real,boundarySizeZmax,1.0,,"length Z of domain")) ((Real,boundarySizeXmin,1.0,,"length X of domain")) ((Real,boundarySizeYmin,1.0,,"length Y of domain")) ((Real,boundarySizeZmin,1.0,,"length Z of domain")) ((Vector3r,directionA,Vector3r(1,0,0),,"length Z of domain")) ((Vector3r,directionB,Vector3r(0,1,0),,"length Z of domain")) ((Vector3r,directionC,Vector3r(0,0,1),,"length Z of domain")) ((Real,calAreaStep,10.0,,"length Z of domain")) ((Real,extremeDist,0.5,,"boundary to base calculation of octree algorithms")) //FIXME remove when not needed anymore ((Real,subdivisionRatio,0.1,,"smallest size/boundary of octree algorithms")) ((vector,joint_a,,,"a")) ((vector,joint_b,,,"b")) ((vector,joint_c,,,"c")) ((vector,joint_d,,,"d")) /* check for different joint types */ ((bool, persistentPlanes,false,,"check persistence")) ((bool, jointProbabilistic,false,,"check for filename jointProbabilistic")) ((bool, opening,false,,"check for filename opening")) ((bool, boundaries,false,,"check for filename boundaries")) ((bool, slopeFace,false,,"check for filename boundaries")) ((bool, sliceBoundaries,false,,"check for filename boundaries")) ((bool, useGlobalStiffnessTimeStepper,false,,"check for filename boundaries")) /* which contact law to use */ ((bool, useBartonBandis,false,,"whether to use Barton Bandis contact law")) ((bool, useFaceProperties, false, , "use face properties")) ((bool, useOverlapVol,false,,"check for filename opening")) ((std::string,filenamePersistentPlanes,"/home/booncw/yade/BranchA/scripts/Tunnel/jointPersistent.csv",,"filename to look for joint properties")) ((std::string,filenameProbabilistic,"/home/booncw/yade/BranchA/scripts/boon/Tunnel/jointProbabilistic.csv",,"filename to look for joint with probabilistic models")) ((std::string,filenameBoundaries,"/home/booncw/yade/BranchA/scripts/boon/Tunnel/boundaries.csv",,"filename to look for joint with probabilistic models")) ((std::string,filenameOpening,"/home/booncw/yade/BranchA/scripts/boon/Tunnel/opening.csv",,"filename to look for joint outline of joints")) ((std::string,filenameSlopeFace,"/home/booncw/yade/BranchA/scripts/boon/Tunnel/opening.csv",,"filename to look for joint outline of joints")) ((std::string,filenameSliceBoundaries,"/home/booncw/yade/BranchA/scripts/boon/Tunnel/sliceBoundaries.csv",,"filename to look for joint outline of joints")) //((double*, array_a,,,"a")) , /* init */ , /* constructor for private */ Key =""; myfile = "./BlkGen"+Key; output2.open(myfile.c_str(), fstream::app); , //.def("setContactProperties",&TriaxialCompressionEngine::setContactProperties,"Assign a new friction angle (degrees) to dynamic bodies and relative interactions") ); DECLARE_LOGGER; }; #ifdef __cplusplus extern "C" { #endif void dgesv_(const int *N, const int *nrhs, double *Hessian, const int *lda, int *ipiv, double *gradient, const int *ldb, int *info); void dsyev_(const char *jobz, const char *uplo, const int *N, double *A, const int *lda, double *W, double *work, int *lwork, int *info); #ifdef __cplusplus }; #endif REGISTER_SERIALIZABLE(BlockGen); #endif // YADE_POTENTIAL_BLOCKS trunk-2017.01a/pkg/dem/BubbleMat.cpp000066400000000000000000000071351304022710500170570ustar00rootroot00000000000000#include "BubbleMat.hpp" YADE_PLUGIN((BubbleMat)(Ip2_BubbleMat_BubbleMat_BubblePhys)(BubblePhys)(Law2_ScGeom_BubblePhys_Bubble)); /********************** Ip2_BubbleMat_BubbleMat_BubblePhys ****************************/ CREATE_LOGGER(Ip2_BubbleMat_BubbleMat_BubblePhys); void Ip2_BubbleMat_BubbleMat_BubblePhys::go(const shared_ptr& m1, const shared_ptr& m2, const shared_ptr& interaction){ // phys already exists if (interaction->phys) return; shared_ptr phys(new BubblePhys()); interaction->phys = phys; } /********************** BubblePhys ****************************/ CREATE_LOGGER(BubblePhys); void BubblePhys::computeCoeffs(Real pctMaxForce, Real surfaceTension, Real c1) { Real Fmax = pctMaxForce*c1*rAvg; Real logPct = log(pctMaxForce/4); Dmax = pctMaxForce*rAvg*logPct; Real dfdd = c1/(logPct+1); coeffB = dfdd/Fmax; coeffA = Fmax/exp(coeffB*Dmax); fN = 0.1*Fmax; } Real BubblePhys::computeForce(Real separation, Real surfaceTension, Real rAvg, int newtonIter, Real newtonTol, Real c1, Real fN, BubblePhys* phys) { if (separation >= phys->Dmax) { Real f,df,g,retOld,residual; Real c2 = 1./(4*c1*rAvg); Real ret = fN; int i = 0; do { //[Chan2011], Loop solves modified form of equation (25) using Newton-Raphson method retOld = ret; g = log(ret*c2); f = separation*c1 - ret*g; df = g+1; ret += f/df; if(ret <= 0.0){ //Need to make sure ret > 0, otherwise the next iteration will try to evaluate the natural logarithm of a negative number, which results in NaN ret = 0.9*fabs(ret); residual = newtonTol*2; //Also, if, by chance, retOld = 0.9*ret it would cause the loop to exit based on the boolean residual > newtonTol, so we force the next iteration by setting residual = newtonTol*2 } else {residual = fabs(ret - retOld)/retOld;} if (i++ > newtonIter) { throw runtime_error("BubblePhys::computeForce: no convergence\n"); } } while (residual > newtonTol); return ret; } else { //Artificial Extension of [Chan2011] equation 25 to approximiate behaviour outside the valid regime (large penetration cases) return phys->coeffA*exp(phys->coeffB*separation); } } /********************** Law2_ScGeom_BubblePhys_Bubble ****************************/ CREATE_LOGGER(Law2_ScGeom_BubblePhys_Bubble); bool Law2_ScGeom_BubblePhys_Bubble::go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I){ ScGeom* geom=static_cast(_geom.get()); BubblePhys* phys=static_cast(_phys.get()); if(geom->penetrationDepth <= 0.0) { return false; } if (I->isFresh(scene)) { c1 = 2*Mathr::PI*surfaceTension; phys->rAvg = .5*(geom->refR1 + geom->refR2); phys->computeCoeffs(pctMaxForce,surfaceTension,c1); } Real &fN = phys->fN; fN = phys->computeForce(-geom->penetrationDepth, surfaceTension, phys->rAvg, phys->newtonIter, phys->newtonTol, c1, fN, phys); phys->fN = fN; Vector3r &normalForce = phys->normalForce; normalForce = fN*geom->normal; int id1 = I->getId1(), id2 = I->getId2(); if (!scene->isPeriodic) { State* b1 = Body::byId(id1,scene)->state.get(); State* b2 = Body::byId(id2,scene)->state.get(); applyForceAtContactPoint(-normalForce, geom->contactPoint , id1, b1->se3.position, id2, b2->se3.position); } else { scene->forces.addForce(id1,-normalForce); scene->forces.addForce(id2,normalForce); scene->forces.addTorque(id1,(geom->radius1-0.5*geom->penetrationDepth)* geom->normal.cross(normalForce)); scene->forces.addTorque(id2,(geom->radius2-0.5*geom->penetrationDepth)* geom->normal.cross(normalForce)); } return true; } trunk-2017.01a/pkg/dem/BubbleMat.hpp000066400000000000000000000100761304022710500170620ustar00rootroot00000000000000#pragma once #include #include #include #include namespace py=boost::python; /********************** BubbleMat ****************************/ class BubbleMat : public Material { public: YADE_CLASS_BASE_DOC_ATTRS_CTOR(BubbleMat,Material,"material for bubble interactions, for use with other Bubble classes", ((Real,surfaceTension,0.07197,,"The surface tension in the fluid surrounding the bubbles. The default value is that of water at 25 degrees Celcius.")) , createIndex(); density=1000; ); REGISTER_CLASS_INDEX(BubbleMat,Material); }; REGISTER_SERIALIZABLE(BubbleMat); /********************** BubblePhys ****************************/ class BubblePhys : public IPhys { private: Real coeffA,coeffB; //Coefficents for artificial curve public: void computeCoeffs(Real pctMaxForce,Real surfaceTension, Real c1); static Real computeForce(Real separation, Real surfaceTension, Real rAvg, int newtonIter, Real newtonTol, Real c1, Real fN, BubblePhys* phys); virtual ~BubblePhys(){}; YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(BubblePhys,IPhys,"Physics of bubble-bubble interactions, for use with BubbleMat", ((Vector3r,normalForce,Vector3r::Zero(),,"Normal force")) ((Real,surfaceTension,NaN,,"Surface tension of the surrounding liquid")) ((Real,fN,NaN,,"Contact normal force")) ((Real,rAvg,NaN,,"Average radius of the two interacting bubbles")) ((Real,Dmax,NaN,,"Maximum penetrationDepth of the bubbles before the force displacement curve changes to an artificial exponential curve. Setting this value will have no effect. See Law2_ScGeom_BubblePhys_Bubble::pctMaxForce for more information")) ((Real,newtonIter,50,,"Maximum number of force iterations allowed")) ((Real,newtonTol,1e-6,,"Convergence criteria for force iterations")) , createIndex(); , .def("computeForce",&BubblePhys::computeForce,"Computes the normal force acting between the two interacting bubbles using the Newton-Rhapson method") .staticmethod("computeForce") ); DECLARE_LOGGER; REGISTER_CLASS_INDEX(BubblePhys,IPhys); }; REGISTER_SERIALIZABLE(BubblePhys); /********************** Ip2_BubbleMat_BubbleMat_BubblePhys ****************************/ class Ip2_BubbleMat_BubbleMat_BubblePhys : public IPhysFunctor{ public: virtual void go(const shared_ptr& m1, const shared_ptr& m2, const shared_ptr& interaction); FUNCTOR2D(BubbleMat,BubbleMat); DECLARE_LOGGER; YADE_CLASS_BASE_DOC_ATTRS(Ip2_BubbleMat_BubbleMat_BubblePhys,IPhysFunctor,"Generates bubble interactions.Used in the contact law Law2_ScGeom_BubblePhys_Bubble.", ); }; REGISTER_SERIALIZABLE(Ip2_BubbleMat_BubbleMat_BubblePhys); /********************** Law2_ScGeom_BubblePhys_Bubble ****************************/ class Law2_ScGeom_BubblePhys_Bubble : public LawFunctor{ private: Real c1; //Coeff used for many contacts public: virtual bool go(shared_ptr& _geom, shared_ptr& _phys, Interaction* interaction); FUNCTOR2D(GenericSpheresContact,BubblePhys); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Law2_ScGeom_BubblePhys_Bubble,LawFunctor,"Constitutive law for Bubble model.", ((Real,pctMaxForce,0.1,,"Chan[2011] states the contact law is valid only for small interferences; therefore an exponential force-displacement curve models the contact stiffness outside that regime (large penetration). This artificial stiffening ensures that bubbles will not pass through eachother or completely overlap during the simulation. The maximum force is Fmax = (2*pi*surfaceTension*rAvg). pctMaxForce is the percentage of the maximum force dictates the separation threshold, Dmax, for each contact. Penetrations less than Dmax calculate the reaction force from the derived contact law, while penetrations equal to or greater than Dmax calculate the reaction force from the artificial exponential curve.")) ((Real,surfaceTension,0.07197,,"The surface tension in the liquid surrounding the bubbles. The default value is that of water at 25 degrees Celcius.")) , /*ctor*/, ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_ScGeom_BubblePhys_Bubble); trunk-2017.01a/pkg/dem/CapillaryPhys.cpp000066400000000000000000000030461304022710500200030ustar00rootroot00000000000000#include #include YADE_PLUGIN((CapillaryPhys)(Ip2_FrictMat_FrictMat_CapillaryPhys)); // The following code was moved from Ip2_FrictMat_FrictMat_CapillaryPhys.cpp void Ip2_FrictMat_FrictMat_CapillaryPhys::go( const shared_ptr& b1 //FrictMat , const shared_ptr& b2 // FrictMat , const shared_ptr& interaction) { ScGeom* geom = YADE_CAST(interaction->geom.get()); if(geom) { if(!interaction->phys) { const shared_ptr& sdec1 = YADE_PTR_CAST(b1); const shared_ptr& sdec2 = YADE_PTR_CAST(b2); if (!interaction->phys) interaction->phys = shared_ptr(new CapillaryPhys()); const shared_ptr& contactPhysics = YADE_PTR_CAST(interaction->phys); Real Ea = sdec1->young; Real Eb = sdec2->young; Real Va = sdec1->poisson; Real Vb = sdec2->poisson; Real Da = geom->radius1; // FIXME - multiply by factor of sphere interaction distance (so sphere interacts at bigger range that its geometrical size) Real Db = geom->radius2; // FIXME - as above Real fa = sdec1->frictionAngle; Real fb = sdec2->frictionAngle; Real Kn = 2*Ea*Da*Eb*Db/(Ea*Da+Eb*Db);//harmonic average of two stiffnesses Real Ks = 2*Ea*Da*Va*Eb*Db*Vb/(Ea*Da*Va+Eb*Db*Va);//harmonic average of two stiffnesses with ks=V*kn for each sphere contactPhysics->tangensOfFrictionAngle = std::tan(std::min(fa,fb)); contactPhysics->kn = Kn; contactPhysics->ks = Ks; } } }; trunk-2017.01a/pkg/dem/CapillaryPhys.hpp000066400000000000000000000067421304022710500200160ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by luc Scholtes * * luc.scholtes@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include class CapillaryPhys : public FrictPhys { public : int currentIndexes [4]; // used for faster interpolation (stores previous positions in tables) virtual ~CapillaryPhys() {}; YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(CapillaryPhys,FrictPhys,"Physics (of interaction) for :yref:`Law2_ScGeom_CapillaryPhys_Capillarity`.", ((bool,meniscus,false,Attr::readonly,"True when a meniscus with a non-zero liquid volume (:yref:`vMeniscus`) has been computed for this interaction")) ((bool,isBroken,false,,"Might be set to true by the user to make liquid bridge inactive (capillary force is zero)")) ((Real,capillaryPressure,0.,,"Value of the capillary pressure Uc. Defined as Ugas-Uliquid, obtained from :yref:`corresponding Law2 parameter`")) ((Real,vMeniscus,0.,,"Volume of the meniscus")) ((Real,Delta1,0.,,"Defines the surface area wetted by the meniscus on the smallest grains of radius R1 (R1` + :yref:`nn33`.")) ((Real,nn33,0.,,":math:`\\iint_A n_3 n_3 \\, dS`, $A$ being the liquid-gas surface of the meniscus, $\\vec n$ the associated normal, and $(1,2,3)$ a local basis with $3$ the meniscus orientation (:yref:`ScGeom.normal`). NB: $A$ = 2 :yref:`nn11` + :yref:`nn33`.")) ,, createIndex();currentIndexes[0]=currentIndexes[1]=currentIndexes[2]=currentIndexes[3]=0; , ); REGISTER_CLASS_INDEX(CapillaryPhys,FrictPhys); }; REGISTER_SERIALIZABLE(CapillaryPhys); class Ip2_FrictMat_FrictMat_CapillaryPhys : public IPhysFunctor { public : virtual void go( const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction); FUNCTOR2D(FrictMat,FrictMat); YADE_CLASS_BASE_DOC_ATTRS_CTOR(Ip2_FrictMat_FrictMat_CapillaryPhys,IPhysFunctor, "RelationShips to use with :yref:`Law2_ScGeom_CapillaryPhys_Capillarity`.\n\n In these RelationShips all the interaction attributes are computed. \n\n.. warning::\n\tas in the others :yref:`Ip2 functors`, most of the attributes are computed only once, when the interaction is new.",,;); }; REGISTER_SERIALIZABLE(Ip2_FrictMat_FrictMat_CapillaryPhys); trunk-2017.01a/pkg/dem/CapillaryPhys1.cpp000066400000000000000000000036461304022710500200720ustar00rootroot00000000000000//keep this #ifdef as long as you don't really want to realize a final version publicly, it will save compilation time for everyone else //when you want it compiled, you can just uncomment the following line // #define CAPILLARYPHYS1 #ifdef CAPILLARYPHYS1 #include #include #include #include CapillaryPhys1::~CapillaryPhys1() { } YADE_PLUGIN((CapillaryPhys1)); YADE_PLUGIN((Ip2_FrictMat_FrictMat_CapillaryPhys1)); void Ip2_FrictMat_FrictMat_CapillaryPhys1::go( const shared_ptr& b1 //FrictMat , const shared_ptr& b2 // FrictMat , const shared_ptr& interaction) { ScGeom* geom = YADE_CAST(interaction->geom.get()); if(geom) { if(!interaction->phys) { const shared_ptr& sdec1 = YADE_PTR_CAST(b1); const shared_ptr& sdec2 = YADE_PTR_CAST(b2); if (!interaction->phys) interaction->phys = shared_ptr(new CapillaryPhys1()); const shared_ptr& contactPhysics = YADE_PTR_CAST(interaction->phys); Real Ea = sdec1->young; Real Eb = sdec2->young; Real Va = sdec1->poisson; Real Vb = sdec2->poisson; Real Da = geom->radius1; // FIXME - multiply by factor of sphere interaction distance (so sphere interacts at bigger range that its geometrical size) Real Db = geom->radius2; // FIXME - as above Real fa = sdec1->frictionAngle; Real fb = sdec2->frictionAngle; Real Kn = 2*Ea*Da*Eb*Db/(Ea*Da+Eb*Db);//harmonic average of two stiffnesses Real Ks = 2*Ea*Da*Va*Eb*Db*Vb/(Ea*Da*Va+Eb*Db*Va);//harmonic average of two stiffnesses with ks=V*kn for each sphere contactPhysics->tangensOfFrictionAngle = std::tan(std::min(fa,fb)); contactPhysics->kn = Kn; contactPhysics->ks = Ks; contactPhysics->computeBridge =computeDefault; } } }; #endif //CAPILLARYPHYS1 trunk-2017.01a/pkg/dem/CapillaryPhys1.hpp000066400000000000000000000124661304022710500200770ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by luc Scholtes * * luc.scholtes@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include class MeniscusPhysicalData { public: double R; double volume; double distance; double surface; double energy; double force; double succion; double delta1; double delta2; double arcLength; bool ending; //default ctor MeniscusPhysicalData() : R(0), volume(0), distance(0), surface(0), energy(0), force(0), succion(0), delta1(0), delta2(0), arcLength(0), ending(1) {} //ctor with input values MeniscusPhysicalData(const double& r, const double& v, const double& d, const double& s, const double& e, const double& f, const double& p, const double& a1, const double& a2, const double& arc, bool end) : R(r), volume(v), distance(d), surface(s), energy(e), force(f), succion(p), delta1(a1), delta2(a2), arcLength(arc), ending(end) {} //a minimal list of operators for the interpolation //these operators are requirements for the DataType template parameter of interpolate() //FIXME: algebra operations must include energy, perimeter, and any other new variable for including them in the interpolation MeniscusPhysicalData& operator+= (const MeniscusPhysicalData& m2) { R+=m2.R; volume+=m2.volume; distance+=m2.distance; surface+=m2.surface; energy+=m2.energy; force+=m2.force; succion+=m2.succion; delta1+=m2.delta1; delta2+=m2.delta2; arcLength+=m2.arcLength; ending=(ending && m2.ending); return *this;} MeniscusPhysicalData operator* (const double& fact) const { return MeniscusPhysicalData(fact*R, fact*volume, fact*distance, fact*surface, fact*energy, fact*force, fact*succion, fact*delta1, fact*delta2, fact*arcLength, ending);} const MeniscusPhysicalData& operator= (const MeniscusPhysicalData& m1) { R=m1.R; volume=m1.volume; distance=m1.distance; surface=m1.surface; energy=m1.energy; force=m1.force; succion=m1.succion; delta1=m1.delta1; delta2=m1.delta2; arcLength=m1.arcLength; ending=m1.ending; return *this;} }; //The structure for the meniscus: physical properties + cached values for fast interpolation class Meniscus { public: typedef MeniscusPhysicalData Data; Data data; //the variables of Laplace's problem DT::Cell_handle cell; //pointer to the last location in the triangulation, for faster locate() std::vector normals;// 4 normals relative to the current cell Meniscus() : data(), cell(DT::Cell_handle()), normals(std::vector()) {} }; class CapillaryPhys1 : public FrictPhys { public : int currentIndexes [4]; // used for faster interpolation (stores previous positions in tables) Meniscus m; virtual ~CapillaryPhys1(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(CapillaryPhys1,FrictPhys,"Physics (of interaction) for Law2_ScGeom_CapillaryPhys_Capillarity.", ((bool,meniscus,false,,"Presence of a meniscus if true")) ((bool,isBroken,false,,"If true, capillary force is zero and liquid bridge is inactive.")) ((bool,computeBridge,true,,"If true, capillary bridge will be computed if not it will be ignored.")) ((Real,capillaryPressure,0.,,"Value of the capillary pressure Uc defines as Ugas-Uliquid")) ((Real,vMeniscus,0.,,"Volume of the menicus")) ((Real,Delta1,0.,,"Defines the surface area wetted by the meniscus on the smallest grains of radius R1 (R1& b1, const shared_ptr& b2, const shared_ptr& interaction); FUNCTOR2D(FrictMat,FrictMat); YADE_CLASS_BASE_DOC_ATTRS_CTOR(Ip2_FrictMat_FrictMat_CapillaryPhys1,IPhysFunctor, "RelationShips to use with Law2_ScGeom_CapillaryPhys_Capillarity1\n\n In these RelationShips all the interaction attributes are computed. \n\n.. warning::\n\tas in the others :yref:`Ip2 functors`, most of the attributes are computed only once, when the interaction is new.", ((bool,computeDefault,true,,"bool to assign the default value of computeBridge.")),; ); }; REGISTER_SERIALIZABLE(Ip2_FrictMat_FrictMat_CapillaryPhys1); trunk-2017.01a/pkg/dem/CapillaryStressRecorder.cpp000066400000000000000000000120101304022710500220200ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by luc scholtes * * luc.scholtes@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "CapillaryStressRecorder.hpp" #include #include #include #include #include #include #include YADE_PLUGIN((CapillaryStressRecorder)); CREATE_LOGGER(CapillaryStressRecorder); void CapillaryStressRecorder::action() { shared_ptr& bodies = scene->bodies; // at the beginning of the file; write column titles if(out.tellp()==0){ out<<"iteration Scap11 Scap22 Scap33 Scap12 Scap13 Scap23 Uc Sr w"< >::iterator itFirst = scene->engines.begin(); vector >::iterator itLast = scene->engines.end(); for ( ;itFirst!=itLast; ++itFirst ) { if ( ( *itFirst )->getClassName() == "TriaxialCompressionEngine") { LOG_DEBUG ( "stress controller engine found" ); triaxialCompressionEngine = YADE_PTR_CAST ( *itFirst ); } } if ( !triaxialCompressionEngine ) { LOG_ERROR ("Stress controller engine not found, the recorder cannot be used."); return;} } Real f1_cap_x=0, f1_cap_y=0, f1_cap_z=0, x1=0, y1=0, z1=0, x2=0, y2=0, z2=0; Real sig11_cap=0, sig22_cap=0, sig33_cap=0, sig12_cap=0, sig13_cap=0, sig23_cap=0, Vwater = 0, capillaryPressure = 0; int j = 0; InteractionContainer::iterator ii = scene->interactions->begin(); InteractionContainer::iterator iiEnd = scene->interactions->end(); for( ; ii!=iiEnd ; ++ii ) { if ((*ii)->isReal()) { const shared_ptr& interaction = *ii; CapillaryPhys* meniscusParameters = static_cast(interaction->phys.get()); if (meniscusParameters->meniscus) { j=j+1; unsigned int id1 = interaction -> getId1(); unsigned int id2 = interaction -> getId2(); Vector3r fcap = meniscusParameters->fCap; f1_cap_x=fcap[0]; f1_cap_y=fcap[1]; f1_cap_z=fcap[2]; Body* de1 = (*bodies)[id1].get(); Body* de2 = (*bodies)[id2].get(); x1 = de1->state->pos[0]; y1 = de1->state->pos[1]; z1 = de1->state->pos[2]; x2 = de2->state->pos[0]; y2 = de2->state->pos[1]; z2 = de2->state->pos[2]; /// capillary stresses from contact forces sig11_cap = sig11_cap + f1_cap_x*(x1 - x2); sig22_cap = sig22_cap + f1_cap_y*(y1 - y2); sig33_cap = sig33_cap + f1_cap_z*(z1 - z2); sig12_cap = sig12_cap + f1_cap_x*(y1 - y2); sig13_cap = sig13_cap + f1_cap_x*(z1 - z2); sig23_cap = sig23_cap + f1_cap_y*(z1 - z2); /// Liquid volume Vwater += meniscusParameters->vMeniscus; capillaryPressure=meniscusParameters->capillaryPressure; } } } /// Sample volume Real V = ( triaxialCompressionEngine->height ) * ( triaxialCompressionEngine->width ) * ( triaxialCompressionEngine->depth ); /// Solid volume Real Vs = 0, Rbody = 0, SR = 0; BodyContainer::iterator bi = bodies->begin(); BodyContainer::iterator biEnd = bodies->end(); for ( ; bi!=biEnd; ++bi) { shared_ptr b = *bi; if (b->shape->getClassIndex()!=Sphere::getClassIndexStatic()) continue; Sphere* sphere = static_cast(b->shape.get()); if (sphere) { Rbody = sphere->radius; SR+=Rbody; Vs += 1.333*Mathr::PI*(Rbody*Rbody*Rbody); } } Real Vv = V - Vs; Real Sr = 100*Vwater/Vv; if (Sr>100) Sr=100; Real w = 100*Vwater/V; if (w>(100*Vv/V)) w=100*(Vv/V); /// homogeneized capillary stresses Real SIG_11_cap=0, SIG_22_cap=0, SIG_33_cap=0, SIG_12_cap=0, SIG_13_cap=0, SIG_23_cap=0; SIG_11_cap = sig11_cap/V; SIG_22_cap = sig22_cap/V; SIG_33_cap = sig33_cap/V; SIG_12_cap = sig12_cap/V; SIG_13_cap = sig13_cap/V; SIG_23_cap = sig23_cap/V; out << boost::lexical_cast ( scene->iter ) << " " << boost::lexical_cast(SIG_11_cap) << " " << boost::lexical_cast(SIG_22_cap) << " " << boost::lexical_cast(SIG_33_cap) << " " << boost::lexical_cast(SIG_12_cap) << " " << boost::lexical_cast(SIG_13_cap)<< " " << boost::lexical_cast(SIG_23_cap)<< " " << boost::lexical_cast(capillaryPressure) << " " << boost::lexical_cast(Sr)<< " " << boost::lexical_cast(w)<< " " << endl; } trunk-2017.01a/pkg/dem/CapillaryStressRecorder.hpp000066400000000000000000000022271304022710500220360ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by luc Scholtes * * luc.scholtes@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include class TriaxialCompressionEngine; class CapillaryStressRecorder : public Recorder { private : shared_ptr triaxialCompressionEngine; public : virtual void action(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(CapillaryStressRecorder,Recorder,"Records information from capillary meniscii on samples submitted to triaxial compressions. Classical sign convention (tension positiv) is used for capillary stresses. -> New formalism needs to be tested!!!",,initRun=true;); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(CapillaryStressRecorder); trunk-2017.01a/pkg/dem/CapillaryTriaxialTest.cpp000066400000000000000000000445351304022710500215050ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * Copyright (C) 2006 by luc Scholtes * * luc.scholtes@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "CapillaryTriaxialTest.hpp" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include // random #include #include #include #include typedef pair BasicSphere; //! generate a list of non-overlapping spheres string GenerateCloud_water(vector& sphere_list, Vector3r lowerCorner, Vector3r upperCorner, long number, Real rad_std_dev, Real porosity); CapillaryTriaxialTest::~CapillaryTriaxialTest () { } bool CapillaryTriaxialTest::generate(std::string& message) { // unsigned int startId=boost::numeric::bounds::highest(), endId=0; // record forces from group 2 message=""; scene = shared_ptr(new Scene); createActors(scene); positionRootBody(scene); shared_ptr body; if(boxWalls) { // bottom box Vector3r center = Vector3r( (lowerCorner[0]+upperCorner[0])/2, lowerCorner[1]-thickness/2.0, (lowerCorner[2]+upperCorner[2])/2); Vector3r halfSize = Vector3r( wallOversizeFactor*std::abs(lowerCorner[0]-upperCorner[0])/2+thickness, thickness/2.0, wallOversizeFactor*std::abs(lowerCorner[2]-upperCorner[2])/2+thickness); createBox(body,center,halfSize,wall_bottom_wire); if(wall_bottom) { scene->bodies->insert(body); triaxialcompressionEngine->wall_bottom_id = body->getId(); //triaxialStateRecorder->wall_bottom_id = body->getId(); } //forcerec->id = body->getId(); // top box center = Vector3r( (lowerCorner[0]+upperCorner[0])/2, upperCorner[1]+thickness/2.0, (lowerCorner[2]+upperCorner[2])/2); halfSize = Vector3r( wallOversizeFactor*std::abs(lowerCorner[0]-upperCorner[0])/2+thickness, thickness/2.0, wallOversizeFactor*std::abs(lowerCorner[2]-upperCorner[2])/2+thickness); createBox(body,center,halfSize,wall_top_wire); if(wall_top) { scene->bodies->insert(body); triaxialcompressionEngine->wall_top_id = body->getId(); //triaxialStateRecorder->wall_top_id = body->getId(); } // box 1 center = Vector3r( lowerCorner[0]-thickness/2.0, (lowerCorner[1]+upperCorner[1])/2, (lowerCorner[2]+upperCorner[2])/2); halfSize = Vector3r( thickness/2.0, wallOversizeFactor*std::abs(lowerCorner[1]-upperCorner[1])/2+thickness, wallOversizeFactor*std::abs(lowerCorner[2]-upperCorner[2])/2+thickness); createBox(body,center,halfSize,wall_1_wire); if(wall_1) { scene->bodies->insert(body); triaxialcompressionEngine->wall_left_id = body->getId(); //triaxialStateRecorder->wall_left_id = body->getId(); } // box 2 center = Vector3r( upperCorner[0]+thickness/2.0, (lowerCorner[1]+upperCorner[1])/2, (lowerCorner[2]+upperCorner[2])/2); halfSize = Vector3r( thickness/2.0, wallOversizeFactor*std::abs(lowerCorner[1]-upperCorner[1])/2+thickness, wallOversizeFactor*std::abs(lowerCorner[2]-upperCorner[2])/2+thickness); createBox(body,center,halfSize,wall_2_wire); if(wall_2) { scene->bodies->insert(body); triaxialcompressionEngine->wall_right_id = body->getId(); //triaxialStateRecorder->wall_right_id = body->getId(); } // box 3 center = Vector3r( (lowerCorner[0]+upperCorner[0])/2, (lowerCorner[1]+upperCorner[1])/2, lowerCorner[2]-thickness/2.0); halfSize = Vector3r( wallOversizeFactor*std::abs(lowerCorner[0]-upperCorner[0])/2+thickness, wallOversizeFactor*std::abs(lowerCorner[1]-upperCorner[1])/2+thickness, thickness/2.0); createBox(body,center,halfSize,wall_3_wire); if(wall_3) { scene->bodies->insert(body); triaxialcompressionEngine->wall_back_id = body->getId(); //triaxialStateRecorder->wall_back_id = body->getId(); } // box 4 center = Vector3r( (lowerCorner[0]+upperCorner[0])/2, (lowerCorner[1]+upperCorner[1])/2, upperCorner[2]+thickness/2.0); halfSize = Vector3r( wallOversizeFactor*std::abs(lowerCorner[0]-upperCorner[0])/2+thickness, wallOversizeFactor*std::abs(lowerCorner[1]-upperCorner[1])/2+thickness, thickness/2.0); createBox(body,center,halfSize,wall_3_wire); if(wall_4) { scene->bodies->insert(body); triaxialcompressionEngine->wall_front_id = body->getId(); //triaxialStateRecorder->wall_front_id = body->getId(); } } //convert the original sphere vector (with clump info) to a BasicSphere vector. vector sphere_list; typedef boost::tuple tupleVector3rRealInt; if(importFilename!=""){ vector >sphereListClumpInfo = Shop::loadSpheresFromFile(importFilename,lowerCorner,upperCorner); FOREACH(tupleVector3rRealInt t, sphereListClumpInfo){ sphere_list.push_back(make_pair(boost::get<0>(t),boost::get<1>(t))); }; } else message+=GenerateCloud_water(sphere_list, lowerCorner, upperCorner, numberOfGrains, Rdispersion, 0.75); vector::iterator it = sphere_list.begin(); vector::iterator it_end = sphere_list.end(); for (;it!=it_end; ++it) { cerr << "sphere (" << it->first << " " << it->second << ")"<first,it->second,false,true); scene->bodies->insert(body); } return true; // return "Generated a sample inside box of dimensions: (" // + boost::lexical_cast(lowerCorner[0]) + "," // + boost::lexical_cast(lowerCorner[1]) + "," // + boost::lexical_cast(lowerCorner[2]) + ") and (" // + boost::lexical_cast(upperCorner[0]) + "," // + boost::lexical_cast(upperCorner[1]) + "," // + boost::lexical_cast(upperCorner[2]) + ")."; } void CapillaryTriaxialTest::createSphere(shared_ptr& body, Vector3r position, Real radius, bool big, bool dynamic ) { body = shared_ptr(new Body); body->groupMask=2; shared_ptr physics(new FrictMat); shared_ptr aabb(new Aabb); shared_ptr iSphere(new Sphere); Quaternionr q(Mathr::SymmetricRandom(),Mathr::SymmetricRandom(),Mathr::SymmetricRandom(),Mathr::SymmetricRandom()); q.normalize(); // q.FromAxisAngle( Vector3r(0,0,1),0); body->setDynamic(dynamic); body->state->angVel = Vector3r(0,0,0); body->state->vel = Vector3r(0,0,0); body->state->mass = 4.0/3.0*Mathr::PI*radius*radius*radius*density; body->state->inertia = Vector3r( 2.0/5.0*body->state->mass*radius*radius, 2.0/5.0*body->state->mass*radius*radius, 2.0/5.0*body->state->mass*radius*radius); body->state->se3 = Se3r(position,q); physics->young = sphereYoungModulus; physics->poisson = sphereKsDivKn; physics->frictionAngle = sphereFrictionDeg * Mathr::PI/180.0; if((!dynamic) && (!boxWalls)) { physics->young = boxYoungModulus; physics->poisson = boxKsDivKn; physics->frictionAngle = boxFrictionDeg * Mathr::PI/180.0; } aabb->color = Vector3r(0,1,0); iSphere->radius = radius; iSphere->color = Vector3r(Mathr::UnitRandom(),Mathr::UnitRandom(),Mathr::UnitRandom()); iSphere->wire = false; body->shape = iSphere; body->bound = aabb; body->material = physics; } void CapillaryTriaxialTest::createBox(shared_ptr& body, Vector3r position, Vector3r extents, bool wire) { body = shared_ptr(new Body); body->groupMask=2; shared_ptr physics(new FrictMat); shared_ptr aabb(new Aabb); shared_ptr iBox(new Box); body->setDynamic(false); body->state->angVel = Vector3r(0,0,0); body->state->vel = Vector3r(0,0,0); body->state->mass = 0; //physics->mass = extents[0]*extents[1]*extents[2]*density*2; body->state->inertia = Vector3r( body->state->mass*(extents[1]*extents[1]+extents[2]*extents[2])/3 , body->state->mass*(extents[0]*extents[0]+extents[2]*extents[2])/3 , body->state->mass*(extents[1]*extents[1]+extents[0]*extents[0])/3 ); // physics->mass = 0; // physics->inertia = Vector3r(0,0,0); body->state->se3 = Se3r(position,Quaternionr::Identity()); physics->young = boxYoungModulus; physics->poisson = boxKsDivKn; physics->frictionAngle = boxFrictionDeg * Mathr::PI/180.0; aabb->color = Vector3r(1,0,0); iBox->extents = extents; iBox->color = Vector3r(1,1,1); iBox->wire = wire; body->bound = aabb; body->shape = iBox; body->material = physics; } void CapillaryTriaxialTest::createActors(shared_ptr& scene) { Real distanceFactor = 1.3;//Create potential interactions as soon as the distance is less than factor*(rad1+rad2) shared_ptr interactionGeometryDispatcher(new IGeomDispatcher); shared_ptr iS2IS4SContactGeometry(new Ig2_Sphere_Sphere_ScGeom); iS2IS4SContactGeometry->interactionDetectionFactor = distanceFactor;//Detect potential distant interaction (meniscii) interactionGeometryDispatcher->add(iS2IS4SContactGeometry); interactionGeometryDispatcher->add(new Ig2_Box_Sphere_ScGeom); shared_ptr interactionPhysicsDispatcher(new IPhysDispatcher); // interactionPhysicsDispatcher->add("Ip2_FrictMat_FrictMat_FrictPhys"); // Unhandled exception: St13runtime_error : Class `Ip2_FrictMat_FrictMat_FrictPhys' could not be cast to required 2D Functor /// OLD //interactionPhysicsDispatcher->add("BodyMacroParameters","BodyMacroParameters","MacroMicroElasticRelationshipsWater"); /// NEW shared_ptr ss(new Ip2_FrictMat_FrictMat_CapillaryPhys); interactionPhysicsDispatcher->add(ss); shared_ptr boundDispatcher = shared_ptr(new BoundDispatcher); shared_ptr collider(new InsertionSortCollider); shared_ptr bo1sphere(new Bo1_Sphere_Aabb); bo1sphere->aabbEnlargeFactor = distanceFactor;//Detect potential distant interaction (meniscii) collider->boundDispatcher->add(bo1sphere); collider->boundDispatcher->add(new Bo1_Box_Aabb); shared_ptr gravityCondition(new GravityEngine); gravityCondition->gravity = gravity; shared_ptr globalStiffnessTimeStepper(new GlobalStiffnessTimeStepper); globalStiffnessTimeStepper->timeStepUpdateInterval = timeStepUpdateInterval; globalStiffnessTimeStepper->defaultDt = defaultDt; shared_ptr elasticContactLaw(new ElasticContactLaw); elasticContactLaw->neverErase = true; // capillary shared_ptr capillaryCohesiveLaw(new Law2_ScGeom_CapillaryPhys_Capillarity); capillaryCohesiveLaw->capillaryPressure = capillaryPressure; // capillaryCohesiveLaw->fusionDetection = fusionDetection; // capillaryCohesiveLaw->binaryFusion = binaryFusion; //shared_ptr stiffnesscounter(new StiffnessCounter); //stiffnesscounter->interval = timeStepUpdateInterval; // moving walls to regulate the stress applied + compress when the packing is dense an stable //cerr << "triaxialcompressionEngine = shared_ptr (new TriaxialCompressionEngine);" << std::endl; triaxialcompressionEngine = shared_ptr (new TriaxialCompressionEngine); triaxialcompressionEngine-> stiffnessUpdateInterval = wallStiffnessUpdateInterval;// = stiffness update interval triaxialcompressionEngine-> radiusControlInterval = radiusControlInterval;// = stiffness update interval triaxialcompressionEngine-> sigmaIsoCompaction = sigmaIsoCompaction; triaxialcompressionEngine-> sigmaLateralConfinement = sigmaLateralConfinement; triaxialcompressionEngine->max_vel = maxWallVelocity; triaxialcompressionEngine-> thickness = thickness; triaxialcompressionEngine->strainRate = strainRate; triaxialcompressionEngine->StabilityCriterion = StabilityCriterion; triaxialcompressionEngine->autoCompressionActivation = autoCompressionActivation; triaxialcompressionEngine->internalCompaction = internalCompaction; triaxialcompressionEngine->maxMultiplier = maxMultiplier; triaxialcompressionEngine->finalMaxMultiplier = finalMaxMultiplier; triaxialcompressionEngine->Key = Key; triaxialcompressionEngine->frictionAngleDegree = sphereFrictionDeg; //cerr << "fin de section triaxialcompressionEngine = shared_ptr (new TriaxialCompressionEngine);" << std::endl; // recording global stress triaxialStateRecorder = shared_ptr(new TriaxialStateRecorder); triaxialStateRecorder-> file = WallStressRecordFile + Key; triaxialStateRecorder-> iterPeriod = recordIntervalIter; //triaxialStateRecorderer-> thickness = thickness; // recording capillary stress capillaryStressRecorder = shared_ptr(new CapillaryStressRecorder); capillaryStressRecorder -> file = capillaryStressRecordFile + Key; capillaryStressRecorder -> iterPeriod = recordIntervalIter; #if 0 // moving walls to regulate the stress applied //cerr << "triaxialstressController = shared_ptr (new TriaxialStressController);" << std::endl; triaxialstressController = shared_ptr (new TriaxialStressController); triaxialstressController-> stiffnessUpdateInterval = 20;// = recordIntervalIter triaxialstressController-> sigma_iso = sigma_iso; triaxialstressController-> max_vel = 0.0001; triaxialstressController-> thickness = thickness; triaxialstressController->wall_bottom_activated = false; triaxialstressController->wall_top_activated = false; //cerr << "fin de sezction triaxialstressController = shared_ptr (new TriaxialStressController);" << std::endl; #endif scene->engines.clear(); scene->engines.push_back(shared_ptr(new ForceResetter)); // scene->engines.push_back(sdecTimeStepper); scene->engines.push_back(collider); scene->engines.push_back(interactionGeometryDispatcher); scene->engines.push_back(interactionPhysicsDispatcher); scene->engines.push_back(elasticContactLaw); // capillary //scene->engines.push_back(stiffnesscounter); //scene->engines.push_back(stiffnessMatrixTimeStepper); scene->engines.push_back(globalStiffnessTimeStepper); if(water) { scene->engines.push_back(capillaryCohesiveLaw); scene->engines.push_back(capillaryStressRecorder); } scene->engines.push_back(triaxialcompressionEngine); scene->engines.push_back(triaxialStateRecorder); //scene->engines.push_back(gravityCondition); scene->engines.push_back(shared_ptr (new NewtonIntegrator)); //if(!rotationBlocked) // scene->engines.push_back(orientationIntegrator); //scene->engines.push_back(triaxialstressController); } void CapillaryTriaxialTest::positionRootBody(shared_ptr& scene) { } string GenerateCloud_water(vector& sphere_list, Vector3r lowerCorner, Vector3r upperCorner, long number, Real rad_std_dev, Real porosity) { typedef boost::minstd_rand StdGenerator; static StdGenerator generator; static boost::variate_generator > random1(generator, boost::uniform_real<>(0,1)); // static boost::variate_generator > // randomN(generator, boost::normal_distribution<>(aggregateMeanRadius,aggregateSigmaRadius)); sphere_list.clear(); long tries = 1000; //nb of tries for positionning the next sphere Vector3r dimensions = upperCorner - lowerCorner; Real mean_radius = std::pow(dimensions.x()*dimensions.y()*dimensions.z()*(1-porosity)/(3.1416*1.3333*number),0.333333); //cerr << mean_radius; Real Rmin=mean_radius, Rmax=mean_radius; std::cerr << "generating aggregates ... "; long t, i; for (i=0; i (sphere_list[j].first-s.first).squaredNorm()) overlap=true; if (!overlap){ sphere_list.push_back(s); Rmin = std::min(Rmin,s.second); Rmax = std::max(Rmax,s.second); break;} } if (t==tries) return "More than " + boost::lexical_cast(tries) + " tries while generating sphere number " + boost::lexical_cast(i+1) + "/" + boost::lexical_cast(number) + "."; } return "Generated a sample with " + boost::lexical_cast(number) + "spheres inside box of dimensions: (" + boost::lexical_cast(dimensions[0]) + "," + boost::lexical_cast(dimensions[1]) + "," + boost::lexical_cast(dimensions[2]) + ")." + " mean radius=" + boost::lexical_cast(mean_radius) + + " Rmin =" + boost::lexical_cast(Rmin) + + " Rmax =" + boost::lexical_cast(Rmax) + "."; } YADE_PLUGIN((CapillaryTriaxialTest)); trunk-2017.01a/pkg/dem/CapillaryTriaxialTest.hpp000066400000000000000000000225711304022710500215060ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * Copyright (C) 2006 by luc Scholtes * * luc.scholtes@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include class ForceRecorder; class AveragePositionRecorder; class VelocityRecorder; class TriaxialStressController; class TriaxialCompressionEngine; class TriaxialStateRecorder; class CapillaryStressRecorder; class GlobalStiffnessTimeStepper; /*! \brief Triaxial test on unsaturated sphere packings This preprocessor is a variant of TriaxialTest, including the model of capillary forces developed as part of the PhD of Luc Scholtès. See the documentation of Law2_ScGeom_CapillaryPhys_Capillarity or the main page https://yade-dem.org/wiki/CapillaryTriaxialTest, for more details. Results obtained with this preprocessor were reported for instance in "Scholtes et al. Micromechanics of granular materials with capillary effects. International Journal of Engineering Science 2009,(47)1, 64-75." */ class CapillaryTriaxialTest : public FileGenerator { private : Vector3r gravity; Vector3r spheresColor; bool wall_top ,wall_bottom ,wall_1 ,wall_2 ,wall_3 ,wall_4 ,wall_top_wire ,wall_bottom_wire ,wall_1_wire ,wall_2_wire ,wall_3_wire ,wall_4_wire ,spheresRandomColor; shared_ptr triaxialcompressionEngine; shared_ptr triaxialstressController; shared_ptr triaxialStateRecorder; shared_ptr capillaryStressRecorder; shared_ptr globalStiffnessTimeStepper; void createBox(shared_ptr& body, Vector3r position, Vector3r extents,bool wire); void createSphere(shared_ptr& body, Vector3r position, Real radius,bool big,bool dynamic); void createActors(shared_ptr& scene); void positionRootBody(shared_ptr& scene); typedef pair BasicSphere; public : ~CapillaryTriaxialTest (); bool generate(std::string& message); YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY( CapillaryTriaxialTest,FileGenerator,"This preprocessor is a variant of TriaxialTest, including the model of capillary forces developed as part of the PhD of Luc Scholtès. See the documentation of Law2_ScGeom_CapillaryPhys_Capillarity or the main page https://yade-dem.org/wiki/CapillaryTriaxialTest, for more details.\n\n Results obtained with this preprocessor were reported for instance in 'Scholtes et al. Micromechanics of granular materials with capillary effects. International Journal of Engineering Science 2009,(47)1, 64-75.'" , ((Vector3r,lowerCorner,Vector3r(0,0,0),,"Lower corner of the box.")) ((Vector3r,upperCorner,Vector3r(1,1,1),,"Upper corner of the box.")) ((string,importFilename,"",,"File with positions and sizes of spheres.")) ((string,Key,"",,"A code that is added to output filenames.")) ((string,fixedBoxDims,"",,"string that contains some subset (max. 2) of {'x','y','z'} ; contains axes will have box dimension hardcoded, even if box is scaled as mean_radius is prescribed: scaling will be applied on the rest.")) ((Real,capillaryPressure,0,,"Define succion in the packing [Pa]. This is the value used in the capillary model.")) ((bool,water,true,,"activate capillary model")) ((bool,fusionDetection,false,,"test overlaps between liquid bridges on modify forces if overlaps exist")) ((bool,binaryFusion,true,,"Defines how overlapping bridges affect the capillary forces (see :yref:`CapillaryTriaxialTest::fusionDetection`). If binary=true, the force is null as soon as there is an overlap detected, if not, the force is divided by the number of overlaps.")) ((string,WallStressRecordFile,"./WallStressesWater"+Key,,"")) ((string,capillaryStressRecordFile,"./capStresses"+Key,,"")) ((string,contactStressRecordFile,"./contStresses"+Key,,"")) ((bool,internalCompaction,false,,"flag for choosing between moving boundaries or increasing particles sizes during the compaction stage.")) ((bool,biaxial2dTest,false,,"FIXME : what is that?")) ((bool,fixedPoroCompaction,false,,"flag to choose an isotropic compaction until a fixed porosity choosing a same translation speed for the six walls")) ((bool,autoCompressionActivation,true,,"Do we just want to generate a stable packing under isotropic pressure (false) or do we want the triaxial loading to start automatically right after compaction stage (true)?")) ((bool,autoUnload,true,,"auto adjust the isotropic stress state from :yref:`TriaxialTest::sigmaIsoCompaction` to :yref:`TriaxialTest::sigmaLateralConfinement` if they have different values. See docs for :yref:`TriaxialCompressionEngine::autoUnload`")) ((bool,autoStopSimulation,false,,"freeze the simulation when conditions are reached (don't activate this if you want to be able to run/stop from Qt GUI)")) ((bool,noFiles,false,,"Do not create any files during run (.xml, .spheres, wall stress records)")) ((bool,facetWalls,false,,"Use facets for boundaries (not tested)")) ((bool,wallWalls,false,,"Use walls for boundaries (not tested)")) ((bool,boxWalls,true,,"Use boxes for boundaries (recommended).")) ((Real,fixedPorosity,1,,"FIXME : what is that?")) ((Real,thickness,0.001,,"thickness of boundaries. It is arbitrary and should have no effect")) ((Real,maxMultiplier,1.01,,"max multiplier of diameters during internal compaction (initial fast increase)")) ((Real,finalMaxMultiplier,1.001,,"max multiplier of diameters during internal compaction (secondary precise adjustment)")) ((Real,Rdispersion,0.3,,"Normalized standard deviation of generated sizes.")) ((Real,radiusMean,-1,,"Mean radius. If negative (default), autocomputed to as a function of box size and :yref:`TriaxialTest::numberOfGrains`")) ((Real,sphereYoungModulus,15000000.0,,"Stiffness of spheres.")) ((Real,sphereKsDivKn,0.5,,"Ratio of shear vs. normal contact stiffness for spheres.")) ((Real,sphereFrictionDeg,18.0,,"Friction angle [°] of spheres assigned just before triaxial testing.")) ((Real,compactionFrictionDeg,sphereFrictionDeg,,"Friction angle [°] of spheres during compaction (different values result in different porosities)]. This value is overridden by :yref:`TriaxialTest::sphereFrictionDeg` before triaxial testing.")) ((Real,boxYoungModulus,15000000.0,,"Stiffness of boxes.")) ((Real,maxWallVelocity,10,,"max velocity of boundaries. Usually useless, but can help stabilizing the system in some cases.")) ((Real,boxKsDivKn,0.5,,"Ratio of shear vs. normal contact stiffness for boxes.")) ((Real,boxFrictionDeg,0.0,,"Friction angle [°] of boundaries contacts.")) ((Real,density,2600,,"density of spheres")) ((Real,strainRate,1,,"Strain rate in triaxial loading.")) ((Real,defaultDt,0.0001,,"Max time-step. Used as initial value if defined. Latter adjusted by the time stepper.")) ((Real,dampingForce,0.2,,"Coefficient of Cundal-Non-Viscous damping (applied on on the 3 components of forces)")) ((Real,dampingMomentum,0.2,,"Coefficient of Cundal-Non-Viscous damping (applied on on the 3 components of torques)")) ((Real,StabilityCriterion,0.01,,"Value of unbalanced force for which the system is considered stable. Used in conditionals to switch between loading stages.")) ((Real,wallOversizeFactor,1.3,,"Make boundaries larger than the packing to make sure spheres don't go out during deformation.")) ((Real,sigmaIsoCompaction,-50000,,"Confining stress during isotropic compaction (< 0 for real - compressive - compaction).")) ((Real,sigmaLateralConfinement,-50000,,"Lateral stress during triaxial loading (< 0 for classical compressive cases). An isotropic unloading is performed if the value is not equal to :yref:`CapillaryTriaxialTest::SigmaIsoCompaction`.")) ((int,timeStepUpdateInterval,50,,"interval for :yref:`GlobalStiffnessTimeStepper`")) ((int,timeStepOutputInterval,50,,"interval for outputing general information on the simulation (stress,unbalanced force,...)")) ((int,wallStiffnessUpdateInterval,10,,"interval for updating the stiffness of sample/boundaries contacts")) ((int,radiusControlInterval,10,,"interval between size changes when growing spheres.")) ((int,numberOfGrains,400,,"Number of generated spheres.")) ((int,recordIntervalIter,20,,"interval between file outputs")) , /* init */ , /* constructor */ wall_top = true; wall_bottom = true; wall_1 = true; wall_2 = true; wall_3 = true; wall_4 = true; wall_top_wire = true; wall_bottom_wire = true; wall_1_wire = true; wall_2_wire = true; wall_3_wire = true; wall_4_wire = true; spheresColor = Vector3r(0.8,0.3,0.3); spheresRandomColor = false; WallStressRecordFile = "./WallStresses"+Key; gravity = Vector3r(0,-9.81,0); , //.def("setContactProperties",&TriaxialCompressionEngine::setContactProperties,"Assign a new friction angle (degrees) to dynamic bodies and relative interactions") ); // DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(CapillaryTriaxialTest); trunk-2017.01a/pkg/dem/CohesiveFrictionalContactLaw.cpp000066400000000000000000000335521304022710500227640ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2007 by Bruno Chareyre * * Copyright (C) 2008 by Janek Kozicki * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "CohesiveFrictionalContactLaw.hpp" #include #include #include YADE_PLUGIN((CohesiveFrictionalContactLaw)(Law2_ScGeom6D_CohFrictPhys_CohesionMoment)(CohFrictMat)(CohFrictPhys)(Ip2_CohFrictMat_CohFrictMat_CohFrictPhys)); CREATE_LOGGER(Law2_ScGeom6D_CohFrictPhys_CohesionMoment); Real Law2_ScGeom6D_CohFrictPhys_CohesionMoment::getPlasticDissipation() {return (Real) plasticDissipation;} void Law2_ScGeom6D_CohFrictPhys_CohesionMoment::initPlasticDissipation(Real initVal) {plasticDissipation.reset(); plasticDissipation+=initVal;} Vector3r CohFrictPhys::getRotStiffness() {return Vector3r(ktw,kr,kr);} Real Law2_ScGeom6D_CohFrictPhys_CohesionMoment::normElastEnergy() { Real normEnergy=0; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; CohFrictPhys* phys = YADE_CAST(I->phys.get()); if (phys) { normEnergy += 0.5*(phys->normalForce.squaredNorm()/phys->kn); } } return normEnergy; } Real Law2_ScGeom6D_CohFrictPhys_CohesionMoment::shearElastEnergy() { Real shearEnergy=0; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; CohFrictPhys* phys = YADE_CAST(I->phys.get()); if (phys) { shearEnergy += 0.5*(phys->shearForce.squaredNorm()/phys->ks); } } return shearEnergy; } Real Law2_ScGeom6D_CohFrictPhys_CohesionMoment::bendingElastEnergy() { Real bendingEnergy=0; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; CohFrictPhys* phys = YADE_CAST(I->phys.get()); if (phys) { bendingEnergy += 0.5*(phys->moment_bending.squaredNorm()/phys->kr); } } return bendingEnergy; } Real Law2_ScGeom6D_CohFrictPhys_CohesionMoment::twistElastEnergy() { Real twistEnergy=0; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; CohFrictPhys* phys = YADE_CAST(I->phys.get()); if (phys) { twistEnergy += 0.5*(phys->moment_twist.squaredNorm()/phys->ktw); } } return twistEnergy; } Real Law2_ScGeom6D_CohFrictPhys_CohesionMoment::totalElastEnergy() { Real totalEnergy=0; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; CohFrictPhys* phys = YADE_CAST(I->phys.get()); if (phys) { totalEnergy += 0.5*(phys->normalForce.squaredNorm()/phys->kn); totalEnergy += 0.5*(phys->shearForce.squaredNorm()/phys->ks); totalEnergy += 0.5*(phys->moment_bending.squaredNorm()/phys->kr); totalEnergy += 0.5*(phys->moment_twist.squaredNorm()/phys->ktw); } } return totalEnergy; } void CohesiveFrictionalContactLaw::action() { if(!functor) functor=shared_ptr(new Law2_ScGeom6D_CohFrictPhys_CohesionMoment); functor->always_use_moment_law = always_use_moment_law; functor->shear_creep=shear_creep; functor->twist_creep=twist_creep; functor->creep_viscosity=creep_viscosity; functor->scene=scene; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; functor->go(I->geom, I->phys, I.get());} } bool Law2_ScGeom6D_CohFrictPhys_CohesionMoment::go(shared_ptr& ig, shared_ptr& ip, Interaction* contact) { const Real& dt = scene->dt; const int &id1 = contact->getId1(); const int &id2 = contact->getId2(); ScGeom6D* geom = YADE_CAST (ig.get()); CohFrictPhys* phys = YADE_CAST (ip.get()); Vector3r& shearForce = phys->shearForce; if (contact->isFresh(scene)) shearForce = Vector3r::Zero(); Real un = geom->penetrationDepth; Real Fn = phys->kn*(un-phys->unp); if (phys->fragile && (-Fn)> phys->normalAdhesion) { // BREAK due to tension return false; } else { if ((-Fn)> phys->normalAdhesion) {//normal plasticity Fn=-phys->normalAdhesion; phys->unp = un+phys->normalAdhesion/phys->kn; if (phys->unpMax>=0 && -phys->unp>phys->unpMax) // Actually unpMax should be defined as a function of the average particule sizes for instance return false; } phys->normalForce = Fn*geom->normal; State* de1 = Body::byId(id1,scene)->state.get(); State* de2 = Body::byId(id2,scene)->state.get(); ///////////////////////// CREEP START /////////// if (shear_creep) shearForce -= phys->ks*(shearForce*dt/creep_viscosity); ///////////////////////// CREEP END //////////// Vector3r& shearForce = geom->rotate(phys->shearForce); const Vector3r& dus = geom->shearIncrement(); //Linear elasticity giving "trial" shear force shearForce -= phys->ks*dus; Real Fs = phys->shearForce.norm(); Real maxFs = phys->shearAdhesion; if (!phys->cohesionDisablesFriction || maxFs==0) maxFs += Fn*phys->tangensOfFrictionAngle; maxFs = std::max((Real) 0, maxFs); if (Fs > maxFs) {//Plasticity condition on shear force if (phys->fragile && !phys->cohesionBroken) { phys->SetBreakingState(); maxFs = max((Real) 0, Fn*phys->tangensOfFrictionAngle); } maxFs = maxFs / Fs; Vector3r trialForce=shearForce; shearForce *= maxFs; if (scene->trackEnergy || traceEnergy){ Real sheardissip=((1/phys->ks)*(trialForce-shearForce))/*plastic disp*/ .dot(shearForce)/*active force*/; if(sheardissip>0) { plasticDissipation+=sheardissip; if (scene->trackEnergy) scene->energy->add(sheardissip,"shearDissip",shearDissipIx,/*reset*/false);} } if (Fn<0) phys->normalForce = Vector3r::Zero();//Vector3r::Zero() } //Apply the force applyForceAtContactPoint(-phys->normalForce-shearForce, geom->contactPoint, id1, de1->se3.position, id2, de2->se3.position + (scene->isPeriodic ? scene->cell->intrShiftPos(contact->cellDist): Vector3r::Zero())); /// Moment law /// if (phys->momentRotationLaw && (!phys->cohesionBroken || always_use_moment_law)) { if (!useIncrementalForm){ if (twist_creep) { Real viscosity_twist = creep_viscosity * std::pow((2 * std::min(geom->radius1,geom->radius2)),2) / 16.0; Real angle_twist_creeped = geom->getTwist() * (1 - dt/viscosity_twist); Quaternionr q_twist(AngleAxisr(geom->getTwist(),geom->normal)); Quaternionr q_twist_creeped(AngleAxisr(angle_twist_creeped,geom->normal)); Quaternionr q_twist_delta(q_twist_creeped * q_twist.conjugate()); geom->twistCreep = geom->twistCreep * q_twist_delta; } phys->moment_twist = (geom->getTwist()*phys->ktw)*geom->normal; phys->moment_bending = geom->getBending() * phys->kr; } else{ // Use incremental formulation to compute moment_twis and moment_bending (no twist_creep is applied) if (twist_creep) throw std::invalid_argument("Law2_ScGeom6D_CohFrictPhys_CohesionMoment: no twis creep is included if the incremental form for the rotations is used."); Vector3r relAngVel = geom->getRelAngVel(de1,de2,dt); // *** Bending ***// Vector3r relAngVelBend = relAngVel - geom->normal.dot(relAngVel)*geom->normal; // keep only the bending part Vector3r relRotBend = relAngVelBend*dt; // relative rotation due to rolling behaviour // incremental formulation for the bending moment (as for the shear part) Vector3r& momentBend = phys->moment_bending; momentBend = geom->rotate(momentBend); // rotate moment vector (updated) momentBend = momentBend-phys->kr*relRotBend; // ---------------------------------------------------------------------------------------- // *** Torsion ***// Vector3r relAngVelTwist = geom->normal.dot(relAngVel)*geom->normal; Vector3r relRotTwist = relAngVelTwist*dt; // component of relative rotation along n FIXME: sign? // incremental formulation for the torsional moment Vector3r& momentTwist = phys->moment_twist; momentTwist = geom->rotate(momentTwist); // rotate moment vector (updated) momentTwist = momentTwist-phys->ktw*relRotTwist; // FIXME: sign? } /// Plasticity /// // limit rolling moment to the plastic value, if required if (phys->maxRollPl>=0.){ // do we want to apply plasticity? Real RollMax = phys->maxRollPl*phys->normalForce.norm(); if (!useIncrementalForm) LOG_WARN("If :yref:`Law2_ScGeom6D_CohFrictPhys_CohesionMoment::useIncrementalForm` is false, then plasticity will not be applied correctly (the total formulation would not reproduce irreversibility)."); Real scalarRoll = phys->moment_bending.norm(); if (scalarRoll>RollMax){ // fix maximum rolling moment Real ratio = RollMax/scalarRoll; phys->moment_bending *= ratio; if (scene->trackEnergy){ Real bendingdissip=((1/phys->kr)*(scalarRoll-RollMax)*RollMax)/*active force*/; if(bendingdissip>0) scene->energy->add(bendingdissip,"bendingDissip",bendingDissipIx,/*reset*/false);} } } // limit twisting moment to the plastic value, if required if (phys->maxTwistPl>=0.){ // do we want to apply plasticity? Real TwistMax = phys->maxTwistPl*phys->normalForce.norm(); if (!useIncrementalForm) LOG_WARN("If :yref:`Law2_ScGeom6D_CohFrictPhys_CohesionMoment::useIncrementalForm` is false, then plasticity will not be applied correctly (the total formulation would not reproduce irreversibility)."); Real scalarTwist= phys->moment_twist.norm(); if (scalarTwist>TwistMax){ // fix maximum rolling moment Real ratio = TwistMax/scalarTwist; phys->moment_twist *= ratio; if (scene->trackEnergy){ Real twistdissip=((1/phys->ktw)*(scalarTwist-TwistMax)*TwistMax)/*active force*/; if(twistdissip>0) scene->energy->add(twistdissip,"twistDissip",twistDissipIx,/*reset*/false);} } } // Apply moments now Vector3r moment = phys->moment_twist + phys->moment_bending; scene->forces.addTorque(id1,-moment); scene->forces.addTorque(id2, moment); } /// Moment law END /// } return true; } void Ip2_CohFrictMat_CohFrictMat_CohFrictPhys::go(const shared_ptr& b1 // CohFrictMat , const shared_ptr& b2 // CohFrictMat , const shared_ptr& interaction) { CohFrictMat* sdec1 = static_cast(b1.get()); CohFrictMat* sdec2 = static_cast(b2.get()); ScGeom6D* geom = YADE_CAST(interaction->geom.get()); //Create cohesive interractions only once if (setCohesionNow && cohesionDefinitionIteration==-1) cohesionDefinitionIteration=scene->iter; if (setCohesionNow && cohesionDefinitionIteration!=-1 && cohesionDefinitionIteration!=scene->iter) { cohesionDefinitionIteration = -1; setCohesionNow = 0;} if (geom) { const auto normalAdhPreCalculated = (normalCohesion) ? (*normalCohesion)(b1->id,b2->id) : std::min(sdec1->normalCohesion,sdec2->normalCohesion); const auto shearAdhPreCalculated = (shearCohesion) ? (*shearCohesion)(b1->id,b2->id) : std::min(sdec1->shearCohesion,sdec2->shearCohesion); if (!interaction->phys) { interaction->phys = shared_ptr(new CohFrictPhys()); CohFrictPhys* contactPhysics = YADE_CAST(interaction->phys.get()); Real Ea = sdec1->young; Real Eb = sdec2->young; Real Va = sdec1->poisson; Real Vb = sdec2->poisson; Real Da = geom->radius1; Real Db = geom->radius2; Real fa = sdec1->frictionAngle; Real fb = sdec2->frictionAngle; Real Kn = 2.0*Ea*Da*Eb*Db/(Ea*Da+Eb*Db);//harmonic average of two stiffnesses // harmonic average of alphas parameters Real AlphaKr, AlphaKtw; if (sdec1->alphaKr && sdec2->alphaKr) AlphaKr = 2.0*sdec1->alphaKr*sdec2->alphaKr/(sdec1->alphaKr+sdec2->alphaKr); else AlphaKr = 0; if (sdec1->alphaKtw && sdec2->alphaKtw) AlphaKtw = 2.0*sdec1->alphaKtw*sdec2->alphaKtw/(sdec1->alphaKtw+sdec2->alphaKtw); else AlphaKtw=0; Real Ks; if (Va && Vb) Ks = 2.0*Ea*Da*Va*Eb*Db*Vb/(Ea*Da*Va+Eb*Db*Vb);//harmonic average of two stiffnesses with ks=V*kn for each sphere else Ks=0; contactPhysics->kr = Da*Db*Ks*AlphaKr; contactPhysics->ktw = Da*Db*Ks*AlphaKtw; contactPhysics->tangensOfFrictionAngle = std::tan(std::min(fa,fb)); if ((setCohesionOnNewContacts || setCohesionNow) && sdec1->isCohesive && sdec2->isCohesive) { contactPhysics->cohesionBroken = false; contactPhysics->normalAdhesion = normalAdhPreCalculated*pow(std::min(Db, Da),2); contactPhysics->shearAdhesion = shearAdhPreCalculated*pow(std::min(Db, Da),2); geom->initRotations(*(Body::byId(interaction->getId1(),scene)->state),*(Body::byId(interaction->getId2(),scene)->state)); contactPhysics->fragile=(sdec1->fragile || sdec2->fragile); } contactPhysics->kn = Kn; contactPhysics->ks = Ks; contactPhysics->maxRollPl = min(sdec1->etaRoll*Da,sdec2->etaRoll*Db); contactPhysics->maxTwistPl = min(sdec1->etaTwist*Da,sdec2->etaTwist*Db); contactPhysics->momentRotationLaw=(sdec1->momentRotationLaw && sdec2->momentRotationLaw); } else {// !isNew, but if setCohesionNow, all contacts are initialized like if they were newly created CohFrictPhys* contactPhysics = YADE_CAST(interaction->phys.get()); if ((setCohesionNow && sdec1->isCohesive && sdec2->isCohesive) || contactPhysics->initCohesion) { contactPhysics->cohesionBroken = false; contactPhysics->normalAdhesion = normalAdhPreCalculated*pow(std::min(geom->radius2, geom->radius1),2); contactPhysics->shearAdhesion = shearAdhPreCalculated*pow(std::min(geom->radius2, geom->radius1),2); geom->initRotations(*(Body::byId(interaction->getId1(),scene)->state),*(Body::byId(interaction->getId2(),scene)->state)); contactPhysics->fragile=(sdec1->fragile || sdec2->fragile); contactPhysics->initCohesion=false; } } } }; trunk-2017.01a/pkg/dem/CohesiveFrictionalContactLaw.hpp000066400000000000000000000311521304022710500227630ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2007 by Bruno Chareyre * * Copyright (C) 2008 by Janek Kozicki * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include #include #include #include #include // The following code was moved from CohFrictMat.hpp class CohFrictMat : public FrictMat { public : virtual ~CohFrictMat () {}; /// Serialization YADE_CLASS_BASE_DOC_ATTRS_CTOR(CohFrictMat,FrictMat,"", ((bool,isCohesive,true,,"")) ((Real,alphaKr,2.0,,"Dimensionless rolling stiffness.")) ((Real,alphaKtw,2.0,,"Dimensionless twist stiffness.")) ((Real,etaRoll,-1.,,"Dimensionless rolling (aka 'bending') strength. If negative, rolling moment will be elastic.")) ((Real,etaTwist,-1.,,"Dimensionless twisting strength. If negative, twist moment will be elastic.")) ((Real,normalCohesion,-1,,"Tensile strength, homogeneous to a pressure. If negative the normal force is purely elastic.")) ((Real,shearCohesion,-1,,"Shear strength, homogeneous to a pressure. If negative the shear force is purely elastic.")) ((bool,fragile,true,,"do cohesion disappear when contact strength is exceeded")) ((bool,momentRotationLaw,false,,"Use bending/twisting moment at contact. The contact will have moments only if both bodies have this flag true. See :yref:`CohFrictPhys::cohesionDisablesFriction` for details.")) , createIndex(); ); /// Indexable REGISTER_CLASS_INDEX(CohFrictMat,FrictMat); }; REGISTER_SERIALIZABLE(CohFrictMat); // The following code was moved from CohFrictPhys.hpp class CohFrictPhys : public FrictPhys { public : virtual ~CohFrictPhys() {}; void SetBreakingState() {cohesionBroken = true; normalAdhesion = 0; shearAdhesion = 0;}; virtual Vector3r getRotStiffness(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(CohFrictPhys,FrictPhys,"", ((bool,cohesionDisablesFriction,false,,"is shear strength the sum of friction and adhesion or only adhesion?")) ((bool,cohesionBroken,true,,"is cohesion active? Set to false at the creation of a cohesive contact, and set to true when a fragile contact is broken")) ((bool,fragile,true,,"do cohesion disappear when contact strength is exceeded?")) ((Real,kr,0,,"rotational stiffness [N.m/rad]")) ((Real,ktw,0,,"twist stiffness [N.m/rad]")) ((Real,maxRollPl,0.0,,"Coefficient of rolling friction (negative means elastic).")) ((Real,maxTwistPl,0.0,,"Coefficient of twisting friction (negative means elastic).")) ((Real,normalAdhesion,0,,"tensile strength")) ((Real,shearAdhesion,0,,"cohesive part of the shear strength (a frictional term might be added depending on :yref:`CohFrictPhys::cohesionDisablesFriction`)")) ((Real,unp,0,,"plastic normal displacement, only used for tensile behaviour and if :yref:`CohFrictPhys::fragile` =false.")) ((Real,unpMax,0,,"maximum value of plastic normal displacement (counted positively), after that the interaction breaks even if :yref:`CohFrictPhys::fragile` =false. A negative value (i.e. -1) means no maximum.")) ((bool,momentRotationLaw,false,,"use bending/twisting moment at contacts. See :yref:`Law2_ScGeom6D_CohFrictPhys_CohesionMoment::always_use_moment_law` for details.")) ((bool,initCohesion,false,,"Initialize the cohesive behaviour with current state as equilibrium state (same as :yref:`Ip2_CohFrictMat_CohFrictMat_CohFrictPhys::setCohesionNow` but acting on only one interaction)")) ((Real,creep_viscosity,-1,,"creep viscosity [Pa.s/m].")) // internal attributes ((Vector3r,moment_twist,Vector3r(0,0,0),,"Twist moment")) ((Vector3r,moment_bending,Vector3r(0,0,0),,"Bending moment")) , createIndex(); ); /// Indexable REGISTER_CLASS_INDEX(CohFrictPhys,FrictPhys); }; REGISTER_SERIALIZABLE(CohFrictPhys); class Law2_ScGeom6D_CohFrictPhys_CohesionMoment: public LawFunctor{ public: OpenMPAccumulator plasticDissipation; Real normElastEnergy(); Real shearElastEnergy(); Real bendingElastEnergy(); Real twistElastEnergy(); Real totalElastEnergy(); Real getPlasticDissipation(); void initPlasticDissipation(Real initVal=0); virtual bool go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Law2_ScGeom6D_CohFrictPhys_CohesionMoment,LawFunctor,"Law for linear traction-compression-bending-twisting, with cohesion+friction and Mohr-Coulomb plasticity surface. This law adds adhesion and moments to :yref:`Law2_ScGeom_FrictPhys_CundallStrack`.\n\nThe normal force is (with the convention of positive tensile forces) $F_n=min(k_n*(u_n-u_n^p), a_n)$, with $a_n$ the normal adhesion and $u_n^p$ the plastic part of normal displacement. The shear force is $F_s=k_s*u_s$, the plasticity condition defines the maximum value of the shear force, by default $F_s^{max}=F_n*tan(\\phi)+a_s$, with $\\phi$ the friction angle and $a_s$ the shear adhesion. If :yref:`CohFrictPhys::cohesionDisableFriction` is True, friction is ignored as long as adhesion is active, and the maximum shear force is only $F_s^{max}=a_s$.\n\nIf the maximum tensile or maximum shear force is reached and :yref:`CohFrictPhys::fragile` =True (default), the cohesive link is broken, and $a_n, a_s$ are set back to zero. If a tensile force is present, the contact is lost, else the shear strength is $F_s^{max}=F_n*tan(\\phi)$. If :yref:`CohFrictPhys::fragile` =False, the behaviour is perfectly plastic, and the shear strength is kept constant.\n\nIf :yref:`Law2_ScGeom6D_CohFrictPhys_CohesionMoment::momentRotationLaw` =True, bending and twisting moments are computed using a linear law with moduli respectively $k_t$ and $k_r$, so that the moments are : $M_b=k_b*\\Theta_b$ and $M_t=k_t*\\Theta_t$, with $\\Theta_{b,t}$ the relative rotations between interacting bodies (details can be found in [Bourrier2013]_). The maximum value of moments can be defined and takes the form of rolling friction. Cohesive -type moment may also be included in the future.\n\nCreep at contact is implemented in this law, as defined in [Hassan2010]_. If activated, there is a viscous behaviour of the shear and twisting components, and the evolution of the elastic parts of shear displacement and relative twist is given by $du_{s,e}/dt=-F_s/\\nu_s$ and $d\\Theta_{t,e}/dt=-M_t/\\nu_t$.", ((bool,neverErase,false,,"Keep interactions even if particles go away from each other (only in case another constitutive law is in the scene, e.g. :yref:`Law2_ScGeom_CapillaryPhys_Capillarity`)")) ((bool,always_use_moment_law,false,,"If true, use bending/twisting moments at all contacts. If false, compute moments only for cohesive contacts.")) ((bool,shear_creep,false,,"activate creep on the shear force, using :yref:`CohesiveFrictionalContactLaw::creep_viscosity`.")) ((bool,twist_creep,false,,"activate creep on the twisting moment, using :yref:`CohesiveFrictionalContactLaw::creep_viscosity`.")) ((bool,traceEnergy,false,,"Define the total energy dissipated in plastic slips at contacts. Note that it will not reflect any energy associated to de-bonding, as it may occur for fragile contacts, nor does it include plastic dissipation in traction.")) ((bool,useIncrementalForm,false,,"use the incremental formulation to compute bending and twisting moments. Creep on the twisting moment is not included in such a case.")) ((int,shearDissipIx,-1,(Attr::hidden|Attr::noSave),"Index for shear dissipation (with O.trackEnergy)")) ((int,bendingDissipIx,-1,(Attr::hidden|Attr::noSave),"Index for bending dissipation (with O.trackEnergy)")) ((int,twistDissipIx,-1,(Attr::hidden|Attr::noSave),"Index for twist dissipation (with O.trackEnergy)")) ((Real,creep_viscosity,1,,"creep viscosity [Pa.s/m]. probably should be moved to Ip2_CohFrictMat_CohFrictMat_CohFrictPhys.")) ,, .def("normElastEnergy",&Law2_ScGeom6D_CohFrictPhys_CohesionMoment::normElastEnergy,"Compute normal elastic energy.") .def("shearElastEnergy",&Law2_ScGeom6D_CohFrictPhys_CohesionMoment::shearElastEnergy,"Compute shear elastic energy.") .def("bendingElastEnergy",&Law2_ScGeom6D_CohFrictPhys_CohesionMoment::bendingElastEnergy,"Compute bending elastic energy.") .def("twistElastEnergy",&Law2_ScGeom6D_CohFrictPhys_CohesionMoment::twistElastEnergy,"Compute twist elastic energy.") .def("elasticEnergy",&Law2_ScGeom6D_CohFrictPhys_CohesionMoment::totalElastEnergy,"Compute total elastic energy.") .def("plasticDissipation",&Law2_ScGeom6D_CohFrictPhys_CohesionMoment::getPlasticDissipation,"Total energy dissipated in plastic slips at all CohFrictPhys contacts. Computed only if :yref:`Law2_ScGeom_FrictPhys_CundallStrack::traceEnergy` is true.") .def("initPlasticDissipation",&Law2_ScGeom6D_CohFrictPhys_CohesionMoment::initPlasticDissipation,"Initialize cummulated plastic dissipation to a value (0 by default).") ); FUNCTOR2D(ScGeom6D,CohFrictPhys); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_ScGeom6D_CohFrictPhys_CohesionMoment); class CohesiveFrictionalContactLaw : public GlobalEngine { shared_ptr functor; public : long iter;/// used for checking if new iteration void action(); YADE_CLASS_BASE_DOC_ATTRS(CohesiveFrictionalContactLaw,GlobalEngine,"[DEPRECATED] Loop over interactions applying :yref:`Law2_ScGeom6D_CohFrictPhys_CohesionMoment` on all interactions.\n\n.. note::\n Use :yref:`InteractionLoop` and :yref:`Law2_ScGeom6D_CohFrictPhys_CohesionMoment` instead of this class for performance reasons.", ((bool,neverErase,false,,"Keep interactions even if particles go away from each other (only in case another constitutive law is in the scene, e.g. :yref:`Law2_ScGeom_CapillaryPhys_Capillarity`)")) ((bool,always_use_moment_law,false,,"If true, use bending/twisting moments at all contacts. If false, compute moments only for cohesive contacts.")) ((bool,shear_creep,false,,"activate creep on the shear force, using :yref:`CohesiveFrictionalContactLaw::creep_viscosity`.")) ((bool,twist_creep,false,,"activate creep on the twisting moment, using :yref:`CohesiveFrictionalContactLaw::creep_viscosity`.")) ((Real,creep_viscosity,false,,"creep viscosity [Pa.s/m]. probably should be moved to Ip2_CohFrictMat_CohFrictMat_CohFrictPhys...")) ); }; REGISTER_SERIALIZABLE(CohesiveFrictionalContactLaw); // The following code was moved from Ip2_CohFrictMat_CohFrictMat_CohFrictPhys.hpp class Ip2_CohFrictMat_CohFrictMat_CohFrictPhys : public IPhysFunctor { public : virtual void go( const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction); int cohesionDefinitionIteration; YADE_CLASS_BASE_DOC_ATTRS_CTOR(Ip2_CohFrictMat_CohFrictMat_CohFrictPhys,IPhysFunctor, "Generates cohesive-frictional interactions with moments, used in the contact law :yref:`Law2_ScGeom6D_CohFrictPhys_CohesionMoment`. The normal/shear stiffness and friction definitions are the same as in :yref:`Ip2_FrictMat_FrictMat_FrictPhys`, check the documentation there for details.\n\nAdhesions related to the normal and the shear components are calculated from :yref:`CohFrictMat::normalCohesion` ($C_n$) and :yref:`CohFrictMat::shearCohesion` ($C_s$). For particles of size $R_1$,$R_2$ the adhesion will be $a_i=C_i min(R_1,R_2)^2$, $i=n,s$.\n\nTwist and rolling stiffnesses are proportional to the shear stiffness through dimensionless factors alphaKtw and alphaKr, such that the rotational stiffnesses are defined by $k_s \\alpha_i R_1 R_2$, $i=tw\\,r$", ((bool,setCohesionNow,false,,"If true, assign cohesion to all existing contacts in current time-step. The flag is turned false automatically, so that assignment is done in the current timestep only.")) ((bool,setCohesionOnNewContacts,false,,"If true, assign cohesion at all new contacts. If false, only existing contacts can be cohesive (also see :yref:`Ip2_CohFrictMat_CohFrictMat_CohFrictPhys::setCohesionNow`), and new contacts are only frictional.")) ((shared_ptr,normalCohesion,,,"Instance of :yref:`MatchMaker` determining tensile strength")) ((shared_ptr,shearCohesion,,,"Instance of :yref:`MatchMaker` determining cohesive part of the shear strength (a frictional term might be added depending on :yref:`CohFrictPhys::cohesionDisablesFriction`)")) , cohesionDefinitionIteration = -1; ); FUNCTOR2D(CohFrictMat,CohFrictMat); }; REGISTER_SERIALIZABLE(Ip2_CohFrictMat_CohFrictMat_CohFrictPhys); trunk-2017.01a/pkg/dem/CohesiveTriaxialTest.cpp000066400000000000000000000350421304022710500213230ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2007 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "CohesiveTriaxialTest.hpp" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include // random #include #include #include #include typedef pair BasicSphere; //! make a list of spheres non-overlapping sphere string GenerateCloud_cohesive(vector& sphere_list, Vector3r lowerCorner, Vector3r upperCorner, long number, Real rad_std_dev, Real porosity); CohesiveTriaxialTest::~CohesiveTriaxialTest (){} bool CohesiveTriaxialTest::generate(std::string& message) { // unsigned int startId=boost::numeric::bounds::highest(), endId=0; // record forces from group 2 scene = shared_ptr(new Scene); createActors(scene); positionRootBody(scene); shared_ptr body; if(boxWalls) { // bottom box Vector3r center = Vector3r( (lowerCorner[0]+upperCorner[0])/2, lowerCorner[1]-thickness/2.0, (lowerCorner[2]+upperCorner[2])/2); Vector3r halfSize = Vector3r( 1.5*std::abs(lowerCorner[0]-upperCorner[0])/2+thickness, thickness/2.0, 1.5*std::abs(lowerCorner[2]-upperCorner[2])/2+thickness); createBox(body,center,halfSize,wall_bottom_wire); if(wall_bottom) { scene->bodies->insert(body); triaxialcompressionEngine->wall_bottom_id = body->getId(); //triaxialStateRecorder->wall_bottom_id = body->getId(); // forcerec->startId = body->getId(); // forcerec->endId = body->getId(); } //forcerec->id = body->getId(); // top box center = Vector3r( (lowerCorner[0]+upperCorner[0])/2, upperCorner[1]+thickness/2.0, (lowerCorner[2]+upperCorner[2])/2); halfSize = Vector3r( 1.5*std::abs(lowerCorner[0]-upperCorner[0])/2+thickness, thickness/2.0, 1.5*std::abs(lowerCorner[2]-upperCorner[2])/2+thickness); createBox(body,center,halfSize,wall_top_wire); if(wall_top) { scene->bodies->insert(body); triaxialcompressionEngine->wall_top_id = body->getId(); //triaxialStateRecorder->wall_top_id = body->getId(); } // box 1 center = Vector3r( lowerCorner[0]-thickness/2.0, (lowerCorner[1]+upperCorner[1])/2, (lowerCorner[2]+upperCorner[2])/2); halfSize = Vector3r( thickness/2.0, 1.5*std::abs(lowerCorner[1]-upperCorner[1])/2+thickness, 1.5*std::abs(lowerCorner[2]-upperCorner[2])/2+thickness); createBox(body,center,halfSize,wall_1_wire); if(wall_1) { scene->bodies->insert(body); triaxialcompressionEngine->wall_left_id = body->getId(); //triaxialStateRecorder->wall_left_id = body->getId(); } // box 2 center = Vector3r( upperCorner[0]+thickness/2.0, (lowerCorner[1]+upperCorner[1])/2, (lowerCorner[2]+upperCorner[2])/2); halfSize = Vector3r( thickness/2.0, 1.5*std::abs(lowerCorner[1]-upperCorner[1])/2+thickness, 1.5*std::abs(lowerCorner[2]-upperCorner[2])/2+thickness); createBox(body,center,halfSize,wall_2_wire); if(wall_2) { scene->bodies->insert(body); triaxialcompressionEngine->wall_right_id = body->getId(); //triaxialStateRecorder->wall_right_id = body->getId(); } // box 3 center = Vector3r( (lowerCorner[0]+upperCorner[0])/2, (lowerCorner[1]+upperCorner[1])/2, lowerCorner[2]-thickness/2.0); halfSize = Vector3r( 1.5*std::abs(lowerCorner[0]-upperCorner[0])/2+thickness, 1.5*std::abs(lowerCorner[1]-upperCorner[1])/2+thickness, thickness/2.0); createBox(body,center,halfSize,wall_3_wire); if(wall_3) { scene->bodies->insert(body); triaxialcompressionEngine->wall_back_id = body->getId(); //triaxialStateRecorder->wall_back_id = body->getId(); } // box 4 center = Vector3r( (lowerCorner[0]+upperCorner[0])/2, (lowerCorner[1]+upperCorner[1])/2, upperCorner[2]+thickness/2.0); halfSize = Vector3r( 1.5*std::abs(lowerCorner[0]-upperCorner[0])/2+thickness, 1.5*std::abs(lowerCorner[1]-upperCorner[1])/2+thickness, thickness/2.0); createBox(body,center,halfSize,wall_3_wire); if(wall_4) { scene->bodies->insert(body); triaxialcompressionEngine->wall_front_id = body->getId(); //triaxialStateRecorder->wall_front_id = body->getId(); } } //convert the original sphere vector (with clump info) to a BasicSphere vector. vector sphere_list; typedef boost::tuple tupleVector3rRealInt; if(importFilename!=""){ vector >sphereListClumpInfo = Shop::loadSpheresFromFile(importFilename,lowerCorner,upperCorner); FOREACH(tupleVector3rRealInt t, sphereListClumpInfo){ sphere_list.push_back(make_pair(boost::get<0>(t),boost::get<1>(t))); }; } else message=GenerateCloud_cohesive(sphere_list, lowerCorner, upperCorner, numberOfGrains, radiusDeviation, 0.75); vector::iterator it = sphere_list.begin(); vector::iterator it_end = sphere_list.end(); for (;it!=it_end; ++it) { cerr << "sphere (" << it->first << " " << it->second << endl; createSphere(body,it->first,it->second,true); scene->bodies->insert(body); } return true; } void CohesiveTriaxialTest::createSphere(shared_ptr& body, Vector3r position, Real radius, bool dynamic ) { body = shared_ptr(new Body); body->groupMask=2; shared_ptr physics(new CohFrictMat); shared_ptr aabb(new Aabb); shared_ptr iSphere(new Sphere); Quaternionr q(Mathr::SymmetricRandom(),Mathr::SymmetricRandom(),Mathr::SymmetricRandom(),Mathr::SymmetricRandom()); q.normalize(); body->state->blockedDOFs=State::DOF_NONE; body->state->angVel = Vector3r(0,0,0); body->state->vel = Vector3r(0,0,0); body->state->mass = 4.0/3.0*Mathr::PI*radius*radius*radius*density; body->state->inertia = Vector3r( 2.0/5.0*body->state->mass*radius*radius, 2.0/5.0*body->state->mass*radius*radius, 2.0/5.0*body->state->mass*radius*radius); body->state->se3 = Se3r(position,q); physics->young = sphereYoungModulus; physics->poisson = sphereKsDivKn; physics->frictionAngle = sphereFrictionDeg * Mathr::PI/180.0; physics->shearCohesion = shearCohesion; physics->normalCohesion = normalCohesion; physics->momentRotationLaw = 1; if((!dynamic) && (!boxWalls)) { physics->young = boxYoungModulus; physics->poisson = boxKsDivKn; physics->frictionAngle = boxFrictionDeg * Mathr::PI/180.0; } aabb->color = Vector3r(0,1,0); iSphere->radius = radius; iSphere->color = Vector3r(Mathr::UnitRandom(),Mathr::UnitRandom(),Mathr::UnitRandom()); iSphere->wire = false; body->shape = iSphere; body->bound = aabb; body->material = physics; } void CohesiveTriaxialTest::createBox(shared_ptr& body, Vector3r position, Vector3r extents, bool wire) { body = shared_ptr(new Body); body->groupMask=2; shared_ptr physics(new CohFrictMat); shared_ptr aabb(new Aabb); shared_ptr iBox(new Box); body->state->blockedDOFs=State::DOF_ALL; body->state->angVel = Vector3r(0,0,0); body->state->vel = Vector3r(0,0,0); body->state->mass = 0; //physics->mass = extents[0]*extents[1]*extents[2]*density*2; body->state->inertia = Vector3r( body->state->mass*(extents[1]*extents[1]+extents[2]*extents[2])/3 , body->state->mass*(extents[0]*extents[0]+extents[2]*extents[2])/3 , body->state->mass*(extents[1]*extents[1]+extents[0]*extents[0])/3 ); // physics->mass = 0; // physics->inertia = Vector3r(0,0,0); body->state->se3 = Se3r(position,Quaternionr::Identity()); physics->young = boxYoungModulus; physics->poisson = boxKsDivKn; physics->frictionAngle = boxFrictionDeg * Mathr::PI/180.0; physics->shearCohesion = 0; physics->normalCohesion = 0; physics->momentRotationLaw = 0; aabb->color = Vector3r(1,0,0); iBox->extents = extents; iBox->color = Vector3r(1,1,1); iBox->wire = wire; body->bound = aabb; body->shape = iBox; body->material = physics; } void CohesiveTriaxialTest::createActors(shared_ptr& scene) { shared_ptr interactionGeometryDispatcher(new IGeomDispatcher); shared_ptr s1(new Ig2_Sphere_Sphere_ScGeom6D); interactionGeometryDispatcher->add(s1); shared_ptr s2(new Ig2_Box_Sphere_ScGeom6D); interactionGeometryDispatcher->add(s2); shared_ptr cohesiveFrictionalRelationships = shared_ptr (new Ip2_CohFrictMat_CohFrictMat_CohFrictPhys); cohesiveFrictionalRelationships->setCohesionOnNewContacts = setCohesionOnNewContacts; shared_ptr interactionPhysicsDispatcher(new IPhysDispatcher); interactionPhysicsDispatcher->add(cohesiveFrictionalRelationships); shared_ptr collider(new InsertionSortCollider); collider->boundDispatcher->add(new Bo1_Sphere_Aabb); collider->boundDispatcher->add(new Bo1_Box_Aabb); shared_ptr newton(new NewtonIntegrator); newton->damping=dampingMomentum; shared_ptr globalStiffnessTimeStepper(new GlobalStiffnessTimeStepper); globalStiffnessTimeStepper->timeStepUpdateInterval = timeStepUpdateInterval; globalStiffnessTimeStepper->defaultDt = defaultDt; globalStiffnessTimeStepper->timestepSafetyCoefficient = 0.2; shared_ptr cohesiveFrictionalContactLaw(new CohesiveFrictionalContactLaw); triaxialcompressionEngine = shared_ptr (new TriaxialCompressionEngine); triaxialcompressionEngine-> stiffnessUpdateInterval = wallStiffnessUpdateInterval;// = stiffness update interval triaxialcompressionEngine-> radiusControlInterval = radiusControlInterval;// = stiffness update interval triaxialcompressionEngine-> sigma_iso = sigmaIsoCompaction; triaxialcompressionEngine-> sigmaLateralConfinement = sigmaLateralConfinement; triaxialcompressionEngine-> sigmaIsoCompaction = sigmaIsoCompaction; triaxialcompressionEngine-> max_vel = 1; triaxialcompressionEngine-> thickness = thickness; triaxialcompressionEngine->strainRate = strainRate; triaxialcompressionEngine->StabilityCriterion = StabilityCriterion; triaxialcompressionEngine->autoCompressionActivation = autoCompressionActivation; triaxialcompressionEngine->internalCompaction = internalCompaction; triaxialcompressionEngine->maxMultiplier = maxMultiplier; // recording global stress triaxialStateRecorder = shared_ptr(new TriaxialStateRecorder); triaxialStateRecorder-> file = WallStressRecordFile; triaxialStateRecorder-> iterPeriod = recordIntervalIter; //triaxialStateRecorder-> thickness = thickness; scene->engines.clear(); scene->engines.push_back(shared_ptr(new ForceResetter)); scene->engines.push_back(collider); scene->engines.push_back(interactionGeometryDispatcher); scene->engines.push_back(interactionPhysicsDispatcher); scene->engines.push_back(cohesiveFrictionalContactLaw); scene->engines.push_back(triaxialcompressionEngine); scene->engines.push_back(globalStiffnessTimeStepper); scene->engines.push_back(triaxialStateRecorder); //scene->engines.push_back(hydraulicForceEngine);//<-------------HYDRAULIC ENGINE HERE scene->engines.push_back(newton); } void CohesiveTriaxialTest::positionRootBody(shared_ptr& scene) { shared_ptr aabb(new Aabb); aabb->color = Vector3r(0,0,1); } string GenerateCloud_cohesive(vector& sphere_list, Vector3r lowerCorner, Vector3r upperCorner, long number, Real rad_std_dev, Real porosity) { typedef boost::minstd_rand StdGenerator; static StdGenerator generator; static boost::variate_generator > random1(generator, boost::uniform_real<>(0,1)); // static boost::variate_generator > // randomN(generator, boost::normal_distribution<>(aggregateMeanRadius,aggregateSigmaRadius)); sphere_list.clear(); long tries = 1000; //nb of tries for positionning the next sphere Vector3r dimensions = upperCorner - lowerCorner; Real mean_radius = std::pow(dimensions.x()*dimensions.y()*dimensions.z()*(1-porosity)/(3.1416*1.3333*number),0.333333); //cerr << mean_radius; std::cerr << "generating aggregates ... "; long t, i; for (i=0; i (sphere_list[j].first-s.first).squaredNorm()) overlap=true; if (!overlap) { sphere_list.push_back(s); break; } } if (t==tries) return "More than " + boost::lexical_cast(tries) + " tries while generating sphere number " + boost::lexical_cast(i+1) + "/" + boost::lexical_cast(number) + "."; } return "Generated a sample with " + boost::lexical_cast(number) + "spheres inside box of dimensions: (" + boost::lexical_cast(dimensions[0]) + "," + boost::lexical_cast(dimensions[1]) + "," + boost::lexical_cast(dimensions[2]) + ")."; } YADE_PLUGIN((CohesiveTriaxialTest)); trunk-2017.01a/pkg/dem/CohesiveTriaxialTest.hpp000066400000000000000000000202401304022710500213220ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2007 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include class TriaxialStressController; class TriaxialCompressionEngine; class TriaxialStateRecorder; /*! \brief Triaxial test on unsaturated sphere packings This preprocessor is a variant of TriaxialTest using the cohesive-frictional contact law with moments. See TriaxialTest documentation. */ class CohesiveTriaxialTest : public FileGenerator { private : Vector3r gravity; Vector3r spheresColor; bool wall_top ,wall_bottom ,wall_1 ,wall_2 ,wall_3 ,wall_4 ,wall_top_wire ,wall_bottom_wire ,wall_1_wire ,wall_2_wire ,wall_3_wire ,wall_4_wire ,spheresRandomColor; shared_ptr triaxialcompressionEngine; shared_ptr triaxialstressController; shared_ptr triaxialStateRecorder; void createBox(shared_ptr& body, Vector3r position, Vector3r extents,bool wire); void createSphere(shared_ptr& body, Vector3r position, Real radius,bool dynamic); void createActors(shared_ptr& scene); void positionRootBody(shared_ptr& scene); public : //CohesiveTriaxialTest (); ~CohesiveTriaxialTest (); virtual bool generate(std::string& message); YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY( CohesiveTriaxialTest,FileGenerator,"This preprocessor is a variant of TriaxialTest using the cohesive-frictional contact law with moments. It sets up a scene for cohesive triaxial tests. See full documentation at http://yade-dem.org/wiki/TriaxialTest.\n\n Cohesion is initially 0 by default. The suggested usage is to define cohesion values in a second step, after isotropic compaction : define shear and normal cohesions in :yref:`Ip2_CohFrictMat_CohFrictMat_CohFrictPhys`, then turn :yref:`Ip2_CohFrictMat_CohFrictMat_CohFrictPhys`::setCohesionNow true to assign them at each contact at next iteration." , ((Vector3r,lowerCorner,Vector3r(0,0,0),,"Lower corner of the box.")) ((Vector3r,upperCorner,Vector3r(1,1,1),,"Upper corner of the box.")) ((string,importFilename,"",,"File with positions and sizes of spheres.")) ((string,Key,"",,"A code that is added to output filenames.")) ((string,fixedBoxDims,"",,"string that contains some subset (max. 2) of {'x','y','z'} ; contains axes will have box dimension hardcoded, even if box is scaled as mean_radius is prescribed: scaling will be applied on the rest.")) ((string,WallStressRecordFile,"./CohesiveWallStresses"+Key,,"")) ((bool,internalCompaction,false,,"flag for choosing between moving boundaries or increasing particles sizes during the compaction stage.")) ((bool,biaxial2dTest,false,,"FIXME : what is that?")) ((bool,fixedPoroCompaction,false,,"flag to choose an isotropic compaction until a fixed porosity choosing a same translation speed for the six walls")) ((bool,autoCompressionActivation,true,,"Do we just want to generate a stable packing under isotropic pressure (false) or do we want the triaxial loading to start automatically right after compaction stage (true)?")) ((bool,autoUnload,true,,"auto adjust the isotropic stress state from :yref:`TriaxialTest`::sigmaIsoCompaction to :yref:`TriaxialTest::sigmaLateralConfinement` if they have different values. See docs for :yref:`TriaxialCompressionEngine::autoUnload`")) ((bool,autoStopSimulation,false,,"freeze the simulation when conditions are reached (don't activate this if you want to be able to run/stop from Qt GUI)")) ((bool,noFiles,false,,"Do not create any files during run (.xml, .spheres, wall stress records)")) ((bool,facetWalls,false,,"Use facets for boundaries (not tested)")) ((bool,wallWalls,false,,"Use walls for boundaries (not tested)")) ((bool,boxWalls,true,,"Use boxes for boundaries (recommended).")) ((Real,fixedPorosity,1,,"FIXME : what is that?")) ((Real,thickness,0.001,,"thickness of boundaries. It is arbitrary and should have no effect")) ((Real,maxMultiplier,1.01,,"max multiplier of diameters during internal compaction (initial fast increase)")) ((Real,finalMaxMultiplier,1.001,,"max multiplier of diameters during internal compaction (secondary precise adjustment)")) ((Real,radiusDeviation,0.3,,"Normalized standard deviation of generated sizes.")) ((Real,radiusMean,-1,,"Mean radius. If negative (default), autocomputed to as a function of box size and :yref:`TriaxialTest::numberOfGrains`")) ((Real,sphereYoungModulus,15000000.0,,"Stiffness of spheres.")) ((Real,sphereKsDivKn,0.5,,"Ratio of shear vs. normal contact stiffness for spheres.")) ((Real,sphereFrictionDeg,18.0,,"Friction angle [°] of spheres assigned just before triaxial testing.")) ((Real,compactionFrictionDeg,sphereFrictionDeg,,"Friction angle [°] of spheres during compaction (different values result in different porosities)]. This value is overridden by :yref:`TriaxialTest::sphereFrictionDeg` before triaxial testing.")) ((Real,normalCohesion,0,,"Material parameter used to define contact strength in tension.")) ((Real,shearCohesion,0,,"Material parameter used to define shear strength of contacts.")) ((bool,setCohesionOnNewContacts,false,,"create cohesionless (False) or cohesive (True) interactions for new contacts.")) ((Real,boxYoungModulus,15000000.0,,"Stiffness of boxes.")) ((Real,maxWallVelocity,10,,"max velocity of boundaries. Usually useless, but can help stabilizing the system in some cases.")) ((Real,boxKsDivKn,0.5,,"Ratio of shear vs. normal contact stiffness for boxes.")) ((Real,boxFrictionDeg,0.0,,"Friction angle [°] of boundaries contacts.")) ((Real,density,2600,,"density of spheres")) ((Real,strainRate,0.1,,"Strain rate in triaxial loading.")) ((Real,defaultDt,0.001,,"Max time-step. Used as initial value if defined. Latter adjusted by the time stepper.")) ((Real,dampingForce,0.2,,"Coefficient of Cundal-Non-Viscous damping (applied on on the 3 components of forces)")) ((Real,dampingMomentum,0.2,,"Coefficient of Cundal-Non-Viscous damping (applied on on the 3 components of torques)")) ((Real,StabilityCriterion,0.01,,"Value of unbalanced force for which the system is considered stable. Used in conditionals to switch between loading stages.")) ((Real,wallOversizeFactor,1.3,,"Make boundaries larger than the packing to make sure spheres don't go out during deformation.")) ((Real,sigmaIsoCompaction,-50000,,"Confining stress during isotropic compaction (< 0 for real - compressive - compaction).")) ((Real,sigmaLateralConfinement,-50000,,"Lateral stress during triaxial loading (< 0 for classical compressive cases). An isotropic unloading is performed if the value is not equal to :yref:`TriaxialTest::sigmaIsoCompaction`.")) ((int,timeStepUpdateInterval,50,,"interval for :yref:`GlobalStiffnessTimeStepper`")) ((int,wallStiffnessUpdateInterval,10,,"interval for updating the stiffness of sample/boundaries contacts")) ((int,radiusControlInterval,10,,"interval between size changes when growing spheres.")) ((int,numberOfGrains,400,,"Number of generated spheres.")) ((int,recordIntervalIter,20,,"interval between file outputs")) , /* init */ , /* constructor */ wall_top = true; wall_bottom = true; wall_1 = true; wall_2 = true; wall_3 = true; wall_4 = true; wall_top_wire = true; wall_bottom_wire = true; wall_1_wire = true; wall_2_wire = true; wall_3_wire = true; wall_4_wire = true; spheresColor = Vector3r(0.8,0.3,0.3); spheresRandomColor = false; WallStressRecordFile = "./CohesiveWallStresses"+Key; gravity = Vector3r(0,-9.81,0); , //.def("setContactProperties",&TriaxialCompressionEngine::setContactProperties,"Assign a new friction angle (degrees) to dynamic bodies and relative interactions") ); }; REGISTER_SERIALIZABLE(CohesiveTriaxialTest); trunk-2017.01a/pkg/dem/ConcretePM.cpp000066400000000000000000000573201304022710500172220ustar00rootroot00000000000000// 2007,2008 © Václav Šmilauer #include"ConcretePM.hpp" #include #include #include #include #include #include #include YADE_PLUGIN((CpmState)(CpmMat)(Ip2_CpmMat_CpmMat_CpmPhys)(Ip2_FrictMat_CpmMat_FrictPhys)(CpmPhys)(Law2_ScGeom_CpmPhys_Cpm) #ifdef YADE_OPENGL (Gl1_CpmPhys) #endif (CpmStateUpdater)); /********************** Ip2_CpmMat_CpmMat_CpmPhys ****************************/ CREATE_LOGGER(Ip2_FrictMat_CpmMat_FrictPhys); void Ip2_FrictMat_CpmMat_FrictPhys::go(const shared_ptr& pp1, const shared_ptr& pp2, const shared_ptr& interaction){ TIMING_DELTAS_START(); const shared_ptr& mat1 = YADE_PTR_CAST(pp1); const shared_ptr& mat2 = YADE_PTR_CAST(pp2); Ip2_FrictMat_FrictMat_FrictPhys iPhysFunctor = Ip2_FrictMat_FrictMat_FrictPhys(); iPhysFunctor.frictAngle = frictAngle; iPhysFunctor.go(mat1,mat2,interaction); TIMING_DELTAS_CHECKPOINT("end of Ip2_FritPhys"); } CREATE_LOGGER(Ip2_CpmMat_CpmMat_CpmPhys); void Ip2_CpmMat_CpmMat_CpmPhys::go(const shared_ptr& pp1, const shared_ptr& pp2, const shared_ptr& interaction){ // no updates of an already existing contact necessary if (interaction->phys) return; TIMING_DELTAS_START(); shared_ptr cpmPhys(new CpmPhys()); interaction->phys = cpmPhys; CpmMat* mat1 = YADE_CAST(pp1.get()); CpmMat* mat2 = YADE_CAST(pp2.get()); // check unassigned values if (!mat1->neverDamage) { assert(!std::isnan(mat1->sigmaT)); assert(!std::isnan(mat1->epsCrackOnset)); assert(!std::isnan(mat1->relDuctility)); } if (!mat2->neverDamage) { assert(!std::isnan(mat2->sigmaT)); assert(!std::isnan(mat2->epsCrackOnset)); assert(!std::isnan(mat2->relDuctility)); } cpmPhys->damLaw = mat1->damLaw; // bodies sharing the same material; no averages necessary if (mat1->id>=0 && mat1->id == mat2->id) { cpmPhys->E = mat1->young; cpmPhys->G = mat1->young*mat1->poisson; cpmPhys->tanFrictionAngle = tan(mat1->frictionAngle); cpmPhys->undamagedCohesion = mat1->sigmaT; cpmPhys->isCohesive = (cohesiveThresholdIter < 0 || scene->iter < cohesiveThresholdIter); #define _CPATTR(a) cpmPhys->a=mat1->a _CPATTR(epsCrackOnset); _CPATTR(relDuctility); _CPATTR(equivStrainShearContrib); _CPATTR(neverDamage); _CPATTR(dmgTau); _CPATTR(dmgRateExp); _CPATTR(plTau); _CPATTR(plRateExp); _CPATTR(isoPrestress); #undef _CPATTR } else { // averaging over both materials #define _AVGATTR(a) cpmPhys->a=.5*(mat1->a+mat2->a) Real e = (!E) ? .5*(mat1->young + mat2->young) : (*E)(mat1->id,mat2->id,mat1->young,mat2->young); cpmPhys->E = e; cpmPhys->G = .5*(mat1->poisson + mat2->poisson)*cpmPhys->E; cpmPhys->tanFrictionAngle = tan(.5*(mat1->frictionAngle + mat2->frictionAngle)); cpmPhys->undamagedCohesion = .5*(mat1->sigmaT + mat2->sigmaT); cpmPhys->isCohesive = (cohesiveThresholdIter < 0 || scene->iter < cohesiveThresholdIter); _AVGATTR(epsCrackOnset); _AVGATTR(relDuctility); _AVGATTR(equivStrainShearContrib); cpmPhys->neverDamage = (mat1->neverDamage || mat2->neverDamage); _AVGATTR(dmgTau); _AVGATTR(dmgRateExp); _AVGATTR(plTau); _AVGATTR(plRateExp); _AVGATTR(isoPrestress); #undef _AVGATTR } // NOTE: some params are not assigned until in Law2_ScGeom_CpmPhys_Cpm, since they need geometry as well; those are: // crossSection, kn, ks, refLength TIMING_DELTAS_CHECKPOINT("end of Ip2_CpmPhys"); } /********************** CpmPhys ****************************/ CREATE_LOGGER(CpmPhys); // !! at least one virtual function in the .cpp file CpmPhys::~CpmPhys(){}; long CpmPhys::cummBetaIter=0, CpmPhys::cummBetaCount=0; Real CpmPhys::solveBeta(const Real c, const Real N){ #ifdef YADE_DEBUG cummBetaCount++; #endif const int maxIter = 20; const Real maxError = 1e-12; Real f, ret = 0.; for(int i = 0; i < maxIter; i++){ #ifdef YADE_DEBUG cummBetaIter++; #endif Real aux = c*exp(N*ret)+exp(ret); f = log(aux); if (std::abs(f) < maxError) return ret; Real df = (c*N*exp(N*ret)+exp(ret))/aux; ret -= f/df; } LOG_FATAL("No convergence after "<= epsN*omega) { // unloading, no viscous stress dmgStrain = epsN*omega; LOG_TRACE("Elastic/unloading, no viscous overstress"); return 0.; } Real c = epsCrackOnset*(1-omega)*pow(dmgTau/dt,dmgRateExp)*pow(epsN*omega-dmgStrain,dmgRateExp-1.); Real beta = solveBeta(c,dmgRateExp); Real deltaDmgStrain = (epsN*omega-dmgStrain)*exp(beta); dmgStrain += deltaDmgStrain; LOG_TRACE("deltaDmgStrain="<& I, *scene->interactions){ if(!I->isReal()) continue; CpmPhys* phys = dynamic_cast(I->phys.get()); if(phys) { ret += 0.5*phys->normalForce.squaredNorm()/((1-(phys->epsN>0?phys->omega:0))*phys->kn); ret += 0.5*phys->shearForce.squaredNorm()/phys->ks; } } return ret; #endif } #ifdef YADE_DEBUG #define CPM_YADE_DEBUG_A \ if(std::isnan(epsN)){\ /*LOG_FATAL("refLength="<refLength<<"; pos1="<se31.position<<"; pos2="<se32.position<<"; displacementN="<displacementN());*/ \ throw runtime_error("!! epsN==NaN !!");\ } #else #define CPM_YADE_DEBUG_A #endif #define YADE_VERIFY(condition) if(!(condition)){LOG_FATAL("Verification `"<<#condition<<"' failed!"); LOG_FATAL("in interaction #"<getId1()<<"+#"<getId2()); Omega::instance().saveSimulation("/tmp/verificationFailed.xml"); throw;} #define NNAN(a) YADE_VERIFY(!std::isnan(a)); #define NNANV(v) YADE_VERIFY(!std::isnan(v[0])); assert(!std::isnan(v[1])); assert(!std::isnan(v[2])); bool Law2_ScGeom_CpmPhys_Cpm::go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I){ TIMING_DELTAS_START(); ScGeom* geom=static_cast(_geom.get()); CpmPhys* phys=static_cast(_phys.get()); /* just the first time */ if (I->isFresh(scene)) { const shared_ptr b1 = Body::byId(I->id1,scene); const shared_ptr b2 = Body::byId(I->id2,scene); const int sphereIndex = Sphere::getClassIndexStatic(); const int facetIndex = Facet::getClassIndexStatic(); const int wallIndex = Wall::getClassIndexStatic(); const int boxIndex = Box::getClassIndexStatic(); const int b1index = b1->shape->getClassIndex(); const int b2index = b2->shape->getClassIndex(); if (b1index == sphereIndex && b2index == sphereIndex) { // both bodies are spheres const Vector3r& pos1 = Body::byId(I->id1,scene)->state->pos; const Vector3r& pos2 = Body::byId(I->id2,scene)->state->pos; Real minRad = (geom->refR1 <= 0? geom->refR2 : (geom->refR2 <=0? geom->refR1 : std::min(geom->refR1,geom->refR2))); Vector3r shift2 = scene->isPeriodic? Vector3r(scene->cell->hSize*I->cellDist.cast()) : Vector3r::Zero(); phys->refLength = (pos2 - pos1 + shift2).norm(); phys->crossSection = Mathr::PI*pow(minRad,2); phys->refPD = geom->refR1 + geom->refR2 - phys->refLength; } else if (b1index == facetIndex || b2index == facetIndex || b1index == wallIndex || b2index == wallIndex || b1index == boxIndex || b2index == boxIndex) { // one body is facet or wall or box shared_ptr sphere, plane; if (b1index == facetIndex || b1index == wallIndex || b1index == boxIndex) { plane = b1; sphere = b2; } else { plane = b2; sphere = b1; } Real rad = ( (Sphere*) sphere->shape.get() )->radius; phys->refLength = rad; phys->crossSection = Mathr::PI*pow(rad,2); phys->refPD = 0.; } phys->kn = phys->crossSection*phys->E/phys->refLength; phys->ks = phys->crossSection*phys->G/phys->refLength; phys->epsFracture = phys->epsCrackOnset*phys->relDuctility; } /* shorthands */ Real& epsN(phys->epsN); Vector3r& epsT(phys->epsT); Vector3r& epsTPl(phys->epsTPl); Real& kappaD(phys->kappaD); /* Real& epsPlSum(phys->epsPlSum); */ const Real& E(phys->E); \ const Real& undamagedCohesion(phys->undamagedCohesion); const Real& tanFrictionAngle(phys->tanFrictionAngle); const Real& G(phys->G); const Real& crossSection(phys->crossSection); const Real& omegaThreshold(this->omegaThreshold); const Real& epsCrackOnset(phys->epsCrackOnset); Real& relResidualStrength(phys->relResidualStrength); /*const Real& relDuctility(phys->relDuctility); */ const Real& epsFracture(phys->epsFracture); const int& damLaw(phys->damLaw); const bool& neverDamage(phys->neverDamage); Real& omega(phys->omega); Real& sigmaN(phys->sigmaN); Vector3r& sigmaT(phys->sigmaT); Real& Fn(phys->Fn); Vector3r& Fs(phys->Fs); /* for python access */ const bool& isCohesive(phys->isCohesive); #ifdef CPM_MATERIAL_MODEL const Real& dt = scene->dt; const Real& dmgTau(phys->dmgTau); const Real& plTau(phys->plTau); const Real& yieldLogSpeed(this->yieldLogSpeed); const int& yieldSurfType(this->yieldSurfType); const Real& yieldEllipseShift(this->yieldEllipseShift); #endif Real& epsNPl(phys->epsNPl); const Real& epsSoft(this->epsSoft); const Real& relKnSoft(this->relKnSoft); TIMING_DELTAS_CHECKPOINT("GO A"); epsN = - (-phys->refPD + geom->penetrationDepth) / phys->refLength; //epsT = geom->rotate(epsT); geom->rotate(epsT); //epsT += geom->shearIncrement() / (phys->refLength + phys->refPD) ; epsT += geom->shearIncrement() / phys->refLength; /* debugging */ CPM_YADE_DEBUG_A NNAN(epsN); NNANV(epsT); /* constitutive law */ #ifdef CPM_MATERIAL_MODEL CPM_MATERIAL_MODEL #else /* simplified public model */ epsN += phys->isoPrestress/E; /* very simplified version of the constitutive law */ Real xi2 = std::pow(phys->equivStrainShearContrib,2); Real epsNorm = std::sqrt(std::pow(std::max(epsN-epsNPl,0.),2)+xi2*epsT.squaredNorm()); kappaD = std::max(epsNorm,kappaD); /* internal variable, max positive strain (non-decreasing) */ omega = isCohesive? phys->funcG(kappaD,epsCrackOnset,epsFracture,neverDamage,damLaw) : 1.; /* damage variable (non-decreasing, as funcG is also non-decreasing) */ sigmaN = (1-(epsN-epsNPl>0?omega:0))*E*(epsN-epsNPl); /* damage taken in account in tension only */ if((epsSoft<0) && (epsN-epsNPlsigmaN){ /*assert(sigmaNSoft>sigmaN);*/ epsNPl+=(sigmaN-sigmaNSoft)/E; sigmaN=sigmaNSoft; } } sigmaT = G*(epsT-epsTPl); /* trial stress */ Real yieldSigmaT = std::max((Real)0.,undamagedCohesion*(1-omega)-sigmaN*tanFrictionAngle); /* Mohr-Coulomb law with damage */ if (sigmaT.squaredNorm() > yieldSigmaT*yieldSigmaT) { Real scale = yieldSigmaT/sigmaT.norm(); sigmaT *= scale; /* stress return */ epsTPl += sigmaT*(1-scale)/G; } relResidualStrength = isCohesive? (kappaDisoPrestress; NNAN(sigmaN); NNANV(sigmaT); NNAN(crossSection); if (!neverDamage) { NNAN(kappaD); NNAN(epsFracture); NNAN(omega); } /* handle broken contacts */ if (epsN>0. && ((isCohesive && omega>omegaThreshold) || !isCohesive)) { /* if (isCohesive) { */ const shared_ptr& body1 = Body::byId(I->getId1(),scene), body2 = Body::byId(I->getId2(),scene); assert(body1); assert(body2); const shared_ptr& st1 = YADE_PTR_CAST(body1->state), st2 = YADE_PTR_CAST(body2->state); /* nice article about openMP::critical vs. scoped locks: http://www.thinkingparallel.com/2006/08/21/scoped-locking-vs-critical-in-openmp-a-personal-shootout/ */ { boost::mutex::scoped_lock lock(st1->updateMutex); st1->numBrokenCohesive += 1; /* st1->epsPlBroken += epsPlSum; */ } { boost::mutex::scoped_lock lock(st2->updateMutex); st2->numBrokenCohesive += 1; /* st2->epsPlBroken += epsPlSum; */ } /* } */ return false; } Fn = sigmaN*crossSection; phys->normalForce = -Fn*geom->normal; Fs = sigmaT*crossSection; phys->shearForce = -Fs; TIMING_DELTAS_CHECKPOINT("GO B"); Body::id_t id1 = I->getId1(); Body::id_t id2 = I->getId2(); State* b1 = Body::byId(id1,scene)->state.get(); State* b2 = Body::byId(id2,scene)->state.get(); Vector3r f = -phys->normalForce - phys->shearForce; if (!scene->isPeriodic) { applyForceAtContactPoint(f, geom->contactPoint , id1, b1->se3.position, id2, b2->se3.position); } else { scene->forces.addForce(id1,f); scene->forces.addForce(id2,-f); scene->forces.addTorque(id1,(geom->radius1+.5*(phys->refPD-geom->penetrationDepth))*geom->normal.cross(f)); scene->forces.addTorque(id2,(geom->radius2+.5*(phys->refPD-geom->penetrationDepth))*geom->normal.cross(f)); } TIMING_DELTAS_CHECKPOINT("rest"); return true; } #ifdef YADE_OPENGL /********************** Gl1_CpmPhys ****************************/ #include #include CREATE_LOGGER(Gl1_CpmPhys); bool Gl1_CpmPhys::contactLine=true; bool Gl1_CpmPhys::dmgLabel=true; bool Gl1_CpmPhys::dmgPlane=false; bool Gl1_CpmPhys::epsNLabel=true; bool Gl1_CpmPhys::epsT=false; bool Gl1_CpmPhys::epsTAxes=false; bool Gl1_CpmPhys::normal=false; Real Gl1_CpmPhys::colorStrainRatio=-1; void Gl1_CpmPhys::go(const shared_ptr& ip, const shared_ptr& i, const shared_ptr& b1, const shared_ptr& b2, bool wireFrame){ const shared_ptr& phys = boost::static_pointer_cast(ip); const shared_ptr& geom = YADE_PTR_CAST(i->geom); // FIXME: get the scene for periodicity; ugly! Scene* scene=Omega::instance().getScene().get(); //Vector3r lineColor(phys->omega,1-phys->omega,0.0); /* damaged links red, undamaged green */ Vector3r lineColor = Shop::scalarOnColorScale(1.-phys->relResidualStrength); if(colorStrainRatio>0) lineColor = Shop::scalarOnColorScale(phys->epsN/(phys->epsCrackOnset*colorStrainRatio)); // FIXME: should be computed by the renderer; for now, use the real values //Vector3r pos1=geom->se31.position, pos2=geom->se32.position; Vector3r pos1 = scene->bodies->operator[](i->id1)->state->pos, pos2 = scene->bodies->operator[](i->id2)->state->pos; if (scene->isPeriodic) { Vector3r dPos = pos2 - pos1; pos1=scene->cell->wrapShearedPt(pos1); Vector3r shift2 = scene->isPeriodic? Vector3r(scene->cell->hSize*i->cellDist.cast()) : Vector3r::Zero();\ pos2 = pos1 + dPos + shift2; //phys->refLength = (pos2 - pos1 + shift2).norm(); //pos2=pos1+(geom->se32.position-geom->se31.position); } /* if (scene->isPeriodic) { Vector3r temp = pos2 - pos1; pos1 = scene->cell->wrapShearedPt(pos1); pos2 = pos1 + temp; } */ if (contactLine) GLUtils::GLDrawLine(pos1,pos2,lineColor); if (dmgLabel) { GLUtils::GLDrawNum(phys->omega,0.5*(pos1+pos2),lineColor); } else if (epsNLabel) { GLUtils::GLDrawNum(phys->epsN,0.5*(pos1+pos2),lineColor); } if (phys->omega>0 && dmgPlane) { Real halfSize = sqrt(1-phys->relResidualStrength)*.5*.705*sqrt(phys->crossSection); Vector3r midPt = .5*Vector3r(pos1+pos2); glDisable(GL_CULL_FACE); glPushMatrix(); glTranslatev(midPt); Quaternionr q; q.setFromTwoVectors(Vector3r::UnitZ(),geom->normal); AngleAxisr aa(q); glRotatef(aa.angle()*Mathr::RAD_TO_DEG,aa.axis()[0],aa.axis()[1],aa.axis()[2]); glBegin(GL_POLYGON); glColor3v(lineColor); glVertex3d(halfSize,0.,0.); glVertex3d(.5*halfSize,.866*halfSize,0.); glVertex3d(-.5*halfSize,.866*halfSize,0.); glVertex3d(-halfSize,0.,0.); glVertex3d(-.5*halfSize,-.866*halfSize,0.); glVertex3d(.5*halfSize,-.866*halfSize,0.); glEnd(); glPopMatrix(); } Vector3r cp = boost::static_pointer_cast(i->geom)->contactPoint; if (scene->isPeriodic) {cp = scene->cell->wrapShearedPt(cp);} if (epsT) { Real maxShear = (phys->undamagedCohesion-phys->sigmaN*phys->tanFrictionAngle)/phys->G; Real relShear = phys->epsT.norm()/maxShear; Real scale = phys->refLength; Vector3r dirShear = phys->epsT; dirShear.normalize(); if(epsTAxes){ GLUtils::GLDrawLine(cp-Vector3r(scale,0,0),cp+Vector3r(scale,0,0)); GLUtils::GLDrawLine(cp-Vector3r(0,scale,0),cp+Vector3r(0,scale,0)); GLUtils::GLDrawLine(cp-Vector3r(0,0,scale),cp+Vector3r(0,0,scale)); } GLUtils::GLDrawArrow(cp,cp+dirShear*relShear*scale,Vector3r(1.,0.,0.)); GLUtils::GLDrawLine(cp+dirShear*relShear*scale,cp+dirShear*scale,Vector3r(.3,.3,.3)); /* normal strain */ GLUtils::GLDrawArrow(cp,cp+geom->normal*(phys->epsN/maxShear),Vector3r(0.,1.,0.)); } //if(normal) GLUtils::GLDrawArrow(cp,cp+geom->normal*.5*phys->equilibriumDist,Vector3r(0.,1.,0.)); } #endif /********************** CpmStateUpdater ****************************/ CREATE_LOGGER(CpmStateUpdater); //Real CpmStateUpdater::maxOmega=0.; //Real CpmStateUpdater::avgRelResidual=0.; void CpmStateUpdater::update(Scene* _scene){ Scene *scene = _scene? _scene : Omega::instance().getScene().get(); vector bodyStats; bodyStats.resize(scene->bodies->size()); assert(bodyStats[0].nCohLinks == 0); // should be initialized by dfault ctor avgRelResidual = 0; Real nAvgRelResidual = 0; Matrix3r identity = Matrix3r::Identity(); Real dmg; Matrix3r incr; FOREACH(const shared_ptr& I, *scene->interactions){ if (!I) continue; if (!I->isReal()) continue; shared_ptr phys = YADE_PTR_DYN_CAST(I->phys); if (!phys) continue; const Body::id_t id1 = I->getId1(), id2 = I->getId2(); GenericSpheresContact* geom = YADE_CAST(I->geom.get()); const Vector3r& n = geom->normal; const Real& Fn = phys->Fn; const Vector3r& Fs = phys->Fs; //stress[i,j] += geom->refLength*(Fn*n[i]*n[j]+0.5*(Fs[i]*n[j]+Fs[j]*n[i])); //stress += geom->refLength*(Fn*outer(n,n)+.5*(outer(Fs,n)+outer(n,Fs))); Matrix3r stress = phys->refLength*(Fn*n*n.transpose()+.5*(Fs*n.transpose()+n*Fs.transpose())); bodyStats[id1].stress += stress; bodyStats[id2].stress += stress; bodyStats[id1].nLinks++; bodyStats[id2].nLinks++; if (!phys->isCohesive) continue; bodyStats[id1].nCohLinks++; bodyStats[id1].dmgSum += (1-phys->relResidualStrength); // bodyStats[id1].epsPlSum += phys->epsPlSum; bodyStats[id2].nCohLinks++; bodyStats[id2].dmgSum += (1-phys->relResidualStrength); // bodyStats[id2].epsPlSum += phys->epsPlSum; maxOmega = std::max(maxOmega,phys->omega); avgRelResidual += phys->relResidualStrength; nAvgRelResidual += 1; for (int i=0; i<3; i++) { for (int j=0; j<3; j++) { dmg = 1-phys->relResidualStrength; incr = -identity*dmg*1.5 + n*n.transpose()*dmg*7.5; bodyStats[id1].damageTensor += incr; bodyStats[id2].damageTensor += incr; } } } // Real tr; FOREACH(shared_ptr B, *scene->bodies){ if (!B) continue; const Body::id_t& id = B->getId(); // add damaged contacts that have already been deleted CpmState* state = dynamic_cast(B->state.get()); if (!state) continue; state->stress = bodyStats[id].stress; int cohLinksWhenever = bodyStats[id].nCohLinks+state->numBrokenCohesive; if (cohLinksWhenever>0) { state->normDmg = (bodyStats[id].dmgSum+state->numBrokenCohesive)/cohLinksWhenever; // state->normEpsPl = (bodyStats[id].epsPlSum+state->epsPlBroken)/cohLinksWhenever; if (state->normDmg>1) { LOG_WARN("#"<damageTensor = bodyStats[id].damageTensor / cohLinksWhenever; } else { state->normDmg = 0; /*state->normEpsPl=0;*/ state->damageTensor = Matrix3r::Zero(); } B->shape->color = Vector3r(state->normDmg,1-state->normDmg,B->state->blockedDOFs==State::DOF_ALL?0:1); nAvgRelResidual += 0.5*state->numBrokenCohesive; // add half or broken interactions, other body has the other half Sphere* sphere = dynamic_cast(B->shape.get()); if(!sphere) continue; Real& r = sphere->radius; state->stress = bodyStats[id].stress/(4/3.*Mathr::PI*r*r*r/.62)*.5; } avgRelResidual /= nAvgRelResidual; } #undef YADE_VERIFY #undef NNAN #undef NNANV trunk-2017.01a/pkg/dem/ConcretePM.hpp000066400000000000000000000477731304022710500172420ustar00rootroot00000000000000// 2008 © Václav Šmilauer /* === HIGH LEVEL OVERVIEW OF CPM === Concrete Particle Model (ConcretePM, Cpm) is a set of classes for modelling mechanical behavior of concrete. Several classes are needed for Cpm. 1. CpmMat (Cpm material) deriving from BodyMacroParameters, which additionally has some information about damage on the body, cummulative plastic strain etc. 2. Ip2_CpmMat_CpmMat_CpmPhys is 2-ary functor for creating CpmPhys from CpmMat's of 2 bodies that collide. Some parameters of the CpmPhys created are computed from CpmMat's, others are passed as parameters of the functor. 3. CpmPhys (Cpm (interaction)Physics) holds various parameters as well as internal variables of the contact that can change as result of plasticity, damage, viscosity. 4. Law2_ScGeom_CpmPhys_Cpm is constitutive law that takes geometry of the interaction (ScGeom) and CpmPhys, computing forces on both bodies and updating contact variables. The model itself is defined in the macro CPM_MATERIAL_MODEL, but due to commercial reasons, those about 30 lines of code cannot be disclosed now and the macro is defined in an external file. The model will be, however, described in enough detail in my thesis (once it is written), along with calibration procedures; it features damage, plasticity and viscosity and is quite tunable (rigidity, poisson's ratio, compressive/tensile strength ratio, fracture energy, behavior under confinement, rate-dependence). There are other classes, which are not strictly necessary: * CpmGlobalCharacteristics computes a few information about individual bodies based on interactions they are involved in. It is probably quite useless now since volumetricStrain is not used in the constitutive law anymore. * Gl1_CpmPhys draws interaction physics (color for damage and a few other); rarely used, though. * CpmStateUpdater changes bodies' colors depending on average damage of their interactions and number of interactions that were already fully broken and have disappeared. This engine contains its own loop (2 loops, more precisely) over all bodies and is run periodically to update colors. */ #pragma once #include #include #include #include #include #include #include #include namespace py=boost::python; /********************************************************************************* * * C P M S T A T E * *********************************************************************************/ /* Cpm state information about each body. None of that is used for computation (at least not now), only for post-processing. */ class CpmState: public State { YADE_CLASS_BASE_DOC_ATTRS_CTOR(CpmState,State,"State information about body use by :yref:`cpm-model`.\n\nNone of that is used for computation (at least not now), only for post-processing.", ((Real,epsVolumetric,0,,"Volumetric strain around this body (unused for now)")) ((int,numBrokenCohesive,0,,"Number of (cohesive) contacts that damaged completely")) ((int,numContacts,0,,"Number of contacts with this body")) ((Real,normDmg,0,,"Average damage including already deleted contacts (it is really not damage, but 1-relResidualStrength now)")) //((Real,epsPlBroken,0,,"Plastic strain on contacts already deleted (bogus values)")) //((Real,normEpsPl,0,,"Sum of plastic strains normalized by number of contacts (bogus values)")) ((Matrix3r,stress,Matrix3r::Zero(),,"Stress tensor of the spherical particle (under assumption that particle volume = pi*r*r*r*4/3.) for packing fraction 0.62")) ((Matrix3r,damageTensor,Matrix3r::Zero(),,"Damage tensor computed with microplane theory averaging. state.damageTensor.trace() = state.normDmg")), /*ctor*/ createIndex(); ); REGISTER_CLASS_INDEX(CpmState,State); }; REGISTER_SERIALIZABLE(CpmState); /********************************************************************************* * * C P M M A T * *********************************************************************************/ /* This class holds information associated with each body */ class CpmMat: public FrictMat { public: virtual shared_ptr newAssocState() const { return shared_ptr(new CpmState); } virtual bool stateTypeOk(State* s) const { return (bool)dynamic_cast(s); } YADE_CLASS_BASE_DOC_ATTRS_CTOR(CpmMat,FrictMat,"Concrete material, for use with other Cpm classes. \n\n.. note::\n\n\t:yref:`Density` is initialized to 4800 kgm⁻³automatically, which gives approximate 2800 kgm⁻³ on 0.5 density packing.\n\nConcrete Particle Model (CPM)\n\n\n:yref:`CpmMat` is particle material, :yref:`Ip2_CpmMat_CpmMat_CpmPhys` averages two particles' materials, creating :yref:`CpmPhys`, which is then used in interaction resultion by :yref:`Law2_ScGeom_CpmPhys_Cpm`. :yref:`CpmState` is associated to :yref:`CpmMat` and keeps state defined on particles rather than interactions (such as number of completely damaged interactions).\n\nThe model is contained in externally defined macro CPM_MATERIAL_MODEL, which features damage in tension, plasticity in shear and compression and rate-dependence. For commercial reasons, rate-dependence and compression-plasticity is not present in reduced version of the model, used when CPM_MATERIAL_MODEL is not defined. The full model will be described in detail in my (Václav Šmilauer) thesis along with calibration procedures (rigidity, poisson's ratio, compressive/tensile strength ratio, fracture energy, behavior under confinement, rate-dependent behavior).\n\nEven the public model is useful enough to run simulation on concrete samples, such as :ysrc:`uniaxial tension-compression test`.", ((Real,sigmaT,NaN,,"Initial cohesion [Pa]")) ((bool,neverDamage,false,,"If true, no damage will occur (for testing only).")) ((Real,epsCrackOnset,NaN,,"Limit elastic strain [-]")) ((Real,relDuctility,NaN,,"relative ductility of bonds in normal direction")) ((Real,equivStrainShearContrib,0,,"Coefficient of shear contribution to equivalent strain")) ((int,damLaw,1,,"Law for damage evolution in uniaxial tension. 0 for linear stress-strain softening branch, 1 (default) for exponential damage evolution law")) ((Real,dmgTau,((void)"deactivated if negative",-1),,"Characteristic time for normal viscosity. [s]")) ((Real,dmgRateExp,0,,"Exponent for normal viscosity function. [-]")) ((Real,plTau,((void)"deactivated if negative",-1),,"Characteristic time for visco-plasticity. [s]")) ((Real,plRateExp,0,,"Exponent for visco-plasticity function. [-]")) ((Real,isoPrestress,0,,"Isotropic prestress of the whole specimen. [Pa]")), createIndex(); density=4800; ); REGISTER_CLASS_INDEX(CpmMat,FrictMat); }; REGISTER_SERIALIZABLE(CpmMat); /********************************************************************************* * * C P M P H Y S * *********************************************************************************/ /*! @brief representation of a single interaction of the CPM type: storage for relevant parameters. * * Evolution of the contact is governed by Law2_ScGeom_CpmPhys_Cpm: * that includes damage effects and chages of parameters inside CpmPhys. * */ class CpmPhys: public NormShearPhys { public: static long cummBetaIter, cummBetaCount; /*! auxiliary variable for visualization, recalculated in Law2_ScGeom_CpmPhys_Cpm at every iteration */ // Fn and Fs are also stored as Vector3r normalForce, shearForce in NormShearPhys Real omega = 0, Fn = 0, sigmaN, epsN = 0, relResidualStrength, kappaD = 0, epsNPl = 0; Vector3r sigmaT, Fs, epsTPl, epsT; static Real solveBeta(const Real c, const Real N); Real computeDmgOverstress(Real dt); Real computeViscoplScalingFactor(Real sigmaTNorm, Real sigmaTYield,Real dt); /* damage evolution law */ static Real funcG(const Real& kappaD, const Real& epsCrackOnset, const Real& epsFracture, const bool& neverDamage, const int& damLaw); static Real funcGDKappa(const Real& kappaD, const Real& epsCrackOnset, const Real& epsFracture, const bool& neverDamage, const int& damLaw); /* inverse damage evolution law */ static Real funcGInv(const Real& omega, const Real& epsCrackOnset, const Real& epsFracture, const bool& neverDamage, const int& damLaw); void setDamage(Real dmg); void setRelResidualStrength(Real r); virtual ~CpmPhys(); #define _ZERO_VECTOR3R(v) v = Vector3r::Zero() YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(CpmPhys,NormShearPhys,"Representation of a single interaction of the Cpm type: storage for relevant parameters.\n\n Evolution of the contact is governed by :yref:`Law2_ScGeom_CpmPhys_Cpm`, that includes damage effects and chages of parameters inside CpmPhys. See :yref:`cpm-model` for details.", ((Real,E,NaN,,"normal modulus (stiffness / crossSection) [Pa]")) ((Real,G,NaN,,"shear modulus [Pa]")) ((Real,tanFrictionAngle,NaN,,"tangens of internal friction angle [-]")) ((Real,undamagedCohesion,NaN,,"virgin material cohesion [Pa]")) ((Real,crossSection,NaN,,"equivalent cross-section associated with this contact [m²]")) ((Real,refLength,NaN,,"initial length of interaction [m]")) ((Real,refPD,NaN,,"initial penetration depth of interaction [m] (used with ScGeom)")) ((Real,epsCrackOnset,NaN,,"strain at which the material starts to behave non-linearly")) ((Real,relDuctility,NaN,,"Relative ductility of bonds in normal direction")) ((Real,epsFracture,NaN,,"strain at which the bond is fully broken [-]")) ((Real,equivStrainShearContrib,NaN,,"Coefficient of shear contribution to equivalent strain")) ((Real,dmgTau,-1,,"characteristic time for damage (if non-positive, the law without rate-dependence is used)")) ((Real,dmgRateExp,0,,"exponent in the rate-dependent damage evolution")) ((Real,dmgStrain,0,,"damage strain (at previous or current step)")) ((Real,dmgOverstress,0,,"damage viscous overstress (at previous step or at current step)")) ((Real,plTau,-1,,"characteristic time for viscoplasticity (if non-positive, no rate-dependence for shear)")) ((Real,plRateExp,0,,"exponent in the rate-dependent viscoplasticity")) ((Real,isoPrestress,0,,"\"prestress\" of this link (used to simulate isotropic stress)")) ((bool,neverDamage,false,,"the damage evolution function will always return virgin state")) ((int,damLaw,1,,"Law for softening part of uniaxial tension. 0 for linear, 1 for exponential (default)")) //((Real,epsPlSum,0,,"cummulative shear plastic strain measure (scalar) on this contact")) ((bool,isCohesive,false,,"if not cohesive, interaction is deleted when distance is greater than zero.")) , // ctors createIndex(); epsN = 0; _ZERO_VECTOR3R(epsT); _ZERO_VECTOR3R(Fs); _ZERO_VECTOR3R(epsTPl); , .def_readonly("omega",&CpmPhys::omega,"Damage internal variable |yupdate|") .def_readonly("Fn",&CpmPhys::Fn,"Magnitude of normal force |yupdate|") .def_readonly("Fs",&CpmPhys::Fs,"Magnitude of shear force |yupdate|") .def_readonly("epsN",&CpmPhys::epsN,"Current normal strain |yupdate|") .def_readonly("epsT",&CpmPhys::epsT,"Current shear strain |yupdate|") .def_readonly("sigmaN",&CpmPhys::sigmaN,"Current normal stress |yupdate|") .def_readonly("sigmaT",&CpmPhys::sigmaT,"Current shear stress |yupdate|") .def_readonly("kappaD",&CpmPhys::kappaD,"Up to now maximum normal strain (semi-norm), non-decreasing in time |yupdate|") .def_readonly("epsNPl",&CpmPhys::epsNPl,"normal plastic strain (initially zero) |yupdate|") .def_readonly("epsTPl",&CpmPhys::epsTPl,"shear plastic strain (initially zero) |yupdate|") .def_readonly("relResidualStrength",&CpmPhys::relResidualStrength,"Relative residual strength |yupdate|") .def_readonly("cummBetaIter",&CpmPhys::cummBetaIter,"Cummulative number of iterations inside CpmMat::solveBeta (for debugging).") .def_readonly("cummBetaCount",&CpmPhys::cummBetaCount,"Cummulative number of calls of CpmMat::solveBeta (for debugging).") .def("funcG",&CpmPhys::funcG,(py::arg("kappaD"),py::arg("epsCrackOnset"),py::arg("epsFracture"),py::arg("neverDamage")=false,py::arg("damLaw")=1),"Damage evolution law, evaluating the $\\omega$ parameter. $\\kappa_D$ is historically maximum strain, *epsCrackOnset* ($\\varepsilon_0$) = :yref:`CpmPhys.epsCrackOnset`, *epsFracture* = :yref:`CpmPhys.epsFracture`; if *neverDamage* is ``True``, the value returned will always be 0 (no damage). TODO") .staticmethod("funcG") .def("funcGInv",&CpmPhys::funcGInv,(py::arg("omega"),py::arg("epsCrackOnset"),py::arg("epsFracture"),py::arg("neverDamage")=false,py::arg("damLaw")=1),"Inversion of damage evolution law, evaluating the $\\kappa_D$ parameter. $\\omega$ is damage, for other parameters see funcG function") .staticmethod("funcGInv") .def("setDamage",&CpmPhys::setDamage,"TODO") .def("setRelResidualStrength",&CpmPhys::setRelResidualStrength,"TODO") ); #undef _ZERO_VECTOR3R DECLARE_LOGGER; REGISTER_CLASS_INDEX(CpmPhys,NormShearPhys); }; REGISTER_SERIALIZABLE(CpmPhys); /********************************************************************************* * * I P 2 * *********************************************************************************/ /*! @brief Convert macroscopic properties to CpmPhys with corresponding parameters. * * */ class Ip2_CpmMat_CpmMat_CpmPhys: public IPhysFunctor{ public: virtual void go(const shared_ptr& pp1, const shared_ptr& pp2, const shared_ptr& interaction); FUNCTOR2D(CpmMat,CpmMat); DECLARE_LOGGER; YADE_CLASS_BASE_DOC_ATTRS(Ip2_CpmMat_CpmMat_CpmPhys,IPhysFunctor,"Convert 2 :yref:`CpmMat` instances to :yref:`CpmPhys` with corresponding parameters. Uses simple (arithmetic) averages if material are different. Simple copy of parameters is performed if the :yref:`material` is shared between both particles. See :yref:`cpm-model` for detals.", ((long,cohesiveThresholdIter,10,,"Should new contacts be cohesive? They will before this iter#, they will not be afterwards. If 0, they will never be. If negative, they will always be created as cohesive (10 by default).")) ((shared_ptr,E,,,"Instance of :yref:`MatchMaker` determining how to compute interaction's normal modulus. If ``None``, average value is used.")) ); }; REGISTER_SERIALIZABLE(Ip2_CpmMat_CpmMat_CpmPhys); class Ip2_FrictMat_CpmMat_FrictPhys: public IPhysFunctor{ public: virtual void go(const shared_ptr& pp1, const shared_ptr& pp2, const shared_ptr& interaction); FUNCTOR2D(FrictMat,CpmMat); DECLARE_LOGGER; YADE_CLASS_BASE_DOC_ATTRS(Ip2_FrictMat_CpmMat_FrictPhys,IPhysFunctor,"Convert :yref:`CpmMat` instance and :yref:`FrictMat` instance to :yref:`FrictPhys` with corresponding parameters (young, poisson, frictionAngle). Uses simple (arithmetic) averages if material parameters are different.", ((shared_ptr,frictAngle,,,"See :yref:`Ip2_FrictMat_FrictMat_FrictPhys`.")) ); }; REGISTER_SERIALIZABLE(Ip2_FrictMat_CpmMat_FrictPhys); /********************************************************************************* * * L A W 2 * *********************************************************************************/ class Law2_ScGeom_CpmPhys_Cpm: public LawFunctor{ public: virtual bool go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I); Real elasticEnergy(); Real yieldSigmaTMagnitude(Real sigmaN, Real omega, Real undamagedCohesion, Real tanFrictionAngle) { #ifdef CPM_MATERIAL_MODEL return CPM_YIELD_SIGMA_T_MAGNITUDE(sigmaN); #else //return max((Real)0.,undamagedCohesion*(1-omega)-sigmaN*tanFrictionAngle); throw std::runtime_error("Full CPM model not available in this build"); #endif } //void go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I); FUNCTOR2D(GenericSpheresContact,CpmPhys); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Law2_ScGeom_CpmPhys_Cpm,LawFunctor,"Constitutive law for the :yref:`cpm-model`.", ((int,yieldSurfType,2,,"yield function: 0: mohr-coulomb (original); 1: parabolic; 2: logarithmic, 3: log+lin_tension, 4: elliptic, 5: elliptic+log")) ((Real,yieldLogSpeed,.1,,"scaling in the logarithmic yield surface (should be <1 for realistic results; >=0 for meaningful results)")) ((Real,yieldEllipseShift,NaN,,"horizontal scaling of the ellipse (shifts on the +x axis as interactions with +y are given)")) ((Real,omegaThreshold,((void)">=1. to deactivate, i.e. never delete any contacts",1.),,"damage after which the contact disappears (<1), since omega reaches 1 only for strain →+∞")) ((Real,epsSoft,((void)"approximates confinement (for -3e-3) -20MPa precisely, -100MPa a little over, -200 and -400 are OK (secant)",1.),,"Strain at which softening in compression starts (non-negative to deactivate). The default value is such that plasticity does not occur")) ((Real,relKnSoft,.3,,"Relative rigidity of the softening branch in compression (0=perfect elastic-plastic, <0 softening, >0 hardening)")), /*ctor*/, .def("yieldSigmaTMagnitude",&Law2_ScGeom_CpmPhys_Cpm::yieldSigmaTMagnitude,(py::arg("sigmaN"),py::arg("omega"),py::arg("undamagedCohesion"),py::arg("tanFrictionAngle")),"Return radius of yield surface for given material and state parameters; uses attributes of the current instance (*yieldSurfType* etc), change them before calling if you need that.") .def("elasticEnergy",&Law2_ScGeom_CpmPhys_Cpm::elasticEnergy,"Compute and return the total elastic energy in all \"CpmPhys\" contacts") ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_ScGeom_CpmPhys_Cpm); /********************************************************************************* * * C P M O P E N G L * *********************************************************************************/ #ifdef YADE_OPENGL #include class Gl1_CpmPhys: public GlIPhysFunctor { public: virtual void go(const shared_ptr&,const shared_ptr&,const shared_ptr&,const shared_ptr&,bool wireFrame); virtual ~Gl1_CpmPhys() {}; RENDERS(CpmPhys); DECLARE_LOGGER; YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_CpmPhys,GlIPhysFunctor,"Render :yref:`CpmPhys` objects of interactions.", ((bool,contactLine,true,,"Show contact line")) ((bool,dmgLabel,true,,"Numerically show contact damage parameter")) ((bool,dmgPlane,false,,"[what is this?]")) ((bool,epsT,false,,"Show shear strain ")) ((bool,epsTAxes,false,,"Show axes of shear plane ")) ((bool,normal,false,,"Show contact normal")) ((Real,colorStrainRatio,-1,,"If positive, set the interaction (wire) color based on $\\eps_N$ normalized by $\\eps_0$ × :yref:`colorStrainRatio` ($\\eps_0$ = :yref:`CpmPhys.epsCrackOnset` ). Otherwise, color based on the residual strength.")) ((bool,epsNLabel,false,,"Numerically show normal strain")) ); }; REGISTER_SERIALIZABLE(Gl1_CpmPhys); #endif /********************************************************************************* * * C P M S T A T E U P D A T E R * *********************************************************************************/ class CpmStateUpdater: public PeriodicEngine { struct BodyStats{ int nCohLinks; int nLinks; Real dmgSum /*, epsPlSum*/; Matrix3r stress; Matrix3r damageTensor; BodyStats(): nCohLinks(0), nLinks(0), dmgSum(0.) /*, epsPlSum(0.)*/, stress(Matrix3r::Zero()), damageTensor(Matrix3r::Zero()) {} }; public: virtual void action(){ update(scene); } void update(Scene* rb=NULL); YADE_CLASS_BASE_DOC_ATTRS_CTOR(CpmStateUpdater,PeriodicEngine,"Update :yref:`CpmState` of bodies based on state variables in :yref:`CpmPhys` of interactions with this bod. In particular, bodies' colors and :yref:`CpmState::normDmg` depending on average :yref:`damage` of their interactions and number of interactions that were already fully broken and have disappeared is updated. This engine contains its own loop (2 loops, more precisely) over all bodies and should be run periodically to update colors during the simulation, if desired.", ((Real,avgRelResidual,NaN,,"Average residual strength at last run.")) ((Real,maxOmega,NaN,,"Globally maximum damage parameter at last run.")), initRun=true; ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(CpmStateUpdater); trunk-2017.01a/pkg/dem/DelaunayInterpolation.hpp000066400000000000000000000161401304022710500215350ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Bruno Chareyre * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include #include #include ///////////////////////////////////////////////////////////////////// /* TYPES: Triangulation_vertex_base_with_id_3: we redefine a vertex base including an index for each vertex (available in CGAL in 2D but not in 3D), MeniscusPhysicalData: the physical variables describing a capillary bridge, with a few algebraic operators for computing weighted averages Meniscus: a structure combining MeniscusPhysicalData with some cached data allowing faster operations in multiple queries (pointer to the last cell found and its normals) FUNCTIONS: getIncidentVtxWeights: an interpolation algorithm which is 20x faster than the natural neighbor interpolation of CGAL. returns a list of vertices incident to a query point and their respective weights interpolate: uses the results of getIncidentVtxWeights combined with a data array to return a weighted average, may be used with arbitrary data types provided they have the required algebraic operators main: example usage */ ///////////////////////////////////////////////////////////////////// namespace CGAL { //Vertex base including an index for each vertex, adapted from CGAL::Triangulation_vertex_base_with_id_2 template < typename GT, typename Vb = Triangulation_vertex_base_with_info_3 > class Triangulation_vertex_base_with_id_3 : public Vb { int _id; public: typedef typename Vb::Cell_handle Cell_handle; typedef typename Vb::Point Point; template < typename TDS3 > struct Rebind_TDS { typedef typename Vb::template Rebind_TDS::Other Vb3; typedef Triangulation_vertex_base_with_id_3 Other; }; Triangulation_vertex_base_with_id_3(): Vb() {} Triangulation_vertex_base_with_id_3(const Point & p): Vb(p) {} Triangulation_vertex_base_with_id_3(const Point & p, Cell_handle c): Vb(p, c) {} Triangulation_vertex_base_with_id_3(Cell_handle c): Vb(c) {} unsigned int id() const { return this->info(); } unsigned int& id() { return this->info(); } }; // The function returning vertices and their weights for an arbitrary point in R3 space. // The returned triplet contains: // - the output iterator pointing to the filled vector of vertices // - the sum of weights for normalisation // - a bool telling if the query point was located inside the convex hull of the data points template Triple< OutputIterator, // iterator with value type std::pair typename Dt::Geom_traits::FT, // Should provide 0 and 1 bool > getIncidentVtxWeights(const Dt& dt, const typename Dt::Geom_traits::Point_3& Q, OutputIterator nn_out, typename Dt::Geom_traits::FT & norm_coeff, std::vector& normals, typename Dt::Cell_handle& start = CGAL_TYPENAME_DEFAULT_ARG Dt::Cell_handle()) { //helpful array for permutations const int comb [6] = {1, 2, 3, 0, 1, 2}; typedef typename Dt::Geom_traits Gt; typedef typename Dt::Cell_handle Cell_handle; typedef typename Dt::Locate_type Locate_type; typedef typename Gt::FT Coord_type; CGAL_triangulation_precondition (dt.dimension()== 3); Locate_type lt; int li, lj; Cell_handle c = dt.locate( Q, lt, li, lj, start); bool updateNormals = (c!=start || normals.size()<4); if (updateNormals) normals.clear(); if ( lt == Dt::VERTEX ) { *nn_out++= std::make_pair(c->vertex(li),Coord_type(1)); return make_triple(nn_out,norm_coeff=Coord_type(1),true); } else if (dt.is_infinite(c)) return make_triple(nn_out, Coord_type(1), false);//point outside the convex-hull norm_coeff=0; for ( int k=0;k<4;k++ ) { if (updateNormals) { normals.push_back(cross_product(c->vertex(comb[k])->point()-c->vertex(comb[k+1])->point(),c->vertex(comb[k])->point()-c->vertex(comb[k+2])->point())); normals[k] = normals[k]/ ((c->vertex(k)->point()-c->vertex(comb[k])->point())*normals[k]); } Coord_type closeness = ((Q-c->vertex(comb[k])->point())*normals[k]); Coord_type w = closeness; *nn_out++= std::make_pair(c->vertex(k),w); norm_coeff += w; } start = c; return make_triple(nn_out,norm_coeff,true); } } //END NAMESPACE CGAL typedef CGAL::Exact_predicates_inexact_constructions_kernel K; typedef CGAL::Delaunay_triangulation_3::Geom_traits Traits; typedef CGAL::Triangulation_vertex_base_with_id_3 Vb; typedef CGAL::Triangulation_cell_base_3 Cb; typedef CGAL::Triangulation_data_structure_3 Tds; typedef CGAL::Delaunay_triangulation_3 DT; typedef std::vector< std::pair< DT::Vertex_handle, K::FT> > Vertex_weight_vector; template typename DataOwner::Data interpolate1 (const Dt& dt, const typename Dt::Geom_traits::Point_3& Q, DataOwner& owner, const std::vector& rawData, bool reset) { K::FT norm; Vertex_weight_vector coords; if (reset) owner.cell = dt.cells_begin(); CGAL::Triple,K::FT, bool> result = CGAL::getIncidentVtxWeights(dt, Q,std::back_inserter(coords), norm, owner.normals , owner.cell); typename DataOwner::Data data = typename DataOwner::Data();//initialize null solution if (!result.third) return data;// out of the convex hull, we return the null solution //else, we compute the weighted sum for (unsigned int k=0; kid()]*coords[k].second); if (!data.ending) return data*(1./result.second); else return typename DataOwner::Data(); } template typename DataOwner::Data interpolate2 (const Dt& dt, const typename Dt::Geom_traits::Point_3& Q, DataOwner& owner, const std::vector& rawData, bool reset) { K::FT norm; Vertex_weight_vector coords; if (reset) owner.cell = dt.cells_begin(); CGAL::Triple,K::FT, bool> result = CGAL::getIncidentVtxWeights(dt, Q,std::back_inserter(coords), norm, owner.normals , owner.cell); typename DataOwner::Data data = typename DataOwner::Data();//initialize null solution if (!result.third) return data;// out of the convex hull, we return the null solution //else, we compute the weighted sum for (unsigned int k=0; kid()]*coords[k].second); if (!data.ending) return data*(1./result.second); else return typename DataOwner::Data(); } trunk-2017.01a/pkg/dem/DemXDofGeom.hpp000066400000000000000000000020031304022710500173120ustar00rootroot00000000000000// 2009 © Václav Šmilauer #pragma once #include /*! Abstract class that unites ScGeom and L3Geom, created for the purposes of GlobalStiffnessTimeStepper. It might be removed in the future. */ class GenericSpheresContact: public IGeom{ YADE_CLASS_BASE_DOC_ATTRS_CTOR(GenericSpheresContact,IGeom, "Class uniting :yref:`ScGeom` and :yref:`L3Geom`, for the purposes of :yref:`GlobalStiffnessTimeStepper`. (It might be removed in the future). Do not use this class directly.", ((Vector3r,normal,,,"Unit vector oriented along the interaction, from particle #1, towards particle #2. |yupdate|")) ((Vector3r,contactPoint,,,"some reference point for the interaction (usually in the middle). |ycomp|")) ((Real,refR1,,,"Reference radius of particle #1. |ycomp|")) ((Real,refR2,,,"Reference radius of particle #2. |ycomp|")), createIndex(); ); REGISTER_CLASS_INDEX(GenericSpheresContact,IGeom); virtual ~GenericSpheresContact() {}; }; REGISTER_SERIALIZABLE(GenericSpheresContact); trunk-2017.01a/pkg/dem/Disp2DPropLoadEngine.cpp000066400000000000000000000173561304022710500211040ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2008 by Jerome Duriez * * jerome.duriez@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "Disp2DPropLoadEngine.hpp" #include #include #include #include #include YADE_PLUGIN((Disp2DPropLoadEngine)); void Disp2DPropLoadEngine::postLoad(Disp2DPropLoadEngine&) { std::string outputFile="DirSearch" + Key + "Yade"; ofile.open(outputFile.c_str(), std::ios::app); if (!boost::filesystem::exists( outputFile.c_str() )) ofile<<"theta (!angle in plane (gamma,-du) ) dtau (kPa) dsigma (kPa) dgamma (m) du (m) tau0 (kPa) sigma0 (kPa) d2W coordSs0 coordTot0 coordSsF coordTotF (Yade)" << endl; } void Disp2DPropLoadEngine::action() { if(LOG) cerr << "debut applyCondi !!" << endl; leftbox = Body::byId(id_boxleft); rightbox = Body::byId(id_boxright); frontbox = Body::byId(id_boxfront); backbox = Body::byId(id_boxback); topbox = Body::byId(id_topbox); boxbas = Body::byId(id_boxbas); if(firstIt) { it_begin=scene->iter; H0=topbox->state->pos.y(); X0=topbox->state->pos.x(); Vector3r F_sup=scene->forces.getForce(id_topbox); Fn0=F_sup.y(); Ft0=F_sup.x(); Real OnlySsInt=0 // the half number of real sphere-sphere (only) interactions, at the beginning of the perturbation ,TotInt=0 // the half number of all the real interactions, at the beginning of the perturbation ; InteractionContainer::iterator ii = scene->interactions->begin(); InteractionContainer::iterator iiEnd = scene->interactions->end(); for( ; ii!=iiEnd ; ++ii ) { if ((*ii)->isReal()) { TotInt++; const shared_ptr& b1 = Body::byId( (*ii)->getId1() ); const shared_ptr& b2 = Body::byId( (*ii)->getId2() ); if ( (b1->isDynamic()) && (b2->isDynamic()) ) OnlySsInt++; } } coordSs0 = OnlySsInt/8590; // 8590 is the number of spheres in the CURRENT case coordTot0 = TotInt / 8596; // 8596 is the number of bodies in the CURRENT case firstIt=false; } if ( (scene->iter-it_begin) < nbre_iter) { letDisturb(); } else if ( (scene->iter-it_begin) == nbre_iter) { stopMovement(); string fileName=Key + "DR"+boost::lexical_cast (nbre_iter)+"ItAtV_"+boost::lexical_cast (v)+"done.xml"; // Omega::instance().saveSimulation ( fileName ); saveData(); } } void Disp2DPropLoadEngine::letDisturb() { const Real& dt = scene->dt; dgamma=cos(theta*Mathr::PI/180.0)*v*dt; dh=sin(theta*Mathr::PI/180.0)*v*dt; Real Ysup = topbox->state->pos.y(); Real Ylat = leftbox->state->pos.y(); // Changes in vertical and horizontal position : topbox->state->pos += Vector3r(dgamma,dh,0); leftbox->state->pos += Vector3r(dgamma/2.0,dh/2.0,0); rightbox->state->pos += Vector3r(dgamma/2.0,dh/2.0,0); Real Ysup_mod = topbox->state->pos.y(); Real Ylat_mod = leftbox->state->pos.y(); // with the corresponding velocities : topbox->state->vel=Vector3r(dgamma/dt,dh/dt,0); leftbox->state->vel = Vector3r((dgamma/dt)/2.0,dh/(2.0*dt),0); rightbox->state->vel = Vector3r((dgamma/dt)/2.0,dh/(2.0*dt),0); // Then computation of the angle of the rotation to be done : computeAlpha(); if (alpha == Mathr::PI/2.0) // Case of the very beginning { dalpha = - atan( dgamma / (Ysup_mod -Ylat_mod) ); } else { Real A = (Ysup_mod - Ylat_mod) * 2.0*tan(alpha) / (2.0*(Ysup - Ylat) + dgamma*tan(alpha) ); dalpha = atan( (A - tan(alpha))/(1.0 + A * tan(alpha))); } Quaternionr qcorr(AngleAxisr(dalpha,Vector3r::UnitZ())); if(LOG) cout << "Quaternion associe a la rotation incrementale : " << qcorr.w() << " " << qcorr.x() << " " << qcorr.y() << " " << qcorr.z() << endl; // On applique la rotation en changeant l'orientation des plaques, leurs vang et en affectant donc alpha leftbox->state->ori = qcorr*leftbox->state->ori; leftbox->state->angVel = Vector3r(0,0,1)*dalpha/dt; rightbox->state->ori = qcorr*leftbox->state->ori; rightbox->state->angVel = Vector3r(0,0,1)*dalpha/dt; } void Disp2DPropLoadEngine::computeAlpha() { Quaternionr orientationLeftBox,orientationRightBox; orientationLeftBox = leftbox->state->ori; orientationRightBox = rightbox->state->ori; if(orientationLeftBox.matrix()!=orientationRightBox.matrix()) { cout << "WARNING !!! your lateral boxes have not the same orientation, you're not in the case of a box imagined for creating these engines" << endl; } AngleAxisr aa(orientationLeftBox); alpha=Mathr::PI/2.0-aa.angle(); // right if the initial orientation of the body (on the beginning of the simulation) is q =(1,0,0,0) = FromAxisAngle((0,0,1),0) } void Disp2DPropLoadEngine::stopMovement() { // annulation de la vitesse de la plaque du haut topbox->state->vel = Vector3r(0,0,0); // de la plaque gauche leftbox->state->vel = Vector3r(0,0,0); leftbox->state->angVel = Vector3r(0,0,0); // de la plaque droite rightbox->state->vel = Vector3r(0,0,0); rightbox->state->angVel = Vector3r(0,0,0); } void Disp2DPropLoadEngine::saveData() { Real Xleft = leftbox->state->pos.x() + (YADE_CAST(leftbox->shape.get()))->extents.x(); Real Xright = rightbox->state->pos.x() - (YADE_CAST(rightbox->shape.get()))->extents.x(); Real Zfront = frontbox->state->pos.z() - YADE_CAST(frontbox->shape.get())->extents.z(); Real Zback = backbox->state->pos.z() + (YADE_CAST(backbox->shape.get()))->extents.z(); Real Scontact = (Xright-Xleft)*(Zfront-Zback); // that's so the value of section at the middle of the height of the box InteractionContainer::iterator ii = scene->interactions->begin(); InteractionContainer::iterator iiEnd = scene->interactions->end(); Real OnlySsInt=0 // the half number of real sphere-sphere (only) interactions, at the end of the perturbation ,TotInt=0 // the half number of all the real interactions, at the end of the perturbation ; for( ; ii!=iiEnd ; ++ii ) { if ((*ii)->isReal()) { TotInt++; const shared_ptr& b1 = Body::byId( (*ii)->getId1() ); const shared_ptr& b2 = Body::byId( (*ii)->getId2() ); if ( (b1->isDynamic()) && (b2->isDynamic()) ) OnlySsInt++; } } Real coordSs = OnlySsInt/8590, // 8590 is the number of spheres in the CURRENT case coordTot = TotInt / 8596; // 8596 is the number of bodies in the CURRENT case Vector3r F_sup = scene->forces.getForce(id_topbox); Real dFn=F_sup.y()-Fn0 // OK pour le signe ,dFt=(F_sup.x()-Ft0) ,du=-( topbox->state->pos.y() - H0 ) // OK pour le signe (>0 en compression) ,dgamma=topbox->state->pos.x()-X0 ,SigN0 = (Fn0/Scontact)/1000 // en kPa, pour comparer à Fortran ,Tau0 = -(Ft0/Scontact)/1000 // en kPa, pour comparer à Fortran, Ok pour le signe, cf p. Yade29 ,dSigN= (dFn/Scontact)/1000 // Ok pour le signe ,dTau = -(dFt/Scontact)/1000 // Ok pour le signe, idem que Tau0 ,d2W = dSigN * du + dTau * dgamma ; ofile << boost::lexical_cast (theta) << " "<< boost::lexical_cast (dTau) << " " << boost::lexical_cast (dSigN) << " " << boost::lexical_cast (dgamma)<<" " << boost::lexical_cast (du) << " " << boost::lexical_cast (Tau0) << " " << boost::lexical_cast (SigN0) << " " << boost::lexical_cast (d2W) << " " << boost::lexical_cast (coordSs0) << " " << boost::lexical_cast (coordTot0) << " " << boost::lexical_cast (coordSs) << " " << boost::lexical_cast (coordTot) < #include #include class Disp2DPropLoadEngine : public BoundaryController { private : Real dgamma // the increment of horizontal displacement in one timestep, part of the disturbation ,dh // the increment of vertical displacement in one timestep, part of the disturbation ,H0 // the height of the top box, at the beginnig of the application of the disturbation ,X0 // the X-position of the top box, at the beginnig of the application of the disturbation ,Fn0,Ft0// the normal and tangential force acting on the top box, at... ,coordSs0,coordTot0 ; std::ofstream ofile; Real alpha // angle from the lower plate to the left box (trigo wise), as in other shear Engines, but here the Engine is able to find itself its value ! ,dalpha // the increment over alpha ; bool firstIt;// true if this is the first iteration, false else. int it_begin// the number of the it at which the computation starts ; shared_ptr leftbox; shared_ptr rightbox; shared_ptr frontbox; shared_ptr backbox; shared_ptr topbox; shared_ptr boxbas; void saveData(); void letDisturb(); void stopMovement(); // to cancel all the velocities public : void action() ,computeAlpha() ; void postLoad(Disp2DPropLoadEngine&); YADE_CLASS_BASE_DOC_ATTRS_CTOR(Disp2DPropLoadEngine,BoundaryController, "Disturbs a simple shear sample in a given displacement direction\n\nThis engine allows one to apply, on a simple shear sample, a loading controlled by du/dgamma = cste, which is equivalent to du + cste' * dgamma = 0 (proportionnal path loadings).\nTo do so, the upper plate of the simple shear box is moved in a given direction (corresponding to a given du/dgamma), whereas lateral plates are moved so that the box remains closed.\nThis engine can easily be used to perform directionnal probes, with a python script launching successivly the same .xml which contains this engine, after having modified the direction of loading (see *theta* attribute). That's why this Engine contains a *saveData* procedure which can save data on the state of the sample at the end of the loading (in case of successive loadings - for successive directions - through a python script, each line would correspond to one direction of loading).", ((Body::id_t,id_topbox,3,,"the id of the upper wall")) ((Body::id_t,id_boxbas,1,,"the id of the lower wall")) ((Body::id_t,id_boxleft,0,,"the id of the left wall")) ((Body::id_t,id_boxright,2,,"the id of the right wall")) ((Body::id_t,id_boxfront,5,,"the id of the wall in front of the sample")) ((Body::id_t,id_boxback,4,,"the id of the wall at the back of the sample")) ((Real,theta,0.0,,"the angle, in a (gamma,h=-u) plane from the gamma - axis to the perturbation vector (trigo wise) [degrees]")) ((Real,v,0.0,,"the speed at which the perturbation is imposed. In case of samples which are more sensitive to normal loadings than tangential ones, one possibility is to take v = V_shear - | (V_shear-V_comp)*sin(theta) | => v=V_shear in shear; V_comp in compression [m/s]")) ((int,nbre_iter,0,,"the number of iterations of loading to perform")) ((string,Key,"",,"string to add at the names of the saved files, and of the output file filled by *saveData*")) ((bool,LOG,false,,"boolean controling the output of messages on the screen")), firstIt=true; alpha=Mathr::PI/2.0; ) }; REGISTER_SERIALIZABLE(Disp2DPropLoadEngine); trunk-2017.01a/pkg/dem/DomainLimiter.cpp000066400000000000000000000354721304022710500177640ustar00rootroot00000000000000#include #include #include YADE_PLUGIN((DomainLimiter)(LawTester) #ifdef YADE_OPENGL (GlExtra_LawTester)(GlExtra_OctreeCubes) #endif ); void DomainLimiter::action(){ std::list out; FOREACH(const shared_ptr& b, *scene->bodies){ if((!b) or ((mask>0) and ((b->groupMask & mask)==0))) continue; const Sphere* sphere = dynamic_cast(b->shape.get()); if (sphere){ //Delete only spheres const Vector3r& p(b->state->pos); if(p[0]hi[0] || p[1]hi[1] || p[2]hi[2]) { out.push_back(b->id); nDeleted++; mDeleted+=b->state->mass; Real r = sphere->radius; vDeleted+=(4/3.)*Mathr::PI*pow(r,3); } } } FOREACH(Body::id_t id, out){ scene->bodies->erase(id,false); } } #include #include #include #include #include #include CREATE_LOGGER(LawTester); void LawTester::postLoad(LawTester&){ if(ids.size()==0) return; // uninitialized object, don't do nothing at all if(ids.size()!=2) throw std::invalid_argument("LawTester.ids: exactly two values must be given."); if(disPath.empty() && rotPath.empty()) throw invalid_argument("LawTester.{disPath,rotPath}: at least one point must be given."); if(pathSteps.empty()) throw invalid_argument("LawTester.pathSteps: at least one value must be given."); size_t pathSize=max(disPath.size(),rotPath.size()); // update path points _path.clear(); _path.push_back(Vector6r::Zero()); for(size_t i=0; i()=Vector3r(i()=Vector3r(i Inew=scene->interactions->find(ids[0],ids[1]); string strIds("##"+boost::lexical_cast(ids[0])+"+"+boost::lexical_cast(ids[1])); // interaction not found at initialization if(!I && (!Inew || !Inew->isReal())){ LOG_WARN("Interaction "<isReal())) throw std::runtime_error("LawTester: interaction "+strIds+" was deleted"+(Inew?" (is not real anymore).":".")); // different interaction object if(I && Inew && I!=Inew) throw std::logic_error("LawTester: interacion "+strIds+" is a different object now?!"); assert(Inew); bool doInit=(!I); if(doInit) I=Inew; id1=I->getId1(); id2=I->getId2(); // test object types GenericSpheresContact* gsc=dynamic_cast(I->geom.get()); ScGeom* scGeom=dynamic_cast(I->geom.get()); L3Geom* l3Geom=dynamic_cast(I->geom.get()); L6Geom* l6Geom=dynamic_cast(I->geom.get()); ScGeom6D* scGeom6d=dynamic_cast(I->geom.get()); bool hasRot=(l6Geom || scGeom6d); //NormShearPhys* phys=dynamic_cast(I->phys.get()); //Disabled because of warning if(!gsc) throw std::invalid_argument("LawTester: IGeom of "+strIds+" not a GenericSpheresContact."); if(!scGeom && !l3Geom) throw std::invalid_argument("LawTester: IGeom of "+strIds+" is neither ScGeom, nor L3Geom (or L6Geom)."); assert(!((bool)scGeom && (bool)l3Geom)); // nonsense // get body objects State *state1=Body::byId(id1,scene)->state.get(), *state2=Body::byId(id2,scene)->state.get(); scene->forces.sync(); if(state1->blockedDOFs!=State::DOF_ALL) { LOG_INFO("Blocking all DOFs for #"<blockedDOFs=State::DOF_ALL;} if(state2->blockedDOFs!=State::DOF_ALL) { LOG_INFO("Blocking all DOFs for #"<blockedDOFs=State::DOF_ALL;} if(step-1>*(_pathT.rbegin())){ LOG_INFO("Last step done, setting zero velocities on #"<vel=state1->angVel=state2->vel=state2->angVel=Vector3r::Zero(); uTest=uTestNext; if(doneHook.empty()){ LOG_INFO("No doneHook set, dying."); dead=true; } else{ LOG_INFO("Running doneHook: "<()=Vector3r(NaN,NaN,NaN); if(!l3Geom){ // IGeom's that don't have local axes axX=gsc->normal; /* just in case */ axX.normalize(); if(doInit){ // initialization of the new interaction -- define local axes // take vector in the y or z direction, depending on its length; arbitrary, but one of them is sure to be non-zero axY=axX.cross(std::abs(axX[1])trsf); axX=trsf.row(0); axY=trsf.row(1); axZ=trsf.row(2); uGeom.head<3>()=l3Geom->u; if(l6Geom) uGeom.tail<3>()=l6Geom->phi; } // perform all shearing by translation, as it does not induce bending if(hasRot && rotWeight!=0){ LOG_INFO("LawTester.rotWeight set to 0 (was "<contactPoint; refLength=gsc->refR1+gsc->refR2; renderLength=.5*refLength; // here we go ahead, finally Vector6r uu=linearInterpolate(step,_pathT,_path,_interpPos); Vector6r dUU=uu-uuPrev; uuPrev=uu; Vector3r dU(dUU.head<3>()), dPhi(dUU.tail<3>()); //Vector3r dU=u-uPrev.head<3>(); uPrev.head<3>()=u; //Vector3r dPhi=phi-uPrev.tail<3>(); uPrev.tail<3>()=phi; if(displIsRel){ LOG_DEBUG("Relative displacement diff is "<refR1+gsc->refR2<<")"); dU*=refLength; } LOG_DEBUG("Absolute diff is: displacement "<()+=dU; uTestNext.tail<3>()+=dPhi; // reset velocities where displacement is controlled //for(int i=0; i<3; i++){ if(forceControl[i]==0){ state1.vel[i]=0; state2.vel[i]=0; } // shear is applied as rotation of id2: dε=r₁dθ → dθ=dε/r₁; Vector3r vel[2],angVel[2]; //State* states[]={state1,state2}; for(int i=0; i<2; i++){ int sign=(i==0?-1:1); Real weight=(i==0?1-idWeight:idWeight); // FIXME: this should not use refR1, but real CP-particle distance perhaps? Real radius=(i==0?gsc->refR1:gsc->refR2); Real relRad=radius/refLength; // signed and weighted displacement/rotation to be applied on this sphere (reversed for #0) // some rotations must cancel the sign, by multiplying by sign again Vector3r ddU=sign*dU*weight; // twist can be still distributed with idWeight (!) Vector3r ddPhi=sign*dPhi*(1-relRad); /* shear angles must distribute to both, otherwise it would induce shear */ ddPhi[0]=sign*dPhi[0]*weight; // twist can be still distributed with idWeight vel[i]=angVel[i]=Vector3r::Zero(); // normal displacement vel[i]+=axX*ddU[0]/scene->dt; // shear rotation // multiplication by sign cancels sign in ddU, since rotation is non-symmetric (to increase shear, both spheres have the same rotation) // (unlike shear displacement, which is symmetric) // rotation around Z (which gives y-shear) must be inverted: +ry gives +εzm while -rz gives +εy Real rotZ=-sign*rotWeight*ddU[1]/radius, rotY=sign*rotWeight*ddU[2]/radius; angVel[i]+=(rotY*axY+rotZ*axZ)/scene->dt; // shear displacement // angle that is traversed by a sphere in order to give desired ddU when displaced on the branch of r1+r2 // FIXME: is the branch value correct here?! Real arcAngleY=atan((1-rotWeight)*ddU[1]/radius), arcAngleZ=atan((1-rotWeight)*ddU[2]/radius); // same, but without the atan, which can be disregarded for small increments: // Real arcAngleY=(1-rotWeight)*ddU[1]/radius, arcAngleZ=(1-rotWeight)*ddU[2]/radius; vel[i]+=axY*radius*sin(arcAngleY)/scene->dt; vel[i]+=axZ*radius*sin(arcAngleZ)/scene->dt; // compensate distance increase caused by motion along the perpendicular axis // cos(argAngle*) is always positive, regardless of the orientation // and the compensation is always in the -εx sense (-sign → +1 for #0, -1 for #1) vel[i]+=-sign*axX*radius*((1-cos(arcAngleY))+(1-cos(arcAngleZ)))/scene->dt; // rotation, convert from local to global angVel[i]+=trsf.transpose()*ddPhi; LOG_DEBUG("vel="<renderLength<=0) return; glColor3v(Vector3r(1,0,1)); // switch to local coordinates glTranslatev(tester->contPt); //glMultMatrixd(Eigen::Affine3d(tester->trsf.transpose()).data()); glMultMatrix(Eigen::Transform(tester->trsf.transpose()).data()); glDisable(GL_LIGHTING); //glColor3v(Vector3r(1,0,1)); //glBegin(GL_LINES); glVertex3v(Vector3r::Zero()); glVertex3v(.1*Vector3r::Ones()); glEnd(); //GLUtils::GLDrawText(string("This is the contact point!"),Vector3r::Zero(),Vector3r(1,0,1)); // local axes glLineWidth(2.); for(int i=0; i<3; i++){ Vector3r pt=Vector3r::Zero(); pt[i]=.5*tester->renderLength; Vector3r color=.3*Vector3r::Ones(); color[i]=1; GLUtils::GLDrawLine(Vector3r::Zero(),pt,color); GLUtils::GLDrawText(string(i==0?"x":(i==1?"y":"z")),pt,color); } // put the origin to the initial (no-shear) point, so that the current point appears at the contact point glTranslatev(Vector3r(0,tester->uTestNext[1],tester->uTestNext[2])); const int t(tester->step); const vector& TT(tester->_pathT); const vector& VV(tester->_path); size_t numSegments=TT.size(); const Vector3r colorBefore=Vector3r(.7,1,.7), colorAfter=Vector3r(1,.7,.7); // scale displacement, if they have the strain meaning Real scale=1; if(tester->displIsRel) scale=tester->refLength; // find maximum displacement, draw axes in the shear plane Real displMax=0; FOREACH(const Vector6r& v, VV) displMax=max(v.head<3>().squaredNorm(),displMax); displMax=1.2*scale*sqrt(displMax); glLineWidth(1.); GLUtils::GLDrawLine(Vector3r(0,-displMax,0),Vector3r(0,displMax,0),Vector3r(.5,0,0)); GLUtils::GLDrawLine(Vector3r(0,0,-displMax),Vector3r(0,0,displMax),Vector3r(.5,0,0)); // draw displacement path glLineWidth(4.); for(size_t segment=0; segment()*scale, &to=-VV[segment+1].head<3>()*scale; // current segment if(t>t0 && t>data[i]; } OctreeBox ob; Vector3r mn(data[0],data[1],data[2]), mx(data[3],data[4],data[5]); ob.center=.5*(mn+mx); ob.extents=(.5*(mx-mn)); ob.level=(int)data[6]; ob.fill=(int)data[7]; // for(int i=0; i<=ob.level; i++) cerr<<"\t"; cerr<fillRangeDraw[1]) continue; if(ob.levellevelRangeDraw[1]) continue; bool doFill=(ob.fill>=fillRangeFill[0] && ob.fill<=fillRangeFill[1] && (ob.fill!=0 || !noFillZero)); // -2: empty // -1: recursion limit, empty // 0: subdivided // 1: recursion limit, full // 2: full Vector3r color=(ob.fill==-2?Vector3r(1,0,0):(ob.fill==-1?Vector3r(1,1,0):(ob.fill==0?Vector3r(0,0,1):(ob.fill==1)?Vector3r(0,1,0):(ob.fill==2)?Vector3r(0,1,1):Vector3r(1,1,1)))); glColor3v(color); glPushMatrix(); glTranslatev(ob.center); glScalef(2*ob.extents[0],2*ob.extents[1],2*ob.extents[2]); if (doFill) glutSolidCube(1); else glutWireCube(1); glPopMatrix(); } } #endif /* YADE_OPENGL */ trunk-2017.01a/pkg/dem/DomainLimiter.hpp000066400000000000000000000206641304022710500177660ustar00rootroot00000000000000 #include #include #include class DomainLimiter: public PeriodicEngine{ public: virtual void action(); YADE_CLASS_BASE_DOC_ATTRS(DomainLimiter,PeriodicEngine,"Delete particles that are out of axis-aligned box given by *lo* and *hi*.", ((Vector3r,lo,Vector3r(0,0,0),,"Lower corner of the domain.")) ((Vector3r,hi,Vector3r(0,0,0),,"Upper corner of the domain.")) ((long,nDeleted,0,Attr::readonly,"Cummulative number of particles deleted.")) ((Real,mDeleted,0,,"Mass of deleted particles.")) ((Real,vDeleted,0,,"Volume of deleted particles.")) ((int,mask,-1,,"If mask is defined, only particles with corresponding groupMask will be deleted.")) ); }; REGISTER_SERIALIZABLE(DomainLimiter); class LawTester: public PartialEngine{ Body::id_t id1,id2; // shorthands for local use public: void init(); virtual void action(); void postLoad(LawTester&); void warnDeprec(const string& s1, const string& s2){ if(!warnedDeprecPtRot){ warnedDeprecPtRot=true; LOG_WARN("LawTester."<(); } Vector3r get_ptGeom(){ warnDeprec("ptGeom","uGeom.head()"); return uGeom.head<3>(); } Vector3r get_rotOurs(){ warnDeprec("rotOurs","uTest.tail()"); return uTest.tail<3>(); } Vector3r get_rotGeom(){ warnDeprec("rotGeom","uGeom.tail()"); return uGeom.tail<3>(); } DECLARE_LOGGER; YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(LawTester,PartialEngine,"Prescribe and apply deformations of an interaction in terms of local normal and shear displacements and rotations (using either :yref:`disPpath` and :yref:`rotPath` [or :yref:`path` in the future]). Supported :yref:`IGeom` types are :yref:`ScGeom`, :yref:`L3Geom` and :yref:`L6Geom`. \n\nSee :ysrc:`scripts/test/law-test.py` for an example.", ((vector,disPath,,Attr::triggerPostLoad,"Loading path, where each Vector3 contains desired normal displacement and two components of the shear displacement (in local coordinate system, which is being tracked automatically. If shorter than :yref:`rotPath`, the last value is repeated.")) ((vector,rotPath,,Attr::triggerPostLoad,"Rotational components of the loading path, where each item contains torsion and two bending rotations in local coordinates. If shorter than :yref:`path`, the last value is repeated.")) ((vector,hooks,,,"Python commands to be run when the corresponding point in path is reached, before doing other things in that particular step. See also :yref:`doneHook`. ")) ((Vector6r,uGeom,Vector6r::Zero(),,"Current generalized displacements (3 displacements, 3 rotations), as stored in the interation itself. They should corredpond to :yref:`uTest`, otherwise a bug is indicated.")) ((Vector6r,uTest,Vector6r::Zero(),,"Current generalized displacements (3 displacements, 3 rotations), as they should be according to this :yref:`LawTester`. Should correspond to :yref:`uGeom`.")) ((Vector6r,uTestNext,Vector6r::Zero(),Attr::hidden,"The value of uTest in the next step; since uTest is computed before uGeom is updated (in the next time step), uTest and uGeom would be always shifted by one timestep.")) ((bool,warnedDeprecPtRot,false,Attr::hidden,"Flag to say that the user was already warned about using deprecated ptOurg/ptGeom/rotOurs/rotGeom.")) ((Vector3r,shearTot,Vector3r::Zero(),Attr::hidden,"Current displacement in global coordinates; only used internally with ScGeom.")) ((bool,displIsRel,true,,"Whether displacement values in *disPath* are normalized by reference contact length (r1+r2 for 2 spheres).")) //((Vector3i,forceControl,Vector3i::Zero(),,"Select which components of path (non-zero value) have force (stress) rather than displacement (strain) meaning.")) ((vector,pathSteps,((void)"(constant step)",vector(1,1)),Attr::triggerPostLoad,"Step number for corresponding values in :yref:`path`; if shorter than path, distance between last 2 values is used for the rest.")) ((vector,_pathT,,(Attr::readonly|Attr::noSave),"Time value corresponding to points on path, computed from *pathSteps*. Length is always the same as path.")) ((vector,_path,,(Attr::readonly|Attr::noSave),"Generalized displacement path values, computed from *disPath* and *rotPath* by appending zero initial value, and possibly repeating the last value to make lengths of *disPath* and *rotPath* match.")) ((shared_ptr,I,,(Attr::hidden),"Interaction object being tracked.")) // axX, axY, axZ could be replaced by references to rows in trsf; perhaps do that in the future (in such a case, trsf would not be noSave) ((Vector3r,axX,,Attr::hidden,"Local x-axis in global coordinates (normal of the contact) |yupdate|")) ((Vector3r,axY,,Attr::hidden,"Local y-axis in global coordinates; perpendicular to axX; initialized arbitrarily, but tracked to be consistent. |yupdate|")) ((Vector3r,axZ,,(Attr::hidden|Attr::noSave),"Local z-axis in global coordinates; computed from axX and axY. |yupdate|")) ((Matrix3r,trsf,,(Attr::noSave|Attr::readonly),"Transformation matrix for the local coordinate system. |yupdate|")) ((size_t,_interpPos,0,(Attr::readonly|Attr::hidden),"State cookie for the interpolation routine.")) ((Vector6r,uuPrev,Vector6r::Zero(),(Attr::readonly),"Generalized displacement values reached in the previous step, for knowing which increment to apply in the current step.")) ((int,step,1,,"Step number in which this engine is active; determines position in path, using pathSteps.")) ((string,doneHook,,,"Python command (as string) to run when end of the path is achieved. If empty, the engine will be set :yref:`dead`.")) ((Real,renderLength,0,,"Characteristic length for the purposes of rendering, set equal to the smaller radius.")) ((Real,refLength,0,(Attr::readonly),"Reference contact length, for rendering only.")) ((Vector3r,contPt,Vector3r::Zero(),Attr::hidden,"Contact point (for rendering only)")) ((Real,idWeight,1,,"Float, usually ∈〈0,1〉, determining on how are displacements distributed between particles (0 for id1, 1 for id2); intermediate values will apply respective part to each of them. This parameter is ignored with 6-DoFs :yref:`IGeom`.")) ((Real,rotWeight,1,,"Float ∈〈0,1〉 determining whether shear displacement is applied as rotation or displacement on arc (0 is displacement-only, 1 is rotation-only). Not effective when mutual rotation is specified.")) // reset force components along individual axes, instead of blocking DOFs which have no specific direction (for the force control) , /* init */ , /* ctor */ , /* py */ .add_property("ptOurs",&LawTester::get_ptOurs,"first 3 components of uTest |ydeprecated|") .add_property("ptGeom",&LawTester::get_ptGeom,"first 3 components of uGeom |ydeprecated|") .add_property("rotOurs",&LawTester::get_rotOurs,"last 3 components of uTest |ydeprecated|") .add_property("rotGeom",&LawTester::get_rotGeom,"last 3 components of uGeom |ydeprecated|") ); }; REGISTER_SERIALIZABLE(LawTester); #ifdef YADE_OPENGL #include class GlExtra_LawTester: public GlExtraDrawer{ public: DECLARE_LOGGER; virtual void render(); YADE_CLASS_BASE_DOC_ATTRS(GlExtra_LawTester,GlExtraDrawer,"Find an instance of :yref:`LawTester` and show visually its data.", ((shared_ptr,tester,,,"Associated :yref:`LawTester` object.")) ); }; REGISTER_SERIALIZABLE(GlExtra_LawTester); class GlExtra_OctreeCubes: public GlExtraDrawer{ public: struct OctreeBox{ Vector3r center, extents; int fill; int level; }; std::vector boxes; void postLoad(GlExtra_OctreeCubes&); virtual void render(); YADE_CLASS_BASE_DOC_ATTRS(GlExtra_OctreeCubes,GlExtraDrawer,"Render boxed read from file", ((string,boxesFile,,Attr::triggerPostLoad,"File to read boxes from; ascii files with ``x0 y0 z0 x1 y1 z1 c`` records, where ``c`` is an integer specifying fill (0 for wire, 1 for filled).")) ((Vector2i,fillRangeFill,Vector2i(2,2),,"Range of fill indices that will be filled.")) ((Vector2i,fillRangeDraw,Vector2i(-2,2),,"Range of fill indices that will be rendered.")) ((Vector2i,levelRangeDraw,Vector2i(-2,2),,"Range of levels that will be rendered.")) ((bool,noFillZero,true,,"Do not fill 0-fill boxed (those that are further subdivided)")) ); }; REGISTER_SERIALIZABLE(GlExtra_OctreeCubes); #endif trunk-2017.01a/pkg/dem/ElasticContactLaw.cpp000066400000000000000000000122271304022710500205640ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2005 by Bruno Chareyre bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include"ElasticContactLaw.hpp" #include #include #include #include #include YADE_PLUGIN((Law2_ScGeom_FrictPhys_CundallStrack)(Law2_ScGeom_ViscoFrictPhys_CundallStrack)(ElasticContactLaw)); #if 1 Real Law2_ScGeom_FrictPhys_CundallStrack::getPlasticDissipation() {return (Real) plasticDissipation;} void Law2_ScGeom_FrictPhys_CundallStrack::initPlasticDissipation(Real initVal) {plasticDissipation.reset(); plasticDissipation+=initVal;} Real Law2_ScGeom_FrictPhys_CundallStrack::elasticEnergy() { Real energy=0; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; FrictPhys* phys = dynamic_cast(I->phys.get()); if(phys) { energy += 0.5*(phys->normalForce.squaredNorm()/phys->kn + phys->shearForce.squaredNorm()/phys->ks);} } return energy; } #endif void ElasticContactLaw::action() { if(!functor) functor=shared_ptr(new Law2_ScGeom_FrictPhys_CundallStrack); functor->neverErase=neverErase; functor->scene=scene; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; #ifdef YADE_DEBUG // these checks would be redundant in the functor (LawDispatcher does that already) if(!dynamic_cast(I->geom.get()) || !dynamic_cast(I->phys.get())) continue; #endif functor->go(I->geom, I->phys, I.get()); } } CREATE_LOGGER(Law2_ScGeom_FrictPhys_CundallStrack); bool Law2_ScGeom_FrictPhys_CundallStrack::go(shared_ptr& ig, shared_ptr& ip, Interaction* contact){ int id1 = contact->getId1(), id2 = contact->getId2(); ScGeom* geom= static_cast(ig.get()); FrictPhys* phys = static_cast(ip.get()); if(geom->penetrationDepth <0){ if (neverErase) { phys->shearForce = Vector3r::Zero(); phys->normalForce = Vector3r::Zero();} else return false; } Real& un=geom->penetrationDepth; phys->normalForce=phys->kn*std::max(un,(Real) 0)*geom->normal; Vector3r& shearForce = geom->rotate(phys->shearForce); const Vector3r& shearDisp = geom->shearIncrement(); shearForce -= phys->ks*shearDisp; Real maxFs = phys->normalForce.squaredNorm()*std::pow(phys->tangensOfFrictionAngle,2); if (!scene->trackEnergy && !traceEnergy){//Update force but don't compute energy terms (see below)) // PFC3d SlipModel, is using friction angle. CoulombCriterion if( shearForce.squaredNorm() > maxFs ){ Real ratio = sqrt(maxFs) / shearForce.norm(); shearForce *= ratio;} } else { //almost the same with additional Vector3r instatinated for energy tracing, //duplicated block to make sure there is no cost for the instanciation of the vector when traceEnergy==false if(shearForce.squaredNorm() > maxFs){ Real ratio = sqrt(maxFs) / shearForce.norm(); Vector3r trialForce=shearForce;//store prev force for definition of plastic slip //define the plastic work input and increment the total plastic energy dissipated shearForce *= ratio; Real dissip=((1/phys->ks)*(trialForce-shearForce))/*plastic disp*/ .dot(shearForce)/*active force*/; if (traceEnergy) plasticDissipation += dissip; else if(dissip>0) scene->energy->add(dissip,"plastDissip",plastDissipIx,/*reset*/false); } // compute elastic energy as well scene->energy->add(0.5*(phys->normalForce.squaredNorm()/phys->kn+phys->shearForce.squaredNorm()/phys->ks),"elastPotential",elastPotentialIx,/*reset at every timestep*/true); } if (!scene->isPeriodic && !sphericalBodies) { State* de1 = Body::byId(id1,scene)->state.get(); State* de2 = Body::byId(id2,scene)->state.get(); applyForceAtContactPoint(-phys->normalForce-shearForce, geom->contactPoint, id1, de1->se3.position, id2, de2->se3.position);} else {//we need to use correct branches in the periodic case, the following apply for spheres only Vector3r force = -phys->normalForce-shearForce; scene->forces.addForce(id1,force); scene->forces.addForce(id2,-force); scene->forces.addTorque(id1,(geom->radius1-0.5*geom->penetrationDepth)* geom->normal.cross(force)); scene->forces.addTorque(id2,(geom->radius2-0.5*geom->penetrationDepth)* geom->normal.cross(force)); } return true; } bool Law2_ScGeom_ViscoFrictPhys_CundallStrack::go(shared_ptr& ig, shared_ptr& ip, Interaction* contact){ ScGeom* geom= static_cast(ig.get()); ViscoFrictPhys* phys = static_cast(ip.get()); if (shearCreep) { const Real& dt=scene->dt; geom->rotate(phys->creepedShear); phys->creepedShear+= creepStiffness*phys->ks*(phys->shearForce-phys->creepedShear)*dt/viscosity; phys->shearForce -= phys->ks*((phys->shearForce-phys->creepedShear)*dt/viscosity);} return Law2_ScGeom_FrictPhys_CundallStrack::go(ig,ip,contact); } trunk-2017.01a/pkg/dem/ElasticContactLaw.hpp000066400000000000000000000111231304022710500205630ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2005 by Bruno Chareyre bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include #include class Law2_ScGeom_FrictPhys_CundallStrack: public LawFunctor{ public: OpenMPAccumulator plasticDissipation; virtual bool go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I); Real elasticEnergy (); Real getPlasticDissipation(); void initPlasticDissipation(Real initVal=0); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Law2_ScGeom_FrictPhys_CundallStrack,LawFunctor,"Law for linear compression, and Mohr-Coulomb plasticity surface without cohesion.\nThis law implements the classical linear elastic-plastic law from [CundallStrack1979]_ (see also [Pfc3dManual30]_). The normal force is (with the convention of positive tensile forces) $F_n=\\min(k_n u_n, 0)$. The shear force is $F_s=k_s u_s$, the plasticity condition defines the maximum value of the shear force : $F_s^{\\max}=F_n\\tan(\\phi)$, with $\\phi$ the friction angle.\n\nThis law is well tested in the context of triaxial simulation, and has been used for a number of published results (see e.g. [Scholtes2009b]_ and other papers from the same authors). It is generalised by :yref:`Law2_ScGeom6D_CohFrictPhys_CohesionMoment`, which adds cohesion and moments at contact.", ((bool,neverErase,false,,"Keep interactions even if particles go away from each other (only in case another constitutive law is in the scene, e.g. :yref:`Law2_ScGeom_CapillaryPhys_Capillarity`)")) ((bool,sphericalBodies,true,,"If true, compute branch vectors from radii (faster), else use contactPoint-position. Turning this flag true is safe for sphere-sphere contacts and a few other specific cases. It will give wrong values of torques on facets or boxes.")) ((bool,traceEnergy,false,,"Define the total energy dissipated in plastic slips at all contacts. This will trace only plastic energy in this law, see O.trackEnergy for a more complete energies tracing")) ((int,plastDissipIx,-1,(Attr::hidden|Attr::noSave),"Index for plastic dissipation (with O.trackEnergy)")) ((int,elastPotentialIx,-1,(Attr::hidden|Attr::noSave),"Index for elastic potential energy (with O.trackEnergy)")) ,, .def("elasticEnergy",&Law2_ScGeom_FrictPhys_CundallStrack::elasticEnergy,"Compute and return the total elastic energy in all \"FrictPhys\" contacts") .def("plasticDissipation",&Law2_ScGeom_FrictPhys_CundallStrack::getPlasticDissipation,"Total energy dissipated in plastic slips at all FrictPhys contacts. Computed only if :yref:`Law2_ScGeom_FrictPhys_CundallStrack::traceEnergy` is true.") .def("initPlasticDissipation",&Law2_ScGeom_FrictPhys_CundallStrack::initPlasticDissipation,"Initialize cummulated plastic dissipation to a value (0 by default).") ); FUNCTOR2D(ScGeom,FrictPhys); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_ScGeom_FrictPhys_CundallStrack); class Law2_ScGeom_ViscoFrictPhys_CundallStrack: public Law2_ScGeom_FrictPhys_CundallStrack{ public: virtual bool go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Law2_ScGeom_ViscoFrictPhys_CundallStrack,Law2_ScGeom_FrictPhys_CundallStrack,"Law similar to :yref:`Law2_ScGeom_FrictPhys_CundallStrack` with the addition of shear creep at contacts.", ((bool,shearCreep,false,," ")) ((Real,viscosity,1,," ")) ((Real,creepStiffness,1,," ")) ,, ); FUNCTOR2D(ScGeom,ViscoFrictPhys); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_ScGeom_ViscoFrictPhys_CundallStrack); class ElasticContactLaw : public GlobalEngine{ shared_ptr functor; public : void action(); YADE_CLASS_BASE_DOC_ATTRS(ElasticContactLaw,GlobalEngine,"[DEPRECATED] Loop over interactions applying :yref:`Law2_ScGeom_FrictPhys_CundallStrack` on all interactions.\n\n.. note::\n Use :yref:`InteractionLoop` and :yref:`Law2_ScGeom_FrictPhys_CundallStrack` instead of this class for performance reasons.", ((bool,neverErase,false,,"Keep interactions even if particles go away from each other (only in case another constitutive law is in the scene, e.g. :yref:`Law2_ScGeom_CapillaryPhys_Capillarity`)")) ); }; REGISTER_SERIALIZABLE(ElasticContactLaw); trunk-2017.01a/pkg/dem/FacetTopologyAnalyzer.cpp000066400000000000000000000155101304022710500215030ustar00rootroot00000000000000#include"FacetTopologyAnalyzer.hpp" #include #include #include CREATE_LOGGER(FacetTopologyAnalyzer); YADE_PLUGIN((FacetTopologyAnalyzer)); #ifndef FACET_TOPO void FacetTopologyAnalyzer::action(){ throw runtime_error("FACET_TOPO was not enabled in Facet.hpp at compile-time. Do not use FacetTopologyAnalyzer or recompile."); } #else void FacetTopologyAnalyzer::action(){ commonEdgesFound=0; LOG_DEBUG("Projection axis for analysis is "< > vv; // minimum facet edge length (tolerance scale) Real minSqLen=numeric_limits::infinity(); FOREACH(const shared_ptr& b, *scene->bodies){ shared_ptr f=YADE_PTR_DYN_CAST(b->shape); if(!f) continue; const Vector3r& pos=b->state->pos; for(size_t i=0; i<3; i++){ vv.push_back(shared_ptr(new VertexData(b->getId(),i,f->vertices[i]+pos,(f->vertices[i]+pos).dot(projectionAxis)))); minSqLen=min(minSqLen,(f->vertices[i]-f->vertices[(i+1)%3]).squaredNorm()); } } LOG_DEBUG("Added data for "<coord-vv[i]->coord)<=tolerance){ shared_ptr &vi=vv[i], &vj=vv[j]; if(std::abs(vi->pos[0]-vj->pos[0])<=tolerance && std::abs(vi->pos[1]-vj->pos[1])<=tolerance && std::abs(vi->pos[2]-vj->pos[2])<=tolerance && (vi->pos-vj->pos).squaredNorm()<=tolerance*tolerance){ // OK, these two vertices touch // LOG_TRACE("Vertices "<id<<"/"<vertexNo<<" and "<id<<"/"<vertexNo<<" close enough."); // add vertex to the nextIndetical of the one that has lower index; the one that is added will have isLowestIndex=false if(vi->indexindex){ vi->nextIdentical.push_back(vj); vj->isLowestIndex=false; } else{ vj->nextIdentical.push_back(vi); vi->isLowestIndex=false; } } } } // identity chains start always at lower indices, this way we get all of them sort(vv.begin(),vv.end(),VertexIndexComparator()); int maxVertexId=0; FOREACH(shared_ptr& v, vv){ if(v->vertexId<0){ assert(v->isLowestIndex); v->vertexId=maxVertexId++; } FOREACH(shared_ptr& vNext, v->nextIdentical){ vNext->vertexId=v->vertexId; } if(v->vertexId>=0) continue; // already assigned } LOG_DEBUG("Found "< > topo(scene->bodies->size()); // initialized with the default ctor FOREACH(shared_ptr& v, vv){ if(!topo[v->id]) topo[v->id]=shared_ptr(new FacetTopology(v->id)); topo[v->id]->vertices[v->vertexNo]=v->vertexId; } // make sure all facets have their vertex id's assigned // add non-empty ones to topo1 that will be used for adjacency search afterwards vector > topo1; for(size_t i=0; i t=topo[i]; if(!t) continue; if(t->vertices[0]<0 || t->vertices[1]<0 || t->vertices[2]<0){ LOG_FATAL("Facet #"<vertices[0]<<","<vertices[1]<<","<vertices[2]); throw logic_error("Facet vertex has no integrized vertex assigned?!"); } topo1.push_back(t); } std::sort(topo1.begin(),topo1.end(),FacetTopology::MinVertexComparator()); size_t nTopo=topo1.size(); for(size_t i=0; i& ti(topo1[i]); long tiMaxVertex=ti->maxVertex(); while(++j &tj(topo1[j]); /* since facets are sorted by their min vertex id, we know that it is safe to skip all the rest as soon as max vertex of ti one is smaller than min vertex of tj, as i<=j */ if(tj->minVertex()>tiMaxVertex) break; vector vvv; // array of common vertices for(size_t k=0; k<3; k++){ if (ti->vertices[k]==tj->vertices[0]) vvv.push_back(ti->vertices[k]); else if(ti->vertices[k]==tj->vertices[1]) vvv.push_back(ti->vertices[k]); else if(ti->vertices[k]==tj->vertices[2]) vvv.push_back(ti->vertices[k]); } if(vvv.size()<2) continue; assert(vvv.size()!=3 /* same coords? nonsense*/ ); assert(vvv.size()==2); // from here, we know ti and tj are adjacent vector edge(2,0); int &ei(edge[0]),&ej(edge[1]); // identify what edge are we at, for both facets for(int k=0; k<2; k++){ for(edge[k]=0; edge[k]<3; edge[k]++){ const shared_ptr& tt( k==0 ? ti : tj); size_t v1=tt->vertices[edge[k]],v2=tt->vertices[(edge[k]+1)%3]; if((vvv[0]==v1 && vvv[1]==v2) || (vvv[0]==v2 && vvv[1]==v1)) break; if(edge[k]==2){ LOG_FATAL("No edge identified for 2 vertices "<id<<" is: "<vertices[0]<<","<vertices[1]<<","<vertices[2]<<")"); throw logic_error("No edge identified for given vertices."); } } } // add adjacency information to the facet itself Facet *f1=YADE_CAST((*scene->bodies)[ti->id]->shape.get()), *f2=YADE_CAST((*scene->bodies)[tj->id]->shape.get()); f1->edgeAdjIds[ei]=ti->id; f2->edgeAdjIds[ej]=tj->id; // normals are in the sense of vertex rotation (right-hand rule); therefore, if vertices of the adjacent edge are opposite on each facet, normals are in the same direction bool invNormals=(ti->vertices[ei]==tj->vertices[ej]); assert( ( invNormals && (ti->vertices[ ei ]==tj->vertices[ej]) && (ti->vertices[(ei+1)%3]==tj->vertices[(ej+1)%3]) ) || (!invNormals && (ti->vertices[(ei+1)%3]==tj->vertices[ej]) && (ti->vertices[ ei ]==tj->vertices[(ej+1)%3]) )); // angle between normals const shared_ptr& b1=Body::byId(ti->id,scene); const shared_ptr& b2=Body::byId(tj->id,scene); Vector3r n1g=b1->state->ori*f1->normal, n2g=b2->state->ori*f2->normal; //TRVAR2(n1g,n2g); Vector3r contEdge1g=b1->state->ori*(f1->vertices[(ei+1)%3]-f1->vertices[ei]); // vector of the edge of contact in global coords Quaternionr q12; q12.setFromTwoVectors(n1g,(invNormals?-1.:1.)*n2g); AngleAxisr aa12(q12); Real halfAngle=.5*aa12.angle(); assert(halfAngle>=0 && halfAngle<=Mathr::HALF_PI); if(aa12.axis().dot(contEdge1g)<0 /* convex contact from the side of +n1 */ ) halfAngle*=-1.; f1->edgeAdjHalfAngle[ei]=halfAngle; f2->edgeAdjHalfAngle[ej]=(invNormals ? -halfAngle : halfAngle); commonEdgesFound++; LOG_TRACE("Found adjacent #"<id<<"+#"<id<<"; common edges "< #pragma once #include #include /*! Initializer for filling adjacency geometry data for facets. * * Common vertices and common edges are identified and mutual angle between facet faces * is written to Facet instances. * If facets don't move with respect to each other, this must be done only at the beginning. */ class FacetTopologyAnalyzer: public GlobalEngine{ struct VertexData{ VertexData(Body::id_t _id, int _vertexNo, Vector3r _pos, Real _coord): id(_id), vertexNo(_vertexNo), coord(_coord), pos(_pos){index=3*id+vertexNo; isLowestIndex=true; vertexId=-1;} //! Facet (body id) that we represent Body::id_t id; //! vertex number within this Facet int vertexNo; //! projected coordinate along projectionAxis Real coord; //! global coordinates Vector3r pos; //! index of this vertex (canonical ordering) size_t index; //! is this vertex the first one in the "identity" graph? bool isLowestIndex; //! vertices that are "identical" with this one, but have higer indices vector > nextIdentical; //! id of vertex, once they have id's assigned long vertexId; }; struct VertexComparator{ bool operator()(const shared_ptr& v1, const shared_ptr& v2){return v1->coordcoord;} }; struct VertexIndexComparator{ bool operator()(const shared_ptr& v1, const shared_ptr& v2){return v1->indexindex;} }; struct FacetTopology{ FacetTopology(Body::id_t _id): id(_id){vertices[0]=vertices[1]=vertices[2]=-1;} //! integrized vertices long vertices[3]; //! facet id, for back reference Body::id_t id; long minVertex(){return min(vertices[0],min(vertices[1],vertices[2]));} long maxVertex(){return max(vertices[0],max(vertices[1],vertices[2]));} struct MinVertexComparator{ bool operator()(const shared_ptr& t1, const shared_ptr& t2){ return t1->minVertex()minVertex();} }; }; public: void action(); YADE_CLASS_BASE_DOC_ATTRS(FacetTopologyAnalyzer,GlobalEngine,"Initializer for filling adjacency geometry data for facets.\n\nCommon vertices and common edges are identified and mutual angle between facet faces is written to Facet instances. If facets don't move with respect to each other, this must be done only at the beginng.", ((Vector3r,projectionAxis,Vector3r::UnitX(),,"Axis along which to do the initial vertex sort")) ((Real,relTolerance,1e-4,,"maximum distance of 'identical' vertices, relative to minimum facet size")) ((long,commonEdgesFound,0,,"how many common edges were identified during last run. |yupdate|")) ((long,commonVerticesFound,0,,"how many common vertices were identified during last run. |yupdate|")) ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(FacetTopologyAnalyzer); trunk-2017.01a/pkg/dem/FlatGridCollider.cpp000066400000000000000000000113761304022710500203760ustar00rootroot00000000000000// 2010 © Václav Šmilauer #include #include #include #include //#include YADE_PLUGIN((FlatGridCollider)); CREATE_LOGGER(FlatGridCollider); bool FlatGridCollider::isActivated(){ // keep interactions trequested for deletion as potential (forget removal requests) // scene->interactions->clearPendingErase(); if(!newton) return true; // handle verlet distance fastestBodyMaxDist+=sqrt(newton->maxVelocitySq)*scene->dt; if(fastestBodyMaxDist>verletDist) return true; return false; } void FlatGridCollider::action(){ if(!newton){ FOREACH(const shared_ptr& e, scene->engines){ newton=YADE_PTR_DYN_CAST(e); if(newton) break; } if(!newton){ throw runtime_error("FlatGridCollider: Unable to find NewtonIntegrator in engines."); } } fastestBodyMaxDist=0; // make interaction loop delete unseen potential interactions scene->interactions->iterColliderLastRun=scene->iter; // adjust grid if necessary updateGrid(); FOREACH(const shared_ptr& b, *scene->bodies){ if(!b) continue; // deleted bodies updateBodyCells(b); } updateCollisions(); } // called from the ctor void FlatGridCollider::initIndices(){ sphereIdx=facetIdx=wallIdx=boxIdx=-1; sphereIdx=Sphere::getClassIndexStatic(); LOG_DEBUG("sphereIdx="<& b){ if(!b->shape) return; const Shape* shape(b->shape.get()); // Sphere if(shape->getClassIndex()==sphereIdx){ Real r=static_cast(shape)->radius+verletDist; const Vector3r& C=b->state->pos; // create "bounding cells" and traverse them one by one; integrized coords can be _outside_ grid, they will be forced to closest cells before insertion Vector3i cMn=grid.pt2int(C-Vector3r(r,r,r)), cMx=grid.pt2int(C+Vector3r(r,r,r)), cC=grid.pt2int(C), cPt; LOG_TRACE("Sphere #"<id<<", C="<id<<" to cell ("<getClassName()+"!"); } void FlatGridCollider::updateCollisions(){ shared_ptr& intrs=scene->interactions; const long& iter=scene->iter; // create interactions for all combinations of bodies within one cell FOREACH(const Grid::idVector& v, grid.data){ size_t sz=v.size(); for(size_t i=0; i& I=intrs->find(id1,id2); if(I){ I->iterLastSeen=iter; continue; } // no interaction yet if(!Collider::mayCollide(Body::byId(id1,scene).get(),Body::byId(id2,scene).get())) continue; intrs->insert(shared_ptr(new Interaction(id1,id2))); LOG_TRACE("Created new interaction #"< #include class NewtonIntegrator; class FlatGridCollider: public Collider{ struct Grid{ typedef std::vector idVector; Vector3i size; Vector3r mn, mx; Real step; // convert point into its integral coordinates (can be outside grid, use fitGrid to coords inside) Vector3i pt2int(const Vector3r& pt){ Vector3i ret; for(int i=0;i<3;i++)ret[i]=floor((pt[i]-mn[1])/step); return ret; } std::vector data; // force integral coordinate inside (0,sz-1) int fit(int i, int sz) const { return max(0,min(i,sz-1)); } Vector3i fitGrid(const Vector3i& v){ return Vector3i(fit(v[0],size[0]),fit(v[1],size[1]),fit(v[2],size[2])); } // linearize x,y,z → n in data vector size_t lin(int x, int y, int z) const { return fit(x,size[0])+size[0]*fit(y,size[1])+size[0]*size[1]*fit(z,size[2]); } // return vector of ids at (x,y,z) idVector& operator()(int x, int y, int z){ return data[lin(x,y,z)];} idVector& operator()(const Vector3i& v){ return data[lin(v[0],v[1],v[2])];} const idVector& operator()(int x, int y, int z) const { return data[lin(x,y,z)];} }; Grid grid; int sphereIdx, facetIdx, wallIdx, boxIdx; // needed for maxVelSq shared_ptr newton; // track maximum distance of fastest body, at every step in isActivated Real fastestBodyMaxDist; void initIndices(); void updateGrid(); void updateBodyCells(const shared_ptr& b); void updateCollisions(); virtual void action(); virtual bool isActivated(); DECLARE_LOGGER; YADE_CLASS_BASE_DOC_ATTRS_CTOR(FlatGridCollider,Collider,"Non-optimized grid collider, storing grid as dense flat array. Each body is assigned to (possibly multiple) cells, which are arranged in regular grid between *aabbMin* and *aabbMax*, with cell size *step* (same in all directions). Bodies outsize (*aabbMin*, *aabbMax*) are handled gracefully, assigned to closest cells (this will create spurious potential interactions). *verletDist* determines how much is each body enlarged to avoid collision detection at every step.\n\n.. note::\n\tThis collider keeps all cells in linear memory array, therefore will be memory-inefficient for sparse simulations.\n\n.. warning::\n\tobjects :yref:`Body::bound` are not used, :yref:`BoundFunctors` are not used either: assigning cells to bodies is hard-coded internally. Currently handles :yref:`Shapes` are: :yref:`Sphere`.\n\n.. note::\n\tPeriodic boundary is not handled (yet).\n\n", ((Real,verletDist,0,,"Length by which enlarge space occupied by each particle; avoids running collision detection at every step.")) ((Vector3r,aabbMin,Vector3r::Zero(),,"Lower corner of grid.")) ((Vector3r,aabbMax,Vector3r::Zero(),,"Upper corner of grid (approximate, might be rouded up to *minStep*.")) ((Real,step,0,,"Step in the grid (cell size)")), initIndices(); ); }; REGISTER_SERIALIZABLE(FlatGridCollider); trunk-2017.01a/pkg/dem/ForceTorqueRecorder.cpp000066400000000000000000000017441304022710500211460ustar00rootroot00000000000000#include"ForceTorqueRecorder.hpp" YADE_PLUGIN((ForceRecorder)(TorqueRecorder)); CREATE_LOGGER(ForceRecorder); void ForceRecorder::action(){ totalForce=Vector3r::Zero(); FOREACH(Body::id_t id, ids){ if (!(scene->bodies->exists(id))) continue; totalForce+=scene->forces.getForce(id); }; //Save data to a file out<iter<<" "<bodies->exists(id))) continue; Body* b=Body::byId(id,scene).get(); Vector3r tmpPos = b->state->pos; Vector3r radiusVector = tmpAxis.cross(tmpAxis.cross(tmpPos - zeroPoint)); totalTorque+=tmpAxis.dot(scene->forces.getTorque(id)+radiusVector.cross(scene->forces.getForce(id))); }; //Save data to a file out<iter<<" "< #include class ForceRecorder: public Recorder { public: virtual void action(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(ForceRecorder,Recorder,"Engine saves the resultant force affecting to bodies, listed in `ids`. For instance, can be useful for defining the forces, which affects to _buldozer_ during its work.", ((std::vector,ids,,,"List of bodies whose state will be measured")) ((Vector3r,totalForce,Vector3r::Zero(),,"Resultant force, returning by the function.")) , initRun=true; , ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(ForceRecorder); class TorqueRecorder: public Recorder { public: virtual void action(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(TorqueRecorder,Recorder,"Engine saves the total torque according to the given axis and ZeroPoint, the force is taken from bodies, listed in `ids` For instance, can be useful for defining the torque, which affects on ball mill during its work.", ((std::vector,ids,,,"List of bodies whose state will be measured")) ((Vector3r,rotationAxis,Vector3r::UnitX(),,"Rotation axis")) ((Vector3r,zeroPoint,Vector3r::Zero(),,"Point of rotation center")) ((Real,totalTorque,0,,"Resultant torque, returning by the function.")), initRun=true; ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(TorqueRecorder); trunk-2017.01a/pkg/dem/FrictPhys.cpp000066400000000000000000000060461304022710500171350ustar00rootroot00000000000000#include "FrictPhys.hpp" #include YADE_PLUGIN((FrictPhys)(ViscoFrictPhys)(Ip2_FrictMat_FrictMat_ViscoFrictPhys)(Ip2_FrictMat_FrictMat_FrictPhys)); // The following code was moved from Ip2_FrictMat_FrictMat_FrictPhys.hpp void Ip2_FrictMat_FrictMat_FrictPhys::go( const shared_ptr& b1 , const shared_ptr& b2 , const shared_ptr& interaction) { if(interaction->phys) return; const shared_ptr& mat1 = YADE_PTR_CAST(b1); const shared_ptr& mat2 = YADE_PTR_CAST(b2); Real Ra,Rb;//Vector3r normal; assert(dynamic_cast(interaction->geom.get()));//only in debug mode GenericSpheresContact* sphCont=YADE_CAST(interaction->geom.get()); Ra=sphCont->refR1>0?sphCont->refR1:sphCont->refR2; Rb=sphCont->refR2>0?sphCont->refR2:sphCont->refR1; interaction->phys = shared_ptr(new FrictPhys()); const shared_ptr& contactPhysics = YADE_PTR_CAST(interaction->phys); Real Ea = mat1->young; Real Eb = mat2->young; Real Va = mat1->poisson; Real Vb = mat2->poisson; //harmonic average of the two stiffnesses when (2*Ri*Ei) is the stiffness of a contact point on sphere "i" Real Kn = 2*Ea*Ra*Eb*Rb/(Ea*Ra+Eb*Rb); //same for shear stiffness Real Ks = 2*Ea*Ra*Va*Eb*Rb*Vb/(Ea*Ra*Va+Eb*Rb*Vb); Real frictionAngle = (!frictAngle) ? std::min(mat1->frictionAngle,mat2->frictionAngle) : (*frictAngle)(mat1->id,mat2->id,mat1->frictionAngle,mat2->frictionAngle); contactPhysics->tangensOfFrictionAngle = std::tan(frictionAngle); contactPhysics->kn = Kn; contactPhysics->ks = Ks; }; void Ip2_FrictMat_FrictMat_ViscoFrictPhys::go( const shared_ptr& b1 , const shared_ptr& b2 , const shared_ptr& interaction) { if(interaction->phys) return; const shared_ptr& mat1 = YADE_PTR_CAST(b1); const shared_ptr& mat2 = YADE_PTR_CAST(b2); interaction->phys = shared_ptr(new ViscoFrictPhys()); const shared_ptr& contactPhysics = YADE_PTR_CAST(interaction->phys); Real Ea = mat1->young; Real Eb = mat2->young; Real Va = mat1->poisson; Real Vb = mat2->poisson; Real Ra,Rb;//Vector3r normal; assert(dynamic_cast(interaction->geom.get()));//only in debug mode GenericSpheresContact* sphCont=YADE_CAST(interaction->geom.get()); Ra=sphCont->refR1>0?sphCont->refR1:sphCont->refR2; Rb=sphCont->refR2>0?sphCont->refR2:sphCont->refR1; //harmonic average of the two stiffnesses when (Ri.Ei/2) is the stiffness of a contact point on sphere "i" Real Kn = 2*Ea*Ra*Eb*Rb/(Ea*Ra+Eb*Rb); //same for shear stiffness Real Ks = 2*Ea*Ra*Va*Eb*Rb*Vb/(Ea*Ra*Va+Eb*Rb*Vb); Real frictionAngle = (!frictAngle) ? std::min(mat1->frictionAngle,mat2->frictionAngle) : (*frictAngle)(mat1->id,mat2->id,mat1->frictionAngle,mat2->frictionAngle); contactPhysics->tangensOfFrictionAngle = std::tan(frictionAngle); contactPhysics->kn = Kn; contactPhysics->ks = Ks; }; trunk-2017.01a/pkg/dem/FrictPhys.hpp000066400000000000000000000107201304022710500171340ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2007 by Bruno CHAREYRE * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include class FrictPhys: public NormShearPhys { public : virtual ~FrictPhys() {}; YADE_CLASS_BASE_DOC_ATTRS_CTOR(FrictPhys,NormShearPhys,"The simple linear elastic-plastic interaction with friction angle, like in the traditional [CundallStrack1979]_", ((Real,tangensOfFrictionAngle,NaN,,"tan of angle of friction")), createIndex() ); REGISTER_CLASS_INDEX(FrictPhys,NormShearPhys); }; REGISTER_SERIALIZABLE(FrictPhys); class ViscoFrictPhys: public FrictPhys { public : virtual ~ViscoFrictPhys() {}; YADE_CLASS_BASE_DOC_ATTRS_CTOR(ViscoFrictPhys,FrictPhys,"Temporary version of :yref:`FrictPhys` for compatibility with e.g. :yref:`Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity`", ((Vector3r,creepedShear,Vector3r(0,0,0),(Attr::readonly),"Creeped force (parallel)")), createIndex() ); REGISTER_CLASS_INDEX(ViscoFrictPhys,FrictPhys); }; REGISTER_SERIALIZABLE(ViscoFrictPhys); // The following code was moved from Ip2_FrictMat_FrictMat_FrictPhys.hpp class Ip2_FrictMat_FrictMat_FrictPhys: public IPhysFunctor{ public: virtual void go(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction); FUNCTOR2D(FrictMat,FrictMat); YADE_CLASS_BASE_DOC_ATTRS(Ip2_FrictMat_FrictMat_FrictPhys,IPhysFunctor,"Create a :yref:`FrictPhys` from two :yref:`FrictMats`. The compliance of one sphere under point load is defined here as $1/(E.D)$, with $E$ the stiffness of the sphere and $D$ its diameter. The compliance of the contact itself will be the sum of compliances from each sphere, i.e. $1/(E_1.D_1)+1/(E_2.D_2)$ in the general case, or $2/(E.D)$ in the special case of equal sizes and equal stiffness. Note that summing compliances corresponds to an harmonic average of stiffnesss (as in e.g. [Scholtes2009a]_), which is how kn is actually computed in the :yref:`Ip2_FrictMat_FrictMat_FrictPhys` functor:\n\n $k_n = \\frac{E_1D_1*E_2D_2}{E_1D_1+E_2D_2}=\\frac{k_1*k_2}{k_1+k_2}$, with $k_i=E_iD_i$.\n\n The shear stiffness ks of one sphere is defined via the material parameter :yref:`ElastMat::poisson`, as ks=poisson*kn, and the resulting shear stiffness of the interaction will be also an harmonic average. In the case of a contact between a :yref:`ViscElMat` and a :yref:`FrictMat`, be sure to set :yref:`FrictMat::young` and :yref:`FrictMat::poisson`, otherwise the default value will be used.", ((shared_ptr,frictAngle,,,"Instance of :yref:`MatchMaker` determining how to compute interaction's friction angle. If ``None``, minimum value is used.")) ); }; REGISTER_SERIALIZABLE(Ip2_FrictMat_FrictMat_FrictPhys); class Ip2_FrictMat_FrictMat_ViscoFrictPhys: public Ip2_FrictMat_FrictMat_FrictPhys{ public: virtual void go(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction); FUNCTOR2D(FrictMat,FrictMat); YADE_CLASS_BASE_DOC_ATTRS(Ip2_FrictMat_FrictMat_ViscoFrictPhys,Ip2_FrictMat_FrictMat_FrictPhys,"Create a :yref:`FrictPhys` from two :yref:`FrictMats`. The compliance of one sphere under symetric point loads is defined here as 1/(E.r), with E the stiffness of the sphere and r its radius, and corresponds to a compliance 1/(2.E.r)=1/(E.D) from each contact point. The compliance of the contact itself will be the sum of compliances from each sphere, i.e. 1/(E.D1)+1/(E.D2) in the general case, or 1/(E.r) in the special case of equal sizes. Note that summing compliances corresponds to an harmonic average of stiffnesss, which is how kn is actually computed in the :yref:`Ip2_FrictMat_FrictMat_FrictPhys` functor.\n\nThe shear stiffness ks of one sphere is defined via the material parameter :yref:`ElastMat::poisson`, as ks=poisson*kn, and the resulting shear stiffness of the interaction will be also an harmonic average.", ); }; REGISTER_SERIALIZABLE(Ip2_FrictMat_FrictMat_ViscoFrictPhys); trunk-2017.01a/pkg/dem/FrictViscoPM.cpp000066400000000000000000000252761304022710500175400ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2014 by Klaus Thoeni * * klaus.thoeni@newcastle.edu.au * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include"FrictViscoPM.hpp" #include #include #include YADE_PLUGIN((FrictViscoMat)(FrictViscoPhys)(Ip2_FrictViscoMat_FrictViscoMat_FrictViscoPhys)(Ip2_FrictMat_FrictViscoMat_FrictViscoPhys)(Law2_ScGeom_FrictViscoPhys_CundallStrackVisco)); FrictViscoMat::~FrictViscoMat(){} /********************** Ip2_FrictViscoMat_FrictMat_FrictViscoPhys ****************************/ CREATE_LOGGER(FrictViscoPhys); FrictViscoPhys::~FrictViscoPhys(){}; /********************** Ip2_FrictViscoMat_FrictMat_FrictViscoPhys ****************************/ CREATE_LOGGER(Ip2_FrictViscoMat_FrictViscoMat_FrictViscoPhys); void Ip2_FrictViscoMat_FrictViscoMat_FrictViscoPhys::go(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction){ LOG_TRACE( "Ip2_FrictViscoMat_FrictViscoMat_FrictViscoPhys::go - contact law" ); if(interaction->phys) return; const shared_ptr& mat1 = YADE_PTR_CAST(b1); const shared_ptr& mat2 = YADE_PTR_CAST(b2); interaction->phys = shared_ptr(new FrictViscoPhys()); const shared_ptr& contactPhysics = YADE_PTR_CAST(interaction->phys); Real Ea = mat1->young; Real Eb = mat2->young; Real Va = mat1->poisson; Real Vb = mat2->poisson; Real Ra,Rb; assert(dynamic_cast(interaction->geom.get()));//only in debug mode GenericSpheresContact* sphCont=YADE_CAST(interaction->geom.get()); Ra=sphCont->refR1>0?sphCont->refR1:sphCont->refR2; Rb=sphCont->refR2>0?sphCont->refR2:sphCont->refR1; // calculate stiffness from MatchMaker or use harmonic avarage as usual if not given Real Kn = (kn) ? (*kn)(mat1->id,mat2->id) : 2.*Ea*Ra*Eb*Rb/(Ea*Ra+Eb*Rb); Real Ks = (kRatio) ? (*kRatio)(mat1->id,mat2->id)*Kn : 2.*Ea*Ra*Va*Eb*Rb*Vb/(Ea*Ra*Va+Eb*Rb*Vb); Real frictionAngle = (!frictAngle) ? std::min(mat1->frictionAngle,mat2->frictionAngle) : (*frictAngle)(mat1->id,mat2->id,mat1->frictionAngle,mat2->frictionAngle); contactPhysics->tangensOfFrictionAngle = std::tan(frictionAngle); contactPhysics->kn = Kn; contactPhysics->ks = Ks; /************************/ /* DAMPING COEFFICIENTS */ /************************/ Real betana = mat1->betan; Real betanb = mat2->betan; // inclusion of local viscous damping if (betana!=0 || betanb!=0){ Body::id_t ida = interaction->getId1(); // get id body 1 Body::id_t idb = interaction->getId2(); // get id body 2 State* dea = Body::byId(ida,scene)->state.get(); State* deb = Body::byId(idb,scene)->state.get(); const shared_ptr& ba=Body::byId(ida,scene); const shared_ptr& bb=Body::byId(idb,scene); Real mbar = (!ba->isDynamic() && bb->isDynamic()) ? deb->mass : ((!bb->isDynamic() && ba->isDynamic()) ? dea->mass : (dea->mass*deb->mass / (dea->mass + deb->mass))); // get equivalent mass if both bodies are dynamic, if not set it equal to the one of the dynamic body TRVAR2(Kn,mbar); contactPhysics->cn_crit = 2.*sqrt(mbar*Kn); // Critical damping coefficient (normal direction) contactPhysics->cn = contactPhysics->cn_crit * ( (betana!=0 && betanb!=0) ? ((betana+betanb)/2.) : ( (betanb==0) ? betana : betanb )); // Damping normal coefficient } else contactPhysics->cn=0.; TRVAR1(contactPhysics->cn); } /********************** Ip2_FrictViscoMat_FrictMat_FrictViscoPhys ****************************/ CREATE_LOGGER(Ip2_FrictMat_FrictViscoMat_FrictViscoPhys); void Ip2_FrictMat_FrictViscoMat_FrictViscoPhys::go(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction){ LOG_TRACE( "Ip2_FrictMat_FrictViscoMat_FrictViscoPhys::go - contact law" ); if(interaction->phys) return; const shared_ptr& mat1 = YADE_PTR_CAST(b1); const shared_ptr& mat2 = YADE_PTR_CAST(b2); interaction->phys = shared_ptr(new FrictViscoPhys()); const shared_ptr& contactPhysics = YADE_PTR_CAST(interaction->phys); Real Ea = mat1->young; Real Eb = mat2->young; Real Va = mat1->poisson; Real Vb = mat2->poisson; Real Ra,Rb; assert(dynamic_cast(interaction->geom.get()));//only in debug mode GenericSpheresContact* sphCont=YADE_CAST(interaction->geom.get()); Ra=sphCont->refR1>0?sphCont->refR1:sphCont->refR2; Rb=sphCont->refR2>0?sphCont->refR2:sphCont->refR1; // calculate stiffness from MatchMaker or use harmonic avarage as usual if not given Real Kn = (kn) ? (*kn)(mat1->id,mat2->id) : 2.*Ea*Ra*Eb*Rb/(Ea*Ra+Eb*Rb); Real Ks = (kRatio) ? (*kRatio)(mat1->id,mat2->id)*Kn : 2.*Ea*Ra*Va*Eb*Rb*Vb/(Ea*Ra*Va+Eb*Rb*Vb); Real frictionAngle = (!frictAngle) ? std::min(mat1->frictionAngle,mat2->frictionAngle) : (*frictAngle)(mat1->id,mat2->id,mat1->frictionAngle,mat2->frictionAngle); contactPhysics->tangensOfFrictionAngle = std::tan(frictionAngle); contactPhysics->kn = Kn; contactPhysics->ks = Ks; /************************/ /* DAMPING COEFFICIENTS */ /************************/ Real betanb = mat2->betan; // inclusion of local viscous damping if (betanb!=0){ Body::id_t ida = interaction->getId1(); // get id body 1 Body::id_t idb = interaction->getId2(); // get id body 2 State* dea = Body::byId(ida,scene)->state.get(); State* deb = Body::byId(idb,scene)->state.get(); const shared_ptr& ba=Body::byId(ida,scene); const shared_ptr& bb=Body::byId(idb,scene); Real mbar = (!ba->isDynamic() && bb->isDynamic()) ? deb->mass : ((!bb->isDynamic() && ba->isDynamic()) ? dea->mass : (dea->mass*deb->mass / (dea->mass + deb->mass))); // get equivalent mass if both bodies are dynamic, if not set it equal to the one of the dynamic body TRVAR2(Kn,mbar); contactPhysics->cn_crit = 2.*sqrt(mbar*Kn); // Critical damping coefficient (normal direction) contactPhysics->cn = contactPhysics->cn_crit * betanb; // Damping normal coefficient } else contactPhysics->cn=0.; TRVAR1(contactPhysics->cn); } /********************** Law2_ScGeom_FrictViscoPhys_CundallStrackVisco ****************************/ // #if 1 Real Law2_ScGeom_FrictViscoPhys_CundallStrackVisco::getPlasticDissipation() {return (Real) plasticDissipation;} void Law2_ScGeom_FrictViscoPhys_CundallStrackVisco::initPlasticDissipation(Real initVal) {plasticDissipation.reset(); plasticDissipation+=initVal;} Real Law2_ScGeom_FrictViscoPhys_CundallStrackVisco::elasticEnergy() { Real energy=0; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; FrictPhys* phys = dynamic_cast(I->phys.get()); if(phys) { energy += 0.5*(phys->normalForce.squaredNorm()/phys->kn + phys->shearForce.squaredNorm()/phys->ks);} } return energy; } // #endif CREATE_LOGGER(Law2_ScGeom_FrictViscoPhys_CundallStrackVisco); bool Law2_ScGeom_FrictViscoPhys_CundallStrackVisco::go(shared_ptr& ig, shared_ptr& ip, Interaction* contact) { LOG_TRACE( "Law2_ScGeom_FrictViscoPhys_CundallStrackVisco::go - create interaction physics" ); int id1 = contact->getId1(), id2 = contact->getId2(); ScGeom* geom= static_cast(ig.get()); FrictViscoPhys* phys = static_cast(ip.get()); if(geom->penetrationDepth <0){ if (neverErase) { phys->shearForce = Vector3r::Zero(); phys->normalForce = Vector3r::Zero();} else return false; } Real& un=geom->penetrationDepth; phys->normalForce = phys->kn*std::max(un,(Real) 0) * geom->normal; /************************/ /* DAMPING CONTRIBUTION */ /************************/ // define shifts to handle periodicity const Vector3r shift2 = scene->isPeriodic ? scene->cell->intrShiftPos(contact->cellDist): Vector3r::Zero(); const Vector3r shiftVel = scene->isPeriodic ? scene->cell->intrShiftVel(contact->cellDist): Vector3r::Zero(); State* de1 = Body::byId(id1,scene)->state.get(); State* de2 = Body::byId(id2,scene)->state.get(); // get incident velocity Vector3r incidentV = geom->getIncidentVel(de1, de2, scene->dt, shift2, shiftVel); Vector3r incidentVn = geom->normal.dot(incidentV)*geom->normal; // contact normal velocity phys->normalViscous = phys->cn*incidentVn; phys->normalForce -= phys->normalViscous; // shear force Vector3r& shearForce = geom->rotate(phys->shearForce); const Vector3r& shearDisp = geom->shearIncrement(); shearForce -= phys->ks*shearDisp; Real maxFs = phys->normalForce.squaredNorm()*std::pow(phys->tangensOfFrictionAngle,2); if (!scene->trackEnergy && !traceEnergy){//Update force but don't compute energy terms (see below)) // PFC3d SlipModel, is using friction angle. CoulombCriterion if( shearForce.squaredNorm() > maxFs ){ Real ratio = sqrt(maxFs) / shearForce.norm(); shearForce *= ratio;} } else { //almost the same with additional Vector3r instatinated for energy tracing, //duplicated block to make sure there is no cost for the instanciation of the vector when traceEnergy==false if(shearForce.squaredNorm() > maxFs){ Real ratio = sqrt(maxFs) / shearForce.norm(); Vector3r trialForce=shearForce;//store prev force for definition of plastic slip //define the plastic work input and increment the total plastic energy dissipated shearForce *= ratio; Real dissip=((1/phys->ks)*(trialForce-shearForce))/*plastic disp*/ .dot(shearForce)/*active force*/; if (traceEnergy) plasticDissipation += dissip; else if(dissip>0) scene->energy->add(dissip,"plastDissip",plastDissipIx,/*reset*/false); } // compute elastic energy as well scene->energy->add(0.5*(phys->normalForce.squaredNorm()/phys->kn+phys->shearForce.squaredNorm()/phys->ks),"elastPotential",elastPotentialIx,/*reset at every timestep*/true); } if (!scene->isPeriodic && !sphericalBodies) { applyForceAtContactPoint(-phys->normalForce-shearForce, geom->contactPoint, id1, de1->se3.position, id2, de2->se3.position);} else {//we need to use correct branches in the periodic case, the following apply for spheres only Vector3r force = -phys->normalForce-shearForce; scene->forces.addForce(id1,force); scene->forces.addForce(id2,-force); scene->forces.addTorque(id1,(geom->radius1-0.5*geom->penetrationDepth)* geom->normal.cross(force)); scene->forces.addTorque(id2,(geom->radius2-0.5*geom->penetrationDepth)* geom->normal.cross(force)); } return true; } trunk-2017.01a/pkg/dem/FrictViscoPM.hpp000066400000000000000000000173461304022710500175440ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2014 by Klaus Thoeni * * klaus.thoeni@newcastle.edu.au * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ /** === OVERVIEW OF FrictViscoPM === A particle model for friction and viscous damping in normal direction. The damping coefficient has to be defined with the material whereas the contact stiffness kn and ks/kn can be defined with the Ip2 functor. Remarks: - maybe there is a better way of implementing this without copying from ElasticContactLaw - maybe we can combine some ideas of this contact law with other contact laws */ #pragma once #include #include #include #include #include #include /** This class holds information associated with each body */ class FrictViscoMat: public FrictMat { public: virtual ~FrictViscoMat(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(FrictViscoMat,FrictMat,"Material for use with the FrictViscoPM classes", ((Real,betan,0.,,"Fraction of the viscous damping coefficient in normal direction equal to $\\frac{c_{n}}{C_{n,crit}}$.")) , createIndex(); ); DECLARE_LOGGER; REGISTER_CLASS_INDEX(FrictViscoMat,FrictMat); }; REGISTER_SERIALIZABLE(FrictViscoMat); /** This class holds information associated with each interaction */ class FrictViscoPhys: public FrictPhys { public: virtual ~FrictViscoPhys(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(FrictViscoPhys,FrictPhys,"Representation of a single interaction of the FrictViscoPM type, storage for relevant parameters", ((Real,cn_crit,NaN,,"Normal viscous constant for ctitical damping defined as $\\c_{n}=C_{n,crit}\\beta_n$.")) ((Real,cn,NaN,,"Normal viscous constant defined as $\\c_{n}=c_{n,crit}\\beta_n$.")) ((Vector3r,normalViscous,Vector3r::Zero(),,"Normal viscous component")) , createIndex(); , ); DECLARE_LOGGER; REGISTER_CLASS_INDEX(FrictViscoPhys,FrictPhys); }; REGISTER_SERIALIZABLE(FrictViscoPhys); /** 2d functor creating IPhys (Ip2) taking FrictViscoMat and FrictViscoMat of 2 bodies, returning type FrictViscoPhys */ class Ip2_FrictViscoMat_FrictViscoMat_FrictViscoPhys: public IPhysFunctor{ public: virtual void go(const shared_ptr& pp1, const shared_ptr& pp2, const shared_ptr& interaction); FUNCTOR2D(FrictViscoMat,FrictViscoMat); YADE_CLASS_BASE_DOC_ATTRS(Ip2_FrictViscoMat_FrictViscoMat_FrictViscoPhys,IPhysFunctor,"Converts 2 :yref:`FrictViscoMat` instances to :yref:`FrictViscoPhys` with corresponding parameters. Basically this functor corresponds to :yref:`Ip2_FrictMat_FrictMat_FrictPhys` with the only difference that damping in normal direction can be considered.", ((shared_ptr,kn,,,"Instance of :yref:`MatchMaker` determining how to compute interaction's normal contact stiffnesses. If this value is not given the elastic properties (i.e. young) of the two colliding materials are used to calculate the stiffness.")) ((shared_ptr,kRatio,,,"Instance of :yref:`MatchMaker` determining how to compute interaction's shear contact stiffnesses. If this value is not given the elastic properties (i.e. poisson) of the two colliding materials are used to calculate the stiffness.")) ((shared_ptr,frictAngle,,,"Instance of :yref:`MatchMaker` determining how to compute interaction's friction angle. If ``None``, minimum value is used.")) ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Ip2_FrictViscoMat_FrictViscoMat_FrictViscoPhys); /** 2d functor creating IPhys (Ip2) taking FrictMat and FrictViscoMat of 2 bodies, returning type FrictViscoPhys */ class Ip2_FrictMat_FrictViscoMat_FrictViscoPhys: public IPhysFunctor{ public: virtual void go(const shared_ptr& pp1, const shared_ptr& pp2, const shared_ptr& interaction); FUNCTOR2D(FrictMat,FrictViscoMat); DEFINE_FUNCTOR_ORDER_2D(FrictMat,FrictViscoMat); YADE_CLASS_BASE_DOC_ATTRS(Ip2_FrictMat_FrictViscoMat_FrictViscoPhys,IPhysFunctor,"Converts a :yref:`FrictMat` and :yref:`FrictViscoMat` instance to :yref:`FrictViscoPhys` with corresponding parameters. Basically this functor corresponds to :yref:`Ip2_FrictMat_FrictMat_FrictPhys` with the only difference that damping in normal direction can be considered.", ((shared_ptr,kn,,,"Instance of :yref:`MatchMaker` determining how to compute interaction's normal contact stiffnesses. If this value is not given the elastic properties (i.e. young) of the two colliding materials are used to calculate the stiffness.")) ((shared_ptr,kRatio,,,"Instance of :yref:`MatchMaker` determining how to compute interaction's shear contact stiffnesses. If this value is not given the elastic properties (i.e. poisson) of the two colliding materials are used to calculate the stiffness.")) ((shared_ptr,frictAngle,,,"Instance of :yref:`MatchMaker` determining how to compute interaction's friction angle. If ``None``, minimum value is used.")) ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Ip2_FrictMat_FrictViscoMat_FrictViscoPhys); /** 2d functor creating the interaction law (Law2) based on SphereContactGeometry (ScGeom) and FrictViscoPhys of 2 bodies, returning type FrictViscoPM */ class Law2_ScGeom_FrictViscoPhys_CundallStrackVisco: public LawFunctor{ public: OpenMPAccumulator plasticDissipation; virtual bool go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I); Real elasticEnergy (); Real getPlasticDissipation(); void initPlasticDissipation(Real initVal=0); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Law2_ScGeom_FrictViscoPhys_CundallStrackVisco,LawFunctor,"Constitutive law for the FrictViscoPM. Corresponds to :yref:`Law2_ScGeom_FrictPhys_CundallStrack` with the only difference that viscous damping in normal direction can be considered.", ((bool,neverErase,false,,"Keep interactions even if particles go away from each other (only in case another constitutive law is in the scene, e.g. :yref:`Law2_ScGeom_CapillaryPhys_Capillarity`)")) ((bool,sphericalBodies,true,,"If true, compute branch vectors from radii (faster), else use contactPoint-position. Turning this flag true is safe for sphere-sphere contacts and a few other specific cases. It will give wrong values of torques on facets or boxes.")) ((bool,traceEnergy,false,,"Define the total energy dissipated in plastic slips at all contacts. This will trace only plastic energy in this law, see O.trackEnergy for a more complete energies tracing")) ((int,plastDissipIx,-1,(Attr::hidden|Attr::noSave),"Index for plastic dissipation (with O.trackEnergy)")) ((int,elastPotentialIx,-1,(Attr::hidden|Attr::noSave),"Index for elastic potential energy (with O.trackEnergy)")) ,, .def("elasticEnergy",&Law2_ScGeom_FrictViscoPhys_CundallStrackVisco::elasticEnergy,"Compute and return the total elastic energy in all \"FrictViscoPhys\" contacts") .def("plasticDissipation",&Law2_ScGeom_FrictViscoPhys_CundallStrackVisco::getPlasticDissipation,"Total energy dissipated in plastic slips at all FrictPhys contacts. Computed only if :yref:Law2_ScGeom_FrictViscoPhys_CundallStrackVisco::traceEnergy` is true.") .def("initPlasticDissipation",&Law2_ScGeom_FrictViscoPhys_CundallStrackVisco::initPlasticDissipation,"Initialize cummulated plastic dissipation to a value (0 by default).") ); FUNCTOR2D(ScGeom,FrictViscoPhys); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_ScGeom_FrictViscoPhys_CundallStrackVisco); trunk-2017.01a/pkg/dem/GeneralIntegratorInsertionSortCollider.cpp000066400000000000000000000224361304022710500250600ustar00rootroot00000000000000// 2009 © Václav Šmilauer #include"GeneralIntegratorInsertionSortCollider.hpp" #include #include #include #include #include #include #include #include #include YADE_PLUGIN((GeneralIntegratorInsertionSortCollider)) CREATE_LOGGER(GeneralIntegratorInsertionSortCollider); // STRIDE bool GeneralIntegratorInsertionSortCollider::isActivated(){ // activated if number of bodies changes (hence need to refresh collision information) // or the time of scheduled run already came, or we were never scheduled yet if(!strideActive) return true; if(!integrator) return true; if(fastestBodyMaxDist<0){fastestBodyMaxDist=0; return true;} fastestBodyMaxDist=integrator->maxVelocitySq; if(fastestBodyMaxDist>=1 || fastestBodyMaxDist==0) return true; if((size_t)BB[0].size!=2*scene->bodies->size()) return true; if(scene->interactions->dirty) return true; if(scene->doSort) { scene->doSort=false; return true; } return false; } void GeneralIntegratorInsertionSortCollider::action(){ #ifdef ISC_TIMING timingDeltas->start(); #endif long nBodies=(long)scene->bodies->size(); InteractionContainer* interactions=scene->interactions.get(); scene->interactions->iterColliderLastRun=-1; // periodicity changed, force reinit if(scene->isPeriodic != periodic){ for(int i=0; i<3; i++) BB[i].vec.clear(); periodic=scene->isPeriodic; } // pre-conditions // adjust storage size bool doInitSort=false; if (doSort) { doInitSort=true; doSort=false; } if(BB[0].size!=2*nBodies){ long BBsize=BB[0].size; LOG_DEBUG("Resize bounds containers from "<200 || BBsize==0) doInitSort=true; assert((BBsize%2)==0); for(int i=0; i<3; i++){ BB[i].vec.reserve(2*nBodies); // add lower and upper bounds; coord is not important, will be updated from bb shortly for(long id=BBsize/2; idbodies->size()); // update periodicity assert(BB[0].axis==0); assert(BB[1].axis==1); assert(BB[2].axis==2); if(periodic) for(int i=0; i<3; i++) BB[i].updatePeriodicity(scene); if(verletDist<0){ Real minR=std::numeric_limits::infinity(); FOREACH(const shared_ptr& b, *scene->bodies){ if(!b || !b->shape) continue; Sphere* s=dynamic_cast(b->shape.get()); if(!s) continue; minR=min(s->radius,minR); } if (std::isinf(minR)) LOG_ERROR("verletDist is set to 0 because no spheres were found. It will result in suboptimal performances, consider setting a positive verletDist in your script."); // if no spheres, disable stride verletDist=std::isinf(minR) ? 0 : std::abs(verletDist)*minR; } // update bounds via boundDispatcher boundDispatcher->scene=scene; boundDispatcher->sweepDist=verletDist; boundDispatcher->minSweepDistFactor=minSweepDistFactor; boundDispatcher->targetInterv=targetInterv; boundDispatcher->updatingDispFactor=updatingDispFactor; boundDispatcher->action(); // if interactions are dirty, force reinitialization if(scene->interactions->dirty){ doInitSort=true; scene->interactions->dirty=false; } // STRIDE if(verletDist>0){ // get the Integrator, to ask for the maximum velocity value if(!integrator){ FOREACH(shared_ptr& e, scene->engines){ integrator=YADE_PTR_DYN_CAST(e); if(integrator) break; } if(!integrator){ throw runtime_error("InsertionSortCollider.verletDist>0, but unable to locate any Integrator within O.engines."); } } } ISC_CHECKPOINT("init"); // STRIDE // get us ready for strides, if they were deactivated if(!strideActive && verletDist>0 && integrator->maxVelocitySq>=0){ // maxVelocitySq is a really computed value strideActive=true; } if(strideActive){ assert(verletDist>0); assert(strideActive); assert(integrator->maxVelocitySq>=0); integrator->updatingDispFactor=updatingDispFactor; } else { /* !strideActive */ boundDispatcher->sweepDist=0; } ISC_CHECKPOINT("bound"); // copy bounds along given axis into our arrays for(long i=0; i<2*nBodies; i++){ for(int j=0; j<3; j++){ VecBounds& BBj=BB[j]; const Body::id_t id=BBj[i].id; const shared_ptr& b=Body::byId(id,scene); if(b){ const shared_ptr& bv=b->bound; // coordinate is min/max if has bounding volume, otherwise both are the position. Add periodic shift so that we are inside the cell // watch out for the parentheses around ?: within ?: (there was unwanted conversion of the Reals to bools!) BBj[i].coord=((BBj[i].flags.hasBB=((bool)bv)) ? (BBj[i].flags.isMin ? bv->min[j] : bv->max[j]) : (b->state->pos[j])) - (periodic ? BBj.cellDim*BBj[i].period : 0.); } else { BBj[i].flags.hasBB=false; /* for vanished body, keep the coordinate as-is, to minimize inversions. */ } // if initializing periodic, shift coords & record the period into BBj[i].period if(doInitSort && periodic) { BBj[i].coord=cellWrap(BBj[i].coord,0,BBj.cellDim,BBj[i].period); } } } // for each body, copy its minima and maxima, for quick checks of overlaps later BOOST_STATIC_ASSERT(sizeof(Vector3r)==3*sizeof(Real)); for(Body::id_t id=0; id& b=Body::byId(id,scene); if(b){ const shared_ptr& bv=b->bound; if(bv) { memcpy(&minima[3*id],&bv->min,3*sizeof(Real)); memcpy(&maxima[3*id],&bv->max,3*sizeof(Real)); } // ⇐ faster than 6 assignments else{ const Vector3r& pos=b->state->pos; memcpy(&minima[3*id],&pos,3*sizeof(Real)); memcpy(&maxima[3*id],&pos,3*sizeof(Real)); } } else { memset(&minima[3*id],0,3*sizeof(Real)); memset(&maxima[3*id],0,3*sizeof(Real)); } } ISC_CHECKPOINT("copy"); // process interactions that the constitutive law asked to be erased // interactions->erasePending(*this,scene); interactions->conditionalyEraseNonReal(*this,scene); ISC_CHECKPOINT("erase"); // sort // the regular case if(!doInitSort && !sortThenCollide){ /* each inversion in insertionSort calls handleBoundInversion, which in turns may add/remove interaction */ if(!periodic) for(int i=0; i<3; i++) insertionSort(BB[i],interactions,scene); else for(int i=0; i<3; i++) insertionSortPeri(BB[i],interactions,scene); } // create initial interactions (much slower) else { if(doInitSort){ // the initial sort is in independent in 3 dimensions, may be run in parallel; it seems that there is no time gain running in parallel, though // important to reset loInx for periodic simulation (!!) for(int i=0; i<3; i++) { BB[i].loIdx=0; std::sort(BB[i].vec.begin(),BB[i].vec.end()); } numReinit++; } else { // sortThenCollide if(!periodic) for(int i=0; i<3; i++) insertionSort(BB[i],interactions,scene,false); else for(int i=0; i<3; i++) insertionSortPeri(BB[i],interactions,scene,false); } // traverse the container along requested axis assert(sortAxis==0 || sortAxis==1 || sortAxis==2); VecBounds& V=BB[sortAxis]; // go through potential aabb collisions, create interactions as necessary if(!periodic){ for(long i=0; i<2*nBodies; i++){ // start from the lower bound (i.e. skipping upper bounds) // skip bodies without bbox, because they don't collide if(!(V[i].flags.isMin && V[i].flags.hasBB)) continue; const Body::id_t& iid=V[i].id; // go up until we meet the upper bound for(long j=i+1; /* handle case 2. of swapped min/max */ j<2*nBodies && V[j].id!=iid; j++){ const Body::id_t& jid=V[j].id; // take 2 of the same condition (only handle collision [min_i..max_i]+min_j, not [min_i..max_i]+min_i (symmetric) if(!V[j].flags.isMin) continue; /* abuse the same function here; since it does spatial overlap check first, it is OK to use it */ handleBoundInversion(iid,jid,interactions,scene); assert(j<2*nBodies-1); } } } else { // periodic case: see comments above for(long i=0; i<2*nBodies; i++){ if(!(V[i].flags.isMin && V[i].flags.hasBB)) continue; const Body::id_t& iid=V[i].id; long cnt=0; // we might wrap over the periodic boundary here; that's why the condition is different from the aperiodic case for(long j=V.norm(i+1); V[j].id!=iid; j=V.norm(j+1)){ const Body::id_t& jid=V[j].id; if(!V[j].flags.isMin) continue; handleBoundInversionPeri(iid,jid,interactions,scene); if(cnt++>2*(long)nBodies){ LOG_FATAL("Uninterrupted loop in the initial sort?"); throw std::logic_error("loop??"); } } } } } ISC_CHECKPOINT("sort&collide"); } trunk-2017.01a/pkg/dem/GeneralIntegratorInsertionSortCollider.hpp000066400000000000000000000023011304022710500250520ustar00rootroot00000000000000// 2014 Burak ER #pragma once #include /*! Adaptive Integration Sort Collider: Changing the Integrator dependence from Newton Integrator to Arbitrary Integrators. Arbitrary integrators should use the Integrator interface. */ #ifdef ISC_TIMING #define ISC_CHECKPOINT(cpt) timingDeltas->checkpoint(cpt) #else #define ISC_CHECKPOINT(cpt) #endif class Integrator; class GeneralIntegratorInsertionSortCollider: public InsertionSortCollider{ // we need this to find out about current maxVelocitySq shared_ptr integrator; // if False, no type of striding is used public: virtual bool isActivated(); //override this function to change NewtonIntegrator dependency. virtual void action(); //override this function to change behaviour with the NewtonIntegrator dependency. YADE_CLASS_BASE_DOC(GeneralIntegratorInsertionSortCollider,InsertionSortCollider," This class is the adaptive version of the InsertionSortCollider and changes the NewtonIntegrator dependency of the collider algorithms to the Integrator interface which is more general."); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(GeneralIntegratorInsertionSortCollider); trunk-2017.01a/pkg/dem/GlobalStiffnessTimeStepper.cpp000066400000000000000000000225561304022710500224750ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include"GlobalStiffnessTimeStepper.hpp" #include #include #include #include #include #include #include #include CREATE_LOGGER(GlobalStiffnessTimeStepper); YADE_PLUGIN((GlobalStiffnessTimeStepper)); GlobalStiffnessTimeStepper::~GlobalStiffnessTimeStepper() {} void GlobalStiffnessTimeStepper::findTimeStepFromBody(const shared_ptr& body, Scene * ncb) { State* sdec=body->state.get(); Vector3r& stiffness= stiffnesses[body->getId()]; Vector3r& Rstiffness=Rstiffnesses[body->getId()]; if(body->isClump()) {// if clump, we sum stifnesses of all members const shared_ptr& clump=YADE_PTR_CAST(body->shape); FOREACH(Clump::MemberMap::value_type& B, clump->members){ const shared_ptr& b = Body::byId(B.first,scene); stiffness+=stiffnesses[b->getId()]; Rstiffness+=Rstiffnesses[b->getId()]; if (viscEl == true){ viscosities[body->getId()]+=viscosities[b->getId()]; Rviscosities[body->getId()]+=Rviscosities[b->getId()]; } } } if(!sdec || stiffness==Vector3r::Zero()){ if (densityScaling) sdec->densityScaling = min(1.0001*sdec->densityScaling, timestepSafetyCoefficient*pow(defaultDt/targetDt,2.0)); return; // not possible to compute! } //Determine the elastic minimum eigenperiod (and if required determine also the viscous one separately and take the minimum of the two) //Elastic Real dtx, dty, dtz; Real dt = max( max (stiffness.x(), stiffness.y()), stiffness.z() ); if (dt!=0) { dt = sdec->mass/dt; computedSomething = true;}//dt = squared eigenperiod of translational motion else dt = Mathr::MAX_REAL; if (Rstiffness.x()!=0) { dtx = sdec->inertia.x()/Rstiffness.x(); computedSomething = true;}//dtx = squared eigenperiod of rotational motion around x else dtx = Mathr::MAX_REAL; if (Rstiffness.y()!=0) { dty = sdec->inertia.y()/Rstiffness.y(); computedSomething = true;} else dty = Mathr::MAX_REAL; if (Rstiffness.z()!=0) { dtz = sdec->inertia.z()/Rstiffness.z(); computedSomething = true;} else dtz = Mathr::MAX_REAL; Real Rdt = std::min( std::min (dtx, dty), dtz );//Rdt = smallest squared eigenperiod for elastic rotational motions dt = 1.41044*timestepSafetyCoefficient*std::sqrt(std::min(dt,Rdt));//1.41044 = sqrt(2) //Viscous if (viscEl == true){ Vector3r& viscosity = viscosities[body->getId()]; Vector3r& Rviscosity = Rviscosities[body->getId()]; Real dtx_visc, dty_visc, dtz_visc; Real dt_visc = max(max(viscosity.x(), viscosity.y()), viscosity.z() ); if (dt_visc!=0) { dt_visc = sdec->mass/dt_visc; computedSomething = true;}//dt = eigenperiod of the viscous translational motion else {dt_visc = Mathr::MAX_REAL;} if (Rviscosity.x()!=0) { dtx_visc = sdec->inertia.x()/Rviscosity.x(); computedSomething = true;}//dtx = eigenperiod of viscous rotational motion around x else dtx_visc = Mathr::MAX_REAL; if (Rviscosity.y()!=0) { dty_visc = sdec->inertia.y()/Rviscosity.y(); computedSomething = true;} else dty_visc = Mathr::MAX_REAL; if (Rviscosity.z()!=0) { dtz_visc = sdec->inertia.z()/Rviscosity.z(); computedSomething = true;} else dtz_visc = Mathr::MAX_REAL; Real Rdt_visc = std::min( std::min (dtx_visc, dty_visc), dtz_visc );//Rdt = smallest squared eigenperiod for viscous rotational motions dt_visc = 2*timestepSafetyCoefficient*std::min(dt_visc,Rdt_visc); //Take the minimum between the elastic and viscous minimum eigenperiod. dt = std::min(dt,dt_visc); } //if there is a target dt, then we apply density scaling on the body, the inertia used in Newton will be mass*scaling, the weight is unmodified if (densityScaling) { sdec->densityScaling = min(sdec->densityScaling,timestepSafetyCoefficient*pow(dt /targetDt,2.0)); newDt=targetDt; } //else we update dt normaly else {newDt = std::min(dt,newDt);} } bool GlobalStiffnessTimeStepper::isActivated() { return (active && ((!computedOnce) || (scene->iter % timeStepUpdateInterval == 0) || (scene->iter < (long int) 2) )); } void GlobalStiffnessTimeStepper::computeTimeStep(Scene* ncb) { // for some reason, this line is necessary to have correct functioning (no idea _why_) // see scripts/test/compare-identical.py, run with or without active=active. active=active; if (defaultDt<0) defaultDt= timestepSafetyCoefficient*Shop::PWaveTimeStep(Omega::instance().getScene()); computeStiffnesses(ncb); shared_ptr& bodies = ncb->bodies; newDt = Mathr::MAX_REAL; computedSomething=false; BodyContainer::iterator bi = bodies->begin(); BodyContainer::iterator biEnd = bodies->end(); for( ; bi!=biEnd ; ++bi ){ shared_ptr b = *bi; if (b->isDynamic() && !b->isClumpMember()) findTimeStepFromBody(b, ncb); } if(densityScaling) (newDt=targetDt); if(computedSomething || densityScaling){ previousDt = min ( min(newDt , maxDt), 1.05*previousDt );// at maximum, dt will be multiplied by 1.05 in one iterration, this is to prevent brutal switches from 0.000... to 1 in some computations scene->dt=previousDt; computedOnce = true;} else if (!computedOnce) scene->dt=defaultDt; // LOG_INFO("computed timestep " << newDt << // (scene->dt==newDt ? string(", applied") : // string(", BUT timestep is ")+boost::lexical_cast(scene->dt))<<"."); } void GlobalStiffnessTimeStepper::computeStiffnesses(Scene* rb){ /* check size */ size_t size=stiffnesses.size(); if(sizebodies->size()){ size=rb->bodies->size(); stiffnesses.resize(size); Rstiffnesses.resize(size); if (viscEl == true){ viscosities.resize(size); Rviscosities.resize(size); } } /* reset stored values */ memset(& stiffnesses[0],0,sizeof(Vector3r)*size); memset(&Rstiffnesses[0],0,sizeof(Vector3r)*size); if (viscEl == true){ memset(& viscosities[0],0,sizeof(Vector3r)*size); memset(&Rviscosities[0],0,sizeof(Vector3r)*size); } FOREACH(const shared_ptr& contact, *rb->interactions){ if(!contact->isReal()) continue; GenericSpheresContact* geom=YADE_CAST(contact->geom.get()); assert(geom); NormShearPhys* phys=YADE_CAST(contact->phys.get()); assert(phys); // all we need for getting stiffness Vector3r& normal=geom->normal; Real& kn=phys->kn; Real& ks=phys->ks; Real& radius1=geom->refR1; Real& radius2=geom->refR2; Real fn = (static_cast (contact->phys.get()))->normalForce.squaredNorm(); if (fn==0) continue;//Is it a problem with some laws? I still don't see why. //Diagonal terms of the translational stiffness matrix Vector3r diag_stiffness = Vector3r(std::pow(normal.x(),2),std::pow(normal.y(),2),std::pow(normal.z(),2)); diag_stiffness *= kn-ks; diag_stiffness = diag_stiffness + Vector3r(1,1,1)*ks; //diagonal terms of the rotational stiffness matrix // Vector3r branch1 = currentContactGeometry->normal*currentContactGeometry->radius1; // Vector3r branch2 = currentContactGeometry->normal*currentContactGeometry->radius2; Vector3r diag_Rstiffness = Vector3r(std::pow(normal.y(),2)+std::pow(normal.z(),2), std::pow(normal.x(),2)+std::pow(normal.z(),2), std::pow(normal.x(),2)+std::pow(normal.y(),2)); diag_Rstiffness *= ks; // If contact moments are present, add the diagonal of (n⊗n*k_twist + (I-n⊗n)*k_roll = (k_twist-k_roll)*n⊗n + I*k_roll ) : Vector3r kr = (static_cast (contact->phys.get()))->getRotStiffness(); //get the vector (k_twist,k_roll,k_roll) Vector3r nn (std::pow(normal.x(),2),std::pow(normal.y(),2),std::pow(normal.z(),2));//n⊗n Vector3r diag_Mstiffness= (kr[0]-kr[1])*nn + Vector3r(1,1,1)*kr[1]; stiffnesses [contact->getId1()]+=diag_stiffness; Rstiffnesses[contact->getId1()]+=diag_Rstiffness*pow(radius1,2)+ diag_Mstiffness; stiffnesses [contact->getId2()]+=diag_stiffness; Rstiffnesses[contact->getId2()]+=diag_Rstiffness*pow(radius2,2)+ diag_Mstiffness; //Same for the Viscous part, if required if (viscEl == true){ ViscElPhys* viscPhys = YADE_CAST(contact->phys.get()); assert(viscPhys); Real& cn=viscPhys->cn; Real& cs=viscPhys->cs; //Diagonal terms of the translational viscous matrix Vector3r diag_viscosity = Vector3r(std::pow(normal.x(),2),std::pow(normal.y(),2),std::pow(normal.z(),2)); diag_viscosity *= cn-cs; diag_viscosity = diag_viscosity + Vector3r(1,1,1)*cs; //diagonal terms of the rotational viscous matrix Vector3r diag_Rviscosity = Vector3r(std::pow(normal.y(),2)+std::pow(normal.z(),2), std::pow(normal.x(),2)+std::pow(normal.z(),2), std::pow(normal.x(),2)+std::pow(normal.y(),2)); diag_Rviscosity *= cs; // Add the contact stiffness matrix to the two particles one viscosities [contact->getId1()]+=diag_viscosity; Rviscosities[contact->getId1()]+=diag_Rviscosity*pow(radius1,2); viscosities [contact->getId2()]+=diag_viscosity; Rviscosities[contact->getId2()]+=diag_Rviscosity*pow(radius2,2); } } } trunk-2017.01a/pkg/dem/GlobalStiffnessTimeStepper.hpp000066400000000000000000000070611304022710500224740ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include /*! \brief Compute the critical timestep of the leap-frog scheme based on global stiffness of bodies See usage details in TriaxialTest documentation (TriaxialTest is also a good example of how to use this class) */ class Interaction; class BodyContainer; class Scene; class GlobalStiffnessTimeStepper : public TimeStepper { private : vector stiffnesses; vector Rstiffnesses; vector viscosities; vector Rviscosities; void computeStiffnesses(Scene*); Real newDt; bool computedSomething, computedOnce; void findTimeStepFromBody(const shared_ptr& body, Scene * ncb); public : virtual ~GlobalStiffnessTimeStepper(); virtual void computeTimeStep(Scene*); virtual bool isActivated(); YADE_CLASS_BASE_DOC_ATTRS_CTOR( GlobalStiffnessTimeStepper,TimeStepper,"An engine assigning the time-step as a fraction of the minimum eigen-period in the problem. The derivation is detailed in the chapter on `DEM formulation `_. The viscEl option enables to evaluate the timestep in a similar way for the visco-elastic contact law :yref:`Law2_ScGeom_ViscElPhys_Basic`, more detail in :yref:`GlobalStiffnessTimestepper::viscEl`. ", ((Real,defaultDt,-1,,"used as the initial value of the timestep (especially useful in the first steps when no contact exist). If negative, it will be defined by :yref:`utils.PWaveTimeStep` * :yref:`GlobalStiffnessTimeStepper::timestepSafetyCoefficient`")) ((Real,maxDt,Mathr::MAX_REAL,,"if positive, used as max value of the timestep whatever the computed value")) ((Real,previousDt,1,,"last computed dt |yupdate|")) ((Real,timestepSafetyCoefficient,0.8,,"safety factor between the minimum eigen-period and the final assigned dt (less than 1)")) ((bool,densityScaling,false,,"|yupdate| don't modify this value if you don't plan to modify the scaling factor manually for some bodies. In most cases, it is enough to set :yref:`NewtonIntegrator::densityScaling` and let this one be adjusted automatically.")) ((Real,targetDt,1,,"if :yref:`NewtonIntegrator::densityScaling` is active, this value will be used as the simulation timestep and the scaling will use this value of dt as the target value. The value of targetDt is arbitrary and should have no effect in the result in general. However if some bodies have imposed velocities, for instance, they will move more or less per each step depending on this value.")) ((bool,viscEl,false,,"To use with :yref:`ViscElPhys`. if True, evaluate separetly the minimum eigen-period in the problem considering only the elastic contribution on one hand (spring only), and only the viscous contribution on the other hand (dashpot only). Take then the minimum of the two and use the safety coefficient :yref:`GlobalStiffnessTimestepper::timestepSafetyCoefficient` to take into account the possible coupling between the two contribution.")), computedOnce=false;) DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(GlobalStiffnessTimeStepper); trunk-2017.01a/pkg/dem/HertzMindlin.cpp000066400000000000000000000670271304022710500176370ustar00rootroot00000000000000// 2010 © Chiara Modenese #include"HertzMindlin.hpp" #include #include #include YADE_PLUGIN( (MindlinPhys) (Ip2_FrictMat_FrictMat_MindlinPhys) (Law2_ScGeom_MindlinPhys_MindlinDeresiewitz) (Law2_ScGeom_MindlinPhys_HertzWithLinearShear) (Law2_ScGeom_MindlinPhys_Mindlin) (MindlinCapillaryPhys) (Ip2_FrictMat_FrictMat_MindlinCapillaryPhys) ); Real Law2_ScGeom_MindlinPhys_Mindlin::getfrictionDissipation() {return (Real) frictionDissipation;} Real Law2_ScGeom_MindlinPhys_Mindlin::getshearEnergy() {return (Real) shearEnergy;} Real Law2_ScGeom_MindlinPhys_Mindlin::getnormDampDissip() {return (Real) normDampDissip;} Real Law2_ScGeom_MindlinPhys_Mindlin::getshearDampDissip() {return (Real) shearDampDissip;} /******************** Ip2_FrictMat_FrictMat_MindlinPhys *******/ CREATE_LOGGER(Ip2_FrictMat_FrictMat_MindlinPhys); void Ip2_FrictMat_FrictMat_MindlinPhys::go(const shared_ptr& b1,const shared_ptr& b2, const shared_ptr& interaction){ if(interaction->phys) return; // no updates of an already existing contact necessary shared_ptr contactPhysics(new MindlinPhys()); interaction->phys = contactPhysics; FrictMat* mat1 = YADE_CAST(b1.get()); FrictMat* mat2 = YADE_CAST(b2.get()); /* from interaction physics */ Real Ea = mat1->young; Real Eb = mat2->young; Real Va = mat1->poisson; Real Vb = mat2->poisson; Real fa = mat1->frictionAngle; Real fb = mat2->frictionAngle; /* from interaction geometry */ GenericSpheresContact* scg = YADE_CAST(interaction->geom.get()); Real Da = scg->refR1>0 ? scg->refR1 : scg->refR2; Real Db = scg->refR2; //Vector3r normal=scg->normal; //The variable set but not used /* calculate stiffness coefficients */ Real Ga = Ea/(2*(1+Va)); Real Gb = Eb/(2*(1+Vb)); Real G = (Ga+Gb)/2; // average of shear modulus Real V = (Va+Vb)/2; // average of poisson's ratio Real E = Ea*Eb/((1.-std::pow(Va,2))*Eb+(1.-std::pow(Vb,2))*Ea); // Young modulus Real R = Da*Db/(Da+Db); // equivalent radius Real Rmean = (Da+Db)/2.; // mean radius Real Kno = 4./3.*E*sqrt(R); // coefficient for normal stiffness Real Kso = 2*sqrt(4*R)*G/(2-V); // coefficient for shear stiffness Real frictionAngle = (!frictAngle) ? std::min(fa,fb) : (*frictAngle)(mat1->id,mat2->id,mat1->frictionAngle,mat2->frictionAngle); Real Adhesion = 4.*Mathr::PI*R*gamma; // calculate adhesion force as predicted by DMT theory /* pass values calculated from above to MindlinPhys */ contactPhysics->tangensOfFrictionAngle = std::tan(frictionAngle); //contactPhysics->prevNormal = scg->normal; // used to compute relative rotation contactPhysics->kno = Kno; // this is just a coeff contactPhysics->kso = Kso; // this is just a coeff contactPhysics->adhesionForce = Adhesion; contactPhysics->kr = krot; contactPhysics->ktw = ktwist; contactPhysics->maxBendPl = eta*Rmean; // does this make sense? why do we take Rmean? /* compute viscous coefficients */ if(en && betan) throw std::invalid_argument("Ip2_FrictMat_FrictMat_MindlinPhys: only one of en, betan can be specified."); if(es && betas) throw std::invalid_argument("Ip2_FrictMat_FrictMat_MindlinPhys: only one of es, betas can be specified."); // en or es specified, just compute alpha, otherwise alpha remains 0 if(en || es){ Real logE = log((*en)(mat1->id,mat2->id)); contactPhysics->alpha = -sqrt(5/6.)*2*logE/sqrt(pow(logE,2)+pow(Mathr::PI,2))*sqrt(2*E*sqrt(R)); // (see Tsuji, 1992), also [Antypov2011] eq. 17 } // betan specified, use that value directly; otherwise give zero else{ contactPhysics->betan=betan ? (*betan)(mat1->id,mat2->id) : 0; contactPhysics->betas=betas ? (*betas)(mat1->id,mat2->id) : contactPhysics->betan; } } /* Function to count the number of adhesive contacts in the simulation at each time step */ Real Law2_ScGeom_MindlinPhys_Mindlin::contactsAdhesive() // It is returning something rather than zero only if includeAdhesion is set to true { Real contactsAdhesive=0; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; MindlinPhys* phys = dynamic_cast(I->phys.get()); if (phys->isAdhesive) {contactsAdhesive += 1;} } return contactsAdhesive; } /* Function which returns the ratio between the number of sliding contacts to the total number at a given time */ Real Law2_ScGeom_MindlinPhys_Mindlin::ratioSlidingContacts() { Real ratio(0); int count(0); FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; MindlinPhys* phys = dynamic_cast(I->phys.get()); if (phys->isSliding) {ratio+=1;} count++; } ratio/=count; return ratio; } /* Function to get the NORMAL elastic potential energy of the system */ Real Law2_ScGeom_MindlinPhys_Mindlin::normElastEnergy() { Real normEnergy=0; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; ScGeom* scg = dynamic_cast(I->geom.get()); MindlinPhys* phys = dynamic_cast(I->phys.get()); if (phys) { if (includeAdhesion) {normEnergy += (std::pow(scg->penetrationDepth,5./2.)*2./5.*phys->kno - phys->adhesionForce*scg->penetrationDepth);} else {normEnergy += std::pow(scg->penetrationDepth,5./2.)*2./5.*phys->kno;} // work done in the normal direction. NOTE: this is the integral } } return normEnergy; } /* Function to get the adhesion energy of the system */ Real Law2_ScGeom_MindlinPhys_Mindlin::adhesionEnergy() { Real adhesionEnergy=0; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; ScGeom* scg = dynamic_cast(I->geom.get()); MindlinPhys* phys = dynamic_cast(I->phys.get()); if (phys && includeAdhesion) { Real R=scg->radius1*scg->radius2/(scg->radius1+scg->radius2); Real gammapi=phys->adhesionForce/(4.*R); adhesionEnergy += gammapi*pow(phys->radius,2);} // note that contact radius is calculated if we calculate energy components } return adhesionEnergy; } bool Law2_ScGeom_MindlinPhys_MindlinDeresiewitz::go(shared_ptr& ig, shared_ptr& ip, Interaction* contact){ Body::id_t id1(contact->getId1()), id2(contact->getId2()); ScGeom* geom = static_cast(ig.get()); MindlinPhys* phys=static_cast(ip.get()); const Real uN=geom->penetrationDepth; if (uN<0) { if (neverErase) {phys->shearForce = phys->normalForce = Vector3r::Zero(); phys->kn=phys->ks=0; return true;} else {return false;} } // normal force Real Fn=phys->kno*pow(uN,3/2.); phys->normalForce=Fn*geom->normal; // exactly zero would not work with the shear formulation, and would give zero shear force anyway if(Fn==0) return true; //phys->kn=3./2.*phys->kno*std::pow(uN,0.5); // update stiffness, not needed // contact radius Real R=geom->radius1*geom->radius2/(geom->radius1+geom->radius2); phys->radius=pow(Fn*pow(R,3/2.)/phys->kno,1/3.); // shear force: transform, but keep the old value for now geom->rotate(phys->usTotal); //Vector3r usOld=phys->usTotal; //The variable set but not used Vector3r dUs=geom->shearIncrement(); phys->usTotal-=dUs; #if 0 Vector3r shearIncrement; shearIncrement=geom->shearIncrement(); Fs-=ks*shearIncrement; // Mohr-Coulomb slip Real maxFs2=pow(Fn,2)*pow(phys->tangensOfFrictionAngle,2); if(Fs.squaredNorm()>maxFs2) Fs*=sqrt(maxFs2)/Fs.norm(); #endif // apply forces Vector3r f=-phys->normalForce-phys->shearForce; scene->forces.addForce(id1,f); scene->forces.addForce(id2,-f); scene->forces.addTorque(id1,(geom->radius1-.5*geom->penetrationDepth)*geom->normal.cross(f)); scene->forces.addTorque(id2,(geom->radius2-.5*geom->penetrationDepth)*geom->normal.cross(f)); return true; } bool Law2_ScGeom_MindlinPhys_HertzWithLinearShear::go(shared_ptr& ig, shared_ptr& ip, Interaction* contact){ Body::id_t id1(contact->getId1()), id2(contact->getId2()); ScGeom* geom = static_cast(ig.get()); MindlinPhys* phys=static_cast(ip.get()); const Real uN=geom->penetrationDepth; if (uN<0) { if (neverErase) {phys->shearForce = phys->normalForce = Vector3r::Zero(); phys->kn=phys->ks=0; return true;} else return false; } // normal force Real Fn=phys->kno*pow(uN,3/2.); phys->normalForce=Fn*geom->normal; //phys->kn=3./2.*phys->kno*std::pow(uN,0.5); // update stiffness, not needed // shear force Vector3r& Fs=geom->rotate(phys->shearForce); Real ks= nonLin>0 ? phys->kso*std::pow(uN,0.5) : phys->kso; Vector3r shearIncrement; if(nonLin>1){ State *de1=Body::byId(id1,scene)->state.get(), *de2=Body::byId(id2,scene)->state.get(); Vector3r shiftVel=scene->isPeriodic ? Vector3r(scene->cell->velGrad*scene->cell->hSize*contact->cellDist.cast()) : Vector3r::Zero(); Vector3r shift2 = scene->isPeriodic ? Vector3r(scene->cell->hSize*contact->cellDist.cast()): Vector3r::Zero(); Vector3r incidentV = geom->getIncidentVel(de1, de2, scene->dt, shift2, shiftVel, /*preventGranularRatcheting*/ nonLin>2 ); Vector3r incidentVn = geom->normal.dot(incidentV)*geom->normal; // contact normal velocity Vector3r incidentVs = incidentV-incidentVn; // contact shear velocity shearIncrement=incidentVs*scene->dt; } else { shearIncrement=geom->shearIncrement(); } Fs-=ks*shearIncrement; // Mohr-Coulomb slip Real maxFs2=pow(Fn,2)*pow(phys->tangensOfFrictionAngle,2); if(Fs.squaredNorm()>maxFs2) Fs*=sqrt(maxFs2)/Fs.norm(); // apply forces Vector3r f=-phys->normalForce-phys->shearForce; /* should be a reference returned by geom->rotate */ assert(phys->shearForce==Fs); scene->forces.addForce(id1,f); scene->forces.addForce(id2,-f); scene->forces.addTorque(id1,(geom->radius1-.5*geom->penetrationDepth)*geom->normal.cross(f)); scene->forces.addTorque(id2,(geom->radius2-.5*geom->penetrationDepth)*geom->normal.cross(f)); return true; } /******************** Law2_ScGeom_MindlinPhys_Mindlin *********/ CREATE_LOGGER(Law2_ScGeom_MindlinPhys_Mindlin); bool Law2_ScGeom_MindlinPhys_Mindlin::go(shared_ptr& ig, shared_ptr& ip, Interaction* contact){ const Real& dt = scene->dt; // get time step Body::id_t id1 = contact->getId1(); // get id body 1 Body::id_t id2 = contact->getId2(); // get id body 2 State* de1 = Body::byId(id1,scene)->state.get(); State* de2 = Body::byId(id2,scene)->state.get(); ScGeom* scg = static_cast(ig.get()); MindlinPhys* phys = static_cast(ip.get()); const shared_ptr& b1=Body::byId(id1,scene); const shared_ptr& b2=Body::byId(id2,scene); bool useDamping=(phys->betan!=0. || phys->betas!=0. || phys->alpha!=0.); bool LinDamp=true; if (phys->alpha!=0.) {LinDamp=false;} // use non linear damping // tangential and normal stiffness coefficients, recomputed from betan,betas at every step Real cn=0, cs=0; /****************/ /* NORMAL FORCE */ /****************/ Real uN = scg->penetrationDepth; // get overlapping if (uN<0) { if (neverErase) {phys->shearForce = phys->normalForce = Vector3r::Zero(); phys->kn=phys->ks=0; return true;} else return false; } /* Hertz-Mindlin's formulation (PFC) Note that the normal stiffness here is a secant value (so as it is cannot be used in the GSTS) In the first place we get the normal force and then we store kn to be passed to the GSTS */ Real Fn = phys->kno*std::pow(uN,1.5); // normal Force (scalar) if (includeAdhesion) { Fn -= phys->adhesionForce; // include adhesion force to account for the effect of Van der Waals interactions phys->isAdhesive = (Fn<0); // set true the bool to count the number of adhesive contacts } phys->normalForce = Fn*scg->normal; // normal Force (vector) if (calcEnergy){ Real R=scg->radius1*scg->radius2/(scg->radius1+scg->radius2); phys->radius=pow((Fn+(includeAdhesion?phys->adhesionForce:0.))*pow(R,3/2.)/phys->kno,1/3.); // attribute not used anywhere, we do not need it } /*******************************/ /* TANGENTIAL NORMAL STIFFNESS */ /*******************************/ phys->kn = 3./2.*phys->kno*std::pow(uN,0.5); // here we store the value of kn to compute the time step /******************************/ /* TANGENTIAL SHEAR STIFFNESS */ /******************************/ phys->ks = phys->kso*std::pow(uN,0.5); // get tangential stiffness (this is a tangent value, so we can pass it to the GSTS) /************************/ /* DAMPING COEFFICIENTS */ /************************/ // Inclusion of local damping if requested // viscous damping is defined for both linear and non-linear elastic case if (useDamping && LinDamp){ Real mbar = (!b1->isDynamic() && b2->isDynamic()) ? de2->mass : ((!b2->isDynamic() && b1->isDynamic()) ? de1->mass : (de1->mass*de2->mass / (de1->mass + de2->mass))); // get equivalent mass if both bodies are dynamic, if not set it equal to the one of the dynamic body //Real mbar = de1->mass*de2->mass / (de1->mass + de2->mass); // equivalent mass Real Cn_crit = 2.*sqrt(mbar*phys->kn); // Critical damping coefficient (normal direction) Real Cs_crit = 2.*sqrt(mbar*phys->ks); // Critical damping coefficient (shear direction) // Note: to compare with the analytical solution you provide cn and cs directly (since here we used a different method to define c_crit) cn = Cn_crit*phys->betan; // Damping normal coefficient cs = Cs_crit*phys->betas; // Damping tangential coefficient if(phys->kn<0 || phys->ks<0){ cerr<<"Negative stiffness kn="<kn<<" ks="<ks<<" for ##"<getId()<<"+"<getId()<<", step "<iter<isDynamic() && b2->isDynamic()) ? de2->mass : ((!b2->isDynamic() && b1->isDynamic()) ? de1->mass : (de1->mass*de2->mass / (de1->mass + de2->mass))); // get equivalent mass if both bodies are dynamic, if not set it equal to the one of the dynamic body cn = phys->alpha*sqrt(mbar)*pow(uN,0.25); // normal viscous coefficient, see also [Antypov2011] eq. 10 cs = cn; // same value for shear viscous coefficient } /***************/ /* SHEAR FORCE */ /***************/ Vector3r& shearElastic = phys->shearElastic; // reference for shearElastic force // Define shifts to handle periodicity const Vector3r shift2 = scene->isPeriodic ? scene->cell->intrShiftPos(contact->cellDist): Vector3r::Zero(); const Vector3r shiftVel = scene->isPeriodic ? scene->cell->intrShiftVel(contact->cellDist): Vector3r::Zero(); // 1. Rotate shear force shearElastic = scg->rotate(shearElastic); Vector3r prev_FsElastic = shearElastic; // save shear force at previous time step // 2. Get incident velocity, get shear and normal components Vector3r incidentV = scg->getIncidentVel(de1, de2, dt, shift2, shiftVel, preventGranularRatcheting); Vector3r incidentVn = scg->normal.dot(incidentV)*scg->normal; // contact normal velocity Vector3r incidentVs = incidentV - incidentVn; // contact shear velocity // 3. Get shear force (incrementally) shearElastic = shearElastic - phys->ks*(incidentVs*dt); /**************************************/ /* VISCOUS DAMPING (Normal direction) */ /**************************************/ // normal force must be updated here before we apply the Mohr-Coulomb criterion if (useDamping){ // get normal viscous component phys->normalViscous = cn*incidentVn; Vector3r normTemp = phys->normalForce - phys->normalViscous; // temporary normal force // viscous force should not exceed the value of current normal force, i.e. no attraction force should be permitted if particles are non-adhesive // if particles are adhesive, then fixed the viscous force at maximum equal to the adhesion force // *** enforce normal force to zero if no adhesion is permitted *** if (phys->adhesionForce==0.0 || !includeAdhesion){ if (normTemp.dot(scg->normal)<0.0){ phys->normalForce = Vector3r::Zero(); phys->normalViscous = phys->normalViscous + normTemp; // normal viscous force is such that the total applied force is null - it is necessary to compute energy correctly! } else{phys->normalForce -= phys->normalViscous;} } else if (includeAdhesion && phys->adhesionForce!=0.0){ // *** limit viscous component to the max adhesive force *** if (normTemp.dot(scg->normal)<0.0 && (phys->normalViscous.norm() > phys->adhesionForce) ){ Real normVisc = phys->normalViscous.norm(); Vector3r normViscVector = phys->normalViscous/normVisc; phys->normalViscous = phys->adhesionForce*normViscVector; phys->normalForce -= phys->normalViscous; } // *** apply viscous component - in the presence of adhesion *** else {phys->normalForce -= phys->normalViscous;} } if (calcEnergy) {normDampDissip += phys->normalViscous.dot(incidentVn*dt);} // calc dissipation of energy due to normal damping } /*************************************/ /* SHEAR DISPLACEMENT (elastic only) */ /*************************************/ Vector3r& us_elastic = phys->usElastic; us_elastic = scg->rotate(us_elastic); // rotate vector Vector3r prevUs_el = us_elastic; // store previous elastic shear displacement (already rotated) us_elastic -= incidentVs*dt; // add shear increment /****************************************/ /* SHEAR DISPLACEMENT (elastic+plastic) */ /****************************************/ Vector3r& us_total = phys->usTotal; us_total = scg->rotate(us_total); // rotate vector Vector3r prevUs_tot = us_total; // store previous total shear displacement (already rotated) us_total -= incidentVs*dt; // add shear increment NOTE: this vector is not passed into the failure criterion, hence it holds also the plastic part of the shear displacement bool noShearDamp = false; // bool to decide whether we need to account for shear damping dissipation or not /********************/ /* MOHR-COULOMB law */ /********************/ phys->isSliding=false; phys->shearViscous=Vector3r::Zero(); // reset so that during sliding, the previous values is not there Fn = phys->normalForce.norm(); if (!includeAdhesion) { Real maxFs = Fn*phys->tangensOfFrictionAngle; if (shearElastic.squaredNorm() > maxFs*maxFs){ phys->isSliding=true; noShearDamp = true; // no damping is added in the shear direction, hence no need to account for shear damping dissipation Real ratio = maxFs/shearElastic.norm(); shearElastic *= ratio; phys->shearForce = shearElastic; /*store only elastic shear displacement*/ us_elastic*= ratio; if (calcEnergy) {frictionDissipation += (us_total-prevUs_tot).dot(shearElastic);} // calculate energy dissipation due to sliding behavior } else if (useDamping){ // add current contact damping if we do not slide and if damping is requested phys->shearViscous = cs*incidentVs; // get shear viscous component phys->shearForce = shearElastic - phys->shearViscous;} else if (!useDamping) {phys->shearForce = shearElastic;} // update the shear force at the elastic value if no damping is present and if we passed MC } else { // Mohr-Coulomb formulation adpated due to the presence of adhesion (see Thornton, 1991). Real maxFs = phys->tangensOfFrictionAngle*(phys->adhesionForce+Fn); // adhesionForce already included in normalForce (above) if (shearElastic.squaredNorm() > maxFs*maxFs){ phys->isSliding=true; noShearDamp = true; // no damping is added in the shear direction, hence no need to account for shear damping dissipation Real ratio = maxFs/shearElastic.norm(); shearElastic *= ratio; phys->shearForce = shearElastic; /*store only elastic shear displacement*/ us_elastic *= ratio; if (calcEnergy) {frictionDissipation += (us_total-prevUs_tot).dot(shearElastic);} // calculate energy dissipation due to sliding behavior } else if (useDamping){ // add current contact damping if we do not slide and if damping is requested phys->shearViscous = cs*incidentVs; // get shear viscous component phys->shearForce = shearElastic - phys->shearViscous;} else if (!useDamping) {phys->shearForce = shearElastic;} // update the shear force at the elastic value if no damping is present and if we passed MC } /************************/ /* SHEAR ELASTIC ENERGY */ /************************/ // NOTE: shear elastic energy calculation must come after the MC criterion, otherwise displacements and forces are not updated if (calcEnergy) { shearEnergy += (us_elastic-prevUs_el).dot((shearElastic+prev_FsElastic)/2.); // NOTE: no additional energy if we perform sliding since us_elastic and prevUs_el will hold the same value (in fact us_elastic is only keeping the elastic part). We work out the area of the trapezium. } /**************************************************/ /* VISCOUS DAMPING (energy term, shear direction) */ /**************************************************/ if (useDamping){ // get normal viscous component (the shear one is calculated inside Mohr-Coulomb criterion, see above) if (calcEnergy) {if (!noShearDamp) {shearDampDissip += phys->shearViscous.dot(incidentVs*dt);}} // calc energy dissipation due to viscous linear damping } /****************/ /* APPLY FORCES */ /****************/ if (!scene->isPeriodic) applyForceAtContactPoint(-phys->normalForce - phys->shearForce, scg->contactPoint , id1, de1->se3.position, id2, de2->se3.position); else { // in scg we do not wrap particles positions, hence "applyForceAtContactPoint" cannot be used Vector3r force = -phys->normalForce - phys->shearForce; scene->forces.addForce(id1,force); scene->forces.addForce(id2,-force); scene->forces.addTorque(id1,(scg->radius1-0.5*scg->penetrationDepth)* scg->normal.cross(force)); scene->forces.addTorque(id2,(scg->radius2-0.5*scg->penetrationDepth)* scg->normal.cross(force)); } /********************************************/ /* MOMENT CONTACT LAW */ /********************************************/ if (includeMoment){ // *** Bending ***// // new code to compute relative particle rotation (similar to the way the shear is computed) // use scg function to compute relAngVel Vector3r relAngVel = scg->getRelAngVel(de1,de2,dt); //Vector3r relAngVel = (b2->state->angVel-b1->state->angVel); Vector3r relAngVelBend = relAngVel - scg->normal.dot(relAngVel)*scg->normal; // keep only the bending part Vector3r relRot = relAngVelBend*dt; // relative rotation due to rolling behaviour // incremental formulation for the bending moment (as for the shear part) Vector3r& momentBend = phys->momentBend; momentBend = scg->rotate(momentBend); // rotate moment vector (updated) momentBend = momentBend-phys->kr*relRot; // add incremental rolling to the rolling vector // ---------------------------------------------------------------------------------------- // *** Torsion ***// Vector3r relAngVelTwist = scg->normal.dot(relAngVel)*scg->normal; Vector3r relRotTwist = relAngVelTwist*dt; // component of relative rotation along n // incremental formulation for the torsional moment Vector3r& momentTwist = phys->momentTwist; momentTwist = scg->rotate(momentTwist); // rotate moment vector (updated) momentTwist = momentTwist-phys->ktw*relRotTwist; #if 0 // code to compute the relative particle rotation if (includeMoment){ Real rMean = (scg->radius1+scg->radius2)/2.; // sliding motion Vector3r duS1 = scg->radius1*(phys->prevNormal-scg->normal); Vector3r duS2 = scg->radius2*(scg->normal-phys->prevNormal); // rolling motion Vector3r duR1 = scg->radius1*dt*b1->state->angVel.cross(scg->normal); Vector3r duR2 = -scg->radius2*dt*b2->state->angVel.cross(scg->normal); // relative position of the old contact point with respect to the new one Vector3r relPosC1 = duS1+duR1; Vector3r relPosC2 = duS2+duR2; Vector3r duR = (relPosC1+relPosC2)/2.; // incremental displacement vector (same radius is temporarily assumed) // check wheter rolling will be present, if not do nothing Vector3r x=scg->normal.cross(duR); Vector3r normdThetaR(Vector3r::Zero()); // initialize if(x.squaredNorm()==0) { /* no rolling */ } else { Vector3r normdThetaR = x/x.norm(); // moment unit vector phys->dThetaR = duR.norm()/rMean*normdThetaR;} // incremental rolling // incremental formulation for the bending moment (as for the shear part) Vector3r& momentBend = phys->momentBend; momentBend = scg->rotate(momentBend); // rotate moment vector momentBend = momentBend+phys->kr*phys->dThetaR; // add incremental rolling to the rolling vector FIXME: is the sign correct? #endif // check plasticity condition (only bending part for the moment) Real MomentMax = phys->maxBendPl*phys->normalForce.norm(); Real scalarMoment = phys->momentBend.norm(); if (MomentMax>0){ if(scalarMoment > MomentMax) { Real ratio = MomentMax/scalarMoment; // to fix the moment to its yielding value phys->momentBend *= ratio; } } // apply moments Vector3r moment = phys->momentTwist+phys->momentBend; scene->forces.addTorque(id1,-moment); scene->forces.addTorque(id2,moment); } return true; // update variables //phys->prevNormal = scg->normal; } // The following code was moved from Ip2_FrictMat_FrictMat_MindlinCapillaryPhys.cpp void Ip2_FrictMat_FrictMat_MindlinCapillaryPhys::go( const shared_ptr& b1 //FrictMat , const shared_ptr& b2 // FrictMat , const shared_ptr& interaction) { if(interaction->phys) return; // no updates of an already existing contact necessary shared_ptr contactPhysics(new MindlinCapillaryPhys()); interaction->phys = contactPhysics; FrictMat* mat1 = YADE_CAST(b1.get()); FrictMat* mat2 = YADE_CAST(b2.get()); /* from interaction physics */ Real Ea = mat1->young; Real Eb = mat2->young; Real Va = mat1->poisson; Real Vb = mat2->poisson; Real fa = mat1->frictionAngle; Real fb = mat2->frictionAngle; /* from interaction geometry */ GenericSpheresContact* scg = YADE_CAST(interaction->geom.get()); Real Da = scg->refR1>0 ? scg->refR1 : scg->refR2; Real Db = scg->refR2; //Vector3r normal=scg->normal; //The variable set but not used /* calculate stiffness coefficients */ Real Ga = Ea/(2*(1+Va)); Real Gb = Eb/(2*(1+Vb)); Real G = (Ga+Gb)/2; // average of shear modulus Real V = (Va+Vb)/2; // average of poisson's ratio Real E = Ea*Eb/((1.-std::pow(Va,2))*Eb+(1.-std::pow(Vb,2))*Ea); // Young modulus Real R = Da*Db/(Da+Db); // equivalent radius Real Rmean = (Da+Db)/2.; // mean radius Real Kno = 4./3.*E*sqrt(R); // coefficient for normal stiffness Real Kso = 2*sqrt(4*R)*G/(2-V); // coefficient for shear stiffness Real frictionAngle = std::min(fa,fb); Real Adhesion = 4.*Mathr::PI*R*gamma; // calculate adhesion force as predicted by DMT theory /* pass values calculated from above to MindlinCapillaryPhys */ contactPhysics->tangensOfFrictionAngle = std::tan(frictionAngle); //mindlinPhys->prevNormal = scg->normal; // used to compute relative rotation contactPhysics->kno = Kno; // this is just a coeff contactPhysics->kso = Kso; // this is just a coeff contactPhysics->adhesionForce = Adhesion; contactPhysics->kr = krot; contactPhysics->ktw = ktwist; contactPhysics->maxBendPl = eta*Rmean; // does this make sense? why do we take Rmean? /* compute viscous coefficients */ if(en && betan) throw std::invalid_argument("Ip2_FrictMat_FrictMat_MindlinCapillaryPhys: only one of en, betan can be specified."); if(es && betas) throw std::invalid_argument("Ip2_FrictMat_FrictMat_MindlinCapillaryPhys: only one of es, betas can be specified."); // en or es specified, just compute alpha, otherwise alpha remains 0 if(en || es){ Real logE = log((*en)(mat1->id,mat2->id)); contactPhysics->alpha = -sqrt(5/6.)*2*logE/sqrt(pow(logE,2)+pow(Mathr::PI,2))*sqrt(2*E*sqrt(R)); // (see Tsuji, 1992) } // betan specified, use that value directly; otherwise give zero else{ contactPhysics->betan=betan ? (*betan)(mat1->id,mat2->id) : 0; contactPhysics->betas=betas ? (*betas)(mat1->id,mat2->id) : contactPhysics->betan; } }; trunk-2017.01a/pkg/dem/HertzMindlin.hpp000066400000000000000000000336661304022710500176460ustar00rootroot00000000000000// 2010 © Chiara Modenese // /* === HIGH LEVEL OVERVIEW OF MINDLIN === Mindlin is a set of classes to include the Hertz-Mindlin formulation for the contact stiffnesses. The DMT formulation is also considered (for adhesive particles, rigid and small bodies). */ #pragma once #include #include #include #include #include #include #include #include #include /******************** MindlinPhys *********************************/ class MindlinPhys: public FrictPhys{ public: virtual ~MindlinPhys() {}; YADE_CLASS_BASE_DOC_ATTRS_CTOR(MindlinPhys,FrictPhys,"Representation of an interaction of the Hertz-Mindlin type.", ((Real,kno,0.0,,"Constant value in the formulation of the normal stiffness")) ((Real,kso,0.0,,"Constant value in the formulation of the tangential stiffness")) ((Real,kr,0.0,,"Rotational stiffness")) ((Real,ktw,0.0,,"Rotational stiffness")) ((Real,maxBendPl,0.0,,"Coefficient to determine the maximum plastic moment to apply at the contact")) ((Vector3r,normalViscous,Vector3r::Zero(),,"Normal viscous component")) ((Vector3r,shearViscous,Vector3r::Zero(),,"Shear viscous component")) ((Vector3r,shearElastic,Vector3r::Zero(),,"Total elastic shear force")) ((Vector3r,usElastic,Vector3r::Zero(),,"Total elastic shear displacement (only elastic part)")) ((Vector3r,usTotal,Vector3r::Zero(),,"Total elastic shear displacement (elastic+plastic part)")) //((Vector3r,prevNormal,Vector3r::Zero(),,"Save previous contact normal to compute relative rotation")) ((Vector3r,momentBend,Vector3r::Zero(),,"Artificial bending moment to provide rolling resistance in order to account for some degree of interlocking between particles")) ((Vector3r,momentTwist,Vector3r::Zero(),,"Artificial twisting moment (no plastic condition can be applied at the moment)")) //((Vector3r,dThetaR,Vector3r::Zero(),,"Incremental rolling vector")) ((Real,radius,NaN,,"Contact radius (only computed with :yref:`Law2_ScGeom_MindlinPhys_Mindlin::calcEnergy`)")) //((Real,gamma,0.0,"Surface energy parameter [J/m^2] per each unit contact surface, to derive DMT formulation from HM")) ((Real,adhesionForce,0.0,,"Force of adhesion as predicted by DMT")) ((bool,isAdhesive,false,,"bool to identify if the contact is adhesive, that is to say if the contact force is attractive")) ((bool,isSliding,false,,"check if the contact is sliding (useful to calculate the ratio of sliding contacts)")) // Contact damping ratio as for linear elastic contact law ((Real,betan,0.0,,"Normal Damping Ratio. Fraction of the viscous damping coefficient (normal direction) equal to $\\frac{c_{n}}{C_{n,crit}}$.")) ((Real,betas,0.0,,"Shear Damping Ratio. Fraction of the viscous damping coefficient (shear direction) equal to $\\frac{c_{s}}{C_{s,crit}}$.")) // Contact damping ratio for non-linear elastic contact law (of Hertz-Mindlin type) ((Real,alpha,0.0,,"Constant coefficient to define contact viscous damping for non-linear elastic force-displacement relationship.")) // temporary ((Vector3r,prevU,Vector3r::Zero(),,"Previous local displacement; only used with :yref:`Law2_L3Geom_FrictPhys_HertzMindlin`.")) ((Vector2r,Fs,Vector2r::Zero(),,"Shear force in local axes (computed incrementally)")) , createIndex()); REGISTER_CLASS_INDEX(MindlinPhys,FrictPhys); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(MindlinPhys); /******************** Ip2_FrictMat_FrictMat_MindlinPhys *******/ class Ip2_FrictMat_FrictMat_MindlinPhys: public IPhysFunctor{ public : virtual void go(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction); FUNCTOR2D(FrictMat,FrictMat); YADE_CLASS_BASE_DOC_ATTRS( Ip2_FrictMat_FrictMat_MindlinPhys,IPhysFunctor,"Calculate some physical parameters needed to obtain \ the normal and shear stiffnesses according to the Hertz-Mindlin formulation (as implemented in PFC).\n\n\ Viscous parameters can be specified either using coefficients of restitution ($e_n$, $e_s$) or viscous \ damping ratio ($\\beta_n$, $\\beta_s$). The following rules apply:\n#. If the $\\beta_n$ ($\\beta_s$) \ ratio is given, it is assigned to :yref:`MindlinPhys.betan` (:yref:`MindlinPhys.betas`) directly.\n#. \ If $e_n$ is given, :yref:`MindlinPhys.betan` is computed using $\\beta_n=-(\\log e_n)/\\sqrt{\\pi^2+(\\log e_n)^2}$. \ The same applies to $e_s$, :yref:`MindlinPhys.betas`.\n#. It is an error (exception) to specify both $e_n$ \ and $\\beta_n$ ($e_s$ and $\\beta_s$).\n#. If neither $e_n$ nor $\\beta_n$ is given, zero value \ for :yref:`MindlinPhys.betan` is used; there will be no viscous effects.\n#.If neither $e_s$ nor $\\beta_s$ \ is given, the value of :yref:`MindlinPhys.betan` is used for :yref:`MindlinPhys.betas` as well.\n\nThe \ $e_n$, $\\beta_n$, $e_s$, $\\beta_s$ are :yref:`MatchMaker` objects; they can be constructed from float \ values to always return constant value.\n\nSee :ysrc:`scripts/test/shots.py` for an example of specifying \ $e_n$ based on combination of parameters.", ((Real,gamma,0.0,,"Surface energy parameter [J/m^2] per each unit contact surface, to derive DMT formulation from HM")) ((Real,eta,0.0,,"Coefficient to determine the plastic bending moment")) ((Real,krot,0.0,,"Rotational stiffness for moment contact law")) ((Real,ktwist,0.0,,"Torsional stiffness for moment contact law")) ((shared_ptr,en,,,"Normal coefficient of restitution $e_n$.")) ((shared_ptr,es,,,"Shear coefficient of restitution $e_s$.")) ((shared_ptr,betan,,,"Normal viscous damping ratio $\\beta_n$.")) ((shared_ptr,betas,,,"Shear viscous damping ratio $\\beta_s$.")) ((shared_ptr,frictAngle,,,"Instance of :yref:`MatchMaker` determining how to compute the friction angle of an interaction. If ``None``, minimum value is used.")) ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Ip2_FrictMat_FrictMat_MindlinPhys); class Law2_ScGeom_MindlinPhys_MindlinDeresiewitz: public LawFunctor{ public: virtual bool go(shared_ptr&, shared_ptr&, Interaction*); FUNCTOR2D(ScGeom,MindlinPhys); YADE_CLASS_BASE_DOC_ATTRS(Law2_ScGeom_MindlinPhys_MindlinDeresiewitz,LawFunctor, "Hertz-Mindlin contact law with partial slip solution, as described in [Thornton1991]_.", ((bool,neverErase,false,,"Keep interactions even if particles go away from each other (only in case another constitutive law is in the scene, e.g. :yref:`Law2_ScGeom_CapillaryPhys_Capillarity`)")) ); }; REGISTER_SERIALIZABLE(Law2_ScGeom_MindlinPhys_MindlinDeresiewitz); class Law2_ScGeom_MindlinPhys_HertzWithLinearShear: public LawFunctor{ public: virtual bool go(shared_ptr&, shared_ptr&, Interaction*); FUNCTOR2D(ScGeom,MindlinPhys); YADE_CLASS_BASE_DOC_ATTRS(Law2_ScGeom_MindlinPhys_HertzWithLinearShear,LawFunctor, "Constitutive law for the Hertz formulation (using :yref:`MindlinPhys.kno`) and linear beahvior in shear (using :yref:`MindlinPhys.kso` for stiffness and :yref:`FrictPhys.tangensOfFrictionAngle`). \n\n.. note:: No viscosity or damping. If you need those, look at :yref:`Law2_ScGeom_MindlinPhys_Mindlin`, which also includes non-linear Mindlin shear.", ((bool,neverErase,false,,"Keep interactions even if particles go away from each other (only in case another constitutive law is in the scene, e.g. :yref:`Law2_ScGeom_CapillaryPhys_Capillarity`)")) ((int,nonLin,0,,"Shear force nonlinearity (the value determines how many features of the non-linearity are taken in account). 1: ks as in HM 2: shearElastic increment computed as in HM 3. granular ratcheting disabled.")) ); }; REGISTER_SERIALIZABLE(Law2_ScGeom_MindlinPhys_HertzWithLinearShear); /******************** Law2_ScGeom_MindlinPhys_Mindlin *********/ class Law2_ScGeom_MindlinPhys_Mindlin: public LawFunctor{ public: virtual bool go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I); Real normElastEnergy(); Real adhesionEnergy(); Real getfrictionDissipation(); Real getshearEnergy(); Real getnormDampDissip(); Real getshearDampDissip(); Real contactsAdhesive(); Real ratioSlidingContacts(); FUNCTOR2D(ScGeom,MindlinPhys); YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(Law2_ScGeom_MindlinPhys_Mindlin,LawFunctor,"Constitutive law for the Hertz-Mindlin formulation. It includes non linear elasticity in the normal direction as predicted by Hertz for two non-conforming elastic contact bodies. In the shear direction, instead, it reseambles the simplified case without slip discussed in Mindlin's paper, where a linear relationship between shear force and tangential displacement is provided. Finally, the Mohr-Coulomb criterion is employed to established the maximum friction force which can be developed at the contact. Moreover, it is also possible to include the effect of linear viscous damping through the definition of the parameters $\\beta_{n}$ and $\\beta_{s}$.", ((bool,preventGranularRatcheting,true,,"bool to avoid granular ratcheting")) ((bool,includeAdhesion,false,,"bool to include the adhesion force following the DMT formulation. If true, also the normal elastic energy takes into account the adhesion effect.")) ((bool,calcEnergy,false,,"bool to calculate energy terms (shear potential energy, dissipation of energy due to friction and dissipation of energy due to normal and tangential damping)")) ((bool,includeMoment,false,,"bool to consider rolling resistance (if :yref:`Ip2_FrictMat_FrictMat_MindlinPhys::eta` is 0.0, no plastic condition is applied.)")) ((bool,neverErase,false,,"Keep interactions even if particles go away from each other (only in case another constitutive law is in the scene, e.g. :yref:`Law2_ScGeom_CapillaryPhys_Capillarity`)")) //((bool,LinDamp,true,,"bool to activate linear viscous damping (if false, en and es have to be defined in place of betan and betas)")) ((OpenMPAccumulator,frictionDissipation,,Attr::noSave,"Energy dissipation due to sliding")) ((OpenMPAccumulator,shearEnergy,,Attr::noSave,"Shear elastic potential energy")) ((OpenMPAccumulator,normDampDissip,,Attr::noSave,"Energy dissipated by normal damping")) ((OpenMPAccumulator,shearDampDissip,,Attr::noSave,"Energy dissipated by tangential damping")) , /* init */ , /* ctor */ , /* py */ .def("contactsAdhesive",&Law2_ScGeom_MindlinPhys_Mindlin::contactsAdhesive,"Compute total number of adhesive contacts.") .def("ratioSlidingContacts",&Law2_ScGeom_MindlinPhys_Mindlin::ratioSlidingContacts,"Return the ratio between the number of contacts sliding to the total number at a given time.") .def("normElastEnergy",&Law2_ScGeom_MindlinPhys_Mindlin::normElastEnergy,"Compute normal elastic potential energy. It handles the DMT formulation if :yref:`Law2_ScGeom_MindlinPhys_Mindlin::includeAdhesion` is set to true.") ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_ScGeom_MindlinPhys_Mindlin); // The following code was moved from Ip2_FrictMat_FrictMat_MindlinCapillaryPhys.hpp class MindlinCapillaryPhys : public MindlinPhys { public : int currentIndexes [4]; // used for faster interpolation (stores previous positions in tables) virtual ~MindlinCapillaryPhys() {}; YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(MindlinCapillaryPhys,MindlinPhys,"Adds capillary physics to Mindlin's interaction physics.", ((bool,meniscus,false,Attr::readonly,"True when a meniscus with a non-zero liquid volume (:yref:`vMeniscus`) has been computed for this interaction")) ((bool,isBroken,false,,"Might be set to true by the user to make liquid bridge inactive (capillary force is zero)")) ((Real,capillaryPressure,0.,,"Value of the capillary pressure Uc. Defined as Ugas-Uliquid, obtained from :yref:`corresponding Law2 parameter`")) ((Real,vMeniscus,0.,,"Volume of the meniscus")) ((Real,Delta1,0.,,"Defines the surface area wetted by the meniscus on the smallest grains of radius R1 (R1& b1, const shared_ptr& b2, const shared_ptr& interaction); FUNCTOR2D(FrictMat,FrictMat); YADE_CLASS_BASE_DOC_ATTRS(Ip2_FrictMat_FrictMat_MindlinCapillaryPhys,IPhysFunctor, "RelationShips to use with Law2_ScGeom_CapillaryPhys_Capillarity\n\n In these RelationShips all the interaction attributes are computed. \n\n.. warning::\n\tas in the others :yref:`Ip2 functors`, most of the attributes are computed only once, when the interaction is new.", ((Real,gamma,0.0,,"Surface energy parameter [J/m^2] per each unit contact surface, to derive DMT formulation from HM")) ((Real,eta,0.0,,"Coefficient to determine the plastic bending moment")) ((Real,krot,0.0,,"Rotational stiffness for moment contact law")) ((Real,ktwist,0.0,,"Torsional stiffness for moment contact law")) ((shared_ptr,en,,,"Normal coefficient of restitution $e_n$.")) ((shared_ptr,es,,,"Shear coefficient of restitution $e_s$.")) ((shared_ptr,betan,,,"Normal viscous damping ratio $\\beta_n$.")) ((shared_ptr,betas,,,"Shear viscous damping ratio $\\beta_s$.")) ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Ip2_FrictMat_FrictMat_MindlinCapillaryPhys); trunk-2017.01a/pkg/dem/Ig2_Box_Sphere_ScGeom.cpp000066400000000000000000000163341304022710500212170ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * Copyright (C) 2006 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include"Ig2_Box_Sphere_ScGeom.hpp" #include #include #include #include #include bool Ig2_Box_Sphere_ScGeom::go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { const Se3r& se31=state1.se3; const Se3r& se32=state2.se3; bool inside=true; Vector3r pt1,pt2,normal; Real depth; Box* obb = static_cast(cm1.get()); Sphere* s = static_cast(cm2.get()); Vector3r extents = obb->extents; // FIXME: do we need rotation matrix? Can't quaternion do just fine? Matrix3r boxAxisT=se31.orientation.toRotationMatrix(); Matrix3r boxAxis = boxAxisT.transpose(); Vector3r relPos21 = se32.position+shift2-se31.position; // relative position of centroids // cOnBox_boxLocal is the sphere centroid (in box-local coordinates), but projected onto box if it is outside. // _boxLocal means that ROTATION is local and origin is in box's origin Vector3r cOnBox_boxLocal=boxAxis*relPos21; if (cOnBox_boxLocal[0]<-extents[0]){cOnBox_boxLocal[0]=-extents[0]; inside=false; } if (cOnBox_boxLocal[0]> extents[0]){cOnBox_boxLocal[0]= extents[0]; inside=false; } if (cOnBox_boxLocal[1]<-extents[1]){cOnBox_boxLocal[1]=-extents[1]; inside=false; } if (cOnBox_boxLocal[1]> extents[1]){cOnBox_boxLocal[1]= extents[1]; inside=false; } if (cOnBox_boxLocal[2]<-extents[2]){cOnBox_boxLocal[2]=-extents[2]; inside=false; } if (cOnBox_boxLocal[2]> extents[2]){cOnBox_boxLocal[2]= extents[2]; inside=false; } shared_ptr scm; if (inside){ // sphere center inside box. find largest `cOnBox_boxLocal' value: // minCBoxDist_index is the coordinate index that minimizes extents[minCBoxDist_index]-std::abs(cOnBox_boxLocal[minCBoxDist_index] (sphere center closest to box boundary) // where cOnBox_boxLocal is minimal (i.e. where sphere center is closest perpendicularly to the box) Real minCBoxDist=extents[0]-std::abs(cOnBox_boxLocal[0]); int minCBoxDist_index=0; for (int i=1; i<3; i++){Real tt=extents[i]-std::abs(cOnBox_boxLocal[i]); if (tt0)?1.0:-1.0; normal = boxAxisT*normal_boxLocal; normal.normalize(); // se32 is sphere's se3 /* * * _--(pt1)-_ BOX * +------~-----x-----~----------------+ * | / ^ \ | * | / | (normal)*minCBoxDist | * | | x | | * | \ | c ≡ se32->position | * | \ | / | * | ~ | / SPHERE | * | ^~~ x ~~^ | * | (pt2) | * +-----------------------------------+ * * */ pt1 = se32.position+normal*minCBoxDist; pt2 = se32.position-normal*s->radius; Vector3r normal = pt1-pt2; normal.normalize(); bool isNew=!c->geom; if (isNew) scm = shared_ptr(new ScGeom()); else scm = YADE_PTR_CAST(c->geom); // contact point is in the middle of overlapping volumes //(in the direction of penetration, which is normal to the box surface closest to sphere center) of overlapping volumes scm->contactPoint = 0.5*(pt1+pt2); // scm->normal = normal; scm->penetrationDepth = (pt1-pt2).norm(); scm->radius1 = s->radius; scm->radius2 = s->radius; c->geom = scm; scm->precompute(state1,state2,scene,c,normal,isNew,shift2,true); } else { // outside Vector3r cOnBox_box = boxAxisT*cOnBox_boxLocal; // projection of sphere's center on closest box surface - relative to box's origin, but GLOBAL orientation! Vector3r cOnBox_sphere = cOnBox_box-relPos21; // same, but origin in sphere's center depth=s->radius-cOnBox_sphere.norm(); if (depth<0 && !c->isReal() && !force) return false; /* * +-----------------------------------+ * | | * | se31->position | * | pt2 × | * | × / cOnBox_box | * | pt1 / | * +------~-----×-----~----------------+ * / ^ \ * / | cOnBox_sphere * | × | * \ c ≡ se32->position * \ / * ~ / * ^~~ ~ ~~^ * */ pt1=cOnBox_box+se31.position; cOnBox_sphere.normalize(); // we want only direction in the following pt2=se32.position+shift2+cOnBox_sphere*s->radius; bool isNew=!c->geom; if (isNew) scm = shared_ptr(new ScGeom()); else scm = YADE_PTR_CAST(c->geom); scm->contactPoint = 0.5*(pt1+pt2); scm->penetrationDepth = depth; scm->radius1 = s->radius; scm->radius2 = s->radius; c->geom = scm; //FIXME : NOT TESTED : do we precompute correctly if boxes are moving? scm->precompute(state1,state2,scene,c,-cOnBox_sphere,isNew,shift2,false); } return true; } bool Ig2_Box_Sphere_ScGeom::goReverse(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { c->swapOrder(); return go(cm2,cm1,state2,state1,-shift2,force,c); } YADE_PLUGIN((Ig2_Box_Sphere_ScGeom)); bool Ig2_Box_Sphere_ScGeom6D::go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { bool isNew = !c->geom; if (Ig2_Box_Sphere_ScGeom::go(cm1,cm2,state1,state2,shift2,force,c)) { if (isNew) {//generate a 6DOF interaction from the 3DOF one generated by Ig2_Box_Sphere_ScGeom shared_ptr sc(new ScGeom6D()); *(YADE_PTR_CAST(sc)) = *(YADE_PTR_CAST(c->geom)); c->geom=sc; } YADE_PTR_CAST(c->geom)->precomputeRotations(state1,state2,isNew,false); return true; } else return false; } bool Ig2_Box_Sphere_ScGeom6D::goReverse(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { c->swapOrder(); return go(cm2,cm1,state2,state1,-shift2,force,c); } YADE_PLUGIN((Ig2_Box_Sphere_ScGeom6D)); trunk-2017.01a/pkg/dem/Ig2_Box_Sphere_ScGeom.hpp000066400000000000000000000047621304022710500212260ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2004 by Olivier Galizzi * * olivier.galizzi@imag.fr * * Copyright (C) 2004 by Janek Kozicki * * cosurgi@berlios.de * * Copyright (C) 2006 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include class Ig2_Box_Sphere_ScGeom : public IGeomFunctor { public : virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); YADE_CLASS_BASE_DOC(Ig2_Box_Sphere_ScGeom,IGeomFunctor,"Create an interaction geometry :yref:`ScGeom` from :yref:`Box` and :yref:`Sphere`, representing the box with a projected virtual sphere of same radius.") FUNCTOR2D(Box,Sphere); DEFINE_FUNCTOR_ORDER_2D(Box,Sphere); }; REGISTER_SERIALIZABLE(Ig2_Box_Sphere_ScGeom); class Ig2_Box_Sphere_ScGeom6D : public Ig2_Box_Sphere_ScGeom { public : virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); YADE_CLASS_BASE_DOC(Ig2_Box_Sphere_ScGeom6D,Ig2_Box_Sphere_ScGeom,"Create an interaction geometry :yref:`ScGeom6D` from :yref:`Box` and :yref:`Sphere`, representing the box with a projected virtual sphere of same radius.") FUNCTOR2D(Box,Sphere); DEFINE_FUNCTOR_ORDER_2D(Box,Sphere); }; REGISTER_SERIALIZABLE(Ig2_Box_Sphere_ScGeom6D); trunk-2017.01a/pkg/dem/Ig2_Facet_Sphere_ScGeom.cpp000066400000000000000000000152621304022710500215100ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2008 by Sergei Dorofeenko * * sega@users.berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include"Ig2_Facet_Sphere_ScGeom.hpp" #include #include #include #include #include #include #include YADE_PLUGIN((Ig2_Facet_Sphere_ScGeom)(Ig2_Facet_Sphere_ScGeom6D)(Ig2_Wall_Sphere_ScGeom)); CREATE_LOGGER(Ig2_Facet_Sphere_ScGeom); bool Ig2_Facet_Sphere_ScGeom::go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { TIMING_DELTAS_START(); const Se3r& se31=state1.se3; const Se3r& se32=state2.se3; Facet* facet = static_cast(cm1.get()); /* could be written as (needs to be tested): * Vector3r cl=se31.orientation.Conjugate()*(se32.position-se31.position); */ Matrix3r facetAxisT=se31.orientation.toRotationMatrix(); Matrix3r facetAxis = facetAxisT.transpose(); // local orientation Vector3r cl = facetAxis*(se32.position + shift2 - se31.position); // "contact line" in facet-local coords // // BEGIN everything in facet-local coordinates // Vector3r normal = facet->normal; Real L = normal.dot(cl); if (L<0) {normal=-normal; L=-L; } Real sphereRadius = static_cast(cm2.get())->radius; if (L>sphereRadius && !c->isReal() && !force) { // no contact, but only if there was no previous contact; ortherwise, the constitutive law is responsible for setting Interaction::isReal=false TIMING_DELTAS_CHECKPOINT("Ig2_Facet_Sphere_ScGeom"); return false; } Vector3r cp = cl - L*normal; const Vector3r* ne = facet->ne; Real penetrationDepth=0; Real bm = ne[0].dot(cp); int m=0; for (int i=1; i<3; ++i) { Real b=ne[i].dot(cp); if (bmicr-sh; if (icr<0) { LOG_WARN("a radius of a facet's inscribed circle less than zero! So, shrinkFactor is too large and would be reduced to zero."); shrinkFactor=0; icr = facet->icr; sh = 0; } if (bmicr) // contact with vertex m // cp = facet->vertices[m]; cp = facet->vu[m]*(facet->vl[m]-sh); else if (cp.dot(ne[m=(m+1>2)?0:m+1])>icr) // contact with vertex m+1 // cp = facet->vertices[(m+1>2)?0:m+1]; cp = facet->vu[m]*(facet->vl[m]-sh); normal = cl-cp; Real norm=normal.norm(); normal/=norm; penetrationDepth = sphereRadius - norm; } // // END everything in facet-local coordinates // if (penetrationDepth>0 || c->isReal()) { shared_ptr scm; bool isNew = !c->geom; if (c->geom) scm = YADE_PTR_CAST(c->geom); else scm = shared_ptr(new ScGeom()); normal = facetAxisT*normal; // in global orientation scm->contactPoint = se32.position + shift2 - (sphereRadius-0.5*penetrationDepth)*normal; scm->penetrationDepth = penetrationDepth; scm->radius1 = 2*sphereRadius; scm->radius2 = sphereRadius; if (isNew) c->geom = scm; scm->precompute(state1,state2,scene,c,normal,isNew,shift2,false/*avoidGranularRatcheting only for sphere-sphere*/); TIMING_DELTAS_CHECKPOINT("Ig2_Facet_Sphere_ScGeom"); return true; } TIMING_DELTAS_CHECKPOINT("Ig2_Facet_Sphere_ScGeom"); return false; } bool Ig2_Facet_Sphere_ScGeom::goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { c->swapOrder(); //LOG_WARN("Swapped interaction order for "<getId2()<<"&"<getId1()); return go(cm2,cm1,state2,state1,-shift2,force,c); } bool Ig2_Facet_Sphere_ScGeom6D::go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { bool isNew = !c->geom; if (Ig2_Facet_Sphere_ScGeom::go(cm1,cm2,state1,state2,shift2,force,c)) { if (isNew) {//generate a 6DOF interaction from the 3DOF one generated by Ig2_Facet_Sphere_ScGeom shared_ptr sc(new ScGeom6D()); *(YADE_PTR_CAST(sc)) = *(YADE_PTR_CAST(c->geom)); c->geom=sc; } YADE_PTR_CAST(c->geom)->precomputeRotations(state1,state2,isNew,false); return true; } else return false; } bool Ig2_Facet_Sphere_ScGeom6D::goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { c->swapOrder(); return go(cm2,cm1,state2,state1,-shift2,force,c); } /********* Wall + Sphere **********/ bool Ig2_Wall_Sphere_ScGeom::go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c){ Wall* wall=static_cast(cm1.get()); const Real radius=static_cast(cm2.get())->radius; const int& ax(wall->axis); Real dist=(state2.pos)[ax]+shift2[ax]-state1.pos[ax]; // signed "distance" between centers if(!c->isReal() && std::abs(dist)>radius && !force) { return false; }// wall and sphere too far from each other // contact point is sphere center projected onto the wall Vector3r contPt=state2.pos+shift2; contPt[ax]=state1.pos[ax]; Vector3r normal(0.,0.,0.); // wall interacting from both sides: normal depends on sphere's position assert(wall->sense==-1 || wall->sense==0 || wall->sense==1); if(wall->sense==0) normal[ax]=dist>0?1.:-1.; else normal[ax]=wall->sense==1?1.:-1; bool isNew=!c->geom; if(isNew) c->geom=shared_ptr(new ScGeom()); const shared_ptr& ws=YADE_PTR_CAST(c->geom); ws->radius1=ws->radius2=radius; // do the same as for facet-sphere: wall's "radius" is the same as the sphere's radius ws->contactPoint=contPt; ws->penetrationDepth=-(std::abs(dist)-radius); // ws->normal is assigned by precompute ws->precompute(state1,state2,scene,c,normal,isNew,shift2,noRatch); return true; } trunk-2017.01a/pkg/dem/Ig2_Facet_Sphere_ScGeom.hpp000066400000000000000000000066451304022710500215220ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2008 by Sergei Dorofeenko * * sega@users.berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include #include class Ig2_Facet_Sphere_ScGeom : public IGeomFunctor { public : virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); YADE_CLASS_BASE_DOC_ATTRS(Ig2_Facet_Sphere_ScGeom,IGeomFunctor,"Create/update a :yref:`ScGeom` instance representing intersection of :yref:`Facet` and :yref:`Sphere`.", ((Real,shrinkFactor,((void)"no shrinking",0),,"The radius of the inscribed circle of the facet is decreased by the value of the sphere's radius multipled by *shrinkFactor*. From the definition of contact point on the surface made of facets, the given surface is not continuous and becomes in effect surface covered with triangular tiles, with gap between the separate tiles equal to the sphere's radius multiplied by 2×*shrinkFactor*. If zero, no shrinking is done.")) ); DECLARE_LOGGER; FUNCTOR2D(Facet,Sphere); DEFINE_FUNCTOR_ORDER_2D(Facet,Sphere); }; REGISTER_SERIALIZABLE(Ig2_Facet_Sphere_ScGeom); class Ig2_Facet_Sphere_ScGeom6D : public Ig2_Facet_Sphere_ScGeom { public : virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); YADE_CLASS_BASE_DOC(Ig2_Facet_Sphere_ScGeom6D,Ig2_Facet_Sphere_ScGeom,"Create an interaction geometry :yref:`ScGeom6D` from :yref:`Facet` and :yref:`Sphere`, representing the Facet with a projected virtual sphere of same radius.") FUNCTOR2D(Facet,Sphere); DEFINE_FUNCTOR_ORDER_2D(Facet,Sphere); }; REGISTER_SERIALIZABLE(Ig2_Facet_Sphere_ScGeom6D); class Ig2_Wall_Sphere_ScGeom: public IGeomFunctor{ public: virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); YADE_CLASS_BASE_DOC_ATTRS(Ig2_Wall_Sphere_ScGeom,IGeomFunctor,"Create/update a :yref:`ScGeom` instance representing intersection of :yref:`Wall` and :yref:`Sphere`.", ((bool,noRatch,true,,"Avoid granular ratcheting")) ); FUNCTOR2D(Wall,Sphere); DEFINE_FUNCTOR_ORDER_2D(Wall,Sphere); }; REGISTER_SERIALIZABLE(Ig2_Wall_Sphere_ScGeom); trunk-2017.01a/pkg/dem/Ig2_PB_PB_ScGeom.cpp000077500000000000000000002756121304022710500200540ustar00rootroot00000000000000/*CWBoon 2016 */ /* Please cite: */ /* CW Boon, GT Houlsby, S Utili (2013). A new algorithm for contact detection between convex polygonal and polyhedral particles in the discrete element method. Computers and Geotechnics 44, 73-82. */ /* The numerical library is changed from CPLEX to CLP because subscription to the academic initiative is required to use CPLEX for free */ #ifdef YADE_POTENTIAL_BLOCKS #include"Ig2_PB_PB_ScGeom.hpp" #include #include //#include #include #include #include #include #include #include #include #include #include #include #include #include #include YADE_PLUGIN((Ig2_PB_PB_ScGeom) //#ifdef YADE_OPENGL // (Gl1_Ig2_PB_PB_ScGeom) // #endif ); CREATE_LOGGER(Ig2_PB_PB_ScGeom); bool Ig2_PB_PB_ScGeom::go(const shared_ptr& cm1,const shared_ptr& cm2,const State& state1, const State& state2, const Vector3r& shift2, const bool& force,const shared_ptr& c) { PotentialBlock *s1=static_cast(cm1.get()); PotentialBlock *s2=static_cast(cm2.get()); /* Short circuit if both particles are boundary particles */ if((s1->isBoundary==true)&&(s2->isBoundary==true)) {return false;} if((s1->isLining==true)&&(s2->isLining==true)) {return false;} if((s1->erase==true)&&(s2->isLining==true)) {return false;} if((s1->isLining==true)&&(s2->erase==true)) {return false;} bool hasGeom = false; Vector3r contactPt(0,0,0); shared_ptr scm; shared_ptr phys; double stepBisection = 0.001*std::min(s1->R,s2->R); if(stepBisectionR<<", R2: "<R<<", stepBisection: "<getId1()<<", id2: "<getId2()<geom){ hasGeom = true; scm=YADE_PTR_CAST(c->geom); if (scm->penetrationDepth>stepBisection ){ stepBisection = 0.5*scm->penetrationDepth;} if(stepBisectionpenetrationDepth<contactPoint; }else{ scm=shared_ptr(new ScGeom()); c->geom=scm; contactPt = 0.5*(state1.pos+state2.pos); } bool hasPhys=false; if(c->phys){ phys=YADE_PTR_CAST(c->phys); hasPhys=true; shearDir = phys->shearDir; //normalization should take place in the Contact Law } if(s1->isLining == true || s2->isLining==true){ double overlap = 0.0; if (s1->isLining == true){ contactPt = state1.pos; fA= evaluatePB(cm2,state2, contactPt); if(fA<0.0){ contact = true; avgNormal = contactPt; //getNormal(cm2,state2,contactPt); // avgNormal.normalize(); //avgNormal = -avgNormal; Vector3r step = avgNormal*stepBisection; int locationStuck = 5; getPtOnParticle2(cm2,state2,contactPt, -1.0*step, ptOnP2); overlap = (ptOnP2-contactPt).norm();// overlap; //avgNormal = contactPt; //avgNormal.normalize(); }else{contact=false;} }else{ contactPt = state2.pos; fB= evaluatePB(cm1,state1, contactPt); if (fB < 0.0){ contact = true; avgNormal = contactPt; //getNormal(cm1,state1,contactPt); // avgNormal.normalize(); avgNormal = -avgNormal; Vector3r step = avgNormal*stepBisection; int locationStuck = 5; getPtOnParticle2(cm1,state1,contactPt, 1.0*step, ptOnP1); overlap = (ptOnP1-contactPt).norm();// overlap; //avgNormal = contactPt; //avgNormal.normalize(); //avgNormal = -avgNormal; }else{contact=false;} } if (contact == true || c->isReal() || force){ if (contact == true){ scm->precompute(state1,state2,scene,c,avgNormal,!(hasGeom),Vector3r(0,0,0)/*shift 2 */, false /* avoidGranularRatcheting */); //Assign contact point and normal after precompute!!!! scm->contactPoint = contactPt; scm->penetrationDepth=overlap; if(std::isnan(avgNormal.norm())){std::cout<<"avgNormal: "<normal = avgNormal; if(hasPhys){ phys->normal= avgNormal; phys->ptOnP1 = contactPt; phys->ptOnP1 = ptOnP1; phys->ptOnP2 = ptOnP2; phys->initial1 = scm->contactPoint; phys->gap = scm->penetrationDepth; phys->tension = std::max(s1->tension[0],s2->tension[0]); phys->cohesion = std::max(s1->cohesion[0],s2->cohesion[0]); phys->jointLength = std::max(s1->liningLength,s2->liningLength); phys->contactArea = phys->jointLength*phys->unitWidth2D; } }else{ //scm->normal = Vector3r(0,0,0); scm->precompute(state1,state2,scene,c,avgNormal,!(hasGeom),Vector3r(0,0,0)/*shift 2 */, false /* avoidGranularRatcheting */); //Assign contact point and normal after precompute!!!! scm->contactPoint = contactPt;scm->penetrationDepth=-1.0; //scm->normal = Vector3r(0,0,0); } return true; }else{ scm->contactPoint = contactPt;scm->penetrationDepth=-1.0;scm->normal = Vector3r(0,0,0); return false; } } bool convergeFeasibility = true; fA= evaluatePB(cm1,state1, contactPt); fB = evaluatePB(cm2,state2, contactPt); //if (fA < -pow(10.0,-6) && fB < -pow(10.0,-6) ){ // contact = true; //}else{ contact = startingPointFeasibilityCLP( cm1, state1, cm2, state2, contactPt, convergeFeasibility); //} fA= evaluatePB(cm1,state1, contactPt); fB = evaluatePB(cm2,state2, contactPt); if (fA*fB<0.0){ std::cout<<"after clp fA: "<isBoundary: "<isBoundary<<", s2->isBoundary: "<isBoundary<isReal() || force){ if (contact == true){ normalP1 = getNormal(cm1,state1,contactPt); normalP1.normalize(); normalP2 = getNormal(cm2,state2,contactPt); normalP2.normalize(); //if(s1->isBoundary==true){avgNormal=normalP1;}else if(s2->isBoundary==true){avgNormal=-normalP2;}else{avgNormal = (normalP1 - normalP2);} #if 0 if(s1->isBoundary==true){avgNormal=normalP1;}else if(s2->isBoundary==true){avgNormal=-normalP2;}else{ avgNormal = (normalP1 - normalP2); } #endif avgNormal = (normalP1 - normalP2); avgNormal.normalize(); if(s1->fixedNormal==true){ avgNormal = s1->boundaryNormal;} if(s2->fixedNormal==true){ avgNormal = -s2->boundaryNormal;} Vector3r step = avgNormal*stepBisection; int locationStuck = 2; getPtOnParticle2(cm1,state1,contactPt, step, ptOnP1); getPtOnParticle2(cm2,state2,contactPt, -1.0*step, ptOnP2); Real penetrationDepth = (ptOnP2-ptOnP1).norm();// overlap; //std::cout<<"contactpoint: "<normal= avgNormal; phys->ptOnP1 = ptOnP1; phys->ptOnP2 = ptOnP2; phys->initial1 = scm->contactPoint; phys->gap = scm->penetrationDepth; bool calJointLength = phys->calJointLength; double jointLength = phys->jointLength; int smallerID = 1; bool twoD = phys->twoDimension; shearDir = phys->shearDir; shearDir.normalize(); /* Get contact area */ phys->prevJointLength = jointLength; double prevContactArea = phys->contactArea; phys->contactArea = getAreaPolygon2(cm1, state1, cm2, state2, contactPt, avgNormal, smallerID,calJointLength,shearDir,jointLength, twoD); //polygon2 if(jointLength < pow(10,-11) || std::isnan(jointLength) || calJointLength == false ) {jointLength = 1.0; /*std::min(s1->R,s2->R);*/} phys->jointLength = jointLength; phys->smallerID = smallerID; /* Get plane physical properties */ double phi_b1=0.0; double phi_b2=0.0; double phi_r1=0.0; double phi_r2=0.0; double JRC1=0.0; double JRC2=0.0; double JSC1=0.0; double JSC2=0.0; double cohesion1=0.0; double cohesion2=0.0; double sigmaC1=0.0; double sigmaC2=0.0; double asperity1=0.0;double asperity2=0.0;double tension1=0.0;double tension2=0.0; int jointType1 = 0; double lambda01=0.0;double lambda02=0.0;double heatCapacity1=0.0; double heatCapacity2 = 0.0; double hwater1 = 0.0; double hwater2 = 0.0; bool intactRock1=false; bool intactRock2=false;int noActive1 = 0; int noActive2 =0; int jointType2 = 0; if(phys->useFaceProperties ){ double f1 = evaluatePhys(cm1, state1, contactPt, phi_b1, phi_r1, JRC1, JSC1, cohesion1, sigmaC1, asperity1, tension1,lambda01,heatCapacity1,hwater1,intactRock1, noActive1, jointType1); double f2 = evaluatePhys(cm2, state2, contactPt, phi_b2, phi_r2, JRC2, JSC2, cohesion2, sigmaC2, asperity2, tension2,lambda02, heatCapacity2,hwater2,intactRock2, noActive2, jointType2); if(s1->isBoundary == true){ phys->phi_b = phi_b1; phys->phi_r = phi_r1; phys->JRC =JRC1; phys->JCS = JSC1; phys->cohesion = cohesion1; phys->sigmaC = sigmaC1; phys->asperity = asperity1; phys->tension = tension1; phys->lambda0 = lambda01; phys->heatCapacities = heatCapacity1; phys->hwater = hwater1; phys->jointType = jointType1; }else if(s2->isBoundary == true){ phys->phi_b = phi_b2; phys->phi_r = phi_r2; phys->JRC = JRC2; phys->JCS = JSC2; phys->cohesion = cohesion2; phys->sigmaC = sigmaC2; phys->asperity = asperity2; phys->tension = tension2; phys->lambda0 = lambda02; phys->heatCapacities = heatCapacity2; phys->hwater = hwater2; phys->jointType = jointType2; }else{ phys->phi_b = std::min(phi_b1,phi_b2); phys->phi_r = std::min(phi_r1,phi_r2); phys->JRC = 0.5*(JRC1+JRC2); phys->JCS = 0.5*(JSC1+JSC2); phys->cohesion = std::min(cohesion1,cohesion2); phys->sigmaC = 0.5*(sigmaC1 + sigmaC2); phys->asperity = 0.5*(asperity1+asperity2); phys->tension = std::min(tension1,tension2); phys->lambda0 = std::max(lambda01,lambda02); phys->heatCapacities = std::max(heatCapacity1,heatCapacity2); phys->hwater = std::max(hwater1,hwater2); phys->intactRock = true; phys->jointType = std::max(jointType1,jointType2); if(intactRock1==false || intactRock2 == false){ phys->intactRock = false;} } if(noActive1 == 1 || noActive2 == 1){phys->rockJointContact = true;}else{phys->rockJointContact = false; } } } scm->precompute(state1,state2,scene,c,avgNormal,!(hasGeom),Vector3r(0,0,0)/*shift 2 */, false /* avoidGranularRatcheting */); //Assign contact point and normal after precompute!!!! scm->contactPoint = contactPt; scm->penetrationDepth=penetrationDepth; if(std::isnan(avgNormal.norm())){std::cout<<"avgNormal: "<normal = avgNormal; }else{ //scm->normal = Vector3r(0,0,0); scm->precompute(state1,state2,scene,c,avgNormal,!(hasGeom),Vector3r(0,0,0)/*shift 2 */, false /* avoidGranularRatcheting */); //Assign contact point and normal after precompute!!!! scm->contactPoint = contactPt;scm->penetrationDepth=-1.0; //scm->normal = Vector3r(0,0,0); } return true; }else{ scm->contactPoint = contactPt;scm->penetrationDepth=-1.0;scm->normal = Vector3r(0,0,0); return false; } return false; } double Ig2_PB_PB_ScGeom::evaluatePhys(const shared_ptr& cm1, const State& state1, const Vector3r newTrial, double& phi_b, double& phi_r, double& JRC, double& JSC, double& cohesion, double& sigmaC, double& asperity, double& tension,double& lambda0,double& heatCapacity, double &hwater, bool &intactRock, int &activePlanesNo, int& jointType){ PotentialBlock *s1=static_cast(cm1.get()); ///////////////////Transforming trial values to local frame of particles////////////////// Vector3r tempP1 = newTrial - state1.pos; /* Direction cosines */ Vector3r localP1 = state1.ori.conjugate()*tempP1; Real x = localP1.x(); Real y = localP1.y(); Real z = localP1.z(); int planeNo = s1->a.size(); if (s1->phi_b.size() == 0){ return 0.0; } Real pSum2 = 0.0; int activeNo = 0; intactRock = true; for (int i=0; ia[i]*x + s1->b[i]*y + s1->c[i]*z - s1->d[i]; if (planehwater[i]; phi_b = s1->phi_b[i]; phi_r = s1->phi_r[i]; tension = s1->tension[i]; cohesion = s1->cohesion[i]; heatCapacity =s1->heatCapacity[i]; jointType = s1->jointType[i]; } JRC += s1->JRC[i]; JSC += s1->JCS[i]; sigmaC += s1->sigmaC[i]; asperity += s1->asperity[i]; lambda0 +=s1->lambda0[i]; hwater = std::max(hwater,s1->hwater[i]); phi_b = std::min(phi_b,s1->phi_b[i]); phi_r = std::min(phi_r,s1->phi_r[i]); tension = std::min(tension,s1->tension[i]); cohesion = std::min(cohesion,s1->cohesion[i]); heatCapacity =std::max(heatCapacity, s1->heatCapacity[i]); jointType = std::max(jointType,s1->jointType[i]); if(s1->intactRock[i] == false){intactRock = false;} activeNo++; //if(lambda0>pow(10,-5)){std::cout<<"lambda0: "<lambda0: "<lambda0[i]<<", i: "<0){ phi_b = phi_b; phi_r = phi_r; JRC = JRC/static_cast(activeNo); JSC = JSC/static_cast(activeNo); JRC = JRC/static_cast(activeNo); cohesion = cohesion; sigmaC = sigmaC/static_cast(activeNo); asperity = asperity/static_cast(activeNo); tension = tension; lambda0 = lambda0/static_cast(activeNo); heatCapacity = heatCapacity; jointType = jointType; hwater = hwater; }else{ phi_b = s1->phi_b[0]; phi_r = s1->phi_r[0]; JRC = s1->JRC[0]; JSC = s1->JCS[0]; cohesion = s1->cohesion[0]; sigmaC = s1->sigmaC[0]; asperity = s1->asperity[0]; tension = s1->tension[0]; lambda0 = s1->lambda0[0]; heatCapacity = 0.0; jointType = jointType; hwater = -1.0; } Real r = s1->r; Real R = s1->R; Real k = s1->k; /* Additional sphere */ Real sphere = (pow(x,2) + pow(y,2) + pow(z,2))/pow(R,2); /* Complete potential particle */ Real f = pSum2 - pow(r,2); activePlanesNo = activeNo; return f; } double Ig2_PB_PB_ScGeom::getSignedArea(const Vector3r pt1, const Vector3r pt2, const Vector3r pt3){ /* if positive, counter clockwise, 2nd point makes a larger angle */ /* if negative, clockwise, 3rd point makes a larger angle */ Eigen::MatrixXd triangle(4,2); triangle(0,0) = pt1.x(); triangle(0,1) = pt1.y(); // triangle(0,2) = pt1.z(); triangle(1,0) = pt2.x(); triangle(1,1) = pt2.y(); // triangle(1,2) = pt2.z(); triangle(2,0) = pt3.x(); triangle(2,1) = pt3.y(); // triangle(2,2) = pt3.z(); triangle(3,0) = pt1.x(); triangle(3,1) = pt1.y(); // triangle(3,2) = pt1.z(); double determinant = getDet(triangle); return determinant; //triangle.determinant(); } double Ig2_PB_PB_ScGeom::getAreaPolygon2(const shared_ptr& cm1, const State& state1, const shared_ptr& cm2, const State& state2,const Vector3r contactPoint, const Vector3r contactNormal, int& smaller, bool calJointLength, Vector3r shearDir, double& jointLength, bool twoD){ const double PI = 3.14159265358979323846; int countParticleA = 0; int countParticleB = 0;double areaTri = 0.0; PotentialBlock *s1=static_cast(cm1.get()); PotentialBlock *s2=static_cast(cm2.get()); double bisectionStepSize = 1.0;//*std::min(s1->R, s2->R); Vector3r ptOnBoundary = contactPoint; Matrix3r rotationMatrix; int count = 1; Vector3r orthogonalDir = Vector3r(contactNormal.y(), -contactNormal.x(),0.0); if(orthogonalDir.norm() 0.0){ /*counter-clockwise */ newSearchDir = -newSearchDir; } if (count == 0){ firstAxis = searchDirOri.cross(newSearchDir); } searchDirOri = newSearchDir; searchDir = searchDirOri;//*bisectionStepSize; prevPoint = ptOnBoundary; Vector3r ptOnP1(0,0,0); Vector3r ptOnP2(0,0,0); if( getPtOnParticleAreaNormal(cm1,state1,ptOnBoundary, searchDir, prevNoA, ptOnP1, searchDirA, newNoA)){ prevNoA = newNoA; }else{ std::cout<<"no intersection A? "< pow(10,-6)) { if( p1.norm()= 2){ area1(0,1) = prevPoint.x();area1(0,2) = ptOnBoundary.x(); area2(0,1) = prevPoint.y();area2(0,2) = ptOnBoundary.y(); area3(0,1) = prevPoint.z(); area3(0,2) = ptOnBoundary.z(); area1(1,1) = prevPoint.y();area1(1,2) = ptOnBoundary.y(); area2(1,1) = prevPoint.z();area2(1,2) = ptOnBoundary.z(); area3(1,1) = prevPoint.x(); area3(1,2) = ptOnBoundary.x(); area1(2,1) = 1.0; area1(2,2) = 1.0; area2(2,1) = 1.0; area2(2,2) = 1.0; area3(2,1) = 1.0; area3(2,2) = 1.0; areaTri += 0.5*sqrt(( pow(area1.determinant(),2) + pow(area2.determinant(),2) + pow(area3.determinant(),2) )); } if(count==1){ secondPoint = ptOnBoundary; } //#if 0 if(count==10){ distanceBackup = (newPt-secondPoint).norm(); areaTri = 0.0; } if(count>12){ if ( fabs((newPt-secondPoint).norm() - distanceBackup )60){ std::cout<<"area polygon count: "< tol);// && (newPt-secondPoint).norm() > tol) ); //std::cout<<"area polygon count: "< pow(10,-5)){searchDir = jointLength*searchDir;} Vector3r ptOnP1(0,0,0); Vector3r ptOnP2(0,0,0); getPtOnParticleArea(cm1,state1,contactPoint, searchDir, ptOnP1); getPtOnParticleArea(cm2,state2,contactPoint, searchDir, ptOnP2); if( (ptOnP1 - contactPoint).squaredNorm() < (ptOnP2 - contactPoint).squaredNorm() ){ ptOnBoundary1 = ptOnP1; }else{ ptOnBoundary1 = ptOnP2; } getPtOnParticleArea(cm1,state1,contactPoint, -searchDir, ptOnP1); getPtOnParticleArea(cm2,state2,contactPoint, -searchDir, ptOnP2); if( (ptOnP1 - contactPoint).squaredNorm() < (ptOnP2 - contactPoint).squaredNorm() ){ ptOnBoundary2 = ptOnP1; }else{ ptOnBoundary2 = ptOnP2; } jointLength = (ptOnBoundary1- ptOnBoundary2).norm(); } //std::cout<<"searchDir: "< countParticleB){smaller =1;}else{smaller =2;} return areaTri; } bool Ig2_PB_PB_ScGeom::getPtOnParticleAreaNormal(const shared_ptr& cm1, const State& state1, const Vector3r previousPt, const Vector3r prevDir, const int prevNo, Vector3r& newPt, Vector3r& newNormal, int& newNo){ //intersect a line and a plane other than the ID of the previous plane PotentialBlock *s1=static_cast(cm1.get()); //Matrix3r Q1 = state1.ori.toRotationMatrix(); Quaternionr Q1 = state1.ori; int planeNo = s1->a.size(); Vector3r intersection (0,0,0); double closestDistance = pow(10,11); newNo = -1; double fA = evaluatePB(cm1,state1, previousPt); //std::cout<<"fA: "<a[i], s1->b[i], s1->c[i]); planeNormal = Q1*planeNormal; double d = -1.0*( planeNormal.x()*(-state1.pos.x()) + planeNormal.y()*(-state1.pos.y()) + planeNormal.z()*(-state1.pos.z()) - s1->d[i] -s1->r); double dotProd = planeNormal.dot(prevDir); if(Mathr::Sign(dotProd) > 0.0 && fabs(dotProd) > pow(10.0,-3) ){ //planeNormal and searchDirection converges double u = (planeNormal.dot(previousPt) - d)/(planeNormal.dot(-prevDir)); Vector3r newPoint = previousPt + u*prevDir; if (fabs(planeNormal.dot(newPoint) - d ) > pow(10,-5) ){ std::cout<<"distance to plane: "<< fabs(planeNormal.dot(newPoint) - d ) <<", planeNormal: "<a[j], s1->b[j], s1->c[j]); planeNormal1 = Q1*planeNormal1; double d1 = -1.0*( planeNormal1.x()*(-state1.pos.x()) + planeNormal1.y()*(-state1.pos.y()) + planeNormal1.z()*(-state1.pos.z()) - s1->d[j] -s1->r); double check1 = planeNormal1.dot(newPoint) - d1; double check1ori = planeNormal1.dot(previousPt) - d1; double dotCheck = planeNormal1.dot(prevDir); std::cout<<"j: "<0.0001){std::cout<<"check : "<& cm1, const State& state1, Vector3r midPoint, Vector3r normal, Vector3r& ptOnParticle){ PotentialBlock *s1=static_cast(cm1.get()); ptOnParticle = midPoint; Real f = evaluatePB(cm1,state1, ptOnParticle); //SecondOrderCorrection(cm1,state1, ptOnParticle); Real fprevious = f; Real fOri =evaluatePB(cm1,state1,ptOnParticle); int counter = 0; //normal.normalize(); Vector3r step = normal*Mathr::Sign(f) *-1.0; Vector3r bracketA(0,0,0); Vector3r bracketB(0,0,0); Vector3r prevPt = ptOnParticle; do{ prevPt = ptOnParticle; ptOnParticle += step; fprevious = f; f = evaluatePB(cm1,state1, ptOnParticle); //SecondOrderCorrection(cm1,state1, ptOnParticle); counter++; if (counter == 50000 ){ //LOG_WARN("Initial point searching exceeded 500 iterations!"); std::cout<<"ptonparticleArea search exceeded 50000 iterations! step:"< 0.0 ); bracketA = ptOnParticle; bracketB = prevPt; //ptOnParticle -step; Vector3r zero(0,0,0); BrentZeroSurf(cm1,state1,bracketA, bracketB, zero); ptOnParticle = zero; //if( fabs(f)>0.1){std::cout<<"getInitial point f:"<& cm1, const State& state1, const shared_ptr& cm2, const State& state2, Vector3r& contactPt){ bool converge = true; PotentialBlock *s1=static_cast(cm1.get()); PotentialBlock *s2=static_cast(cm2.get()); int planeNoA = s1->a.size(); int planeNoB = s2->a.size(); int totalPlanes = planeNoA+planeNoB; Matrix3r QA = state1.ori.toRotationMatrix(); /*direction cosine */ Matrix3r QB = state2.ori.toRotationMatrix(); /*direction cosine */ double blasQ1[3*3]; double blasQ2[3*3]; double blasP1Q [planeNoA*3]; double d1 [planeNoA]; double blasP2Q [planeNoB*3]; double d2 [planeNoB]; int blasCount = 0; for(int i=0; i<3; i++){ for(int j=0; j<3; j++){ blasQ1[blasCount]=QA(j,i); blasQ2[blasCount]=QB(j,i); blasCount++; } } double blasP1[planeNoA*3]; for(int i=0; ia[i]; blasP1[3*i+1]=s1->b[i]; blasP1[3*i+2]=s1->c[i]; d1[i] = s1->d[i] + s1->r; } double blasP2[planeNoB*3]; for(int i=0; ia[i]; blasP2[3*i+1]=s2->b[i]; blasP2[3*i+2]=s2->c[i]; d2[i] = s2->d[i] + s2->r; } int incx =1; int incy=1; int blas3 = 3; char blasNT = 'N'; char blasT= 'T'; double blas0 = 0.0; double blas1 = 1.0; double blasNeg1 = -1.0; double HessTemp[3*totalPlanes]; dgemm_(&blasNT, &blasNT, &blas3, &planeNoA, &blas3, &blas1, &blasQ1[0], &blas3, &blasP1[0], &blas3, &blas0, &blasP1Q[0], &blas3); /*Matrix mulitplication Q1*P1 */ dgemm_(&blasNT, &blasNT, &blas3, &planeNoB, &blas3, &blas1, &blasQ2[0], &blas3, &blasP2[0], &blas3, &blas0, &blasP2Q[0], &blas3); /*Matrix mulitplication Q2*P2 */ for(unsigned int k=0; k orival+ backtrack*0.01*blasFprime){ backtrack *= 0.5; dcopy_(&varNo, &xx[0], &incx, &blasNewX[0], &incy); daxpy_(&varNo, &backtrack, &blasStep[0], &incx, &blasNewX[0], &incy); /* d = B - A*x */ // dcopy_(&totalPlanes, &B[0], &incx, &D[0], &incy); // dgemv_(&blasT, &blas3, &totalPlanes, &blasNeg1, &Atranspose[0], &blas3, &blasNewX[0], &incx, &blas1, &D[0], &incy); val=0.0; for(int i=0; i49){std::cout<<"custom analytic center iter: "<& cm1, const State& state1, const shared_ptr& cm2, const State& state2, Vector3r &contactPoint, bool &convergeFeasibility){ //timingDeltas->start(); Vector3r xGlobal (0,0,0); double rescale = 1.0; bool converge = true; /* minimise s */ /* s.t. Ax - s <= d*/ PotentialBlock *s1=static_cast(cm1.get()); PotentialBlock *s2=static_cast(cm2.get()); /* Parameters for particles A and B */ int planeNoA = s1->a.size(); int planeNoB = s2->a.size(); Matrix3r Q1 = state1.ori.toRotationMatrix().transpose(); //(state1.ori.conjugate()).toRotationMatrix(); Matrix3r Q2 = state2.ori.toRotationMatrix().transpose(); //(state2.ori.conjugate()).toRotationMatrix(); Eigen::MatrixXd A1 = Eigen::MatrixXd::Zero(planeNoA,3); for (int i=0; i < planeNoA; i++){ A1(i,0) = s1->a[i]/rescale; A1(i,1) = s1->b[i]/rescale; A1(i,2) = s1->c[i]/rescale; } Eigen::MatrixXd A2 = Eigen::MatrixXd::Zero(planeNoB,3); for (int i=0; i < planeNoB; i++){ A2(i,0) = s2->a[i]/rescale; A2(i,1) =s2->b[i]/rescale; A2(i,2) = s2->c[i]/rescale; } Eigen::MatrixXd AQ1 = A1*Q1; Eigen::MatrixXd AQ2 = A2*Q2; Eigen::MatrixXd pos1(3,1); pos1(0,0) = rescale*state1.pos.x(); pos1(1,0) = rescale*state1.pos.y(); pos1(2,0) = rescale*state1.pos.z(); Eigen::MatrixXd Q1pos1 = AQ1*pos1; Eigen::MatrixXd pos2(3,1); pos2(0,0) = rescale*state2.pos.x(); pos2(1,0) = rescale*state2.pos.y(); pos2(2,0) = rescale*state2.pos.z(); Eigen::MatrixXd Q2pos2 = AQ2*pos2; // Eigen::MatrixXd xinit(3,1); Eigen::MatrixXd b1 = Q1pos1;// - AQ1*xinit; Eigen::MatrixXd b2 = Q2pos2;// - AQ2*xinit; double constraintInit[planeNoA+planeNoB]; for (int i=0; id[i] + s1->r + Q1pos1(i,0); } for(int i=0; id[i] + s2->r + Q2pos2(i,0); } for (int k = 0; k < numberRows; k++) { rowLower[k] = -COIN_DBL_MAX; } for (int i = 0; i < planeNoA;i++){ int rowIndex[] = {0, 1, 2, 3}; double rowValue[] = {AQ1(i,0), AQ1(i,1), AQ1(i,2), -1.0}; model2.addRow(4, rowIndex, rowValue,rowLower[i], rowUpper[i]); } for (int i = 0; i < planeNoB;i++){ int rowIndex[] = {0, 1, 2, 3}; double rowValue[] = {AQ2(i,0), AQ2(i,1), AQ2(i,2), -1.0}; model2.addRow(4, rowIndex, rowValue,rowLower[planeNoA+i], rowUpper[planeNoA+i]); } model2.setLogLevel(0); model2.scaling(0); model2.setPrimalTolerance(pow(10,-9)) ; model2.primal(); //model2.writeMps("a.mps"); // Alternatively getColSolution() double * columnPrimal = model2.primalColumnSolution(); xGlobal = Vector3r(columnPrimal[0],columnPrimal[1],columnPrimal[2])/rescale; contactPoint = xGlobal; s = columnPrimal[3]; if(s>-pow(10,-15) || model2.status()!=0 ){ return false; }else{ return true; } } void Ig2_PB_PB_ScGeom::BrentZeroSurf(const shared_ptr& cm1, const State& state1, const Vector3r bracketA, const Vector3r bracketB, Vector3r& zero){ Real a = 0.0; Real b = 1.0; Real t = pow(10,-16); Real m = 0.0; Real p = 0.0; Real q = 0.0; Real r = 0.0; Real s = 0.0; Real c = 0.0; Real d = 0.0; Real e = 0.0; Vector3r bracketRange = bracketB- bracketA; Real fa = evaluatePB(cm1,state1, bracketA); //evaluateFNoSphere(cm1,state1, bracketA); // Real fb = evaluatePB(cm1,state1, bracketB); //evaluateFNoSphere(cm1,state1, bracketB); // if(fa*fb > 0.00001){ std::cout<<"fa: "< 0.0){ c = a; fc = fa; d = b-a; e = d; } if(fabs(fc) < fabs(fb) ){ a = b; b = c; c = a; fa = fb; fb = fc; fc = fa; } } tol = 2.0*DBL_EPSILON*fabs(b) + t; m = 0.5*(c-b); if (fabs(m) > tol && fabs(fb) > pow(10,-13) ){ if(fabs(e) < tol || fabs(fa) <= fabs(fb) ){ d = m; e = d; }else{ s = fb/fa; if(fabs(a - c) 0.0){ q = -q; }else{ p = -p; } s = e; e = d; if(( 2.0*p < (3.0*m*q - fabs(tol*q))) && (p < fabs(0.5*s*q)) ){ d = p/q; }else{ d = m; e = d; } } a = b; fa = fb; Real h = 0.0; if(fabs(d) >tol){ h = d; }else if(m > 0.0){ h = tol; }else{ h = - tol; } b = b + h; // h*m_unitVec; zero = bracketA + b*bracketRange; fb = evaluatePB(cm1,state1, zero); //evaluateFNoSphere(cm1,state1, zero); // }else{ zero = bracketA + b*bracketRange; //std::cout<<"b: "< tol && fabs(fb) > pow(10,-13) ); } /* Routine to get value of function (constraint) at a particular position */ double Ig2_PB_PB_ScGeom::evaluatePB(const shared_ptr& cm1, const State& state1, const Vector3r newTrial){ PotentialBlock *s1=static_cast(cm1.get()); ///////////////////Transforming trial values to local frame of particles////////////////// Vector3r tempP1 = newTrial - state1.pos; /* Direction cosines */ //state1.ori.normalize(); Vector3r localP1 = state1.ori.conjugate()*tempP1; Real x = localP1.x(); Real y = localP1.y(); Real z = localP1.z(); int planeNo = s1->a.size(); Real r = s1->r; int insideCount = 0; for (int i=0; ia[i]*x + s1->b[i]*y + s1->c[i]*z - s1->d[i]-r; //-pow(10,-10); if (Mathr::Sign(plane)*1.0<0.0){ insideCount++; } } /* Complete potential particle */ Real f = 1.0; if (insideCount == planeNo){ f = -1.0;} return f; } Vector3r Ig2_PB_PB_ScGeom::getNormal(const shared_ptr& cm1, const State& state1, const Vector3r newTrial){ PotentialBlock *s1=static_cast(cm1.get()); ///////////////////Transforming trial values to local frame of particles////////////////// Vector3r tempP1 = newTrial - state1.pos; /* Direction cosines */ Vector3r localP1(0,0,0); localP1 = state1.ori.conjugate()*tempP1; //the body has been rotated by state.ori. So I will need to rotate the frame by state.ori too Real x = localP1[0]; Real y = localP1[1]; Real z = localP1[2]; ////////////////////////////// assembling potential planes particle 1////////////////////////////// int planeNo = s1->a.size(); vectorp; Real pSum2 = 0.0; bool isSphere = true; int minNo = 0; double closestDistance = pow(10,12); for (int i=0; ia[i]*x + s1->b[i]*y + s1->c[i]*z -s1-> d[i]; if (planea[i],s1->b[i],s1->c[i]); double dist = normal.dot(Vector3r(0,1,0)); if(fabs(dist)<0.99 ){minNo = i; closestDistance = fabs(plane); } }else{ minNo = i; closestDistance = fabs(plane); } } plane = 0.0; }else{isSphere = false;} p.push_back(plane); pSum2 += pow(p[i],2); } Real r = s1->r; Real R = s1->R; Real k = s1->k; /* Additional sphere */ Real sphere = (pow(x,2) + pow(y,2) + pow(z,2))/pow(R,2); /* Complete potential particle */ Real f = (1.0-k)*(pSum2/pow(r,2)-1.0)+k*(sphere -1.0); //////////////////////////////// local first derivitive particle 1 ///////////////////////////////////// Real pdxSum = 0.0; Real pdySum = 0.0; Real pdzSum = 0.0; for (int i=0; ia[i]*p[i]); pdySum += (s1->b[i]*p[i]); pdzSum += (s1->c[i]*p[i]); } Real fdx = 2.0 * pdxSum; Real fdy = 2.0 * pdySum; Real fdz = 2.0 * pdzSum; if (isSphere == true){ fdx = s1->a[minNo];//2.0*x; // fdy = s1->b[minNo]; //2.0*y; // fdz = s1->c[minNo]; //2.0*z; // } ///////////////////// Assembling rotation matrix Qt for particle 1 ////////////////////////////// Matrix3r Q1=Eigen::Matrix3d::Zero(); //if(state1.ori==Quaternionr(1,0,0,0)){ // Q1.setIdentity(); //}else{ Real q0 = state1.ori.w(); Real q1 = state1.ori.x(); Real q2 = state1.ori.y(); Real q3 = state1.ori.z(); Q1(0,0) = 2.0*pow(q0,2.0) -1.0 + 2.0*pow(q1,2.0); Q1(0,1) = 2.0*q1*q2 + 2.0*q0*q3; Q1(0,2) = 2.0*q1*q3 - 2.0*q0*q2; Q1(1,0) = 2.0*q1*q2 - 2.0*q0*q3; Q1(1,1) = 2.0*pow(q0,2.0) -1.0 + 2.0*pow(q2,2.0); Q1(1,2) = 2.0*q2*q3 + 2.0*q0*q1; Q1(2,0) = 2.0*q1*q3 + 2.0*q0*q2; Q1(2,1) = 2.0*q2*q3 - 2.0*q0*q1; Q1(2,2) = 2.0*pow(q0,2) -1.0 + 2.0*pow(q3,2.0); //Matrix3r Q1n = state1.ori.toRotationMatrix(); //Matrix3r Q1c = state1.ori.conjugate().toRotationMatrix(); //std::cout<<"Q1: "<& cm1, const State& state1, const shared_ptr& cm2, const State& state2, Vector3r &contactPt){ PotentialBlock *s1=static_cast(cm1.get()); PotentialBlock *s2=static_cast(cm2.get()); Vector3r xGlobal(0.0,0.0,0.0); /* Parameters for particles A and B */ double rA = s1->r; double kA = s1->k; double RA = s1->R; double rB = s2->r; double kB = s2->k; double RB = s2->R; int planeNoA = s1->a.size(); int planeNoB = s2->a.size(); /* Variables to keep things neat */ double ksA = RA/sqrt(kA); double kpA = rA/sqrt(1.0 - kA); double ksB = RB/sqrt(kB); double kpB = rB/sqrt(1.0 - kB); int NUMCON = 3 + 1+ planeNoA + planeNoB; int NUMVAR = 6 + 2 + planeNoA + planeNoB; /* LINEAR CONSTRAINTS */ MSKboundkeye bkc[NUMCON]; bkc[0] = MSK_BK_FX; bkc[1] = MSK_BK_FX; bkc[2] = MSK_BK_FX; bkc[3] = MSK_BK_FX; for(int i=0; id[i]; }; for(int i=0; id[i]; }; /* BOUNDS */ MSKboundkeye bkx[NUMVAR ]; bkx[0] = MSK_BK_FR; bkx[1] = MSK_BK_FR; bkx[2] = MSK_BK_FR; bkx[3] = MSK_BK_FR; bkx[4] = MSK_BK_FR; bkx[5] = MSK_BK_FR; bkx[6] = MSK_BK_FR; bkx[7] = MSK_BK_FR; for(int i=0; i aval; vector aptrb; vector aptre; vector asub; Matrix3r Q1 = state1.ori.toRotationMatrix(); Matrix3r Q2 = state2.ori.toRotationMatrix(); int totalCount = 0; /* column 0 xA*/ aptrb.push_back(0); int count = 0; if(fabs(Q1(0,0))>pow(10,-15) ){ aval.push_back(ksA*Q1(0,0)); asub.push_back(0); count++; } if(fabs(Q1(1,0) )>pow(10,-15) ){ aval.push_back(ksA*Q1(1,0)); asub.push_back(1); count++; } if(fabs(Q1(2,0) )>pow(10,-15) ){ aval.push_back(ksA*Q1(2,0)); asub.push_back(2); count++; } for(int i=0; i < planeNoA; i++){ if(fabs(s1->a[i]) > pow(10,-15) ){ aval.push_back(ksA*s1->a[i]); asub.push_back(4+i); count++; } } aptre.push_back(count); totalCount += count; /* column 1 yA*/ aptrb.push_back(aptre[0]); count = 0; if(fabs(Q1(0,1) )>pow(10,-15) ){ aval.push_back(ksA*Q1(0,1)); asub.push_back(0); count++; } if(fabs(Q1(1,1))>pow(10,-15) ){ aval.push_back(ksA*Q1(1,1)); asub.push_back(1); count++; } if(fabs(Q1(2,1) )>pow(10,-15) ){ aval.push_back(ksA*Q1(2,1)); asub.push_back(2); count++; } for(int i=0; i < planeNoA; i++){ if(fabs(s1->b[i]) > pow(10,-15) ){ aval.push_back(ksA*s1->b[i]); asub.push_back(4+i); count++; } } aptre.push_back(aptrb[1] + count); totalCount += count; /* column 2 zA*/ aptrb.push_back(aptre[1]); count = 0; if(fabs(Q1(0,2) )>pow(10,-15) ){ aval.push_back(ksA*Q1(0,2)); asub.push_back(0); count++; } if(fabs(Q1(1,2))>pow(10,-15) ){ aval.push_back(ksA*Q1(1,2)); asub.push_back(1); count++; } if(fabs(Q1(2,2) )>pow(10,-15) ){ aval.push_back(ksA*Q1(2,2)); asub.push_back(2); count++; } for(int i=0; i < planeNoA; i++){ if(fabs(s1->c[i]) > pow(10,-15) ){ aval.push_back(ksA*s1->c[i]); asub.push_back(4+i); count++; } } aptre.push_back(aptrb[2] + count); totalCount += count; /* column 3 xB*/ aptrb.push_back(aptre[2]); count = 0; if(fabs(Q2(0,0))>pow(10,-15) ){ aval.push_back(-ksB*Q2(0,0)); asub.push_back(0); count++; } if(fabs(Q2(1,0) )>pow(10,-15) ){ aval.push_back(-ksB*Q2(1,0)); asub.push_back(1); count++; } if(fabs(Q2(2,0) )>pow(10,-15) ){ aval.push_back(-ksB*Q2(2,0)); asub.push_back(2); count++; } for(int i=0; i < planeNoB; i++){ if(fabs(s2->a[i]) > pow(10,-15) ){ aval.push_back(ksB*s2->a[i]); asub.push_back(4+planeNoA +i); count++; } } aptre.push_back(aptrb[3] + count); totalCount += count; /* column 4 yB*/ aptrb.push_back(aptre[3]); count = 0; if(fabs(Q2(0,1))>pow(10,-15) ){ aval.push_back(-ksB*Q2(0,1)); asub.push_back(0); count++; } if(fabs(Q2(1,1) )>pow(10,-15) ){ aval.push_back(-ksB*Q2(1,1)); asub.push_back(1); count++; } if(fabs(Q2(2,1) )>pow(10,-15) ){ aval.push_back(-ksB*Q2(2,1)); asub.push_back(2); count++; } for(int i=0; i < planeNoB; i++){ if(fabs(s2->b[i]) > pow(10,-15) ){ aval.push_back(ksB*s2->b[i]); asub.push_back(4+planeNoA+i); count++; } } aptre.push_back(aptrb[4] + count); totalCount += count; /* column 5 zB*/ aptrb.push_back(aptre[4]); count = 0; if(fabs(Q2(0,2))>pow(10,-15) ){ aval.push_back(-ksB*Q2(0,2)); asub.push_back(0); count++; } if(fabs(Q2(1,2) )>pow(10,-15) ){ aval.push_back(-ksB*Q2(1,2)); asub.push_back(1); count++; } if(fabs(Q2(2,2) )>pow(10,-15) ){ aval.push_back(-ksB*Q2(2,2)); asub.push_back(2); count++; } for(int i=0; i < planeNoB; i++){ if(fabs(s2->c[i]) > pow(10,-15) ){ aval.push_back(ksB*s2->c[i]); asub.push_back(4+planeNoA+i); count++; } } aptre.push_back(aptrb[5] + count); totalCount += count; /*column 6 */ aptrb.push_back(aptre[5]); aval.push_back(1.0); asub.push_back(3); aptre.push_back(aptrb[6]+1); totalCount += 1; /*column 7 */ aptrb.push_back(aptre[6]); aval.push_back(-1.0); asub.push_back(3); aptre.push_back(aptrb[7]+1); totalCount += 1; /*column 8 + i*/ for(int i=0; i < planeNoA; i++){ aptrb.push_back(aptre[8-1+i]); aval.push_back(-1.0*kpA); asub.push_back(4 + i); aptre.push_back(aptrb[8+i]+1); } totalCount += planeNoA; /*column 8 + planeNoA + i */ for(int i=0; i < planeNoB; i++){ aptrb.push_back(aptre[ 8 + planeNoA-1+i]); aval.push_back(-1.0*kpB); asub.push_back(4 + planeNoA + i); aptre.push_back(aptrb[8 + planeNoA+i]+1); } totalCount += planeNoB; MSKidxt i,j,csubA[1+ 3 + planeNoA], csubB[1+ 3 + planeNoB] ; double xx[NUMVAR]; MSKenv_t & env=mosekEnv; MSKtask_t task; MSKrescodee & r=mosekTaskEnv; if ( r==MSK_RES_OK ) { /* Directs the log stream to the 'printstr' function. */ // MSK_linkfunctoenvstream(env,MSK_STREAM_LOG,NULL,NULL); //printstr // MSK_linkfunctoenvstream(env,MSK_STREAM_LOG,NULL,NULL); } if ( r==MSK_RES_OK ) { /* Create the optimization task. */ r = MSK_maketask(env,NUMCON,NUMVAR,&task); if ( r==MSK_RES_OK ) { // MSK_linkfunctotaskstream(task,MSK_STREAM_LOG,NULL,printstr); /* Give MOSEK an estimate of the size of the input data. This is done to increase the speed of inputting data. However, it is optional. */ if (r == MSK_RES_OK) r = MSK_putmaxnumvar(task,NUMVAR); if (r == MSK_RES_OK) r = MSK_putmaxnumcon(task,NUMCON); int NUMANZ = totalCount; if (r == MSK_RES_OK) r = MSK_putmaxnumanz(task,NUMANZ); /* APBend 'NUMCON' empty constraints. The constraints will initially have no bounds. */ if ( r == MSK_RES_OK ) r = MSK_aPBend(task,MSK_ACC_CON,NUMCON); /* APBend 'NUMVAR' variables. The variables will initially be fixed at zero (x=0). */ if ( r == MSK_RES_OK ) r = MSK_aPBend(task,MSK_ACC_VAR,NUMVAR); /* Optionally add a constant term to the objective. */ if ( r ==MSK_RES_OK ) r = MSK_putcfix(task,0.0); for(j=0; j& cm1, const State& state1, Vector3r midPoint, Vector3r normal, Vector3r& ptOnParticle){ PotentialBlock *s1=static_cast(cm1.get()); ptOnParticle = midPoint; Real f = evaluatePB(cm1,state1, ptOnParticle);//evaluateFNoSphere(cm1,state1, ptOnParticle); // Real fprevious = f; int counter = 0; //normal.normalize(); Vector3r step = normal*Mathr::Sign(f) *-1.0; Vector3r bracketA(0,0,0); Vector3r bracketB(0,0,0); do{ ptOnParticle += step; fprevious = f; f = evaluatePB(cm1,state1, ptOnParticle); //evaluateFNoSphere(cm1,state1, ptOnParticle); // counter++; if (counter == 50000 ){ //LOG_WARN("Initial point searching exceeded 500 iterations!"); std::cout<<"ptonparticle2 search exceeded 50000 iterations! step:"< 0.0 ); bracketA = ptOnParticle; bracketB = ptOnParticle -step; Vector3r zero(0,0,0); BrentZeroSurf(cm1,state1,bracketA, bracketB, zero); ptOnParticle = zero; //if( fabs(f)>0.1){std::cout<<"getInitial point f:"<& cm1, const State& state1, const shared_ptr& cm2, const State& state2, Vector3r &contactPt, bool warmstart){ //timingDeltas->start(); PotentialBlock *s1=static_cast(cm1.get()); PotentialBlock *s2=static_cast(cm2.get()); Vector3r xGlobal(0.0,0.0,0.0); int iter = 0; int totalIter = 0; /* Parameters for particles A and B */ double rA = s1->r;double kA = s1->k;double RA = s1->R; double rB = s2->r;double kB = s2->k;double RB = s2->R; int planeNoA = s1->a.size();int planeNoB = s2->a.size(); int varNo = 3+1+planeNoA+planeNoB; int planeNoAB = planeNoA + planeNoB; int varNo2 = varNo*varNo; int planeNoA3 = 3+planeNoA; int planeNoB3=3+planeNoB; int planeNoA2 =planeNoA*planeNoA; int planeNoB2=planeNoB*planeNoB; Matrix3r QA = state1.ori.conjugate().toRotationMatrix(); /*direction cosine */ Matrix3r QB = state2.ori.conjugate().toRotationMatrix(); /*direction cosine */ int blas3 = 3; char blasNT = 'N'; char blasT= 'T'; int blas1planeNoA = std::max(1,planeNoA); int blas1planeNoB = std::max(1,planeNoB); int blas1planeNoAB = std::max(1,planeNoAB); double blas0 = 0.0; double blas1 = 1.0; double blasNeg1 = -1.0; double blasQA[9]; double blasQB[9]; double blasPosA[3]; double blasPosB[3]; double blasContactPt[3]; double blasC[varNo]; for (int i=0; ia[i]*blasLocalP1[0] + s1->b[i]*blasLocalP1[1] + s1->c[i]*blasLocalP1[2] - s1->d[i]; if (planea[i]; blasP1[i+planeNoA] = s1->b[i]; blasP1[i+2*planeNoA] = s1->c[i]; blasD1[i] = s1->d[i]; } //Eigen::MatrixXd P1Q = P1*QA; //transA = 'N'; transB = 'N'; blasM = planeNoA; blasN = 3; blasK = 3; // blasLDA = std::max(1,blasM); blasLDC = std::max(1,blasM); blasLDB = 3; blasAlpha=1.0; blasBeta = 0.0; //dgemm_(&transA, &transB, &blasM, &blasN, &blasK, &blasAlpha, &blasP1[0], &blasLDA, &blasQA[0], &blasLDB, &blasBeta, &blasP1Q[0], &blasLDC); dgemm_(&blasNT, &blasNT, &planeNoA, &blas3, &blas3, &blas1, &blasP1[0], &blas1planeNoA, &blasQA[0], &blasLDB, &blas0, &blasP1Q[0], &blas1planeNoA); Real sphereA = (pow(blasLocalP1[0],2) + pow(blasLocalP1[1],2) + pow(blasLocalP1[2],2))/pow(RA,2); Real sA = (1.0-kA)*(pertSumA2/pow(rA,2) - 1.0)+kA*(sphereA -1.0); /* fB */ double blasTemPB2[3]; double blasLocalP2[3]; for(int i=0; i<3; i++){ blasTemPB2[i] = blasContactPt[i] - blasPosB[i]; } //transA = 'N'; blasM = 3; blasN = 3; blasLDA = 3; blasAlpha=1.0; blasBeta = 0.0; //dgemv_(&transA, &blasM, &blasN, &blasAlpha, &blasQB[0], &blasLDA, &blasTemPB2[0], &incx, &blasBeta, &blasLocalP2[0], &incy); dgemv_(&blasNT, &blas3, &blas3, &blas1, &blasQB[0], &blas3, &blasTemPB2[0], &incx, &blas0, &blasLocalP2[0], &incy); // Vector3r temPB2 = contactPt - posB; // Vector3r localP2 = QB*temPB2; /*P2Q*/ //Eigen::MatrixXd P2 = Eigen::MatrixXd::Zero(planeNoB,3); /*d2*/ //Eigen::MatrixXd d2 = Eigen::MatrixXd::Zero(planeNoB,1); double blasP2[planeNoB*3]; double blasD2[planeNoB]; double blasP2Q[planeNoB*3]; double pertSumB2 = 0.0; for (int i=0; ia[i]*blasLocalP2[0] + s2->b[i]*blasLocalP2[1] + s2->c[i]*blasLocalP2[2] - s2->d[i]; if (planea[i]; blasP2[i+planeNoB] = s2->b[i]; blasP2[i+2*planeNoB] = s2->c[i]; blasD2[i] = s2->d[i]; } //Eigen::MatrixXd P2Q = P2*QB; //transA = 'N'; transB = 'N'; blasM = planeNoB; blasN = 3; blasK = 3; //blasLDA = std::max(1,blasM); blasLDC = std::max(1,blasM); blasLDB = 3; blasAlpha=1.0; blasBeta = 0.0; // dgemm_(&transA, &transB, &blasM, &blasN, &blasK, &blasAlpha, &blasP2[0], &blasLDA, &blasQB[0], &blasLDB, &blasBeta, &blasP2Q[0], &blasLDC); dgemm_(&blasNT, &blasNT, &planeNoB, &blas3, &blas3, &blasAlpha, &blasP2[0], &blas1planeNoB, &blasQB[0], &blas3, &blasBeta, &blasP2Q[0], &blas1planeNoB); Real sphereB = (pow(blasLocalP2[0],2) + pow(blasLocalP2[1],2) + pow(blasLocalP2[2],2))/pow(RB,2); Real sB = (1.0-kB)*(pertSumB2/pow(rB,2) - 1.0)+kB*(sphereB -1.0); //sPert = fabs(fA-fB); s = std::max(sqrt(fabs(sA+1.0)), sqrt(fabs(sB+1.0))) + sPert; //sqrt(fA+fB+2.0)+sPert; //sqrt(std::max(fabs(fA+1.0), fabs(fB+1.0))) + sPert; // //x[3] = s; blasX[3]= s; /////////////////// algebra formulation of the SOCP /////////////////// /* c */ // Eigen::MatrixXd c=Eigen::MatrixXd::Zero(varNo,1); // c[3] = 1.0; double blasA1[(3+planeNoA)*varNo]; double blasA2[(3+planeNoB)*varNo]; /* Second order cone constraints */ /* A1 */ //Eigen::MatrixXd A1(3+planeNoA,varNo); //Matrix3r QAs=kAs*QA; //cwise() double blasQAs[9]; int noElements=9; double scaleFactor = kAs; dcopy_(&noElements, &blasQA[0], &incx, &blasQAs[0], &incx); dscal_(&noElements, &scaleFactor, &blasQAs[0], &incx); // A1 << QAs,Eigen::MatrixXd::Zero(3,1+planeNoAB), // Eigen::MatrixXd::Zero(planeNoA,4),kAp*Eigen::MatrixXd::Identity(planeNoA, planeNoA),Eigen::MatrixXd::Zero(planeNoA,planeNoB); memset(blasA1,0.0,sizeof(blasA1)); for (int i=0; i<3; i++){ blasA1[i] = blasQAs[i]; blasA1[i+planeNoA3] = blasQAs[i+3]; blasA1[i+2*planeNoA3] = blasQAs[i+6]; } for (int i=0; icheckpoint("setup"); while(totalIter<500){ penalty = 1.0/t; /* Newton's method */ /* s=x[3]; */ s=blasX[3]; /* temp variables */ /* w1 = A1*x + b1; */ noElements = 3+planeNoA; dcopy_(&noElements, &blasB1[0], &incx, &blasW1[0], &incy); //transA = 'N'; blasM = 3+planeNoA; blasN = varNo; //blasLDA = 3+planeNoA; blasAlpha = 1.0; blasBeta = 1.0; incx =1; incy=1; //dgemv_(&transA, &blasM, &blasN, &blasAlpha, &blasA1[0], &blasLDA, &blasX[0], &incx, &blasBeta, &blasW1[0], &incy); dgemv_(&blasNT, &planeNoA3, &varNo, &blas1, &blasA1[0], &planeNoA3, &blasX[0], &incx, &blas1, &blasW1[0], &incy); /* w2 = A2*x + b2; */ noElements = 3+planeNoB; dcopy_(&noElements, &blasB2[0], &incx, &blasW2[0], &incy); //transA = 'N'; blasM = 3+planeNoB; blasN = varNo; //blasLDA = 3+planeNoB; blasAlpha = 1.0; blasBeta = 1.0; //dgemv_(&transA, &blasM, &blasN, &blasAlpha, &blasA2[0], &blasLDA, &blasX[0], &incx, &blasBeta, &blasW2[0], &incy); dgemv_(&blasNT, &planeNoB3, &varNo, &blas1, &blasA2[0], &planeNoB3, &blasX[0], &incx, &blas1, &blasW2[0], &incy); /* u1 = s*s - w1.dot(w1); */ /* u2 = s*s - w2.dot(w2); */ //noElements = 3+planeNoA; blasW1dot = ddot_(&planeNoA3, &blasW1[0], &incx, &blasW1[0], &incy); //noElements = 3+planeNoB; blasW2dot = ddot_(&planeNoB3, &blasW2[0], &incx, &blasW2[0], &incy); u1 =s*s -blasW1dot; u2 =s*s -blasW2dot; /* wL = bL - AL*x; */ noElements = planeNoAB; dcopy_(&noElements, &blasBL[0], &incx, &blasWL[0], &incy); //transA = 'N'; blasN = varNo; //blasM = planeNoAB; blasLDA = std::max(1,planeNoAB); blasAlpha = -1.0; blasBeta = 1.0; //dgemv_(&transA, &blasM, &blasN, &blasAlpha, &blasAL[0], &blasLDA, &blasX[0], &incx, &blasBeta, &blasWL[0], &incy); dgemv_(&blasNT, &planeNoAB, &varNo, &blasNeg1, &blasAL[0], &blas1planeNoAB, &blasX[0], &incx, &blas1, &blasWL[0], &incy); for (int i=0; icheckpoint("assemble H and g"); //std::cout<<"before Chol, totalIter: "<checkpoint("Cholesky"); //fprime = step.transpose()*g; //noElements = varNo; blasFprime = ddot_(&varNo, &blasStep[0], &incx, &blasGrad[0], &incy); wLlogsum = 0.0; for (int i=0; i0){ minWL = blasWL[0]; } for(int i=0; i0){ minWL = blasWL[0]; } for(int i=0; icheckpoint("barrier search"); wLlogsum = 0.0; for (int i=0; i val + backtrack*0.01*blasFprime){ backtrack = 0.5*backtrack; //for (int i = 0; icheckpoint("line search"); noElements = varNo; dcopy_(&noElements, &blasNewX[0], &incx, &blasX[0], &incy); if(blasFprime >0.0){ std::cout<<"count: "<0.001 ){std::cout<<"inside fA-fB: "<checkpoint("newton"); return true; } t = std::min(t*mu, (2.0*m+1.0)/tol); iter = 0; totalIter = totalIter+1; } if(totalIter>100){ std::cout<<"totalIter: "<checkpoint("complete"); } return ( true ); } #endif // YADE_POTENTIAL_BLOCKS trunk-2017.01a/pkg/dem/Ig2_PB_PB_ScGeom.hpp000077500000000000000000000150521304022710500200470ustar00rootroot00000000000000/*CWBoon 2016 */ /* Please cite: */ /* CW Boon, GT Houlsby, S Utili (2013). A new algorithm for contact detection between convex polygonal and polyhedral particles in the discrete element method. Computers and Geotechnics 44, 73-82. */ /* The numerical library is changed from CPLEX to CLP because subscription to the academic initiative is required to use CPLEX for free */ #ifdef YADE_POTENTIAL_BLOCKS #pragma once #include #include #include #include #include #include #include # if 0 #include #include #include #include #endif #include #include #include #include #include //#include "/home/boon/coin-Clp/Clp/src/ClpSimplex.hpp" //#include "/home/boon/coin-Clp/CoinUtils/src/CoinHelperFunctions.hpp" //#include "/home/boon/coin-Clp/CoinUtils/src/CoinTime.hpp" //#include "/home/boon/coin-Clp/CoinUtils/src/CoinBuild.hpp" //#include "/home/boon/coin-Clp/CoinUtils/src/CoinModel.hpp" #include #include class Ig2_PB_PB_ScGeom: public IGeomFunctor { //protected: //static std::ofstream output; #if 0 std::string myfile; std::string Key; MSKrescodee mosekTaskEnv; MSKenv_t mosekEnv; #endif public : virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& se32, const Vector3r& shift2, const bool& force, const shared_ptr& c); double getSignedArea(const Vector3r pt1,const Vector3r pt2, const Vector3r pt3); double evaluatePB(const shared_ptr& cm1, const State& state1, const Vector3r newTrial); void getPtOnParticle2(const shared_ptr& cm1, const State& state1, Vector3r previousPt, Vector3r normal, Vector3r& newlocalPoint); void getPtOnParticleArea(const shared_ptr& cm1, const State& state1, Vector3r previousPt, Vector3r normal, Vector3r& newlocalPoint); bool getPtOnParticleAreaNormal(const shared_ptr& cm1, const State& state1, const Vector3r previousPt, const Vector3r prevDir, const int prevNo, Vector3r& newlocalPoint, Vector3r& newNormal, int& newNo); bool contactPtMosekF2(const shared_ptr& cm1, const State& state1, const shared_ptr& cm2, const State& state2, Vector3r &contactPt); double getDet(const Eigen::MatrixXd A); bool customSolve(const shared_ptr& cm1, const State& state1, const shared_ptr& cm2, const State& state2, Vector3r &contactPt, bool warmstart); double evaluatePhys(const shared_ptr& cm1, const State& state1, const Vector3r newTrial, double& phi_b, double& phi_r, double& JRC, double& JSC, double& cohesion, double& sigmaC, double& asperity, double& tension, double &lambda0, double &heatCapacity, double &hwater, bool &intactRock, int &activePlanesNo, int &jointType); Vector3r getNormal(const shared_ptr& cm1, const State& state1, const Vector3r newTrial); void BrentZeroSurf(const shared_ptr& cm1, const State& state1, const Vector3r bracketA, const Vector3r bracketB, Vector3r& zero); bool startingPointFeasibilityCLP(const shared_ptr& cm1, const State& state1, const shared_ptr& cm2, const State& state2, Vector3r &contactPoint, bool &convergeFeasibility); bool customSolveAnalyticCentre(const shared_ptr& cm1, const State& state1, const shared_ptr& cm2, const State& state2, Vector3r& contactPt); double getAreaPolygon2(const shared_ptr& cm1, const State& state1, const shared_ptr& cm2, const State& state2, const Vector3r contactPt, const Vector3r contactNormal, int& smaller, bool calJointLength, Vector3r shearDir, double& jointLength, bool twoDimension); ///////////////////////////////////////////////////////////////////////////////////////////////////// YADE_CLASS_BASE_DOC_ATTRS_CTOR(Ig2_PB_PB_ScGeom,IGeomFunctor,"PB", ((double, accuracyTol, pow(10,-7),, "accuracy desired, tolerance criteria for SOCP")) ((double, stepAngle, pow(10,-2),, "accuracy desired, tolerance criteria for SOCP")) ((double,interactionDetectionFactor,1.0,,"bool to avoid granular ratcheting")) ((Vector3r, twoDdir, Vector3r(0,1,0),, "to get radius of curvature")) ((bool,twoDimension,false,,"bool to avoid granular ratcheting")), //((std::string,myfile,"./PotentialBlocks"+"","string")), //timingDeltas=shared_ptr(new TimingDeltas); //mosekTaskEnv = MSK_makeenv(&mosekEnv,NULL,NULL,NULL,NULL); //mosekTaskEnv = MSK_initenv(mosekEnv); ); FUNCTOR2D(PotentialBlock,PotentialBlock); // needed for the dispatcher, even if it is symmetric DEFINE_FUNCTOR_ORDER_2D(PotentialBlock,PotentialBlock); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Ig2_PB_PB_ScGeom); #ifdef __cplusplus extern "C" { #endif /* LAPACK LU */ //int dgesv(int varNo, int varNo2, double *H, int varNo3, int *pivot, double* g, int varNo4, int info){ extern void dgesv_(const int *N, const int *nrhs, double *Hessian, const int *lda, int *ipiv, double *gradient, const int *ldb, int *info); // int ans; // dgesv_(&varNo, &varNo2, H, &varNo3, pivot,g, &varNo4, &ans); // return ans; //} /* LAPACK Cholesky */ extern void dpbsv_(const char *uplo, const int *n, const int *kd, const int *nrhs, double *AB, const int *ldab, double *B, const int *ldb, int *info); /* LAPACK QR */ extern void dgels_(const char *Trans, const int *m, const int *n, const int *nrhs, double *A, const int *lda, double *B, const int *ldb, const double *work, const int *lwork, int *info); /*BLAS */ extern void dgemm_(const char *transA, const char *transB, const int *m, const int *n, const int *k, const double *alpha, double *A, const int *lda, double *B, const int *ldb, const double *beta, double *C, const int *ldc); extern void dgemv_(const char *trans, const int *m, const int *n, const double *alpha, double *A, const int *lda, double *x, const int *incx, const double *beta, double *y, const int *incy); extern void dcopy_(const int *N, double *x, const int *incx, double *y, const int *incy); extern double ddot_(const int *N, double *x, const int *incx, double *y, const int *incy); extern void daxpy_(const int *N, const double *da, double *dx, const int *incx, double *dy, const int *incy); extern void dscal_(const int *N, const double *alpha, double *x, const int *incx); void dsyev_(const char *jobz, const char *uplo, const int *N, double *A, const int *lda, double *W, double *work, int *lwork, int *info); #ifdef __cplusplus }; #endif #endif // YADE_POTENTIAL_BLOCKS trunk-2017.01a/pkg/dem/Ig2_PP_PP_ScGeom.cpp000066400000000000000000001642341304022710500201020ustar00rootroot00000000000000/*CWBoon 2015 */ /* C.W. Boon, G.T. Houlsby, S. Utili (2013). A new contact detection algorithm for three-dimensional non-spherical particles. Powder Technology, 248, pp 94-102. */ /* code for calling MOSEK was for ver 6. Please uncomment if you have the licence */ #ifdef YADE_POTENTIAL_PARTICLES #include "Ig2_PP_PP_ScGeom.hpp" #include #include //#include #include #include #include #include #include #include #include #include #include #include #include #include #include YADE_PLUGIN((Ig2_PP_PP_ScGeom) //#ifdef YADE_OPENGL // (Gl1_Ig2_PP_PP_ScGeom) // #endif ); CREATE_LOGGER(Ig2_PP_PP_ScGeom); bool Ig2_PP_PP_ScGeom::go(const shared_ptr& cm1,const shared_ptr& cm2,const State& state1, const State& state2, const Vector3r& shift2, const bool& force,const shared_ptr& c) { PotentialParticle *s1=static_cast(cm1.get()); PotentialParticle *s2=static_cast(cm2.get()); /* Short circuit if both particles are boundary particles */ if((s1->isBoundary==true)&&(s2->isBoundary==true)) { return false; } bool hasGeom = false; Vector3r contactPt(0,0,0); shared_ptr scm; Real stepBisection = 0.001*std::min(s1->R,s2->R); if(stepBisectionR<<", R2: "<R<<", stepBisection: "<getId1()<<", id2: "<getId2()<geom) { hasGeom = true; scm=YADE_PTR_CAST(c->geom); if (scm->penetrationDepth>stepBisection ) { stepBisection = 0.5*scm->penetrationDepth; } if(stepBisectionpenetrationDepth<contactPoint; } else { scm=shared_ptr(new ScGeom()); c->geom=scm; contactPt = 0.5*(state1.pos+state2.pos); } converge = true; fA= evaluatePP(cm1,state1, contactPt); fB = evaluatePP(cm2,state2, contactPt); //Default does not have warmstart //if(fA < 0.0 && fB <0.0){ // converge = customSolve(cm1,state1,cm2,state2,contactPt,true); //}else{ converge = customSolve(cm1,state1,cm2,state2,contactPt,false); //} // if you have mosek uncomment this. Mosek is more robust but slightly slower as an external library #ifdef YADE_MOSEK /* Mosek */ if( converge==false ) { //std::cout<<"mosek used"<start(); if (fA < 0.0 && fB < 0.0 && converge == true) { contact = true; } else { contact = false; contactPt = 0.5*(state1.pos+state2.pos); } //////////////////////////////////////////////////////////* PASS VARIABLES TO ScGeom Functor *///////////////////////////////////////////////////////////// //* 1. Get overlap *// //* 2. Get information on active planes. //////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////////// if (contact == true || c->isReal() || force) { if (contact == true) { normalP1 = getNormal(cm1,state1,contactPt); normalP1.normalize(); normalP2 = getNormal(cm2,state2,contactPt); normalP2.normalize(); //if(s1->isBoundary==true){avgNormal=normalP1;}else if(s2->isBoundary==true){avgNormal=-normalP2;}else{avgNormal = (normalP1 - normalP2);} avgNormal = (normalP1 - normalP2); avgNormal.normalize(); if(s1->fixedNormal==true) { avgNormal = s1->boundaryNormal; } if(s2->fixedNormal==true) { avgNormal = -s2->boundaryNormal; } Vector3r step = avgNormal*stepBisection; //int locationStuck = 2; getPtOnParticle2(cm1,state1,contactPt, step, ptOnP1); getPtOnParticle2(cm2,state2,contactPt, -1.0*step, ptOnP2); vector points; Real penetrationDepth = (ptOnP2-ptOnP1).norm();// overlap; //std::cout<<"contactpoint: "<precompute(state1,state2,scene,c,avgNormal,!(hasGeom),Vector3r(0,0,0)/*shift 2 */, false /* avoidGranularRatcheting */); //Assign contact point and normal after precompute!!!! scm->contactPoint = contactPt; scm->penetrationDepth=penetrationDepth; if(std::isnan(avgNormal.norm())) { //std::cout<<"avgNormal: "<normal = avgNormal; } else { //scm->normal = Vector3r(0,0,0); scm->precompute(state1,state2,scene,c,avgNormal,!(hasGeom),Vector3r(0,0,0)/*shift 2 */, false /* avoidGranularRatcheting */); //Assign contact point and normal after precompute!!!! scm->contactPoint = contactPt; scm->penetrationDepth=-1.0; //scm->normal = Vector3r(0,0,0); } return true; } else { scm->contactPoint = contactPt; scm->penetrationDepth=-1.0; scm->normal = Vector3r(0,0,0); return false; } return false; } void Ig2_PP_PP_ScGeom::BrentZeroSurf(const shared_ptr& cm1, const State& state1, const Vector3r bracketA, const Vector3r bracketB, Vector3r& zero) { Real a = 0.0; Real b = 1.0; Real t = pow(10,-16); Real m = 0.0; Real p = 0.0; Real q = 0.0; Real r = 0.0; Real s = 0.0; Real c = 0.0; Real d = 0.0; Real e = 0.0; Vector3r bracketRange = bracketB- bracketA; Real fa = evaluatePP(cm1,state1, bracketA); //evaluateFNoSphere(cm1,state1, bracketA); // Real fb = evaluatePP(cm1,state1, bracketB); //evaluateFNoSphere(cm1,state1, bracketB); // if(fa*fb > 0.00001) { //std::cout<<"fa: "< 0.0) { c = a; fc = fa; d = b-a; e = d; } if(fabs(fc) < fabs(fb) ) { a = b; b = c; c = a; fa = fb; fb = fc; fc = fa; } } tol = 2.0*DBL_EPSILON*fabs(b) + t; m = 0.5*(c-b); if (fabs(m) > tol && fabs(fb) > pow(10,-13) ) { if(fabs(e) < tol || fabs(fa) <= fabs(fb) ) { d = m; e = d; } else { s = fb/fa; if(fabs(a - c) 0.0) { q = -q; } else { p = -p; } s = e; e = d; if(( 2.0*p < (3.0*m*q - fabs(tol*q))) && (p < fabs(0.5*s*q)) ) { d = p/q; } else { d = m; e = d; } } a = b; fa = fb; Real h = 0.0; if(fabs(d) >tol) { h = d; } else if(m > 0.0) { h = tol; } else { h = - tol; } b = b + h; // h*m_unitVec; zero = bracketA + b*bracketRange; fb = evaluatePP(cm1,state1, zero); //evaluateFNoSphere(cm1,state1, zero); // } else { zero = bracketA + b*bracketRange; //std::cout<<"b: "< tol && fabs(fb) > pow(10,-13) ); } /* Routine to get value of function (constraint) at a particular position */ Real Ig2_PP_PP_ScGeom::evaluatePP(const shared_ptr& cm1, const State& state1, const Vector3r newTrial) { PotentialParticle *s1=static_cast(cm1.get()); ///////////////////Transforming trial values to local frame of particles////////////////// Vector3r tempP1 = newTrial - state1.pos; /* Direction cosines */ //state1.ori.normalize(); Vector3r localP1 = state1.ori.conjugate()*tempP1; Real x = localP1.x(); Real y = localP1.y(); Real z = localP1.z(); int planeNo = s1->a.size(); Real pSum2 = 0.0; for (int i=0; ia[i]*x + s1->b[i]*y + s1->c[i]*z - s1->d[i]; if (planer; Real R = s1->R; Real k = s1->k; /* Additional sphere */ Real sphere = (pow(x,2) + pow(y,2) + pow(z,2))/pow(R,2); /* Complete potential particle */ Real f = (1.0-k)*(pSum2/pow(r,2) - 1.0)+k*(sphere -1.0); return f; } Vector3r Ig2_PP_PP_ScGeom::getNormal(const shared_ptr& cm1, const State& state1, const Vector3r newTrial) { PotentialParticle *s1=static_cast(cm1.get()); ///////////////////Transforming trial values to local frame of particles////////////////// Vector3r tempP1 = newTrial - state1.pos; /* Direction cosines */ Vector3r localP1(0,0,0); localP1 = state1.ori.conjugate()*tempP1; //the body has been rotated by state.ori. So I will need to rotate the frame by state.ori too Real x = localP1[0]; Real y = localP1[1]; Real z = localP1[2]; ////////////////////////////// assembling potential planes particle 1////////////////////////////// int planeNo = s1->a.size(); vectorp; Real pSum2 = 0.0; for (int i=0; ia[i]*x + s1->b[i]*y + s1->c[i]*z -s1-> d[i]; if (planer; Real R = s1->R; Real k = s1->k; /* Additional sphere */ //Real sphere = (pow(x,2) + pow(y,2) + pow(z,2))/pow(R,2); /* Complete potential particle */ //Real f = (1.0-k)*(pSum2/pow(r,2)-1.0)+k*(sphere -1.0); //////////////////////////////// local first derivitive particle 1 ///////////////////////////////////// Real pdxSum = 0.0; Real pdySum = 0.0; Real pdzSum = 0.0; for (int i=0; ia[i]*p[i]); pdySum += (s1->b[i]*p[i]); pdzSum += (s1->c[i]*p[i]); } Real fdx = 2.0*(1.0-k) * pdxSum/pow(r,2) + 2.0*k*x/pow(R,2); Real fdy = 2.0*(1.0-k) * pdySum/pow(r,2) + 2.0*k*y/pow(R,2); Real fdz = 2.0*(1.0-k) * pdzSum/pow(r,2) + 2.0*k*z/pow(R,2); ///////////////////// Assembling rotation matrix Qt for particle 1 ////////////////////////////// Matrix3r Q1=Eigen::Matrix3d::Zero();; //if(state1.ori==Quaternionr(1,0,0,0)){ // Q1.setIdentity(); //}else{ Real q0 = state1.ori.w(); Real q1 = state1.ori.x(); Real q2 = state1.ori.y(); Real q3 = state1.ori.z(); Q1(0,0) = 2.0*pow(q0,2.0) -1.0 + 2.0*pow(q1,2.0); Q1(0,1) = 2.0*q1*q2 + 2.0*q0*q3; Q1(0,2) = 2.0*q1*q3 - 2.0*q0*q2; Q1(1,0) = 2.0*q1*q2 - 2.0*q0*q3; Q1(1,1) = 2.0*pow(q0,2.0) -1.0 + 2.0*pow(q2,2.0); Q1(1,2) = 2.0*q2*q3 + 2.0*q0*q1; Q1(2,0) = 2.0*q1*q3 + 2.0*q0*q2; Q1(2,1) = 2.0*q2*q3 - 2.0*q0*q1; Q1(2,2) = 2.0*pow(q0,2) -1.0 + 2.0*pow(q3,2.0); //Matrix3r Q1n = state1.ori.toRotationMatrix(); //Matrix3r Q1c = state1.ori.conjugate().toRotationMatrix(); //std::cout<<"Q1: "<& cm1, const State& state1, const shared_ptr& cm2, const State& state2, Vector3r &contactPt) { PotentialParticle *s1=static_cast(cm1.get()); PotentialParticle *s2=static_cast(cm2.get()); Vector3r xGlobal(0.0,0.0,0.0); /* Parameters for particles A and B */ Real rA = s1->r; Real kA = s1->k; Real RA = s1->R; Real rB = s2->r; Real kB = s2->k; Real RB = s2->R; int planeNoA = s1->a.size(); int planeNoB = s2->a.size(); /* Variables to keep things neat */ Real ksA = RA/sqrt(kA); Real kpA = rA/sqrt(1.0 - kA); Real ksB = RB/sqrt(kB); Real kpB = rB/sqrt(1.0 - kB); int NUMCON = 3 + 1+ planeNoA + planeNoB; int NUMVAR = 6 + 2 + planeNoA + planeNoB; /* LINEAR CONSTRAINTS */ MSKboundkeye bkc[NUMCON]; bkc[0] = MSK_BK_FX; bkc[1] = MSK_BK_FX; bkc[2] = MSK_BK_FX; bkc[3] = MSK_BK_FX; for(int i=0; id[i]; }; for(int i=0; id[i]; }; /* BOUNDS */ MSKboundkeye bkx[NUMVAR ]; bkx[0] = MSK_BK_FR; bkx[1] = MSK_BK_FR; bkx[2] = MSK_BK_FR; bkx[3] = MSK_BK_FR; bkx[4] = MSK_BK_FR; bkx[5] = MSK_BK_FR; bkx[6] = MSK_BK_FR; bkx[7] = MSK_BK_FR; for(int i=0; i aval; vector aptrb; vector aptre; vector asub; Matrix3r Q1 = state1.ori.toRotationMatrix(); Matrix3r Q2 = state2.ori.toRotationMatrix(); int totalCount = 0; /* column 0 xA*/ aptrb.push_back(0); int count = 0; if(fabs(Q1(0,0))>pow(10,-15) ) { aval.push_back(ksA*Q1(0,0)); asub.push_back(0); count++; } if(fabs(Q1(1,0) )>pow(10,-15) ) { aval.push_back(ksA*Q1(1,0)); asub.push_back(1); count++; } if(fabs(Q1(2,0) )>pow(10,-15) ) { aval.push_back(ksA*Q1(2,0)); asub.push_back(2); count++; } for(int i=0; i < planeNoA; i++) { if(fabs(s1->a[i]) > pow(10,-15) ) { aval.push_back(ksA*s1->a[i]); asub.push_back(4+i); count++; } } aptre.push_back(count); totalCount += count; /* column 1 yA*/ aptrb.push_back(aptre[0]); count = 0; if(fabs(Q1(0,1) )>pow(10,-15) ) { aval.push_back(ksA*Q1(0,1)); asub.push_back(0); count++; } if(fabs(Q1(1,1))>pow(10,-15) ) { aval.push_back(ksA*Q1(1,1)); asub.push_back(1); count++; } if(fabs(Q1(2,1) )>pow(10,-15) ) { aval.push_back(ksA*Q1(2,1)); asub.push_back(2); count++; } for(int i=0; i < planeNoA; i++) { if(fabs(s1->b[i]) > pow(10,-15) ) { aval.push_back(ksA*s1->b[i]); asub.push_back(4+i); count++; } } aptre.push_back(aptrb[1] + count); totalCount += count; /* column 2 zA*/ aptrb.push_back(aptre[1]); count = 0; if(fabs(Q1(0,2) )>pow(10,-15) ) { aval.push_back(ksA*Q1(0,2)); asub.push_back(0); count++; } if(fabs(Q1(1,2))>pow(10,-15) ) { aval.push_back(ksA*Q1(1,2)); asub.push_back(1); count++; } if(fabs(Q1(2,2) )>pow(10,-15) ) { aval.push_back(ksA*Q1(2,2)); asub.push_back(2); count++; } for(int i=0; i < planeNoA; i++) { if(fabs(s1->c[i]) > pow(10,-15) ) { aval.push_back(ksA*s1->c[i]); asub.push_back(4+i); count++; } } aptre.push_back(aptrb[2] + count); totalCount += count; /* column 3 xB*/ aptrb.push_back(aptre[2]); count = 0; if(fabs(Q2(0,0))>pow(10,-15) ) { aval.push_back(-ksB*Q2(0,0)); asub.push_back(0); count++; } if(fabs(Q2(1,0) )>pow(10,-15) ) { aval.push_back(-ksB*Q2(1,0)); asub.push_back(1); count++; } if(fabs(Q2(2,0) )>pow(10,-15) ) { aval.push_back(-ksB*Q2(2,0)); asub.push_back(2); count++; } for(int i=0; i < planeNoB; i++) { if(fabs(s2->a[i]) > pow(10,-15) ) { aval.push_back(ksB*s2->a[i]); asub.push_back(4+planeNoA +i); count++; } } aptre.push_back(aptrb[3] + count); totalCount += count; /* column 4 yB*/ aptrb.push_back(aptre[3]); count = 0; if(fabs(Q2(0,1))>pow(10,-15) ) { aval.push_back(-ksB*Q2(0,1)); asub.push_back(0); count++; } if(fabs(Q2(1,1) )>pow(10,-15) ) { aval.push_back(-ksB*Q2(1,1)); asub.push_back(1); count++; } if(fabs(Q2(2,1) )>pow(10,-15) ) { aval.push_back(-ksB*Q2(2,1)); asub.push_back(2); count++; } for(int i=0; i < planeNoB; i++) { if(fabs(s2->b[i]) > pow(10,-15) ) { aval.push_back(ksB*s2->b[i]); asub.push_back(4+planeNoA+i); count++; } } aptre.push_back(aptrb[4] + count); totalCount += count; /* column 5 zB*/ aptrb.push_back(aptre[4]); count = 0; if(fabs(Q2(0,2))>pow(10,-15) ) { aval.push_back(-ksB*Q2(0,2)); asub.push_back(0); count++; } if(fabs(Q2(1,2) )>pow(10,-15) ) { aval.push_back(-ksB*Q2(1,2)); asub.push_back(1); count++; } if(fabs(Q2(2,2) )>pow(10,-15) ) { aval.push_back(-ksB*Q2(2,2)); asub.push_back(2); count++; } for(int i=0; i < planeNoB; i++) { if(fabs(s2->c[i]) > pow(10,-15) ) { aval.push_back(ksB*s2->c[i]); asub.push_back(4+planeNoA+i); count++; } } aptre.push_back(aptrb[5] + count); totalCount += count; /*column 6 */ aptrb.push_back(aptre[5]); aval.push_back(1.0); asub.push_back(3); aptre.push_back(aptrb[6]+1); totalCount += 1; /*column 7 */ aptrb.push_back(aptre[6]); aval.push_back(-1.0); asub.push_back(3); aptre.push_back(aptrb[7]+1); totalCount += 1; /*column 8 + i*/ for(int i=0; i < planeNoA; i++) { aptrb.push_back(aptre[8-1+i]); aval.push_back(-1.0*kpA); asub.push_back(4 + i); aptre.push_back(aptrb[8+i]+1); } totalCount += planeNoA; /*column 8 + planeNoA + i */ for(int i=0; i < planeNoB; i++) { aptrb.push_back(aptre[ 8 + planeNoA-1+i]); aval.push_back(-1.0*kpB); asub.push_back(4 + planeNoA + i); aptre.push_back(aptrb[8 + planeNoA+i]+1); } totalCount += planeNoB; MSKidxt i,j,csubA[1+ 3 + planeNoA], csubB[1+ 3 + planeNoB] ; Real xx[NUMVAR]; MSKenv_t & env=mosekEnv; MSKtask_t task; MSKrescodee & r=mosekTaskEnv; if ( r==MSK_RES_OK ) /* Directs the log stream to the 'printstr' function. */ // MSK_linkfunctoenvstream(env,MSK_STREAM_LOG,NULL,NULL); //printstr // MSK_linkfunctoenvstream(env,MSK_STREAM_LOG,NULL,NULL); f ( r==MSK_RES_OK ) /* Create the optimization task. */ r = MSK_maketask(env,NUMCON,NUMVAR,&task); if ( r==MSK_RES_OK ) { // MSK_linkfunctotaskstream(task,MSK_STREAM_LOG,NULL,printstr); /* Give MOSEK an estimate of the size of the input data. This is done to increase the speed of inputting data. However, it is optional. */ if (r == MSK_RES_OK) r = MSK_putmaxnumvar(task,NUMVAR); if (r == MSK_RES_OK) r = MSK_putmaxnumcon(task,NUMCON); int NUMANZ = totalCount; if (r == MSK_RES_OK) r = MSK_putmaxnumanz(task,NUMANZ); /* Append 'NUMCON' empty constraints. The constraints will initially have no bounds. */ if ( r == MSK_RES_OK ) r = MSK_append(task,MSK_ACC_CON,NUMCON); /* Append 'NUMVAR' variables. The variables will initially be fixed at zero (x=0). */ if ( r == MSK_RES_OK ) r = MSK_append(task,MSK_ACC_VAR,NUMVAR); /* Optionally add a constant term to the objective. */ if ( r ==MSK_RES_OK ) r = MSK_putcfix(task,0.0); for(j=0; j& cm1, const State& state1, Vector3r midPoint, Vector3r normal, Vector3r& ptOnParticle) { //PotentialParticle *s1=static_cast(cm1.get()); ptOnParticle = midPoint; Real f = evaluatePP(cm1,state1, ptOnParticle);//evaluateFNoSphere(cm1,state1, ptOnParticle); // Real fprevious = f; int counter = 0; //normal.normalize(); Vector3r step = normal*Mathr::Sign(f) *-1.0; Vector3r bracketA(0,0,0); Vector3r bracketB(0,0,0); do { ptOnParticle += step; fprevious = f; f = evaluatePP(cm1,state1, ptOnParticle); //evaluateFNoSphere(cm1,state1, ptOnParticle); // counter++; if (counter == 50000 ) { //LOG_WARN("Initial point searching exceeded 500 iterations!"); //std::cout<<"ptonparticle2 search exceeded 50000 iterations! step:"< 0.0 ); bracketA = ptOnParticle; bracketB = ptOnParticle -step; Vector3r zero(0,0,0); BrentZeroSurf(cm1,state1,bracketA, bracketB, zero); ptOnParticle = zero; //if( fabs(f)>0.1){std::cout<<"getInitial point f:"<& cm1, const State& state1, const shared_ptr& cm2, const State& state2, Vector3r &contactPt, bool warmstart) { //timingDeltas->start(); PotentialParticle *s1=static_cast(cm1.get()); PotentialParticle *s2=static_cast(cm2.get()); Vector3r xGlobal(0.0,0.0,0.0); int iter = 0; int totalIter = 0; /* Parameters for particles A and B */ Real rA = s1->r; Real kA = s1->k; Real RA = s1->R; Real rB = s2->r; Real kB = s2->k; Real RB = s2->R; int planeNoA = s1->a.size(); int planeNoB = s2->a.size(); int varNo = 3+1+planeNoA+planeNoB; int planeNoAB = planeNoA + planeNoB; int varNo2 = varNo*varNo; int planeNoA3 = 3+planeNoA; int planeNoB3=3+planeNoB; //int planeNoA2 =planeNoA*planeNoA; //int planeNoB2=planeNoB*planeNoB; Matrix3r QA = state1.ori.conjugate().toRotationMatrix(); /*direction cosine */ Matrix3r QB = state2.ori.conjugate().toRotationMatrix(); /*direction cosine */ int blas3 = 3; char blasNT = 'N'; char blasT= 'T'; int blas1planeNoA = std::max(1,planeNoA); int blas1planeNoB = std::max(1,planeNoB); int blas1planeNoAB = std::max(1,planeNoAB); Real blas0 = 0.0; Real blas1 = 1.0; Real blasNeg1 = -1.0; Real blasQA[9]; Real blasQB[9]; Real blasPosA[3]; Real blasPosB[3]; Real blasContactPt[3]; Real blasC[varNo]; for (int i=0; ia[i]*blasLocalP1[0] + s1->b[i]*blasLocalP1[1] + s1->c[i]*blasLocalP1[2] - s1->d[i]; if (planea[i]; blasP1[i+planeNoA] = s1->b[i]; blasP1[i+2*planeNoA] = s1->c[i]; blasD1[i] = s1->d[i]; } //Eigen::MatrixXd P1Q = P1*QA; //transA = 'N'; transB = 'N'; blasM = planeNoA; blasN = 3; blasK = 3; // blasLDA = std::max(1,blasM); blasLDC = std::max(1,blasM); blasLDB = 3; blasAlpha=1.0; blasBeta = 0.0; //dgemm_(&transA, &transB, &blasM, &blasN, &blasK, &blasAlpha, &blasP1[0], &blasLDA, &blasQA[0], &blasLDB, &blasBeta, &blasP1Q[0], &blasLDC); dgemm_(&blasNT, &blasNT, &planeNoA, &blas3, &blas3, &blas1, &blasP1[0], &blas1planeNoA, &blasQA[0], &blasLDB, &blas0, &blasP1Q[0], &blas1planeNoA); Real sphereA = (pow(blasLocalP1[0],2) + pow(blasLocalP1[1],2) + pow(blasLocalP1[2],2))/pow(RA,2); Real sA = (1.0-kA)*(pertSumA2/pow(rA,2) - 1.0)+kA*(sphereA -1.0); /* fB */ Real blasTempP2[3]; Real blasLocalP2[3]; for(int i=0; i<3; i++) { blasTempP2[i] = blasContactPt[i] - blasPosB[i]; } //transA = 'N'; blasM = 3; blasN = 3; blasLDA = 3; blasAlpha=1.0; blasBeta = 0.0; //dgemv_(&transA, &blasM, &blasN, &blasAlpha, &blasQB[0], &blasLDA, &blasTempP2[0], &incx, &blasBeta, &blasLocalP2[0], &incy); dgemv_(&blasNT, &blas3, &blas3, &blas1, &blasQB[0], &blas3, &blasTempP2[0], &incx, &blas0, &blasLocalP2[0], &incy); // Vector3r tempP2 = contactPt - posB; // Vector3r localP2 = QB*tempP2; /*P2Q*/ //Eigen::MatrixXd P2 = Eigen::MatrixXd::Zero(planeNoB,3); /*d2*/ //Eigen::MatrixXd d2 = Eigen::MatrixXd::Zero(planeNoB,1); Real blasP2[planeNoB*3]; Real blasD2[planeNoB]; Real blasP2Q[planeNoB*3]; Real pertSumB2 = 0.0; for (int i=0; ia[i]*blasLocalP2[0] + s2->b[i]*blasLocalP2[1] + s2->c[i]*blasLocalP2[2] - s2->d[i]; if (planea[i]; blasP2[i+planeNoB] = s2->b[i]; blasP2[i+2*planeNoB] = s2->c[i]; blasD2[i] = s2->d[i]; } //Eigen::MatrixXd P2Q = P2*QB; //transA = 'N'; transB = 'N'; blasM = planeNoB; blasN = 3; blasK = 3; //blasLDA = std::max(1,blasM); blasLDC = std::max(1,blasM); blasLDB = 3; blasAlpha=1.0; blasBeta = 0.0; // dgemm_(&transA, &transB, &blasM, &blasN, &blasK, &blasAlpha, &blasP2[0], &blasLDA, &blasQB[0], &blasLDB, &blasBeta, &blasP2Q[0], &blasLDC); dgemm_(&blasNT, &blasNT, &planeNoB, &blas3, &blas3, &blasAlpha, &blasP2[0], &blas1planeNoB, &blasQB[0], &blas3, &blasBeta, &blasP2Q[0], &blas1planeNoB); Real sphereB = (pow(blasLocalP2[0],2) + pow(blasLocalP2[1],2) + pow(blasLocalP2[2],2))/pow(RB,2); Real sB = (1.0-kB)*(pertSumB2/pow(rB,2) - 1.0)+kB*(sphereB -1.0); //sPert = fabs(fA-fB); s = std::max(sqrt(fabs(sA+1.0)), sqrt(fabs(sB+1.0))) + sPert; //sqrt(fA+fB+2.0)+sPert; //sqrt(std::max(fabs(fA+1.0), fabs(fB+1.0))) + sPert; // //x[3] = s; blasX[3]= s; /////////////////// algebra formulation of the SOCP /////////////////// /* c */ // Eigen::MatrixXd c=Eigen::MatrixXd::Zero(varNo,1); // c[3] = 1.0; Real blasA1[(3+planeNoA)*varNo]; Real blasA2[(3+planeNoB)*varNo]; /* Second order cone constraints */ /* A1 */ //Eigen::MatrixXd A1(3+planeNoA,varNo); //Matrix3r QAs=kAs*QA; //cwise() Real blasQAs[9]; int noElements=9; Real scaleFactor = kAs; dcopy_(&noElements, &blasQA[0], &incx, &blasQAs[0], &incx); dscal_(&noElements, &scaleFactor, &blasQAs[0], &incx); // A1 << QAs,Eigen::MatrixXd::Zero(3,1+planeNoAB), // Eigen::MatrixXd::Zero(planeNoA,4),kAp*Eigen::MatrixXd::Identity(planeNoA, planeNoA),Eigen::MatrixXd::Zero(planeNoA,planeNoB); memset(blasA1,0.0,sizeof(blasA1)); for (int i=0; i<3; i++) { blasA1[i] = blasQAs[i]; blasA1[i+planeNoA3] = blasQAs[i+3]; blasA1[i+2*planeNoA3] = blasQAs[i+6]; } for (int i=0; icheckpoint("setup"); while(totalIter<500) { penalty = 1.0/t; /* Newton's method */ /* s=x[3]; */ s=blasX[3]; /* temp variables */ /* w1 = A1*x + b1; */ noElements = 3+planeNoA; dcopy_(&noElements, &blasB1[0], &incx, &blasW1[0], &incy); //transA = 'N'; blasM = 3+planeNoA; blasN = varNo; //blasLDA = 3+planeNoA; blasAlpha = 1.0; blasBeta = 1.0; incx =1; incy=1; //dgemv_(&transA, &blasM, &blasN, &blasAlpha, &blasA1[0], &blasLDA, &blasX[0], &incx, &blasBeta, &blasW1[0], &incy); dgemv_(&blasNT, &planeNoA3, &varNo, &blas1, &blasA1[0], &planeNoA3, &blasX[0], &incx, &blas1, &blasW1[0], &incy); /* w2 = A2*x + b2; */ noElements = 3+planeNoB; dcopy_(&noElements, &blasB2[0], &incx, &blasW2[0], &incy); //transA = 'N'; blasM = 3+planeNoB; blasN = varNo; //blasLDA = 3+planeNoB; blasAlpha = 1.0; blasBeta = 1.0; //dgemv_(&transA, &blasM, &blasN, &blasAlpha, &blasA2[0], &blasLDA, &blasX[0], &incx, &blasBeta, &blasW2[0], &incy); dgemv_(&blasNT, &planeNoB3, &varNo, &blas1, &blasA2[0], &planeNoB3, &blasX[0], &incx, &blas1, &blasW2[0], &incy); /* u1 = s*s - w1.dot(w1); */ /* u2 = s*s - w2.dot(w2); */ //noElements = 3+planeNoA; blasW1dot = ddot_(&planeNoA3, &blasW1[0], &incx, &blasW1[0], &incy); //noElements = 3+planeNoB; blasW2dot = ddot_(&planeNoB3, &blasW2[0], &incx, &blasW2[0], &incy); u1 =s*s -blasW1dot; u2 =s*s -blasW2dot; /* wL = bL - AL*x; */ noElements = planeNoAB; dcopy_(&noElements, &blasBL[0], &incx, &blasWL[0], &incy); //transA = 'N'; blasN = varNo; //blasM = planeNoAB; blasLDA = std::max(1,planeNoAB); blasAlpha = -1.0; blasBeta = 1.0; //dgemv_(&transA, &blasM, &blasN, &blasAlpha, &blasAL[0], &blasLDA, &blasX[0], &incx, &blasBeta, &blasWL[0], &incy); dgemv_(&blasNT, &planeNoAB, &varNo, &blasNeg1, &blasAL[0], &blas1planeNoAB, &blasX[0], &incx, &blas1, &blasWL[0], &incy); for (int i=0; icheckpoint("assemble H and g"); //std::cout<<"before Chol, totalIter: "<checkpoint("Cholesky"); //fprime = step.transpose()*g; //noElements = varNo; blasFprime = ddot_(&varNo, &blasStep[0], &incx, &blasGrad[0], &incy); wLlogsum = 0.0; for (int i=0; i0) { minWL = blasWL[0]; } for(int i=0; i0) { minWL = blasWL[0]; } for(int i=0; icheckpoint("barrier search"); wLlogsum = 0.0; for (int i=0; i val + backtrack*0.01*blasFprime) { backtrack = 0.5*backtrack; //for (int i = 0; icheckpoint("line search"); noElements = varNo; dcopy_(&noElements, &blasNewX[0], &incx, &blasX[0], &incy); if(blasFprime >0.0) { //std::cout<<"count: "<0.001 ) { //std::cout<<"inside fA-fB: "<checkpoint("newton"); return true; } t = std::min(t*mu, (2.0*m+1.0)/tol); iter = 0; totalIter = totalIter+1; } if(totalIter>100) { //std::cout<<"totalIter: "<checkpoint("complete"); } return ( true ); } #endif // YADE_POTENTIAL_PARTICLES trunk-2017.01a/pkg/dem/Ig2_PP_PP_ScGeom.hpp000066400000000000000000000105431304022710500201000ustar00rootroot00000000000000/*CWBoon 2015 */ /* C.W. Boon, G.T. Houlsby, S. Utili (2013). A new contact detection algorithm for three-dimensional non-spherical particles. Powder Technology, 248, pp 94-102. */ /* code for calling MOSEK was for ver 6. Please uncomment if you have the licence */ #pragma once #ifdef YADE_POTENTIAL_PARTICLES #include #include #include #include #include #include #include # ifdef YADE_MOSEK #include #include #include #include #endif class Ig2_PP_PP_ScGeom: public IGeomFunctor { #ifdef YADE_MOSEK protected: std::string myfile; std::string Key; MSKrescodee mosekTaskEnv; MSKenv_t mosekEnv; #endif public : virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& se32, const Vector3r& shift2, const bool& force, const shared_ptr& c); Real evaluatePP(const shared_ptr& cm1, const State& state1, const Vector3r newTrial); void getPtOnParticle2(const shared_ptr& cm1, const State& state1, Vector3r previousPt, Vector3r normal, Vector3r& newlocalPoint); bool contactPtMosekF2(const shared_ptr& cm1, const State& state1, const shared_ptr& cm2, const State& state2, Vector3r &contactPt); bool customSolve(const shared_ptr& cm1, const State& state1, const shared_ptr& cm2, const State& state2, Vector3r &contactPt, bool warmstart); Vector3r getNormal(const shared_ptr& cm1, const State& state1, const Vector3r newTrial); void BrentZeroSurf(const shared_ptr& cm1, const State& state1, const Vector3r bracketA, const Vector3r bracketB, Vector3r& zero); ///////////////////////////////////////////////////////////////////////////////////////////////////// YADE_CLASS_BASE_DOC_ATTRS_CTOR(Ig2_PP_PP_ScGeom,IGeomFunctor,"EXPERIMENTAL. IGeom functor for PotentialParticle - PotentialParticle pair", ((Real, accuracyTol, pow(10,-7),, "accuracy desired, tolerance criteria for SOCP")) ((Real,interactionDetectionFactor,1.0,,"bool to avoid granular ratcheting")), //((std::string,myfile,"./PotentialParticles"+"","string")), //timingDeltas=shared_ptr(new TimingDeltas); //mosekTaskEnv = MSK_makeenv(&mosekEnv,NULL,NULL,NULL,NULL); //mosekTaskEnv = MSK_initenv(mosekEnv); ); FUNCTOR2D(PotentialParticle,PotentialParticle); // needed for the dispatcher, even if it is symmetric DEFINE_FUNCTOR_ORDER_2D(PotentialParticle,PotentialParticle); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Ig2_PP_PP_ScGeom); #ifdef __cplusplus extern "C" { #endif /* LAPACK LU */ //int dgesv(int varNo, int varNo2, Real *H, int varNo3, int *pivot, Real* g, int varNo4, int info){ extern void dgesv_(const int *N, const int *nrhs, Real *Hessian, const int *lda, int *ipiv, Real *gradient, const int *ldb, int *info); // int ans; // dgesv_(&varNo, &varNo2, H, &varNo3, pivot,g, &varNo4, &ans); // return ans; //} /* LAPACK Cholesky */ extern void dpbsv_(const char *uplo, const int *n, const int *kd, const int *nrhs, Real *AB, const int *ldab, Real *B, const int *ldb, int *info); /* LAPACK QR */ extern void dgels_(const char *Trans, const int *m, const int *n, const int *nrhs, Real *A, const int *lda, Real *B, const int *ldb, const Real *work, const int *lwork, int *info); /*BLAS */ extern void dgemm_(const char *transA, const char *transB, const int *m, const int *n, const int *k, const Real *alpha, Real *A, const int *lda, Real *B, const int *ldb, const Real *beta, Real *C, const int *ldc); extern void dgemv_(const char *trans, const int *m, const int *n, const Real *alpha, Real *A, const int *lda, Real *x, const int *incx, const Real *beta, Real *y, const int *incy); extern void dcopy_(const int *N, Real *x, const int *incx, Real *y, const int *incy); extern Real ddot_(const int *N, Real *x, const int *incx, Real *y, const int *incy); extern void daxpy_(const int *N, const Real *da, Real *dx, const int *incx, Real *dy, const int *incy); extern void dscal_(const int *N, const Real *alpha, Real *x, const int *incx); void dsyev_(const char *jobz, const char *uplo, const int *N, Real *A, const int *lda, Real *W, Real *work, int *lwork, int *info); #ifdef __cplusplus }; #endif #endif // YADE_POTENTIAL_PARTICLES trunk-2017.01a/pkg/dem/Ig2_Sphere_Sphere_ScGeom.cpp000066400000000000000000000066121304022710500217130ustar00rootroot00000000000000// © 2004 Janek Kozicki // © 2007 Bruno Chareyre // © 2008 Václav Šmilauer #include"Ig2_Sphere_Sphere_ScGeom.hpp" #include #include #include #include #include #include bool Ig2_Sphere_Sphere_ScGeom::go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { TIMING_DELTAS_START(); const Se3r& se31=state1.se3; const Se3r& se32=state2.se3; const Sphere *s1=static_cast(cm1.get()), *s2=static_cast(cm2.get()); Vector3r normal=(se32.position+shift2)-se31.position; if (!c->isReal() && !force) {//don't fast-check distance if geometry will be updated anyway Real penetrationDepthSq=pow(interactionDetectionFactor*(s1->radius+s2->radius),2) - normal.squaredNorm(); if (penetrationDepthSq<0) { TIMING_DELTAS_CHECKPOINT("Ig2_Sphere_Sphere_ScGeom"); return false; } } shared_ptr scm; bool isNew = !c->geom; if(!isNew) scm=YADE_PTR_CAST(c->geom); else { scm=shared_ptr(new ScGeom()); c->geom=scm; } Real norm=normal.norm(); normal/=norm; // normal is unit vector now #ifdef YADE_DEBUG if(norm==0) throw runtime_error(("Zero distance between spheres #"+boost::lexical_cast(c->getId1())+" and #"+boost::lexical_cast(c->getId2())+".").c_str()); #endif Real penetrationDepth=s1->radius+s2->radius-norm; scm->contactPoint=se31.position+(s1->radius-0.5*penetrationDepth)*normal;//0.5*(pt1+pt2); scm->penetrationDepth=penetrationDepth; scm->radius1=s1->radius; scm->radius2=s2->radius; scm->precompute(state1,state2,scene,c,normal,isNew,shift2,avoidGranularRatcheting); TIMING_DELTAS_CHECKPOINT("Ig2_Sphere_Sphere_ScGeom"); return true; } bool Ig2_Sphere_Sphere_ScGeom::goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { return go(cm1,cm2,state2,state1,-shift2,force,c); } YADE_PLUGIN((Ig2_Sphere_Sphere_ScGeom)); bool Ig2_Sphere_Sphere_ScGeom6D::go( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { bool isNew = !c->geom; if (Ig2_Sphere_Sphere_ScGeom::go(cm1,cm2,state1,state2,shift2,force,c)){//the 3 DOFS from ScGeom are updated here if (isNew) {//generate a 6DOF interaction from the 3DOF one generated by Ig2_Sphere_Sphere_ScGeom shared_ptr sc (new ScGeom6D()); *(YADE_PTR_CAST(sc)) = *(YADE_PTR_CAST(c->geom)); c->geom=sc;} if (updateRotations) YADE_PTR_CAST(c->geom)->precomputeRotations(state1,state2,isNew,creep); return true; } else return false; } bool Ig2_Sphere_Sphere_ScGeom6D::goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { return go(cm1,cm2,state2,state1,-shift2,force,c); } YADE_PLUGIN((Ig2_Sphere_Sphere_ScGeom6D)); trunk-2017.01a/pkg/dem/Ig2_Sphere_Sphere_ScGeom.hpp000066400000000000000000000116301304022710500217140ustar00rootroot00000000000000// © 2004 Janek Kozicki // © 2007 Bruno Chareyre // © 2008 Václav Šmilauer #pragma once #include #include class Ig2_Sphere_Sphere_ScGeom: public IGeomFunctor{ public: virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); YADE_CLASS_BASE_DOC_ATTRS(Ig2_Sphere_Sphere_ScGeom,IGeomFunctor, "Create/update a :yref:`ScGeom` instance representing the geometry of a contact point between two :yref:`Spheres` s.", ((Real,interactionDetectionFactor,1,,"Enlarge both radii by this factor (if >1), to permit creation of distant interactions.\n\nInteractionGeometry will be computed when interactionDetectionFactor*(rad1+rad2) > distance.\n\n.. note::\n\t This parameter is functionally coupled with :yref:`Bo1_Sphere_Aabb::aabbEnlargeFactor`, which will create larger bounding boxes and should be of the same value.")) ((bool,avoidGranularRatcheting,true,,"Define relative velocity so that ratcheting is avoided. It applies for sphere-sphere contacts. It eventualy also apply for sphere-emulating interactions (i.e. convertible into the ScGeom type), if the virtual sphere's motion is defined correctly (see e.g. :yref:`Ig2_Sphere_ChainedCylinder_CylScGeom`.\n\n" "Short explanation of what we want to avoid :\n\n" "Numerical ratcheting is best understood considering a small elastic cycle at a contact between two grains : assuming b1 is fixed, impose this displacement to b2 :\n\n" "#. translation *dx* in the normal direction\n" "#. rotation *a*\n" "#. translation *-dx* (back to the initial position)\n" "#. rotation *-a* (back to the initial orientation)\n\n\n" "If the branch vector used to define the relative shear in rotation×branch is not constant (typically if it is defined from the vector center→contactPoint), then the shear displacement at the end of this cycle is not zero: rotations *a* and *-a* are multiplied by branches of different lengths.\n\n" "It results in a finite contact force at the end of the cycle even though the positions and orientations are unchanged, in total contradiction with the elastic nature of the problem. It could also be seen as an *inconsistent energy creation or loss*. Given that DEM simulations tend to generate oscillations around equilibrium (damped mass-spring), it can have a significant impact on the evolution of the packings, resulting for instance in slow creep in iterations under constant load.\n\n" "The solution adopted here to avoid ratcheting is as proposed by McNamara and co-workers. They analyzed the ratcheting problem in detail - even though they comment on the basis of a cycle that differs from the one shown above. One will find interesting discussions in e.g. [McNamara2008]_, even though solution it suggests is not fully applied here (equations of motion are not incorporating alpha, in contradiction with what is suggested by McNamara et al.).\n\n" )) ); FUNCTOR2D(Sphere,Sphere); // needed for the dispatcher, even if it is symmetric DEFINE_FUNCTOR_ORDER_2D(Sphere,Sphere); }; REGISTER_SERIALIZABLE(Ig2_Sphere_Sphere_ScGeom); class Ig2_Sphere_Sphere_ScGeom6D: public Ig2_Sphere_Sphere_ScGeom{ public: virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); YADE_CLASS_BASE_DOC_ATTRS(Ig2_Sphere_Sphere_ScGeom6D,Ig2_Sphere_Sphere_ScGeom,"Create/update a :yref:`ScGeom6D` instance representing the geometry of a contact point between two :yref:`Spheres`, including relative rotations.", ((bool,updateRotations,true,,"Precompute relative rotations. Turning this false can speed up simulations when rotations are not needed in constitutive laws (e.g. when spheres are compressed without cohesion and moment in early stage of a triaxial test), but is not foolproof. Change this value only if you know what you are doing.")) ((bool,creep,false,,"Substract rotational creep from relative rotation. The rotational creep :yref:`ScGeom6D::twistCreep` is a quaternion and has to be updated inside a constitutive law, see for instance :yref:`Law2_ScGeom6D_CohFrictPhys_CohesionMoment`." )) ); FUNCTOR2D(Sphere,Sphere); // needed for the dispatcher, even if it is symmetric DEFINE_FUNCTOR_ORDER_2D(Sphere,Sphere); }; REGISTER_SERIALIZABLE(Ig2_Sphere_Sphere_ScGeom6D); trunk-2017.01a/pkg/dem/InelastCohFrictPM.cpp000066400000000000000000000265671304022710500205120ustar00rootroot00000000000000#include "InelastCohFrictPM.hpp" YADE_PLUGIN((InelastCohFrictMat)(InelastCohFrictPhys)(Ip2_2xInelastCohFrictMat_InelastCohFrictPhys)(Law2_ScGeom6D_InelastCohFrictPhys_CohesionMoment)); void Ip2_2xInelastCohFrictMat_InelastCohFrictPhys::go(const shared_ptr& b1 // InelastCohFrictMat , const shared_ptr& b2 // InelastCohFrictMat , const shared_ptr& interaction) { InelastCohFrictMat* sdec1 = static_cast(b1.get()); InelastCohFrictMat* sdec2 = static_cast(b2.get()); ScGeom6D* geom = YADE_CAST(interaction->geom.get()); //FIXME : non cohesive contact are not implemented, it would be useful to use setCohesionNow, setCohesionOnNewContacts etc ... if (geom) { if (!interaction->phys) { interaction->phys = shared_ptr(new InelastCohFrictPhys()); InelastCohFrictPhys* contactPhysics = YADE_CAST(interaction->phys.get()); Real pi = 3.14159265; Real r1 = geom->radius1; Real r2 = geom->radius2; Real f1 = sdec1->frictionAngle; Real f2 = sdec2->frictionAngle; contactPhysics->tangensOfFrictionAngle = tan(min(f1,f2)); // harmonic average of modulus contactPhysics->knC = 2.0*sdec1->compressionModulus*r1*sdec2->compressionModulus*r2/(sdec1->compressionModulus*r1+sdec2->compressionModulus*r2); contactPhysics->knT = 2.0*sdec1->tensionModulus*r1*sdec2->tensionModulus*r2/(sdec1->tensionModulus*r1+sdec2->tensionModulus*r2); contactPhysics->ks = 2.0*sdec1->shearModulus*r1*sdec2->shearModulus*r2/(sdec1->shearModulus*r1+sdec2->shearModulus*r2); // harmonic average of coeficients for bending and twist coeficients Real AlphaKr = 2.0*sdec1->alphaKr*sdec2->alphaKr/(sdec1->alphaKr+sdec2->alphaKr); Real AlphaKtw = 2.0*sdec1->alphaKtw*sdec2->alphaKtw/(sdec1->alphaKtw+sdec2->alphaKtw); contactPhysics->kr = r1*r2*contactPhysics->ks*AlphaKr; contactPhysics->ktw = r1*r2*contactPhysics->ks*AlphaKtw; contactPhysics->kTCrp = contactPhysics->knT*min(sdec1->creepTension,sdec2->creepTension); contactPhysics->kRCrp = contactPhysics->kr*min(sdec1->creepBending,sdec2->creepBending); contactPhysics->kTwCrp = contactPhysics->ktw*min(sdec1->creepTwist,sdec2->creepTwist); contactPhysics->kRUnld = contactPhysics->kr*min(sdec1->unloadBending,sdec2->unloadBending); contactPhysics->kTUnld = contactPhysics->knT*min(sdec1->unloadTension,sdec2->unloadTension); contactPhysics->kTwUnld = contactPhysics->ktw*min(sdec1->unloadTwist,sdec2->unloadTwist); contactPhysics->maxElC = min(sdec1->sigmaCompression,sdec2->sigmaCompression)*pow(min(r2, r1),2); contactPhysics->maxElT = min(sdec1->sigmaTension,sdec2->sigmaTension)*pow(min(r2, r1),2); contactPhysics->maxElB = min(sdec1->nuBending,sdec2->nuBending)*pow(min(r2, r1),3); contactPhysics->maxElTw = min(sdec1->nuTwist,sdec2->nuTwist)*pow(min(r2, r1),3); contactPhysics->shearAdhesion = min(sdec1->shearCohesion,sdec2->shearCohesion)*pow(min(r1, r2),2); contactPhysics->maxExten = min(sdec1->epsilonMaxTension*r1,sdec2->epsilonMaxTension*r2); contactPhysics->maxContract = min(sdec1->epsilonMaxCompression*r1,sdec2->epsilonMaxCompression*r2); contactPhysics->maxBendMom = min(sdec1->etaMaxBending,sdec2->etaMaxBending)*pow(min(r2, r1),3); contactPhysics->maxTwist = 2*pi*min(sdec1->etaMaxTwist,sdec2->etaMaxTwist); } } }; Real Law2_ScGeom6D_InelastCohFrictPhys_CohesionMoment::normElastEnergy() { //FIXME : this have to be checked and adapted Real normEnergy=0; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; InelastCohFrictPhys* phys = YADE_CAST(I->phys.get()); if (phys) { normEnergy += 0.5*(phys->normalForce.squaredNorm()/phys->kn); } } return normEnergy; } Real Law2_ScGeom6D_InelastCohFrictPhys_CohesionMoment::shearElastEnergy() { //FIXME : this have to be checked and adapted Real shearEnergy=0; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; InelastCohFrictPhys* phys = YADE_CAST(I->phys.get()); if (phys) { shearEnergy += 0.5*(phys->shearForce.squaredNorm()/phys->ks); } } return shearEnergy; } bool Law2_ScGeom6D_InelastCohFrictPhys_CohesionMoment::go(shared_ptr& ig, shared_ptr& ip, Interaction* contact) { //FIXME : non cohesive contact are not implemented, it would be useful to use setCohesionNow, setCohesionOnNewContacts etc ... const int &id1 = contact->getId1(); const int &id2 = contact->getId2(); const Real& dt = scene->dt; ScGeom6D* geom = YADE_CAST (ig.get()); InelastCohFrictPhys* phys = YADE_CAST (ip.get()); if (contact->isFresh(scene)) phys->shearForce = Vector3r::Zero(); Real un = geom->penetrationDepth-phys->unp; Real Fn; State* de1 = Body::byId(id1,scene)->state.get(); State* de2 = Body::byId(id2,scene)->state.get(); if(un<=0){/// tension /// if(-un>phys->maxExten || phys->isBroken){//plastic failure. phys->isBroken=1; phys->normalForce=phys->shearForce=phys->moment_twist=phys->moment_bending=Vector3r(0,0,0); return false; } Fn=phys->knT*un; //elasticity if(-Fn>phys->maxElT || phys->onPlastT){ //so we are on plastic deformation. phys->onPlastT=1; phys->onPlastC=1; //if plasticity is reached on tension, set it to compression too. if(phys->maxCrpRchdT[0]kTUnld*(un-phys->maxCrpRchdT[0])+phys->maxCrpRchdT[1]; } else{//loading on plastic deformation : creep. Fn = -phys->maxElT+phys->kTCrp*(un+phys->maxElT/phys->knT); phys->maxCrpRchdT[0]=un; //new maximum is reached. phys->maxCrpRchdT[1]=Fn; } if (Fn>0){ //so the contact just passed the equilibrium state, set new "unp" who stores the plastic equilibrium state. phys->unp=geom->penetrationDepth; phys->maxCrpRchdT[0]=1e20; phys->maxElT=0; } } else{ //elasticity phys->maxCrpRchdT[0]=un; phys->maxCrpRchdT[1]=Fn; } } else{/// compression /// similar to tension. if(un>phys->maxContract || phys->isBroken){ phys->isBroken=1; phys->normalForce=phys->shearForce=phys->moment_twist=phys->moment_bending=Vector3r(0,0,0); if(geom->penetrationDepth<=0){ //do not erase the contact while penetrationDepth<0 because it would be recreated at next timestep. return false; } return true; } Fn=phys->knC*un; if(Fn>phys->maxElC || phys->onPlastC){ phys->onPlastC=1; if(phys->maxCrpRchdC[0]>un){ Fn = phys->kTUnld*(un-phys->maxCrpRchdC[0])+phys->maxCrpRchdC[1]; } else{ Fn = phys->maxElC+phys->kTCrp*(un-phys->maxElC/phys->knC); phys->maxCrpRchdC[0]=un; phys->maxCrpRchdC[1]=Fn; } if (Fn<0){ phys->unp=geom->penetrationDepth; phys->maxCrpRchdC[0]=-1e20; phys->maxElC=0; } } else{ phys->maxCrpRchdC[0]=un; phys->maxCrpRchdC[1]=Fn; } } /// Shear /// Vector3r shearForce = geom->rotate(phys->shearForce); const Vector3r& dus = geom->shearIncrement(); //Linear elasticity giving "trial" shear force shearForce += phys->ks*dus; Real Fs = shearForce.norm(); Real maxFs = phys->shearAdhesion; if (maxFs==0)maxFs = Fn*phys->tangensOfFrictionAngle; maxFs = std::max((Real) 0, maxFs); if (Fs > maxFs) {//Plasticity condition on shear force if (!phys->cohesionBroken) { phys->cohesionBroken=1; phys->shearAdhesion=0; maxFs = max((Real) 0, Fn*phys->tangensOfFrictionAngle); } maxFs = maxFs / Fs; shearForce *= maxFs; } //rotational moment are only applied if the cohesion is not broken. /// Twist /// the twist law is driven by twist displacement ("getTwist()"). if(!phys->cohesionBroken){ Real twist = geom->getTwist() - phys->twp; Real twistM=twist*phys->ktw; //elastic twist moment. bool sgnChanged=0; //whether the twist moment just passed the equilibrium state. if(!contact->isFresh(scene) && phys->moment_twist.dot(twistM*geom->normal)<0)sgnChanged=1; if(std::abs(twist)>phys->maxTwist){ phys->cohesionBroken=1; twistM=0; } else{ if(std::abs(twistM)>phys->maxElTw || phys->onPlastTw){ //plastic deformation. phys->onPlastTw=1; if(std::abs(phys->maxCrpRchdTw[0])>std::abs(twist)){ //unloading/reloading twistM = phys->kTwUnld*(twist-phys->maxCrpRchdTw[0])+phys->maxCrpRchdTw[1]; } else{//creep loading. int sign = twist<0?-1:1; twistM = sign*phys->maxElTw+phys->kTwCrp*(twist-sign*phys->maxElTw/phys->ktw); //creep phys->maxCrpRchdTw[0]=twist; //new maximum reached phys->maxCrpRchdTw[1]=twistM; } if(sgnChanged){ phys->maxElTw=0; phys->twp=geom->getTwist(); phys->maxCrpRchdTw[0]=0; } } else{ //elasticity phys->maxCrpRchdTw[0]=twist; phys->maxCrpRchdTw[1]=twistM; } } phys->moment_twist = twistM * geom->normal; } else phys->moment_twist=Vector3r(0,0,0); /// Bending /// incremental form. if(!phys->cohesionBroken){ Vector3r bendM = phys->moment_bending; Vector3r relAngVel = geom->getRelAngVel(de1,de2,dt); Vector3r relRotBend = (relAngVel - geom->normal.dot(relAngVel)*geom->normal)*dt; // relative rotation due to rolling behaviour bendM = geom->rotate(phys->moment_bending); // rotate moment vector (updated) phys->pureCreep=geom->rotate(phys->pureCreep); // pure creep is updated to compute the damage. Vector3r bendM_elast = bendM-phys->kr*relRotBend; if(bendM_elast.norm()>phys->maxElB || phys->onPlastB){ // plastic behavior phys->onPlastB=1; bendM=bendM-phys->kDam*relRotBend; //trial bending if(bendM.norm()moment_bending.norm()){ // if bending decreased, we are unloading ... bendM = bendM+phys->kDam*relRotBend-phys->kRUnld*relRotBend; // ... so undo bendM and apply unload coefficient. Vector3r newPureCreep = phys->pureCreep-phys->kRCrp*relRotBend; // trial pure creep. phys->pureCreep = newPureCreep.norm()pureCreep.norm()?newPureCreep:phys->pureCreep+phys->kRCrp*relRotBend; // while unloading, pure creep must decrease. phys->kDam=phys->kr+(phys->kRCrp-phys->kr)*(phys->maxCrpRchdB.norm()-phys->maxElB)/(phys->maxBendMom-phys->maxElB); // compute the damage coefficient. } else{ // bending increased, so we are loading (bendM has to be unchanged). Vector3r newPureCreep = phys->pureCreep-phys->kRCrp*relRotBend; phys->pureCreep = newPureCreep.norm()>phys->pureCreep.norm()?newPureCreep:phys->pureCreep+phys->kRCrp*relRotBend; // while loading, pure creep must increase. if(phys->pureCreep.norm()pureCreep; // bending moment can't be greather than pure creep. if(phys->pureCreep.norm()>phys->maxCrpRchdB.norm()) phys->maxCrpRchdB=phys->pureCreep; // maxCrpRchdB must follow the maximum of pure creep. if(phys->pureCreep.norm()>phys->maxBendMom){ phys->cohesionBroken=1; bendM=bendM_elast=Vector3r(0,0,0); } } phys->moment_bending=bendM; } else{//elasticity phys->pureCreep=phys->moment_bending=phys->maxCrpRchdB=bendM_elast; phys->kDam=phys->kRCrp; } } phys->shearForce=shearForce; phys->normalForce=-Fn*geom->normal; applyForceAtContactPoint(phys->normalForce+phys->shearForce, geom->contactPoint, id1, de1->se3.position, id2, de2->se3.position + (scene->isPeriodic ? scene->cell->intrShiftPos(contact->cellDist): Vector3r::Zero())); scene->forces.addTorque(id1,-phys->moment_bending-phys->moment_twist); scene->forces.addTorque(id2,phys->moment_bending+phys->moment_twist); return true; } trunk-2017.01a/pkg/dem/InelastCohFrictPM.hpp000066400000000000000000000160611304022710500205030ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2012 by Ignacio Olmedo nolmedo.manich@gmail.com * * Copyright (C) 2012 by François Kneib francois.kneib@gmail.com * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include "CohesiveFrictionalContactLaw.hpp" class InelastCohFrictMat : public FrictMat { public : virtual ~InelastCohFrictMat () {}; /// Serialization YADE_CLASS_BASE_DOC_ATTRS_CTOR(InelastCohFrictMat,FrictMat,"", ((Real,tensionModulus,0.0,,"Tension elasticity modulus")) ((Real,compressionModulus,0.0,,"Compresion elasticity modulus")) ((Real,shearModulus,0.0,,"shear elasticity modulus")) ((Real,alphaKr,2.0,,"Dimensionless coefficient used for the rolling stiffness.")) ((Real,alphaKtw,2.0,,"Dimensionless coefficient used for the twist stiffness.")) ((Real,nuBending,0.0,,"Bending elastic stress limit")) ((Real,nuTwist,0.0,,"Twist elastic stress limit")) ((Real,sigmaTension,0.0,,"Tension elastic stress limit")) ((Real,sigmaCompression,0.0,,"Compression elastic stress limit")) ((Real,shearCohesion,0.0,,"Shear elastic stress limit")) ((Real,creepTension,0.0,,"Tension/compression creeping coefficient. Usual values between 0 and 1.")) ((Real,creepBending,0.0,,"Bending creeping coefficient. Usual values between 0 and 1.")) ((Real,creepTwist,0.0,,"Twist creeping coefficient. Usual values between 0 and 1.")) ((Real,unloadTension,0.0,,"Tension/compression plastic unload coefficient. Usual values between 0 and +infinity.")) ((Real,unloadBending,0.0,,"Bending plastic unload coefficient. Usual values between 0 and +infinity.")) ((Real,unloadTwist,0.0,,"Twist plastic unload coefficient. Usual values between 0 and +infinity.")) ((Real,epsilonMaxTension,0.0,,"Maximal plastic strain tension")) ((Real,epsilonMaxCompression,0.0,,"Maximal plastic strain compression")) ((Real,etaMaxBending,0.0,,"Maximal plastic bending strain")) ((Real,etaMaxTwist,0.0,,"Maximal plastic twist strain")), createIndex(); ); /// Indexable REGISTER_CLASS_INDEX(InelastCohFrictMat,FrictMat); }; REGISTER_SERIALIZABLE(InelastCohFrictMat); class InelastCohFrictPhys : public FrictPhys { public : virtual ~InelastCohFrictPhys() {}; YADE_CLASS_BASE_DOC_ATTRS_CTOR(InelastCohFrictPhys,FrictPhys,"", ((bool,cohesionBroken,false,,"is cohesion active? will be set false when a fragile contact is broken")) ((Real,knT,0,,"tension stiffness")) ((Real,knC,0,,"compression stiffness")) ((Real,ktw,0,,"twist shear stiffness")) ((Real,ks,0,,"shear stiffness")) ((Real,kr,0,,"bending stiffness")) ((Real,maxElB,0.0,,"Maximum bending elastic moment.")) ((Real,maxElTw,0.0,,"Maximum twist elastic moment.")) ((Real,maxElT,0.0,,"Maximum tension elastic force.")) ((Real,maxElC,0.0,,"Maximum compression elastic force.")) ((Real,shearAdhesion,0,,"Maximum elastic shear force (cohesion).")) ((Real,kTCrp,0.0,,"Tension/compression creep stiffness")) ((Real,kRCrp,0.0,,"Bending creep stiffness")) ((Real,kTwCrp,0.0,,"Twist creep stiffness")) ((Real,kTUnld,0.0,,"Tension/compression plastic unload stiffness")) ((Real,kRUnld,0.0,,"Bending plastic unload stiffness")) ((Real,kTwUnld,0.0,,"Twist plastic unload stiffness")) ((Real,maxExten,0.0,,"Plastic failure extension (stretching).")) ((Real,maxContract,0.0,,"Plastic failure contraction (shrinkage).")) ((Real,maxBendMom,0.0,,"Plastic failure bending moment.")) ((Real,maxTwist,0.0,,"Plastic failure twist angle")) ((bool,isBroken,false,,"true if compression plastic fracture achieved")) ((Real,unp,0,,"plastic normal penetration depth describing the equilibrium state.")) ((Real,twp,0,,"plastic twist penetration depth describing the equilibrium state.")) ((bool,onPlastB,false,Attr::readonly,"true if plasticity achieved on bending")) ((bool,onPlastTw,false,Attr::readonly,"true if plasticity achieved on twisting")) ((bool,onPlastT,false,Attr::readonly,"true if plasticity achieved on traction")) ((bool,onPlastC,false,Attr::readonly,"true if plasticity achieved on compression")) ((Vector2r,maxCrpRchdT,Vector2r(0,0),Attr::readonly,"maximal extension reached on plastic deformation. maxCrpRchdT[0] stores un and maxCrpRchdT[1] stores Fn.")) ((Vector2r,maxCrpRchdC,Vector2r(0,0),Attr::readonly,"maximal compression reached on plastic deformation. maxCrpRchdC[0] stores un and maxCrpRchdC[1] stores Fn.")) ((Vector2r,maxCrpRchdTw,Vector2r(0,0),Attr::readonly,"maximal twist reached on plastic deformation. maxCrpRchdTw[0] stores twist angle and maxCrpRchdTw[1] stores twist moment.")) ((Vector3r,maxCrpRchdB,Vector3r(0,0,0),Attr::readonly,"maximal bending moment reached on plastic deformation.")) ((Vector3r,moment_twist,Vector3r(0,0,0),(Attr::readonly),"Twist moment")) ((Vector3r,moment_bending,Vector3r(0,0,0),(Attr::readonly),"Bending moment")) ((Vector3r,pureCreep,Vector3r(0,0,0),(Attr::readonly),"Pure creep curve, used for comparison in calculation.")) ((Real,kDam,0,(Attr::readonly),"Damage coefficient on bending, computed from maximum bending moment reached and pure creep behaviour. Its values will vary between :yref:`InelastCohFrictPhys::kr` and :yref:`InelastCohFrictPhys::kRCrp` .")) // internal attributes , createIndex(); ); /// Indexable REGISTER_CLASS_INDEX(InelastCohFrictPhys,FrictPhys); }; REGISTER_SERIALIZABLE(InelastCohFrictPhys); class Ip2_2xInelastCohFrictMat_InelastCohFrictPhys : public IPhysFunctor { public : virtual void go(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction); int cohesionDefinitionIteration; YADE_CLASS_BASE_DOC_ATTRS_CTOR(Ip2_2xInelastCohFrictMat_InelastCohFrictPhys,IPhysFunctor, "Generates cohesive-frictional interactions with moments. Used in the contact law :yref:`Law2_ScGeom6D_InelastCohFrictPhys_CohesionMoment`.", , cohesionDefinitionIteration = -1; ); FUNCTOR2D(InelastCohFrictMat,InelastCohFrictMat); }; REGISTER_SERIALIZABLE(Ip2_2xInelastCohFrictMat_InelastCohFrictPhys); class Law2_ScGeom6D_InelastCohFrictPhys_CohesionMoment: public LawFunctor{ public: Real normElastEnergy(); Real shearElastEnergy(); virtual bool go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Law2_ScGeom6D_InelastCohFrictPhys_CohesionMoment,LawFunctor,"This law is currently under developpement. Final version and documentation will come before the end of 2014.", ,, .def("normElastEnergy",&Law2_ScGeom6D_InelastCohFrictPhys_CohesionMoment::normElastEnergy,"Compute normal elastic energy.") .def("shearElastEnergy",&Law2_ScGeom6D_InelastCohFrictPhys_CohesionMoment::shearElastEnergy,"Compute shear elastic energy.") ); FUNCTOR2D(ScGeom6D,InelastCohFrictPhys); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_ScGeom6D_InelastCohFrictPhys_CohesionMoment); trunk-2017.01a/pkg/dem/Integrator.cpp000066400000000000000000000237321304022710500173410ustar00rootroot00000000000000#include #include #include #ifdef YADE_OPENMP #include #endif YADE_PLUGIN((Integrator)); void observer::operator()( const stateVector& x , Real t ) const { this->integrator->scene->time=t; this->integrator->setCurrentStates(x); } //! Integrator's pseudo-ctor (factory), taking nested lists of slave engines (might be moved to real ctor perhaps) void Integrator::action(){ } void Integrator::system(const stateVector& currentstates, stateVector& derivatives, Real time) { #ifdef YADE_OPENMP //prevent https://bugs.launchpad.net/yade/+bug/923929 ensureSync(); #endif //Calculate orientation maxVelocitySq=-1; setCurrentStates(currentstates); scene->time=time; const int size=(int)slaves.size(); for(int i=0; i& e, slaves[i]) { e->scene=scene; if(!e->dead && e->isActivated()) e->action(); } } derivatives=getSceneStateDot(); /* std::cout<bodies->size(); scene->forces.sync(); accumstatedotofthescene.resize(2*scene->bodies->size()*7); YADE_PARALLEL_FOREACH_BODY_BEGIN(const shared_ptr& b, scene->bodies){ const Body::id_t& id=b->getId(); Vector3r force=Vector3r::Zero(); Vector3r vel_current; Vector3r moment=Vector3r::Zero(); Vector3r angvel_current; Quaternionr ori_current; Quaternionr angvelquat; Quaternionr oridot_current; if(!b->isClumpMember()) { Real mass=b->state->mass; Vector3r inertia=b->state->inertia; vel_current=b->state->vel; angvel_current=b->state->angVel; ori_current=b->state->ori; // clumps forces if(b->isClump()) { b->shape->cast().addForceTorqueFromMembers(b->state.get(),scene,force,moment); #ifdef YADE_OPENMP //it is safe here, since only one thread will read/write scene->forces.addTorqueUnsynced(id,moment); scene->forces.addForceUnsynced(id,force); #else scene->forces.addTorque(id,moment); scene->forces.addForce(id,force); #endif } force=scene->forces.getForce(id); moment=scene->forces.getTorque(id); /* * Calculation of accelerations * */ force[0]=force[0]/mass; force[1]= force[1]/mass; force[2]= force[2]/mass; //Calculate linear acceleration moment[0]=moment[0]/inertia[0]; moment[1]= moment[1]/inertia[1]; moment[2]= moment[2]/inertia[2]; //Calculate angular acceleration //Check for fixation /* This code block needs optimization */ string str="xyzXYZ"; // Very very very hard coding!!!!! Fixation seems not handled fine by state structure, should be improved. for(int i=0; i<3; i++) if(b->state->blockedDOFs_vec_get().find(str[i]) != std::string::npos){ force[i]=0;vel_current[i]=0;} for(int i=3; i<6; i++) if(b->state->blockedDOFs_vec_get().find(str[i]) != std::string::npos){ moment[i-3]=0;angvel_current[i-3]=0;} angvelquat = Quaternionr(0.0,angvel_current[0],angvel_current[1],angvel_current[2]); oridot_current=Quaternionr(0.5*(angvelquat*ori_current).coeffs()); // if (densityScaling) accel*=state->densityScaling; } else { //is clump member force=Vector3r::Zero(); moment=Vector3r::Zero(); vel_current=Vector3r::Zero(); angvel_current=Vector3r::Zero(); oridot_current=Quaternionr(0,0,0,0);// zero change in quaternion with respect to time } /*Orientation differantion is straight forward.*/ accumstatedotofthescene[id*7+0]=vel_current[0]; accumstatedotofthescene[(id+numberofscenebodies)*7+0]=force[0]; accumstatedotofthescene[id*7+1]=vel_current[1]; accumstatedotofthescene[(id+numberofscenebodies)*7+1]=force[1]; accumstatedotofthescene[id*7+2]=vel_current[2]; accumstatedotofthescene[(id+numberofscenebodies)*7+2]=force[2]; accumstatedotofthescene[id*7+3]=oridot_current.w(); accumstatedotofthescene[(id+numberofscenebodies)*7+3]=moment[0]; accumstatedotofthescene[id*7+4]=oridot_current.x(); accumstatedotofthescene[(id+numberofscenebodies)*7+4]=moment[1]; accumstatedotofthescene[id*7+5]=oridot_current.y(); accumstatedotofthescene[(id+numberofscenebodies)*7+5]=moment[2]; accumstatedotofthescene[id*7+6]=oridot_current.z(); accumstatedotofthescene[(id+numberofscenebodies)*7+6]=0; } YADE_PARALLEL_FOREACH_BODY_END(); } catch(std::exception& e){ LOG_FATAL("Unhandled exception at Integrator::getSceneStateDot the exception information : "<bodies->size(); accumstateofthescene.resize(2*scene->bodies->size()*7); YADE_PARALLEL_FOREACH_BODY_BEGIN(const shared_ptr& b, scene->bodies){ const Body::id_t& id=b->getId(); Vector3r pos_current=b->state->pos; Vector3r vel_current=b->state->vel; Quaternionr ori=b->state->ori; Vector3r angvel=b->state->angVel; accumstateofthescene[id*7+0]=pos_current[0]; accumstateofthescene[(id+numberofscenebodies)*7+0]=vel_current[0]; accumstateofthescene[id*7+1]=pos_current[1]; accumstateofthescene[(id+numberofscenebodies)*7+1]=vel_current[1]; accumstateofthescene[id*7+2]=pos_current[2]; accumstateofthescene[(id+numberofscenebodies)*7+2]=vel_current[2]; accumstateofthescene[id*7+3]=ori.w(); accumstateofthescene[(id+numberofscenebodies)*7+3]=angvel[0]; accumstateofthescene[id*7+4]=ori.x(); accumstateofthescene[(id+numberofscenebodies)*7+4]=angvel[1]; accumstateofthescene[id*7+5]=ori.y(); accumstateofthescene[(id+numberofscenebodies)*7+5]=angvel[2]; accumstateofthescene[id*7+6]=ori.z(); accumstateofthescene[(id+numberofscenebodies)*7+6]=0; } YADE_PARALLEL_FOREACH_BODY_END(); } catch(std::exception& e){ LOG_FATAL("Unhandled exception at Integrator::getCurrentStates the exception information : "<bodies->size(); //Zero max velocity for each thread #ifdef YADE_OPENMP FOREACH(Real& thrMaxVSq, threadMaxVelocitySq) { thrMaxVSq=0; } #endif YADE_PARALLEL_FOREACH_BODY_BEGIN(const shared_ptr& b, scene->bodies){ if(b->isClumpMember()) continue; const Body::id_t& id=b->getId(); Vector3r pos_current; pos_current<state->pos=pos_current; b->state->vel=vel_current; b->state->ori=ori; //std::cout<<"Setting orientation to "<state->ori.normalize(); //Normalize orientation //std::cout<<"Setting angvel to "<state->angVel=angvel; #ifdef YADE_OPENMP Real& thrMaxVSq=threadMaxVelocitySq[omp_get_thread_num()]; thrMaxVSq=max(thrMaxVSq,b->state->vel.squaredNorm()); #else maxVelocitySq=max(maxVelocitySq,b->state->vel.squaredNorm());// Set maximum velocity of the scene #endif if(b->isClump()) Clump::moveMembers(b,scene,this); } YADE_PARALLEL_FOREACH_BODY_END(); #ifdef YADE_OPENMP FOREACH(const Real& thrMaxVSq, threadMaxVelocitySq) { maxVelocitySq=max(maxVelocitySq,thrMaxVSq); } #endif } catch(std::exception& e){ LOG_FATAL("Unhandled exception at Integrator::setCurrentStates the exception information : "<& b, scene->bodies){ // if(b->isClump()) continue; scene->forces.addForce(b->getId(),Vector3r(0,0,0)); } YADE_PARALLEL_FOREACH_BODY_END(); syncEnsured=true; } #endif void Integrator::saveMaximaDisplacement(const shared_ptr& b){ if (!b->bound) return;//clumps for instance, have no bounds, hence not saved Vector3r disp=b->state->pos-b->bound->refPos; Real maxDisp=max(std::abs(disp[0]),max(std::abs(disp[1]),std::abs(disp[2]))); if (!maxDisp || maxDispbound->sweepLength) {/*b->bound->isBounding = (updatingDispFactor>0 && (updatingDispFactor*maxDisp)bound->sweepLength);*/ maxDisp=0.5;//not 0, else it will be seen as "not updated" by the collider, but less than 1 means no colliding } else {/*b->bound->isBounding = false;*/ maxDisp=2;/*2 is more than 1, enough to trigger collider*/} maxVelocitySq=max(maxVelocitySq,maxDisp); } void Integrator::slaves_set(const boost::python::list& slaves2){ std::cout<<"Adding slaves"; int len=boost::python::len(slaves2); slaves.clear(); for(int i=0; i > > serialGroup(slaves2[i]); if (serialGroup.check()){ slaves.push_back(serialGroup()); continue; } boost::python::extract > serialAlone(slaves2[i]); if (serialAlone.check()){ vector > aloneWrap; aloneWrap.push_back(serialAlone()); slaves.push_back(aloneWrap); continue; } PyErr_SetString(PyExc_TypeError,"Engines that are given to Integrator should be in two cases (a) in an ordered group, (b) alone engines"); boost::python::throw_error_already_set(); } } boost::python::list Integrator::slaves_get(){ boost::python::list ret; FOREACH(vector >& grp, slaves){ if(grp.size()==1) ret.append(boost::python::object(grp[0])); else ret.append(boost::python::object(grp)); } return ret; } trunk-2017.01a/pkg/dem/Integrator.hpp000066400000000000000000000060561304022710500173460ustar00rootroot00000000000000#pragma once #include class Integrator; typedef std::vector stateVector;// Currently, we are unable to use Eigen library within odeint /*Observer used to update the state of the scene*/ class observer { Integrator* integrator; public: observer(Integrator* _in):integrator(_in){} void operator()( const stateVector& /* x */ , Real /* t */ ) const; }; //[ ode_wrapper template< class Obj , class Mem > class ode_wrapper { Obj m_obj; Mem m_mem; public: ode_wrapper( Obj obj , Mem mem ) : m_obj( obj ) , m_mem( mem ) { } template< class State , class Deriv , class Time > void operator()( const State &x , Deriv &dxdt , Time t ) { (m_obj.*m_mem)( x , dxdt , t ); } }; template< class Obj , class Mem > ode_wrapper< Obj , Mem > make_ode_wrapper( Obj obj , Mem mem ) { return ode_wrapper< Obj , Mem >( obj , mem ); } //] class Integrator: public TimeStepper { public: stateVector accumstateofthescene;//pos+vel stateVector accumstatedotofthescene;//only the accelerations stateVector resetstate;//last state before integration attempt Real timeresetvalue; inline void evaluateQuaternions(const stateVector &); //evaluate quaternions after integration typedef vector > > slaveContainer; #ifdef YADE_OPENMP vector threadMaxVelocitySq; #endif virtual void action(); virtual void system(const stateVector&, stateVector&, Real); //System function to calculate the derivatives of states virtual bool isActivated(){return true;} // py access boost::python::list slaves_get(); stateVector& getSceneStateDot(); bool saveCurrentState(Scene const* ourscene);//Before any integration attempt state of the scene should be saved. bool resetLastState(void);//Before any integration attempt state of the scene should be saved. void slaves_set(const boost::python::list& slaves); stateVector& getCurrentStates(void); bool setCurrentStates(stateVector); Real updatingDispFactor;//(experimental) Displacement factor used to trigger bound update: the bound is updated only if updatingDispFactor*disp>sweepDist when >0, else all bounds are updated. void saveMaximaDisplacement(const shared_ptr& b); #ifdef YADE_OPENMP void ensureSync(); bool syncEnsured; #endif YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Integrator,TimeStepper,"Integration Engine Interface.", ((slaveContainer,slaves,,,"[will be overridden]")) ((Real,integrationsteps,,,"all integrationsteps count as all succesfull substeps")) ((Real,maxVelocitySq,NaN,,"store square of max. velocity, for informative purposes; computed again at every step. |yupdate|")) , /*ctor*/ #ifdef YADE_OPENMP threadMaxVelocitySq.resize(omp_get_max_threads()); syncEnsured=false; #endif , /*py*/ .add_property("slaves",&Integrator::slaves_get,&Integrator::slaves_set,"List of lists of Engines to calculate the force acting on the particles; to obtain the derivatives of the states, engines inside will be run sequentially."); ); }; REGISTER_SERIALIZABLE(Integrator); trunk-2017.01a/pkg/dem/Ip2_ElastMat.cpp000066400000000000000000000043601304022710500174430ustar00rootroot00000000000000#include "Ip2_ElastMat.hpp" #include #include YADE_PLUGIN((Ip2_ElastMat_ElastMat_NormPhys)(Ip2_ElastMat_ElastMat_NormShearPhys)); void Ip2_ElastMat_ElastMat_NormPhys::go( const shared_ptr& b1 , const shared_ptr& b2 , const shared_ptr& interaction) { if(interaction->phys) return; const shared_ptr& mat1 = YADE_PTR_CAST(b1); const shared_ptr& mat2 = YADE_PTR_CAST(b2); Real Ea = mat1->young; Real Eb = mat2->young; interaction->phys = shared_ptr(new NormPhys()); const shared_ptr& phys = YADE_PTR_CAST(interaction->phys); Real Kn; const GenericSpheresContact* geom=dynamic_cast(interaction->geom.get()); if (geom) { Real Ra,Rb;//Vector3r normal; Ra=geom->refR1>0?geom->refR1:geom->refR2; Rb=geom->refR2>0?geom->refR2:geom->refR1; //harmonic average of the two stiffnesses when (Ri.Ei/2) is the stiffness of a contact point on sphere "i" Kn = 2*Ea*Ra*Eb*Rb/(Ea*Ra+Eb*Rb); } else { Kn = 2*Ea*Eb/(Ea+Eb); } phys->kn = Kn; }; void Ip2_ElastMat_ElastMat_NormShearPhys::go( const shared_ptr& b1 , const shared_ptr& b2 , const shared_ptr& interaction) { if(interaction->phys) return; const shared_ptr& mat1 = YADE_PTR_CAST(b1); const shared_ptr& mat2 = YADE_PTR_CAST(b2); Real Ea = mat1->young; Real Eb = mat2->young; Real Va = mat1->poisson; Real Vb = mat2->poisson; interaction->phys = shared_ptr(new NormShearPhys()); const shared_ptr& phys = YADE_PTR_CAST(interaction->phys); Real Kn=0.0, Ks=0.0; GenericSpheresContact* geom=dynamic_cast(interaction->geom.get()); if (geom) { Real Ra,Rb;//Vector3r normal; Ra=geom->refR1>0?geom->refR1:geom->refR2; Rb=geom->refR2>0?geom->refR2:geom->refR1; //harmonic average of the two stiffnesses when (Ri.Ei/2) is the stiffness of a contact point on sphere "i" Kn = 2*Ea*Ra*Eb*Rb/(Ea*Ra+Eb*Rb); Ks = 2*Ea*Ra*Va*Eb*Rb*Vb/(Ea*Ra*Va+Eb*Rb*Vb); } else { Kn = 2*Ea*Eb/(Ea+Eb); Kn = 2*Ea*Va*Eb*Vb/(Ea*Va+Eb*Vb); } phys->kn = Kn; phys->ks = Ks; }; trunk-2017.01a/pkg/dem/Ip2_ElastMat.hpp000066400000000000000000000017761304022710500174600ustar00rootroot00000000000000 #include #include #include class Ip2_ElastMat_ElastMat_NormPhys: public IPhysFunctor{ public: virtual void go(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction); FUNCTOR2D(ElastMat,ElastMat); YADE_CLASS_BASE_DOC_ATTRS(Ip2_ElastMat_ElastMat_NormPhys,IPhysFunctor,"Create a :yref:`NormPhys` from two :yref:`ElastMats`. TODO. EXPERIMENTAL", ); }; REGISTER_SERIALIZABLE(Ip2_ElastMat_ElastMat_NormPhys); class Ip2_ElastMat_ElastMat_NormShearPhys: public IPhysFunctor{ public: virtual void go(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction); FUNCTOR2D(ElastMat,ElastMat); YADE_CLASS_BASE_DOC_ATTRS(Ip2_ElastMat_ElastMat_NormShearPhys,IPhysFunctor,"Create a :yref:`NormShearPhys` from two :yref:`ElastMats`. TODO. EXPERIMENTAL", ); }; REGISTER_SERIALIZABLE(Ip2_ElastMat_ElastMat_NormShearPhys); trunk-2017.01a/pkg/dem/JointedCohesiveFrictionalPM.cpp000066400000000000000000000361741304022710500225610ustar00rootroot00000000000000/* LucScholtes2010 */ #include"JointedCohesiveFrictionalPM.hpp" #include #include #include YADE_PLUGIN((JCFpmMat)(JCFpmState)(JCFpmPhys)(Ip2_JCFpmMat_JCFpmMat_JCFpmPhys)(Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM)); /********************** Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM ****************************/ CREATE_LOGGER(Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM); bool Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM::go(shared_ptr& ig, shared_ptr& ip, Interaction* contact){ const int &id1 = contact->getId1(); const int &id2 = contact->getId2(); ScGeom* geom = static_cast(ig.get()); JCFpmPhys* phys = static_cast(ip.get()); Body* b1 = Body::byId(id1,scene).get(); Body* b2 = Body::byId(id2,scene).get(); Real Dtensile=phys->FnMax/phys->kn; string fileCracks = "cracks_"+Key+".txt"; /// Defines the interparticular distance used for computation Real D = 0; /*this is for setting the equilibrium distance between all cohesive elements in the first contact detection*/ if ( contact->isFresh(scene) ) { phys->normalForce = Vector3r::Zero(); phys->shearForce = Vector3r::Zero(); if ((smoothJoint) && (phys->isOnJoint)) { phys->jointNormal = geom->normal.dot(phys->jointNormal)*phys->jointNormal; //to set the joint normal colinear with the interaction normal phys->jointNormal.normalize(); phys->initD = std::abs((b1->state->pos - b2->state->pos).dot(phys->jointNormal)); // to set the initial gap as the equilibrium gap } else { phys->initD = geom->penetrationDepth; } } if ( smoothJoint && phys->isOnJoint ) { if ( phys->more || ( phys-> jointCumulativeSliding > (2*min(geom->radius1,geom->radius2)) ) ) { if (!neverErase) return false; else { phys->shearForce = Vector3r::Zero(); phys->normalForce = Vector3r::Zero(); phys->isCohesive =0; phys->FnMax = 0; phys->FsMax = 0; return true; // do we need this? -> yes if it ends the loop (avoid the following calculations) } } else { D = phys->initD - std::abs((b1->state->pos - b2->state->pos).dot(phys->jointNormal)); } } else { D = geom->penetrationDepth - phys->initD; } phys->crackJointAperture = D<0? -D : 0.; // for DFNFlow /* Determination of interaction */ if (D < 0) { //spheres do not touch if ( !phys->isCohesive) { if (!neverErase) return false; else { phys->shearForce = Vector3r::Zero(); phys->normalForce = Vector3r::Zero(); phys->isCohesive =0; phys->FnMax = 0; phys->FsMax = 0; return true; // do we need this? not sure -> yes, it ends the loop (avoid the following calculations) } } if ( phys->isCohesive && (phys->FnMax>0) && (std::abs(D)>Dtensile) ) { // update body state with the number of broken bonds JCFpmState* st1=dynamic_cast(b1->state.get()); JCFpmState* st2=dynamic_cast(b2->state.get()); st1->tensBreak+=1; st2->tensBreak+=1; st1->tensBreakRel+=1.0/st1->noIniLinks; st2->tensBreakRel+=1.0/st2->noIniLinks; // create a text file to record properties of the broken bond (iteration, position, type (tensile), cross section and contact normal orientation) if (recordCracks){ std::ofstream file (fileCracks.c_str(), !cracksFileExist ? std::ios::trunc : std::ios::app); if(file.tellp()==0){ file <<"i p0 p1 p2 t s norm0 norm1 norm2"<isOnJoint)) { crackNormal=phys->jointNormal; } else {crackNormal=geom->normal;} file << boost::lexical_cast ( scene->iter )<<" "<< boost::lexical_cast ( geom->contactPoint[0] ) <<" "<< boost::lexical_cast ( geom->contactPoint[1] ) <<" "<< boost::lexical_cast ( geom->contactPoint[2] ) <<" "<< 0 <<" "<< boost::lexical_cast ( 0.5*(geom->radius1+geom->radius2) ) <<" "<< boost::lexical_cast ( crackNormal[0] ) <<" "<< boost::lexical_cast ( crackNormal[1] ) <<" "<< boost::lexical_cast ( crackNormal[2] ) << endl; } cracksFileExist=true; /// Timos if (!neverErase) return false; else { phys->shearForce = Vector3r::Zero(); phys->normalForce = Vector3r::Zero(); phys->isCohesive =0; phys->FnMax = 0; phys->FsMax = 0; phys->isBroken = true; return true; // do we need this? not sure -> yes, it ends the loop (avoid the following calculations) } // return true; // do we need this? no } } /* NormalForce */ Real Fn = 0; Fn = phys->kn*D; /* ShearForce */ Vector3r& shearForce = phys->shearForce; Real jointSliding=0; if ((smoothJoint) && (phys->isOnJoint)) { /// incremental formulation (OK?) Vector3r relativeVelocity = (b2->state->vel - b1->state->vel); // angVel are not taken into account as particles on joint don't rotate ???? Vector3r slidingVelocity = relativeVelocity - phys->jointNormal.dot(relativeVelocity)*phys->jointNormal; Vector3r incrementalSliding = slidingVelocity*scene->dt; shearForce -= phys->ks*incrementalSliding; jointSliding = incrementalSliding.norm(); phys->jointCumulativeSliding += jointSliding; } else { shearForce = geom->rotate(phys->shearForce); const Vector3r& incrementalShear = geom->shearIncrement(); shearForce -= phys->ks*incrementalShear; } /* Mohr-Coulomb criterion */ Real maxFs = phys->FsMax + Fn*phys->tanFrictionAngle; Real scalarShearForce = shearForce.norm(); if (scalarShearForce > maxFs) { if (scalarShearForce != 0) shearForce*=maxFs/scalarShearForce; else shearForce=Vector3r::Zero(); if ((smoothJoint) && (phys->isOnJoint)) {phys->dilation=phys->jointCumulativeSliding*phys->tanDilationAngle-D; phys->initD+=(jointSliding*phys->tanDilationAngle);} // take into account shear cracking -> are those lines critical? -> TODO testing with and without if ( phys->isCohesive ) { // update body state with the number of broken bonds JCFpmState* st1=dynamic_cast(b1->state.get()); JCFpmState* st2=dynamic_cast(b2->state.get()); st1->shearBreak+=1; st2->shearBreak+=1; st1->shearBreakRel+=1.0/st1->noIniLinks; st2->shearBreakRel+=1.0/st2->noIniLinks; // create a text file to record properties of the broken bond (iteration, position, type (shear), cross section and contact normal orientation) if (recordCracks){ std::ofstream file (fileCracks.c_str(), !cracksFileExist ? std::ios::trunc : std::ios::app); if(file.tellp()==0){ file <<"i p0 p1 p2 t s norm0 norm1 norm2"<isOnJoint)) { crackNormal=phys->jointNormal; } else {crackNormal=geom->normal;} file << boost::lexical_cast ( scene->iter )<<" "<< boost::lexical_cast ( geom->contactPoint[0] ) <<" "<< boost::lexical_cast ( geom->contactPoint[1] ) <<" "<< boost::lexical_cast ( geom->contactPoint[2] ) <<" "<< 1 <<" "<< boost::lexical_cast ( 0.5*(geom->radius1+geom->radius2) ) <<" "<< boost::lexical_cast ( crackNormal[0] ) <<" "<< boost::lexical_cast ( crackNormal[1] ) <<" "<< boost::lexical_cast ( crackNormal[2] ) << endl; } cracksFileExist=true; // set the contact properties to friction if in compression, delete contact if in tension phys->isBroken = true; phys->isCohesive = 0; phys->FnMax = 0; phys->FsMax = 0; // shearForce *= Fn*phys->tanFrictionAngle/scalarShearForce; // now or at the next timestep? if ( D < 0 ) { // spheres do not touch if (!neverErase) return false; else { phys->shearForce = Vector3r::Zero(); phys->normalForce = Vector3r::Zero(); return true; // do we need this? not sure -> yes, it ends the loop (avoid the following calculations) } } // return true; // do we need this one? no } } /* Apply forces */ if ((smoothJoint) && (phys->isOnJoint)) { phys->normalForce = Fn*phys->jointNormal; } else { phys->normalForce = Fn*geom->normal; } Vector3r f = phys->normalForce + shearForce; /// applyForceAtContactPoint computes torque also and, for now, we don't want rotation for particles on joint (some errors in calculation due to specific geometry) //applyForceAtContactPoint(f, geom->contactPoint, I->getId2(), b2->state->pos, I->getId1(), b1->state->pos, scene); scene->forces.addForce (id1,-f); scene->forces.addForce (id2, f); // simple solution to avoid torque computation for particles interacting on a smooth joint if ( (phys->isOnJoint)&&(smoothJoint) ) return true; /// those lines are needed if rootBody->forces.addForce and rootBody->forces.addMoment are used instead of applyForceAtContactPoint -> NOTE need to check for accuracy!!! scene->forces.addTorque(id1,(geom->radius1-0.5*geom->penetrationDepth)* geom->normal.cross(-f)); scene->forces.addTorque(id2,(geom->radius2-0.5*geom->penetrationDepth)* geom->normal.cross(-f)); return true; } CREATE_LOGGER(Ip2_JCFpmMat_JCFpmMat_JCFpmPhys); void Ip2_JCFpmMat_JCFpmMat_JCFpmPhys::go(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction){ /* avoid updates of interaction if it already exists */ if( interaction->phys ) return; ScGeom* geom=dynamic_cast(interaction->geom.get()); assert(geom); const shared_ptr& yade1 = YADE_PTR_CAST(b1); const shared_ptr& yade2 = YADE_PTR_CAST(b2); JCFpmState* st1=dynamic_cast(Body::byId(interaction->getId1(),scene)->state.get()); JCFpmState* st2=dynamic_cast(Body::byId(interaction->getId2(),scene)->state.get()); shared_ptr contactPhysics(new JCFpmPhys()); /* From material properties */ Real E1 = yade1->young; Real E2 = yade2->young; Real v1 = yade1->poisson; Real v2 = yade2->poisson; Real f1 = yade1->frictionAngle; Real f2 = yade2->frictionAngle; Real SigT1 = yade1->tensileStrength; Real SigT2 = yade2->tensileStrength; Real Coh1 = yade1->cohesion; Real Coh2 = yade2->cohesion; /* From interaction geometry */ Real R1= geom->radius1; Real R2= geom->radius2; contactPhysics->crossSection = Mathr::PI*pow(min(R1,R2),2); /* Pass values to JCFpmPhys. In case of a "jointed" interaction, the following values will be replaced by other ones later (in few if(){} blocks)*/ // frictional properties contactPhysics->kn = 2.*E1*R1*E2*R2/(E1*R1+E2*R2); if ( (v1==0)&&(v2==0) ) contactPhysics->ks = 0; else contactPhysics->ks = 2.*E1*R1*v1*E2*R2*v2/(E1*R1*v1+E2*R2*v2); contactPhysics->tanFrictionAngle = std::tan(std::min(f1,f2)); // cohesive properties ///to set if the contact is cohesive or not if ( ((cohesiveTresholdIteration < 0) || (scene->iter < cohesiveTresholdIteration)) && (std::min(SigT1,SigT2)>0 || std::min(Coh1,Coh2)>0) && (yade1->type == yade2->type)){ contactPhysics->isCohesive=true; st1->noIniLinks++; st2->noIniLinks++; } if ( contactPhysics->isCohesive ) { contactPhysics->FnMax = std::min(SigT1,SigT2)*contactPhysics->crossSection; contactPhysics->FsMax = std::min(Coh1,Coh2)*contactPhysics->crossSection; } /// +++ Jointed interactions ->NOTE: geom->normal is oriented from 1 to 2 / jointNormal from plane to sphere if ( st1->onJoint && st2->onJoint ) { if ( (((st1->jointNormal1.cross(st2->jointNormal1)).norm()<0.1) && (st1->jointNormal1.dot(st2->jointNormal1)<0)) || (((st1->jointNormal1.cross(st2->jointNormal2)).norm()<0.1) && (st1->jointNormal1.dot(st2->jointNormal2)<0)) || (((st1->jointNormal1.cross(st2->jointNormal3)).norm()<0.1) && (st1->jointNormal1.dot(st2->jointNormal3)<0)) ) { contactPhysics->isOnJoint = true; contactPhysics->jointNormal = st1->jointNormal1; } else if ( (((st1->jointNormal2.cross(st2->jointNormal1)).norm()<0.1) && (st1->jointNormal2.dot(st2->jointNormal1)<0)) || (((st1->jointNormal2.cross(st2->jointNormal2)).norm()<0.1) && (st1->jointNormal2.dot(st2->jointNormal2)<0)) || (((st1->jointNormal2.cross(st2->jointNormal3)).norm()<0.1) && (st1->jointNormal2.dot(st2->jointNormal3)<0)) ) { contactPhysics->isOnJoint = true; contactPhysics->jointNormal = st1->jointNormal2; } else if ( (((st1->jointNormal3.cross(st2->jointNormal1)).norm()<0.1) && (st1->jointNormal3.dot(st2->jointNormal1)<0)) || (((st1->jointNormal3.cross(st2->jointNormal2)).norm()<0.1) && (st1->jointNormal3.dot(st2->jointNormal2)<0)) || (((st1->jointNormal3.cross(st2->jointNormal3)).norm()<0.1) && (st1->jointNormal3.dot(st2->jointNormal3)<0)) ) { contactPhysics->isOnJoint = true; contactPhysics->jointNormal = st1->jointNormal3; } else if ( (st1->joint>3 || st2->joint>3) && ( ( ((st1->jointNormal1.cross(st2->jointNormal1)).norm()>0.1) && ((st1->jointNormal1.cross(st2->jointNormal2)).norm()>0.1) && ((st1->jointNormal1.cross(st2->jointNormal3)).norm()>0.1) ) || ( ((st1->jointNormal2.cross(st2->jointNormal1)).norm()>0.1) && ((st1->jointNormal2.cross(st2->jointNormal2)).norm()>0.1) && ((st1->jointNormal2.cross(st2->jointNormal3)).norm()>0.1) ) || ( ((st1->jointNormal3.cross(st2->jointNormal1)).norm()>0.1) && ((st1->jointNormal3.cross(st2->jointNormal2)).norm()>0.1) && ((st1->jointNormal3.cross(st2->jointNormal3)).norm()>0.1) ) ) ) { contactPhysics->isOnJoint = true; contactPhysics->more = true; contactPhysics->jointNormal = geom->normal; } } ///to specify joint properties if ( contactPhysics->isOnJoint ) { Real jf1 = yade1->jointFrictionAngle; Real jf2 = yade2->jointFrictionAngle; Real jkn1 = yade1->jointNormalStiffness; Real jkn2 = yade2->jointNormalStiffness; Real jks1 = yade1->jointShearStiffness; Real jks2 = yade2->jointShearStiffness; Real jdil1 = yade1->jointDilationAngle; Real jdil2 = yade2->jointDilationAngle; Real jcoh1 = yade1->jointCohesion; Real jcoh2 = yade2->jointCohesion; Real jSigT1 = yade1->jointTensileStrength; Real jSigT2 = yade2->jointTensileStrength; contactPhysics->tanFrictionAngle = std::tan(std::min(jf1,jf2)); //contactPhysics->kn = jointNormalStiffness*2.*R1*R2/(R1+R2); // very first expression from Luc //contactPhysics->kn = (jkn1+jkn2)/2.0*2.*R1*R2/(R1+R2); // after putting jointNormalStiffness in material contactPhysics->kn = ( jkn1 + jkn2 ) /2.0 * contactPhysics->crossSection; // for a size independant expression contactPhysics->ks = ( jks1 + jks2 ) /2.0 * contactPhysics->crossSection; // for a size independant expression contactPhysics->tanDilationAngle = std::tan(std::min(jdil1,jdil2)); ///to set if the contact is cohesive or not if ( ((cohesiveTresholdIteration < 0) || (scene->iter < cohesiveTresholdIteration)) && (std::min(jcoh1,jcoh2)>0 || std::min(jSigT1,jSigT2)>0) ) { contactPhysics->isCohesive=true; st1->noIniLinks++; st2->noIniLinks++; } else { contactPhysics->isCohesive=false; contactPhysics->FnMax=0; contactPhysics->FsMax=0; } if ( contactPhysics->isCohesive ) { contactPhysics->FnMax = std::min(jSigT1,jSigT2)*contactPhysics->crossSection; contactPhysics->FsMax = std::min(jcoh1,jcoh2)*contactPhysics->crossSection; } } interaction->phys = contactPhysics; } JCFpmPhys::~JCFpmPhys(){} trunk-2017.01a/pkg/dem/JointedCohesiveFrictionalPM.hpp000066400000000000000000000224531304022710500225610ustar00rootroot00000000000000/* lucScholtes2010 */ #pragma once #include #include #include #include /** This class holds information associated with each body state*/ class JCFpmState: public State { YADE_CLASS_BASE_DOC_ATTRS_CTOR(JCFpmState,State,"JCFpm state information about each body.", ((int,tensBreak,0,,"Number of tensile breakages. [-]")) ((int,shearBreak,0,,"Number of shear breakages. [-]")) ((int,noIniLinks,0,,"Number of initial cohesive interactions. [-]")) ((Real,tensBreakRel,0,,"Relative number (in [0;1], compared with :yref:`noIniLinks`) of tensile breakages. [-]")) ((Real,shearBreakRel,0,,"Relative number (in [0;1], compared with :yref:`noIniLinks`) of shear breakages. [-]")) ((bool,onJoint,false,,"Identifies if the particle is on a joint surface.")) ((int,joint,0,,"Indicates the number of joint surfaces to which the particle belongs (0-> no joint, 1->1 joint, etc..). [-]")) ((Vector3r,jointNormal1,Vector3r::Zero(),,"Specifies the normal direction to the joint plane 1. Rk: the ideal here would be to create a vector of vector wich size is defined by the joint integer (as much joint normals as joints). However, it needs to make the pushback function works with python since joint detection is done through a python script. lines 272 to 312 of cpp file should therefore be adapted. [-]")) ((Vector3r,jointNormal2,Vector3r::Zero(),,"Specifies the normal direction to the joint plane 2. [-]")) ((Vector3r,jointNormal3,Vector3r::Zero(),,"Specifies the normal direction to the joint plane 3. [-]")) , createIndex(); ); REGISTER_CLASS_INDEX(JCFpmState,State); }; REGISTER_SERIALIZABLE(JCFpmState); /** This class holds information associated with each body */ class JCFpmMat: public FrictMat { public: virtual shared_ptr newAssocState() const { return shared_ptr(new JCFpmState); } virtual bool stateTypeOk(State* s) const { return (bool)dynamic_cast(s); } YADE_CLASS_BASE_DOC_ATTRS_CTOR(JCFpmMat,FrictMat,"Possibly jointed, cohesive frictional material, for use with other JCFpm classes", ((Real,cohesion,0.,,"Defines the maximum admissible tangential force in shear, for Fn=0, in the matrix (:yref:`FsMax` = cohesion * :yref:`crossSection`). [Pa]")) ((Real,jointCohesion,0.,,"Defines the :yref:`maximum admissible tangential force in shear`, for Fn=0, on the joint surface. [Pa]")) ((Real,jointDilationAngle,0,,"Defines the dilatancy of the joint surface (only valid for :yref:`smooth contact logic`). [rad]")) ((Real,jointFrictionAngle,-1,,"Defines Coulomb friction on the joint surface. [rad]")) ((Real,jointNormalStiffness,0.,,"Defines the normal stiffness on the joint surface. [Pa/m]")) ((Real,jointShearStiffness,0.,,"Defines the shear stiffness on the joint surface. [Pa/m]")) ((Real,jointTensileStrength,0.,,"Defines the :yref:`maximum admissible normal force in traction` on the joint surface. [Pa]")) ((int,type,0,,"If particles of two different types interact, it will be with friction only (no cohesion).[-]")) ((Real,tensileStrength,0.,,"Defines the maximum admissible normal force in traction in the matrix (:yref:`FnMax` = tensileStrength * :yref:`crossSection`). [Pa]")) , createIndex(); ); REGISTER_CLASS_INDEX(JCFpmMat,FrictMat); }; REGISTER_SERIALIZABLE(JCFpmMat); /** This class holds information associated with each interaction */ class JCFpmPhys: public NormShearPhys { public: virtual ~JCFpmPhys(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(JCFpmPhys,NormShearPhys,"Representation of a single interaction of the JCFpm type, storage for relevant parameters", ((Real,initD,0,,"equilibrium distance for interacting particles. Computed as the interparticular distance at first contact detection.")) ((bool,isCohesive,false,,"If false, particles interact in a frictional way. If true, particles are bonded regarding the given :yref:`cohesion` and :yref:`tensile strength` (or their jointed variants).")) ((bool,more,false,,"specifies if the interaction is crossed by more than 3 joints. If true, interaction is deleted (temporary solution).")) ((bool,isOnJoint,false,,"defined as true when both interacting particles are :yref:`on joint` and are in opposite sides of the joint surface. In this case, mechanical parameters of the interaction are derived from the ''joint...'' material properties of the particles. Furthermore, the normal of the interaction may be re-oriented (see :yref:`Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM.smoothJoint`).")) ((Real,tanFrictionAngle,0,,"tangent of Coulomb friction angle for this interaction (auto. computed). [-]")) ((Real,crossSection,0,,"crossSection=pi*Rmin^2. [m2]")) ((Real,FnMax,0,,"positiv value computed from :yref:`tensile strength` (or joint variant) to define the maximum admissible normal force in traction: Fn >= -FnMax. [N]")) ((Real,FsMax,0,,"computed from :yref:`cohesion` (or jointCohesion) to define the maximum admissible tangential force in shear, for Fn=0. [N]")) ((Vector3r,jointNormal,Vector3r::Zero(),,"normal direction to the joint, deduced from e.g. :yref:``.")) ((Real,jointCumulativeSliding,0,,"sliding distance for particles interacting on a joint. Used, when :yref:`` is true, to take into account dilatancy due to shearing. [-]")) ((Real,tanDilationAngle,0,,"tangent of the angle defining the dilatancy of the joint surface (auto. computed from :yref:`JCFpmMat.jointDilationAngle`). [-]")) ((Real,dilation,0,,"defines the normal displacement in the joint after sliding treshold. [m]")) ((bool,isBroken,false,,"flag for broken interactions")) ((Real,crackJointAperture,0,,"Relative displacement between 2 spheres (in case of a crack it is equivalent of the crack aperture)")) , createIndex(); , ); DECLARE_LOGGER; REGISTER_CLASS_INDEX(JCFpmPhys,NormShearPhys); }; REGISTER_SERIALIZABLE(JCFpmPhys); /** 2d functor creating InteractionPhysics (Ip2) taking JCFpmMat and JCFpmMat of 2 bodies, returning type JCFpmPhys */ class Ip2_JCFpmMat_JCFpmMat_JCFpmPhys: public IPhysFunctor{ public: virtual void go(const shared_ptr& pp1, const shared_ptr& pp2, const shared_ptr& interaction); FUNCTOR2D(JCFpmMat,JCFpmMat); DECLARE_LOGGER; YADE_CLASS_BASE_DOC_ATTRS(Ip2_JCFpmMat_JCFpmMat_JCFpmPhys,IPhysFunctor,"Converts 2 :yref:`JCFpmMat` instances to one :yref:`JCFpmPhys` instance, with corresponding parameters. See :yref:`JCFpmMat` and [Duriez2016]_ for details", ((int,cohesiveTresholdIteration,1,,"should new contacts be cohesive? If strictly negativ, they will in any case. If positiv, they will before this iter, they won't afterward.")) ); }; REGISTER_SERIALIZABLE(Ip2_JCFpmMat_JCFpmMat_JCFpmPhys); /** 2d functor creating the interaction law (Law2) based on SphereContactGeometry (ScGeom) and JCFpmPhys of 2 bodies, returning type JointedCohesiveFrictionalPM */ class Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM: public LawFunctor{ public: virtual bool go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I); FUNCTOR2D(ScGeom,JCFpmPhys); YADE_CLASS_BASE_DOC_ATTRS(Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM,LawFunctor,"Interaction law for cohesive frictional material, e.g. rock, possibly presenting joint surfaces, that can be mechanically described with a smooth contact logic [Ivars2011]_ (implemented in Yade in [Scholtes2012]_). See examples/jointedCohesiveFrictionalPM for script examples. Joint surface definitions (through stl meshes or direct definition with gts module) are illustrated there.", ((string,Key,"",,"string specifying the name of saved file 'cracks___.txt', when :yref:`recordCracks` is true.")) ((bool,cracksFileExist,false,,"if true (and if :yref:`recordCracks`), data are appended to an existing 'cracksKey' text file; otherwise its content is reset.")) ((bool,smoothJoint,false,,"if true, interactions of particles belonging to joint surface (:yref:`JCFpmPhys.isOnJoint`) are handled according to a smooth contact logic [Ivars2011]_, [Scholtes2012]_.")) ((bool,recordCracks,false,,"if true, data about interactions that lose their cohesive feature are stored in a text file cracksKey.txt (see :yref:`Key` and :yref:`cracksFileExist`). It contains 9 columns: the break iteration, the 3 coordinates of the contact point, the type (1 means shear break, while 0 corresponds to tensile break), the ''cross section'' (mean radius of the 2 spheres) and the 3 coordinates of the contact normal.")) ((bool,neverErase,false,,"Keep interactions even if particles go away from each other (only in case another constitutive law is in the scene")) ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_ScGeom_JCFpmPhys_JointedCohesiveFrictionalPM); trunk-2017.01a/pkg/dem/KinemC__Engine.cpp000066400000000000000000000105411304022710500200070ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2008 by Jerome Duriez * * jerome.duriez@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include YADE_PLUGIN((KinemCTDEngine)(KinemCNDEngine)(KinemCNLEngine)(KinemCNSEngine)); void KinemCTDEngine::action() { KinemSimpleShearBox::getBoxes_Dt(); scene->forces.sync(); Real current_NormalForce=(scene->forces.getForce(id_topbox)).y(); KinemSimpleShearBox::computeScontact(); current_sigma=current_NormalForce/(1000.0*Scontact); // so we have the current value of sigma, in kPa if( ((compSpeed > 0) && (current_sigma < targetSigma)) || ((compSpeed < 0) && (current_sigma > targetSigma)) ) { if(temoin!=0) temoin=0; letMove(0.0,-compSpeed*dt); } else if (temoin==0) { stopMovement(); string f; if (compSpeed > 0) f="Sigmax_"; else f="Sigmin_"; Omega::instance().saveSimulation(Key + f +boost::lexical_cast (floor(targetSigma)) + "kPaReached.xml"); temoin=1; } for(unsigned int j=0;j0)&&(current_sigma > sigma_save[j]) ) || ((compSpeed<0)&&(current_sigma < sigma_save[j])) ) && (temoin_save[j]==0)) { stopMovement(); Omega::instance().saveSimulation(Key + "SigInt_" +boost::lexical_cast (floor(current_sigma)) + "kPareached.xml"); temoin_save[j]=1; } } } void KinemCNDEngine::action() { KinemSimpleShearBox::getBoxes_Dt(); if( ((shearSpeed > 0) && (gamma<=gammalim)) || ((shearSpeed < 0) /*&& (gamma>=gammalim)*/ ) ) { if(temoinfin!=0) temoinfin=0; letMove(shearSpeed * dt,0); gamma+=shearSpeed * dt; } else { stopMovement(); if(temoinfin==0) { Omega::instance().saveSimulation(Key + "endShear.xml"); temoinfin=1; } } for(unsigned int j=0;j0)&&(gamma > gamma_save[j]) ) || ((shearSpeed<0)&&(gamma < gamma_save[j])) ) && (temoin_save[j]==0) ) { stopMovement(); // reset of all the speeds before the save Omega::instance().saveSimulation(Key+"_"+boost::lexical_cast (floor(gamma*1000)) + "mmsheared.xml"); temoin_save[j]=1; } } } void KinemCNLEngine::action() { if(LOG) cout << "debut applyCondi du CNCEngine !!" << endl; KinemSimpleShearBox::getBoxes_Dt(); if(LOG) cout << "gamma = " << boost::lexical_cast(gamma) << " et gammalim = " << boost::lexical_cast(gammalim) << endl; if(gamma<=gammalim) { if(LOG) cout << "Je suis bien dans la partie gamma < gammalim" << endl; if(temoin==0) { if(LOG) cout << "Je veux maintenir la Force a f0 = : " << f0 << endl; temoin=1; } computeDY(0.0); letMove(shearSpeed*dt,deltaH); gamma+=shearSpeed * dt; } else if (temoin<2) { stopMovement(); it_stop=scene->iter; cout << "Shear stopped : gammaLim reached at it "<< it_stop << endl; temoin=2; } else if (temoin==2 && (scene->iter==(it_stop+5000)) ) { Omega::instance().saveSimulation(Key + "endShear" +boost::lexical_cast ( scene->iter ) + ".xml"); Omega::instance().pause(); } for(unsigned int j=0;j gamma_save[j]) && (temoin_save[j]==0)) { stopMovement(); // reset of all the speeds before the save Omega::instance().saveSimulation(Key+"_"+boost::lexical_cast (floor(gamma*1000)) +"_" +boost::lexical_cast (floor(gamma*10000)-10*floor(gamma*1000))+ "mmsheared.xml"); temoin_save[j]=1; } } } void KinemCNSEngine::action() { if(LOG) cerr << "debut applyCondi !!" << endl; KinemSimpleShearBox::getBoxes_Dt(); if(gamma<=gammalim) { computeDY(KnC); letMove(shearSpeed * dt,deltaH); gamma+=shearSpeed * dt; if(temoin==0) { temoin=1; } } else if (temoin<2) { stopMovement(); it_stop=scene->iter; cout << "Cisaillement arrete : gammaLim atteint a l'iteration "<< it_stop << endl; temoin=2; } else if (temoin==2 && (scene->iter==(it_stop+5000)) ) { Omega::instance().saveSimulation(Key + "finCis" +boost::lexical_cast (scene->iter ) + ".xml"); Omega::instance().pause(); } } trunk-2017.01a/pkg/dem/KinemC__Engine.hpp000066400000000000000000000164461304022710500200260ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2008 by Jerome Duriez * * jerome.duriez@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include class KinemCTDEngine : public KinemSimpleShearBox { private : Real current_sigma // Computed in kPa ; int temoin; public : virtual ~KinemCTDEngine() {}; void action(); // ; YADE_CLASS_BASE_DOC_ATTRS_CTOR(KinemCTDEngine,KinemSimpleShearBox, "To compress a simple shear sample by moving the upper box in a vertical way only, so that the tangential displacement (defined by the horizontal gap between the upper and lower boxes) remains constant (thus, the CTD = Constant Tangential Displacement).\n \t The lateral boxes move also to keep always contact. All that until this box is submitted to a given stress (:yref:`targetSigma`). Moreover saves are executed at each value of stresses stored in the vector :yref:`sigma_save`, and at :yref:`targetSigma`", ((Real,compSpeed,0.0,,"(vertical) speed of the upper box : >0 for real compression, <0 for unloading [$m/s$]")) ((std::vector,sigma_save,,,"vector with the values of sigma at which a save of the simulation should be performed [$kPa$]")) ((Real,targetSigma,0.0,,"the value of sigma at which the compression should stop [$kPa$]")), temoin=0; ) }; REGISTER_SERIALIZABLE(KinemCTDEngine); class KinemCNDEngine : public KinemSimpleShearBox { private : int temoinfin; public : void action(); protected : YADE_CLASS_BASE_DOC_ATTRS_CTOR(KinemCNDEngine,KinemSimpleShearBox, "To apply a Constant Normal Displacement (CND) shear for a parallelogram box\n\n \tThis engine, designed for simulations implying a simple shear box (:yref:`SimpleShear` Preprocessor or scripts/simpleShear.py), allows one to perform a constant normal displacement shear, by translating horizontally the upper plate, while the lateral ones rotate so that they always keep contact with the lower and upper walls.", ((Real,shearSpeed,0.0,,"the speed at which the shear is performed : speed of the upper plate [m/s]")) ((Real,gammalim,0.0,,"the value of the tangential displacement at wich the displacement is stopped [m]")) ((Real,gamma,0.0,,"the current value of the tangential displacement")) ((std::vector,gamma_save,,,"vector with the values of gamma at which a save of the simulation is performed [m]")), temoinfin=0; ); }; REGISTER_SERIALIZABLE(KinemCNDEngine); class KinemCNLEngine : public KinemSimpleShearBox { private : int temoin,// utile pour savoir ou on en est it_stop ; public : void action() ; YADE_CLASS_BASE_DOC_ATTRS_CTOR(KinemCNLEngine,KinemSimpleShearBox, "To apply a constant normal stress shear (i.e. Constant Normal Load : CNL) for a parallelogram box (simple shear box : :yref:`SimpleShear` Preprocessor or scripts/simpleShear.py)\n\nThis engine allows one to translate horizontally the upper plate while the lateral ones rotate so that they always keep contact with the lower and upper walls.\n\nIn fact the upper plate can move not only horizontally but also vertically, so that the normal stress acting on it remains constant (this constant value is not chosen by the user but is the one that exists at the beginning of the simulation)\n\nThe right vertical displacements which will be allowed are computed from the rigidity Kn of the sample over the wall (so to cancel a deltaSigma, a normal dplt deltaSigma*S/(Kn) is set)\n\nThe movement is moreover controlled by the user via a :yref:`shearSpeed` which will be the speed of the upper wall, and by a maximum value of horizontal displacement :yref:`gammalim`, after which the shear stops.\n\n.. note::\n\tNot only the positions of walls are updated but also their speeds, which is all but useless considering the fact that in the contact laws these velocities of bodies are used to compute values of tangential relative displacements.\n\n.. warning::\n\tBecause of this last point, if you want to use later saves of simulations executed with this Engine, but without that stopMovement was executed, your boxes will keep their speeds => you will have to cancel them 'by hand' in the .xml.\n", ((Real,shearSpeed,0.0,,"the speed at wich the shearing is performed : speed of the upper plate [m/s]")) ((Real,gammalim,0.0,,"the value of tangential displacement (of upper plate) at wich the shearing is stopped [m]")) ((Real,gamma,0.0,,"current value of tangential displacement [m]")) ((std::vector,gamma_save,,,"vector with the values of gamma at which a save of the simulation is performed [m]")), // ((Real,coeff_dech,1.0,,"in the case of the use of 'Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity' for ex, where kn(unload)#kn(load). The engine cares to find the value at the first run BROKEN actually")), temoin=0; it_stop=0; ); }; REGISTER_SERIALIZABLE(KinemCNLEngine); class KinemCNSEngine : public KinemSimpleShearBox { private : int temoin,it_stop ; public : void action() ; YADE_CLASS_BASE_DOC_ATTRS_CTOR(KinemCNSEngine,KinemSimpleShearBox, "To apply a Constant Normal Stifness (CNS) shear for a parallelogram box (simple shear)\n\nThis engine, useable in simulations implying one deformable parallelepipedic box, allows one to translate horizontally the upper plate while the lateral ones rotate so that they always keep contact with the lower and upper walls. The upper plate can move not only horizontally but also vertically, so that the normal rigidity defined by DeltaF(upper plate)/DeltaU(upper plate) = constant (= :yref:`KnC` defined by the user).\n\nThe movement is moreover controlled by the user via a :yref:`shearSpeed` which is the horizontal speed of the upper wall, and by a maximum value of horizontal displacement :yref:`gammalim` (of the upper plate), after which the shear stops.\n\n.. note::\n\t not only the positions of walls are updated but also their speeds, which is all but useless considering the fact that in the contact laws these velocities of bodies are used to compute values of tangential relative displacements.\n\n.. warning::\n\tBut, because of this last point, if you want to use later saves of simulations executed with this Engine, but without that stopMovement was executed, your boxes will keep their speeds => you will have to cancel them by hand in the .xml", ((Real,shearSpeed,0.0,,"the speed at wich the shearing is performed : speed of the upper plate [m/s]")) ((Real,gammalim,0.0,,"the value of tangential displacement (of upper plate) at wich the shearing is stopped [m]")) ((Real,gamma,0.0,,"current value of tangential displacement [m]")) ((Real,KnC,10.0e6,,"the normal rigidity chosen by the user [MPa/mm] - the conversion in Pa/m will be made")), temoin=0; it_stop=0; ); }; REGISTER_SERIALIZABLE(KinemCNSEngine); trunk-2017.01a/pkg/dem/KinemSimpleShearBox.cpp000066400000000000000000000131511304022710500210660ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2010 by Jerome Duriez * * jerome.duriez@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include #include #include #include YADE_PLUGIN((KinemSimpleShearBox)) void KinemSimpleShearBox::computeAlpha() { Quaternionr orientationLeftBox,orientationRightBox; orientationLeftBox = leftbox->state->ori; orientationRightBox = rightbox->state->ori; if(orientationLeftBox.matrix()!=orientationRightBox.matrix()) { cout << "WARNING !!! your lateral boxes have not the same orientation, you're not in the case of a box imagined for creating these engines" << endl; } Real angle; AngleAxisr aa(orientationLeftBox); angle = aa.angle(); // orientationLeftBox.ToAxisAngle(axis,angle); alpha=Mathr::PI/2.0-angle; // right if the initial orientation of the body (on the beginning of the simulation) is q =(1,0,0,0) = FromAxisAngle((0,0,1),0) } void KinemSimpleShearBox::computeScontact() { Real Xleft = leftbox->state->pos.x() + (YADE_CAST(leftbox->shape.get()))->extents.x(); Real Xright = rightbox->state->pos.x() - (YADE_CAST(rightbox->shape.get()))->extents.x(); Real Zfront = frontbox->state->pos.z() - YADE_CAST(frontbox->shape.get())->extents.z(); Real Zback = backbox->state->pos.z() + (YADE_CAST(backbox->shape.get()))->extents.z(); Scontact = (Xright-Xleft)*(Zfront-Zback); // that's so the value of section at the middle of the height of the box } void KinemSimpleShearBox::letMove(Real dX, Real dY) { if(LOG) cout << "It : " << scene->iter << endl; // const Real& dt = scene->dt; // dt value obtained by getBoxes_Dt Real Ysup = topbox->state->pos.y(); Real Ylat = leftbox->state->pos.y(); // Changes in vertical and horizontal velocities : topbox->state->vel = Vector3r(dX/dt,dY/dt,0); leftbox->state->vel = Vector3r(dX/(2.0 * dt),dY/(2.0 * dt),0); rightbox->state->vel = Vector3r(dX/(2.0 * dt),dY/(2.0*dt),0); if(LOG) cout << "dY that will be applied by NewtonIntegrator :" << dY << endl; Real Ysup_mod = Ysup + dY; Real Ylat_mod = Ylat + dY; computeAlpha(); // Then computation of the angle of the rotation,dalpha, to be done : if (alpha == Mathr::PI/2.0) // Case of the very beginning { dalpha = - atan( dX / (Ysup_mod -Ylat_mod) ); } else { Real A = (Ysup_mod - Ylat_mod) * 2.0*tan(alpha) / (2.0*(Ysup - Ylat) + dX*tan(alpha) ); dalpha = atan( (A - tan(alpha))/(1.0 + A * tan(alpha))); } Quaternionr qcorr(AngleAxisr(dalpha,Vector3r::UnitZ())); // Rotation is applied through velocities (and NewtonIntegrator) leftbox->state->angVel = Vector3r(0,0,1)*dalpha/dt; rightbox->state->angVel = Vector3r(0,0,1)*dalpha/dt; } void KinemSimpleShearBox::stopMovement() { // upper plate's speed is zeroed topbox->state->vel = Vector3r(0,0,0); // same for left box leftbox->state->vel = Vector3r(0,0,0); leftbox->state->angVel = Vector3r(0,0,0); // and for rightbox rightbox->state->vel = Vector3r(0,0,0); rightbox->state->angVel = Vector3r(0,0,0); } void KinemSimpleShearBox::computeStiffness() { int nbre_contacts = 0; stiffness=0.0; InteractionContainer::iterator ii = scene->interactions->begin(); InteractionContainer::iterator iiEnd = scene->interactions->end(); for( ; ii!=iiEnd ; ++ii ) { if ((*ii)->isReal()) { const shared_ptr& contact = *ii; Real fn = (static_cast(contact->phys.get()))->normalForce.norm(); if (fn!=0) { int id1 = contact->getId1(), id2 = contact->getId2(); if ( id_topbox==id1 || id_topbox==id2 ) { FrictPhys* currentContactPhysics = static_cast ( contact->phys.get() ); stiffness += currentContactPhysics->kn; nbre_contacts += 1; } } } } if(LOG) cout << "nbre billes en contacts : " << nbre_contacts << endl; if(LOG) cout << "rigidite echantillon calculee : " << stiffness << endl; } void KinemSimpleShearBox::getBoxes_Dt() { leftbox = Body::byId(id_boxleft); rightbox = Body::byId(id_boxright); frontbox = Body::byId(id_boxfront); backbox = Body::byId(id_boxback); topbox = Body::byId(id_topbox); boxbas = Body::byId(id_boxbas); dt = scene->dt; } void KinemSimpleShearBox::computeDY(Real KnC) { scene->forces.sync(); Vector3r fSup=scene->forces.getForce(id_topbox); if(firstRun) { alpha=Mathr::PI/2.0;; y0 = topbox->state->pos.y(); f0 = fSup.y(); firstRun=false; } computeStiffness(); Real hCurrent = topbox->state->pos.y(); computeScontact(); Real fDesired = f0 + KnC * 1.0e9 * Scontact * (hCurrent-y0); // The value of the force desired, with the fact that KnC is in MPa/mm if( stiffness==0 ) { deltaH=0; cerr << "Stiffness(sample) = 0 => DNC in fact : not CNL or CNS..." << endl; } else { deltaH = ( fSup.y() - fDesired )/(stiffness); } if(LOG) cout << "Alors q je veux KnC = " << KnC << " depuis f0 = " << f0 << " et y0 = " << y0 << endl; if(LOG) cout << "deltaH a permettre normalement :" << deltaH << endl; deltaH = (1-wallDamping)*deltaH; if(LOG) cout << "deltaH apres amortissement :" << deltaH << endl; if(std::abs(deltaH) > max_vel*scene->dt) { deltaH=deltaH/std::abs(deltaH)*max_vel*scene->dt; if(LOG) cout << "Correction appliquee pour ne pas depasser vmax(comp)" << endl; } } trunk-2017.01a/pkg/dem/KinemSimpleShearBox.hpp000066400000000000000000000114161304022710500210750ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2010 by Jerome Duriez * * jerome.duriez@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include class KinemSimpleShearBox : public BoundaryController { protected : Real Scontact // computed by computeScontact() ,dt // value of the time step, obtained in getBoxes_Dt ,stiffness // the normal stifness on the sample acting below the upper plate. Computed by computeStiffness ,dalpha // the increment over alpha, due to vertical displacement of upper box ,deltaH // the vertical increment of displacement to allow on the upper plate on this time step to verify either the constant normal stress or the constant normal stifness. Computed here by computeDY(..) ; shared_ptr leftbox; shared_ptr rightbox; shared_ptr frontbox; shared_ptr backbox; shared_ptr topbox; shared_ptr boxbas; void computeAlpha() ,computeScontact() ,stopMovement() // to cancel all velocities when end of the loading is reached ,letMove(Real dgamma,Real dH) //dgamma and dH being computed by different ways in the different Kinem... Engines ,computeStiffness() // computes the stiffness of the contact sample - upper side. Useful for CNL and CNS loads ,computeDY(Real KnC) // computes vertical displacement to perform to obey to the stiffness of the shear wanted : KnC. Useful for CNL (for which KnC = 0) and CNS loads ,getBoxes_Dt() ; YADE_CLASS_BASE_DOC_ATTRS_CTOR(KinemSimpleShearBox,BoundaryController, "This class is supposed to be a mother class for all Engines performing loadings on the simple shear box of :yref:`SimpleShear`. It is not intended to be used by itself, but its declaration and implentation will thus contain all what is useful for all these Engines. The script simpleShear.py illustrates the use of the various corresponding Engines.", ((Real,alpha,Mathr::PI/2.0,,"the angle from the lower box to the left box (trigo wise). Measured by this Engine. Has to be saved, but not to be changed by the user.")) ((std::vector,temoin_save,,,"vector (same length as 'gamma_save' for ex), with 0 or 1 depending whether the save for the corresponding value of gamma has been done (1) or not (0). Has to be saved, but not to be changed by the user.")) ((Body::id_t,id_topbox,3,,"the id of the upper wall")) ((Body::id_t,id_boxbas,1,,"the id of the lower wall")) ((Body::id_t,id_boxleft,0,,"the id of the left wall")) ((Body::id_t,id_boxright,2,,"the id of the right wall")) ((Body::id_t,id_boxfront,5,,"the id of the wall in front of the sample")) ((Body::id_t,id_boxback,4,,"the id of the wall at the back of the sample")) ((Real,max_vel,1.0,,"to limit the speed of the vertical displacements done to control $\\sigma$ (CNL or CNS cases) [$m/s$]")) ((Real,wallDamping,0.2,,"the vertical displacements done to to control $\\sigma$ (CNL or CNS cases) are in fact damped, through this wallDamping")) ((bool,firstRun,true,,"boolean set to false as soon as the engine has done its job one time : useful to know if initial height of, and normal force sustained by, the upper box are known or not (and thus if they have to be initialized). Has to be saved, but not to be changed by the user.")) ((Real,f0,0.0,,"the (vertical) force acting on the upper plate on the very first time step (determined by the Engine). Controls of the loadings in case of :yref:`KinemCNSEngine` or :yref:`KinemCNLEngine` will be done according to this initial value [$N$]. Has to be saved, but not to be changed by the user.")) ((Real,y0,0.0,,"the height of the upper plate at the very first time step : the engine finds its value [$m$]. Has to be saved, but not to be changed by the user.")) ((bool,LOG,false,,"boolean controling the output of messages on the screen")) //FIXME : surely something better to use here ((string,Key,"",,"string to add at the names of the saved files")), /* leftbox = Body::byId(id_boxleft,scene); rightbox = Body::byId(id_boxright,scene); frontbox = Body::byId(id_boxfront,scene); backbox = Body::byId(id_boxback,scene); topbox = Body::byId(id_topbox,scene); boxbas = Body::byId(id_boxbas,scene);*/ Scontact = 0.0; dt = 0.0; stiffness=0.0; dalpha=0.0; deltaH=0.0; ); }; REGISTER_SERIALIZABLE(KinemSimpleShearBox); trunk-2017.01a/pkg/dem/KnKsLaw.cpp000066400000000000000000000266441304022710500165420ustar00rootroot00000000000000#ifdef YADE_POTENTIAL_PARTICLES #include "KnKsLaw.hpp" #include #include #include #include YADE_PLUGIN((Law2_SCG_KnKsPhys_KnKsLaw)(Ip2_FrictMat_FrictMat_KnKsPhys)(KnKsPhys) ); /********************** Law2_Dem3DofGeom_RockPMPhys_Rpm ****************************/ CREATE_LOGGER(Law2_SCG_KnKsPhys_KnKsLaw); bool Law2_SCG_KnKsPhys_KnKsLaw::go(shared_ptr& ig, shared_ptr& ip, Interaction* contact) { //const Real& dt = scene->dt; int id1 = contact->getId1(); int id2 = contact->getId2(); ScGeom* geom= static_cast(ig.get()); KnKsPhys* phys = static_cast(ip.get()); State* de1 = Body::byId(id1,scene)->state.get(); State* de2 = Body::byId(id2,scene)->state.get(); Shape* shape1 = Body::byId(id1,scene)->shape.get(); Shape* shape2 = Body::byId(id2,scene)->shape.get(); PotentialParticle *s1=static_cast(shape1); PotentialParticle *s2=static_cast(shape2); Vector3r& shearForce = phys->shearForce; Real un=geom->penetrationDepth; TRVAR3(geom->penetrationDepth,de1->se3.position,de2->se3.position); /* Need to initialise in python. In the 1st time step. All the particles in contact (controlled by initialOverlap) are identified. The interactions are set to tensile and cohesive (tensionBroken = false and cohesionBroken = false). If there is no initial tension or cohesion, the contact law is run in a tensionless or cohesionless mode */ if(geom->penetrationDepth <0.0 ) { if (neverErase) { phys->shearForce = Vector3r::Zero(); phys->normalForce = Vector3r::Zero(); phys->normalViscous = Vector3r::Zero(); geom->normal = Vector3r::Zero(); phys->tensionBroken = true; } else { scene->interactions->requestErase(id1,id2); return false; } return true; } //Vector3r shearForceBeforeRotate = shearForce; Vector3r shiftVel = Vector3r(0,0,0); //scene->isPeriodic ? (Vector3r)((scene->cell->velGrad*scene->cell->Hsize)*Vector3r((Real) contact->cellDist[0],(Real) contact->cellDist[1],(Real) contact->cellDist[2])) : Vector3r::Zero(); geom->rotate(shearForce); //AndGetShear(shearForce,phys->prevNormal,de1,de2,dt,shiftVel,/*avoid ratcheting*/false); //Vector3r shearForceAfterRotate = shearForce; //Linear elasticity giving "trial" shear force Vector3r shift2(0,0,0); Vector3r incidentV = geom->getIncidentVel(de1, de2, scene->dt, shift2, shiftVel, /*preventGranularRatcheting*/false ); Vector3r incidentVn = geom->normal.dot(incidentV)*geom->normal; // contact normal velocity Vector3r incidentVs = incidentV-incidentVn; // contact shear velocity Vector3r shearIncrement=incidentVs*scene->dt; phys->shearDir = shearIncrement; phys->shearIncrementForCD += shearIncrement.norm(); double du = 0.0; //double debugFn = 0.0; //double u_prev = fabs(phys->u_cumulative); if(phys->shearDir.norm() > pow(10,-15)) { phys->shearDir.normalize(); } double degradeLength = phys->brittleLength; /*jointLength = 100u_peak */ /* Elastic and plastic displacement can have negative signs but must be consistent throughout the simulation */ if(phys->initialShearDir.norm() < pow(10,-11)) { phys->initialShearDir = phys->shearDir; du = shearIncrement.norm(); if(fabs(phys->mobilizedShear)>0.99999) { phys->u_cumulative += du; phys->cumulative_us += du; } else { phys->u_elastic +=du; } } else { du = Mathr::Sign(phys->initialShearDir.dot(phys->shearDir))*shearIncrement.norm(); //check cumulative shear displacement if(fabs(phys->mobilizedShear) > 0.99999) { if(du>0.0) { //if negative it means it is unloading phys->u_cumulative += du; phys->cumulative_us += du; } else { phys->u_elastic +=du; } } else { phys->u_elastic +=du; } } /* Original */ if(phys->twoDimension) { phys->contactArea = phys->unitWidth2D*phys->jointLength; } if(s1->isBoundary == true || s2->isBoundary==true) { phys->tensionBroken = true; phys->cohesionBroken = true; } if(!Talesnick) { un = un-initialOverlapDistance; if (phys->jointType==3) { phys->prevSigma = un*phys->kn_i/(1.0-un/phys->maxClosure); } else { phys->prevSigma = phys->kn*un; } //} phys->normalForce = phys->prevSigma*std::max(pow(10,-15),phys->contactArea)*geom->normal; } phys->Knormal_area = phys->kn*std::max(pow(10,-8),phys->contactArea); if((un <0.0 && fabs(phys->prevSigma)>phys->tension && phys->tensionBroken == false /* first time tension is broken */) || (un<0.0 && phys->tensionBroken==true)) { if (neverErase) { phys->shearForce = Vector3r::Zero(); phys->normalForce = Vector3r::Zero(); phys->normalViscous = Vector3r::Zero(); geom->normal = Vector3r::Zero(); phys->tensionBroken = true; } else { return false; } return true; } /*ORIGINAL */ Vector3r c1x = geom->contactPoint - de1->pos; Vector3r c2x = geom->contactPoint - de2->pos; incidentV = (de2->vel+de2->angVel.cross(c2x)) - (de1->vel+de1->angVel.cross(c1x)); incidentVn = geom->normal.dot(incidentV)*geom->normal; // contact normal velocity incidentVs = incidentV-incidentVn; // contact shear velocity shearIncrement=incidentVs*scene->dt; if(!Talesnick) { double Ks=0.0; if(phys->jointType == 3) { Ks = phys->ks_i*pow(phys->prevSigma,0.6); } else { Ks = phys->ks; } shearForce -= Ks*shearIncrement*std::max(pow(10,-11),phys->contactArea); } phys->Kshear_area = phys->ks*std::max(pow(10,-11),phys->contactArea); const shared_ptr& b1=Body::byId(id1,scene); const shared_ptr& b2=Body::byId(id2,scene); Real mbar = (!b1->isDynamic() && b2->isDynamic()) ? de2->mass : ((!b2->isDynamic() && b1->isDynamic()) ? de1->mass : (de1->mass*de2->mass / (de1->mass + de2->mass))); // get equivalent mass if both bodies are dynamic, if not set it equal to the one of the dynamic body Real Cn_crit = 2.*sqrt(mbar*phys->Knormal_area); // Knormal_area Critical damping coefficient (normal direction) Real Cs_crit = 2.*sqrt(mbar*phys->Kshear_area); // Kshear_area Critical damping coefficient (shear direction) // Note: to compare with the analytical solution you provide cn and cs directly (since here we used a different method to define c_crit) double cn = Cn_crit*phys->viscousDamping; // Damping normal coefficient double cs = Cs_crit*phys->viscousDamping; // Damping tangential coefficient // add normal viscous component if damping is included //double maxFnViscous = phys->normalForce.norm(); phys->normalViscous = cn*incidentVn; //if(phys->normalViscous.norm() > maxFnViscous){ // phys->normalViscous = phys->normalViscous * maxFnViscous/phys->normalViscous.norm(); //} phys->normalForce -= phys->normalViscous; //double baseElevation = geom->contactPoint.z(); /* Water pressure, heat effect */ /* strength degradation */ const double PI = std::atan(1.0)*4; double tan_effective_phi = 0.0; if(s1->isBoundary==true || s2->isBoundary == true || phys->jointType==2 ) { // clay layer at boundary; phys->effective_phi = phys->phi_b; // - 3.25*(1.0-exp(-fabs(phys->cumulative_us)/0.4)); tan_effective_phi = tan(phys->effective_phi/180.0*PI); } else if(phys->intactRock == true) { phys->effective_phi = phys->phi_r + (phys->phi_b-phys->phi_r)*(exp(-fabs(phys->u_cumulative)/degradeLength)); tan_effective_phi = tan(phys->effective_phi/180.0*PI); } else { phys->effective_phi = phys->phi_b; tan_effective_phi = tan(phys->effective_phi/180.0*PI); } /* shear loss */ Vector3r dampedShearForce = shearForce; double cohesiveForce = phys->cohesion*std::max(pow(10,-11),phys->contactArea); Real maxFs = cohesiveForce; if (un>0.0 /*compression*/) { double fN = phys->normalForce.norm(); if(phys->intactRock == true) { if (phys->cohesionBroken == true && allowBreakage == true) { maxFs = std::max( fN,0.0)*tan_effective_phi; } else { maxFs = cohesiveForce+std::max( fN,0.0)*tan_effective_phi; } } else { maxFs = std::max( fN,0.0)*tan_effective_phi; } } if( shearForce.norm() > maxFs ) { Real ratio = maxFs / shearForce.norm(); shearForce *= ratio; dampedShearForce = shearForce; if(allowBreakage == true) { phys->cohesionBroken = true; } phys->shearViscous = Vector3r(0,0,0); } else { /* no damping when it slides */ phys->shearViscous = cs*incidentVs; dampedShearForce = shearForce - phys->shearViscous; } if(shearForce.norm() < pow(10,-11) ) { phys->mobilizedShear = 1.0; } else { phys->mobilizedShear = shearForce.norm()/maxFs; } //we need to use correct branches in the periodic case, the following apply for spheres only Vector3r force = -phys->normalForce-dampedShearForce; if(std::isnan(force.norm())) { //std::cout<<"shearForce: "<normalForce<<", debugFn: "<normalViscous<<", normal: "<normal<<", geom normal: "<normal<<", effective_phi: "<effective_phi<<", shearIncrement: "<forces.addForce(id1,force); scene->forces.addForce(id2,-force); //Vector3r normal = geom->normal; scene->forces.addTorque(id1,c1x.cross(force)); scene->forces.addTorque(id2,-(c2x).cross(force)); phys->prevNormal = geom->normal; return true; } CREATE_LOGGER(Ip2_FrictMat_FrictMat_KnKsPhys); void Ip2_FrictMat_FrictMat_KnKsPhys::go(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction) { const double PI = 3.14159265358979323846; if(interaction->phys) return; ScGeom* scg=YADE_CAST(interaction->geom.get()); assert(scg); const shared_ptr& sdec1 = YADE_PTR_CAST(b1); const shared_ptr& sdec2 = YADE_PTR_CAST(b2); shared_ptr contactPhysics(new KnKsPhys()); //interaction->interactionPhysics = shared_ptr(new MomentPhys()); //const shared_ptr& contactPhysics = YADE_PTR_CAST(interaction->interactionPhysics); /* From interaction physics */ Real fa = sdec1->frictionAngle; Real fb = sdec2->frictionAngle; /* calculate stiffness */ Real Kn= Knormal; Real Ks= Kshear; /* Pass values calculated from above to CSPhys */ contactPhysics->viscousDamping = viscousDamping; contactPhysics->useOverlapVol = useOverlapVol; contactPhysics->kn = Kn; contactPhysics->ks = Ks; contactPhysics->kn_i = Kn; contactPhysics->ks_i = Ks; contactPhysics->u_peak = u_peak; contactPhysics->maxClosure = maxClosure; contactPhysics->cohesionBroken = cohesionBroken; contactPhysics->tensionBroken = tensionBroken; contactPhysics->unitWidth2D = unitWidth2D; contactPhysics->frictionAngle = std::min(fa,fb); if(!useFaceProperties) { contactPhysics->phi_r = std::min(fa,fb)/PI*180.0; contactPhysics->phi_b = contactPhysics->phi_r; } contactPhysics->tanFrictionAngle = std::tan(contactPhysics->frictionAngle); //contactPhysics->initialOrientation1 = Body::byId(interaction->getId1())->state->ori; //contactPhysics->initialOrientation2 = Body::byId(interaction->getId2())->state->ori; contactPhysics->prevNormal = scg->normal; //This is also done in the Contact Law. It is not redundant because this class is only called ONCE! contactPhysics->calJointLength = calJointLength; contactPhysics->twoDimension = twoDimension; contactPhysics->useFaceProperties = useFaceProperties; contactPhysics->brittleLength = brittleLength; interaction->phys = contactPhysics; } CREATE_LOGGER(KnKsPhys); /* KnKsPhys */ KnKsPhys::~KnKsPhys() {} #endif // YADE_POTENTIAL_PARTICLES trunk-2017.01a/pkg/dem/KnKsLaw.hpp000066400000000000000000000235421304022710500165410ustar00rootroot00000000000000#pragma once #ifdef YADE_POTENTIAL_PARTICLES #include #include #include #include #include #include #include class KnKsPhys: public FrictPhys { public: virtual ~KnKsPhys(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(KnKsPhys,FrictPhys,"EXPERIMENTAL. IPhys originally for potential particles", ((vector,lambdaIPOPT,0.0,,"Lagrange multiplier for equality constraints")) ((vector,cstatCPLEX,,,"Lagrange multiplier for equality constraints")) ((vector,rstatCPLEX,,,"Lagrange multiplier for equality constraints")) ((Real,frictionAngle,0.0,,"fric angle")) ((Real,tanFrictionAngle,0.0,,"tangent of fric angle")) ((Vector3r,contactDetectionPt,Vector3r(0,0,0),,"contact detection result")) ((Real, viscousDamping, 0.8, ,"viscousDamping")) ((Real, unitWidth2D, 1.0, ,"viscousDamping")) ((Real, maxClosure, 0.0002, ,"vmi")) ((Real, u_peak, 0.05, ,"peak shear displacement")) ((Real, u_elastic, 0.0, ,"elastic shear displacement")) ((double, brittleLength, 5.0, ,"brittle rock")) ((double, kn_i, 5.0, ,"initial normal stiffness")) ((double, ks_i, 5.0, ,"initial shear stiffness")) ((Vector3r, normalViscous, Vector3r(0,0,0), ,"viscousDamping")) ((Vector3r, shearViscous, Vector3r(0,0,0), ,"viscousDamping")) ((double, hwater, 0.0, ,"height of pore water")) ((bool, rockJointContact, false, ,"brittle rock")) ((bool, intactRock, false, ,"brittle rock")) ((int, jointType, 0, ,"jointType")) ((Real,Kshear_area,0.0,,"kshear area")) ((Real,Knormal_area, 0.0,,"knormal area")) ((Vector3r, shearDir, Vector3r(0,0,0), ,"shear direction")) ((vector, shearForces, , ,"shear direction")) ((Vector3r, shear, Vector3r(0,0,0),, "shear displacement")) ((Vector3r, prevNormal, Vector3r(0.0,0.0,0.0),, "previous Normal")) ((Vector3r, normal, Vector3r(0.0,0.0,0.0),, " normalVector")) ((vector, pointsArea, ,, "intermediate contact points")) ((vector, pointsShear, ,, "points to calculate shear")) ((vector, areaShear, ,, "area to attribute shear")) ((vector, overlapDistances, ,, "area to attribute shear")) ((Real, finalSize, 0.0,, "finalgridsize")) ((int, finalGridNo, 0,, "final number of grids")) ((vector, dualityGap, , ,"duality gap for SOCP")) ((bool, warmstart, false, ,"warmstart for SOCP")) ((int, generation, 0,, "number of subdivisions")) ((int, triNoMain, 24,, "number of subdivisions")) ((int, triNoSub, 6,, "number of subdivisions")) ((Vector3r, initial1, Vector3r(0.0,0.0,0.0),, "midpoint")) ((Vector3r, ptOnP1, Vector3r(0.0,0.0,0.0),, "pt on particle")) ((Vector3r, ptOnP2, Vector3r(0.0,0.0,0.0),, " pt on particle 2")) ((vector, redundantA, , ,"activePlanes for interaction.id1")) ((vector, redundantB, , ,"activePlanes for interaction.id1")) ((vector, activePlanes1, , ,"activePlanes for interaction.id1")) ((vector, activePlanes2, , ,"activePlanes for interaction.id2")) ((vector, activeA1, , ,"activePlanes for interaction.id2")) ((vector, activeB1, , ,"activePlanes for interaction.id2")) ((vector, activeC1, , ,"activePlanes for interaction.id2")) ((vector, activeD1, , ,"activePlanes for interaction.id2")) ((vector, activeA2, , ,"activePlanes for interaction.id2")) ((vector, activeB2, , ,"activePlanes for interaction.id2")) ((vector, activeC2, , ,"activePlanes for interaction.id2")) ((vector, activeD2, , ,"activePlanes for interaction.id2")) ((int, noActive1, 0, ,"activePlanes for interaction.id1")) ((int, noActive2,0 , ,"activePlanes for interaction.id2")) ((int, smallerID,1 , ,"id of particle with smaller plane")) ((Real, cumulative_us, 0.0,, "cumulative translation")) ((Real, cumulativeRotation, 0.0,, "cumulative rotation")) ((Real, mobilizedShear, , ,"mobilizedShear")) ((Real, contactArea, 0.0, ,"contactArea")) ((Real, radCurvFace, , ,"face")) ((double, prevJointLength, 0.0, ,"previous joint length")) ((Real, radCurvCorner, , ,"corners")) ((Real, prevSigma,0.0 , ,"previous normal stress")) ((vector, prevSigmaList,0.0 , ,"previous normal stress")) ((bool, calJointLength, false,, "calculate joint length")) ((bool, useOverlapVol, false,, "calculate overlap volume")) ((bool, calContactArea, false,, "calculate contact area")) ((double, jointLength, 0.0,, "approximatedJointLength")) ((double, shearIncrementForCD, 0.0,, "toSeeWhether it is necessary to update contactArea")) ((Real, overlappingVol,0.0 , ,"overlapping vol")) ((Real, overlappingVolMulti,0.0 , ,"overlapping vol")) ((double, gap_normalized, 0.0,, "distance between particles normalized by particle size. Estimated using Taubin Distance ")) ((double, gap, 0.0,, "distance between particles normalized by particle size. Estimated using Taubin Distance ")) ((bool, findCurv, false,, "to get radius of curvature")) ((bool, useFaceProperties, false,,"boolean to get face properites")) ((Real, cohesion, 0.0, ,"cohesion")) ((Real, tension, 0.0, ,"tension")) ((bool, cohesionBroken, true, ,"cohesion already broken")) ((bool, tensionBroken, true, ,"tension already broken")) ((bool, twoDimension, false, ,"tension already broken")) ((Real, phi_b, 0.0, ,"basic friction angle (degrees)")) ((Real, phi_r, 0.0, ,"residual friction angle (degrees)")) ((Real, asperity, 3.0, ,"asperity height")) ((Real, JRC, 0.0, ,"Joint Roughness Coefficient")) ((Real, JRCmobilized, 0.0, ,"Joint Roughness Coefficient")) ((Real, JCS, 0.0, ,"Joint Roughness Coefficient")) ((Real, sigmaC,0.0 , ,"Joint Roughness Coefficient")) ((Real, u_dilate,0.0 , ,"dilation distance")) ((Real, dilation_angle,0.0 , ,"dilation distance")) /* pore water pressure */ ((Real, lambda0,0.0 , ,"initial pore water pressure to stress ratio")) ((Real, lambda_present,0.0 , ,"Voight&Faust (1992) Sitar et al. (2005)")) ((Real, u_cumulative, 0.0,, "cumulative translation")) ((Vector3r, prevShearDir, Vector3r(0.0,0.0,0.0),, "previous shear direction")) ((Vector3r, initialShearDir, Vector3r(0.0,0.0,0.0),, "previous shear direction")) ((double, delta_porePressure, 0.0,, "change in pore water pressure")) ((double, porePressure, 0.0,, "pore water pressure")) ((double, bandThickness, 0.1,, "clay layer thickness")) ((double, heatCapacities, 0.0,, "clay layer thickness")) ((double, effective_phi, 0.0,, "friction angle in clay after displacement")) ((double, prevOverlap, 0.0,, "friction angle in clay after displacement")) ((Real, h, 0.0,,"cd")), //((Real, cumulativeRotation, 0.0,, "cumulative rotation")) //((Quaternionr, initialOrientation1, Quaternionr(1.0,0.0,0.0,0.0),, "orientation1")) //((Quaternionr, initialOrientation2, Quaternionr(1.0,0.0,0.0,0.0),, "orientation2")), createIndex(); ); REGISTER_CLASS_INDEX(KnKsPhys,FrictPhys); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(KnKsPhys); class Ip2_FrictMat_FrictMat_KnKsPhys: public IPhysFunctor { public: virtual void go(const shared_ptr& pp1, const shared_ptr& pp2, const shared_ptr& interaction); YADE_CLASS_BASE_DOC_ATTRS(Ip2_FrictMat_FrictMat_KnKsPhys,IPhysFunctor,"EXPERIMENTAL. Ip2 functor for :yref:`KnKsPhys`", ((Real,Knormal,0.0,,"allows user to input values directly from python scripts")) ((Real,Kshear,0.0,,"allows user to input values directly from python scripts")) ((Real, unitWidth2D, 1.0, ,"viscousDamping")) ((double, brittleLength, 3.0, ,"brittle rock")) ((double, kn_i, 0.002, ,"brittle rock")) ((double, ks_i, 0.002, ,"brittle rock")) ((double, u_peak, -1.0, ,"brittle rock")) ((double, maxClosure, 0.002, ,"brittle rock")) ((Real, viscousDamping, 0.8, ,"viscousDamping")) ((Real, cohesion, 0.0, ,"viscousDamping")) ((Real, tension, 0.0, ,"viscousDamping")) ((bool, cohesionBroken, true, ,"cohesion")) ((bool, tensionBroken, true, ,"tension")) ((Real, phi_b, 0.0, ,"viscousDamping")) ((bool, useOverlapVol, false,, "calculate overlap volume")) ((bool, useFaceProperties, false,,"boolean to get face properites")) ((bool, calJointLength, false,, "calculate joint length")) ((bool, twoDimension, false, ,"tension already broken")) ); FUNCTOR2D(FrictMat,FrictMat); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Ip2_FrictMat_FrictMat_KnKsPhys); class Law2_SCG_KnKsPhys_KnKsLaw: public LawFunctor { public: static Real Real0; //OpenMPAccumulator plasticDissipation; virtual bool go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I); FUNCTOR2D(ScGeom,KnKsPhys); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Law2_SCG_KnKsPhys_KnKsLaw,LawFunctor,"Law for linear compression, without cohesion and Mohr-Coulomb plasticity surface.\n\n.. note::\n This law uses :yref:`ScGeom`; there is also functionally equivalent :yref:`Law2_Dem3DofGeom_FrictPhys_Basic`, which uses :yref:`Dem3DofGeom` (sphere-box interactions are not implemented for the latest).", ((bool,neverErase,false,,"Keep interactions even if particles go away from each other (only in case another constitutive law is in the scene, e.g. :yref:`Law2_ScGeom_CapillaryPhys_Capillarity`)")) ((bool,preventGranularRatcheting,false,,"bool to avoid granular ratcheting")) ((bool,traceEnergy,false,,"Define the total energy dissipated in plastic slips at all contacts.")) ((bool,Talesnick,false,,"Define the total energy dissipated in plastic slips at all contacts.")) ((double,waterLevel,0.0,,"Define the total energy dissipated in plastic slips at all contacts.")) ((bool, allowBreakage, false, ,"cohesion = 0, once broken")) ((double,initialOverlapDistance,0.0,,"initial overlap distance")) ,, ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_SCG_KnKsPhys_KnKsLaw); #endif // YADE_POTENTIAL_PARTICLES trunk-2017.01a/pkg/dem/KnKsPBLaw.cpp000077500000000000000000000672771304022710500167760ustar00rootroot00000000000000#ifdef YADE_POTENTIAL_BLOCKS #include"KnKsPBLaw.hpp" #include #include #include #include YADE_PLUGIN((Law2_SCG_KnKsPBPhys_KnKsPBLaw)(Ip2_FrictMat_FrictMat_KnKsPBPhys)(KnKsPBPhys) ); /********************** Law2_Dem3DofGeom_RockPMPhys_Rpm ****************************/ CREATE_LOGGER(Law2_SCG_KnKsPBPhys_KnKsPBLaw); bool Law2_SCG_KnKsPBPhys_KnKsPBLaw::go(shared_ptr& ig /* contact geometry */, shared_ptr& ip /* contact physics */, Interaction* contact){ const Real& dt = scene->dt; /* size of time step */ int id1 = contact->getId1(); /* id of Body1 */ int id2 = contact->getId2(); /* id of Body2 */ ScGeom* geom= static_cast(ig.get()); /* contact geometry */ KnKsPBPhys* phys = static_cast(ip.get()); /* contact physics */ State* de1 = Body::byId(id1,scene)->state.get(); /* pointer to Body1 */ State* de2 = Body::byId(id2,scene)->state.get(); /* pointer to Body2 */ Shape* shape1 = Body::byId(id1,scene)->shape.get(); /* pointer to Shape1 */ Shape* shape2 = Body::byId(id2,scene)->shape.get(); /* pointer to Shape2 */ PotentialBlock *s1=static_cast(shape1); PotentialBlock *s2=static_cast(shape2); Vector3r& shearForce = phys->shearForce; /* shear force at previous timestep */ Real un=geom->penetrationDepth; /* overlap distance */ TRVAR3(geom->penetrationDepth,de1->se3.position,de2->se3.position); /* ERASE CONTACT OR RESET PARAMETERS IF NO OVERLAP */ if(geom->penetrationDepth <0.0 ){ if (neverErase) { phys->shearForce = Vector3r::Zero(); phys->normalForce = Vector3r::Zero(); phys->normalViscous = Vector3r::Zero(); geom->normal = Vector3r::Zero(); phys->tensionBroken = true; }else{ scene->interactions->requestErase(id1,id2); return false; } return true; } Vector3r shiftVel = Vector3r(0,0,0); //scene->isPeriodic ? (Vector3r)((scene->cell->velGrad*scene->cell->Hsize)*Vector3r((Real) contact->cellDist[0],(Real) contact->cellDist[1],(Real) contact->cellDist[2])) : Vector3r::Zero(); geom->rotateNonSpherical(shearForce); /*rotate shear force according to new contact plane (normal) */ Vector3r oriShear = shearForce; Vector3r oriNormalF = phys->normalForce; /* CALCULATE SHEAR INCREMENT */ Vector3r shift2(0,0,0); Vector3r incidentV = geom->getIncidentVel(de1, de2, scene->dt, shift2, shiftVel, /*preventGranularRatcheting*/false ); /* get relative velocity */ Vector3r incidentVn = geom->normal.dot(incidentV)*geom->normal; /* get normal relative velocity */ Vector3r incidentVs = incidentV-incidentVn; /* get shear relative velocity */ Vector3r shearIncrement=incidentVs*scene->dt; /* calculate shear increment from shear velocity */ double du = shearIncrement.norm(); /* magnitude of shear increment */ phys->shearDir = shearIncrement; /* get shear direction */ if(phys->shearDir.norm() > pow(10,-15)){ phys->shearDir.normalize(); } if(phys->twoDimension) { phys->contactArea = phys->unitWidth2D*phys->jointLength;} /* contact area in 2D */ if(s1->isBoundary == true || s2->isBoundary==true){phys->tensionBroken = true; phys->cohesionBroken = true;} /* no cohesion and tension if the contact is a boundary*/ /* NORMAL CONTACT FORCE */ double normalStiffness = phys->kn; /* use default stiffness values */ if(Talesnick){ //phys->prevSigma = phys->kn*std::max(un,(Real) 0.0); //phys->normalForce=phys->prevSigma*phys->normal*std::max(pow(10,-15),phys->contactArea); //#if 0 //#if 0 /* linear */ //un = un - 8.0*pow(10.0,-5); double A = 0.5*4.0*pow(10.0,9);//*pow(10.0,9); double B = 0.5*7.4*pow(10.0,4); double expTerm = B*(std::max(un,0.0)) + std::log(A) ; phys->prevSigma = std::max(( (std::exp(expTerm)-A)) / B, 0.0); double Fn = phys->prevSigma*std::max(pow(10,-15),phys->contactArea); phys->normalForce = Fn*geom->normal; phys->kn = (A+ B*phys->prevSigma); //#endif #if 0 /* power */phys->h double Fn = pow(525000*std::max(un,(Real) 0),1.0/0.25)*std::max(pow(10,-11),phys->contactArea); phys->kn = 2.1*pow(10.0,6)*pow(phys->prevSigma,0.75); #endif #if 0 double A = 7.0*pow(10.0,13);//*pow(10.0,9); double B = 1.0*pow(10.0,6); phys->prevSigma = (A*un)*un - B*un; double Fn = phys->prevSigma*std::max(pow(10,-15),phys->contactArea); phys->normalForce = Fn*geom->normal; phys->kn = A*2.0*un - pow(10,6); #endif #if 0 //power double A = 2.1*pow(10.0,6); //4.2*pow(10.0,5); double B = 0.75; //0.88; phys->prevSigma = pow( (1.0-B)*A*std::max(un, 0.0),1.0/(1.0-B) ); double Fn = phys->prevSigma*std::max(pow(10,-14),phys->contactArea); phys->kn = A*pow(phys->prevSigma,B); //1.0/(1.0-B)*pow( (1.0-B)*A,1.0/(1.0-B) ) * pow(std::max(un,0.0), B/(1.0-B)); //A*pow(phys->prevSigma,B); // phys->normalForce = Fn*geom->normal; #endif if (phys->prevSigma > pow(10.0,15) /* || Fn < 0.0 */){ std::cout<<"prevSigma: "<prevSigma/* <<", Fn: "<Knormal_area = phys->kn*std::max(pow(10,-15),phys->contactArea); }else{ if(s1->isBoundary == true || s2->isBoundary==true|| s1->isEastBoundary == true || s2->isEastBoundary==true ){ normalStiffness = phys->kn_i; /* use special stiffness for boundaries */ phys->prevSigma = normalStiffness*un; phys->normalForce = phys->prevSigma*std::max(pow(10,-15),phys->contactArea)*geom->normal; //std::max(pow(10,-15),phys->contactArea)* phys->Knormal_area = normalStiffness*std::max(pow(10,-15),phys->contactArea); }else{ if(s1->isLining==true){normalStiffness=s1->liningStiffness; un = un-s1->liningTensionGap; phys->prevSigma = normalStiffness*un;} else if(s2->isLining==true){normalStiffness=s2->liningStiffness; un = un-s2->liningTensionGap; phys->prevSigma = normalStiffness*un;} else{ un = un-initialOverlapDistance; if(phys->tensionBroken == true){ //if(allowBreakage == false && un > 0.0){phys->tensionBroken = false;} phys->prevSigma = normalStiffness*std::max(un,0.0); }else{ phys->prevSigma = normalStiffness*un; } } /* GENERAL CASE - initialOverlapDistance is the offset distance for tension overlap, i.e. negative overlap */ phys->normalForce = phys->prevSigma*std::max(pow(10,-15),phys->contactArea)*geom->normal; phys->Knormal_area = normalStiffness*std::max(pow(10,-15),phys->contactArea); } } /* ERASE CONTACT IF TENSION IS BROKEN */ if((un <0.0 && fabs(phys->prevSigma)>phys->tension && phys->tensionBroken == false /* first time tension is broken */) || (un<0.0 && phys->tensionBroken==true)){ if (neverErase) { phys->shearForce = Vector3r::Zero(); phys->normalForce = Vector3r::Zero(); phys->normalViscous = Vector3r::Zero(); //geom->normal = Vector3r::Zero(); phys->tensionBroken = true; }else { return false; } return true; } /* SHEAR CONTACT FORCE */ double Ks = 0.0; if(Talesnick){ //shearForce -= phys->ks*shearIncrement*std::max(pow(10,-15),phys->contactArea); #if 0 /* TALESNICK */ /* linear law */ double shearStiffness = 1.0*pow(10.0,8) + 9.7*pow(10.0,4)*phys->prevSigma; /* current sigmaN from above */ /* power law */ //double shearStiffness = 0.95*pow(10.0,6)*pow(phys->prevSigma,0.7); /* current sigmaN from above */ //double shearStiffness = 3.3*pow(10.0,5)*pow(phys->prevSigma,0.88); /* current sigmaN from above */ phys->ks = shearStiffness; Ks = shearStiffness; shearForce -= shearStiffness*shearIncrement*std::max(pow(10,-15),phys->contactArea); #endif //#if 0 phys->ks = 1.9*pow(10.0,6)*pow(phys->prevSigma,0.7); shearForce -= phys->ks*shearIncrement*std::max(pow(10,-14),phys->contactArea); //#endif phys->Kshear_area = phys->ks*std::max(pow(10,-15),phys->contactArea); }else{ Ks= phys->ks; /* use default values */ if(s1->isBoundary == true || s2->isBoundary==true || s1->isEastBoundary == true || s2->isEastBoundary==true){ Ks = phys->ks_i; shearForce -= Ks*shearIncrement*std::max(pow(10,-15),phys->contactArea); phys->Kshear_area = Ks*std::max(pow(10,-15),phys->contactArea); }else{ if(s1->isLining==true){Ks=s1->liningStiffness;} if(s2->isLining==true){Ks=s2->liningStiffness;} shearForce -= Ks*shearIncrement*std::max(pow(10,-15),phys->contactArea); /* GENERAL CASE */ phys->Kshear_area = Ks*std::max(pow(10,-15),phys->contactArea); } } /* CONTACT DAMPING */ Real mass1 = 0.0; Real mass2 = 0.0; const shared_ptr& b1=Body::byId(id1,scene); const shared_ptr& b2=Body::byId(id2,scene); if (b1->isClumpMember() == true){ State* stateClump = Body::byId(b1->clumpId,scene)->state.get(); mass1 = stateClump->mass; } if (b2->isClumpMember() == true){ State* stateClump = Body::byId(b2->clumpId,scene)->state.get(); mass2 = stateClump->mass; } if (b1->isClumpMember() == false && b2->isClumpMember() == false){ mass1 = de1->mass; mass2 = de2->mass; } Real mbar = (!b1->isDynamic() && b2->isDynamic()) ? mass2 : ((!b2->isDynamic() && b1->isDynamic()) ? mass1 : (mass1*mass2 / (mass1 + mass2))); // get equivalent mass Real Cn_crit = 2.*sqrt(mbar*phys->Knormal_area); // Knormal_area Critical damping coefficient (normal direction) 2.*sqrt(mbar*std::min(phys->Knormal_area,phys->Kshear_area)) Real Cs_crit = Cn_crit ; //2.*sqrt(mbar*phys->Kshear_area); // Kshear_area Critical damping coefficient (shear direction) // Note: to compare with the analytical solution you provide cn and cs directly (since here we used a different method to define c_crit) double cn = Cn_crit*phys->viscousDamping; // Damping normal coefficient double cs = Cs_crit*phys->viscousDamping; // Damping tangential coefficient /* Add normal viscous component if damping is included */ phys->normalViscous = cn*incidentVn; phys->normalForce -= phys->normalViscous; /* FRICTION LIMIT */ const double PI = std::atan(1.0)*4; double tan_effective_phi = 0.0; bool useIterativeMethod = false; if(Talesnick){ phys->cumulative_us = phys->cumulative_us + fabs(du); phys->effective_phi = phys->phi_b; tan_effective_phi = tan(phys->effective_phi/180.0*PI); #if 0 double upeak = 2.0*pow(10.0,-6)*pow(phys->prevSigma,0.213); double delta_miu = phys->ks/phys->prevSigma*(1.0 - std::min(fabs(phys->cumulative_us)/upeak, 1.0) ); if (isnan(delta_miu)){delta_miu = phys->ks/phys->prevSigma;} if (shearForce.norm() > phys->normalForce.norm()*phys->effective_phi){ phys->effective_phi = phys->effective_phi + delta_miu*fabs(du); } tan_effective_phi = phys->effective_phi; #endif }else{ if(s1->isBoundary==true || s2->isBoundary == true || phys->jointType==2 ){ // clay layer at boundary; useIterativeMethod=false; //fixme //if (allowBreakage == true) {useIterativeMethod = true;}else{ // useIterativeMethod = false; // phys->effective_phi = phys->phi_b; // - 3.25*(1.0-exp(-fabs(phys->cumulative_us)/0.4)); // tan_effective_phi = tan(phys->effective_phi/180.0*PI); //} }else if(s1->isLining==true){ phys->effective_phi = s1->liningFriction; tan_effective_phi = tan(phys->effective_phi/180.0*PI); }else if(s2->isLining==true){ phys->effective_phi = s2->liningFriction; tan_effective_phi = tan(phys->effective_phi/180.0*PI); }else{ phys->effective_phi = phys->phi_b; //if(s1->isEastBoundary==true || s2->isEastBoundary==true){phys->effective_phi = 0.0;} tan_effective_phi = tan(phys->effective_phi/180.0*PI); } } /* SHEAR CORRECTION */ Vector3r dampedShearForce = shearForce; double cohesiveForce = phys->cohesion*std::max(pow(10,-15),phys->contactArea); Real maxFs = 0.0; double maxShear = 0.0; if (useIterativeMethod == false){ double fN = phys->normalForce.dot(geom->normal); if(std::isnan(fN)){fN=0.0;} if(phys->intactRock == true){ if(allowBreakage == false || phys->cohesionBroken == false){ maxFs = cohesiveForce+ fN*tan_effective_phi; }else{ maxFs = std::max( fN,0.0)*tan_effective_phi; } }else{ maxFs = std::max( fN,0.0)*tan_effective_phi; } if( shearForce.norm() > maxFs ){ Real ratio = maxFs / shearForce.norm(); shearForce *= ratio; shearForce = shearForce; if(allowBreakage == true){phys->cohesionBroken = true;} dampedShearForce = shearForce; phys->shearViscous = Vector3r(0,0,0); }else{ /* no damping when it slides */ phys->shearViscous = Vector3r(0,0,0); //cs*incidentVs; // dampedShearForce = shearForce - phys->shearViscous; } }else{ Vector3r Fs_prev = oriShear; /* shear force before stress update */ Vector3r delta_us = -shearIncrement; /* increment of shear displacement */ double beta = 0.0; /* rate of plastic multiplier */ double beta_prev = phys->cumulative_us; /* accumulated plastic mutliplier before stress update */ double fN = phys->normalForce.norm(); //std::max(pow(10,-15),phys->contactArea); if(std::isnan(fN)){fN=0.0;} double phi =phys->phi_b; Vector3r newFs (0,0,0); double plasticDisp = 0.0; if(!Talesnick){ plasticDisp = stressUpdateVec(ip /*contact physics */, Fs_prev, delta_us, beta_prev, phys->Kshear_area /*shear stiffness */,fN, phi, newFs); }else{ double upeak = 2.0*pow(10.0,-6)*pow(phys->prevSigma,0.213); plasticDisp = stressUpdateVecTalesnick(ip /*contact physics */, Fs_prev, delta_us, beta_prev, phys->Kshear_area /*shear stiffness */,fN, phi, newFs, upeak); } shearForce = newFs; dampedShearForce = newFs; phys->cumulative_us = phys->cumulative_us + plasticDisp; //beta*shearIncrement; /* add plastic displacements */ double miu_peak = tan(phys->phi_b/180.0*PI); double delta_miu = 0.059266; tan_effective_phi = miu_peak - delta_miu*(1.0-exp(-phys->cumulative_us/0.35)); phys->effective_phi = atan(tan_effective_phi)/PI*180.0; maxFs = fN*tan_effective_phi; //if(shearForce.norm()/maxFs > 1.02) {std::cout<<"shearForce.norm()/maxFs: "<shearViscous = Vector3r(0,0,0); //cs*incidentVs; // dampedShearForce = shearForce - phys->shearViscous; } } /* APPLY FORCES */ Vector3r c1x = geom->contactPoint - de1->pos; Vector3r c2x = geom->contactPoint - de2->pos; Vector3r force = -phys->normalForce-dampedShearForce; scene->forces.addForce(id1,force); scene->forces.addForce(id2,-force); Vector3r normal = geom->normal; scene->forces.addTorque(id1,c1x.cross(force)); scene->forces.addTorque(id2,-(c2x).cross(force)); phys->prevNormal = geom->normal; /* RECORDING VALUES AND DEBUGGING */ if(shearForce.norm() < pow(10,-11) ){phys->mobilizedShear = 1.0;}else{phys->mobilizedShear = shearForce.norm()/maxFs;} if(s1->isLining==true){s1->liningTotalPressure = 1.0/s1->liningLength*force; s1->liningNormalPressure=-1.0/s1->liningLength*phys->normalForce; } else if(s2->isLining==true){s2->liningTotalPressure = -1.0/s2->liningLength*force; s2->liningNormalPressure=1.0/s2->liningLength*phys->normalForce; } if(std::isnan(force.norm())){ std::cout<<"shearForce: "<normalForce<<", viscousNormal: "<normalViscous<<", viscousShear: "<shearViscous<<", normal: "<normal<<", geom normal: "<normal<<", effective_phi: "<effective_phi<<", shearIncrement: "<mobilizedShear: "<mobilizedShear<& ip, const Vector3r Fs_prev /*prev shear force*/ , const Vector3r du /*shear displacement increment*/, const double beta_prev /* prev plastic displacements*/, const double Ks /*shear stiffness */,const double fN /*normal force*/, const double phi_b /*peak friction angle*/, Vector3r & newFs /*new shear force*/){ // FUNCTION RETURNS PLASTIC MULTIPLIER RATE (beta) AND CURRENT SHEAR FORCE newFs = Vector3r(0,0,0); double maxFs = 0.0; const double PI = std::atan(1.0)*4; // Define beta_prev as the cumulated plastic multiplier // Define beta as the rate of plastic multiplier at the current time step // Fs_new = Fs_prev + dF // dF = Ks*du_elastic = Ks*(du - du_plastic) = Ks*(du - beta*du_p) double beta = 0.0; //beta is the plastic multiplier double effective_phi = phi_b; double tan_effective_phi = tan(effective_phi/180.0*PI); double miu_peak = tan_effective_phi ; double delta_miu = 0.059266; double function = 0.0; double lambda = 0.0; newFs = Fs_prev + Ks*du; maxFs = fN*(miu_peak-delta_miu*(1.0-exp(-1.0*beta_prev/0.35))); //If new stress after elastic update is outside the previous yield surface if (newFs.norm() - maxFs >pow(10,-11) && fN>pow(10,-11) && (Ks*du).norm()>pow(10,-11) ){ // Fs_new = Fs_prev + dF // dF = Ks*du_elastic = Ks*(du - du_plastic) = Ks*(du - beta*du_p) // where du_p is a unit vector whose sign is Sign((Fs_prev + Ks*du).dot(du))*Sign(du); /* EQUATION TO SOLVE */ /* Solve for beta */ // Fs + Ks*(du - beta*du_p) = N*( miu_peak-delta_miu*(1-exp(beta_prev + beta) ) ) beta = 0.0; //////* ESTABLISH LOWER AND UPPER BOUNDS (positive and negative) FOR BRACKETING beta (plastic multiplier) *////// /* Establish lower bound for lambda*/ /* Lower bound = 0.0, i.e. fully elastic */ /* f_lower_bound <0.0, because it is outside the yield surface */ double lowerBound = 0.0; Vector3r termA = (Fs_prev + Ks*du)/(Ks*lowerBound + 1.0); double beta = beta_prev + lowerBound*termA.norm(); double f_lower_bound = termA.norm() - fN*(miu_peak - delta_miu*(1.0 - exp(-1.0*beta/0.35))); /* Establish upper bound for lambda*/ double upperBound = du.norm()/Fs_prev.norm(); if(std::isnan(upperBound)==true){upperBound=1.0;} if(std::isinf(upperBound)==true || upperBound>pow(10.0,12) ){upperBound=pow(10.0,12);} termA = (Fs_prev + Ks*du)/(Ks*upperBound + 1.0); beta = beta_prev + upperBound*termA.norm(); double f_upper_bound= termA.norm() - fN*(miu_peak - delta_miu*(1.0 - exp(-1.0*beta/0.35))); int iterUpper = 0; while(Mathr::Sign(f_upper_bound)*Mathr::Sign(f_lower_bound)>0.0){ upperBound=5.0*upperBound; termA = (Fs_prev + Ks*du)/(Ks*upperBound + 1.0); beta = beta_prev + upperBound*termA.norm(); f_upper_bound= termA.norm() - fN*(miu_peak - delta_miu*(1.0 - exp(-1.0*beta/0.35))); iterUpper++; if(iterUpper>1000){ std::cout<<"iterUpper: "< pow(10,-14) && fabs(lowerBound-upperBound)> pow(10,-14) ) { midTrial = 0.5*(lowerBound+upperBound); lambda = midTrial; termA = (Fs_prev + Ks*du)/(Ks*lambda + 1.0); beta = beta_prev + lambda*termA.norm(); function = termA.norm() - fN*(miu_peak - delta_miu*(1.0 - exp(-1.0*beta/0.35))); double Fmid = function; if (Mathr::Sign(Fmid) == Mathr::Sign(f_lower_bound)){ lowerBound = midTrial; f_lower_bound=function;}else{upperBound = midTrial;f_upper_bound=function;} iter++; if(iter > 98){ if ( fabs(function) > pow(10,-6) && fabs(lowerBound-upperBound)> pow(10,-6) ){ std::cout<<"iter: "< 1.05){ std::cout<<"newFs.norm()/maxFs: "<& ip, const Vector3r Fs_prev /*prev shear force*/ , const Vector3r du /*shear displacement increment*/, const double beta_prev /* prev plastic displacements*/, const double Ks /*shear stiffness */,const double fN /*normal force*/, const double phi_b /*peak friction angle*/, Vector3r & newFs /*new shear force*/, const double upeak){ // FUNCTION RETURNS PLASTIC MULTIPLIER RATE (beta) AND CURRENT SHEAR FORCE newFs = Vector3r(0,0,0); double maxFs = 0.0; const double PI = std::atan(1.0)*4; // Define beta_prev as the cumulated plastic multiplier // Define beta as the rate of plastic multiplier at the current time step // Fs_new = Fs_prev + dF // dF = Ks*du_elastic = Ks*(du - du_plastic) = Ks*(du - beta*du_p) double beta = 0.0; //beta is the plastic multiplier double effective_phi = phi_b; double tan_effective_phi = tan(effective_phi/180.0*PI); double miu_peak = tan_effective_phi ; double function = 0.0; double lambda = 0.0; newFs = Fs_prev + Ks*du; maxFs = fN*(miu_peak*(1.0-exp(-1.0*beta_prev/upeak))); //If new stress after elastic update is outside the previous yield surface if (newFs.norm() - maxFs >pow(10,-11) && fN>pow(10,-11) && (Ks*du).norm()>pow(10,-11) ){ // Fs_new = Fs_prev + dF // dF = Ks*du_elastic = Ks*(du - du_plastic) = Ks*(du - beta*du_p) // where du_p is a unit vector whose sign is Sign((Fs_prev + Ks*du).dot(du))*Sign(du); /* EQUATION TO SOLVE */ /* Solve for beta */ // Fs + Ks*(du - beta*du_p) = N*( miu_peak-delta_miu*(1-exp(beta_prev + beta) ) ) beta = 0.0; //////* ESTABLISH LOWER AND UPPER BOUNDS (positive and negative) FOR BRACKETING beta (plastic multiplier) *////// /* Establish lower bound for lambda*/ /* Lower bound = 0.0, i.e. fully elastic */ /* f_lower_bound <0.0, because it is outside the yield surface */ double lowerBound = 0.0; Vector3r termA = (Fs_prev + Ks*du)/(Ks*lowerBound + 1.0); double beta = beta_prev + lowerBound*termA.norm(); double f_lower_bound = termA.norm() - fN*(miu_peak*(1.0-exp(-1.0*beta_prev/upeak))); /* Establish upper bound for lambda*/ double upperBound = du.norm()/Fs_prev.norm(); if(std::isnan(upperBound)==true){upperBound=1.0;} if(std::isinf(upperBound)==true || upperBound>pow(10.0,12) ){upperBound=pow(10.0,12);} termA = (Fs_prev + Ks*du)/(Ks*upperBound + 1.0); beta = beta_prev + upperBound*termA.norm(); double f_upper_bound= termA.norm() - fN*(miu_peak*(1.0-exp(-1.0*beta_prev/upeak))); int iterUpper = 0; while(Mathr::Sign(f_upper_bound)*Mathr::Sign(f_lower_bound)>0.0){ upperBound=5.0*upperBound; termA = (Fs_prev + Ks*du)/(Ks*upperBound + 1.0); beta = beta_prev + upperBound*termA.norm(); f_upper_bound= termA.norm() - fN*(miu_peak*(1.0-exp(-1.0*beta_prev/upeak))); iterUpper++; if(iterUpper>1000){ std::cout<<"iterUpper: "< pow(10,-14) && fabs(lowerBound-upperBound)> pow(10,-14) ) { midTrial = 0.5*(lowerBound+upperBound); lambda = midTrial; termA = (Fs_prev + Ks*du)/(Ks*lambda + 1.0); beta = beta_prev + lambda*termA.norm(); function = termA.norm() - fN*(miu_peak*(1.0-exp(-1.0*beta_prev/upeak))); double Fmid = function; if (Mathr::Sign(Fmid) == Mathr::Sign(f_lower_bound)){ lowerBound = midTrial; f_lower_bound=function;}else{upperBound = midTrial;f_upper_bound=function;} iter++; if(iter > 98){ if ( fabs(function) > pow(10,-6) && fabs(lowerBound-upperBound)> pow(10,-6) ){ std::cout<<"iter: "< 1.05){ std::cout<<"newFs.norm()/maxFs: "<& b1, const shared_ptr& b2, const shared_ptr& interaction){ const double PI = 3.14159265358979323846; if(interaction->phys) return; ScGeom* scg=YADE_CAST(interaction->geom.get()); assert(scg); const shared_ptr& sdec1 = YADE_PTR_CAST(b1); const shared_ptr& sdec2 = YADE_PTR_CAST(b2); shared_ptr contactPhysics(new KnKsPBPhys()); //interaction->interactionPhysics = shared_ptr(new MomentPhys()); //const shared_ptr& contactPhysics = YADE_PTR_CAST(interaction->interactionPhysics); /* From interaction physics */ Real fa = sdec1->frictionAngle; Real fb = sdec2->frictionAngle; /* calculate stiffness */ Real Kn= Knormal; Real Ks= Kshear; /* Pass values calculated from above to CSPhys */ contactPhysics->viscousDamping = viscousDamping; contactPhysics->useOverlapVol = useOverlapVol; contactPhysics->kn = Kn; contactPhysics->ks = Ks; contactPhysics->kn_i = kn_i; contactPhysics->ks_i = ks_i; contactPhysics->u_peak = u_peak; contactPhysics->maxClosure = maxClosure; contactPhysics->cohesionBroken = cohesionBroken; contactPhysics->tensionBroken = tensionBroken; contactPhysics->unitWidth2D = unitWidth2D; contactPhysics->frictionAngle = std::min(fa,fb); if(!useFaceProperties){ contactPhysics->phi_r = std::min(fa,fb)/PI*180.0; contactPhysics->phi_b = contactPhysics->phi_r; } contactPhysics->tanFrictionAngle = std::tan(contactPhysics->frictionAngle); //contactPhysics->initialOrientation1 = Body::byId(interaction->getId1())->state->ori; //contactPhysics->initialOrientation2 = Body::byId(interaction->getId2())->state->ori; contactPhysics->prevNormal = scg->normal; //This is also done in the Contact Law. It is not redundant because this class is only called ONCE! contactPhysics->calJointLength = calJointLength; contactPhysics->twoDimension = twoDimension; contactPhysics->useFaceProperties = useFaceProperties; contactPhysics->brittleLength = brittleLength; interaction->phys = contactPhysics; } CREATE_LOGGER(KnKsPBPhys); /* KnKsPBPhys */ KnKsPBPhys::~KnKsPBPhys(){} #endif // YADE_POTENTIAL_BLOCKS trunk-2017.01a/pkg/dem/KnKsPBLaw.hpp000077500000000000000000000247211304022710500167660ustar00rootroot00000000000000#ifdef YADE_POTENTIAL_BLOCKS #pragma once #include #include #include #include #include #include #include class KnKsPBPhys: public FrictPhys { public: virtual ~KnKsPBPhys(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(KnKsPBPhys,FrictPhys,"Simple phys", ((vector,lambdaIPOPT,0.0,,"lagrane multiplier for equality constraints")) ((vector,cstatCPLEX,,,"lagrane multiplier for equality constraints")) ((vector,rstatCPLEX,,,"lagrane multiplier for equality constraints")) ((Real,frictionAngle,0.0,,"fric angle")) ((Real,tanFrictionAngle,0.0,,"tangent of fric angle")) ((Vector3r,contactDetectionPt,Vector3r(0,0,0),,"contact detection result")) ((Real, viscousDamping, 0.8, ,"viscousDamping")) ((Real, unitWidth2D, 1.0, ,"viscousDamping")) ((Real, maxClosure, 0.0002, ,"vmi")) ((Real, u_peak, 0.05, ,"peak shear displacement")) ((Real, u_elastic, 0.0, ,"elastic shear displacement")) ((double, brittleLength, 5.0, ,"brittle rock")) ((double, kn_i, 5.0, ,"initial normal stiffness")) ((double, ks_i, 5.0, ,"initial shear stiffness")) ((Vector3r, normalViscous, Vector3r(0,0,0), ,"viscousDamping")) ((Vector3r, shearViscous, Vector3r(0,0,0), ,"viscousDamping")) ((double, hwater, 0.0, ,"height of pore water")) ((bool, rockJointContact, false, ,"brittle rock")) ((bool, intactRock, false, ,"brittle rock")) ((int, jointType, 0, ,"jointType")) ((Real,Kshear_area,0.0,,"kshear area")) ((Real,Knormal_area, 0.0,,"knormal area")) ((Vector3r, shearDir, Vector3r(0,0,0), ,"shear direction")) ((vector, shearForces, , ,"shear direction")) ((Vector3r, shear, Vector3r(0,0,0),, "shear displacement")) ((Vector3r, prevNormal, Vector3r(0.0,0.0,0.0),, "previous Normal")) ((Vector3r, normal, Vector3r(0.0,0.0,0.0),, " normalVector")) ((vector, pointsArea, ,, "intermediate contact points")) ((vector, pointsShear, ,, "points to calculate shear")) ((vector, areaShear, ,, "area to attribute shear")) ((vector, overlapDistances, ,, "area to attribute shear")) ((Real, finalSize, 0.0,, "finalgridsize")) ((int, finalGridNo, 0,, "final number of grids")) ((vector, dualityGap, , ,"duality gap for SOCP")) ((bool, warmstart, false, ,"warmstart for SOCP")) ((int, generation, 0,, "number of subdivisions")) ((int, triNoMain, 24,, "number of subdivisions")) ((int, triNoSub, 6,, "number of subdivisions")) ((Vector3r, initial1, Vector3r(0.0,0.0,0.0),, "midpoint")) ((Vector3r, ptOnP1, Vector3r(0.0,0.0,0.0),, "pt on particle")) ((Vector3r, ptOnP2, Vector3r(0.0,0.0,0.0),, " pt on particle 2")) ((vector, redundantA, , ,"activePlanes for interaction.id1")) ((vector, redundantB, , ,"activePlanes for interaction.id1")) ((vector, activePlanes1, , ,"activePlanes for interaction.id1")) ((vector, activePlanes2, , ,"activePlanes for interaction.id2")) ((vector, activeA1, , ,"activePlanes for interaction.id2")) ((vector, activeB1, , ,"activePlanes for interaction.id2")) ((vector, activeC1, , ,"activePlanes for interaction.id2")) ((vector, activeD1, , ,"activePlanes for interaction.id2")) ((vector, activeA2, , ,"activePlanes for interaction.id2")) ((vector, activeB2, , ,"activePlanes for interaction.id2")) ((vector, activeC2, , ,"activePlanes for interaction.id2")) ((vector, activeD2, , ,"activePlanes for interaction.id2")) ((int, noActive1, 0, ,"activePlanes for interaction.id1")) ((int, noActive2,0 , ,"activePlanes for interaction.id2")) ((int, smallerID,1 , ,"id of particle with smaller plane")) ((Real, cumulative_us, 0.0,, "cumulative translation")) ((Real, cumulativeRotation, 0.0,, "cumulative rotation")) ((Real, mobilizedShear, , ,"mobilizedShear")) ((Real, contactArea, 0.0, ,"contactArea")) ((Real, radCurvFace, , ,"face")) ((double, prevJointLength, 0.0, ,"previous joint length")) ((Real, radCurvCorner, , ,"corners")) ((Real, prevSigma,0.0 , ,"previous normal stress")) ((vector, prevSigmaList,0.0 , ,"previous normal stress")) ((bool, calJointLength, false,, "calculate joint length")) ((bool, useOverlapVol, false,, "calculate overlap volume")) ((bool, calContactArea, false,, "calculate contact area")) ((double, jointLength, 0.0,, "approximatedJointLength")) ((double, shearIncrementForCD, 0.0,, "toSeeWhether it is necessary to update contactArea")) ((Real, overlappingVol,0.0 , ,"overlapping vol")) ((Real, overlappingVolMulti,0.0 , ,"overlapping vol")) ((double, gap_normalized, 0.0,, "distance between particles normalized by particle size. Estimated using Taubin Distance ")) ((double, gap, 0.0,, "distance between particles normalized by particle size. Estimated using Taubin Distance ")) ((bool, findCurv, false,, "to get radius of curvature")) ((bool, useFaceProperties, false,,"boolean to get face properites")) ((Real, cohesion, 0.0, ,"cohesion")) ((Real, tension, 0.0, ,"tension")) ((bool, cohesionBroken, true, ,"cohesion already broken")) ((bool, tensionBroken, true, ,"tension already broken")) ((bool, twoDimension, false, ,"tension already broken")) ((Real, phi_b, 0.0, ,"basic friction angle (degrees)")) ((Real, phi_r, 0.0, ,"residual friction angle (degrees)")) ((Real, asperity, 3.0, ,"asperity height")) ((Real, JRC, 0.0, ,"Joint Roughness Coefficient")) ((Real, JRCmobilized, 0.0, ,"Joint Roughness Coefficient")) ((Real, JCS, 0.0, ,"Joint Roughness Coefficient")) ((Real, sigmaC,0.0 , ,"Joint Roughness Coefficient")) ((Real, u_dilate,0.0 , ,"dilation distance")) ((Real, dilation_angle,0.0 , ,"dilation distance")) /* pore water pressure */ ((Real, lambda0,0.0 , ,"initial pore water pressure to stress ratio")) ((Real, lambda_present,0.0 , ,"Voight&Faust (1992) Sitar et al. (2005)")) ((Real, u_cumulative, 0.0,, "cumulative translation")) ((Vector3r, prevShearDir, Vector3r(0.0,0.0,0.0),, "previous shear direction")) ((Vector3r, initialShearDir, Vector3r(0.0,0.0,0.0),, "previous shear direction")) ((double, delta_porePressure, 0.0,, "change in pore water pressure")) ((double, porePressure, 0.0,, "pore water pressure")) ((double, bandThickness, 0.1,, "clay layer thickness")) ((double, heatCapacities, 0.0,, "clay layer thickness")) ((double, effective_phi, 0.0,, "friction angle in clay after displacement")) ((double, prevOverlap, 0.0,, "friction angle in clay after displacement")) ((Real, h, 0.0,,"cd")), //((Real, cumulativeRotation, 0.0,, "cumulative rotation")) //((Quaternionr, initialOrientation1, Quaternionr(1.0,0.0,0.0,0.0),, "orientation1")) //((Quaternionr, initialOrientation2, Quaternionr(1.0,0.0,0.0,0.0),, "orientation2")), createIndex(); ); REGISTER_CLASS_INDEX(KnKsPBPhys,FrictPhys); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(KnKsPBPhys); class Ip2_FrictMat_FrictMat_KnKsPBPhys: public IPhysFunctor{ public: virtual void go(const shared_ptr& pp1, const shared_ptr& pp2, const shared_ptr& interaction); YADE_CLASS_BASE_DOC_ATTRS(Ip2_FrictMat_FrictMat_KnKsPBPhys,IPhysFunctor,"Calculation", ((Real,Knormal,0.0,,"allows user to input values directly from python scripts")) ((Real,Kshear,0.0,,"allows user to input values directly from python scripts")) ((Real, unitWidth2D, 1.0, ,"viscousDamping")) ((double, brittleLength, 3.0, ,"brittle rock")) ((double, kn_i, 0.002, ,"brittle rock")) ((double, ks_i, 0.002, ,"brittle rock")) ((double, u_peak, -1.0, ,"brittle rock")) ((double, maxClosure, 0.002, ,"brittle rock")) ((Real, viscousDamping, 0.8, ,"viscousDamping")) ((Real, cohesion, 0.0, ,"viscousDamping")) ((Real, tension, 0.0, ,"viscousDamping")) ((bool, cohesionBroken, true, ,"cohesion")) ((bool, tensionBroken, true, ,"tension")) ((Real, phi_b, 0.0, ,"viscousDamping")) ((bool, useOverlapVol, false,, "calculate overlap volume")) ((bool, useFaceProperties, false,,"boolean to get face properites")) ((bool, calJointLength, false,, "calculate joint length")) ((bool, twoDimension, false, ,"tension already broken")) ); FUNCTOR2D(FrictMat,FrictMat); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Ip2_FrictMat_FrictMat_KnKsPBPhys); class Law2_SCG_KnKsPBPhys_KnKsPBLaw: public LawFunctor{ public: double stressUpdate(shared_ptr& ip, const Vector3r Fs_prev, const Vector3r du, const Vector3r prev_us, const double Kshear_area /*shear stiffness */,const double fN, const double dFn, const double phi_b, Vector3r & newFs); double stressUpdateVec(shared_ptr& ip, const Vector3r Fs_prev, const Vector3r du, const double prev_us, const double Kshear_area /*shear stiffness */,const double fN, const double phi_b, Vector3r & newFs); double stressUpdateVecTalesnick(shared_ptr& ip, const Vector3r Fs_prev, const Vector3r du, const double prev_us, const double Kshear_area /*shear stiffness */,const double fN, const double phi_b, Vector3r & newFs, const double upeak); static Real Real0; //OpenMPAccumulator plasticDissipation; virtual bool go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I); FUNCTOR2D(ScGeom,KnKsPBPhys); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Law2_SCG_KnKsPBPhys_KnKsPBLaw,LawFunctor,"Law for linear compression, without cohesion and Mohr-Coulomb plasticity surface.\n\n.. note::\n This law uses :yref:`ScGeom`; there is also functionally equivalent :yref:`Law2_Dem3DofGeom_FrictPhys_Basic`, which uses :yref:`Dem3DofGeom` (sphere-box interactions are not implemented for the latest).", ((bool,neverErase,false,,"Keep interactions even if particles go away from each other (only in case another constitutive law is in the scene, e.g. :yref:`Law2_ScGeom_CapillaryPhys_Capillarity`)")) ((bool,preventGranularRatcheting,false,,"bool to avoid granular ratcheting")) ((bool,traceEnergy,false,,"Define the total energy dissipated in plastic slips at all contacts.")) ((bool,Talesnick,false,,"Define the total energy dissipated in plastic slips at all contacts.")) ((double,waterLevel,0.0,,"Define the total energy dissipated in plastic slips at all contacts.")) ((bool, allowBreakage, false, ,"cohesion = 0, once broken")) ((double,initialOverlapDistance,0.0,,"initial overlap distance")) ,, ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_SCG_KnKsPBPhys_KnKsPBLaw); #endif // YADE_POTENTIAL_BLOCKS trunk-2017.01a/pkg/dem/L3Geom.cpp000066400000000000000000000415021304022710500163040ustar00rootroot00000000000000 #include #include #include #include #ifdef YADE_OPENGL #include #include #include #endif YADE_PLUGIN((L3Geom)(L6Geom)(Ig2_Sphere_Sphere_L3Geom)(Ig2_Wall_Sphere_L3Geom)(Ig2_Facet_Sphere_L3Geom)(Ig2_Sphere_Sphere_L6Geom)(Law2_L3Geom_FrictPhys_ElPerfPl)(Law2_L6Geom_FrictPhys_Linear) #ifdef YADE_OPENGL (Gl1_L3Geom)(Gl1_L6Geom) #endif ); L3Geom::~L3Geom(){} void L3Geom::applyLocalForceTorque(const Vector3r& localF, const Vector3r& localT, const Interaction* I, Scene* scene, NormShearPhys* nsp) const { Vector2r foo; // avoid undefined ~Vector2r with clang? Vector3r globF=trsf.transpose()*localF; // trsf is orthonormal, therefore inverse==transpose Vector3r x1c(normal*(refR1+.5*u[0])), x2c(-normal*(refR2+.5*u[0])); if(nsp){ nsp->normalForce=normal*globF.dot(normal); nsp->shearForce=globF-nsp->normalForce; } Vector3r globT=Vector3r::Zero(); if(localT!=Vector3r::Zero()){ globT=trsf.transpose()*localT; } // apply force and torque scene->forces.addForce(I->getId1(), globF); scene->forces.addTorque(I->getId1(),x1c.cross( globF)+globT); scene->forces.addForce(I->getId2(),-globF); scene->forces.addTorque(I->getId2(),x2c.cross(-globF)-globT); } void L3Geom::applyLocalForce(const Vector3r& localF, const Interaction* I, Scene* scene, NormShearPhys* nsp) const { applyLocalForceTorque(localF,Vector3r::Zero(),I,scene,nsp); } L6Geom::~L6Geom(){} bool Ig2_Sphere_Sphere_L3Geom::go(const shared_ptr& s1, const shared_ptr& s2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& I){ return genericGo(/*is6Dof*/false,s1,s2,state1,state2,shift2,force,I); }; bool Ig2_Sphere_Sphere_L6Geom::go(const shared_ptr& s1, const shared_ptr& s2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& I){ return genericGo(/*is6Dof*/true,s1,s2,state1,state2,shift2,force,I); }; CREATE_LOGGER(Ig2_Sphere_Sphere_L3Geom); bool Ig2_Sphere_Sphere_L3Geom::genericGo(bool is6Dof, const shared_ptr& s1, const shared_ptr& s2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& I){ // temporary hack only, to not have elastic potential energy in rigid packings with overlapping spheres //if(state1.blockedDOFs==State::DOF_ALL && state2.blockedDOFs==State::DOF_ALL) return false; const Real& r1=s1->cast().radius; const Real& r2=s2->cast().radius; Vector3r relPos=state2.pos+shift2-state1.pos; Real unDistSq=relPos.squaredNorm()-pow(std::abs(distFactor)*(r1+r2),2); if (unDistSq>0 && !I->isReal() && !force) return false; // contact exists, go ahead Real dist=relPos.norm(); Real uN=dist-(r1+r2); Vector3r normal=relPos/dist; Vector3r contPt=state1.pos+(r1+0.5*uN)*normal; handleSpheresLikeContact(I,state1,state2,shift2,is6Dof,normal,contPt,uN,r1,r2); return true; }; /* Generic function to compute L3Geom (with colinear points), used for {sphere,facet,wall}+sphere contacts now */ void Ig2_Sphere_Sphere_L3Geom::handleSpheresLikeContact(const shared_ptr& I, const State& state1, const State& state2, const Vector3r& shift2, bool is6Dof, const Vector3r& normal, const Vector3r& contPt, Real uN, Real r1, Real r2){ // create geometry if(!I->geom){ if(is6Dof) I->geom=shared_ptr(new L6Geom); else I->geom=shared_ptr(new L3Geom); L3Geom& g(I->geom->cast()); g.contactPoint=contPt; g.refR1=r1; g.refR2=r2; g.normal=normal; // g.trsf.setFromTwoVectors(Vector3r::UnitX(),g.normal); // quaternion just from the X-axis; does not seem to work for some reason?! const Vector3r& locX(g.normal); // initial local y-axis orientation, in the xz or xy plane, depending on which component is larger to avoid singularities Vector3r locY=normal.cross(std::abs(normal[1])isPeriodic?scene->cell->intrShiftVel(I->cellDist):Vector3r::Zero())<isPeriodic) relShearVel+=scene->cell->intrShiftVel(I->cellDist); relShearVel-=avgNormal.dot(relShearVel)*avgNormal; Vector3r relShearDu=relShearVel*scene->dt; /* Update of quantities in global coords consists in adding 3 increments we have computed; in global coords (a is any vector) 1. +relShearVel*scene->dt; // mutual motion of the contact 2. -a.cross(normRotVec); // rigid rotation perpendicular to the normal 3. -a.cross(normTwistVec); // rigid rotation parallel to the normal */ // compute current transformation, by updating previous axes // the X axis can be prescribed directly (copy of normal) // the mutual motion on the contact does not change transformation const Matrix3r prevTrsf(g.trsf); // could be reference perhaps, but we need it to compute midTrsf (if applicable) Matrix3r currTrsf; currTrsf.row(0)=currNormal; for(int i=1; i<3; i++){ currTrsf.row(i)=prevTrsf.row(i)-prevTrsf.row(i).cross(normRotVec)-prevTrsf.row(i).cross(normTwistVec); } if((scene->iter % trsfRenorm)==0 && trsfRenorm>0){ currTrsf.row(0).normalize(); currTrsf.row(1)-=currTrsf.row(0)*currTrsf.row(1).dot(currTrsf.row(0)); // take away y projected on x, to stabilize numerically currTrsf.row(1).normalize(); currTrsf.row(2)=currTrsf.row(0).cross(currTrsf.row(1)); currTrsf.row(2).normalize(); #ifdef YADE_DEBUG if(std::abs(currTrsf.determinant()-1)>.05){ LOG_ERROR("##"<getId1()<<"+"<getId2()<<", |trsf|="<geom->cast().phi+=midTrsf*(scene->dt*(state2.angVel-state1.angVel)); } }; bool Ig2_Wall_Sphere_L3Geom::go(const shared_ptr& s1, const shared_ptr& s2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& I){ if(scene->isPeriodic) throw std::logic_error("Ig2_Wall_Sphere_L3Geom does not handle periodic boundary conditions."); const Real& radius=s2->cast().radius; const int& ax(s1->cast().axis); const int& sense(s1->cast().sense); Real dist=state2.pos[ax]+shift2[ax]-state1.pos[ax]; // signed "distance" between centers if(!I->isReal() && std::abs(dist)>radius && !force) { return false; }// wall and sphere too far from each other // contact point is sphere center projected onto the wall Vector3r contPt=state2.pos+shift2; contPt[ax]=state1.pos[ax]; Vector3r normal=Vector3r::Zero(); // wall interacting from both sides: normal depends on sphere's position assert(sense==-1 || sense==0 || sense==1); if(sense==0) normal[ax]=dist>0?1.:-1.; else normal[ax]=(sense==1?1.:-1); Real uN=normal[ax]*dist-radius; // takes in account sense, radius and distance // check that the normal did not change orientation (would be abrup here) if(I->geom && I->geom->cast().normal!=normal){ ostringstream oss; oss<<"Ig2_Wall_Sphere_L3Geom: normal changed from ("<geom->cast().normal<<" to "<getId1()<<"+"<getId2()<<" (with Wall.sense=0, a particle might cross the Wall plane, if Δt is too high)"; throw std::logic_error(oss.str().c_str()); } handleSpheresLikeContact(I,state1,state2,shift2,/*is6Dof*/false,normal,contPt,uN,/*r1*/0,/*r2*/radius); return true; }; bool Ig2_Facet_Sphere_L3Geom::go(const shared_ptr& s1, const shared_ptr& s2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& I){ const Facet& facet(s1->cast()); Real radius=s2->cast().radius; // begin facet-local coordinates Vector3r cogLine=state1.ori.conjugate()*(state2.pos+shift2-state1.pos); // connect centers of gravity Vector3r normal=facet.normal; // trial contact normal Real planeDist=normal.dot(cogLine); if(std::abs(planeDist)>radius && !I->isReal() && !force) return false; // sphere too far if(planeDist<0){normal*=-1; planeDist*=-1; } Vector3r planarPt=cogLine-planeDist*normal; // project sphere center to the facet plane Vector3r contactPt; // facet's point closes to the sphere Real normDotPt[3]; // edge outer normals dot products for(int i=0; i<3; i++) normDotPt[i]=facet.ne[i].dot(planarPt-facet.vertices[i]); short w=(normDotPt[0]>0?1:0)+(normDotPt[1]>0?2:0)+(normDotPt[2]>0?4:0); // bitmask whether the closest point is outside (1,2,4 for respective edges) switch(w){ case 0: contactPt=planarPt; break; // ---: inside triangle case 1: contactPt=getClosestSegmentPt(planarPt,facet.vertices[0],facet.vertices[1]); break; // +-- (n1) case 2: contactPt=getClosestSegmentPt(planarPt,facet.vertices[1],facet.vertices[2]); break; // -+- (n2) case 4: contactPt=getClosestSegmentPt(planarPt,facet.vertices[2],facet.vertices[0]); break; // --+ (n3) case 3: contactPt=facet.vertices[1]; break; // ++- (v1) case 5: contactPt=facet.vertices[0]; break; // +-+ (v0) case 6: contactPt=facet.vertices[2]; break; // -++ (v2) case 7: throw logic_error("Ig2_Facet_Sphere_L3Geom: Impossible sphere-facet intersection (all points are outside the edges). (please report bug)"); // +++ (impossible) default: throw logic_error("Ig2_Facet_Sphere_L3Geom: Nonsense intersection value. (please report bug)"); } normal=cogLine-contactPt; // normal is now the contact normal, still in local coords if(!I->isReal() && normal.squaredNorm()>radius*radius && !force) { return false; } // fast test before sqrt Real dist=normal.norm(); normal/=dist; // normal is unit vector now // end facet-local coordinates normal=state1.ori*normal; // normal is in global coords now handleSpheresLikeContact(I,state1,state2,shift2,/*is6Dof*/false,normal,/*contact pt*/state2.pos+shift2-normal*dist,dist-radius,0,radius); return true; } bool Law2_L3Geom_FrictPhys_ElPerfPl::go(shared_ptr& ig, shared_ptr& ip, Interaction* I){ L3Geom* geom=static_cast(ig.get()); FrictPhys* phys=static_cast(ip.get()); // compute force Vector3r& localF(geom->F); localF=geom->relU().cwiseProduct(Vector3r(phys->kn,phys->ks,phys->ks)); // break if necessary if(localF[0]>0 && !noBreak) return false; if(!noSlip){ // plastic slip, if necessary; non-zero elastic limit only for compression Real maxFs=-min((Real)0.,localF[0]*phys->tangensOfFrictionAngle); Eigen::Map Fs(&localF[1]); //cerr<<"u="<relU()<<", maxFs="<trackEnergy) { scene->energy->add(0.5*(pow(geom->relU()[0],2)*phys->kn+(pow(geom->relU()[1],2)+pow(geom->relU()[2],2))*phys->ks),"elastPotential",elastPotentialIx,/*reset at every timestep*/true); } // apply force: this converts the force to global space, updates NormShearPhys::{normal,shear}Force, applies to particles geom->applyLocalForce(localF,I,scene,phys); return true; } bool Law2_L6Geom_FrictPhys_Linear::go(shared_ptr& ig, shared_ptr& ip, Interaction* I){ L6Geom& geom=ig->cast(); FrictPhys& phys=ip->cast(); // simple linear relationships Vector3r localF=geom.relU().cwiseProduct(Vector3r(phys.kn,phys.ks,phys.ks)); Vector3r localT=charLen*(geom.relPhi().cwiseProduct(Vector3r(phys.kn,phys.ks,phys.ks))); geom.applyLocalForceTorque(localF,localT,I,scene,static_cast(ip.get())); return true; } #ifdef YADE_OPENGL bool Gl1_L3Geom::axesLabels; Real Gl1_L3Geom::axesWd; Real Gl1_L3Geom::axesScale; Real Gl1_L3Geom::uPhiWd; Real Gl1_L3Geom::uScale; Real Gl1_L6Geom::phiScale; void Gl1_L3Geom::go(const shared_ptr& ig, const shared_ptr&, const shared_ptr&, const shared_ptr&, bool){ draw(ig); } void Gl1_L6Geom::go(const shared_ptr& ig, const shared_ptr&, const shared_ptr&, const shared_ptr&, bool){ draw(ig,true,phiScale); } void Gl1_L3Geom::draw(const shared_ptr& ig, bool isL6Geom, const Real& phiScale){ const L3Geom& g(ig->cast()); glTranslatev(g.contactPoint); glMultMatrix(Eigen::Transform(g.trsf.transpose()).data()); Real rMin=g.refR1<=0?g.refR2:(g.refR2<=0?g.refR1:min(g.refR1,g.refR2)); if(axesWd>0){ glLineWidth(axesWd); for(int i=0; i<3; i++){ Vector3r pt=Vector3r::Zero(); pt[i]=.5*rMin*axesScale; Vector3r color=.3*Vector3r::Ones(); color[i]=1; GLUtils::GLDrawLine(Vector3r::Zero(),pt,color); if(axesLabels) GLUtils::GLDrawText(string(i==0?"x":(i==1?"y":"z")),pt,color); } } if(uPhiWd>0){ glLineWidth(uPhiWd); if(uScale!=0) GLUtils::GLDrawLine(Vector3r::Zero(),uScale*g.relU(),Vector3r(0,1,.5)); if(isL6Geom && phiScale>0) GLUtils::GLDrawLine(Vector3r::Zero(),ig->cast().relPhi()/Mathr::PI*rMin*phiScale,Vector3r(.8,0,1)); } glLineWidth(1.); }; #endif trunk-2017.01a/pkg/dem/L3Geom.hpp000066400000000000000000000305361304022710500163160ustar00rootroot00000000000000 #pragma once #include #include #include #include #include #include #include #include #include #include #ifdef YADE_OPENGL #include #endif /* L3Geom Ig2 functor cooperation: 1. functors define genericGo function, which take ``bool is6Dof`` as the first arg; they are called from functors returning both L3Geom and L6Geom (this only applies to sphere+sphere now, since Ig2_{Facet,Wall}_Sphere_L6Geom has not been written yet for lack of interest, though would be trivial) 2. genericGo function computes several parameter specific to shape types; then it calls (if L3GEOM_SPHERESLIKE is defined) handleSpheresLikeContact which contains the common code, given all data necessary. Note that: (a) although L3GEOM_SPHERESLIKE is enabled by default, its performance impact has not been measured yet (the compiler should be smart enough, since it is just factoring out common code). (b) L3Geom only contains contPt and normal, which supposes (in L3Geom::applyLocalForce) that particles' centroids and the contact point are colinear; while this is true for spheres and mostly OK for facets&walls (since they are non-dynamic), it might be adjusted in the future -- L3Geom_Something deriving from L3Geom will be created, and exact branch vectors contained in it will be gotten via virtual method from L3Geom::applyLocalForce. This would be controlled via some approxMask (in the Law2 functor perhaps) so that it is only optional (c) Ig2_Facet_Sphere_L3Geom is only enabled with L3GEOM_SPHERESLIKE */ #define L3GEOM_SPHERESLIKE struct L3Geom: public GenericSpheresContact{ const Real& uN; const Vector2r uT; virtual ~L3Geom(); // utility function // TODO: currently supposes body's centroids are conencted with distance*normal // that will not be true for sphere+facet and others, watch out! // the force is oriented as applied to particle #1 void applyLocalForce(const Vector3r& f, const Interaction* I, Scene* scene, NormShearPhys* nsp=NULL) const; void applyLocalForceTorque(const Vector3r& f, const Vector3r& t, const Interaction* I, Scene* scene, NormShearPhys* nsp=NULL) const; Vector3r relU() const{ return u-u0; } YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(L3Geom,GenericSpheresContact,"Geometry of contact given in local coordinates with 3 degress of freedom: normal and two in shear plane. [experimental]", ((Vector3r,u,Vector3r::Zero(),,"Displacement components, in local coordinates. |yupdate|")) ((Vector3r,u0,Vector3r::Zero(),,"Zero displacement value; u0 should be always subtracted from the *geometrical* displacement *u* computed by appropriate :yref:`IGeomFunctor`, resulting in *u*. This value can be changed for instance\n\n#. by :yref:`IGeomFunctor`, e.g. to take in account large shear displacement value unrepresentable by underlying geomeric algorithm based on quaternions)\n#. by :yref:`LawFunctor`, to account for normal equilibrium position different from zero geometric overlap (set once, just after the interaction is created)\n#. by :yref:`LawFunctor` to account for plastic slip.\n\n.. note:: Never set an absolute value of *u0*, only increment, since both :yref:`IGeomFunctor` and :yref:`LawFunctor` use it. If you need to keep track of plastic deformation, store it in :yref:`IPhys` isntead (this might be changed: have *u0* for :yref:`LawFunctor` exclusively, and a separate value stored (when that is needed) inside classes deriving from :yref:`L3Geom`.")) /* Is it better to store trsf as Matrix3 or Quaternion? * Quaternions are much easier to re-normalize, which we should do to avoid numerical drift. * Multiplication of vector with quaternion is internally done by converting to matrix first, anyway * We need to extract local axes, and that is easier to be done from Matrix3r (columns) */ ((Matrix3r,trsf,Matrix3r::Identity(),,"Transformation (rotation) from global to local coordinates. (the translation part is in :yref:`GenericSpheresContact.contactPoint`)")) ((Vector3r,F,Vector3r::Zero(),,"Applied force in local coordinates [debugging only, will be removed]")) , /*init*/ ((uN,u[0])) ((uT,Vector2r::Map(&u[1]))) , /*ctor*/ createIndex(); , /*py*/ ); REGISTER_CLASS_INDEX(L3Geom,GenericSpheresContact); }; REGISTER_SERIALIZABLE(L3Geom); struct L6Geom: public L3Geom{ virtual ~L6Geom(); Vector3r relPhi() const{ return phi-phi0; } YADE_CLASS_BASE_DOC_ATTRS_CTOR(L6Geom,L3Geom,"Geometric of contact in local coordinates with 6 degrees of freedom. [experimental]", ((Vector3r,phi,Vector3r::Zero(),,"Rotation components, in local coordinates. |yupdate|")) ((Vector3r,phi0,Vector3r::Zero(),,"Zero rotation, should be always subtracted from *phi* to get the value. See :yref:`L3Geom.u0`.")) , /* ctor */ createIndex(); ); REGISTER_CLASS_INDEX(L6Geom,L3Geom); }; REGISTER_SERIALIZABLE(L6Geom); #ifdef YADE_OPENGL struct Gl1_L3Geom: public GlIGeomFunctor{ RENDERS(L3Geom); void go(const shared_ptr&, const shared_ptr&, const shared_ptr&, const shared_ptr&, bool); void draw(const shared_ptr&, bool isL6Geom=false, const Real& phiScale=0); YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_L3Geom,GlIGeomFunctor,"Render :yref:`L3Geom` geometry.", ((bool,axesLabels,false,,"Whether to display labels for local axes (x,y,z)")) ((Real,axesScale,1.,,"Scale local axes, their reference length being half of the minimum radius.")) ((Real,axesWd,1.,,"Width of axes lines, in pixels; not drawn if non-positive")) ((Real,uPhiWd,2.,,"Width of lines for drawing displacements (and rotations for :yref:`L6Geom`); not drawn if non-positive.")) ((Real,uScale,1.,,"Scale local displacements (:yref:`u` - :yref:`u0`); 1 means the true scale, 0 disables drawing local displacements; negative values are permissible.")) ); }; REGISTER_SERIALIZABLE(Gl1_L3Geom); struct Gl1_L6Geom: public Gl1_L3Geom{ RENDERS(L6Geom); void go(const shared_ptr&, const shared_ptr&, const shared_ptr&, const shared_ptr&, bool); YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_L6Geom,Gl1_L3Geom,"Render :yref:`L6Geom` geometry.", ((Real,phiScale,1.,,"Scale local rotations (:yref:`phi` - :yref:`phi0`). The default scale is to draw $\\pi$ rotation with length equal to minimum radius.")) ); }; REGISTER_SERIALIZABLE(Gl1_L6Geom); #endif struct Ig2_Sphere_Sphere_L3Geom: public IGeomFunctor{ virtual bool go(const shared_ptr& s1, const shared_ptr& s2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& I); virtual bool genericGo(bool is6Dof, const shared_ptr& s1, const shared_ptr& s2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& I); // common code for {sphere,facet,wall}+sphere contacts // facet&wall will get separated if L3Geom subclass with exact branch vector is created void handleSpheresLikeContact(const shared_ptr& I, const State& state1, const State& state2, const Vector3r& shift2, bool is6Dof, const Vector3r& normal, const Vector3r& contPt, Real uN, Real r1, Real r2); enum { APPROX_NO_MID_TRSF=1, APPROX_NO_MID_NORMAL=2, APPROX_NO_RENORM_MID_NORMAL=4 }; YADE_CLASS_BASE_DOC_ATTRS(Ig2_Sphere_Sphere_L3Geom,IGeomFunctor,"Incrementally compute :yref:`L3Geom` for contact of 2 spheres. Detailed documentation in py/\\_extraDocs.py", ((bool,noRatch,true,,"See :yref:`Ig2_Sphere_Sphere_ScGeom.avoidGranularRatcheting`.")) ((Real,distFactor,1,,"Create interaction if spheres are not futher than *distFactor* \\*(r1+r2). If negative, zero normal deformation will be set to be the initial value (otherwise, the geometrical distance is the \'\'zero'' one).")) ((int,trsfRenorm,100,,"How often to renormalize :yref:`trsf`; if non-positive, never renormalized (simulation might be unstable)")) ((int,approxMask,0,,"Selectively enable geometrical approximations (bitmask); add the values for approximations to be enabled.\n\n" "== ===============================================================\n" "1 use previous transformation to transform velocities (which are known at mid-steps), instead of mid-step transformation computed as quaternion slerp at t=0.5.\n" "2 do not take average (mid-step) normal when computing relative shear displacement, use previous value instead\n" "4 do not re-normalize average (mid-step) normal, if used.…\n" "== ===============================================================\n\n" "By default, the mask is zero, wherefore none of these approximations is used.\n" )) ); FUNCTOR2D(Sphere,Sphere); DEFINE_FUNCTOR_ORDER_2D(Sphere,Sphere); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Ig2_Sphere_Sphere_L3Geom); struct Ig2_Wall_Sphere_L3Geom: public Ig2_Sphere_Sphere_L3Geom{ virtual bool go(const shared_ptr& s1, const shared_ptr& s2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& I); //virtual bool genericGo(bool is6Dof, const shared_ptr& s1, const shared_ptr& s2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& I); YADE_CLASS_BASE_DOC(Ig2_Wall_Sphere_L3Geom,Ig2_Sphere_Sphere_L3Geom,"Incrementally compute :yref:`L3Geom` for contact between :yref:`Wall` and :yref:`Sphere`. Uses attributes of :yref:`Ig2_Sphere_Sphere_L3Geom`."); FUNCTOR2D(Wall,Sphere); DEFINE_FUNCTOR_ORDER_2D(Wall,Sphere); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Ig2_Wall_Sphere_L3Geom); #ifdef L3GEOM_SPHERESLIKE struct Ig2_Facet_Sphere_L3Geom: public Ig2_Sphere_Sphere_L3Geom{ // get point on segment A..B closest to P; algo: http://local.wasp.uwa.edu.au/~pbourke/geometry/pointline/ static Vector3r getClosestSegmentPt(const Vector3r& P, const Vector3r& A, const Vector3r& B){ Vector3r BA=B-A; Real u=(P.dot(BA)-A.dot(BA))/(BA.squaredNorm()); return A+min((Real)1.,max((Real)0.,u))*BA; } virtual bool go(const shared_ptr& s1, const shared_ptr& s2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& I); YADE_CLASS_BASE_DOC(Ig2_Facet_Sphere_L3Geom,Ig2_Sphere_Sphere_L3Geom,"Incrementally compute :yref:`L3Geom` for contact between :yref:`Facet` and :yref:`Sphere`. Uses attributes of :yref:`Ig2_Sphere_Sphere_L3Geom`."); FUNCTOR2D(Facet,Sphere); DEFINE_FUNCTOR_ORDER_2D(Facet,Sphere); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Ig2_Facet_Sphere_L3Geom); #endif struct Ig2_Sphere_Sphere_L6Geom: public Ig2_Sphere_Sphere_L3Geom{ virtual bool go(const shared_ptr& s1, const shared_ptr& s2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& I); YADE_CLASS_BASE_DOC(Ig2_Sphere_Sphere_L6Geom,Ig2_Sphere_Sphere_L3Geom,"Incrementally compute :yref:`L6Geom` for contact of 2 spheres."); FUNCTOR2D(Sphere,Sphere); DEFINE_FUNCTOR_ORDER_2D(Sphere,Sphere); }; REGISTER_SERIALIZABLE(Ig2_Sphere_Sphere_L6Geom); struct Law2_L3Geom_FrictPhys_ElPerfPl: public LawFunctor{ virtual bool go(shared_ptr&, shared_ptr&, Interaction*); FUNCTOR2D(L3Geom,FrictPhys); YADE_CLASS_BASE_DOC_ATTRS(Law2_L3Geom_FrictPhys_ElPerfPl,LawFunctor,"Basic law for testing :yref:`L3Geom`; it bears no cohesion (unless *noBreak* is ``True``), and plastic slip obeys the Mohr-Coulomb criterion (unless *noSlip* is ``True``).", ((bool,noBreak,false,,"Do not break contacts when particles separate.")) ((bool,noSlip,false,,"No plastic slipping.")) ((int,plastDissipIx,-1,(Attr::noSave|Attr::hidden),"Index of plastically dissipated energy")) ((int,elastPotentialIx,-1,(Attr::hidden|Attr::noSave),"Index for elastic potential energy (with O.trackEnergy)")) ); }; REGISTER_SERIALIZABLE(Law2_L3Geom_FrictPhys_ElPerfPl); struct Law2_L6Geom_FrictPhys_Linear: public Law2_L3Geom_FrictPhys_ElPerfPl{ virtual bool go(shared_ptr&, shared_ptr&, Interaction*); FUNCTOR2D(L6Geom,FrictPhys); YADE_CLASS_BASE_DOC_ATTRS(Law2_L6Geom_FrictPhys_Linear,Law2_L3Geom_FrictPhys_ElPerfPl,"Basic law for testing :yref:`L6Geom` -- linear in both normal and shear sense, without slip or breakage.", ((Real,charLen,1,,"Characteristic length with the meaning of the stiffness ratios bending/shear and torsion/normal.")) ); }; REGISTER_SERIALIZABLE(Law2_L6Geom_FrictPhys_Linear); trunk-2017.01a/pkg/dem/Law2_ScGeom_CapillaryPhys_Capillarity.cpp000066400000000000000000000642631304022710500244720ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by luc Scholtes * * luc.scholtes@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "Law2_ScGeom_CapillaryPhys_Capillarity.hpp" #include #include #include #include #include #include #include #include YADE_PLUGIN((Law2_ScGeom_CapillaryPhys_Capillarity)); void Law2_ScGeom_CapillaryPhys_Capillarity::postLoad(Law2_ScGeom_CapillaryPhys_Capillarity&){ capillary = shared_ptr(new capillarylaw); capillary->fill(("M(r=1)"+suffCapFiles).c_str()); capillary->fill(("M(r=1.1)"+suffCapFiles).c_str()); capillary->fill(("M(r=1.25)"+suffCapFiles).c_str()); capillary->fill(("M(r=1.5)"+suffCapFiles).c_str()); capillary->fill(("M(r=1.75)"+suffCapFiles).c_str()); capillary->fill(("M(r=2)"+suffCapFiles).c_str()); capillary->fill(("M(r=3)"+suffCapFiles).c_str()); capillary->fill(("M(r=4)"+suffCapFiles).c_str()); capillary->fill(("M(r=5)"+suffCapFiles).c_str()); capillary->fill(("M(r=10)"+suffCapFiles).c_str()); } MeniscusParameters::MeniscusParameters() { V = 0; F = 0; delta1 = 0; delta2 = 0; nn11 = 0; nn33 = 0; } MeniscusParameters::MeniscusParameters(const MeniscusParameters &source) { V = source.V; F = source.F; delta1 = source.delta1; delta2 = source.delta2; nn11 = source.nn11; nn33 = source.nn33; } MeniscusParameters::~MeniscusParameters() {} void Law2_ScGeom_CapillaryPhys_Capillarity::action() { if (!scene) cerr << "scene not defined!"; if (!capillary) postLoad(*this);//when the script does not define arguments, postLoad is never called shared_ptr& bodies = scene->bodies; int sphereIndex = Sphere::getClassIndexStatic(); //check for contact model once (assuming that contact model does not change) if (!hertzInitialized){//NOTE: We are assuming that only one type is used in one simulation here FOREACH(const shared_ptr& I, *scene->interactions){ if (I->isReal()) { if (CapillaryPhys::getClassIndexStatic()==I->phys->getClassIndex()) hertzOn=false; else if (MindlinCapillaryPhys::getClassIndexStatic()==I->phys->getClassIndex()) hertzOn=true; else LOG_ERROR("The capillary law is not implemented for interactions using "<phys->getClassName()); bodiesMenisciiList.initialized = false;//must be re-initialized after creation of first real contact in the model hertzInitialized = true; break; } } } if (fusionDetection && !bodiesMenisciiList.initialized) bodiesMenisciiList.prepare(scene,hertzOn); FOREACH(const shared_ptr& interaction, *scene->interactions){ // could be done in parallel as soon as OpenMPVector class (lib/base/openmp-accu.hpp) is extended See http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg10842.html and msg11238.html /// interaction is real if (interaction->isReal()) { CapillaryPhys* cundallContactPhysics=NULL; MindlinCapillaryPhys* mindlinContactPhysics=NULL; /// contact physics depends on the contact law, that is used (either linear model or hertz model) if (!hertzOn) cundallContactPhysics = static_cast(interaction->phys.get());//use CapillaryPhys for linear model else mindlinContactPhysics = static_cast(interaction->phys.get());//use MindlinCapillaryPhys for hertz model unsigned int id1 = interaction->getId1(); unsigned int id2 = interaction->getId2(); /// definition of interacting objects (not necessarily in contact) ScGeom* currentContactGeometry = static_cast(interaction->geom.get()); /// test of interacting bodies geometries since capillarity will be computed between spheres only int geometryIndex1 = (*bodies)[id1]->shape->getClassIndex(); int geometryIndex2 = (*bodies)[id2]->shape->getClassIndex(); if ( !(geometryIndex1 == sphereIndex && geometryIndex2 == sphereIndex) ) { // such interactions won't have a meniscus // thus we will ask for the interaction to be erased in this distant case, as we do w. sphere-sphere interactions below: if(currentContactGeometry->penetrationDepth < 0) scene->interactions->requestErase(interaction); continue;} /// Interacting Grains: // If you want to define a ratio between YADE sphere size and real sphere size Real alpha=1; Real R1 = 0; R1=alpha*std::min(currentContactGeometry->radius2,currentContactGeometry->radius1) ; Real R2 = 0; R2=alpha*std::max(currentContactGeometry->radius2,currentContactGeometry->radius1) ; /// intergranular distance Real D = - alpha * currentContactGeometry->penetrationDepth; if ( D<0 || createDistantMeniscii) { //||(scene->iter < 1) ) // a simplified way to define meniscii everywhere D=max(0.,D); // defines fCap when spheres interpenetrate. D<0 leads to wrong interpolation as D<0 has no solution in the interpolation : this is not physically interpretable!! even if, interpenetration << grain radius. if (!hertzOn) { if (fusionDetection && !cundallContactPhysics->meniscus) bodiesMenisciiList.insert(interaction); cundallContactPhysics->meniscus=true; } else { if (fusionDetection && !mindlinContactPhysics->meniscus) bodiesMenisciiList.insert(interaction); mindlinContactPhysics->meniscus=true; } } Real Dinterpol = D/R2; /// Suction (Capillary pressure): Real Pinterpol = 0; if (!hertzOn) Pinterpol = cundallContactPhysics->isBroken ? 0 : capillaryPressure*(R2/surfaceTension); else Pinterpol = mindlinContactPhysics->isBroken ? 0 : capillaryPressure*(R2/surfaceTension); if (!hertzOn) cundallContactPhysics->capillaryPressure = capillaryPressure; else mindlinContactPhysics->capillaryPressure = capillaryPressure; /// Capillary solution finder: if ((Pinterpol>=0) && (hertzOn? mindlinContactPhysics->meniscus : cundallContactPhysics->meniscus)) { int* currentIndexes = hertzOn? mindlinContactPhysics->currentIndexes : cundallContactPhysics->currentIndexes; //If P=0, we use null solution MeniscusParameters solution(Pinterpol? capillary->interpolate(R1,R2,Dinterpol, Pinterpol, currentIndexes) : MeniscusParameters()); /// If no bridge, delete the interaction if necessary and escape if (!solution.V) { if ((fusionDetection) || (hertzOn ? mindlinContactPhysics->isBroken : cundallContactPhysics->isBroken)) bodiesMenisciiList.remove(interaction); if (D>0) {scene->interactions->requestErase(interaction); continue;} else if ((Pinterpol > 0) && (showError)) { LOG_ERROR("No meniscus found at a contact. capillaryPressure may be too large wrt. the loaded data files."); // V=0 at a contact reveals a problem if and only if uc* > 0 showError = false;}//show error message once / avoid console spam } /// capillary adhesion force Real Finterpol = solution.F; Vector3r fCap = - Finterpol*(2*Mathr::PI*(R2/alpha)*surfaceTension)*currentContactGeometry->normal; if (!hertzOn) cundallContactPhysics->fCap = fCap; else mindlinContactPhysics->fCap = fCap; /// meniscus volume Real Vinterpol = solution.V * pow(R2/alpha,3); if (!hertzOn) { cundallContactPhysics->vMeniscus = Vinterpol; if (Vinterpol != 0) cundallContactPhysics->meniscus = true; else cundallContactPhysics->meniscus = false; } else { mindlinContactPhysics->vMeniscus = Vinterpol; if (Vinterpol != 0) mindlinContactPhysics->meniscus = true; else mindlinContactPhysics->meniscus = false; } /// wetting angles if (!hertzOn) { cundallContactPhysics->Delta1 = min(max(solution.delta1,solution.delta2),90.0); // undesired values greater than 90 degrees (by few degrees) may be present in the capillary files for high r (~ 10) and very low suction and distance cundallContactPhysics->Delta2 = min(solution.delta1,solution.delta2); } else { mindlinContactPhysics->Delta1 = min(max(solution.delta1,solution.delta2),90.0); mindlinContactPhysics->Delta2 = min(solution.delta1,solution.delta2); } // nn11 and nn33 if (!hertzOn) { cundallContactPhysics->nn11 = pow(R2/alpha,2) * solution.nn11; cundallContactPhysics->nn33 = pow(R2/alpha,2) * solution.nn33; } } ///interaction is not real //If the interaction is not real, it should not be in the list } else if (fusionDetection) bodiesMenisciiList.remove(interaction); } if (fusionDetection) checkFusion(); #ifdef YADE_OPENMP const long size=scene->interactions->size(); #pragma omp parallel for schedule(guided) num_threads(ompThreads>0 ? min(ompThreads,omp_get_max_threads()) : omp_get_max_threads()) for(long i=0; i& interaction=(*scene->interactions)[i]; #else FOREACH(const shared_ptr& interaction, *scene->interactions){ #endif if (interaction->isReal()) { CapillaryPhys* cundallContactPhysics=NULL; MindlinCapillaryPhys* mindlinContactPhysics=NULL; if (!hertzOn) cundallContactPhysics = static_cast(interaction->phys.get());//use CapillaryPhys for linear model else mindlinContactPhysics = static_cast(interaction->phys.get());//use MindlinCapillaryPhys for hertz model if ((hertzOn && mindlinContactPhysics->meniscus) || (!hertzOn && cundallContactPhysics->meniscus)) { if (fusionDetection) {//version with effect of fusion //BINARY VERSION : if fusionNumber!=0 then no capillary force short int& fusionNumber = hertzOn?mindlinContactPhysics->fusionNumber:cundallContactPhysics->fusionNumber; if (binaryFusion) { if (fusionNumber!=0) { //cerr << "fusion" << endl; hertzOn?mindlinContactPhysics->fCap:cundallContactPhysics->fCap = Vector3r::Zero(); continue; } } //LINEAR VERSION : capillary force is divided by (fusionNumber + 1) - NOTE : any decreasing function of fusionNumber can be considered in fact else if (fusionNumber !=0) hertzOn?mindlinContactPhysics->fCap:cundallContactPhysics->fCap /= (fusionNumber+1.); } scene->forces.addForce(interaction->getId1(),-(hertzOn?mindlinContactPhysics->fCap:cundallContactPhysics->fCap)); scene->forces.addForce(interaction->getId2(), hertzOn?mindlinContactPhysics->fCap:cundallContactPhysics->fCap ); } } } } capillarylaw::capillarylaw() {} void capillarylaw::fill(const char* filename) { data_complete.push_back(Tableau(filename)); } void Law2_ScGeom_CapillaryPhys_Capillarity::checkFusion() { //Reset fusion numbers FOREACH(const shared_ptr& interaction, *scene->interactions){ // same remark for parallel loops, the most problematic part ? if ( interaction->isReal()) { if (!hertzOn) static_cast(interaction->phys.get())->fusionNumber=0; else static_cast(interaction->phys.get())->fusionNumber=0; } } list< shared_ptr >::iterator firstMeniscus, lastMeniscus, currentMeniscus; Real angle1 = -1.0; Real angle2 = -1.0; for ( int i=0; i< bodiesMenisciiList.size(); ++i ) { // i is the index (or id) of the body being tested CapillaryPhys* cundallInteractionPhysics1=NULL; MindlinCapillaryPhys* mindlinInteractionPhysics1=NULL; CapillaryPhys* cundallInteractionPhysics2=NULL; MindlinCapillaryPhys* mindlinInteractionPhysics2=NULL; if ( !bodiesMenisciiList[i].empty() ) { lastMeniscus = bodiesMenisciiList[i].end(); for ( firstMeniscus=bodiesMenisciiList[i].begin(); firstMeniscus!=lastMeniscus; ++firstMeniscus ) { //FOR EACH MENISCUS ON THIS BODY... currentMeniscus = firstMeniscus; ++currentMeniscus; if (!hertzOn) { cundallInteractionPhysics1 = YADE_CAST((*firstMeniscus)->phys.get()); if (i == (*firstMeniscus)->getId1()) angle1=cundallInteractionPhysics1->Delta1;//get angle of meniscus1 on body i else angle1=cundallInteractionPhysics1->Delta2; } else { mindlinInteractionPhysics1 = YADE_CAST((*firstMeniscus)->phys.get()); if (i == (*firstMeniscus)->getId1()) angle1=mindlinInteractionPhysics1->Delta1;//get angle of meniscus1 on body i else angle1=mindlinInteractionPhysics1->Delta2; } for ( ;currentMeniscus!= lastMeniscus; ++currentMeniscus) {//... CHECK FUSION WITH ALL OTHER MENISCII ON THE BODY if (!hertzOn) { cundallInteractionPhysics2 = YADE_CAST((*currentMeniscus)->phys.get()); if (i == (*currentMeniscus)->getId1()) angle2=cundallInteractionPhysics2->Delta1;//get angle of meniscus2 on body i else angle2=cundallInteractionPhysics2->Delta2; } else { mindlinInteractionPhysics2 = YADE_CAST((*currentMeniscus)->phys.get()); if (i == (*currentMeniscus)->getId1()) angle2=mindlinInteractionPhysics2->Delta1;//get angle of meniscus2 on body i else angle2=mindlinInteractionPhysics2->Delta2; } if (angle1==0 || angle2==0) cerr << "THIS SHOULD NOT HAPPEN!!"<< endl; //cerr << "angle1 = " << angle1 << " | angle2 = " << angle2 << endl; Vector3r normalFirstMeniscus = YADE_CAST((*firstMeniscus)->geom.get())->normal; Vector3r normalCurrentMeniscus = YADE_CAST((*currentMeniscus)->geom.get())->normal; Real normalDot = 0; if ((*firstMeniscus)->getId1() == (*currentMeniscus)->getId1() || (*firstMeniscus)->getId2() == (*currentMeniscus)->getId2()) normalDot = normalFirstMeniscus.dot(normalCurrentMeniscus); else normalDot = - (normalFirstMeniscus.dot(normalCurrentMeniscus)); Real normalAngle = 0; if (normalDot >= 0 ) normalAngle = Mathr::FastInvCos0(normalDot); else normalAngle = ((Mathr::PI) - Mathr::FastInvCos0(-(normalDot))); if ((angle1+angle2)*Mathr::DEG_TO_RAD > normalAngle) { if (!hertzOn) {++(cundallInteractionPhysics1->fusionNumber); ++(cundallInteractionPhysics2->fusionNumber);}//count +1 if 2 meniscii are overlaping else {++(mindlinInteractionPhysics1->fusionNumber); ++(mindlinInteractionPhysics2->fusionNumber);} } } } } } } MeniscusParameters capillarylaw::interpolate(Real R1, Real R2, Real D, Real P, int* index) { if (R1 > R2) { Real R3 = R1; R1 = R2; R2 = R3; } Real R = R2/R1; //cerr << "R = " << R << endl; MeniscusParameters result_inf; MeniscusParameters result_sup; MeniscusParameters result; int i = 0; for ( ; i < (NB_R_VALUES); i++) { Real data_R = data_complete[i].R; //cerr << "i = " << i << endl; if (data_R > R) // Attention a l'ordre ds lequel vont etre ranges les tableau R (croissant) { Tableau& tab_inf=data_complete[i-1]; Tableau& tab_sup=data_complete[i]; Real r=(R-tab_inf.R)/(tab_sup.R-tab_inf.R); result_inf = tab_inf.Interpolate2(D,P,index[0], index[1]); result_sup = tab_sup.Interpolate2(D,P,index[2], index[3]); result.V = result_inf.V*(1-r) + r*result_sup.V; result.F = result_inf.F*(1-r) + r*result_sup.F; result.delta1 = result_inf.delta1*(1-r) + r*result_sup.delta1; result.delta2 = result_inf.delta2*(1-r) + r*result_sup.delta2; result.nn11 = result_inf.nn11*(1-r) + r*result_sup.nn11; result.nn33 = result_inf.nn33*(1-r) + r*result_sup.nn33; i=NB_R_VALUES; //cerr << "i = " << i << endl; } else if (data_complete[i].R == R) { result = data_complete[i].Interpolate2(D,P, index[0], index[1]); i=NB_R_VALUES; } } return result; } Tableau::Tableau() {} Tableau::Tableau(const char* filename) { ifstream file (filename); file >> R; int n_D; //number of D values file >> n_D; if (!file.is_open()) { static bool first=true; if(first) { cout << "WARNING: cannot open files used for capillary law, all forces will be null. Instructions on how to download and install them is found here : https://yade-dem.org/wiki/CapillaryTriaxialTest." << endl; first=false; } return; } for (int i=0; i D ) // ok si D rang�s ds l'ordre croissant { Real rD = (D-full_data[i-1].D)/(full_data[i].D-full_data[i-1].D); result_inf = full_data[i-1].Interpolate3(P, index1); result_sup = full_data[i].Interpolate3(P, index2); result.V = result_inf.V*(1-rD) + rD*result_sup.V; result.F = result_inf.F*(1-rD) + rD*result_sup.F; result.delta1 = result_inf.delta1*(1-rD) + rD*result_sup.delta1; result.delta2 = result_inf.delta2*(1-rD) + rD*result_sup.delta2; result.nn11 = result_inf.nn11*(1-rD) + rD*result_sup.nn11; result.nn33 = result_inf.nn33*(1-rD) + rD*result_sup.nn33; i = full_data.size(); } else if (full_data[i].D == D) { result=full_data[i].Interpolate3(P, index1); i=full_data.size(); } } return result; } TableauD::TableauD() {} TableauD::TableauD(ifstream& file) { int i=0; Real x; int n_lines; //pb: n_lines is real!!! file >> n_lines; file.ignore(200, '\n'); // saute les caract�res (200 au maximum) jusque au caract�re \n (fin de ligne)*_ if (n_lines!=0) for (; i ()); for (int j=0; j < 8; ++j) // [D,P,V,F,delta1,delta2,nn11,nn33] { file >> x; data[i].push_back(x); } } else LOG_ERROR("Problem regarding the capillary file structure (e.g. n_D is not consistent with the actual data), and/or mismatch with the expected structure by the code ! Will segfault"); D = data[i-1][0]; } MeniscusParameters TableauD::Interpolate3(Real P, int& index) { //cerr << "interpolate3" << endl; MeniscusParameters result; int dataSize = data.size(); if (index < dataSize && index>0) { if (data[index][1] >= P && data[index-1][1] < P) { //compteur1+=1; Real Pinf=data[index-1][1]; Real Finf=data[index-1][3]; Real Vinf=data[index-1][2]; Real Delta1inf=data[index-1][4]; Real Delta2inf=data[index-1][5]; Real nn11inf = data[index-1][6]; Real nn33inf = data[index-1][7]; Real Psup=data[index][1]; Real Fsup=data[index][3]; Real Vsup=data[index][2]; Real Delta1sup=data[index][4]; Real Delta2sup=data[index][5]; Real nn11sup = data[index][6]; Real nn33sup = data[index][7]; result.V = Vinf+((Vsup-Vinf)/(Psup-Pinf))*(P-Pinf); result.F = Finf+((Fsup-Finf)/(Psup-Pinf))*(P-Pinf); result.delta1 = Delta1inf+((Delta1sup-Delta1inf)/(Psup-Pinf))*(P-Pinf); result.delta2 = Delta2inf+((Delta2sup-Delta2inf)/(Psup-Pinf))*(P-Pinf); result.nn11 = nn11inf + (nn11sup - nn11inf) / (Psup-Pinf) * (P-Pinf); result.nn33 = nn33inf + (nn33sup - nn33inf) / (Psup-Pinf) * (P-Pinf); return result; } } //compteur2+=1; for (int k=1; k < dataSize; ++k) // Length(data) ?? { if ( data[k][1] > P) // OK si P rangés ds l'ordre croissant { Real Pinf=data[k-1][1]; Real Finf=data[k-1][3]; Real Vinf=data[k-1][2]; Real Delta1inf=data[k-1][4]; Real Delta2inf=data[k-1][5]; Real nn11inf = data[k-1][6]; Real nn33inf = data[k-1][7]; Real Psup=data[k][1]; Real Fsup=data[k][3]; Real Vsup=data[k][2]; Real Delta1sup=data[k][4]; Real Delta2sup=data[k][5]; Real nn11sup = data[k][6]; Real nn33sup = data[k][7]; result.V = Vinf+((Vsup-Vinf)/(Psup-Pinf))*(P-Pinf); result.F = Finf+((Fsup-Finf)/(Psup-Pinf))*(P-Pinf); result.delta1 = Delta1inf+((Delta1sup-Delta1inf)/(Psup-Pinf))*(P-Pinf); result.delta2 = Delta2inf+((Delta2sup-Delta2inf)/(Psup-Pinf))*(P-Pinf); result.nn11 = nn11inf + (nn11sup - nn11inf) / (Psup-Pinf) * (P-Pinf); result.nn33 = nn33inf + (nn33sup - nn33inf) / (Psup-Pinf) * (P-Pinf); index = k; k=dataSize; } else if (data[k][1] == P) { result.V = data[k][2]; result.F = data[k][3]; result.delta1 = data[k][4]; result.delta2 = data[k][5]; result.nn11= data[k][6]; result.nn33= data[k][7]; index = k; k=dataSize; } } return result; } TableauD::~TableauD() {} std::ostream& operator<<(std::ostream& os, Tableau& T) { os << "Tableau : R=" << T.R << endl; for (unsigned int i=0; i& bodies = scene->bodies; Body::id_t MaxId = -1; BodyContainer::iterator bi = bodies->begin(); BodyContainer::iterator biEnd = bodies->end(); for( ; bi!=biEnd ; ++bi ) { MaxId=max(MaxId, (*bi)->getId()); } interactionsOnBody.resize(MaxId+1); for ( unsigned int i=0; i& I, *scene->interactions){ // parallel version using Engine::ompThreads variable not accessible, this function is not one of the Engine.. if (I->isReal()) { if (!hertzOn) {if (static_cast(I->phys.get())->meniscus) insert(I);} else {if (static_cast(I->phys.get())->meniscus) insert(I);} } } return initialized=true; } bool BodiesMenisciiList::insert(const shared_ptr< Interaction >& interaction) { checkLengthBuffer(interaction); interactionsOnBody[interaction->getId1()].push_back(interaction); interactionsOnBody[interaction->getId2()].push_back(interaction); return true; } bool BodiesMenisciiList::remove(const shared_ptr< Interaction >& interaction) { checkLengthBuffer(interaction); interactionsOnBody[interaction->getId1()].remove(interaction); interactionsOnBody[interaction->getId2()].remove(interaction); return true; } void BodiesMenisciiList::checkLengthBuffer(const shared_ptr& interaction) { Body::id_t maxBodyId = std::max(interaction->getId1(), interaction->getId2()); if (unsigned(maxBodyId) >= interactionsOnBody.size()) { interactionsOnBody.resize(maxBodyId+1); } } list< shared_ptr >& BodiesMenisciiList::operator[] (int index) { return interactionsOnBody[index]; } int BodiesMenisciiList::size() { return interactionsOnBody.size(); } void BodiesMenisciiList::display() { list< shared_ptr >::iterator firstMeniscus; list< shared_ptr >::iterator lastMeniscus; for ( unsigned int i=0; igetId1() << ", " << ( *firstMeniscus )->getId2() <<") "; else cerr << "(void)"; } } cerr << endl; } else cerr << "empty" << endl; } } BodiesMenisciiList::BodiesMenisciiList() { initialized=false; } trunk-2017.01a/pkg/dem/Law2_ScGeom_CapillaryPhys_Capillarity.hpp000066400000000000000000000215331304022710500244700ustar00rootroot00000000000000// // C++ Interface: Law2_ScGeom_CapillaryPhys_Capillarity /************************************************************************* * Copyright (C) 2006 by luc Scholtes * * luc.scholtes@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include /** This law allows one to take into account capillary forces/effects between spheres coming from the presence of interparticular liquid bridges (menisci). refs: - (french, lot of documentation) L. Scholtes, PhD thesis -> http://tel.archives-ouvertes.fr/tel-00363961/en/ - (english, less...) L. Scholtes et al. Micromechanics of granular materials with capillary effects. International Journal of Engineering Science 2009,(47)1, 64-75 The law needs ascii files M(r=i) with i=R1/R2 to work (downloaded from https://yade-dem.org/wiki/CapillaryTriaxialTest). They contain a set of results from the resolution of the Laplace-Young equation for different configurations of the interacting geometry (assuming a null wetting angle) and must be placed in the bin directory (where yade exec file is situated) to be taken into account. The control parameter is the capillary pressure (or suction) Delta_u, defined as the difference between gas and liquid pressure: Delta_u = u_gas - u_liquid Liquid bridges properties (volume V, extent over interacting grains delta1 and delta2) are computed as a result of Delta_u and the interacting geometry (spheres radii and interparticular distance) Rk: - the formulation is valid only for pendular menisci involving two grains (pendular regime). - an algorithm was developed by B. Chareyre to identify menisci overlaps on each spheres (menisci fusion). - some assumptions can be made to reduce capillary forces when menisci overlap (binary->F_cap=0 if at least 1 overlap, linear->F_cap=F_cap/numberOfOverlaps) */ /// !!! This version is deprecated. It should be updated to the new formalism -> ToDo !!! /// a class to store meniscus parameters -> Rk: is it really needed since CapillaryPhys exist? class MeniscusParameters { public : Real V; // adimentionnal volume of the meniscus : true volume / Rmax^3, see Annexe 1 of Scholtes2009d Real F; // adimentionnal capillary force for this meniscus : true force / ( 2 * pi * Rmax * superficial tension), (30) of Annexe1 of Scholtes2009d Real delta1; // angle defined Fig 2.5 Scholtes2009d Real delta2; // angle defined Fig 2.5 Scholtes2009d Real nn11; // CapillaryPhys.nn11 / R2^2 Real nn33; // CapillaryPhys.nn33 / R2^2 int index1; int index2; MeniscusParameters(); MeniscusParameters(const MeniscusParameters &source); ~MeniscusParameters(); }; /// R = ratio(RadiusParticle1 on RadiusParticle2). Here, 10 R values from interpolation files (yade/extra/capillaryFiles), R = 1, 1.1, 1.25, 1.5, 1.75, 2, 3, 4, 5, 10 const int NB_R_VALUES = 10; class capillarylaw; // the class defined below (end of file) class Interaction; ///This container class is used to check if meniscii overlap. Wet interactions are put in a series of lists, with one list per body. class BodiesMenisciiList { private: vector< list< shared_ptr > > interactionsOnBody; // would require use of OpenMPVector (lib/base/openmp-accu.hpp) for parallel coding, see http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg10842.html and msg11238.html //shared_ptr empty; public: BodiesMenisciiList(); BodiesMenisciiList(Scene*,bool);//TODO: remove? bool prepare(Scene*,bool); bool insert(const shared_ptr&); bool remove(const shared_ptr&); list< shared_ptr >& operator[] (int); int size(); void display(); void checkLengthBuffer(const shared_ptr&); bool initialized; }; /// This is the constitutive law class Law2_ScGeom_CapillaryPhys_Capillarity : public GlobalEngine { public : void checkFusion(); shared_ptr capillary; BodiesMenisciiList bodiesMenisciiList; void action(); void postLoad(Law2_ScGeom_CapillaryPhys_Capillarity&); bool hertzInitialized; bool hertzOn; bool showError; YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(Law2_ScGeom_CapillaryPhys_Capillarity,GlobalEngine,"This law allows one to take into account capillary forces/effects between spheres coming from the presence of interparticular liquid bridges (menisci).\n\nThe control parameter is the :yref:`capillary pressure` (or suction) Uc = Ugas - Uliquid. Liquid bridges properties (volume V, extent over interacting grains delta1 and delta2) are computed as a result of the defined capillary pressure and of the interacting geometry (spheres radii and interparticular distance).\n\nReferences: in english [Scholtes2009b]_; more detailed, but in french [Scholtes2009d]_.\n\nThe law needs ascii files M(r=i) with i=R1/R2 to work (see https://yade-dem.org/wiki/CapillaryTriaxialTest). These ASCII files contain a set of results from the resolution of the Laplace-Young equation for different configurations of the interacting geometry, assuming a null wetting angle.\n\nIn order to allow capillary forces between distant spheres, it is necessary to enlarge the bounding boxes using :yref:`Bo1_Sphere_Aabb::aabbEnlargeFactor` and make the Ig2 define define distant interactions via :yref:`interactionDetectionFactor`. It is also necessary to disable interactions removal by the constitutive law (:yref:`Law2=True`). The only combinations of laws supported are currently capillary law + :yref:`Law2_ScGeom_FrictPhys_CundallStrack` and capillary law + :yref:`Law2_ScGeom_MindlinPhys_Mindlin` (and the other variants of Hertz-Mindlin).\n\nSee CapillaryPhys-example.py for an example script.", ((Real,capillaryPressure,0.,,"Value of the capillary pressure Uc defined as Uc=Ugas-Uliquid")) ((bool,fusionDetection,false,,"If true potential menisci overlaps are checked, computing :yref:`fusionNumber` for each capillary interaction, and reducing :yref:`fCap` according to :yref:`binaryFusion`")) ((bool,binaryFusion,true,,"If true, capillary forces are set to zero as soon as, at least, 1 overlap (menisci fusion) is detected. Otherwise :yref:`fCap` = :yref:`fCap` / (:yref:`fusionNumber` + 1 )")) ((bool,createDistantMeniscii,false,,"Generate meniscii between distant spheres? Else only maintain the existing ones. For modeling a wetting path this flag should always be false. For a drying path it should be true for one step (initialization) then false, as in the logic of [Scholtes2009c]_")) ((Real,surfaceTension,0.073,,"Value of considered surface tension")) // (0.073 N/m is water tension at 20 Celsius degrees) ((string,suffCapFiles,"",,"Capillary files suffix: M(r=X)suffCapFiles")) ,,/*constructor*/ hertzInitialized = false; hertzOn = false; showError = true; , ); }; class TableauD // Laplace solutions for a given r, and a given D (and a given contact angle): pieces of one capillary file { public: Real D; // one cst D value in each TableauD (the one appearing last line of corresponding group D=cst in the capillary file) std::vector > data; MeniscusParameters Interpolate3(Real P, int& index); // does the interpolation on uc* TableauD(); TableauD(std::ifstream& file); ~TableauD(); }; // Fonction d'ecriture de tableau, utilisee dans le constructeur pour test //TODO: translate this in english class Tableau; std::ostream& operator<<(std::ostream& os, Tableau& T); class Tableau // Laplace solutions for a given r (and a given contact angle): one capillary file { public: Real R; std::vector full_data; // members of full_data are the different TableauD, for different D. MeniscusParameters Interpolate2(Real D, Real P, int& index1, int& index2); // does the interpolation on d* (returning no meniscus when d* > the greatest D of the file) std::ifstream& operator<< (std::ifstream& file); Tableau(); Tableau(const char* filename); ~Tableau(); }; class capillarylaw // class for a whole set of capillary files M(r=..) { public: capillarylaw(); std::vector data_complete; // data_complete includes, in ascending order of r, all capillary files: each Tableau of data_complete is one capillary file MeniscusParameters interpolate(Real R1, Real R2, Real D, Real P, int* index); void fill (const char* filename); }; REGISTER_SERIALIZABLE(Law2_ScGeom_CapillaryPhys_Capillarity); trunk-2017.01a/pkg/dem/Law2_ScGeom_CapillaryPhys_Capillarity1.cpp000066400000000000000000000672311304022710500245510ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by luc Scholtes * * luc.scholtes@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ //Modifs : Parameters renamed as MeniscusParameters //id1/id2 as id1 is the smallest grain, FIXME : wetting angle? //FIXME : in triaxialStressController, change test about null force in updateStiffnessccc //keep this #ifdef as long as you don't really want to realize a final version publicly, it will save compilation time for everyone else //when you want it compiled, you can just uncomment the following line //#define LAW2_SCGEOM_CAPILLARYPHYS_Capillarity1 #ifdef LAW2_SCGEOM_CAPILLARYPHYS_Capillarity1 #include #include #include #include #include #include #include #include #include DT Law2_ScGeom_CapillaryPhys_Capillarity1::dtVbased; DT Law2_ScGeom_CapillaryPhys_Capillarity1::dtPbased; Real Law2_ScGeom_CapillaryPhys_Capillarity1::intEnergy() { Real energy=0; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; ScGeom* currentGeometry = static_cast(I->geom.get()); CapillaryPhys1* phys = dynamic_cast(I->phys.get()); if(phys) { if (phys->SInterface!=0){ energy += liquidTension*(phys->SInterface-4*3.141592653589793238462643383279502884*(pow(currentGeometry->radius1,2))-4*3.141592653589793238462643383279502884*(pow(currentGeometry->radius2,2)));} } } return energy; } Real Law2_ScGeom_CapillaryPhys_Capillarity1::wnInterface() { Real wn=0; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; ScGeom* currentGeometry = static_cast(I->geom.get()); CapillaryPhys1* phys = dynamic_cast(I->phys.get()); if(phys) { if (phys->SInterface!=0){ wn += (phys->SInterface-2*3.141592653589793238462643383279502884*(pow(currentGeometry->radius1,2)*(1+cos(phys->Delta1))+pow(currentGeometry->radius2,2)*(1+cos(phys->Delta2)))); } } } return wn; } Real Law2_ScGeom_CapillaryPhys_Capillarity1::swInterface() { Real sw=0; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; ScGeom* currentGeometry = static_cast(I->geom.get()); CapillaryPhys1* phys = dynamic_cast(I->phys.get()); if(phys) { sw += (2*3.141592653589793238462643383279502884*(pow(currentGeometry->radius1,2)*(1-cos(phys->Delta1))+pow(currentGeometry->radius2,2)*(1-cos(phys->Delta2)))); } } return sw; } Real Law2_ScGeom_CapillaryPhys_Capillarity1::waterVolume() { Real volume=0; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; CapillaryPhys1* phys = dynamic_cast(I->phys.get()); if(phys) { volume += phys->vMeniscus;} } return volume; } void Law2_ScGeom_CapillaryPhys_Capillarity1::triangulateData() { /// We get data from a file and input them in triangulations if (solutions.size()>0) {LOG_WARN("Law2_ScGeom_CapillaryPhys_Capillarity1 asking triangulation for the second time. Ignored."); return;} ifstream file (inputFilename.c_str()); if (!file.is_open()) { LOG_ERROR("No data file found for capillary law. Check path and inputFilename."); return;} // convention R,v,d,s,e,f,p,a1,a2,dummy (just for the example, define your own, // dummy is because has too much values per line - with one useless extra colum,) MeniscusPhysicalData dat; double ending; while ( file.good() ) { file >>dat.succion>>dat.force>>dat.distance>>dat.volume>>dat.surface>>dat.arcLength>>dat.delta1>>dat.delta2>>dat.R>>ending; dat.ending=(bool) ending; solutions.push_back(dat); } file.close(); // Make lists of points with index, so we can use range insertion, more efficient // see http://doc.cgal.org/latest/Triangulation_3/index.html#Triangulation_3SettingInformationWhileInserting std::vector< std::pair > pointsP, pointsV; for (unsigned int k=0; kinteractions->begin(); InteractionContainer::iterator iiEnd = scene->interactions->end(); if (imposePressure) { solver(capillaryPressure,switched); } else{ if (((totalVolumeConstant || (!totalVolumeConstant && firstIteration==1)) && totalVolumeofWater!=-1) || (totalVolumeConstant && totalVolumeofWater==-1)) { if (!totalVolumeConstant) x=1; totalVolumeConstant=1; Real p0=capillaryPressure; Real slope; Real eps=0.0000000001; solver(p0,switched); Real V0=waterVolume(); if (totalVolumeConstant && totalVolumeofWater==-1 && firstIteration==1){ totalVolumeofWater=V0; firstIteration+=1; } Real p1=capillaryPressure+0.1; solver(p1,switched); Real V1=waterVolume(); while (abs((totalVolumeofWater-V1)/totalVolumeofWater)>eps){ slope= (p1-p0)/(V1-V0); p0=p1; V0=V1; p1=p1-slope*(V1-totalVolumeofWater); if (p1<0) { cout<< "The requested volume of water is quite big, the simulation will continue at constant suction.:"<< p0 <interactions->begin(); ii!=iiEnd ; ++ii) { CapillaryPhys1* phys = dynamic_cast((*ii)->phys.get()); if ((*ii)->isReal() && phys-> computeBridge==true) { CapillaryPhys1* cundallContactPhysics=NULL; MindlinCapillaryPhys* mindlinContactPhysics=NULL; if (!hertzOn) cundallContactPhysics = static_cast((*ii)->phys.get());//use CapillaryPhys for linear model else mindlinContactPhysics = static_cast((*ii)->phys.get());//use MindlinCapillaryPhys for hertz model if ((hertzOn && mindlinContactPhysics->meniscus) || (!hertzOn && cundallContactPhysics->meniscus)) { if (fusionDetection) {//version with effect of fusion //BINARY VERSION : if fusionNumber!=0 then no capillary force short int& fusionNumber = hertzOn?mindlinContactPhysics->fusionNumber:cundallContactPhysics->fusionNumber; if (binaryFusion) { if (fusionNumber!=0) { //cerr << "fusion" << endl; hertzOn?mindlinContactPhysics->fCap:cundallContactPhysics->fCap = Vector3r::Zero(); continue; } } //LINEAR VERSION : capillary force is divided by (fusionNumber + 1) - NOTE : any decreasing function of fusionNumber can be considered in fact else if (fusionNumber !=0) hertzOn?mindlinContactPhysics->fCap:cundallContactPhysics->fCap /= (fusionNumber+1.); } scene->forces.addForce((*ii)->getId1(), hertzOn?mindlinContactPhysics->fCap:cundallContactPhysics->fCap); scene->forces.addForce((*ii)->getId2(),-(hertzOn?mindlinContactPhysics->fCap:cundallContactPhysics->fCap)); } } } } void Law2_ScGeom_CapillaryPhys_Capillarity1::checkFusion() { //Reset fusion numbers InteractionContainer::iterator ii = scene->interactions->begin(); InteractionContainer::iterator iiEnd = scene->interactions->end(); for( ; ii!=iiEnd ; ++ii ) { if ((*ii)->isReal()) { if (!hertzOn) static_cast((*ii)->phys.get())->fusionNumber=0; else static_cast((*ii)->phys.get())->fusionNumber=0; } } std::list< shared_ptr >::iterator firstMeniscus, lastMeniscus, currentMeniscus; Real angle1 = -1.0; Real angle2 = -1.0; for ( int i=0; i< bodiesMenisciiList.size(); ++i ) { // i is the index (or id) of the body being tested CapillaryPhys1* cundallInteractionPhysics1=NULL; MindlinCapillaryPhys* mindlinInteractionPhysics1=NULL; CapillaryPhys1* cundallInteractionPhysics2=NULL; MindlinCapillaryPhys* mindlinInteractionPhysics2=NULL; if ( !bodiesMenisciiList[i].empty() ) { lastMeniscus = bodiesMenisciiList[i].end(); for ( firstMeniscus=bodiesMenisciiList[i].begin(); firstMeniscus!=lastMeniscus; ++firstMeniscus ) { //FOR EACH MENISCUS ON THIS BODY... currentMeniscus = firstMeniscus; ++currentMeniscus; if (!hertzOn) { cundallInteractionPhysics1 = YADE_CAST((*firstMeniscus)->phys.get()); if (i == (*firstMeniscus)->getId1()) angle1=cundallInteractionPhysics1->Delta1;//get angle of meniscus1 on body i else angle1=cundallInteractionPhysics1->Delta2; } else { mindlinInteractionPhysics1 = YADE_CAST((*firstMeniscus)->phys.get()); if (i == (*firstMeniscus)->getId1()) angle1=mindlinInteractionPhysics1->Delta1;//get angle of meniscus1 on body i else angle1=mindlinInteractionPhysics1->Delta2; } for ( ; currentMeniscus!= lastMeniscus; ++currentMeniscus) { //... CHECK FUSION WITH ALL OTHER MENISCII ON THE BODY if (!hertzOn) { cundallInteractionPhysics2 = YADE_CAST((*currentMeniscus)->phys.get()); if (i == (*currentMeniscus)->getId1()) angle2=cundallInteractionPhysics2->Delta1;//get angle of meniscus2 on body i else angle2=cundallInteractionPhysics2->Delta2; } else { mindlinInteractionPhysics2 = YADE_CAST((*currentMeniscus)->phys.get()); if (i == (*currentMeniscus)->getId1()) angle2=mindlinInteractionPhysics2->Delta1;//get angle of meniscus2 on body i else angle2=mindlinInteractionPhysics2->Delta2; } if (angle1==0 || angle2==0) cerr << "THIS SHOULD NOT HAPPEN!!"<< endl; Vector3r normalFirstMeniscus = YADE_CAST((*firstMeniscus)->geom.get())->normal; Vector3r normalCurrentMeniscus = YADE_CAST((*currentMeniscus)->geom.get())->normal; Real normalDot = 0; if ((*firstMeniscus)->getId1() == (*currentMeniscus)->getId1() || (*firstMeniscus)->getId2() == (*currentMeniscus)->getId2()) normalDot = normalFirstMeniscus.dot(normalCurrentMeniscus); else normalDot = - (normalFirstMeniscus.dot(normalCurrentMeniscus)); Real normalAngle = 0; if (normalDot >= 0 ) normalAngle = Mathr::FastInvCos0(normalDot); else normalAngle = ((Mathr::PI) - Mathr::FastInvCos0(-(normalDot))); if ((angle1+angle2)*Mathr::DEG_TO_RAD > normalAngle) { if (!hertzOn) { ++(cundallInteractionPhysics1->fusionNumber); //count +1 if 2 meniscii are overlaping ++(cundallInteractionPhysics2->fusionNumber); } else { ++(mindlinInteractionPhysics1->fusionNumber); ++(mindlinInteractionPhysics2->fusionNumber); } }; } } } } } BodiesMenisciiList1::BodiesMenisciiList1(Scene * scene) { initialized=false; prepare(scene); } bool BodiesMenisciiList1::prepare(Scene * scene) { interactionsOnBody.clear(); shared_ptr& bodies = scene->bodies; Body::id_t MaxId = -1; BodyContainer::iterator bi = bodies->begin(); BodyContainer::iterator biEnd = bodies->end(); for( ; bi!=biEnd ; ++bi ) { MaxId=max(MaxId, (*bi)->getId()); } interactionsOnBody.resize(MaxId+1); for ( unsigned int i=0; iinteractions->begin(); InteractionContainer::iterator iiEnd = scene->interactions->end(); for( ; ii!=iiEnd ; ++ii ) { if ((*ii)->isReal()) { if (static_cast((*ii)->phys.get())->meniscus) insert(*ii); } } return initialized=true; } bool BodiesMenisciiList1::insert(const shared_ptr< Interaction >& interaction) { interactionsOnBody[interaction->getId1()].push_back(interaction); interactionsOnBody[interaction->getId2()].push_back(interaction); return true; } bool BodiesMenisciiList1::remove(const shared_ptr< Interaction >& interaction) { interactionsOnBody[interaction->getId1()].remove(interaction); interactionsOnBody[interaction->getId2()].remove(interaction); return true; } list< shared_ptr >& BodiesMenisciiList1::operator[] (int index) { return interactionsOnBody[index]; } int BodiesMenisciiList1::size() { return interactionsOnBody.size(); } void BodiesMenisciiList1::display() { list< shared_ptr >::iterator firstMeniscus; list< shared_ptr >::iterator lastMeniscus; for ( unsigned int i=0; iget() ) cerr << "(" << ( *firstMeniscus )->getId1() << ", " << ( *firstMeniscus )->getId2() <<") "; else cerr << "(void)"; } } cerr << endl; } else cerr << "empty" << endl; } } BodiesMenisciiList1::BodiesMenisciiList1() { initialized=false; } void Law2_ScGeom_CapillaryPhys_Capillarity1::solver(Real suction,bool reset) { if (!scene) cerr << "scene not defined!"; shared_ptr& bodies = scene->bodies; if (dtPbased.number_of_vertices ()<1 ) triangulateData(); if (fusionDetection && !bodiesMenisciiList.initialized) bodiesMenisciiList.prepare(scene); InteractionContainer::iterator ii = scene->interactions->begin(); InteractionContainer::iterator iiEnd = scene->interactions->end(); bool hertzInitialized = false; Real i=0; for (; ii!=iiEnd ; ++ii) { i+=1; CapillaryPhys1* phys = dynamic_cast((*ii)->phys.get());//////////////////////////////////////////////////////////////////////////////////////////// if ((*ii)->isReal() && phys-> computeBridge==true) { const shared_ptr& interaction = *ii; if (!hertzInitialized) {//NOTE: We are assuming that only one type is used in one simulation here if (CapillaryPhys1::getClassIndexStatic()==interaction->phys->getClassIndex()) hertzOn=false; else if (MindlinCapillaryPhys::getClassIndexStatic()==interaction->phys->getClassIndex()) hertzOn=true; else LOG_ERROR("The capillary law is not implemented for interactions using"<phys->getClassName()); } hertzInitialized = true; CapillaryPhys1* cundallContactPhysics=NULL; MindlinCapillaryPhys* mindlinContactPhysics=NULL; /// contact physics depends on the contact law, that is used (either linear model or hertz model) if (!hertzOn) cundallContactPhysics = static_cast(interaction->phys.get());//use CapillaryPhys for linear model else mindlinContactPhysics = static_cast(interaction->phys.get());//use MindlinCapillaryPhys for hertz model unsigned int id1 = interaction->getId1(); unsigned int id2 = interaction->getId2(); /// interaction geometry search (this test is to compute capillarity only between spheres (probably a better way to do that) int geometryIndex1 = (*bodies)[id1]->shape->getClassIndex(); // !!! int geometryIndex2 = (*bodies)[id2]->shape->getClassIndex(); if (!(geometryIndex1 == geometryIndex2)) continue; /// definition of interacting objects (not necessarily in contact) ScGeom* currentContactGeometry = static_cast(interaction->geom.get()); /// Interacting Grains: // If you want to define a ratio between YADE sphere size and real sphere size Real alpha=1; Real R1 = alpha*std::max(currentContactGeometry->radius2,currentContactGeometry->radius1); Real R2 =alpha*std::min(currentContactGeometry->radius2,currentContactGeometry->radius1); shared_ptr& bodies = scene->bodies; Real N=bodies->size(); Real epsilon1,epsilon2; Real ran1= (N-id1+0.5)/(N+1); Real ran2= (N-id2+0.5)/(N+1); epsilon1 = epsilonMean*(2*(ran1-0.5)* disp +1);//addednow epsilon2 = epsilonMean*(2*(ran2-0.5)* disp +1); // cout << epsilon1 << "separate" <penetrationDepth))+epsilon1*R1+epsilon2*R2; if ((currentContactGeometry->penetrationDepth>=0)|| D<=0 || createDistantMeniscii) { //||(scene->iter < 1) ) // a simplified way to define meniscii everywhere if (!hertzOn) { if (fusionDetection && !cundallContactPhysics->meniscus) bodiesMenisciiList.insert((*ii)); cundallContactPhysics->meniscus=true; } else { if (fusionDetection && !mindlinContactPhysics->meniscus) bodiesMenisciiList.insert((*ii)); mindlinContactPhysics->meniscus=true; } } Real Dinterpol = D/R1; /// Suction (Capillary pressure): if (imposePressure || (!imposePressure && totalVolumeConstant)){ Real Pinterpol = 0; if (!hertzOn) Pinterpol = cundallContactPhysics->isBroken ? 0 : suction*R1/liquidTension; else Pinterpol = mindlinContactPhysics->isBroken ? 0 : suction*R1/liquidTension; if (!hertzOn) cundallContactPhysics->capillaryPressure = suction; else mindlinContactPhysics->capillaryPressure = suction; /// Capillary solution finder: if ((Pinterpol>=0) && (hertzOn? mindlinContactPhysics->meniscus : cundallContactPhysics->meniscus)) {//FIXME: need an "else {delete}" MeniscusPhysicalData solution = interpolate1(dtPbased,K::Point_3(R2/R1, Pinterpol, Dinterpol), cundallContactPhysics->m, solutions, reset); /// capillary adhesion force Real Finterpol = solution.force; Vector3r fCap = Finterpol*R1*liquidTension*currentContactGeometry->normal; if (!hertzOn) cundallContactPhysics->fCap = fCap; else mindlinContactPhysics->fCap = fCap; /// meniscus volume //FIXME: hardcoding numerical constants is bad practice generaly, and it probably reveals a flaw in that case (Bruno) Real Vinterpol = solution.volume*pow(R1,3); Real SInterface = solution.surface*pow(R1,2); if (!hertzOn) { cundallContactPhysics->vMeniscus = Vinterpol; cundallContactPhysics->SInterface = SInterface; if (Vinterpol > 0) cundallContactPhysics->meniscus = true; else cundallContactPhysics->meniscus = false; } else { mindlinContactPhysics->vMeniscus = Vinterpol; if (Vinterpol > 0) mindlinContactPhysics->meniscus = true; else mindlinContactPhysics->meniscus = false; } if (cundallContactPhysics->meniscus== false) cundallContactPhysics->SInterface=4*3.141592653589793238462643383279502884*(pow(R1,2))+4*3.141592653589793238462643383279502884*(pow(R2,2)); if (!Vinterpol) { if ((fusionDetection) || (hertzOn ? mindlinContactPhysics->isBroken : cundallContactPhysics->isBroken)) bodiesMenisciiList.remove((*ii)); /// FIXME: the following D>(...) test is wrong, should be based on penetrationDepth, and should "continue" after erasing if (D>((interactionDetectionFactor-1)*(currentContactGeometry->radius2+currentContactGeometry->radius1))) scene->interactions->requestErase(interaction); } /// wetting angles if (!hertzOn) { cundallContactPhysics->Delta1 = max(solution.delta1,solution.delta2); cundallContactPhysics->Delta2 = min(solution.delta1,solution.delta2); } else { mindlinContactPhysics->Delta1 = max(solution.delta1,solution.delta2); mindlinContactPhysics->Delta2 = min(solution.delta1,solution.delta2); } } } else{ if (cundallContactPhysics->vMeniscus==0 and cundallContactPhysics->capillaryPressure!=0){//FIXME: test capillaryPressure consistently (!0 or >0 or >=0?!) Real Pinterpol = 0; if (!hertzOn) Pinterpol = cundallContactPhysics->isBroken ? 0 : cundallContactPhysics->capillaryPressure*R1/liquidTension; else Pinterpol = mindlinContactPhysics->isBroken ? 0 : cundallContactPhysics->capillaryPressure*R1/liquidTension; // if (!hertzOn) cundallContactPhysics->capillaryPressure = suction; // else mindlinContactPhysics->capillaryPressure = suction; /// Capillary solution finder: if ((Pinterpol>=0) && (hertzOn? mindlinContactPhysics->meniscus : cundallContactPhysics->meniscus)) { MeniscusPhysicalData solution = interpolate1(dtPbased,K::Point_3(R2/R1, Pinterpol, Dinterpol), cundallContactPhysics->m, solutions, reset); /// capillary adhesion force Real Finterpol = solution.force; Vector3r fCap = Finterpol*R1*liquidTension*currentContactGeometry->normal; if (!hertzOn) cundallContactPhysics->fCap = fCap; else mindlinContactPhysics->fCap = fCap; /// meniscus volume //FIXME: hardcoding numerical constants is bad practice generaly, and it probably reveals a flaw in that case (Bruno) Real Vinterpol = solution.volume*pow(R1,3); Real SInterface = solution.surface*pow(R1,2); if (!hertzOn) { cundallContactPhysics->vMeniscus = Vinterpol; cundallContactPhysics->SInterface = SInterface; if (Vinterpol > 0) cundallContactPhysics->meniscus = true; else cundallContactPhysics->meniscus = false; } else { mindlinContactPhysics->vMeniscus = Vinterpol; if (Vinterpol > 0) mindlinContactPhysics->meniscus = true; else mindlinContactPhysics->meniscus = false; } if (cundallContactPhysics->meniscus== false) cundallContactPhysics->SInterface=4*3.141592653589793238462643383279502884*(pow(R1,2))+4*3.141592653589793238462643383279502884*(pow(R2,2)); if (!Vinterpol) { if ((fusionDetection) || (hertzOn ? mindlinContactPhysics->isBroken : cundallContactPhysics->isBroken)) bodiesMenisciiList.remove((*ii)); if (D>((interactionDetectionFactor-1)*(currentContactGeometry->radius2+currentContactGeometry->radius1))) scene->interactions->requestErase(interaction); } /// wetting angles if (!hertzOn) { cundallContactPhysics->Delta1 = max(solution.delta1,solution.delta2); cundallContactPhysics->Delta2 = min(solution.delta1,solution.delta2); } else { mindlinContactPhysics->Delta1 = max(solution.delta1,solution.delta2); mindlinContactPhysics->Delta2 = min(solution.delta1,solution.delta2); } } } else{ Real Vinterpol = 0; if (!hertzOn) { Vinterpol = cundallContactPhysics->vMeniscus/pow(R1,3); } else Vinterpol = mindlinContactPhysics->vMeniscus; /// Capillary solution finder: if ((hertzOn? mindlinContactPhysics->meniscus : cundallContactPhysics->meniscus)) { MeniscusPhysicalData solution = interpolate2(dtVbased,K::Point_3(R2/R1, Vinterpol, Dinterpol), cundallContactPhysics->m, solutions,reset); /// capillary adhesion force Real Finterpol = solution.force; Vector3r fCap = Finterpol*R1*liquidTension*currentContactGeometry->normal; if (!hertzOn) cundallContactPhysics->fCap = fCap; else mindlinContactPhysics->fCap = fCap; /// suction and interfacial area Real Pinterpol = solution.succion*liquidTension/R1; Real SInterface = solution.surface*pow(R1,2); if (!hertzOn) { cundallContactPhysics->capillaryPressure = Pinterpol; cundallContactPhysics->SInterface = SInterface; if (Finterpol > 0) cundallContactPhysics->meniscus = true; else{ cundallContactPhysics->vMeniscus=0; cundallContactPhysics->meniscus = false; } } else { mindlinContactPhysics->capillaryPressure = Pinterpol; if (Finterpol > 0) mindlinContactPhysics->meniscus = true; else { cundallContactPhysics->vMeniscus=0; mindlinContactPhysics->meniscus = false; } } if (!Vinterpol) { if ((fusionDetection) || (hertzOn ? mindlinContactPhysics->isBroken : cundallContactPhysics->isBroken)) bodiesMenisciiList.remove((*ii)); if (D>((interactionDetectionFactor-1)*(currentContactGeometry->radius2+currentContactGeometry->radius1))) scene->interactions->requestErase(interaction); } /// wetting angles if (!hertzOn) { cundallContactPhysics->Delta1 = max(solution.delta1,solution.delta2); cundallContactPhysics->Delta2 = min(solution.delta1,solution.delta2); } else { mindlinContactPhysics->Delta1 = max(solution.delta1,solution.delta2); mindlinContactPhysics->Delta2 = min(solution.delta1,solution.delta2); } } } } ///interaction is not real //If the interaction is not real, it should not be in the list } else if (fusionDetection) bodiesMenisciiList.remove((*ii)); } if (fusionDetection) checkFusion(); } #endif //LAW2_SCGEOM_CAPILLARYPHYS_Capillarity1 trunk-2017.01a/pkg/dem/Law2_ScGeom_CapillaryPhys_Capillarity1.hpp000066400000000000000000000176431304022710500245600ustar00rootroot00000000000000// // C++ Interface: Law2_ScGeom_CapillaryPhys_Capillarity /************************************************************************* * Copyright (C) 2006 by luc Scholtes * * luc.scholtes@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include #include #include #include #include #include #include #include /** This law allows one to take into account capillary forces/effects between spheres coming from the presence of interparticular liquid bridges (menisci). refs: - (french, lot of documentation) L. Scholtes, PhD thesis -> http://tel.archives-ouvertes.fr/tel-00363961/en/ - (english, less...) L. Scholtes et al. Micromechanics of granular materials with capillary effects. International Journal of Engineering Science 2009,(47)1, 64-75 The law needs ascii files M(r=i) with i=R1/R2 to work (downloaded from https://yade-dem.org/wiki/CapillaryTriaxialTest). They contain a set of results from the resolution of the Laplace-Young equation for different configurations of the interacting geometry and must be placed in the bin directory (where yade exec file is situated) to be taken into account. The control parameter is the capillary pressure (or suction) Delta_u, defined as the difference between gas and liquid pressure: Delta_u = u_gas - u_liquid Liquid bridges properties (volume V, extent over interacting grains delta1 and delta2) are computed as a result of Delta_u and the interacting geometry (spheres radii and interparticular distance) Rk: - the formulation is valid only for pendular menisci involving two grains (pendular regime). - an algorithm was developed by B. Chareyre to identify menisci overlaps on each spheres (menisci fusion). - some assumptions can be made to reduce capillary forces when menisci overlap (binary->F_cap=0 if at least 1 overlap, linear->F_cap=F_cap/numberOfOverlaps) */ /// !!! This version is deprecated. It should be updated to the new formalism -> ToDo !!! /// R = ratio(RadiusParticle1 on RadiusParticle2). Here, 10 R values from interpolation files (yade/extra/capillaryFiles), R = 1, 0.1, 0.2, 0.3, 0.4, 0.5, 0.6, 0.7, 0.8, 0.9 //const int NB_R_VALUES = 10; // class capillarylaw1; // fait appel a la classe def plus bas class Interaction; ///This container class is used to check if meniscii overlap. Wet interactions are put in a series of lists, with one list per body. class BodiesMenisciiList1 { private: vector< list< shared_ptr > > interactionsOnBody; //shared_ptr empty; public: BodiesMenisciiList1(); BodiesMenisciiList1(Scene* body); bool prepare(Scene* scene); bool insert(const shared_ptr& interaction); bool remove(const shared_ptr& interaction); list< shared_ptr >& operator[] (int index); int size(); void display(); bool initialized; }; /// This is the constitutive law class Law2_ScGeom_CapillaryPhys_Capillarity1 : public GlobalEngine { public : void checkFusion(); static DT dtVbased; static DT dtPbased; std::vector solutions; int switchTriangulation;//to detect switches between P-based and V-based data BodiesMenisciiList1 bodiesMenisciiList; void action(); Real intEnergy(); Real swInterface(); Real wnInterface(); Real waterVolume(); void solver(Real suction, bool reset); void triangulateData(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Law2_ScGeom_CapillaryPhys_Capillarity1,GlobalEngine,"This law allows one to take into account capillary forces/effects between spheres coming from the presence of interparticular liquid bridges (menisci).\n\nThe control parameter is the capillary pressure (or suction) Uc = ugas - Uliquid. Liquid bridges properties (volume V, extent over interacting grains delta1 and delta2) are computed as a result of the defined capillary pressure and of the interacting geometry (spheres radii and interparticular distance).\n\nReferences: in english [Scholtes2009b]_; more detailed, but in french [Scholtes2009d]_.\n\nThe law needs ascii files M(r=i) with i=R1/R2 to work (see https://yade-dem.org/index.php/CapillaryTriaxialTest). These ASCII files contain a set of results from the resolution of the Laplace-Young equation for different configurations of the interacting geometry." "\n\nIn order to allow capillary forces between distant spheres, it is necessary to enlarge the bounding boxes using :yref:`Bo1_Sphere_Aabb::aabbEnlargeFactor` and make the Ig2 define define distant interactions via:yref:`interactionDetectionFactor`. It is also necessary to disable interactions removal by the constitutive law (:yref:`Law2=True`). The only combinations of laws supported are currently capillary law + :yref:`Law2_ScGeom_FrictPhys_CundallStrack` and capillary law + :yref:`Law2_ScGeom_MindlinPhys_Mindlin` (and the other variants of Hertz-Mindlin).\n\nSee CapillaryPhys-example.py for an example script.", ((Real,capillaryPressure,0.,,"Value of the capillary pressure Uc defines as Uc=Ugas-Uliquid")) ((Real,totalVolumeofWater,-1.,,"Value of imposed water volume")) ((Real,liquidTension,0.073,,"Value of the superficial water tension in N/m")) ((Real,epsilonMean,0.,," Mean Value of the roughness"))//old value was epsilon ((Real,disp,0.,," Dispersion from the mean Value of the roughness"))//added now ((Real,interactionDetectionFactor,1.5,,"defines critical distance for deleting interactions. Must be consistent with the Ig2 value.")) ((bool,fusionDetection,false,,"If true potential menisci overlaps are checked")) ((bool,initialized,false,," ")) ((bool,binaryFusion,true,,"If true, capillary forces are set to zero as soon as, at least, 1 overlap (menisci fusion) is detected")) ((bool,hertzOn,false,,"|yupdate| true if hertz model is used")) ((string,inputFilename,string("capillaryfile.txt"),,"the file with meniscus solutions, used for interpolation.")) ((bool,createDistantMeniscii,false,,"Generate meniscii between distant spheres? Else only maintain the existing one. For modeling a wetting path this flag should always be false. For a drying path it should be true for one step (initialization) then false, as in the logic of [Scholtes2009c]_")) ((bool,imposePressure,true,," If True, suction is imposed and is constant if not Volume is imposed-Undrained test")) ((bool,totalVolumeConstant,true,," in undrained test there are 2 options, If True, the total volume of water is imposed,if false the volume of each meniscus is kept constant: in this case capillary pressure can be imposed for initial distribution of meniscus or it is the total volume that can be imposed initially")) ,switchTriangulation=-1, .def("intEnergy",&Law2_ScGeom_CapillaryPhys_Capillarity1::intEnergy,"define the energy of interfaces in unsaturated pendular state") // .def("sninterface",&Law2_ScGeom_CapillaryPhys_Capillarity1::sninterface,"define the amount of solid-non-wetting interfaces in unsaturated pendular state") .def("swInterface",&Law2_ScGeom_CapillaryPhys_Capillarity1::swInterface,"define the amount of solid-wetting interfaces in unsaturated pendular state") .def("wnInterface",&Law2_ScGeom_CapillaryPhys_Capillarity1::wnInterface,"define the amount of wetting-non-wetiing interfaces in unsaturated pendular state") .def("waterVolume",&Law2_ScGeom_CapillaryPhys_Capillarity1::waterVolume,"return the total value of water in the sample") ); }; REGISTER_SERIALIZABLE(Law2_ScGeom_CapillaryPhys_Capillarity1); trunk-2017.01a/pkg/dem/LudingPM.cpp000066400000000000000000000160431304022710500166770ustar00rootroot00000000000000#include"LudingPM.hpp" #include #include #include #include #include YADE_PLUGIN((LudingMat)(LudingPhys)(Ip2_LudingMat_LudingMat_LudingPhys)(Law2_ScGeom_LudingPhys_Basic)); LudingMat::~LudingMat(){} LudingPhys::~LudingPhys(){} void Ip2_LudingMat_LudingMat_LudingPhys::go(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction) { if(interaction->phys) return; LudingMat* mat1 = static_cast(b1.get()); LudingMat* mat2 = static_cast(b2.get()); const Real k11 = mat1->k1; const Real k12 = mat2->k1; const Real kp1 = mat1->kp; const Real kp2 = mat2->kp; const Real kc1 = mat1->kc; const Real kc2 = mat2->kc; const Real G01 = mat1->G0; const Real G02 = mat2->G0; const Real PhiF1 = mat1->PhiF; const Real PhiF2 = mat2->PhiF; LudingPhys* phys = new LudingPhys(); phys->k1 = this->reduced(k11, k12); phys->kp = this->reduced(kp1, kp2); phys->kc = this->reduced(kc1, kc2); phys->PhiF = this->reduced(PhiF1, PhiF2); phys->k2 = 0.0; phys->G0 = this->reduced(G01, G02); Real a1 = 0.0; Real a2 = 0.0; Sphere* s1=dynamic_cast(Body::byId(interaction->getId1())->shape.get()); Sphere* s2=dynamic_cast(Body::byId(interaction->getId2())->shape.get()); if (s1 and s2) { a1 = s1->radius; a2 = s2->radius; } else if (s1 and not(s2)) { a1 = s1->radius; } else { a2 = s2->radius; } if (phys->k1 >= phys->kp) { throw runtime_error("k1 have to be less as kp!"); // [Luding2008], sentence after equation (6); kp = k2^ // [Singh2013], sentence after equation (6) } phys->tangensOfFrictionAngle = std::tan(std::min(mat1->frictionAngle, mat2->frictionAngle)); phys->shearForce = Vector3r(0,0,0); phys->DeltMax = 0.0; phys->DeltNull = 0.0; phys->DeltPMax = phys->kp/(phys->kp-phys->k1)*phys->PhiF*2*a1*a2/(a1+a2); // [Luding2008], equation (7) // [Singh2013], equation (11) phys->DeltPNull = phys->PhiF*2*a1*a2/(a1+a2); // [Singh2013], equation (12) phys->DeltPrev = 0.0; phys->DeltMin = 0.0; interaction->phys = shared_ptr(phys); } Real Ip2_LudingMat_LudingMat_LudingPhys::reduced(Real a1, Real a2){ Real a = (a1?1/a1:0) + (a2?1/a2:0); a = a?1/a:0; return 2.0*a; } bool Law2_ScGeom_LudingPhys_Basic::go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I){ const ScGeom& geom=*static_cast(_geom.get()); LudingPhys& phys=*static_cast(_phys.get()); const int id1 = I->getId1(); const int id2 = I->getId2(); const Real Delt = geom.penetrationDepth; if (Delt<0) { return false; }; const BodyContainer& bodies = *scene->bodies; Real forceHys = 0.0; if (phys.DeltMax/phys.DeltPMax >= 1.0) { // [Luding2008], equation (8) phys.k2 = phys.kp; // [Singh2013], equation (10) } else { phys.k2 = phys.k1 + (phys.kp - phys.k1)*phys.DeltMax/phys.DeltPMax; } if (phys.k2>phys.kp) { phys.k2 = phys.kp; } if (phys.k1>phys.k2) { phys.k1 = phys.k2; } phys.DeltMin = (phys.k2- phys.k1)/(phys.k2 + phys.kc); if (Delt > phys.DeltMax) { phys.DeltMax = Delt; phys.DeltNull = std::min((1.0 - phys.k1/phys.k2)*phys.DeltMax, phys.DeltPNull); // [Luding2008], equation over Fig 1 // [Singh2013], equation (8) } Real k2DeltTtmp = phys.k2*(Delt - phys.DeltNull); // [Luding2008], equation (6) // [Singh2013], equation (6) if ( k2DeltTtmp >= phys.k1*Delt) { if (Delt -phys.kc*Delt and k2DeltTtmp < phys.k1*Delt) { forceHys = k2DeltTtmp; } else if (k2DeltTtmp<=-phys.kc*Delt) { if ((Delt - phys.DeltPrev) < 0) { forceHys = -phys.kc*Delt; phys.DeltMax = Delt*(phys.k2 + phys.kc)/(phys.k2 - phys.k1); // [Singh2013], equation (9) phys.DeltNull = std::min((1.0 - phys.k1/phys.k2)*phys.DeltMax, phys.DeltPNull); // [Luding2008], equation over Fig 1 // [Singh2013], equation (8) } else { forceHys = k2DeltTtmp; } } phys.DeltPrev = Delt; //=================================================================== //=================================================================== //=================================================================== // Copy-paste from ViscoElasticPM const State& de1 = *static_cast(bodies[id1]->state.get()); const State& de2 = *static_cast(bodies[id2]->state.get()); Vector3r& shearForce = phys.shearForce; if (I->isFresh(scene)) shearForce=Vector3r(0,0,0); const Real& dt = scene->dt; shearForce = geom.rotate(shearForce); // Handle periodicity. const Vector3r shift2 = scene->isPeriodic ? scene->cell->intrShiftPos(I->cellDist): Vector3r::Zero(); const Vector3r shiftVel = scene->isPeriodic ? scene->cell->intrShiftVel(I->cellDist): Vector3r::Zero(); const Vector3r c1x = (geom.contactPoint - de1.pos); const Vector3r c2x = (geom.contactPoint - de2.pos - shift2); const Vector3r relativeVelocity = (de1.vel+de1.angVel.cross(c1x)) - (de2.vel+de2.angVel.cross(c2x)) + shiftVel; const Real normalVelocity = geom.normal.dot(relativeVelocity); const Vector3r shearVelocity = relativeVelocity-normalVelocity*geom.normal; shearForce += phys.ks*dt*shearVelocity; // the elastic shear force have a history, but Vector3r shearForceVisc = Vector3r::Zero(); // the viscous shear damping haven't a history because it is a function of the instant velocity phys.normalForce = (forceHys + phys.G0 * normalVelocity)*geom.normal; const Real maxFs = phys.normalForce.squaredNorm() * std::pow(phys.tangensOfFrictionAngle,2); if( shearForce.squaredNorm() > maxFs ) { const Real ratio = sqrt(maxFs) / shearForce.norm(); shearForce *= ratio; } else { // shearForceVisc = phys.cs*shearVelocity; //~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ shearForceVisc = phys.G0*shearVelocity; } //=================================================================== //=================================================================== //=================================================================== if (I->isActive) { const Vector3r f = phys.normalForce + shearForce + shearForceVisc; addForce (id1,-f,scene); addForce (id2, f,scene); addTorque(id1,-c1x.cross(f),scene); addTorque(id2, c2x.cross(f),scene); } return true; } trunk-2017.01a/pkg/dem/LudingPM.hpp000066400000000000000000000055401304022710500167040ustar00rootroot00000000000000#pragma once #include #include #include #include class LudingMat : public Material { public: virtual ~LudingMat(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(LudingMat,Material,"Material for simple Luding`s model of contact [Luding2008]_ ,[Singh2013]_ .\n", ((Real,k1,NaN,,"Slope of loading plastic branch")) ((Real,kp,NaN,,"Slope of unloading and reloading limit elastic branch")) ((Real,kc,NaN,,"Slope of irreversible, tensile adhesive branch")) ((Real,PhiF,NaN,,"Dimensionless plasticity depth")) ((Real,G0,NaN,,"Viscous damping")) ((Real,frictionAngle,NaN,,"Friction angle [rad]")), createIndex(); ); REGISTER_CLASS_INDEX(LudingMat,Material); }; REGISTER_SERIALIZABLE(LudingMat); class LudingPhys : public FrictPhys{ public: virtual ~LudingPhys(); Real R; YADE_CLASS_BASE_DOC_ATTRS_CTOR(LudingPhys,FrictPhys,"IPhys created from :yref:`LudingMat`, for use with :yref:`Law2_ScGeom_LudingPhys_Basic`.", ((Real,k1,NaN,,"Slope of loading plastic branch")) ((Real,k2,NaN,,"Slope of unloading and reloading elastic branch")) ((Real,kp,NaN,,"Slope of unloading and reloading limit elastic branch")) ((Real,kc,NaN,,"Slope of irreversible, tensile adhesive branch")) ((Real,PhiF,NaN,,"Dimensionless plasticity depth")) ((Real,DeltMin,NaN,,"MinimalDelta value of delta")) ((Real,DeltMax,NaN,,"Maximum overlap between particles for a collision")) ((Real,DeltPMax,NaN,,"Maximum overlap between particles for the limit case")) ((Real,DeltNull,NaN,,"Force free overlap, plastic contact deformation")) ((Real,DeltPNull,NaN,,"Max force free overlap, plastic contact deformation")) ((Real,DeltPrev,NaN,,"Previous value of delta")) ((Real,G0,NaN,,"Viscous damping")), createIndex(); ) }; REGISTER_SERIALIZABLE(LudingPhys); class Ip2_LudingMat_LudingMat_LudingPhys: public IPhysFunctor { public : virtual void go(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction); YADE_CLASS_BASE_DOC(Ip2_LudingMat_LudingMat_LudingPhys,IPhysFunctor,"Convert 2 instances of :yref:`LudingMat` to :yref:`LudingPhys` using the rule of consecutive connection."); FUNCTOR2D(LudingMat,LudingMat); private: Real reduced(Real, Real); }; REGISTER_SERIALIZABLE(Ip2_LudingMat_LudingMat_LudingPhys); class Law2_ScGeom_LudingPhys_Basic: public LawFunctor { public : virtual bool go(shared_ptr&, shared_ptr&, Interaction*); private: Real calculateCapillarForce(const ScGeom& geom, LudingPhys& phys); FUNCTOR2D(ScGeom,LudingPhys); YADE_CLASS_BASE_DOC(Law2_ScGeom_LudingPhys_Basic,LawFunctor,"Linear viscoelastic model operating on :yref:`ScGeom` and :yref:`LudingPhys`. See [Luding2008]_ ,[Singh2013]_ for more details."); }; REGISTER_SERIALIZABLE(Law2_ScGeom_LudingPhys_Basic); trunk-2017.01a/pkg/dem/MicroMacroAnalyser.cpp000066400000000000000000000257671304022710500207670ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2008 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef YADE_CGAL #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include "MicroMacroAnalyser.hpp" YADE_PLUGIN((MicroMacroAnalyser)); CREATE_LOGGER(MicroMacroAnalyser); MicroMacroAnalyser::~MicroMacroAnalyser(){ /*delete analyser;*/} //no need, its a shared_ptr now... void MicroMacroAnalyser::postLoad(MicroMacroAnalyser&) { ofile.open(outputFile.c_str(), std::ios::app); if (!boost::filesystem::exists( outputFile.c_str() )) ofile<<"iteration eps1w eps2w eps3w eps11g eps22g eps33g eps12g eps13g eps23g"<< endl; } void MicroMacroAnalyser::action() { //cerr << "MicroMacroAnalyser::action() (interval="<< interval <<", iteration="<< scene->iter<<")" << endl; if (!triaxialCompressionEngine) { vector >::iterator itFirst = scene->engines.begin(); vector >::iterator itLast = scene->engines.end(); for (;itFirst!=itLast; ++itFirst) { if ((*itFirst)->getClassName() == "TriaxialCompressionEngine") { LOG_DEBUG("stress controller engine found"); triaxialCompressionEngine = YADE_PTR_CAST (*itFirst);} } if (!triaxialCompressionEngine) LOG_ERROR("stress controller engine not found"); } if (triaxialCompressionEngine->strain[0]==0) return;// no deformation yet if (!initialized) { setState(1,true,false); //Check file here again, to make sure we write to the correct file when filename is modified after the scene is loaded ofile.open(outputFile.c_str(), std::ios::app); if (!boost::filesystem::exists( outputFile.c_str() )) ofile<<"iteration eps1w eps2w eps3w eps11g eps22g eps33g eps12g eps13g eps23g"<< endl; initialized=true; } else if (scene->iter % interval == 0) { setState(2, true, compIncrt); if (compDeformation) { analyser->computeParticlesDeformation(); //for (int i=0; iParticleDeformation.size();i++) cerr<< analyser->ParticleDeformation[i]<DefToFile(oss.str().c_str()); } CGT::Tenseur_sym3 epsg(analyser->grad_u_total); ofile << scene->iter << analyser->Delta_epsilon(1,1)<<" "<Delta_epsilon(2,2)<<" "<Delta_epsilon(3,3)<<" "<SwitchStates(); } //cerr << "ENDOF MicroMacro::action" << endl; } void MicroMacroAnalyser::setState(unsigned int state, bool save_states, bool computeIncrement) { LOG_INFO("MicroMacroAnalyser::setState"); CGT::TriaxialState& TS = makeState(state); if (state == 2) { analyser->Delta_epsilon(3,3) = analyser->TS1->eps3 - analyser->TS0->eps3; analyser->Delta_epsilon(1,1) = analyser->TS1->eps1 - analyser->TS0->eps1; analyser->Delta_epsilon(2,2) = analyser->TS1->eps2 - analyser->TS0->eps2; if (computeIncrement) { analyser->SetForceIncrements(); analyser->SetDisplacementIncrements(); } } if (save_states) { ostringstream oss; //oss<iter; oss<& bodies = scene->bodies; CGT::TriaxialState* ts=0; if (state==1) ts = analyser->TS0; else if (state==2) ts = analyser->TS1; else LOG_ERROR("state must be 1 or 2, instead of " << state); CGT::TriaxialState& TS = *ts; TS.reset(); long Ng = bodies->size(); TS.mean_radius=0; TS.grains.resize(Ng); BodyContainer::iterator biBegin = bodies->begin(); BodyContainer::iterator biEnd = bodies->end(); BodyContainer::iterator bi = biBegin; Ng = 0; vector fictiousVtx; for (; bi!=biEnd ; ++bi) { const Body::id_t Idg = (*bi)->getId(); TS.grains[Idg].id = Idg; if (!(*bi)->isDynamic()) { if (!nonSphereAsFictious) continue; TS.grains[Idg].isSphere = false; fictiousVtx.push_back(Idg);} else {//then it is a sphere (not a wall) ++Ng; const Sphere* s = YADE_CAST ((*bi)->shape.get()); //const GranularMat* p = YADE_CAST ( ( *bi )->material.get() ); const Vector3r& pos = (*bi)->state->pos; Real rad = s->radius; TS.grains[Idg].sphere = CGT::Sphere(CGT::Point(pos[0],pos[1],pos[2]),rad); // TS.grains[Idg].translation = trans; AngleAxisr aa((*bi)->state->ori); Vector3r rotVec=aa.axis()*aa.angle(); TS.grains[Idg].rotation = CGT::CVector(rotVec[0],rotVec[1],rotVec[2]); TS.box.base = CGT::Point(min(TS.box.base.x(), pos.x()-rad), min(TS.box.base.y(), pos.y()-rad), min(TS.box.base.z(), pos.z()-rad)); TS.box.sommet = CGT::Point(max(TS.box.sommet.x(), pos.x() +rad), max(TS.box.sommet.y(), pos.y() +rad), max(TS.box.sommet.z(), pos.z() +rad)); TS.mean_radius += TS.grains[Idg].sphere.weight(); } } TS.mean_radius /= Ng;//rayon moyen LOG_INFO(" loaded : " << Ng << " grains with mean radius = " << TS.mean_radius); Real FAR = 1e4; if (fictiousVtx.size()==0) { TS.grains.resize(Ng+6); for (int fv=Ng;fvinteractions->begin(); InteractionContainer::iterator iiEnd = scene->interactions->end(); for (; ii!=iiEnd ; ++ii) { if ((*ii)->isReal()) { CGT::TriaxialState::Contact *c = new CGT::TriaxialState::Contact; TS.contacts.push_back(c); CGT::TriaxialState::VectorGrain& grains = TS.grains; Body::id_t id1 = (*ii)->getId1(); Body::id_t id2 = (*ii)->getId2(); c->grain1 = & (TS.grains[id1]); c->grain2 = & (TS.grains[id2]); grains[id1].contacts.push_back(c); grains[id2].contacts.push_back(c); c->normal = CGT::CVector((YADE_CAST ((*ii)->geom.get()))->normal.x(), (YADE_CAST ((*ii)->geom.get()))->normal.y(), (YADE_CAST ((*ii)->geom.get()))->normal.z()); // c->normal = ( grains[id2].sphere.point()-grains[id1].sphere.point() ); // c->normal = c->normal/sqrt ( pow ( c->normal.x(),2 ) +pow ( c->normal.y(),2 ) +pow ( c->normal.z(),2 ) ); c->position = CGT::CVector((YADE_CAST ((*ii)->geom.get()))->contactPoint.x(), (YADE_CAST ((*ii)->geom.get()))->contactPoint.y(), (YADE_CAST ((*ii)->geom.get()))->contactPoint.z()); // c->position = 0.5* ( ( grains[id1].sphere.point()-CGAL::ORIGIN ) + // ( grains[id1].sphere.weight() *c->normal ) + // ( grains[id2].sphere.point()-CGAL::ORIGIN ) - // ( grains[id2].sphere.weight() *c->normal ) ); c->fn = YADE_CAST (((*ii)->phys.get()))->normalForce.dot((YADE_CAST ((*ii)->geom.get()))->normal); Vector3r fs = YADE_CAST ((*ii)->phys.get())->shearForce; c->fs = CGT::CVector(fs.x(),fs.y(),fs.z()); c->old_fn = c->fn; c->old_fs = c->fs; c->frictional_work = 0; } } //Save various parameters if triaxialCompressionEngine is defined if (!triaxialCompressionEngine) { vector >::iterator itFirst = scene->engines.begin(); vector >::iterator itLast = scene->engines.end(); for (;itFirst!=itLast; ++itFirst) { if ((*itFirst)->getClassName() == "TriaxialCompressionEngine") { LOG_DEBUG("stress controller engine found"); triaxialCompressionEngine = YADE_PTR_CAST (*itFirst);} } if (!triaxialCompressionEngine) LOG_INFO("stress controller engine not found");} if (triaxialCompressionEngine) { TS.wszzh = triaxialCompressionEngine->stress[triaxialCompressionEngine->wall_top][1]; TS.wsxxd = triaxialCompressionEngine->stress[triaxialCompressionEngine->wall_right][0]; TS.wsyyfa = triaxialCompressionEngine->stress[triaxialCompressionEngine->wall_front][2]; TS.eps3 = triaxialCompressionEngine->strain[2];//find_parameter("eps3=", Statefile); TS.eps1 = triaxialCompressionEngine->strain[0];//find_parameter("eps1=", Statefile); TS.eps2 = triaxialCompressionEngine->strain[1];//find_parameter("eps2=", Statefile); TS.haut = triaxialCompressionEngine->height;//find_parameter("haut=", Statefile); TS.larg = triaxialCompressionEngine->width;//find_parameter("larg=", Statefile); TS.prof = triaxialCompressionEngine->depth;//find_parameter("prof=", Statefile); TS.porom = 0/*analyser->computeMacroPorosity() crasher?*/;//find_parameter("porom=", Statefile); TS.ratio_f = triaxialCompressionEngine->ComputeUnbalancedForce(scene); //find_parameter("ratio_f=", Statefile); } else TS.wszzh=TS.wsxxd=TS.wsyyfa=TS.eps3=TS.eps1=TS.eps2=TS.haut=TS.larg=TS.prof=TS.porom=TS.ratio_f=0; if (filename!=NULL) TS.to_file(filename); return TS; } // const vector& MicroMacroAnalyser::makeDeformationArray(const char* state_file1, const char* state_file0) // { // return analyser->computeParticlesDeformation(state_file1, state_file0); // } #endif /* YADE_CGAL */ trunk-2017.01a/pkg/dem/MicroMacroAnalyser.hpp000066400000000000000000000066451304022710500207660ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2008 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef YADE_CGAL #pragma once #include #include /*! \brief compute fabric tensor, local porosity, local deformation, and other micromechanicaly defined quantities based on triangulation/tesselation of the packing. */ namespace CGT { class TriaxialState; class Tenseur3; } class TriaxialCompressionEngine; class MicroMacroAnalyser : public GlobalEngine { /// Attributes private : std::ofstream ofile; shared_ptr triaxialCompressionEngine; bool initialized; public : ~MicroMacroAnalyser(); void action(); /// Set current state as initial (state=1) or final (state=2) congiguration for later kinematic analysis on the increment; if requested : save snapshots (with specific format) - possibly including contact forces increments on the state1->state2 interval void setState(unsigned int state, bool save_states = false, bool computeIncrement = false); /// Copy the current simulation in a TriaxialState structure. If filename!=NULL, save it to a file that can be reloaded later for computing strain increments, state must be 1 or 2. CGT::TriaxialState& makeState(unsigned int state, const char* filename = NULL); //const vector& makeDeformationArray(const char* state_file1, const char* state_file0); shared_ptr analyser; void postLoad(MicroMacroAnalyser&); YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(MicroMacroAnalyser,GlobalEngine,"compute fabric tensor, local porosity, local deformation, and other micromechanicaly defined quantities based on triangulation/tesselation of the packing.", ((unsigned int,stateNumber,0,,"A number incremented and appended at the end of output files to reflect increment number.")) ((unsigned int,incrtNumber,1,,"")) ((std::string,outputFile,"MicroMacroAnalysis",,"Base name for increment analysis output file.")) ((std::string,stateFileName,"state",,"Base name of state files.")) ((int,interval,100,,"Number of timesteps between analyzed states.")) ((bool,compDeformation,false,,"Is the engine just saving states or also computing and outputing deformations for each increment?")) ((bool,compIncrt,false,,"Should increments of force and displacements be defined on [n,n+1]? If not, states will be saved with only positions and forces (no displacements).")) ((bool,nonSphereAsFictious,true,,"bodies that are not spheres will be used to defines bounds (else just skipped).")) ,/*init*/ ,/*ctor*/ analyser = shared_ptr (new CGT::KinematicLocalisationAnalyser); analyser->SetConsecutive(true); analyser->SetNO_ZERO_ID(false); initialized = false; ,/*py*/ ); DECLARE_LOGGER; //REGISTER_ATTRIBUTES(GlobalEngine,(stateNumber)(incrtNumber)(outputFile)(stateFileName)(interval)(compDeformation)(compIncrt)); }; REGISTER_SERIALIZABLE(MicroMacroAnalyser); #endif /* YADE_CGAL */ trunk-2017.01a/pkg/dem/MortarMat.cpp000066400000000000000000000076771304022710500171430ustar00rootroot00000000000000// 2016 © Jan Stránský #include"MortarMat.hpp" YADE_PLUGIN((MortarMat)(Ip2_MortarMat_MortarMat_MortarPhys)(MortarPhys)(Law2_ScGeom_MortarPhys_Lourenco)) CREATE_LOGGER(Ip2_MortarMat_MortarMat_MortarPhys); void Ip2_MortarMat_MortarMat_MortarPhys::go(const shared_ptr& material1, const shared_ptr& material2, const shared_ptr& interaction){ if (interaction->phys) return; if (scene->iter >= cohesiveThresholdIter) { LOG_ERROR("MortarMat not implemented for non-cohesive contacts"); } shared_ptr phys(new MortarPhys()); interaction->phys = phys; MortarMat* mat1 = YADE_CAST(material1.get()); MortarMat* mat2 = YADE_CAST(material2.get()); GenericSpheresContact* geom = YADE_CAST(interaction->geom.get()); if (mat1->id>=0 && mat1->id == mat2->id) { #define _CPATTR(a) phys->a=mat1->a _CPATTR(tensileStrength); _CPATTR(compressiveStrength); _CPATTR(cohesion); _CPATTR(ellAspect); _CPATTR(neverDamage); #undef _CPATTR phys->tangensOfFrictionAngle = std::tan(mat1->frictionAngle); } else { // averaging over both materials #define _MINATTR(a) phys->a=std::min(mat1->a,mat2->a) #define _AVGATTR(a) phys->a=.5*(mat1->a+mat2->a) _MINATTR(tensileStrength); _MINATTR(compressiveStrength); _MINATTR(cohesion); _AVGATTR(ellAspect); #undef _AVGATTR #undef _MINATTR phys->neverDamage = mat1->neverDamage || mat2->neverDamage; phys->tangensOfFrictionAngle = std::tan(.5*(mat1->frictionAngle+mat2->frictionAngle)); } // const Real& r1 = geom->refR1; const Real& r2 = geom->refR2; Real minRad = r1 <= 0 ? r2 : r2 <= 0 ? r1 : std::min(r1,r2); phys->crossSection = std::pow(minRad,2); const Real& E1 = mat1->young; const Real& E2 = mat2->young; const Real& n1 = mat1->poisson; const Real& n2 = mat2->poisson; phys->kn = 2*E1*r1*E2*r2/(E1*r1+E2*r2); phys->ks = 2*E1*r1*n1*E2*r2*n2/(E1*r1*n1+E2*r2*n2); } CREATE_LOGGER(MortarPhys); MortarPhys::~MortarPhys(){}; bool MortarPhys::failureCondition(Real sigmaN, Real sigmaT) { bool cond1 = sigmaN - tensileStrength > 0; bool cond2 = sigmaT + sigmaN*tangensOfFrictionAngle - cohesion > 0; bool cond3 = std::pow(sigmaN,2) + std::pow(ellAspect*sigmaT,2) - std::pow(compressiveStrength,2) > 0; return cond1 || cond2 || cond3; } /********************** Law2_ScGeom_MortarPhys_Lourenco ****************************/ CREATE_LOGGER(Law2_ScGeom_MortarPhys_Lourenco); bool Law2_ScGeom_MortarPhys_Lourenco::go(shared_ptr& iGeom, shared_ptr& iPhys, Interaction* interaction){ ScGeom* geom=static_cast(iGeom.get()); MortarPhys* phys=static_cast(iPhys.get()); Body::id_t id1 = interaction->getId1(); Body::id_t id2 = interaction->getId2(); const shared_ptr b1 = Body::byId(id1,scene); const shared_ptr b2 = Body::byId(id2,scene); /* shorthands */ const Real& crossSection(phys->crossSection); Real& sigmaN(phys->sigmaN); Vector3r& sigmaT(phys->sigmaT); Real& kn(phys->kn); Real& ks(phys->ks); Vector3r& normalForce(phys->normalForce); Vector3r& shearForce(phys->shearForce); /* constitutive law */ normalForce = kn*geom->penetrationDepth*geom->normal; geom->rotate(shearForce); shearForce -= ks*geom->shearIncrement(); sigmaN = - normalForce.dot(geom->normal) / crossSection; sigmaT = - shearForce / crossSection; if (!phys->neverDamage && phys->failureCondition(sigmaN,sigmaT.norm())) { return false; } State* s1 = b1->state.get(); State* s2 = b2->state.get(); Vector3r f = - normalForce - shearForce; if (!scene->isPeriodic) { applyForceAtContactPoint(f, geom->contactPoint , id1, s1->se3.position, id2, s2->se3.position); } else { scene->forces.addForce(id1,f); scene->forces.addForce(id2,-f); scene->forces.addTorque(id1,(geom->radius1-.5*(geom->penetrationDepth))*geom->normal.cross(f)); scene->forces.addTorque(id2,(geom->radius2-.5*(geom->penetrationDepth))*geom->normal.cross(f)); } return true; } trunk-2017.01a/pkg/dem/MortarMat.hpp000066400000000000000000000076351304022710500171420ustar00rootroot00000000000000// 2016 © Jan Stránský #pragma once #include #include #include #include #include #include #include #include namespace py=boost::python; class MortarMat: public FrictMat { public: YADE_CLASS_BASE_DOC_ATTRS_CTOR(MortarMat,FrictMat,"Material for mortar interface, used in Ip2_MortarMat_MortarMat_MortarPhys and Law2_ScGeom_MortarPhys_Lourenco. Default values according to ", ((Real,young,1e9,,"Normal elastic modulus [Pa]")) ((Real,poisson,1,,"Shear to normal modulus ratio")) ((Real,frictionAngle,.25,,"Friction angle")) // ((Real,tensileStrength,1e6,,"tensileStrength [Pa]")) ((Real,compressiveStrength,10e6,,"compressiveStrength [Pa]")) ((Real,cohesion,1e6,,"cohesion [Pa]")) ((Real,ellAspect,3,,"aspect ratio of elliptical 'cap'. Value >1 means the ellipse is longer along normal stress axis.")) ((bool,neverDamage,false,,"If true, interactions remain elastic regardless stresses")) , createIndex(); ); REGISTER_CLASS_INDEX(MortarMat,FrictMat); }; REGISTER_SERIALIZABLE(MortarMat); class MortarPhys: public FrictPhys { public: Real sigmaN; Vector3r sigmaT; virtual ~MortarPhys(); bool failureCondition(Real sigmaN, Real sigmaT); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(MortarPhys,FrictPhys,"IPhys class containing parameters of MortarMat. Used by Law2_ScGeom_MortarPhys_Lourenco.", ((Real,tensileStrength,NaN,,"tensileStrength [Pa]")) ((Real,compressiveStrength,NaN,,"compressiveStrength [Pa]")) ((Real,cohesion,NaN,,"cohesion [Pa]")) ((Real,ellAspect,NaN,,"aspect ratio of elliptical 'cap'. Value >1 means the ellipse is longer along normal stress axis.")) ((Real,crossSection,NaN,,"Crosssection of interaction")) ((bool,neverDamage,false,,"If true, interactions remain elastic regardless stresses")) , // ctors createIndex(); , .def_readonly("sigmaN",&MortarPhys::sigmaN,"Current normal stress |yupdate|") .def_readonly("sigmaT",&MortarPhys::sigmaT,"Current shear stress |yupdate|") .def("failureCondition",&MortarPhys::failureCondition,"Failure condition from normal stress and norm of shear stress (false=elastic, true=damaged)") ); DECLARE_LOGGER; REGISTER_CLASS_INDEX(MortarPhys,NormShearPhys); }; REGISTER_SERIALIZABLE(MortarPhys); class Ip2_MortarMat_MortarMat_MortarPhys: public IPhysFunctor{ public: virtual void go(const shared_ptr& material1, const shared_ptr& material2, const shared_ptr& interaction); FUNCTOR2D(MortarMat,MortarMat); DECLARE_LOGGER; YADE_CLASS_BASE_DOC_ATTRS(Ip2_MortarMat_MortarMat_MortarPhys,IPhysFunctor,"Ip2 creating MortarPhys from two MortarMat instances.", ((long,cohesiveThresholdIter,2,,"Should new contacts be cohesive? They will before this iter#, they will not be afterwards. If <=0, they will never be.")) ); }; REGISTER_SERIALIZABLE(Ip2_MortarMat_MortarMat_MortarPhys); class Law2_ScGeom_MortarPhys_Lourenco: public LawFunctor{ public: virtual bool go(shared_ptr& iGeom, shared_ptr& iPhys, Interaction* interaction); FUNCTOR2D(GenericSpheresContact,MortarPhys); YADE_CLASS_BASE_DOC(Law2_ScGeom_MortarPhys_Lourenco,LawFunctor,"Material law for mortar layer according to [Lourenco1994]_. The contact behaves elastic until brittle failure when reaching strength envelope. The envelope has three parts.\n\nTensile with condition $\\sigma_N-f_t$.\n\nShear part with Mohr-Coulomb condition $|\\sigma_T|+\\sigma_N\\tan\\varphi-c$.\n\nCompressive part with condition $\\sigma_N^2+A^2\\sigma_T^2-f_c^2$\n\nThe main idea is to begin simulation with this model and when the contact is broken, to use standard non-cohesive Law2_PolyhedraGeom_PolyhedraPhys_Volumetric." ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_ScGeom_MortarPhys_Lourenco); trunk-2017.01a/pkg/dem/NewtonIntegrator.cpp000066400000000000000000000405031304022710500205270ustar00rootroot00000000000000/************************************************************************* Copyright (C) 2008 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include #include #include #include YADE_PLUGIN((NewtonIntegrator)); CREATE_LOGGER(NewtonIntegrator); // 1st order numerical damping void NewtonIntegrator::cundallDamp1st(Vector3r& force, const Vector3r& vel){ for(int i=0; i<3; i++) force[i]*=1-damping*Mathr::Sign(force[i]*vel[i]); } // 2nd order numerical damping void NewtonIntegrator::cundallDamp2nd(const Real& dt, const Vector3r& vel, Vector3r& accel){ for(int i=0; i<3; i++) accel[i]*= 1 - damping*Mathr::Sign ( accel[i]*(vel[i] + 0.5*dt*accel[i]) ); } Vector3r NewtonIntegrator::computeAccel(const Vector3r& force, const Real& mass, int blockedDOFs){ if(blockedDOFs==0) return (force/mass + gravity); Vector3r ret(Vector3r::Zero()); for(int i=0; i<3; i++) if(!(blockedDOFs & State::axisDOF(i,false))) ret[i]+=force[i]/mass+gravity[i]; return ret; } Vector3r NewtonIntegrator::computeAngAccel(const Vector3r& torque, const Vector3r& inertia, int blockedDOFs){ if(blockedDOFs==0) return torque.cwiseQuotient(inertia); Vector3r ret(Vector3r::Zero()); for(int i=0; i<3; i++) if(!(blockedDOFs & State::axisDOF(i,true))) ret[i]+=torque[i]/inertia[i]; return ret; } void NewtonIntegrator::updateEnergy(const shared_ptr& b, const State* state, const Vector3r& fluctVel, const Vector3r& f, const Vector3r& m){ assert(b->isStandalone() || b->isClump()); // always positive dissipation, by-component: |F_i|*|v_i|*damping*dt (|T_i|*|ω_i|*damping*dt for rotations) if(damping!=0. && state->isDamped){ scene->energy->add(fluctVel.cwiseAbs().dot(f.cwiseAbs())*damping*scene->dt,"nonviscDamp",nonviscDampIx,/*non-incremental*/false); // when the aspherical integrator is used, torque is damped instead of ang acceleration; this code is only approximate scene->energy->add(state->angVel.cwiseAbs().dot(m.cwiseAbs())*damping*scene->dt,"nonviscDamp",nonviscDampIx,false); } // kinetic energy Real Etrans=.5*state->mass*fluctVel.squaredNorm(); Real Erot; // rotational terms if(b->isAspherical()){ Matrix3r mI; mI<inertia[0],0,0, 0,state->inertia[1],0, 0,0,state->inertia[2]; Matrix3r T(state->ori); Erot=.5*b->state->angVel.transpose().dot((T.transpose()*mI*T)*b->state->angVel); } else { Erot=0.5*state->angVel.dot(state->inertia.cwiseProduct(state->angVel)); } if(!kinSplit) scene->energy->add(Etrans+Erot,"kinetic",kinEnergyIx,/*non-incremental*/true); else{ scene->energy->add(Etrans,"kinTrans",kinEnergyTransIx,true); scene->energy->add(Erot,"kinRot",kinEnergyRotIx,true); } // gravitational work (work done by gravity is "negative", since the energy appears in the system from outside) scene->energy->add(-gravity.dot(b->state->vel)*b->state->mass*scene->dt,"gravWork",fieldWorkIx,/*non-incremental*/false); } void NewtonIntegrator::saveMaximaVelocity(const Body::id_t& id, State* state){ #ifdef YADE_OPENMP Real& thrMaxVSq=threadMaxVelocitySq[omp_get_thread_num()]; thrMaxVSq=max(thrMaxVSq,state->vel.squaredNorm()); #else maxVelocitySq=max(maxVelocitySq,state->vel.squaredNorm()); #endif } void NewtonIntegrator::saveMaximaDisplacement(const shared_ptr& b){ if (!b->bound) return;//clumps for instance, have no bounds, hence not saved Vector3r disp=b->state->pos-b->bound->refPos; Real maxDisp=max(std::abs(disp[0]),max(std::abs(disp[1]),std::abs(disp[2]))); if (!maxDisp || maxDispbound->sweepLength) {/*b->bound->isBounding = (updatingDispFactor>0 && (updatingDispFactor*maxDisp)bound->sweepLength);*/ maxDisp=0.5;//not 0, else it will be seen as "not updated" by the collider, but less than 1 means no colliding } else {/*b->bound->isBounding = false;*/ maxDisp=2;/*2 is more than 1, enough to trigger collider*/} #ifdef YADE_OPENMP Real& thrMaxVSq=threadMaxVelocitySq[omp_get_thread_num()]; thrMaxVSq=max(thrMaxVSq,maxDisp); #else maxVelocitySq=max(maxVelocitySq,maxDisp); #endif } void NewtonIntegrator::action() { scene->forces.sync(); bodySelected=(scene->selectedBody>=0); if(warnNoForceReset && scene->forces.lastResetiter) LOG_WARN("O.forces last reset in step "<forces.lastReset<<", while the current step is "<iter<<". Did you forget to include ForceResetter in O.engines?"); const Real& dt=scene->dt; //Take care of user's request to change velGrad. Safe to change it here after the interaction loop. if (scene->cell->velGradChanged || scene->cell->nextVelGrad!=Matrix3r::Zero()) { scene->cell->velGrad=scene->cell->nextVelGrad; scene->cell->velGradChanged=0; scene->cell->nextVelGrad=Matrix3r::Zero();} homoDeform=scene->cell->homoDeform; dVelGrad=scene->cell->velGrad-prevVelGrad; Matrix3r R=.5*(dVelGrad-dVelGrad.transpose()); dSpin=Vector3r(-R(1,2),R(0,2),-R(0,1)); // account for motion of the periodic boundary, if we remember its last position // its velocity will count as max velocity of bodies // otherwise the collider might not run if only the cell were changing without any particle motion // FIXME: will not work for pure shear transformation, which does not change Cell::getSize() if(scene->isPeriodic && ((prevCellSize!=scene->cell->getSize())) && /* initial value */!std::isnan(prevCellSize[0]) ){ cellChanged=true; maxVelocitySq=(prevCellSize-scene->cell->getSize()).squaredNorm()/pow(dt,2); } else { maxVelocitySq=0; cellChanged=false; } #ifdef YADE_BODY_CALLBACK // setup callbacks vector callbackPtrs; FOREACH(const shared_ptr& cb, callbacks){ cerr<<"scene="<"; cb->scene=scene; callbackPtrs.push_back(cb->stepInit()); } assert(callbackPtrs.size()==callbacks.size()); size_t callbacksSize=callbacks.size(); #endif const bool trackEnergy(scene->trackEnergy); const bool isPeriodic(scene->isPeriodic); #ifdef YADE_OPENMP FOREACH(Real& thrMaxVSq, threadMaxVelocitySq) { thrMaxVSq=0; } #endif YADE_PARALLEL_FOREACH_BODY_BEGIN(const shared_ptr& b, scene->bodies){ // clump members are handled inside clumps if(b->isClumpMember()) continue; State* state=b->state.get(); const Body::id_t& id=b->getId(); Vector3r f=Vector3r::Zero(); Vector3r m=Vector3r::Zero(); // clumps forces if(b->isClump()) { b->shape->cast().addForceTorqueFromMembers(state,scene,f,m); #ifdef YADE_OPENMP //it is safe here, since only one thread is adding forces/torques scene->forces.addTorqueUnsynced(id,m); scene->forces.addForceUnsynced(id,f); #else scene->forces.addTorque(id,m); scene->forces.addForce(id,f); #endif } //in most cases, the initial force on clumps will be zero and next line is not changing f and m, but make sure we don't miss something (e.g. user defined forces on clumps) f=scene->forces.getForce(id); m=scene->forces.getTorque(id); #ifdef YADE_DEBUG if(std::isnan(f[0])||std::isnan(f[1])||std::isnan(f[2])) throw runtime_error(("NewtonIntegrator: NaN force acting on #"+boost::lexical_cast(id)+".").c_str()); if(std::isnan(m[0])||std::isnan(m[1])||std::isnan(m[2])) throw runtime_error(("NewtonIntegrator: NaN torque acting on #"+boost::lexical_cast(id)+".").c_str()); if(state->mass<=0 && ((state->blockedDOFs & State::DOF_XYZ) != State::DOF_XYZ)) throw runtime_error(("NewtonIntegrator: #"+boost::lexical_cast(id)+" has some linear accelerations enabled, but State::mass is non-positive.")); if(state->inertia.minCoeff()<=0 && ((state->blockedDOFs & State::DOF_RXRYRZ) != State::DOF_RXRYRZ)) throw runtime_error(("NewtonIntegrator: #"+boost::lexical_cast(id)+" has some angular accelerations enabled, but State::inertia contains non-positive terms.")); #endif // fluctuation velocity does not contain meanfield velocity in periodic boundaries // in aperiodic boundaries, it is equal to absolute velocity Vector3r fluctVel=isPeriodic?scene->cell->bodyFluctuationVel(b->state->pos,b->state->vel,prevVelGrad):state->vel; // numerical damping & kinetic energy if(trackEnergy) updateEnergy(b,state,fluctVel,f,m); // whether to use aspherical rotation integration for this body; for no accelerations, spherical integrator is "exact" (and faster) bool useAspherical=(exactAsphericalRot && b->isAspherical() && state->blockedDOFs!=State::DOF_ALL); // for particles not totally blocked, compute accelerations; otherwise, the computations would be useless if (state->blockedDOFs!=State::DOF_ALL) { // linear acceleration Vector3r linAccel=computeAccel(f,state->mass,state->blockedDOFs); if (densityScaling) linAccel*=state->densityScaling; if(state->isDamped) cundallDamp2nd(dt,fluctVel,linAccel); //This is the convective term, appearing in the time derivation of Cundall/Thornton expression (dx/dt=velGrad*pos -> d²x/dt²=dvelGrad/dt*pos+velGrad*vel), negligible in many cases but not for high speed large deformations (gaz or turbulent flow). if (isPeriodic && homoDeform>1) linAccel+=prevVelGrad*state->vel; //finally update velocity state->vel+=dt*linAccel; // angular acceleration if(!useAspherical){ // uses angular velocity Vector3r angAccel=computeAngAccel(m,state->inertia,state->blockedDOFs); if (densityScaling) angAccel*=state->densityScaling; if(state->isDamped) cundallDamp2nd(dt,state->angVel,angAccel); state->angVel+=dt*angAccel; } else { // uses torque for(int i=0; i<3; i++) if(state->blockedDOFs & State::axisDOF(i,true)) m[i]=0; // block DOFs here if(state->isDamped) cundallDamp1st(m,state->angVel); } // reflect macro-deformation even for non-dynamic bodies } else if (isPeriodic && homoDeform>1) state->vel+=dt*prevVelGrad*state->vel; // update positions from velocities (or torque, for the aspherical integrator) leapfrogTranslate(state,id,dt); if(!useAspherical) leapfrogSphericalRotate(state,id,dt); else leapfrogAsphericalRotate(state,id,dt,m); saveMaximaDisplacement(b); // move individual members of the clump, save maxima velocity (for collider stride) if(b->isClump()) Clump::moveMembers(b,scene,this); #ifdef YADE_BODY_CALLBACK // process callbacks for(size_t i=0; iid<<",cb="<scene<<">"; // <<",force="<scene->forces.getForce(b->id)<<">"; if(callbackPtrs[i]!=NULL) (*(callbackPtrs[i]))(callbacks[i].get(),b.get()); } #endif } YADE_PARALLEL_FOREACH_BODY_END(); #ifdef YADE_OPENMP FOREACH(const Real& thrMaxVSq, threadMaxVelocitySq) { maxVelocitySq=max(maxVelocitySq,thrMaxVSq); } #endif if(scene->isPeriodic) { prevCellSize=scene->cell->getSize(); prevVelGrad=scene->cell->prevVelGrad=scene->cell->velGrad; } } void NewtonIntegrator::leapfrogTranslate(State* state, const Body::id_t& id, const Real& dt){ if (scene->forces.getMoveRotUsed()) state->pos+=scene->forces.getMove(id); // update velocity reflecting changes in the macroscopic velocity field, making the problem homothetic. //NOTE : if the velocity is updated before moving the body, it means the current velGrad (i.e. before integration in cell->integrateAndUpdate) will be effective for the current time-step. Is it correct? If not, this velocity update can be moved just after "state->pos += state->vel*dt", meaning the current velocity impulse will be applied at next iteration, after the contact law. (All this assuming the ordering is resetForces->integrateAndUpdate->contactLaw->PeriCompressor->NewtonsLaw. Any other might fool us.) //NOTE : dVel defined without wraping the coordinates means bodies out of the (0,0,0) period can move realy fast. It has to be compensated properly in the definition of relative velocities (see Ig2 functors and contact laws). //Reflect mean-field (periodic cell) acceleration in the velocity if(scene->isPeriodic && homoDeform) {Vector3r dVel=dVelGrad*state->pos; state->vel+=dVel;} if ( (mask<=0) or ((mask>0) and (Body::byId(id)->maskCompatible(mask))) ) { state->pos+=state->vel*dt; } } void NewtonIntegrator::leapfrogSphericalRotate(State* state, const Body::id_t& id, const Real& dt ) { if(scene->isPeriodic && homoDeform) {state->angVel+=dSpin;} Real angle2=state->angVel.squaredNorm(); if (angle2!=0 and ( (mask<=0) or ((mask>0) and (Body::byId(id)->maskCompatible(mask))) )) {//If we have an angular velocity, we make a rotation Real angle=sqrt(angle2); Quaternionr q(AngleAxisr(angle*dt,state->angVel/angle)); state->ori = q*state->ori; } if(scene->forces.getMoveRotUsed() && scene->forces.getRot(id)!=Vector3r::Zero() and ( (mask<=0) or ((mask>0) and (Body::byId(id)->maskCompatible(mask))) )) { Vector3r r(scene->forces.getRot(id)); Real norm=r.norm(); r/=norm; Quaternionr q(AngleAxisr(norm,r)); state->ori=q*state->ori; } state->ori.normalize(); } void NewtonIntegrator::leapfrogAsphericalRotate(State* state, const Body::id_t& id, const Real& dt, const Vector3r& M){ //FIXME: where to increment angular velocity like this? Only done for spherical rotations at the moment //if(scene->isPeriodic && homoDeform) {state->angVel+=dSpin;} Matrix3r A=state->ori.conjugate().toRotationMatrix(); // rotation matrix from global to local r.f. const Vector3r l_n = state->angMom + dt/2. * M; // global angular momentum at time n const Vector3r l_b_n = A*l_n; // local angular momentum at time n Vector3r angVel_b_n = l_b_n.cwiseQuotient(state->inertia); // local angular velocity at time n if (densityScaling) angVel_b_n*=state->densityScaling; const Quaternionr dotQ_n=DotQ(angVel_b_n,state->ori); // dQ/dt at time n const Quaternionr Q_half = Quaternionr(state->ori.coeffs() + dt/2. * dotQ_n.coeffs()); // Q at time n+1/2 state->angMom+=dt*M; // global angular momentum at time n+1/2 const Vector3r l_b_half = A*state->angMom; // local angular momentum at time n+1/2 Vector3r angVel_b_half = l_b_half.cwiseQuotient(state->inertia); // local angular velocity at time n+1/2 if (densityScaling) angVel_b_half*=state->densityScaling; const Quaternionr dotQ_half=DotQ(angVel_b_half,Q_half); // dQ/dt at time n+1/2 state->ori=Quaternionr(state->ori.coeffs()+dt*dotQ_half.coeffs()); // Q at time n+1 state->angVel=state->ori*angVel_b_half; // global angular velocity at time n+1/2 if(scene->forces.getMoveRotUsed() && scene->forces.getRot(id)!=Vector3r::Zero()) { Vector3r r(scene->forces.getRot(id)); Real norm=r.norm(); r/=norm; Quaternionr q(AngleAxisr(norm,r)); state->ori=q*state->ori; } state->ori.normalize(); } bool NewtonIntegrator::get_densityScaling() { FOREACH(const shared_ptr e, Omega::instance().getScene()->engines) { GlobalStiffnessTimeStepper* ts=dynamic_cast(e.get()); if (ts && densityScaling != ts->densityScaling) LOG_WARN("density scaling is not active in the timeStepper, it will have no effect unless a scaling is specified manually for some bodies");} LOG_WARN("GlobalStiffnessTimeStepper not present in O.engines, density scaling will have no effect unless a scaling is specified manually for some bodies"); return densityScaling;; } void NewtonIntegrator::set_densityScaling(bool dsc) { FOREACH(const shared_ptr e, Omega::instance().getScene()->engines) { GlobalStiffnessTimeStepper* ts=dynamic_cast(e.get()); if (ts) { ts->densityScaling=dsc; densityScaling=dsc; LOG_WARN("GlobalStiffnessTimeStepper found in O.engines and adjusted to match this setting. Revert in the timestepper if you don't want the scaling adjusted automatically."); return; } } LOG_WARN("GlobalStiffnessTimeStepper not found in O.engines. Density scaling will have no effect unless a scaling is specified manually for some bodies"); } // http://www.euclideanspace.com/physics/kinematics/angularvelocity/QuaternionDifferentiation2.pdf Quaternionr NewtonIntegrator::DotQ(const Vector3r& angVel, const Quaternionr& Q){ Quaternionr dotQ; dotQ.w() = (-Q.x()*angVel[0]-Q.y()*angVel[1]-Q.z()*angVel[2])/2; dotQ.x() = ( Q.w()*angVel[0]-Q.z()*angVel[1]+Q.y()*angVel[2])/2; dotQ.y() = ( Q.z()*angVel[0]+Q.w()*angVel[1]-Q.x()*angVel[2])/2; dotQ.z() = (-Q.y()*angVel[0]+Q.x()*angVel[1]+Q.w()*angVel[2])/2; return dotQ; } trunk-2017.01a/pkg/dem/NewtonIntegrator.hpp000066400000000000000000000133511304022710500205350ustar00rootroot00000000000000/************************************************************************* Copyright (C) 2008 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include #include #ifdef YADE_OPENMP #include #endif /*! An engine that can replace the usual series of engines used for integrating the laws of motion. */ class State; class NewtonIntegrator : public FieldApplier{ inline void cundallDamp1st(Vector3r& force, const Vector3r& vel); inline void cundallDamp2nd(const Real& dt, const Vector3r& vel, Vector3r& accel); inline void leapfrogTranslate(State*, const Body::id_t& id, const Real& dt); // leap-frog translate inline void leapfrogSphericalRotate(State*, const Body::id_t& id, const Real& dt); // leap-frog rotate of spherical body inline void leapfrogAsphericalRotate(State*, const Body::id_t& id, const Real& dt, const Vector3r& M); // leap-frog rotate of aspherical body Quaternionr DotQ(const Vector3r& angVel, const Quaternionr& Q); // compute linear and angular acceleration, respecting State::blockedDOFs Vector3r computeAccel(const Vector3r& force, const Real& mass, int blockedDOFs); Vector3r computeAngAccel(const Vector3r& torque, const Vector3r& inertia, int blockedDOFs); void updateEnergy(const shared_ptr&b, const State* state, const Vector3r& fluctVel, const Vector3r& f, const Vector3r& m); #ifdef YADE_OPENMP void ensureSync(); bool syncEnsured; #endif // whether the cell has changed from the previous step bool cellChanged; int homoDeform; // wether a body has been selected in Qt view bool bodySelected; Matrix3r dVelGrad; Vector3r dSpin; public: bool densityScaling;// internal for density scaling Real updatingDispFactor;//(experimental) Displacement factor used to trigger bound update: the bound is updated only if updatingDispFactor*disp>sweepDist when >0, else all bounds are updated. // function to save maximum velocity, for the verlet-distance optimization void saveMaximaVelocity(const Body::id_t& id, State* state); void saveMaximaDisplacement(const shared_ptr& b); bool get_densityScaling (); void set_densityScaling (bool dsc); #ifdef YADE_OPENMP vector threadMaxVelocitySq; #endif virtual void action(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(NewtonIntegrator,GlobalEngine,"Engine integrating newtonian motion equations.", ((Real,damping,0.2,,"damping coefficient for Cundall's non viscous damping (see `numerical damping `_ and [Chareyre2005]_)")) ((Vector3r,gravity,Vector3r::Zero(),,"Gravitational acceleration (effectively replaces GravityEngine).")) ((Real,maxVelocitySq,NaN,,"store square of max. velocity, for informative purposes; computed again at every step. |yupdate|")) ((bool,exactAsphericalRot,true,,"Enable more exact body rotation integrator for :yref:`aspherical bodies` *only*, using formulation from [Allen1989]_, pg. 89.")) ((Matrix3r,prevVelGrad,Matrix3r::Zero(),,"Store previous velocity gradient (:yref:`Cell::velGrad`) to track acceleration. |yupdate|")) #ifdef YADE_BODY_CALLBACK ((vector >,callbacks,,,"List (std::vector in c++) of :yref:`BodyCallbacks` which will be called for each body as it is being processed.")) #endif ((Vector3r,prevCellSize,Vector3r(NaN,NaN,NaN),Attr::hidden,"cell size from previous step, used to detect change and find max velocity")) ((bool,warnNoForceReset,true,,"Warn when forces were not resetted in this step by :yref:`ForceResetter`; this mostly points to :yref:`ForceResetter` being forgotten incidentally and should be disabled only with a good reason.")) // energy tracking ((int,nonviscDampIx,-1,(Attr::hidden|Attr::noSave),"Index of the energy dissipated using the non-viscous damping (:yref:`damping`).")) ((bool,kinSplit,false,,"Whether to separately track translational and rotational kinetic energy.")) ((int,kinEnergyIx,-1,(Attr::hidden|Attr::noSave),"Index for kinetic energy in scene->energies.")) ((int,kinEnergyTransIx,-1,(Attr::hidden|Attr::noSave),"Index for translational kinetic energy in scene->energies.")) ((int,kinEnergyRotIx,-1,(Attr::hidden|Attr::noSave),"Index for rotational kinetic energy in scene->energies.")) ((int,mask,-1,,"If mask defined and the bitwise AND between mask and body`s groupMask gives 0, the body will not move/rotate. Velocities and accelerations will be calculated not paying attention to this parameter.")) , /*ctor*/ densityScaling=false; #ifdef YADE_OPENMP threadMaxVelocitySq.resize(omp_get_max_threads()); syncEnsured=false; #endif ,/*py*/ .add_property("densityScaling",&NewtonIntegrator::get_densityScaling,&NewtonIntegrator::set_densityScaling,"if True, then density scaling [Pfc3dManual30]_ will be applied in order to have a critical timestep equal to :yref:`GlobalStiffnessTimeStepper::targetDt` for all bodies. This option makes the simulation unrealistic from a dynamic point of view, but may speedup quasistatic simulations. In rare situations, it could be useful to not set the scalling factor automatically for each body (which the time-stepper does). In such case revert :yref:`GlobalStiffnessTimeStepper.densityScaling` to False.") ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(NewtonIntegrator); trunk-2017.01a/pkg/dem/NormalInelasticPM.cpp000066400000000000000000000172461304022710500205470ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2008 by Jérôme DURIEZ * * duriez@geo.hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "NormalInelasticPM.hpp" #include #include #include YADE_PLUGIN((NormalInelasticMat)(NormalInelasticityPhys)(Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity)(Ip2_2xNormalInelasticMat_NormalInelasticityPhys)); bool Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity::go(shared_ptr& iG, shared_ptr& iP, Interaction* contact) { int id1 = contact->getId1(); int id2 = contact->getId2(); // cout << "contact entre " << id1 << " et " << id2; NormalInelasticMat* Mat1 = static_cast(Body::byId(id1,scene)->material.get()); ScGeom6D* geom = YADE_CAST(iG.get()); NormalInelasticityPhys* currentContactPhysics = YADE_CAST (iP.get()); Vector3r& shearForce = currentContactPhysics->shearForce; if (contact->isFresh(scene)) { shearForce = Vector3r::Zero(); currentContactPhysics->previousun=0.0; currentContactPhysics->previousFn=0.0; currentContactPhysics->unMax=0.0; } un = geom->penetrationDepth; // >0 for real penetration // Check if there is a real overlap or not. The Ig2... seems to let exist interactions with negative un (= no overlap). Such interactions seem then to have to be deleted here. if ( un < 0 ) { return false;// this, among other things, resets the interaction : geometry and physics variables (as forces, ...) are reset to defaut values } // ******** Computation of normal Force : depends of the history ******* // // cout << " Dans Law2 valeur de kn : " << currentContactPhysics->kn << endl; // cout << "un = " << un << " alors que unMax = "<< currentContactPhysics->unMax << " et previousun = " << currentContactPhysics->previousun << " et previousFn =" << currentContactPhysics->previousFn << endl; if(un >= currentContactPhysics->unMax) // case of virgin load : on the "principal line" (limit state of the (un,Fn) space) { Fn = currentContactPhysics->knLower*un; currentContactPhysics->unMax = std::abs(un); // cout << "je suis dans le calcul normal " << endl; } else// a priori then we need a greater stifness. False in the case when we are already on the limit state, but a correction below will then do the job { currentContactPhysics->kn = currentContactPhysics->knLower* Mat1->coeff_dech; // Incremental computation of the new normal force : Fn = currentContactPhysics->previousFn + currentContactPhysics->kn * (un-currentContactPhysics->previousun); // cout << "je suis dans l'autre calcul" << endl; if(std::abs(Fn) > std::abs(currentContactPhysics->knLower * un)) // check if the limit state is not violated { Fn = currentContactPhysics->knLower*un; // cout << "j'etais dans l'autre calcul mais j'ai corrige pour ne pas depasser la limite" << endl; } if(Fn < 0.0 ) // check to stay >=0 { Fn = 0; // cout << "j'ai corrige pour ne pas etre negatif" << endl; } } currentContactPhysics->normalForce = Fn*geom->normal; // cout << "Fn appliquee " << Fn << endl << endl; // actualisation : currentContactPhysics->previousFn = Fn; currentContactPhysics->previousun = un; // *** End of computation of normal force *** // // ******** Tangential force ******* // if ( un < 0 ) { // BREAK due to tension return false; } else { // Correction of previous shear force to take into account the change in normal: shearForce = geom->rotate(currentContactPhysics->shearForce); // Update of shear force corresponding to shear displacement increment: shearForce -= currentContactPhysics->ks * geom->shearIncrement(); Fs = currentContactPhysics->shearForce.norm(); maxFs = std::max((Real) 0,Fn*currentContactPhysics->tangensOfFrictionAngle); if ( Fs > maxFs ) { maxFs = max((Real) 0, Fn * currentContactPhysics->tangensOfFrictionAngle); maxFs = maxFs / Fs; if (maxFs>1) cerr << "maxFs>1!!!!!!!!!!!!!!!!!!!" << endl; shearForce *= maxFs; if (Fn<0) currentContactPhysics->normalForce = Vector3r::Zero(); } f = currentContactPhysics->normalForce + shearForce; scene->forces.addForce (id1,-f); scene->forces.addForce (id2, f); scene->forces.addTorque(id1,-(geom->radius1-0.5*geom->penetrationDepth)* geom->normal.cross(f)); scene->forces.addTorque(id2, -(geom->radius2-0.5*geom->penetrationDepth)* geom->normal.cross(f)); // *** End of computation of tangential force *** // // ******** Moment law ******* // if(momentRotationLaw) { currentContactPhysics->moment_twist = (geom->getTwist()*currentContactPhysics->kr)*geom->normal ; currentContactPhysics->moment_bending = geom->getBending() * currentContactPhysics->kr; moment = currentContactPhysics->moment_twist + currentContactPhysics->moment_bending; // Limitation by plastic threshold of this part of the moment caused by relative twist and bending if (!momentAlwaysElastic) { Real normeMomentMax = currentContactPhysics->forMaxMoment * std::abs(Fn); if(moment.norm()>normeMomentMax) { moment *= normeMomentMax/moment.norm(); } } scene->forces.addTorque(id1,-moment); scene->forces.addTorque(id2, moment); } // ******** Moment law END ******* // } return true; } void Ip2_2xNormalInelasticMat_NormalInelasticityPhys::go( const shared_ptr& b1 // NormalInelasticMat , const shared_ptr& b2 // NormalInelasticMat , const shared_ptr& interaction) { NormalInelasticMat* sdec1 = static_cast(b1.get()); NormalInelasticMat* sdec2 = static_cast(b2.get()); ScGeom* geom = YADE_CAST(interaction->geom.get()); if(geom) // so it is ScGeom - NON PERMANENT LINK { if(!interaction->phys) { //std::cerr << " isNew, id1: " << interaction->getId1() << " id2: " << interaction->getId2() << "\n"; interaction->phys = shared_ptr(new NormalInelasticityPhys()); NormalInelasticityPhys* contactPhysics = YADE_CAST(interaction->phys.get()); Real Ea = sdec1->young; Real Eb = sdec2->young; Real Va = sdec1->poisson; Real Vb = sdec2->poisson; Real Ra = geom->radius1; Real Rb = geom->radius2; Real fa = sdec1->frictionAngle; Real fb = sdec2->frictionAngle; Real Kn = 2.0*Ea*Ra*Eb*Rb/(Ea*Ra+Eb*Rb);//harmonic average of two stiffnesses Real Ks = 2.0*Ea*Ra*Va*Eb*Rb*Vb/(Ea*Ra*Va+Eb*Rb*Vb);//harmonic average of two stiffnesses with ks=V*kn for each sphere // Jean-Patrick Plassiard, Noura Belheine, Frederic Victor Donze, "A Spherical Discrete Element Model: calibration procedure and incremental response", DOI: 10.1007/s10035-009-0130-x Real Kr = betaR*std::pow((Ra+Rb)/2.0,2)*Ks; contactPhysics->tangensOfFrictionAngle = std::tan(std::min(fa,fb)); contactPhysics->forMaxMoment = 1.0*(Ra+Rb)/2.0; // 1.0 corresponding to ethaR which I don't know exactly where to define as a parameter... // Lot of suppress here around (>) r2276. contactPhysics->knLower = Kn; contactPhysics->kn = Kn; contactPhysics->ks = Ks; contactPhysics->kr = Kr; } } }; trunk-2017.01a/pkg/dem/NormalInelasticPM.hpp000066400000000000000000000136321304022710500205470ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2010 by Jerome Duriez * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include class NormalInelasticMat : public FrictMat { public : virtual ~NormalInelasticMat () {}; /// Serialization YADE_CLASS_BASE_DOC_ATTRS_CTOR(NormalInelasticMat,FrictMat,"Material class for particles whose contact obey to a normal inelasticity (governed by this :yref:`coeff_dech`).", ((Real,coeff_dech,1.0,,"=kn(unload) / kn(load)")) , createIndex(); ); /// Indexable REGISTER_CLASS_INDEX(NormalInelasticMat,FrictMat); }; REGISTER_SERIALIZABLE(NormalInelasticMat); class NormalInelasticityPhys : public FrictPhys { public : virtual ~NormalInelasticityPhys() {}; YADE_CLASS_BASE_DOC_ATTRS_CTOR(NormalInelasticityPhys,FrictPhys, "Physics (of interaction) for using :yref:`Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity` : with inelastic unloadings", ((Real,unMax,0.0,,"the maximum value of penetration depth of the history of this interaction")) ((Real,previousun,0.0,,"the value of this un at the last time step")) ((Real,previousFn,0.0,,"the value of the normal force at the last time step")) ((Real,forMaxMoment,1.0,,"parameter stored for each interaction, and allowing to compute the maximum value of the exchanged torque : TorqueMax= forMaxMoment * NormalForce")) ((Real,kr,0.0,,"the rolling stiffness of the interaction")) ((Real,knLower,0.0,,"the stifness corresponding to a virgin load for example")) // internal attributes ((Vector3r,moment_twist,Vector3r(0,0,0),(Attr::noSave | Attr::readonly),"Twist moment. Defined here, being initialized as it should be, to be used in :yref:`Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity`")) ((Vector3r,moment_bending,Vector3r(0,0,0),(Attr::noSave | Attr::readonly),"Bending moment. Defined here, being initialized as it should be, to be used in :yref:`Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity`")) , createIndex(); ); REGISTER_CLASS_INDEX(NormalInelasticityPhys,FrictPhys); }; REGISTER_SERIALIZABLE(NormalInelasticityPhys); class Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity : public LawFunctor { private : Vector3r moment // the part of the contact torque of the interaction due to relative rotations (a first part is due to contact forces) ,f// contact force ; Real Fn // value of normal force in the interaction ,Fs // shear force ,maxFs; // maximum value of shear force according to Coulomb-like criterion Real un; // value of interpenetration in the interaction public : virtual bool go(shared_ptr&, shared_ptr&, Interaction*); FUNCTOR2D(ScGeom,NormalInelasticityPhys); YADE_CLASS_BASE_DOC_ATTRS_CTOR(Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity, LawFunctor, "Contact law used to simulate granular filler in rock joints [Duriez2009a]_, [Duriez2011]_. It includes possibility of cohesion, moment transfer and inelastic compression behaviour (to reproduce the normal inelasticity observed for rock joints, for the latter).\n\n The moment transfer relation corresponds to the adaptation of the work of Plassiard & Belheine (see in [DeghmReport2006]_ for example), which was realized by J. Kozicki, and is now coded in :yref:`ScGeom6D`.\n\n As others :yref:`LawFunctor`, it uses pre-computed data of the interactions (rigidities, friction angles -with their tan()-, orientations of the interactions); this work is done here in :yref:`Ip2_2xNormalInelasticMat_NormalInelasticityPhys`.\n\n To use this you should also use :yref:`NormalInelasticMat` as material type of the bodies.\n\n The effects of this law are illustrated in examples/normalInelasticity-test.py", ((bool,momentRotationLaw,true,,"boolean, true=> computation of a torque (against relative rotation) exchanged between particles")) ((bool,momentAlwaysElastic,false,,"boolean, true=> the part of the contact torque (caused by relative rotations, which is computed only if momentRotationLaw..) is not limited by a plastic threshold")) , moment=Vector3r::Zero(); f=Vector3r::Zero(); Fn=0.0; Fs=0.0; maxFs=0.0; un=0.0; ); }; REGISTER_SERIALIZABLE(Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity); /*! \brief The RelationShips for using Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity In these RelationShips all the attributes of the interactions (which are of NormalInelasticityPhys type) are computed. WARNING : as in the others Relationships most of the attributes are computed only once : when the interaction is "new" */ class Ip2_2xNormalInelasticMat_NormalInelasticityPhys : public IPhysFunctor { public : virtual void go( const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction); FUNCTOR2D(NormalInelasticMat,NormalInelasticMat); YADE_CLASS_BASE_DOC_ATTRS(Ip2_2xNormalInelasticMat_NormalInelasticityPhys, IPhysFunctor, "Computes interaction attributes (of :yref:`NormalInelasticityPhys` type) from :yref:`NormalInelasticMat` material parameters. For simulations using :yref:`Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity`. Note that, as for others :yref:`Ip2 functors`, most of the attributes are computed only once, when the interaction is new.", ((Real,betaR,0.12,,"Parameter for computing the torque-stifness : T-stifness = betaR * Rmoy^2")) ); }; REGISTER_SERIALIZABLE(Ip2_2xNormalInelasticMat_NormalInelasticityPhys); trunk-2017.01a/pkg/dem/PeriIsoCompressor.cpp000066400000000000000000000550601304022710500206510ustar00rootroot00000000000000 // 2009 © Václav Šmilauer #include #include #include #include #include #include YADE_PLUGIN((PeriIsoCompressor)(PeriTriaxController)(Peri3dController)) CREATE_LOGGER(PeriIsoCompressor); void PeriIsoCompressor::action(){ if(!scene->isPeriodic){ LOG_FATAL("Being used on non-periodic simulation!"); throw; } if(state>=stresses.size()) return; // initialize values if(charLen<=0){ Bound* bv=Body::byId(0,scene)->bound.get(); if(!bv){ LOG_FATAL("No charLen defined and body #0 has no bound"); throw; } const Vector3r sz=bv->max-bv->min; charLen=(sz[0]+sz[1]+sz[2])/3.; LOG_INFO("No charLen defined, taking avg bbox size of body #0 = "<& b, *scene->bodies){ if(!b || !b->bound) continue; for(int i=0; i<3; i++) maxSpan=max(maxSpan,b->bound->max[i]-b->bound->min[i]); } } if(maxDisplPerStep<0) maxDisplPerStep=1e-2*charLen; // this should be tuned somehow… const long& step=scene->iter; Vector3r cellSize=scene->cell->getSize(); //unused: Real cellVolume=cellSize[0]*cellSize[1]*cellSize[2]; Vector3r cellArea=Vector3r(cellSize[1]*cellSize[2],cellSize[0]*cellSize[2],cellSize[0]*cellSize[1]); Real minSize=min(cellSize[0],min(cellSize[1],cellSize[2])), maxSize=max(cellSize[0],max(cellSize[1],cellSize[2])); if(minSize<2.1*maxSpan){ throw runtime_error("Minimum cell size is smaller than 2.1*span_of_the_biggest_body! (periodic collider requirement)"); } if(((step%globalUpdateInt)==0) || avgStiffness<0 || sigma[0]<0 || sigma[1]<0 || sigma[2]<0){ Vector3r sumForces=Shop::totalForceInVolume(avgStiffness,scene); sigma=-Vector3r(sumForces[0]/cellArea[0],sumForces[1]/cellArea[1],sumForces[2]/cellArea[2]); LOG_TRACE("Updated sigma="<0) { sigma+=(avgGrow*avgStiffness)*Vector3r::Ones(); sigAvg+=avgGrow*avgStiffness; } if(std::abs((sigAvg-sigmaGoal)/sigmaGoal)>5e-3) allStressesOK=false; cellGrow=(avgGrow/avgSize)*cellSize; } else{ // handle each dimension separately for(int axis=0; axis<3; axis++){ // Δσ=ΔεE=(Δl/l)×(l×K/A) ↔ Δl=Δσ×A/K // FIXME: either NormShearPhys::{kn,ks} is computed wrong or we have dimensionality problem here // FIXME: that is why the fixup 1e-4 is needed here // FIXME: or perhaps maxDisplaPerStep=1e-2*charLen is too big?? cellGrow[axis]=1e-4*(sigmaGoal-sigma[axis])*cellArea[axis]/(avgStiffness>0?avgStiffness:1); // FIXME: wrong dimensions? See PeriTriaxController if(std::abs(cellGrow[axis])>maxDisplPerStep) cellGrow[axis]=Mathr::Sign(cellGrow[axis])*maxDisplPerStep; cellGrow[axis]=max(cellGrow[axis],-(cellSize[axis]-2.1*maxSpan)); // crude way of predicting sigma, for steps when it is not computed from intrs if(avgStiffness>0) sigma[axis]+=cellGrow[axis]*avgStiffness; // FIXME: dimensions if(std::abs((sigma[axis]-sigmaGoal)/sigmaGoal)>5e-3) allStressesOK=false; } } TRVAR4(cellGrow,sigma,sigmaGoal,avgStiffness); assert(scene->dt>0); for(int axis=0; axis<3; axis++){ scene->cell->velGrad(axis,axis)=cellGrow[axis]/(scene->dt*scene->cell->getSize()[axis]); } // handle state transitions if(allStressesOK){ if((step%globalUpdateInt)==0) currUnbalanced=Shop::unbalancedForce(/*useMaxForce=*/false,scene); if(currUnbalancedcell->trsf(i,i)); //Compute volume of the deformed cell Real volume=scene->cell->hSize.determinant(); //Compute sum(fi*lj) and stiffness stressTensor = Matrix3r::Zero(); Vector3r sumStiff(Vector3r::Zero()); int n=0; // NOTE : This sort of loops on interactions could be removed if we had callbacks in e.g. constitutive laws // → very likely performance hit; do you have some concrete design in mind? // → a vector with functors so we can law->functs->pushback(myThing), and access to the fundamental members (forces, stiffness, normal, etc.). Implementing the second part is less clear in my mind. Inheriting from law::funct(force&, stiffness&, ...)? FOREACH(const shared_ptr&I, *scene->interactions){ if ( !I->isReal() ) continue; NormShearPhys* nsi=YADE_CAST ( I->phys.get() ); GenericSpheresContact* gsc=YADE_CAST ( I->geom.get() ); //Contact force Vector3r f= (-1.)*( nsi->normalForce+nsi->shearForce ); Vector3r branch=Body::byId(I->getId2(),scene)->state->pos + scene->cell->hSize*I->cellDist.cast() -Body::byId(I->getId1(),scene)->state->pos; stressTensor+=f*branch.transpose(); if( !dynCell ){ for ( int i=0; i<3; i++ ) sumStiff[i]+=std::abs ( gsc->normal[i] ) *nsi->kn+ ( 1-std::abs ( gsc->normal[i] ) ) *nsi->ks; n++;} } // Divide by volume as in stressTensor=sum(fi*lj)/Volume (Love equation) stressTensor /= volume; for(int axis=0; axis<3; axis++) stress[axis]=stressTensor(axis,axis); LOG_DEBUG ( "stressTensor : "<cell->getSize(); //FIXME : this is wrong I think (almost sure, B.) Vector3r cellArea=Vector3r(cellSize[1]*cellSize[2],cellSize[0]*cellSize[2],cellSize[0]*cellSize[1]); // initial updates if (maxBodySpan[0]<=0){ FOREACH(const shared_ptr& b,*scene->bodies){ if(!b || !b->bound) continue; for(int i=0; i<3; i++) if ((b->bound->max[i]-b->bound->min[i])bound->max[i]-b->bound->min[i]);} } // check current size if(2.1*maxBodySpan[0]>cellSize[0] || 2.1*maxBodySpan[1]>cellSize[1] || 2.1*maxBodySpan[2]>cellSize[2]){ LOG_DEBUG("cellSize="<iter%globUpdate)==0); if(doUpdate || min(stiff[0],min(stiff[1],stiff[2])) <=0 || dynCell){ strainStressStiffUpdate(); } // set mass to be sum of masses, if not set by the user if(dynCell && std::isnan(mass)){ mass=0; FOREACH(const shared_ptr& b, *scene->bodies){ if(b && b->state) mass+=b->state->mass; } LOG_INFO("Setting cell mass to "<dt>0.); for(int axis=0; axis<3; axis++){ Real& strain_rate = scene->cell->velGrad(axis,axis);//strain rate on axis if(stressMask & (1<dt*(goal[axis]-stress[axis])*cellArea[axis]/(stiff[axis]>0?stiff[axis]:1.); LOG_TRACE(axis<<": stress="<dt; LOG_TRACE ( axis<<": strain="<1e-6");} } } // update stress and strain if (!dynCell) for ( int axis=0; axis<3; axis++ ){ // take in account something like poisson's effect here… //Real bogusPoisson=0.25; int ax1=(axis+1)%3,ax2=(axis+2)%3; //don't modify stress if dynCell, testing only stiff[axis]>0 would not allow switching the control mode in simulations, if (stiff[axis]>0) stress[axis]+=(scene->cell->velGrad(axis,axis)*scene->dt/cellSize[axis])*(stiff[axis]/cellArea[axis]); //-bogusPoisson*(cellGrow[ax1]/refSize[ax1])*(stiff[ax1]/cellArea[ax1])-bogusPoisson*(cellGrow[ax2]/refSize[ax2])*(stiff[ax2]/cellArea[ax2]); } for (int k=0;k<3;k++) strainRate[k]=scene->cell->velGrad(k,k); //Update energy input FIXME: replace trace by norm, so it works for any kind of deformation Real dW=(0.5*(scene->cell->prevVelGrad + scene->cell->velGrad)*stressTensor).trace()*scene->dt*(scene->cell->hSize.determinant()); externalWork+=dW; if(scene->trackEnergy) scene->energy->add(-dW,"velGradWork",velGradWorkIx,/*non-incremental*/false); prevGrow = strainRate; if(allOk){ if(doUpdate || currUnbalanced<0){ currUnbalanced=Shop::unbalancedForce(/*useMaxForce=*/false,scene); LOG_DEBUG("Stress/strain="<< (stressMask&1?stress[0]:strain[0]) <<"," <<(stressMask&2?stress[1]:strain[1])<<"," <<(stressMask&4?stress[2]:strain[2]) <<", goal="<isPeriodic){ LOG_FATAL("Being used on non-periodic simulation!"); throw; } const Real& dt=scene->dt; assert(dt>0); /* "Constructor" (if (step==0) ) ps is the vector of indices, where stress is prescribed pe is the vector of indices, where strain is prescribed example: goal = 0b000110 : ps=(1,2,0,0,0,0), pe=(0,3,4,5,0,0) lenPs (lenPe) is the meaningful length of ps (pe) (the zeros at the end of ps and pe has no meaning), i.e. the number of indices with prescribed stress (strain) */ bool stressBasedSimulation=false; // true when all stresses are prescribed or if all prescribed strains equal zero if (progress==0) { lenPs=0; lenPe=0; ps=Vector6i::Zero(); pe=Vector6i::Zero(); stressGoal = Vector6r::Zero(); strainGoal = Vector6r::Zero(); for (int i=0; i<6; i++){ if (stressMask&(1<operator[](j).operator(k) is k-th element of j-th Vector2r of xxPath //#define PATH_OP_OP(pi,op1i,op2i) paths[pi]->operator[](op1i).operator()(op2i) //#define PATH_OP_OP(pi,op1i,op2i) (pi==0?xxPath:pi==1?yyPath:pi==2?zzPath:pi==3?yzPath:pi==4?zxPath:pi==5?xyPath:NULL)->operator[](op1i).operator()(op2i) #define PATH_OP_OP(pi,op1i,op2i) (pi==0?xxPath:pi==1?yyPath:pi==2?zzPath:pi==3?yzPath:pi==4?zxPath:xyPath)[op1i].operator()(op2i) for (int i=0; i<6; i++) { for (int j=1; j= PATH_OP_OP(i,j,0) ) { throw runtime_error("Peri3dCoontroller.##Path: Time in ##Path must be monothonically increasing"); }} } for (int j=0; j= 1e-9) { // the final value is not 0 (otherwise always absolute values are considered) PATH_OP_OP(i,j,1) *= goal(i)/PATH_OP_OP(i,pathSizes[i]-1,1); } } } // set weather the simulation is "stress based" (all stress components prescribed or all prescribed strains equal zero) if (lenPe == 0) { stressBasedSimulation = true; } else { stressBasedSimulation = true; for (int i=0; i= PATH_OP_OP(i,pathsCounter[i],0)) { pathsCounter[i]++; } } /* values of prescribed stress (strain) rate in respect to prescribed path. The strain indices where stress is prescribed will be overwritten by predictor */ for (int i=0; i 0){ // if at least 1 stress component is prescribed (otherwise prescribed strain is applied in all 6 directions if (progress == 0 && stressBasedSimulation) { // the very first step, use compliance estimation (compliance matrix for elastic isotropic material) Real complianceEstimation[6][6] = { {1/youngEstimation, -poissonEstimation/youngEstimation, -poissonEstimation/youngEstimation, 0,0,0}, {-poissonEstimation/youngEstimation, 1/youngEstimation, -poissonEstimation/youngEstimation, 0,0,0}, {-poissonEstimation/youngEstimation, -poissonEstimation/youngEstimation, 1/youngEstimation, 0,0,0}, {0,0,0, (1+poissonEstimation)/youngEstimation,0,0}, {0,0,0, 0,(1+poissonEstimation)/youngEstimation,0}, {0,0,0, 0,0,(1+poissonEstimation)/youngEstimation}}; for (int i=0; i0){strainRate(j) -= sr*mod;} else {strainRate(j) += sr*mod;} } } } // correction coefficient ix strainRate.maxstd::abs() > maxStrainRate Real srCorr = (strainRate.cwiseAbs().maxCoeff() > maxStrainRate)? (maxStrainRate/strainRate.cwiseAbs().maxCoeff()):1.; strainRate *= srCorr; // Actual action (see the documentation for more info) const Matrix3r& trsf=scene->cell->trsf; // compute rotational and nonrotational (strain in local coordinates) part of trsf Matrix_computeUnitaryPositive(trsf,&rot,&nonrot); // prescribed velocity gradient (strain tensor rate) in global coordinates epsilonRate = voigt_toSymmTensor(strainRate,/*strain=*/true); /* transformation of prescribed strain rate (computed by predictor) into local cell coordinates, multiplying by time to obtain strain increment and adding it to nonrot (current strain in local coordinates)*/ nonrot += rot.transpose()*(epsilonRate*dt)*rot; Matrix3r& velGrad=scene->cell->velGrad; // compute velGrad: // trsf = rot*nonrot // dTrsf = dt*velGrad // trsfNew = trsf + dTrsf*trsf = (I+dTrsf)*trsf = (I+dt*velGrad)*trsf -> velGrad velGrad = ((rot*nonrot)*trsf.inverse()- Matrix3r::Identity()) / dt ; progress += srCorr/nSteps; if (progress >= 1. || strain.cwiseAbs().maxCoeff() > maxStrain) { if(doneHook.empty()){ LOG_INFO("No doneHook set, dying."); dead=true; Omega::instance().pause(); } else{ LOG_INFO("Running doneHook: "< #pragma once #include class PeriIsoCompressor: public BoundaryController{ Real avgStiffness; Real maxDisplPerStep; Vector3r sumForces, sigma; Real currUnbalanced; public: void action(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(PeriIsoCompressor,BoundaryController,"Compress/decompress cloud of spheres by controlling periodic cell size until it reaches prescribed average stress, then moving to next stress value in given stress series.", ((vector,stresses,,,"Stresses that should be reached, one after another")) ((Real,charLen,-1.,,"Characteristic length, should be something like mean particle diameter (default -1=invalid value))")) ((Real,maxSpan,-1.,,"Maximum body span in terms of bbox, to prevent periodic cell getting too small. |ycomp|")) ((Real,maxUnbalanced,1e-4,,"if actual unbalanced force is smaller than this number, the packing is considered stable,")) ((int,globalUpdateInt,20,,"how often to recompute average stress, stiffness and unbalanced force")) ((size_t,state,0,,"Where are we at in the stress series")) ((string,doneHook,"",,"Python command to be run when reaching the last specified stress")) ((bool,keepProportions,true,,"Exactly keep proportions of the cell (stress is controlled based on average, not its components")), /*ctor*/ currUnbalanced=-1; avgStiffness=-1; maxDisplPerStep=-1; sumForces=Vector3r::Zero(); sigma=Vector3r::Zero(); , /*py*/ .def_readonly("currUnbalanced",&PeriIsoCompressor::currUnbalanced,"Current value of unbalanced force") .def_readonly("sigma",&PeriIsoCompressor::sigma,"Current stress value") ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(PeriIsoCompressor); /* Engine for independently controlling stress or strain in periodic simulations. strainStress contains absolute values for the controlled quantity, and stressMask determines meaning of those values (0 for strain, 1 for stress): e.g. ( 1<<0 | 1<<2 ) = 1 | 4 = 5 means that strainStress[0] and strainStress[2] are stress values, and strainStress[1] is strain. See scripts/test/periodic-triax.py for a simple example. */ class PeriTriaxController: public BoundaryController{ public: virtual void action(); void strainStressStiffUpdate(); YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(PeriTriaxController,BoundaryController,"Engine for independently controlling stress or strain in periodic simulations.\n\n``strainStress`` contains absolute values for the controlled quantity, and ``stressMask`` determines meaning of those values (0 for strain, 1 for stress): e.g. ``( 1<<0 | 1<<2 ) = 1 | 4 = 5`` means that ``strainStress[0]`` and ``strainStress[2]`` are stress values, and ``strainStress[1]`` is strain. \n\nSee scripts/test/periodic-triax.py for a simple example.", ((bool,dynCell,false,,"Imposed stress can be controlled using the packing stiffness or by applying the laws of dynamic (dynCell=true). Don't forget to assign a :yref:`mass` to the cell.")) ((Vector3r,goal,Vector3r::Zero(),,"Desired stress or strain values (depending on stressMask), strains defined as ``strain(i)=log(Fii)``.\n\n.. warning:: Strains are relative to the :yref:`O.cell.refSize` (reference cell size), not the current one (e.g. at the moment when the new strain value is set).")) ((int,stressMask,((void)"all strains",0),,"mask determining strain/stress (0/1) meaning for goal components")) ((Vector3r,maxStrainRate,Vector3r(1,1,1),,"Maximum strain rate of the periodic cell.")) ((Real,maxUnbalanced,1e-4,,"maximum unbalanced force.")) ((Real,absStressTol,1e3,,"Absolute stress tolerance")) ((Real,relStressTol,3e-5,,"Relative stress tolerance")) ((Real,growDamping,.25,,"Damping of cell resizing (0=perfect control, 1=no control at all); see also ``wallDamping`` in :yref:`TriaxialStressController`.")) ((int,globUpdate,5,,"How often to recompute average stress, stiffness and unbalaced force.")) ((string,doneHook,,,"python command to be run when the desired state is reached")) ((Vector3r,maxBodySpan,Vector3r::Zero(),,"maximum body dimension |ycomp|")) ((Matrix3r,stressTensor,Matrix3r::Zero(),,"average stresses, updated at every step (only every globUpdate steps recomputed from interactions if !dynCell)")) ((Vector3r,stress,Vector3r::Zero(),,"diagonal terms of the stress tensor")) ((Vector3r,strain,Vector3r::Zero(),,"cell strain |yupdate|")) ((Vector3r,strainRate,Vector3r::Zero(),,"cell strain rate |yupdate|")) ((Vector3r,stiff,Vector3r::Zero(),,"average stiffness (only every globUpdate steps recomputed from interactions) |yupdate|")) ((Real,currUnbalanced,NaN,,"current unbalanced force (updated every globUpdate) |yupdate|")) ((Vector3r,prevGrow,Vector3r::Zero(),,"previous cell grow")) ((Real,mass,NaN,,"mass of the cell (user set); if not set and :yref:`dynCell` is used, it will be computed as sum of masses of all particles.")) ((Real,externalWork,0,,"Work input from boundary controller.")) ((int,velGradWorkIx,-1,(Attr::hidden|Attr::noSave),"Index for work done by velocity gradient, if tracking energy")) ,,, ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(PeriTriaxController); class Peri3dController: public BoundaryController{ public: Vector6r stressOld; Matrix3r sigma, epsilon, epsilonRate, rot, nonrot; virtual void action(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Peri3dController,BoundaryController,"Experimental controller of full strain/stress tensors on periodic cell. Detailed documentation is in py/_extraDocs.py.", ((Vector6r,stress,Vector6r::Zero(),,"Current stress vector ($\\sigma_x$,$\\sigma_y$,$\\sigma_z$,$\\tau_{yz}$,$\\tau_{zx}$,$\\tau_{xy}$)|yupdate|.")) ((Vector6r,strain,Vector6r::Zero(),,"Current strain (deformation) vector ($\\varepsilon_x$,$\\varepsilon_y$,$\\varepsilon_z$,$\\gamma_{yz}$,$\\gamma_{zx}$,$\\gamma_{xy}$) |yupdate|.")) ((Vector6r,strainRate,Vector6r::Zero(),,"Current strain rate vector.")) ((Vector6r,stressRate,Vector6r::Zero(),,"Current stress rate vector (that is prescribed, the actual one slightly differ).")) ((Vector6r,stressIdeal,Vector6r::Zero(),,"Ideal stress vector at current time step.")) ((Vector6r,goal,Vector6r::Zero(),,"Goal state; only the upper triangular matrix is considered; each component is either prescribed stress or strain, depending on :yref:`stressMask`.")) ((int,stressMask,((void)"all strains",0),,"mask determining whether components of :yref:`goal` are strain (0) or stress (1). The order is 00,11,22,12,02,01 from the least significant bit. (e.g. 0b000011 is stress 00 and stress 11).")) ((int,nSteps,1000,,"Number of steps of the simulation.")) ((Real,progress,0.,,"Actual progress of the simulation with Controller.")) ((Real,mod,.1,,"Predictor modificator, by trail-and-error analysis the value 0.1 was found as the best.")) ((string,doneHook,,,"Python command (as string) to run when :yref:`nSteps` is achieved. If empty, the engine will be set :yref:`dead`.")) ((vector,xxPath,vector(1,Vector2r::Ones()),,"\"Time function\" (piecewise linear) for xx direction. Sequence of couples of numbers. First number is time, second number desired value of respective quantity (stress or strain). The last couple is considered as final state (equal to (:yref:`nSteps`, :yref:`goal`)), other values are relative to this state.\n\nExample: nSteps=1000, goal[0]=300, xxPath=((2,3),(4,1),(5,2))\n\nat step 400 (=5*1000/2) the value is 450 (=3*300/2),\n\nat step 800 (=4*1000/5) the value is 150 (=1*300/2),\n\nat step 1000 (=5*1000/5=nSteps) the value is 300 (=2*300/2=goal[0]).\n\nSee example :ysrc:`scripts/test/peri3dController_example1` for illusration.")) ((vector,yyPath,vector(1,Vector2r::Ones()),,"Time function for yy direction, see :yref:`xxPath`")) ((vector,zzPath,vector(1,Vector2r::Ones()),,"Time function for zz direction, see :yref:`xxPath`")) ((vector,yzPath,vector(1,Vector2r::Ones()),,"Time function for yz direction, see :yref:`xxPath`")) ((vector,zxPath,vector(1,Vector2r::Ones()),,"Time function for zx direction, see :yref:`xxPath`")) ((vector,xyPath,vector(1,Vector2r::Ones()),,"Time function for xy direction, see :yref:`xxPath`")) ((Real,maxStrainRate,1e3,,"Maximal absolute value of strain rate (both normal and shear components of :yref:`strain`)")) ((Real,maxStrain,1e6,,"Maximal asolute value of :yref:`strain` allowed in the simulation. If reached, the simulation is considered as finished")) ((Real,youngEstimation,1e20,,"Estimation of macroscopic Young's modulus, used for the first simulation step")) ((Real,poissonEstimation,.25,,"Estimation of macroscopic Poisson's ratio, used used for the first simulation step")) // ((Vector6r,stressGoal,Vector6r::Zero(),Attr::readonly,"Peri3dController internal variable")) ((Vector6r,strainGoal,Vector6r::Zero(),Attr::readonly,"Peri3dController internal variable")) ((Vector6i,pe,Vector6i::Zero(),Attr::readonly,"Peri3dController internal variable")) ((Vector6i,ps,Vector6i::Zero(),Attr::readonly,"Peri3dController internal variable")) ((Vector6i,pathSizes,Vector6i::Zero(),Attr::readonly,"Peri3dController internal variable")) ((Vector6i,pathsCounter,Vector6i::Zero(),Attr::readonly,"Peri3dController internal variable")) ((int,lenPe,0,Attr::readonly,"Peri3dController internal variable")) ((int,lenPs,0,Attr::readonly,"Peri3dController internal variable")) , /*ctor*/ , /*py*/ ); }; REGISTER_SERIALIZABLE(Peri3dController); trunk-2017.01a/pkg/dem/Polyhedra.cpp000066400000000000000000000523611304022710500171520ustar00rootroot00000000000000// © 2013 Jan Elias, http://www.fce.vutbr.cz/STM/elias.j/, elias.j@fce.vutbr.cz // https://www.vutbr.cz/www_base/gigadisk.php?i=95194aa9a #ifdef YADE_CGAL // NDEBUG causes crashes in CGAL sometimes. Anton #ifdef NDEBUG #undef NDEBUG #endif #include "Polyhedra.hpp" YADE_PLUGIN(/* self-contained in hpp: */ (Polyhedra) (PolyhedraGeom) (Bo1_Polyhedra_Aabb) (PolyhedraPhys) (PolyhedraMat) (Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys) (Ip2_FrictMat_PolyhedraMat_FrictPhys) (Law2_PolyhedraGeom_PolyhedraPhys_Volumetric) /* some code in cpp (this file): */ #ifdef YADE_OPENGL (Gl1_Polyhedra) (Gl1_PolyhedraGeom) (Gl1_PolyhedraPhys) #endif ); //********************************************************************************* /* Polyhedra Constructor */ void Polyhedra::Initialize(){ if (init) return; bool isRandom = false; //get vertices int N = (int) v.size(); if (N==0) { //generate randomly while ((int) v.size()<4) GenerateRandomGeometry(); N = (int) v.size(); isRandom = true; } //compute convex hull of vertices std::vector points; points.resize(v.size()); for(int i=0;ipoint().x(),vIter->point().y(),vIter->point().z())); } //list surface triangles for plotting faceTri.clear(); std::transform(P.facets_begin(), P.facets_end(), P.planes_begin(),Plane_equation()); for (Polyhedron::Facet_iterator fIter = P.facets_begin(); fIter != P.facets_end(); fIter++){ Polyhedron::Halfedge_around_facet_circulator hfc0; int n = fIter->facet_degree(); hfc0 = fIter->facet_begin(); int a = std::distance(P.vertices_begin(), hfc0->vertex()); for (int i=2; ivertex())); faceTri.push_back(std::distance(P.vertices_begin(), hfc0->next()->vertex())); } } //compute centroid and volume P_volume_centroid(P, &volume, ¢roid); //check vierd behavior of CGAL in tessalation if(isRandom && volume*1.75<4./3.*3.14*size[0]/2.*size[1]/2.*size[2]/2.) { v.clear(); seed = rand(); Initialize(); } Vector3r translation((-1)*centroid); //set centroid to be [0,0,0] for(int i=0;i& v) { init = false; this->v = v; Initialize(); } void Polyhedra::setVertices4(const Vector3r& v0, const Vector3r& v1,const Vector3r& v2,const Vector3r& v3) { init = false; v.resize(4); v[0] = v0; v[1] = v1; v[2] = v2; v[3] = v3; Initialize(); } //************************************************************************** /* Generator of randomly shaped polyhedron based on Voronoi tessellation*/ void Polyhedra::GenerateRandomGeometry(){ srand(seed); vector nuclei; nuclei.push_back(CGALpoint(5.,5.,5.)); CGALpoint trial; unsigned int iter = 0; bool isOK; //fill box 5x5x5 with randomly located nuclei with restricted minimal mutual distance 0.75 which gives approximate mean mutual distance 1; Real dist_min2 = 0.75*0.75; while(iter<500){ isOK = true; iter++; trial = CGALpoint(Real(rand())/RAND_MAX*5.+2.5,Real(rand())/RAND_MAX*5.+2.5,Real(rand())/RAND_MAX*5.+2.5); for(int i=0;i< (int) nuclei.size();i++) { isOK = pow(nuclei[i].x()-trial.x(),2)+pow(nuclei[i].y()-trial.y(),2)+pow(nuclei[i].z()-trial.z(),2) > dist_min2; if (!isOK) break; } if(isOK){ iter = 0; nuclei.push_back(trial); } } //perform Voronoi tessellation nuclei.erase(nuclei.begin()); Triangulation dt(nuclei.begin(), nuclei.end()); Triangulation::Vertex_handle zero_point = dt.insert(CGALpoint(5.,5.,5.)); v.clear(); std::vector ch_cells; dt.incident_cells(zero_point,std::back_inserter(ch_cells)); for(auto ci = ch_cells.begin(); ci !=ch_cells.end(); ++ci){ v.push_back(FromCGALPoint(dt.dual(*ci))-Vector3r(5.,5.,5.)); } //resize and rotate the voronoi cell Quaternionr Rot(Real(rand())/RAND_MAX,Real(rand())/RAND_MAX,Real(rand())/RAND_MAX,Real(rand())/RAND_MAX); Rot.normalize(); for(int i=0; i< (int) v.size();i++) { v[i] = Rot*(Vector3r(v[i][0]*size[0],v[i][1]*size[1],v[i][2]*size[2])); } //to avoid patological cases (that should not be present, but CGAL works somehow unpredicable) if (v.size() < 8) { cout << "wrong " << v.size() << endl; v.clear(); seed = rand(); GenerateRandomGeometry(); } } //************************************************************************** /* Get polyhdral surfaces */ vector> Polyhedra::GetSurfaces() const { vector> ret(P.size_of_facets()); int i=0; for (Polyhedron::Facet_const_iterator f = P.facets_begin(); f != P.facets_end(); f++, i++){ Polyhedron::Halfedge_around_facet_const_circulator h=f->facet_begin(); do { ret[i].push_back(std::distance(P.vertices_begin(), h->vertex())); } while (++h != f->facet_begin()); } return ret; } //**************************************************************************************** /* Destructor */ Polyhedra::~Polyhedra(){} //**************************************************************************************** /* Destructor */ PolyhedraGeom::~PolyhedraGeom(){} //**************************************************************************************** /* AaBb overlap checker */ void Bo1_Polyhedra_Aabb::go(const shared_ptr& ig, shared_ptr& bv, const Se3r& se3, const Body*){ Polyhedra* t=static_cast(ig.get()); if (!t->IsInitialized()) t->Initialize(); if(!bv){ bv=shared_ptr(new Aabb); } Aabb* aabb=static_cast(bv.get()); //Quaternionr invRot=se3.orientation.conjugate(); int N = (int) t->v.size(); Vector3r v_g, mincoords(0.,0.,0.), maxcoords(0.,0.,0.); for(int i=0; iv[i]; // vertices in global coordinates mincoords = Vector3r(min(mincoords[0],v_g[0]),min(mincoords[1],v_g[1]),min(mincoords[2],v_g[2])); maxcoords = Vector3r(max(maxcoords[0],v_g[0]),max(maxcoords[1],v_g[1]),max(maxcoords[2],v_g[2])); } if (aabbEnlargeFactor>0) { mincoords *= aabbEnlargeFactor; maxcoords *= aabbEnlargeFactor; } aabb->min=se3.position+mincoords; aabb->max=se3.position+maxcoords; } //********************************************************************************** /* Plotting */ #ifdef YADE_OPENGL #include bool Gl1_Polyhedra::wire; void Gl1_Polyhedra::go(const shared_ptr& cm, const shared_ptr&,bool wire2,const GLViewInfo&) { glMaterialv(GL_FRONT,GL_AMBIENT_AND_DIFFUSE,Vector3r(cm->color[0],cm->color[1],cm->color[2])); glColor3v(cm->color); Polyhedra* t=static_cast(cm.get()); vector faceTri = t->GetSurfaceTriangulation(); if (wire || wire2) { glDisable(GL_LIGHTING); glBegin(GL_LINES); for(int tri=0; tri < (int) faceTri.size(); tri+=3) { glOneWire(t, faceTri[tri], faceTri[tri+1]); glOneWire(t, faceTri[tri], faceTri[tri+2]); glOneWire(t, faceTri[tri+1], faceTri[tri+2]); } glEnd(); } else { Vector3r centroid = t->GetCentroid(); glDisable(GL_CULL_FACE); glEnable(GL_LIGHTING); glBegin(GL_TRIANGLES); for(int tri=0; tri < (int) faceTri.size(); tri+=3) { const auto a = faceTri[tri+0]; const auto b = faceTri[tri+1]; const auto c = faceTri[tri+2]; Vector3r n=(t->v[b]-t->v[a]).cross(t->v[c]-t->v[a]); n.normalize(); Vector3r faceCenter=(t->v[a]+t->v[b]+t->v[c])/3.; if((faceCenter-centroid).dot(n)<0) n=-n; glNormal3v(n); glVertex3v(t->v[a]); glVertex3v(t->v[b]); glVertex3v(t->v[c]); } glEnd(); } } void Gl1_PolyhedraGeom::go(const shared_ptr& ig, const shared_ptr&, const shared_ptr&, const shared_ptr&, bool) {draw(ig);} void Gl1_PolyhedraGeom::draw(const shared_ptr& ig){}; GLUquadric* Gl1_PolyhedraPhys::gluQuadric=NULL; Real Gl1_PolyhedraPhys::maxFn; Real Gl1_PolyhedraPhys::refRadius; Real Gl1_PolyhedraPhys::maxRadius; int Gl1_PolyhedraPhys::signFilter; int Gl1_PolyhedraPhys::slices; int Gl1_PolyhedraPhys::stacks; void Gl1_PolyhedraPhys::go(const shared_ptr& ip, const shared_ptr& i, const shared_ptr& b1, const shared_ptr& b2, bool wireFrame){ if(!gluQuadric){ gluQuadric=gluNewQuadric(); if(!gluQuadric) throw runtime_error("Gl1_PolyhedraPhys::go unable to allocate new GLUquadric object (out of memory?)."); } PolyhedraPhys* np=static_cast(ip.get()); shared_ptr ig(i->geom); if(!ig) return; // changed meanwhile? PolyhedraGeom* geom=YADE_CAST(ig.get()); Real fnNorm=np->normalForce.dot(geom->normal); if((signFilter>0 && fnNorm<0) || (signFilter<0 && fnNorm>0)) return; int fnSign=fnNorm>0?1:-1; fnNorm=std::abs(fnNorm); Real radiusScale=1.; maxFn=max(fnNorm,maxFn); Real realMaxRadius; if(maxRadius<0){ refRadius=min(0.03,refRadius); realMaxRadius=refRadius; } else realMaxRadius=maxRadius; Real radius=radiusScale*realMaxRadius*(fnNorm/maxFn); if (radius<=0.) radius = 1E-8; Vector3r color=Shop::scalarOnColorScale(fnNorm*fnSign,-maxFn,maxFn); Vector3r p1=b1->state->pos, p2=b2->state->pos; Vector3r relPos; relPos=p2-p1; Real dist=relPos.norm(); glDisable(GL_CULL_FACE); glPushMatrix(); glTranslatef(p1[0],p1[1],p1[2]); Quaternionr q(Quaternionr().setFromTwoVectors(Vector3r(0,0,1),relPos/dist /* normalized */)); // using Transform with OpenGL: http://eigen.tuxfamily.org/dox/TutorialGeometry.html //glMultMatrixd(Eigen::Affine3d(q).data()); glMultMatrix(Eigen::Transform(q).data()); glColor3v(color); gluCylinder(gluQuadric,radius,radius,dist,slices,stacks); glPopMatrix(); } #endif //********************************************************************************** //!Precompute data needed for rotating tangent vectors attached to the interaction void PolyhedraGeom::precompute(const State& rbp1, const State& rbp2, const Scene* scene, const shared_ptr& c, const Vector3r& currentNormal, bool isNew, const Vector3r& shift2) { if(!isNew) { orthonormal_axis = normal.cross(currentNormal); Real angle = scene->dt*0.5*normal.dot(rbp1.angVel + rbp2.angVel); twist_axis = angle*normal;} else twist_axis=orthonormal_axis=Vector3r::Zero(); //Update contact normal normal=currentNormal; //Precompute shear increment Vector3r c1x = (contactPoint - rbp1.pos); Vector3r c2x = (contactPoint - rbp2.pos + shift2); Vector3r relativeVelocity = (rbp2.vel+rbp2.angVel.cross(c2x)) - (rbp1.vel+rbp1.angVel.cross(c1x)); //keep the shear part only relativeVelocity = relativeVelocity-normal.dot(relativeVelocity)*normal; shearInc = relativeVelocity*scene->dt; } //********************************************************************************** Vector3r& PolyhedraGeom::rotate(Vector3r& shearForce) const { // approximated rotations shearForce -= shearForce.cross(orthonormal_axis); shearForce -= shearForce.cross(twist_axis); //NOTE : make sure it is in the tangent plane? It's never been done before. Is it not adding rounding errors at the same time in fact?... shearForce -= normal.dot(shearForce)*normal; return shearForce; } //********************************************************************************** /* Material law, physics */ void Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys::go( const shared_ptr& b1 , const shared_ptr& b2 , const shared_ptr& interaction) { if(interaction->phys) return; const shared_ptr& mat1 = YADE_PTR_CAST(b1); const shared_ptr& mat2 = YADE_PTR_CAST(b2); interaction->phys = shared_ptr(new PolyhedraPhys()); const shared_ptr& contactPhysics = YADE_PTR_CAST(interaction->phys); Real Kna = mat1->young; Real Knb = mat2->young; Real Ksa = mat1->young*mat1->poisson; Real Ksb = mat2->young*mat2->poisson; Real frictionAngle = std::min(mat1->frictionAngle,mat2->frictionAngle); contactPhysics->tangensOfFrictionAngle = std::tan(frictionAngle); contactPhysics->kn = Kna*Knb/(Kna+Knb); contactPhysics->ks = Ksa*Ksb/(Ksa+Ksb); }; void Ip2_FrictMat_PolyhedraMat_FrictPhys::go(const shared_ptr& pp1, const shared_ptr& pp2, const shared_ptr& interaction){ const shared_ptr& mat1 = YADE_PTR_CAST(pp1); const shared_ptr& mat2 = YADE_PTR_CAST(pp2); Ip2_FrictMat_FrictMat_FrictPhys().go(mat1,mat2,interaction); } //************************************************************************************** Real Law2_PolyhedraGeom_PolyhedraPhys_Volumetric::getPlasticDissipation() {return (Real) plasticDissipation;} void Law2_PolyhedraGeom_PolyhedraPhys_Volumetric::initPlasticDissipation(Real initVal) {plasticDissipation.reset(); plasticDissipation+=initVal;} Real Law2_PolyhedraGeom_PolyhedraPhys_Volumetric::elasticEnergy() { Real energy=0; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; FrictPhys* phys = dynamic_cast(I->phys.get()); if(phys) { energy += 0.5*(phys->normalForce.squaredNorm()/phys->kn + phys->shearForce.squaredNorm()/phys->ks);} } return energy; } //************************************************************************************** // Apply forces on polyhedrons in collision based on geometric configuration bool Law2_PolyhedraGeom_PolyhedraPhys_Volumetric::go(shared_ptr& ig, shared_ptr& ip, Interaction* I){ if (!I->geom) {return true;} const shared_ptr& contactGeom(YADE_PTR_DYN_CAST(I->geom)); if(!contactGeom) {return true;} const Body::id_t idA=I->getId1(), idB=I->getId2(); const shared_ptr& A=Body::byId(idA), B=Body::byId(idB); PolyhedraPhys* phys = dynamic_cast(I->phys.get()); //erase the interaction when aAbB shows separation, otherwise keep it to be able to store previous separating plane for fast detection of separation Vector3r shift2=scene->cell->hSize*I->cellDist.cast(); if (A->bound->min[0] >= B->bound->max[0]+shift2[0] || B->bound->min[0]+shift2[0] >= A->bound->max[0] || A->bound->min[1] >= B->bound->max[1]+shift2[1] || B->bound->min[1]+shift2[1] >= A->bound->max[1] || A->bound->min[2] >= B->bound->max[2]+shift2[2] || B->bound->min[2]+shift2[2] >= A->bound->max[2]) { return false; } //zero penetration depth means no interaction force if(!(contactGeom->equivalentPenetrationDepth > 1E-18) || !(contactGeom->penetrationVolume > 0)) { phys->normalForce = Vector3r(0.,0.,0.); phys->shearForce = Vector3r(0.,0.,0.); return true; } Real prop = std::pow(contactGeom->penetrationVolume,volumePower); Vector3r normalForce=contactGeom->normal*prop*phys->kn; //shear force: in case the polyhdras are separated and come to contact again, one //should not use the previous shear force if (contactGeom->isShearNew) shearForce = Vector3r::Zero(); else shearForce = contactGeom->rotate(shearForce); const Vector3r& shearDisp = contactGeom->shearInc; shearForce -= phys->ks*shearDisp; const Real maxFs = normalForce.squaredNorm()*std::pow(phys->tangensOfFrictionAngle,2); if(shearForce.squaredNorm() > maxFs && maxFs){ //PFC3d SlipModel, is using friction angle. CoulombCriterion Real ratio = sqrt(maxFs) / shearForce.norm(); if (std::isinf(ratio)) { LOG_DEBUG("shearForce.squaredNorm() > maxFs && maxFs: " << (shearForce.squaredNorm() > maxFs && maxFs)); // the condition should be 1 (we are in this branch), but is actually 0 LOG_DEBUG("shearForce: "<trackEnergy && traceEnergy) { const Real dissip=((1/phys->ks)*(trialForce-shearForce)).dot(shearForce); if (traceEnergy) plasticDissipation += dissip; else if(dissip>0) scene->energy->add(dissip,"plastDissip",plastDissipIx,false); // compute elastic energy as well scene->energy->add(0.5*(normalForce.squaredNorm()/phys->kn+shearForce.squaredNorm()/phys->ks), "elastPotential",elastPotentialIx,true); } } else { if (maxFs==0) shearForce = Vector3r::Zero(); scene->energy->add(0.5*(normalForce.squaredNorm()/phys->kn+shearForce.squaredNorm()/phys->ks), "elastPotential",elastPotentialIx,true); } Vector3r F = -normalForce-shearForce; if (contactGeom->equivalentPenetrationDepth != contactGeom->equivalentPenetrationDepth) exit(1); scene->forces.addForce (idA,F); scene->forces.addForce (idB, -F); scene->forces.addTorque(idA, -(A->state->pos-contactGeom->contactPoint).cross(F)); scene->forces.addTorque(idB, (B->state->pos-contactGeom->contactPoint).cross(F)); /* FILE * fin = fopen("Forces.dat","a"); fprintf(fin,"************** IDS %d %d **************\n",idA, idB); Vector3r T = (B->state->pos-contactGeom->contactPoint).cross(F); fprintf(fin,"volume\t%e\n",contactGeom->penetrationVolume); fprintf(fin,"normal_force\t%e\t%e\t%e\n",normalForce[0],normalForce[1],normalForce[2]); fprintf(fin,"shear_force\t%e\t%e\t%e\n",shearForce[0],shearForce[1],shearForce[2]); fprintf(fin,"total_force\t%e\t%e\t%e\n",F[0],F[1],F[2]); fprintf(fin,"torsion\t%e\t%e\t%e\n",T[0],T[1],T[2]); fprintf(fin,"A\t%e\t%e\t%e\n",A->state->pos[0],A->state->pos[1],A->state->pos[2]); fprintf(fin,"B\t%e\t%e\t%e\n",B->state->pos[0],B->state->pos[1],B->state->pos[2]); fprintf(fin,"centroid\t%e\t%e\t%e\n",contactGeom->contactPoint[0],contactGeom->contactPoint[1],contactGeom->contactPoint[2]); fclose(fin); */ //needed to be able to acces interaction forces in other parts of yade phys->normalForce = normalForce; phys->shearForce = shearForce; return true; } #endif // YADE_CGAL trunk-2017.01a/pkg/dem/Polyhedra.hpp000066400000000000000000000376531304022710500171660ustar00rootroot00000000000000// © 2013 Jan Elias, http://www.fce.vutbr.cz/STM/elias.j/, elias.j@fce.vutbr.cz // https://www.vutbr.cz/www_base/gigadisk.php?i=95194aa9a #pragma once #ifdef YADE_CGAL // NDEBUG causes crashes in CGAL sometimes. Anton #ifdef NDEBUG #undef NDEBUG #endif #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #define likely(x) __builtin_expect((x),1) #define unlikely(x) __builtin_expect((x),0) //CGAL definitions - does not work with another kernel!! Why??? typedef CGAL::Exact_predicates_inexact_constructions_kernel K; typedef CGAL::Polyhedron_3 Polyhedron; typedef CGAL::Delaunay_triangulation_3 Triangulation; typedef K::Point_3 CGALpoint; typedef K::Triangle_3 CGALtriangle; typedef K::Vector_3 CGALvector; typedef CGAL::Aff_transformation_3 Transformation; typedef K::Segment_3 Segment; typedef CGAL::Triangle_3 Triangle; typedef CGAL::Plane_3 Plane; typedef CGAL::Line_3 Line; typedef CGAL::Origin CGAL_ORIGIN; typedef CGAL::AABB_tree::iterator>>> CGAL_AABB_tree; //********************************************************************************** class Polyhedra: public Shape{ public: //constructor from Vertices Polyhedra(std::vector V) { createIndex(); v.resize(V.size()); for(int i=0;i<(int) V.size();i++) v[i]=V[i]; Initialize();} //contructor of "random" polyhedra Polyhedra(Vector3r xsize, int xseed) { createIndex(); seed=xseed; size=xsize; v.clear(); Initialize();} virtual ~Polyhedra(); Vector3r GetCentroid(){Initialize(); return centroid;} Vector3r GetInertia(){Initialize(); return inertia;} vector GetSurfaceTriangulation(){Initialize(); return faceTri;} vector> GetSurfaces() const; void Initialize(); bool IsInitialized(){return init;} std::vector GetOriginalVertices(); Real GetVolume(){Initialize(); return volume;} Quaternionr GetOri(){Initialize(); return orientation;} Polyhedron GetPolyhedron(){return P;}; void Clear(){v.clear(); P.clear(); init = 0; size = Vector3r(1.,1.,1.); faceTri.clear();}; void setVertices(const std::vector& v); void setVertices4(const Vector3r& v0, const Vector3r& v1,const Vector3r& v2,const Vector3r& v3); protected: //triangulation of facets for plotting vector faceTri; //centroid = (0,0,0) for random Polyhedra Vector3r centroid; //CGAL structure Polyhedron Polyhedron P; //sign of performed initialization bool init; //centroid Volume Real volume; //centroid inerta - diagonal of the tensor Vector3r inertia; //orientation, that provides diagonal inertia tensor Quaternionr orientation; void GenerateRandomGeometry(); YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(Polyhedra,Shape,"Polyhedral (convex) geometry.", ((std::vector,v,,,"Tetrahedron vertices in global coordinate system.")) ((int,seed, time(NULL),,"Seed for random generator.")) ((Vector3r, size, Vector3r(1.,1.,1.),,"Size of the grain in meters - x,y,z - before random rotation")), /*init*/, /*ctor*/ createIndex(); init = 0, .def("Initialize",&Polyhedra::Initialize,"Initialization") .def("GetVolume",&Polyhedra::GetVolume,"return polyhedra's volume") .def("GetInertia",&Polyhedra::GetInertia,"return polyhedra's inertia tensor") .def("GetOri",&Polyhedra::GetOri,"return polyhedra's orientation") .def("GetCentroid",&Polyhedra::GetCentroid,"return polyhedra's centroid") .def("GetSurfaceTriangulation",&Polyhedra::GetSurfaceTriangulation,"triangulation of facets (for plotting)") .def("GetSurfaces",&Polyhedra::GetSurfaces,"get indices of surfaces' vertices (for postprocessing)") .def("setVertices",&Polyhedra::setVertices,"set vertices and update receiver. Takes a list/tuple of vertices as argument.\n\n.. note:: Causes memory leaks, so if you want to use it maaaany times, use one of setVertices mentioned lower, passing each vertex as individual argument (currently only setVertices(v1,v2,v3,v4) for tetrahedron is implemented, on request it is easy to implement more vertices).") .def("setVertices",&Polyhedra::setVertices4,"set 4 vertices and update receiver. Each vertex is single argument.") ); REGISTER_CLASS_INDEX(Polyhedra,Shape); }; REGISTER_SERIALIZABLE(Polyhedra); //*************************************************************************** /*! Collision configuration for Polyhedra and something. * This is expressed as penetration volume properties: centroid, volume, depth ... * * Self-contained. */ class PolyhedraGeom: public IGeom{ public: virtual ~PolyhedraGeom(); //precompute data for shear evaluation void precompute(const State& rbp1, const State& rbp2, const Scene* scene, const shared_ptr& c, const Vector3r& currentNormal, bool isNew, const Vector3r& shift2); Vector3r& rotate(Vector3r& shearForce) const; //sep_plane is a code storing plane, that previously separated two polyhedras. It is used for faster detection of non-overlap. std::vector sep_plane; bool isShearNew; protected: YADE_CLASS_BASE_DOC_ATTRS_CTOR(PolyhedraGeom,IGeom,"Geometry of interaction between 2 :yref:`vector`, including volumetric characteristics", ((Real,penetrationVolume,NaN,,"Volume of overlap [m³]")) ((Real,equivalentCrossSection,NaN,,"Cross-section area of the overlap (perpendicular to the normal) - not used")) ((Real,equivalentPenetrationDepth,NaN,,"volume / equivalentCrossSection - not used")) ((Vector3r,contactPoint,Vector3r::Zero(),,"Contact point (global coords), centriod of the overlapping polyhedron")) ((Vector3r,shearInc,Vector3r::Zero(),,"Shear displacement increment in the last step")) ((Vector3r,normal,Vector3r::Zero(),,"Normal direction of the interaction")) ((Vector3r,twist_axis,Vector3r::Zero(),,"")) ((Vector3r,orthonormal_axis,Vector3r::Zero(),,"")), createIndex(); sep_plane.assign(3,0); ); //FUNCTOR2D(Tetra,Tetra); REGISTER_CLASS_INDEX(PolyhedraGeom,IGeom); }; REGISTER_SERIALIZABLE(PolyhedraGeom); //*************************************************************************** /*! Creates Aabb from Polyhedra. * * Self-contained. */ class Bo1_Polyhedra_Aabb: public BoundFunctor{ public: void go(const shared_ptr& ig, shared_ptr& bv, const Se3r& se3, const Body*); FUNCTOR1D(Polyhedra); YADE_CLASS_BASE_DOC_ATTRS(Bo1_Polyhedra_Aabb,BoundFunctor,"Create/update :yref:`Aabb` of a :yref:`Polyhedra`", ((Real,aabbEnlargeFactor,((void)"deactivated",-1),,"see :yref:`Bo1_Sphere_Aabb.aabbEnlargeFactor`")) ); }; REGISTER_SERIALIZABLE(Bo1_Polyhedra_Aabb); //*************************************************************************** /*! Elastic material */ class PolyhedraMat: public FrictMat{ public: Real GetStrength(){return strength;}; virtual ~PolyhedraMat(){}; YADE_CLASS_BASE_DOC_ATTRS_CTOR(PolyhedraMat,FrictMat,"Elastic material with Coulomb friction.", ((bool,IsSplitable,0,,"To be splitted ... or not")) ((Real,strength,100,,"Stress at which polyhedra of volume 4/3*pi [mm] breaks.")) ((Real,young,1e8,,"TODO")), /*ctor*/ createIndex(); ); REGISTER_CLASS_INDEX(PolyhedraMat,FrictMat); }; REGISTER_SERIALIZABLE(PolyhedraMat); //*************************************************************************** class PolyhedraPhys: public FrictPhys{ public: virtual ~PolyhedraPhys(){}; YADE_CLASS_BASE_DOC_ATTRS_CTOR(PolyhedraPhys,FrictPhys,"Simple elastic material with friction for volumetric constitutive laws", /*attrs*/ , /*ctor*/ createIndex(); ); REGISTER_CLASS_INDEX(PolyhedraPhys,FrictPhys); }; REGISTER_SERIALIZABLE(PolyhedraPhys); //*************************************************************************** #ifdef YADE_OPENGL #include #include #include #include #include /*! Draw Polyhedra using OpenGL */ class Gl1_Polyhedra: public GlShapeFunctor{ public: virtual void go(const shared_ptr&, const shared_ptr&,bool,const GLViewInfo&); YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_Polyhedra,GlShapeFunctor,"Renders :yref:`Polyhedra` object", ((bool,wire,false,,"Only show wireframe")) ); RENDERS(Polyhedra); }; REGISTER_SERIALIZABLE(Gl1_Polyhedra); struct Gl1_PolyhedraGeom: public GlIGeomFunctor{ RENDERS(PolyhedraGeom); void go(const shared_ptr&, const shared_ptr&, const shared_ptr&, const shared_ptr&, bool); void draw(const shared_ptr&); YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_PolyhedraGeom,GlIGeomFunctor,"Render :yref:`PolyhedraGeom` geometry.", ); }; REGISTER_SERIALIZABLE(Gl1_PolyhedraGeom); class Gl1_PolyhedraPhys: public GlIPhysFunctor{ static GLUquadric* gluQuadric; // needed for gluCylinder, initialized by ::go if no initialized yet public: virtual void go(const shared_ptr&,const shared_ptr&,const shared_ptr&,const shared_ptr&,bool wireFrame); YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_PolyhedraPhys,GlIPhysFunctor,"Renders :yref:`PolyhedraPhys` objects as cylinders of which diameter and color depends on :yref:`PolyhedraPhys::normForce` magnitude.", ((Real,maxFn,0,,"Value of :yref:`NormPhys.normalForce` corresponding to :yref:`maxDiameter`. This value will be increased (but *not decreased* ) automatically.")) ((Real,refRadius,std::numeric_limits::infinity(),,"Reference (minimum) particle radius")) ((int,signFilter,0,,"If non-zero, only display contacts with negative (-1) or positive (+1) normal forces; if zero, all contacts will be displayed.")) ((Real,maxRadius,-1,,"Cylinder radius corresponding to the maximum normal force.")) ((int,slices,6,,"Number of sphere slices; (see `glutCylinder reference `__)")) ( (int,stacks,1,,"Number of sphere stacks; (see `glutCylinder reference `__)")) ); RENDERS(PolyhedraPhys); }; REGISTER_SERIALIZABLE(Gl1_PolyhedraPhys); #endif //*************************************************************************** class Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys: public IPhysFunctor{ public: virtual void go(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction); FUNCTOR2D(PolyhedraMat,PolyhedraMat); YADE_CLASS_BASE_DOC_ATTRS(Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys,IPhysFunctor,"", ); }; REGISTER_SERIALIZABLE(Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys); class Ip2_FrictMat_PolyhedraMat_FrictPhys: public IPhysFunctor{ public: virtual void go(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction); FUNCTOR2D(FrictMat,PolyhedraMat); YADE_CLASS_BASE_DOC_ATTRS(Ip2_FrictMat_PolyhedraMat_FrictPhys,IPhysFunctor,"", ); }; REGISTER_SERIALIZABLE(Ip2_FrictMat_PolyhedraMat_FrictPhys); //*************************************************************************** /*! Calculate physical response based on penetration configuration given by PolyhedraGeom. */ class Law2_PolyhedraGeom_PolyhedraPhys_Volumetric: public LawFunctor{ OpenMPAccumulator plasticDissipation; virtual bool go(shared_ptr&, shared_ptr&, Interaction*); Real elasticEnergy (); Real getPlasticDissipation(); void initPlasticDissipation(Real initVal=0); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Law2_PolyhedraGeom_PolyhedraPhys_Volumetric,LawFunctor,"Calculate physical response of 2 :yref:`vector` in interaction, based on penetration configuration given by :yref:`PolyhedraGeom`. Normal force is proportional to the volume of intersection", ((Real,volumePower,1.,,"Power of volume used in evaluation of normal force. Default is 1.0 - normal force is linearly proportional to volume. 1.0/3.0 would mean that normal force is proportional to the cube root of volume, approximation of penetration depth.")) ((Vector3r,shearForce,Vector3r::Zero(),,"Shear force from last step")) ((bool,traceEnergy,false,,"Define the total energy dissipated in plastic slips at all contacts. This will trace only plastic energy in this law, see O.trackEnergy for a more complete energies tracing")) ((int,plastDissipIx,-1,(Attr::hidden|Attr::noSave),"Index for plastic dissipation (with O.trackEnergy)")) ((int,elastPotentialIx,-1,(Attr::hidden|Attr::noSave),"Index for elastic potential energy (with O.trackEnergy)")) ,, .def("elasticEnergy",&Law2_PolyhedraGeom_PolyhedraPhys_Volumetric::elasticEnergy,"Compute and return the total elastic energy in all \"FrictPhys\" contacts") .def("plasticDissipation",&Law2_PolyhedraGeom_PolyhedraPhys_Volumetric::getPlasticDissipation,"Total energy dissipated in plastic slips at all FrictPhys contacts. Computed only if :yref:`Law2_PolyhedraGeom_PolyhedraPhys_Volumetric::traceEnergy` is true.") .def("initPlasticDissipation",&Law2_PolyhedraGeom_PolyhedraPhys_Volumetric::initPlasticDissipation,"Initialize cummulated plastic dissipation to a value (0 by default).") ); FUNCTOR2D(PolyhedraGeom,PolyhedraPhys); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_PolyhedraGeom_PolyhedraPhys_Volumetric); //*************************************************************************** //compute plane equation from three points on the facet struct Plane_equation { template typename Facet::Plane_3 operator()( Facet& f) { typename Facet::Halfedge_handle h = f.halfedge(); typedef typename Facet::Plane_3 Plane; return Plane( h->vertex()->point(), h->next()->vertex()->point(), h->next()->next()->vertex()->point()); } }; //get Tetrahedron inertia Matrix3r TetraInertiaTensor(Vector3r av,Vector3r bv,Vector3r cv,Vector3r dv); //return intersection of two polyhedrons Polyhedron Polyhedron_Polyhedron_intersection(Polyhedron A, Polyhedron B, CGALpoint X, CGALpoint centroidA, CGALpoint centroidB, std::vector &code); //return intersection of plane & polyhedron Polyhedron Polyhedron_Plane_intersection(Polyhedron A, Plane B, CGALpoint centroid, CGALpoint X); //Test if point is inside Polyhedron bool Is_inside_Polyhedron(Polyhedron P, CGALpoint inside); //return approximate intersection of sphere & polyhedron bool Sphere_Polyhedron_intersection(Polyhedron A, Real r, CGALpoint C, CGALpoint centroid, Real volume, CGALvector normal, Real area); //return volume and centroid of polyhedra bool P_volume_centroid(Polyhedron P, Real * volume, Vector3r * centroid); //CGAL - miniEigen communication Vector3r FromCGALPoint(CGALpoint A); Vector3r FromCGALVector(CGALvector A); CGALpoint ToCGALPoint(Vector3r A); CGALvector ToCGALVector(Vector3r A); //determination of intersection of two polyhedras bool do_intersect(Polyhedron A, Polyhedron B); bool do_intersect(Polyhedron A, Polyhedron B, std::vector &sep_plane); //connect triagular facets if possible Polyhedron Simplify(Polyhedron P, Real lim); //list of facets and edges void PrintPolyhedron(Polyhedron P); void PrintPolyhedron2File(Polyhedron P,FILE* X); //normal by least square fitting of separating segments Vector3r FindNormal(Polyhedron Int, Polyhedron PA, Polyhedron PB); //split polyhedron shared_ptr SplitPolyhedra(const shared_ptr& body, Vector3r direction, Vector3r point); //new polyhedra shared_ptr NewPolyhedra(vector v, shared_ptr mat); #endif // YADE_CGAL trunk-2017.01a/pkg/dem/Polyhedra_Ig2.cpp000066400000000000000000000465631304022710500176620ustar00rootroot00000000000000// © 2013 Jan Elias, http://www.fce.vutbr.cz/STM/elias.j/, elias.j@fce.vutbr.cz // https://www.vutbr.cz/www_base/gigadisk.php?i=95194aa9a #ifdef YADE_CGAL // NDEBUG causes crashes in CGAL sometimes. Anton #ifdef NDEBUG #undef NDEBUG #endif #include "Polyhedra_Ig2.hpp" YADE_PLUGIN(/* self-contained in hpp: */ (Ig2_Polyhedra_Polyhedra_PolyhedraGeom) (Ig2_Wall_Polyhedra_PolyhedraGeom) (Ig2_Facet_Polyhedra_PolyhedraGeom) (Ig2_Sphere_Polyhedra_ScGeom) (Ig2_Polyhedra_Polyhedra_ScGeom) (Ig2_Polyhedra_Polyhedra_PolyhedraGeomOrScGeom) ); //********************************************************************************** /*! Create Polyhedra (collision geometry) from colliding Polyhedras. */ bool Ig2_Polyhedra_Polyhedra_PolyhedraGeom::go( const shared_ptr& shape1, const shared_ptr& shape2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& interaction) { //get polyhedras const Se3r& se31=state1.se3; const Se3r& se32=state2.se3; Polyhedra* A = static_cast(shape1.get()); Polyhedra* B = static_cast(shape2.get()); bool isNew = !interaction->geom; //move and rotate 1st the CGAL structure Polyhedron Matrix3r rot_mat = (se31.orientation).toRotationMatrix(); Vector3r trans_vec = se31.position; const Real& s = interactionDetectionFactor; Transformation t_rot_trans( s*rot_mat(0,0), s*rot_mat(0,1), s*rot_mat(0,2), trans_vec[0], s*rot_mat(1,0), s*rot_mat(1,1), s*rot_mat(1,2), trans_vec[1], s*rot_mat(2,0), s*rot_mat(2,1), s*rot_mat(2,2), trans_vec[2], 1. ); Polyhedron PA = A->GetPolyhedron(); std::transform( PA.points_begin(), PA.points_end(), PA.points_begin(), t_rot_trans); std::transform( PA.facets_begin(), PA.facets_end(), PA.planes_begin(),Plane_equation()); //move and rotate 2nd the CGAL structure Polyhedron rot_mat = (se32.orientation).toRotationMatrix(); trans_vec = se32.position + shift2; t_rot_trans = Transformation( s*rot_mat(0,0), s*rot_mat(0,1), s*rot_mat(0,2), trans_vec[0], s*rot_mat(1,0), s*rot_mat(1,1), s*rot_mat(1,2), trans_vec[1], s*rot_mat(2,0), s*rot_mat(2,1), s*rot_mat(2,2), trans_vec[2], 1. ); Polyhedron PB = B->GetPolyhedron(); std::transform( PB.points_begin(), PB.points_end(), PB.points_begin(), t_rot_trans); std::transform( PB.facets_begin(), PB.facets_end(), PB.planes_begin(),Plane_equation()); shared_ptr bang; if (isNew) { // new interaction bang=shared_ptr(new PolyhedraGeom()); bang->sep_plane.assign(3,0); bang->contactPoint = Vector3r(0,0,0); bang->isShearNew = true; }else{ // use data from old interaction bang=YADE_PTR_CAST(interaction->geom); bang->isShearNew = bang->equivalentPenetrationDepth<=0; } //find intersection Polyhedra Polyhedron Int; Int = Polyhedron_Polyhedron_intersection(PA,PB,ToCGALPoint(bang->contactPoint),ToCGALPoint(se31.position),ToCGALPoint(se32.position+shift2), bang->sep_plane); //volume and centroid of intersection Real volume; Vector3r centroid; P_volume_centroid(Int, &volume, ¢roid); if(std::isnan(volume) || volume<=1E-25 || volume > min(A->GetVolume(),B->GetVolume())) { bang->equivalentPenetrationDepth=0; bang->penetrationVolume=min(A->GetVolume(),B->GetVolume()); bang->normal = (A->GetVolume()>B->GetVolume() ? 1 : -1)*(se32.position+shift2-se31.position); return !isNew; } if ((!Is_inside_Polyhedron(PA, ToCGALPoint(centroid))) or (!Is_inside_Polyhedron(PB, ToCGALPoint(centroid)))) { bang->equivalentPenetrationDepth=0; return !isNew; } if (isNew) interaction->geom = bang; //find normal direction Vector3r normal = FindNormal(Int, PA, PB); if((se32.position+shift2-centroid).dot(normal)<0) normal*=-1; Real area = std::pow(volume,2./3.); // store calculated stuff in bang; some is redundant bang->equivalentCrossSection=area; bang->contactPoint=centroid; bang->penetrationVolume=volume; bang->equivalentPenetrationDepth=volume/area; scene = Omega::instance().getScene().get(); bang->precompute(state1,state2,scene,interaction,normal,bang->isShearNew,shift2); bang->normal=normal; /* FILE * fin = fopen("Interactions.dat","a"); fprintf(fin,"************** IDS %d %d **************\n",interaction->id1, interaction->id2); fprintf(fin,"volume\t%e\n",volume); fprintf(fin,"centroid\t%e\t%e\t%e\n",centroid[0],centroid[1],centroid[2]); PrintPolyhedron2File(PA,fin); PrintPolyhedron2File(PB,fin); PrintPolyhedron2File(Int,fin); fclose(fin); */ return true; } //********************************************************************************** bool Ig2_Polyhedra_Polyhedra_PolyhedraGeom::goReverse( const shared_ptr& shape1, const shared_ptr& shape2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c) { return go(shape1,shape2,state2,state1,-shift2,force,c); } //********************************************************************************** /*! Create Polyhedra (collision geometry) from colliding Polyhedron and Wall. */ bool Ig2_Wall_Polyhedra_PolyhedraGeom::go(const shared_ptr& shape1,const shared_ptr& shape2, const State& state1,const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& interaction) { const int& PA(shape1->cast().axis); const int& sense(shape1->cast().sense); const Se3r& se31=state1.se3; const Se3r& se32=state2.se3; Polyhedra* B = static_cast(shape2.get()); bool isNew = !interaction->geom; //move and rotate also the CGAL structure Polyhedron Matrix3r rot_mat = (se32.orientation).toRotationMatrix(); Vector3r trans_vec = se32.position; Transformation t_rot_trans( rot_mat(0,0),rot_mat(0,1),rot_mat(0,2),trans_vec[0], rot_mat(1,0),rot_mat(1,1),rot_mat(1,2),trans_vec[1], rot_mat(2,0),rot_mat(2,1),rot_mat(2,2),trans_vec[2],1.); Polyhedron PB = B->GetPolyhedron(); std::transform( PB.points_begin(), PB.points_end(), PB.points_begin(), t_rot_trans); std::transform( PB.facets_begin(), PB.facets_end(), PB.planes_begin(),Plane_equation()); //move wall Vector3r normal = Vector3r(0,0,0); if (sense != 0) { normal[PA] = sense; } else { normal[PA] = 1; Real dot = normal.dot(se32.position-se31.position); if (dot<1) { normal[PA] = -1; } } CGALvector CGALnormal = CGALvector(normal[0],normal[1],normal[2]); Plane A = Plane(CGALpoint(se31.position[0],se31.position[1],se31.position[2]),CGALvector(normal[0],normal[1],normal[2])); shared_ptr bang; if (isNew) { // new interaction bang=shared_ptr(new PolyhedraGeom()); bang->contactPoint = Vector3r(0,0,0); bang->isShearNew = true; interaction->geom = bang; }else{ // use data from old interaction bang=YADE_PTR_CAST(interaction->geom); bang->isShearNew = bang->equivalentPenetrationDepth<=0; } //find intersection Polyhedra Polyhedron Int; Int = Polyhedron_Plane_intersection(PB,A,ToCGALPoint(se32.position),ToCGALPoint(bang->contactPoint)); //volume and centroid of intersection Real volume; Vector3r centroid; P_volume_centroid(Int, &volume, ¢roid); if(std::isnan(volume) || volume<=1E-25 || volume > B->GetVolume()) {bang->equivalentPenetrationDepth=0; return true;} if (!Is_inside_Polyhedron(PB, ToCGALPoint(centroid))) {bang->equivalentPenetrationDepth=0; return true;} //calculate area of projection of Intersection into the normal plane Real area = volume/1E-8; // store calculated stuff in bang; some is redundant bang->equivalentCrossSection=area; bang->contactPoint=centroid; bang->penetrationVolume=volume; bang->equivalentPenetrationDepth=volume/area; bang->precompute(state1,state2,scene,interaction,normal,isNew,shift2); bang->normal=FromCGALVector(CGALnormal); return true; } //********************************************************************************** /*! Create Polyhedra (collision geometry) from colliding Polyhedron and Facet. */ bool Ig2_Facet_Polyhedra_PolyhedraGeom::go(const shared_ptr& shape1,const shared_ptr& shape2, const State& state1,const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& interaction){ const Se3r& se31=state1.se3; const Se3r& se32=state2.se3; Facet* A = static_cast(shape1.get()); Polyhedra* B = static_cast(shape2.get()); bool isNew = !interaction->geom; //move and rotate 1st the CGAL structure Polyhedron Matrix3r rot_mat = (se32.orientation).toRotationMatrix(); Vector3r trans_vec = se32.position; Transformation t_rot_trans( rot_mat(0,0),rot_mat(0,1),rot_mat(0,2),trans_vec[0], rot_mat(1,0),rot_mat(1,1),rot_mat(1,2),trans_vec[1], rot_mat(2,0),rot_mat(2,1),rot_mat(2,2),trans_vec[2],1.); Polyhedron PB = B->GetPolyhedron(); std::transform( PB.points_begin(), PB.points_end(), PB.points_begin(), t_rot_trans); std::transform( PB.facets_begin(), PB.facets_end(), PB.planes_begin(),Plane_equation()); //move and rotate facet vector v; v.resize(6); for (int i=0; i<3; i++) v[i] = ToCGALPoint(se31.orientation*A->vertices[i] + se31.position); // vertices in global coordinates //determine CGALpoint f_center((v[0].x()+v[1].x()+v[2].x())/3.,(v[0].y()+v[1].y()+v[2].y())/3.,(v[0].z()+v[1].z()+v[2].z())/3.); CGALvector f_normal = CGAL::cross_product((v[1]-v[0]),(v[2]-v[0])); //chage normal + change order of vertices to get outwarding facet normal for initial tetrahedron if ((ToCGALPoint(se32.position)-f_center)*(f_normal) < 0) { f_normal = (-1)*f_normal; CGALpoint help; help = v[0]; v[0]=v[1]; v[1]=help; } Real f_area = sqrt(f_normal.squared_length()); for (int i=3; i<6; i++) v[i] = v[i-3]-f_normal/f_area*0.05*sqrt(f_area); // vertices in global coordinates Polyhedron PA; //construct polyhedron directly Polyhedron::Halfedge_iterator hei = PA.make_tetrahedron(v[4],v[1],v[0],v[2]); hei = PA.split_vertex(hei, hei->next()->opposite()); hei->vertex()->point() = v[3]; hei = PA.split_facet(hei->next()->next()->next(),hei->next()); hei = PA.split_vertex(hei, hei->next_on_vertex()->next_on_vertex()); hei->vertex()->point() = v[5]; shared_ptr bang; if (isNew) { // new interaction bang=shared_ptr(new PolyhedraGeom()); bang->sep_plane.assign(3,0); bang->contactPoint = Vector3r(0,0,0); bang->isShearNew = true; interaction->geom = bang; } else { // use data from old interaction bang=YADE_PTR_CAST(interaction->geom); bang->isShearNew = bang->equivalentPenetrationDepth<=0; } //find intersection Polyhedra Polyhedron Int; Int = Polyhedron_Polyhedron_intersection(PA,PB,ToCGALPoint(bang->contactPoint),ToCGALPoint(se31.position),ToCGALPoint(se32.position), bang->sep_plane); //volume and centroid of intersection Real volume; Vector3r centroid; P_volume_centroid(Int, &volume, ¢roid); if(std::isnan(volume) || volume<=1E-25 || volume > B->GetVolume()) {bang->equivalentPenetrationDepth=0; return true;} if (!Is_inside_Polyhedron(PB, ToCGALPoint(centroid))) {bang->equivalentPenetrationDepth=0; return true;} //find normal direction Vector3r normal = FindNormal(Int, PA, PB); if((se32.position-centroid).dot(normal)<0) normal*=-1; //calculate area of projection of Intersection into the normal plane Real area = volume/1E-8; // store calculated stuff in bang; some is redundant bang->equivalentCrossSection=area; bang->contactPoint=centroid; bang->penetrationVolume=volume; bang->equivalentPenetrationDepth=volume/area; bang->precompute(state1,state2,scene,interaction,normal,bang->isShearNew,shift2); bang->normal=normal; return true; } //********************************************************************************** /*! Create Polyhedra (collision geometry) from colliding Polyhedron and Sphere. */ bool Ig2_Sphere_Polyhedra_ScGeom::go(const shared_ptr& shape1,const shared_ptr& shape2,const State& state1,const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& interaction){ const Se3r& se31=state1.se3; const Se3r& se32=state2.se3; Sphere* A = static_cast(shape1.get()); Real radius = A->radius; Real r2 = radius*radius; Polyhedra* B = static_cast(shape2.get()); bool isNew = !interaction->geom; shared_ptr geom; // use polyhedron surface triangulation const std::vector faceTri = B->GetSurfaceTriangulation(); // get vertices in global coordinate system std::vector pts(B->v); for (unsigned int i=0; i0) isInside = false; // p0 lies in positive halfspace of triangle, cannot be inside p0a = p0 - dst*n; // p0 projected to triangle plane p10 = p0a-p1; p20 = p0a-p2; p30 = p0a-p3; // inside/outside with respect to individual edges o1 = (p10.cross(p20)).dot(n); o2 = (p20.cross(p30)).dot(n); o3 = (p30.cross(p10)).dot(n); if (o1>0 && o2>0 && o3>0) { // p0a is inside triangle pp = p0a; relTemp = inside; } else { edst2min = DBL_MAX; for (int j=0; j<3; j++) { // iterate over 3 edges end find the closest point of them pa = j==0? p1 : (j==1? p2 : p3); pb = j==0? p2 : (j==1? p3 : p1); r = (((pb-p0a).cross(pa-p0a)).cross(pb-pa)).normalized(); p0aa = p0a + (pa-p0a).dot(r)*r; // projection of p0a on the edge e = pb-pa; en = e.norm(); e /= en; t = (p0aa-pa).dot(e)/en; // parameter of edge line if (t<0.) { ppp = pa; relTemp2=vertex; } else if (t>1.) { ppp = pb; relTemp2=vertex; } else { ppp = p0aa; relTemp2=edge; } edst2 = (ppp-p0).squaredNorm(); if (edst2 < edst2min) { edst2min = edst2; pp = ppp; relTemp = relTemp2; } } } dst2 = (pp-p0).squaredNorm(); if (dst2 < dst2min) { // dst2 is now the minimal squared distance and pp is now the closest found point so far dst2min = dst2; closest = pp; rel = relTemp; } } //****************************************************************************** if (isNew && !(isInside || dst2min<=r2) ) return false; if (isNew) { geom = shared_ptr(new ScGeom()); geom->radius1 = geom->radius2 = radius; interaction->geom = geom; } else { geom = YADE_PTR_CAST(interaction->geom); } Real penetrationDepth; Vector3r normal,contactPoint; if (isInside) { // some artificial tricks for unlikely case normal = se32.position - center; dst = normal.norm(); penetrationDepth = radius; normal /= dst; contactPoint = center + normal*(.5*radius); } else { if (rel==none) { LOG_FATAL("TODO"); } Real coeff = rel==edge? edgeCoeff : (rel==vertex? vertexCoeff : 1.0); normal = closest - center; dst = normal.norm(); normal /= dst; penetrationDepth = radius - dst; contactPoint = center + normal*(radius-.5*penetrationDepth); penetrationDepth *= coeff; } geom->normal = normal; geom->penetrationDepth = penetrationDepth; geom->contactPoint = contactPoint; geom->precompute(state1,state2,scene,interaction,normal,isNew,shift2,false/*avoidGranularRatcheting only for sphere-sphere*/); return true; } //********************************************************************************** /*! Plyhedra -> ScGeom. */ bool Ig2_Polyhedra_Polyhedra_ScGeom::go(const shared_ptr& shape1, const shared_ptr& shape2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& interaction) { const Se3r& se31=state1.se3; const Se3r& se32=state2.se3; shared_ptr geom; bool isNew = !interaction->geom; if (isNew) { Ig2_Polyhedra_Polyhedra_PolyhedraGeom ppGeom = Ig2_Polyhedra_Polyhedra_PolyhedraGeom(); ppGeom.interactionDetectionFactor = interactionDetectionFactor; bool pp = ppGeom.go(shape1,shape2,state2,state1,shift2,force,interaction); if (!pp) { return false; } shared_ptr pGeom = YADE_PTR_CAST(interaction->geom); geom = shared_ptr(new ScGeom()); geom->radius1 = (pGeom->contactPoint-se31.position).norm(); geom->radius2 = (pGeom->contactPoint-se32.position+shift2).norm(); interaction->geom=geom; } else { geom = YADE_PTR_CAST(interaction->geom); } const Real& radius1 = geom->radius1; const Real& radius2 = geom->radius2; Vector3r normal=(se32.position+shift2)-se31.position; Real norm=normal.norm(); normal/=norm; // normal is unit vector now Real penetrationDepth=radius1+radius2-norm; geom->contactPoint=se31.position+(radius1-0.5*penetrationDepth)*normal;//0.5*(pt1+pt2); geom->penetrationDepth=penetrationDepth; scene = Omega::instance().getScene().get(); geom->precompute(state1,state2,scene,interaction,normal,isNew,shift2,false); return true; } bool Ig2_Polyhedra_Polyhedra_ScGeom::goReverse(const shared_ptr& shape1, const shared_ptr& shape2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& interaction) { return go(shape1,shape2,state2,state1,-shift2,force,interaction); } bool Ig2_Polyhedra_Polyhedra_PolyhedraGeomOrScGeom::go(const shared_ptr& shape1, const shared_ptr& shape2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& interaction) { bool isNew = !interaction->geom; if (isNew) { if (createScGeom) { return ig2scGeom->go(shape1,shape2,state1,state2,shift2,force,interaction); } else { return ig2polyhedraGeom->go(shape1,shape2,state1,state2,shift2,force,interaction); } } // ScGeom* scGeom = dynamic_cast(interaction->geom.get()); if (scGeom) { return ig2scGeom->go(shape1,shape2,state1,state2,shift2,force,interaction); } // PolyhedraGeom* pGeom = dynamic_cast(interaction->geom.get()); if (pGeom) { return ig2polyhedraGeom->go(shape1,shape2,state1,state2,shift2,force,interaction); } // LOG_ERROR("TODO, should not happen"); return false; } bool Ig2_Polyhedra_Polyhedra_PolyhedraGeomOrScGeom::goReverse(const shared_ptr& shape1, const shared_ptr& shape2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& interaction) { return go(shape1,shape2,state2,state1,-shift2,force,interaction); } #endif // YADE_CGAL trunk-2017.01a/pkg/dem/Polyhedra_Ig2.hpp000066400000000000000000000154641304022710500176630ustar00rootroot00000000000000// © 2013 Jan Elias, http://www.fce.vutbr.cz/STM/elias.j/, elias.j@fce.vutbr.cz // https://www.vutbr.cz/www_base/gigadisk.php?i=95194aa9a #ifdef YADE_CGAL #include "Polyhedra.hpp" //*************************************************************************** /*! Create Polyhedra (collision geometry) from colliding Polyhedras. */ class Ig2_Polyhedra_Polyhedra_PolyhedraGeom: public IGeomFunctor { public: virtual ~Ig2_Polyhedra_Polyhedra_PolyhedraGeom(){}; virtual bool go(const shared_ptr& shape1, const shared_ptr& shape2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse(const shared_ptr& shape1, const shared_ptr& shape2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); FUNCTOR2D(Polyhedra,Polyhedra); DEFINE_FUNCTOR_ORDER_2D(Polyhedra,Polyhedra); YADE_CLASS_BASE_DOC_ATTRS(Ig2_Polyhedra_Polyhedra_PolyhedraGeom,IGeomFunctor,"Create/update geometry of collision between 2 Polyhedras", ((Real,interactionDetectionFactor,1,,"see :yref:`Ig2_Sphere_Sphere_ScGeom.interactionDetectionFactor`")) ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Ig2_Polyhedra_Polyhedra_PolyhedraGeom); //*************************************************************************** /*! Create Polyhedra (collision geometry) from colliding Wall & Polyhedra. */ class Ig2_Wall_Polyhedra_PolyhedraGeom: public IGeomFunctor { public: virtual ~Ig2_Wall_Polyhedra_PolyhedraGeom(){}; virtual bool go(const shared_ptr& shape1, const shared_ptr& shape2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); FUNCTOR2D(Wall,Polyhedra); DEFINE_FUNCTOR_ORDER_2D(Wall,Polyhedra); YADE_CLASS_BASE_DOC(Ig2_Wall_Polyhedra_PolyhedraGeom,IGeomFunctor,"Create/update geometry of collision between Wall and Polyhedra"); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Ig2_Wall_Polyhedra_PolyhedraGeom); //*************************************************************************** /*! Create Polyhedra (collision geometry) from colliding Facet & Polyhedra. */ class Ig2_Facet_Polyhedra_PolyhedraGeom: public IGeomFunctor { public: virtual ~Ig2_Facet_Polyhedra_PolyhedraGeom(){}; virtual bool go(const shared_ptr& shape1, const shared_ptr& shape2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); FUNCTOR2D(Facet,Polyhedra); DEFINE_FUNCTOR_ORDER_2D(Facet,Polyhedra); YADE_CLASS_BASE_DOC(Ig2_Facet_Polyhedra_PolyhedraGeom,IGeomFunctor,"Create/update geometry of collision between Facet and Polyhedra"); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Ig2_Facet_Polyhedra_PolyhedraGeom); //*************************************************************************** /*! Create Polyhedra (collision geometry) from colliding Sphere & Polyhedra. */ class Ig2_Sphere_Polyhedra_ScGeom: public IGeomFunctor { public: enum PointTriangleRelation { inside, edge, vertex, none }; virtual ~Ig2_Sphere_Polyhedra_ScGeom(){}; virtual bool go(const shared_ptr& shape1, const shared_ptr& shape2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); FUNCTOR2D(Sphere,Polyhedra); DEFINE_FUNCTOR_ORDER_2D(Sphere,Polyhedra); YADE_CLASS_BASE_DOC_ATTRS(Ig2_Sphere_Polyhedra_ScGeom,IGeomFunctor,"Create/update geometry of collision between Sphere and Polyhedra", ((Real,edgeCoeff,1.0,,"multiplier of penetrationDepth when sphere contacts edge (simulating smaller volume of actual intersection or when several polyhedrons has common edge)")) ((Real,vertexCoeff,1.0,,"multiplier of penetrationDepth when sphere contacts vertex (simulating smaller volume of actual intersection or when several polyhedrons has common vertex)")) ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Ig2_Sphere_Polyhedra_ScGeom); //*************************************************************************** /*! Plyhedra -> ScGeom. */ class Ig2_Polyhedra_Polyhedra_ScGeom: public IGeomFunctor { public: virtual ~Ig2_Polyhedra_Polyhedra_ScGeom(){}; virtual bool go(const shared_ptr& shape1, const shared_ptr& shape2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse(const shared_ptr& shape1, const shared_ptr& shape2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); FUNCTOR2D(Polyhedra,Polyhedra); DEFINE_FUNCTOR_ORDER_2D(Polyhedra,Polyhedra); YADE_CLASS_BASE_DOC_ATTRS(Ig2_Polyhedra_Polyhedra_ScGeom,IGeomFunctor,"EXPERIMENTAL. Ig2 functor creating ScGeom from two Polyhedra shapes. The radii are computed as a distance of contact point (computed using Ig2_Polyhedra_Polyhedra_PolyhedraGeom) and center of particle. Tested only for face-face contacts (like brick wall).", ((Real,interactionDetectionFactor,1,,"see Ig2_Sphere_Sphere_ScGeom.interactionDetectionFactor")) ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Ig2_Polyhedra_Polyhedra_ScGeom); class Ig2_Polyhedra_Polyhedra_PolyhedraGeomOrScGeom: public IGeomFunctor { public: virtual ~Ig2_Polyhedra_Polyhedra_PolyhedraGeomOrScGeom(){}; virtual bool go(const shared_ptr& shape1, const shared_ptr& shape2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse(const shared_ptr& shape1, const shared_ptr& shape2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); FUNCTOR2D(Polyhedra,Polyhedra); DEFINE_FUNCTOR_ORDER_2D(Polyhedra,Polyhedra); YADE_CLASS_BASE_DOC_ATTRS(Ig2_Polyhedra_Polyhedra_PolyhedraGeomOrScGeom,IGeomFunctor,"EXPERIMENTAL. A hacky helper Ig2 functor combining two Polyhedra shapes and creating, according to the settings, either ScGeom or PolyhedraGeom.", ((bool,createScGeom,true,,"If true, creates ScGeom on new contacts. Creates PolyhedraGeom otherwise. On existing contacts Ig2_Polyhedra_Polyhedra_PolyhedraGeom or Ig2_Polyhedra_Polyhedra_ScGeom is used according to present IGeom isntance.")) ((shared_ptr,ig2polyhedraGeom,new Ig2_Polyhedra_Polyhedra_PolyhedraGeom,,"Helper Ig2 functor for PolyhedraGeom (to be able to modify its settings)")) ((shared_ptr,ig2scGeom,new Ig2_Polyhedra_Polyhedra_ScGeom,,"Helper Ig2 functor for ScGeom (to be able to modify its settings)")) ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Ig2_Polyhedra_Polyhedra_PolyhedraGeomOrScGeom); //*************************************************************************** #endif // YADE_CGAL trunk-2017.01a/pkg/dem/Polyhedra_splitter.cpp000066400000000000000000000103011304022710500210640ustar00rootroot00000000000000// © 2013 Jan Elias, http://www.fce.vutbr.cz/STM/elias.j/, elias.j@fce.vutbr.cz // https://www.vutbr.cz/www_base/gigadisk.php?i=95194aa9a #ifdef YADE_CGAL // NDEBUG causes crashes in CGAL sometimes. Anton #ifdef NDEBUG #undef NDEBUG #endif #include YADE_PLUGIN((PolyhedraSplitter)); CREATE_LOGGER(PolyhedraSplitter); using PSplitT = std::tuple, Vector3r, Vector3r>; //********************************************************************************* /* Evaluate tensorial stress estimation in polyhedras */ void getStressForEachBody(vector& bStresses){ const shared_ptr& scene=Omega::instance().getScene(); FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; PolyhedraGeom* geom=YADE_CAST(I->geom.get()); PolyhedraPhys* phys=YADE_CAST(I->phys.get()); if(!geom || !phys) continue; Vector3r f=phys->normalForce+phys->shearForce; //Sum f_i*l_j for each contact of each particle const auto cP = geom->contactPoint; bStresses[I->getId1()] -=f*((cP-Body::byId(I->getId1(),scene)->state->pos).transpose()); bStresses[I->getId2()] +=f*((cP-Body::byId(I->getId2(),scene)->state->pos).transpose()); } } //********************************************************************************* /* Size dependent strength */ Real PolyhedraSplitter::getStrength(const Real & volume, const Real & strength) const { //equvalent radius const Real r_eq = pow(volume*3./4./Mathr::PI,1./3.); //r should be in milimeters return strength/(r_eq/1000.); } //********************************************************************************* /* Symmetrization of stress tensor */ void PolyhedraSplitter::Symmetrize(Matrix3r & bStress){ bStress(0,1) = (bStress(0,1) + bStress(1,0))/2.; bStress(0,2) = (bStress(0,2) + bStress(2,0))/2.; bStress(1,2) = (bStress(1,2) + bStress(2,1))/2.; bStress(1,0) = bStress(0,1); bStress(2,0) = bStress(0,2); bStress(2,1) = bStress(1,2); } //********************************************************************************** //split polyhedra void SplitPolyhedraDouble(const PSplitT & split){ const auto & b =(get<0>(split)); const auto & d1=(get<1>(split)); const auto & d2=(get<2>(split)); const Se3r& se3=b->state->se3; const Vector3r pnt = se3.position; shared_ptr B2 = SplitPolyhedra(b, d1, pnt); shared_ptr B3 = SplitPolyhedra(B2, d2, pnt); shared_ptr B4 = SplitPolyhedra(b, d2, pnt); } //********************************************************************************* /* Split if stress exceed strength */ void PolyhedraSplitter::action() { const shared_ptr _rb=shared_ptr(); shared_ptr rb=(_rb?_rb:Omega::instance().getScene()); vector splitsV; vector bStresses (scene->bodies->size(), Matrix3r::Zero()); getStressForEachBody(bStresses); for(const auto b : *(rb->bodies)) { if(!b || !b->material || !b->shape) continue; shared_ptr p=YADE_PTR_DYN_CAST(b->shape); shared_ptr m=YADE_PTR_DYN_CAST(b->material); if(p && m->IsSplitable){ //not real strees, to get real one, it has to be divided by body volume Matrix3r stress = bStresses[b->id]; //get eigenstresses Symmetrize(stress); Matrix3r I_vect(Matrix3r::Zero()), I_valu(Matrix3r::Zero()); matrixEigenDecomposition(stress,I_vect,I_valu); Eigen::Matrix3f::Index min_i, max_i; I_valu.diagonal().minCoeff(&min_i); I_valu.diagonal().maxCoeff(&max_i); //division of stress by volume const Vector3r dirC = I_vect.col(max_i); const Vector3r dirT = I_vect.col(min_i); const Vector3r dir1 = dirC.normalized() + dirT.normalized(); const Vector3r dir2 = dirC.normalized() - dirT.normalized(); //double sigma_t = -comp_stress/2.+ tens_stress; const Real sigma_t = pow(( pow(I_valu(0,0)-I_valu(1,1),2)+ pow(I_valu(0,0)-I_valu(2,2),2)+ pow(I_valu(1,1)-I_valu(2,2),2)) /2.,0.5)/p->GetVolume(); if (sigma_t > getStrength(p->GetVolume(),m->GetStrength())) { splitsV.push_back(std::make_tuple(b, dir1.normalized(), dir2.normalized())); } } } std::for_each(splitsV.begin(), splitsV.end(), &SplitPolyhedraDouble); } #endif // YADE_CGAL trunk-2017.01a/pkg/dem/Polyhedra_splitter.hpp000066400000000000000000000013751304022710500211040ustar00rootroot00000000000000// © 2013 Jan Elias, http://www.fce.vutbr.cz/STM/elias.j/, elias.j@fce.vutbr.cz // https://www.vutbr.cz/www_base/gigadisk.php?i=95194aa9a #pragma once #ifdef YADE_CGAL #include "Polyhedra.hpp" #include //********************************************************************************* /* Polyhedra Splitter */ class PolyhedraSplitter : public PeriodicEngine{ public: virtual void action(); double getStrength(const double & volume, const double & strength) const; void Symmetrize(Matrix3r & bStress); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(PolyhedraSplitter,PeriodicEngine,"Engine that splits polyhedras.", , /*ctor*/ ,/*py*/ ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(PolyhedraSplitter); #endif // YADE_CGAL trunk-2017.01a/pkg/dem/Polyhedra_support.cpp000066400000000000000000000775041304022710500207540ustar00rootroot00000000000000// © 2013 Jan Elias, http://www.fce.vutbr.cz/STM/elias.j/, elias.j@fce.vutbr.cz // https://www.vutbr.cz/www_base/gigadisk.php?i=95194aa9a #ifdef YADE_CGAL // NDEBUG causes crashes in CGAL sometimes. Anton #ifdef NDEBUG #undef NDEBUG #endif #include "Polyhedra.hpp" //EMPRIRICAL CONSTANTS - ADJUST IF SEGMENTATION FAULT OCCUR, IT IS A PROBLEM OF CGAL. THESE ARE USED TO CHECK CGAL IMPUTS //DISTANCE_LIMIT controls numerical issues in calculating intersection. It should be small enough to neglect only extremely //small overlaps, but large enough to prevent errors during computation of convex hull const Real DISTANCE_LIMIT = 2E-11; //MERGE_PLANES_LIMIT - if two facets of two intersecting polyhedron differ less, then they are treated ose one only const Real MERGE_PLANES_LIMIT = 1E-18; //18 //SIMPLIFY_LIMIT - if two facets of one polyhedron differ less, then they are joint into one facet const Real SIMPLIFY_LIMIT = 1E-19; //19 //FIND_NORMAL_LIMIT - to determine which facet of intersection belongs to which polyhedron const Real FIND_NORMAL_LIMIT = 1E-40; //SPLITTER_GAP - creates gap between splitted polyhedrons const Real SPLITTER_GAP = 1E-8; //********************************************************************************** //return volume and centroid of polyhedron bool P_volume_centroid(Polyhedron P, Real * volume, Vector3r * centroid){ Vector3r basepoint = FromCGALPoint(P.vertices_begin()->point()); Vector3r A,B,C,D; (*volume) = 0; Real vtet; (*centroid) = Vector3r(0.,0.,0.); //compute centroid and volume for (Polyhedron::Facet_iterator fIter = P.facets_begin(); fIter != P.facets_end(); fIter++){ Polyhedron::Halfedge_around_facet_circulator hfc0; hfc0 = fIter->facet_begin(); int n = fIter->facet_degree(); A = FromCGALPoint(hfc0->vertex()->point()); C = FromCGALPoint(hfc0->next()->vertex()->point()); for (int i=2; inext()->vertex()->point()); vtet = std::abs((basepoint-C).dot((A-C).cross(B-C)))/6.; *volume += vtet; *centroid = *centroid + (basepoint+A+B+C) / 4. * vtet; } } *centroid = *centroid/(*volume); return true; } //********************************************************************************** //STOLEN FROM TETRA body of Vaclav Smilauer /*! Calculates tetrahedron inertia relative to the origin (0,0,0), with unit density (scales linearly). * See article F. Tonon, "Explicit Exact Formulas for the 3-D Tetrahedron Inertia Tensor in Terms of its Vertex Coordinates", * http://docsdrive.com/pdfs/sciencepublications/jmssp/2005/8-11.pdf * [Tonon2005] */ //Centroid MUST be [0,0,0] Matrix3r TetraInertiaTensor(Vector3r av,Vector3r bv,Vector3r cv,Vector3r dv){ const auto x1 = av[0]; const auto y1 = av[1]; const auto z1 = av[2]; const auto x2 = bv[0]; const auto y2 = bv[1]; const auto z2 = bv[2]; const auto x3 = cv[0]; const auto y3 = cv[1]; const auto z3 = cv[2]; const auto x4 = dv[0]; const auto y4 = dv[1]; const auto z4 = dv[2]; // Jacobian of transformation to the reference 4hedron Real detJ=(x2-x1)*(y3-y1)*(z4-z1)+ (x3-x1)*(y4-y1)*(z2-z1)+ (x4-x1)*(y2-y1)*(z3-z1) -(x2-x1)*(y4-y1)*(z3-z1) -(x3-x1)*(y2-y1)*(z4-z1) -(x4-x1)*(y3-y1)*(z2-z1); detJ=std::abs(detJ); const Real a=detJ*(y1*y1+y1*y2+y2*y2+y1*y3+y2*y3+ y3*y3+y1*y4+y2*y4+y3*y4+y4*y4+z1*z1+z1*z2+ z2*z2+z1*z3+z2*z3+z3*z3+z1*z4+z2*z4+z3*z4+z4*z4)/60.; const Real b=detJ*(x1*x1+x1*x2+x2*x2+x1*x3+x2*x3+x3*x3+ x1*x4+x2*x4+x3*x4+x4*x4+z1*z1+z1*z2+z2*z2+z1*z3+ z2*z3+z3*z3+z1*z4+z2*z4+z3*z4+z4*z4)/60.; const Real c=detJ*(x1*x1+x1*x2+x2*x2+x1*x3+x2*x3+x3*x3+x1*x4+ x2*x4+x3*x4+x4*x4+y1*y1+y1*y2+y2*y2+y1*y3+ y2*y3+y3*y3+y1*y4+y2*y4+y3*y4+y4*y4)/60.; // a' in the article etc. const Real a__=detJ*(2*y1*z1+y2*z1+y3*z1+y4*z1+y1*z2+ 2*y2*z2+y3*z2+y4*z2+y1*z3+y2*z3+2*y3*z3+ y4*z3+y1*z4+y2*z4+y3*z4+2*y4*z4)/120.; const Real b__=detJ*(2*x1*z1+x2*z1+x3*z1+x4*z1+x1*z2+ 2*x2*z2+x3*z2+x4*z2+x1*z3+x2*z3+2*x3*z3+ x4*z3+x1*z4+x2*z4+x3*z4+2*x4*z4)/120.; const Real c__=detJ*(2*x1*y1+x2*y1+x3*y1+x4*y1+x1*y2+ 2*x2*y2+x3*y2+x4*y2+x1*y3+x2*y3+2*x3*y3+ x4*y3+x1*y4+x2*y4+x3*y4+2*x4*y4)/120.; Matrix3r ret; ret<< a , -c__, -b__, -c__, b , -a__, -b__, -a__, c ; return ret; } //********************************************************************************** //distace of point from a plane (squared) with sign Real Oriented_squared_distance(Plane P, CGALpoint x){ Real h = P.a()*x.x()+P.b()*x.y()+P.c()*x.z()+P.d(); return ((h>0.)-(h<0.))*pow(h,2)/(CGALvector(P.a(),P.b(),P.c())).squared_length(); } //********************************************************************************** // test if point is inside polyhedra in strong sence, i.e. boundary location is not enough bool Is_inside_Polyhedron(Polyhedron P, CGALpoint inside){ Polyhedron::Plane_iterator pi; for(pi=P.planes_begin(); pi!=P.planes_end(); ++pi){ if( ! pi->has_on_negative_side(inside)) return false; } return true; } //********************************************************************************** // test if point is inside polyhedra not closer than lim to its boundary bool Is_inside_Polyhedron(Polyhedron P, CGALpoint inside, Real lim){ Polyhedron::Plane_iterator pi; lim = pow(lim,2); for(pi=P.planes_begin(); pi!=P.planes_end(); ++pi){ if(Oriented_squared_distance(*pi, inside)>-lim) return false; } return true; } //********************************************************************************** //test if two polyhedron intersect bool do_intersect(Polyhedron A, Polyhedron B){ std::vector sep_plane; sep_plane.assign(3,0); return do_intersect(A, B, sep_plane); } //********************************************************************************** //test if two polyhedron intersect based on previous data bool do_intersect(Polyhedron A, Polyhedron B, std::vector &sep_plane){ bool found; //check previous separation plane switch (sep_plane[0]){ case 1://separation plane was previously determined as sep_plane[2]-th plane of A polyhedron { if(unlikely((unsigned) sep_plane[2]>=A.size_of_facets())) break; Polyhedron::Facet_iterator fIter = A.facets_begin(); for (int i=0; iplane().has_on_positive_side(vIter->point())) {found = false; break;}; } if(found) return false; } break; case 2://separation plane was previously determined as sep_plane[2]-th plane of B polyhedron { if(unlikely((unsigned) sep_plane[2]>=B.size_of_facets())) break; Polyhedron::Facet_iterator fIter = B.facets_begin(); for (int i=0; iplane().has_on_positive_side(vIter->point())) {found = false; break;}; } if(found) return false; } break; case 3://separation plane was previously given by sep_plane[1]-th and sep_plane[2]-th edge of A & B polyhedrons { if(unlikely((unsigned) sep_plane[1]>=A.size_of_halfedges()/2)) break; if(unlikely((unsigned) sep_plane[2]>=B.size_of_halfedges()/2)) break; Polyhedron::Edge_iterator eIter1 = A.edges_begin(); Polyhedron::Edge_iterator eIter2 = B.edges_begin(); for (int i=0; ivertex()->point(),CGAL::cross_product( (eIter1->vertex()->point() - eIter1->opposite()->vertex()->point()), (eIter2->vertex()->point() - eIter2->opposite()->vertex()->point()))); if (!X.has_on_positive_side(B.vertices_begin()->point())) X = X.opposite(); Real lim = pow(DISTANCE_LIMIT,2); for (Polyhedron::Vertex_iterator vIter = A.vertices_begin(); vIter != A.vertices_end(); ++vIter){ if (Oriented_squared_distance(X, vIter->point())>lim) {found = false; break;}; } for (Polyhedron::Vertex_iterator vIter = B.vertices_begin(); vIter != B.vertices_end(); ++vIter){ if (! X.has_on_positive_side(vIter->point())) {found = false; break;}; } if(found) return false; } break; } //regular test with no previous information about separating plane //test all planes from A int i = 0; for (Polyhedron::Facet_iterator fIter = A.facets_begin(); fIter != A.facets_end(); fIter++, i++){ found = true; for (Polyhedron::Vertex_iterator vIter = B.vertices_begin(); vIter != B.vertices_end(); ++vIter){ if (! fIter->plane().has_on_positive_side(vIter->point())) {found = false; break;}; } if(found) {sep_plane[0] = 1; sep_plane[1] = 1; sep_plane[2] = i; return false;} } //test all planes from B i = 0; for (Polyhedron::Facet_iterator fIter = B.facets_begin(); fIter != B.facets_end(); fIter++, i++){ found = true; for (Polyhedron::Vertex_iterator vIter = A.vertices_begin(); vIter != A.vertices_end(); ++vIter){ if (! fIter->plane().has_on_positive_side(vIter->point())) {found = false; break;}; } if(found) {sep_plane[0] = 2; sep_plane[1] = 2; sep_plane[2] = i; return false;} } //test all pairs of edges from A & B Plane X; CGALvector vA; Real lim = pow(DISTANCE_LIMIT,2); i = 0; for (Polyhedron::Edge_iterator eIter1 = A.edges_begin(); eIter1 != A.edges_end(); ++eIter1, i++){ vA = eIter1->vertex()->point() - eIter1->opposite()->vertex()->point(); int j = 0; for (Polyhedron::Edge_iterator eIter2 = B.edges_begin(); eIter2 != B.edges_end(); ++eIter2, j++){ found = true; X = Plane(eIter1->vertex()->point(),CGAL::cross_product(vA, (eIter2->vertex()->point() - eIter2->opposite()->vertex()->point()))); if (!X.has_on_positive_side(B.vertices_begin()->point())) X = X.opposite(); for (Polyhedron::Vertex_iterator vIter = A.vertices_begin(); vIter != A.vertices_end(); ++vIter){ if (Oriented_squared_distance(X, vIter->point())>lim) {found = false; break;}; } for (Polyhedron::Vertex_iterator vIter = B.vertices_begin(); vIter != B.vertices_end(); ++vIter){ if (! X.has_on_positive_side(vIter->point())) {found = false; break;}; } if(found) { sep_plane[0] = 3; sep_plane[1] = i; sep_plane[2] = j; return false; } } } sep_plane[0] = 0; return true; } //********************************************************************************** //norm of difference between two planes Real PlaneDifference(const Plane &a, const Plane &b){ Real la = sqrt(pow(a.a(),2) + pow(a.b(),2) + pow(a.c(),2) + pow(a.d(),2)); Real lb = sqrt(pow(b.a(),2) + pow(b.b(),2) + pow(b.c(),2) + pow(b.d(),2)); return pow(a.a()/la-b.a()/lb,2) + pow(a.b()/la-b.b()/lb,2) + pow(a.c()/la-b.c()/lb,2) + pow(a.d()/la-b.d()/lb,2); //in case we do not care of the orientation //return min(pow(a.a()/la-b.a()/lb,2) + pow(a.b()/la-b.b()/lb,2) + pow(a.c()/la-b.c()/lb,2) + pow(a.d()/la-b.d()/lb,2),pow(a.a()/la+b.a()/lb,2) + pow(a.b()/la+b.b()/lb,2) + pow(a.c()/la+b.c()/lb,2) + pow(a.d()/la+b.d()/lb,2)); } //********************************************************************************** //connect triagular facets if possible Polyhedron Simplify(Polyhedron P, Real limit){ bool elimination = true; while(elimination){ elimination = false; for (Polyhedron::Edge_iterator hei = P.edges_begin(); hei!=P.edges_end(); ++hei){ if (PlaneDifference(hei->facet()->plane(),hei->opposite()->facet()->plane()) < limit){ if (hei->vertex()->vertex_degree() < 3) hei = P.erase_center_vertex(hei); else if(hei->opposite()->vertex()->vertex_degree() < 3) hei = P.erase_center_vertex(hei->opposite()); else hei = P.join_facet(hei); elimination = true; break; } } } if (P.size_of_facets() < 4) P.clear(); return P; } //********************************************************************************** //list of facets + edges void PrintPolyhedron2File(Polyhedron P,FILE* X){ Vector3r A,B,C; fprintf(X,"*** faces ***\n"); for (Polyhedron::Facet_iterator fIter = P.facets_begin(); fIter!=P.facets_end(); ++fIter){ Polyhedron::Halfedge_around_facet_circulator hfc0; hfc0 = fIter->facet_begin(); int n = fIter->facet_degree(); A = FromCGALPoint(hfc0->vertex()->point()); C = FromCGALPoint(hfc0->next()->vertex()->point()); for (int i=2; inext()->vertex()->point()); fprintf(X,"%e\t%e\t%e\t%e\t%e\t%e\t%e\t%e\t%e\n",A[0],A[1],A[2],B[0],B[1],B[2],C[0],C[1],C[2]); } } fprintf(X,"*** edges ***\n"); for (Polyhedron::Edge_iterator hei = P.edges_begin(); hei!=P.edges_end(); ++hei){ fprintf(X,"%e\t%e\t%e\t%e\t%e\t%e\n", hei->vertex()->point()[0], hei->vertex()->point()[1], hei->vertex()->point()[2], hei->opposite()->vertex()->point()[0], hei->opposite()->vertex()->point()[1], hei->opposite()->vertex()->point()[2]); } } //********************************************************************************** //list of facets + edges void PrintPolyhedron(Polyhedron P){ Vector3r A,B,C; cout << "*** faces ***" << endl; for (Polyhedron::Facet_iterator fIter = P.facets_begin(); fIter!=P.facets_end(); ++fIter){ Polyhedron::Halfedge_around_facet_circulator hfc0; hfc0 = fIter->facet_begin(); int n = fIter->facet_degree(); A = FromCGALPoint(hfc0->vertex()->point()); C = FromCGALPoint(hfc0->next()->vertex()->point()); for (int i=2; inext()->vertex()->point()); cout << A << " "<< B << " "<< C << endl; } } cout << "*** edges ***" << endl; for (Polyhedron::Edge_iterator hei = P.edges_begin(); hei!=P.edges_end(); ++hei){ cout << hei->vertex()->point() << " " << hei->opposite()->vertex()->point() << endl; } } //********************************************************************************** //list of facets void PrintPolyhedronFacets(Polyhedron P){ Vector3r A,B,C; for (Polyhedron::Facet_iterator fIter = P.facets_begin(); fIter!=P.facets_end(); ++fIter){ cout << "***" << endl; Polyhedron::Halfedge_around_facet_circulator hfc0; hfc0 = fIter->facet_begin(); int n = fIter->facet_degree(); for (int i = 0; ivertex()->point() << endl; } } } //********************************************************************************** //solve system of 3x3 by Cramers rule Vector3r SolveLinSys3x3(Matrix3r A, Vector3r y){ //only system 3x3 by Cramers rule Real det = A(0,0)*A(1,1)*A(2,2)+ A(0,1)*A(1,2)*A(2,0)+ A(0,2)*A(1,0)*A(2,1)- A(0,2)*A(1,1)*A(2,0)- A(0,1)*A(1,0)*A(2,2)- A(0,0)*A(1,2)*A(2,1); if (det == 0) { LOG_WARN("error in linear solver"); return Vector3r(0,0,0); } return Vector3r( ( y(0)*A(1,1)*A(2,2)+ A(0,1)*A(1,2)*y(2)+ A(0,2)*y(1)*A(2,1)- A(0,2)*A(1,1)*y(2)- A(0,1)*y(1)*A(2,2)- y(0)*A(1,2)*A(2,1) )/det, ( A(0,0)*y(1)*A(2,2)+ y(0)*A(1,2)*A(2,0)+ A(0,2)*A(1,0)*y(2)- A(0,2)*y(1)*A(2,0)- y(0)*A(1,0)*A(2,2)- A(0,0)*A(1,2)*y(2) )/det, ( A(0,0)*A(1,1)*y(2)+ A(0,1)*y(1)*A(2,0)+ y(0)*A(1,0)*A(2,1)- y(0)*A(1,1)*A(2,0)- A(0,1)*A(1,0)*y(2)- A(0,0)*y(1)*A(2,1) )/det ); } //********************************************************************************** /* * Return convex hull of points * critical point, because CGAL often returnes segmentation fault. * The planes must be sufficiently "different". This is, however, * checked elswhere by DISTANCE_LIMIT variable. */ Polyhedron ConvexHull(vector &planes){ Polyhedron Int; for (const auto p : planes) { if (std::isnan(p.x()) || std::isnan(p.y()) || std::isnan(p.z())) return Int; } if (planes.size()>3) CGAL::convex_hull_3(planes.begin(), planes.end(), Int); return Int; } //********************************************************************************** //determination of normal direction of intersection Vector3r FindNormal(Polyhedron Int, Polyhedron PA, Polyhedron PB){ //determine which plane is from which polyhedra Polyhedron::Plane_iterator pi, pj; std::transform( Int.facets_begin(), Int.facets_end(), Int.planes_begin(),Plane_equation()); std::transform( PA.facets_begin(), PA.facets_end(), PA.planes_begin(), Plane_equation()); std::transform( PB.facets_begin(), PB.facets_end(), PB.planes_begin(), Plane_equation()); vector from_A(Int.size_of_facets()); vector minsA(Int.size_of_facets()); vector minsB(Int.size_of_facets()); int i=0; Real minA, minB, k; for(pi = Int.planes_begin(); pi!=Int.planes_end(); ++pi,i++){ minA = 1.; minB = 1.; for(pj=PA.planes_begin(); pj!=PA.planes_end(); ++pj){ k = PlaneDifference(*pi, *pj); if (k segments; int a,b; for (Polyhedron::Edge_iterator hei = Int.edges_begin(); hei!=Int.edges_end(); ++hei){ a = std::distance(Int.facets_begin(), hei->facet()); b = std::distance(Int.facets_begin(), hei->opposite()->facet()); if ((from_A[a] && !from_A[b]) || (from_A[b] && !from_A[a])) { segments.push_back(Segment(hei->vertex()->point(),hei->opposite()->vertex()->point())); } } //find normal direction Plane fit; linear_least_squares_fitting_3(segments.begin(),segments.end(),fit,CGAL::Dimension_tag<1>()); CGALvector CGALnormal=fit.orthogonal_vector(); CGALnormal = CGALnormal/sqrt(CGALnormal.squared_length()); // reverse direction if projection of the (contact_point-centroid_of_B) vector onto the normal is negative (i.e. the normal points more towards B) return FromCGALVector(CGALnormal); } //********************************************************************************** //prepare data for CGAL convex hull vector MergePlanes(vector planes1, vector planes2, Real limit){ vector P = planes1; bool add; for(vector::iterator i = planes2.begin(); i!=planes2.end(); ++i){ add = true; for(vector::iterator j = planes1.begin(); j!=planes1.end(); ++j){ if (PlaneDifference(*i,*j) < limit){ add = false; break; } } if (add) P.push_back(*i); } return P; } //********************************************************************************** //returnes intersecting polyhedron of polyhedron & plane (possibly empty) Polyhedron Polyhedron_Plane_intersection(Polyhedron A, Plane B, CGALpoint centroid, CGALpoint X){ Polyhedron Intersection; CGALpoint inside; vector planes1, planes2; vector dual_planes; // test if do intersect, find some intersecting point bool intersection_found = false; Real lim = pow(DISTANCE_LIMIT,2); std::transform( A.facets_begin(), A.facets_end(), A.planes_begin(),Plane_equation()); // test centroid of previous intersection if(Is_inside_Polyhedron(A,X,DISTANCE_LIMIT) && Oriented_squared_distance(B,X)<=-lim) { intersection_found = true; inside = X; // find new point by checking polyhedron vertices that lies on negative side of the plane } else { for(Polyhedron::Vertex_iterator vIter = A.vertices_begin(); vIter != A.vertices_end() && !intersection_found ; vIter++){ if(Oriented_squared_distance(B,vIter->point())<=-lim) { if (Oriented_squared_distance(B,centroid)point() + 0.5*CGALvector(vIter->point(),centroid); }else{ CGAL::Object result = CGAL::intersection(Line(vIter->point(),centroid), B); if (const CGALpoint *ipoint = CGAL::object_cast(&result)) { inside = vIter->point() + 0.5*CGALvector(vIter->point(),*ipoint); }else{ LOG_WARN("Error in line-plane intersection"); } } if(Is_inside_Polyhedron(A,inside,DISTANCE_LIMIT) && Oriented_squared_distance(B,inside)<=-lim) intersection_found = true; } } } //no intersectiong point => no intersection polyhedron if(!intersection_found) return Intersection; //set the intersection point to origin Transformation transl_back(CGAL::TRANSLATION, inside - CGALpoint(0.,0.,0.)); Transformation transl(CGAL::TRANSLATION, CGALpoint(0.,0.,0.)-inside); std::transform( A.points_begin(), A.points_end(), A.points_begin(), transl); B = transl.transform(B); //dualize plane planes1.push_back(B); //dualize polyhedron std::transform( A.facets_begin(), A.facets_end(), A.planes_begin(),Plane_equation()); for(Polyhedron::Plane_iterator pi =A.planes_begin(); pi!=A.planes_end(); ++pi) planes2.push_back(*pi);; //merge planes planes1 = MergePlanes(planes1,planes2, MERGE_PLANES_LIMIT);//MERGE_PLANES_LIMIT); for(vector::iterator pi =planes1.begin(); pi!= planes1.end(); ++pi) dual_planes.push_back(CGALpoint(-pi->a()/pi->d(),-pi->b()/pi->d(),-pi->c()/pi->d())); //compute convex hull of it Intersection = ConvexHull(dual_planes); if (Intersection.empty()) return Intersection; //simplify std::transform( Intersection.facets_begin(), Intersection.facets_end(), Intersection.planes_begin(),Plane_equation()); Intersection = Simplify(Intersection, SIMPLIFY_LIMIT); std::transform( Intersection.facets_begin(), Intersection.facets_end(), Intersection.planes_begin(),Plane_equation()); //dualize again dual_planes.clear(); for(Polyhedron::Plane_iterator pi =Intersection.planes_begin(); pi!=Intersection.planes_end(); ++pi) dual_planes.push_back(CGALpoint(-pi->a()/pi->d(),-pi->b()/pi->d(),-pi->c()/pi->d())); //compute convex hull of it Intersection = ConvexHull(dual_planes); if (Intersection.empty()) return Intersection; //return to original position std::transform( Intersection.points_begin(), Intersection.points_end(), Intersection.points_begin(), transl_back); if (Intersection.size_of_facets() < 4) Intersection.clear(); return Intersection; } //********************************************************************************** //returnes intersecting polyhedron of polyhedron & plane defined by direction and point Polyhedron Polyhedron_Plane_intersection(Polyhedron A, Vector3r direction, Vector3r plane_point){ Plane B(ToCGALPoint(plane_point), ToCGALVector(direction)); CGALpoint X = ToCGALPoint(plane_point) - 1E-8*ToCGALVector(direction); return Polyhedron_Plane_intersection(A, B, ToCGALPoint(plane_point), X); } //********************************************************************************** //returnes intersecting polyhedron of two polyhedrons (possibly empty) Polyhedron Polyhedron_Polyhedron_intersection(Polyhedron A, Polyhedron B, CGALpoint X, CGALpoint centroidA, CGALpoint centroidB, std::vector &sep_plane){ Polyhedron Intersection; vector planes1, planes2; vector dual_planes; Polyhedron::Plane_iterator pi; CGALpoint inside(0,0,0); bool intersection_found = false; std::transform( A.facets_begin(), A.facets_end(), A.planes_begin(),Plane_equation()); std::transform( B.facets_begin(), B.facets_end(), B.planes_begin(),Plane_equation()); Matrix3r Amatrix; Vector3r y; // test that X is really inside if(Is_inside_Polyhedron(A,X,DISTANCE_LIMIT) && Is_inside_Polyhedron(B,X,DISTANCE_LIMIT)) { intersection_found = true; inside = X; } else { if (!do_intersect(A, B, sep_plane)) return Intersection; //some intersection point Real dist_S, dist_T; Real lim2 = pow(DISTANCE_LIMIT,2); CGALvector d1; Real factor = sqrt(DISTANCE_LIMIT * 1.5); //test vertices A - not needed, edges are enough for (Polyhedron::Vertex_iterator vIter = A.vertices_begin(); vIter != A.vertices_end() && !intersection_found; vIter++){ d1 = centroidA-vIter->point(); inside = vIter->point() + d1/sqrt(d1.squared_length())*DISTANCE_LIMIT*20.; intersection_found = (Is_inside_Polyhedron(A,inside,DISTANCE_LIMIT) && Is_inside_Polyhedron(B,inside,DISTANCE_LIMIT)); } //test vertices B - necessary for (Polyhedron::Vertex_iterator vIter = B.vertices_begin(); vIter != B.vertices_end() && !intersection_found; vIter++){ d1 = centroidB-vIter->point(); inside = vIter->point() + d1/sqrt(d1.squared_length())*DISTANCE_LIMIT*20.; intersection_found = (Is_inside_Polyhedron(A,inside,DISTANCE_LIMIT) && Is_inside_Polyhedron(B,inside,DISTANCE_LIMIT)); } //test edges for (Polyhedron::Edge_iterator eIter = A.edges_begin(); eIter != A.edges_end() && !intersection_found; eIter++){ for (Polyhedron::Facet_iterator fIter = B.facets_begin(); fIter != B.facets_end() && !intersection_found; fIter++){ dist_S = Oriented_squared_distance(fIter->plane(), eIter->vertex()->point()); dist_T = Oriented_squared_distance(fIter->plane(), eIter->opposite()->vertex()->point()); if (dist_S*dist_T >= 0 || std::abs(dist_S)vertex()->point() + (eIter->opposite()->vertex()->point()-eIter->vertex()->point())*sqrt(std::abs(dist_S))/(sqrt(std::abs(dist_S))+sqrt(std::abs(dist_T))); // the fact that edge intersects the facet (not only its plane) is not explicitely checked, it sufices to check that the resulting point is inside both polyhedras Plane p1 = fIter->plane(); Plane p2 = eIter->facet()->plane(); Plane p3 = eIter->opposite()->facet()->plane(); Amatrix << p1.a(),p1.b(),p1.c(), p2.a(),p2.b(),p2.c(), p3.a(),p3.b(),p3.c(); y = Vector3r(-p1.d()-factor*sqrt(pow(p1.a(),2)+pow(p1.b(),2)+pow(p1.c(),2)),-p2.d()-factor*sqrt(pow(p2.a(),2)+pow(p2.b(),2)+pow(p2.c(),2)),-p3.d()-factor*sqrt(pow(p3.a(),2)+pow(p3.b(),2)+pow(p3.c(),2))); inside = ToCGALPoint(SolveLinSys3x3(Amatrix,y)); intersection_found = (Is_inside_Polyhedron(A,inside,DISTANCE_LIMIT) && Is_inside_Polyhedron (B,inside,DISTANCE_LIMIT)); } } } //Polyhedrons do not intersect if (!intersection_found) return Intersection; //set the intersection point to origin Transformation transl_back(CGAL::TRANSLATION, inside - CGALpoint(0.,0.,0.)); Transformation transl(CGAL::TRANSLATION, CGALpoint(0.,0.,0.)-inside); std::transform( A.points_begin(), A.points_end(), A.points_begin(), transl); std::transform( B.points_begin(), B.points_end(), B.points_begin(), transl); //dualize polyhedrons std::transform( A.facets_begin(), A.facets_end(), A.planes_begin(),Plane_equation()); std::transform( B.facets_begin(), B.facets_end(), B.planes_begin(),Plane_equation()); for(Polyhedron::Plane_iterator pi =A.planes_begin(); pi!=A.planes_end(); ++pi) planes1.push_back(*pi); for(Polyhedron::Plane_iterator pi =B.planes_begin(); pi!=B.planes_end(); ++pi) planes2.push_back(*pi); //merge planes planes1 = MergePlanes(planes1,planes2, MERGE_PLANES_LIMIT);//MERGE_PLANES_LIMIT); for(vector::iterator pi =planes1.begin(); pi!= planes1.end(); ++pi) dual_planes.push_back(CGALpoint(-pi->a()/pi->d(),-pi->b()/pi->d(),-pi->c()/pi->d())); //compute convex hull of it Intersection = ConvexHull(dual_planes); if (Intersection.empty()) return Intersection; //simplify std::transform( Intersection.facets_begin(), Intersection.facets_end(), Intersection.planes_begin(),Plane_equation()); Intersection = Simplify(Intersection, SIMPLIFY_LIMIT); std::transform( Intersection.facets_begin(), Intersection.facets_end(), Intersection.planes_begin(),Plane_equation()); //dualize again dual_planes.clear(); for(Polyhedron::Plane_iterator pi =Intersection.planes_begin(); pi!=Intersection.planes_end(); ++pi) { const auto pX = -pi->a()/pi->d(); const auto pY = -pi->b()/pi->d(); const auto pZ = -pi->c()/pi->d(); if (std::isnan(pX) || std::isnan(pY) || std::isnan(pZ)) { Polyhedron IntersectionEmpty; return IntersectionEmpty; } else { dual_planes.push_back(CGALpoint(-pi->a()/pi->d(),-pi->b()/pi->d(),-pi->c()/pi->d())); } } //compute convex hull of it Intersection = ConvexHull(dual_planes); if (Intersection.empty()) return Intersection; //return to original position std::transform( Intersection.points_begin(), Intersection.points_end(), Intersection.points_begin(), transl_back); if (Intersection.size_of_facets() < 4) Intersection.clear(); return Intersection; } //********************************************************************************** Vector3r FromCGALPoint(CGALpoint A){ return Vector3r(A.x(), A.y(), A.z()); } //********************************************************************************** Vector3r FromCGALVector(CGALvector A){ return Vector3r(A.x(), A.y(), A.z()); } //********************************************************************************** CGALpoint ToCGALPoint(Vector3r A){ return CGALpoint(A[0], A[1], A[2]); } //********************************************************************************** CGALvector ToCGALVector(Vector3r A){ return CGALvector(A[0], A[1], A[2]); } //********************************************************************************** //new polyhedra shared_ptr NewPolyhedra(vector v, shared_ptr mat){ shared_ptr body(new Body); body->material=mat; body->shape=shared_ptr(new Polyhedra()); Polyhedra* A = static_cast(body->shape.get()); A->v = v; A->Initialize(); body->state->pos= A->GetCentroid(); body->state->mass=body->material->density*A->GetVolume(); body->state->inertia =A->GetInertia()*body->material->density; body->state->ori = A->GetOri(); body->bound=shared_ptr(new Aabb); body->setAspherical(true); return body; } //********************************************************************************** //split polyhedra shared_ptr SplitPolyhedra(const shared_ptr& body, const Vector3r direction, const Vector3r point){ Scene* scene=Omega::instance().getScene().get(); const Se3r& se3=body->state->se3; Polyhedra* A = static_cast(body->shape.get()); State* X = static_cast(body->state.get()); const Vector3r OrigPos = X->pos; const Vector3r OrigVel = X->vel; const Vector3r OrigAngVel = X->angVel; //move and rotate CGAL structure Polyhedron Matrix3r rot_mat = (se3.orientation).toRotationMatrix(); Vector3r trans_vec = se3.position; Transformation t_rot_trans( rot_mat(0,0),rot_mat(0,1),rot_mat(0,2),trans_vec[0], rot_mat(1,0),rot_mat(1,1),rot_mat(1,2),trans_vec[1], rot_mat(2,0),rot_mat(2,1),rot_mat(2,2),trans_vec[2],1.); Polyhedron PA = A->GetPolyhedron(); std::transform( PA.points_begin(), PA.points_end(), PA.points_begin(), t_rot_trans); //calculate first splitted polyhedrons Plane B(ToCGALPoint(point-direction*SPLITTER_GAP), ToCGALVector(direction)); Polyhedron S1 = Polyhedron_Plane_intersection(PA, B, ToCGALPoint(se3.position), B.projection(ToCGALPoint(OrigPos)) - 1E-6*ToCGALVector(direction)); B = Plane(ToCGALPoint(point+direction*SPLITTER_GAP), ToCGALVector((-1.)*direction)); Polyhedron S2 = Polyhedron_Plane_intersection(PA, B, ToCGALPoint(se3.position), B.projection(ToCGALPoint(OrigPos)) + 1E-6*ToCGALVector(direction)); //scene->bodies->erase(body->id); //replace original polyhedron A->Clear(); for(Polyhedron::Vertex_iterator vi = S1.vertices_begin(); vi != S1.vertices_end(); vi++) A->v.push_back(FromCGALPoint(vi->point())); A->Initialize(); X->pos = A->GetCentroid(); X->ori = A->GetOri(); X->mass=body->material->density*A->GetVolume(); X->refPos[0] = X->refPos[0]+1.; X->inertia =A->GetInertia()*body->material->density; X->vel = OrigVel + OrigAngVel.cross(X->pos-OrigPos); X->angVel = OrigAngVel; //second polyhedron vector v2; for(Polyhedron::Vertex_iterator vi = S2.vertices_begin(); vi != S2.vertices_end(); vi++) v2.push_back(FromCGALPoint(vi->point())); shared_ptr BP = NewPolyhedra(v2, body->material); BP->shape->color = Vector3r(Real(rand())/RAND_MAX,Real(rand())/RAND_MAX,Real(rand())/RAND_MAX); scene->bodies->insert(BP); //set proper state variables BP->state->vel = OrigVel + OrigAngVel.cross(BP->state->pos-OrigPos); BP->state->angVel = OrigAngVel; return BP; } #endif // YADE_CGAL trunk-2017.01a/pkg/dem/PotentialBlock.cpp000077500000000000000000000072241304022710500201360ustar00rootroot00000000000000/*CWBoon 2015 */ #ifdef YADE_POTENTIAL_BLOCKS //! To implement potential particles (Houlsby 2009) using sphere #include "PotentialBlock.hpp" YADE_PLUGIN((PotentialBlock)); PotentialBlock::~PotentialBlock() { } void PotentialBlock::addPlaneStruct() { planeStruct.push_back(Planes()); } void PotentialBlock::addVertexStruct() { vertexStruct.push_back(Vertices()); } void PotentialBlock::addEdgeStruct() { edgeStruct.push_back(Edges()); } //#if 0 void PotentialBlock::postLoad(PotentialBlock&) { int planeNo = a.size(); for (int i=0; i0.9998){parallel = true;} if (fabs(plane1.dot(plane3))<1.0002 && fabs(plane1.dot(plane3))>0.9998){parallel = true;} if (fabs(plane2.dot(plane3))<1.0002 && fabs(plane2.dot(plane3))>0.9998){parallel = true;} double det = Aplanes.determinant(); if(fabs(det)>pow(10,-15) ){ //if (parallel == false){ int ipiv[3]; int bColNo=1; int info=0; /* LU */ int three =3; dgesv_( &three, &bColNo, Ax, &three, ipiv, D, &three, &info); if (info!=0){ //std::cout<<"linear algebra error"<pow(10,-3)){inside = false;} } #if 0 double planeV1 = d1 - (plane1.x()*vertex[0] + plane1.y()*vertex[1] + plane1.z()*vertex[2]); double planeV2 = d2 - (plane2.x()*vertex[0] + plane2.y()*vertex[1] + plane2.z()*vertex[2]); double planeV3 = d3 - (plane3.x()*vertex[0] + plane3.y()*vertex[1] + plane3.z()*vertex[2]); if (planeV1 <-pow(10,-3) ){ inside = false;} if (planeV2 <-pow(10,-3) ){ inside = false;} if (planeV3 <-pow(10,-3) ){ inside = false;} #endif if (inside == true){ //std::cout<<"vertex: "< #include #include #include #include #include namespace yade{ class PotentialBlock : public Shape { public: struct Planes{ vector vertexID; }; struct Vertices{ vector edgeID; vector planeID; }; struct Edges{ vector vertexID; }; void addPlaneStruct(); void addVertexStruct(); void addEdgeStruct(); vector planeStruct; vector vertexStruct; vector edgeStruct; Eigen::MatrixXd Amatrix; Eigen::MatrixXd Dmatrix; virtual ~PotentialBlock (); void postLoad(PotentialBlock&); YADE_CLASS_BASE_DOC_ATTRS_CTOR(PotentialBlock,Shape,"Geometry of PotentialBlock.", ((bool, isLining, false,, "false")) ((double, liningStiffness, pow(10.0,8),, "lining stiffness")) ((double, liningFriction, 20.0,, "lining stiffness")) ((double, liningLength, 0.0,, "lining stiffness")) ((double, liningTensionGap, 0.0,, "lining stiffness")) ((Vector3r, liningNormalPressure, Vector3r(0,0,0),, "lining stiffness")) ((Vector3r, liningTotalPressure, Vector3r(0,0,0),, "lining stiffness")) ((bool, isBoundary, false,, "boundary")) ((bool, isEastBoundary, false,, "boundary")) ((bool, isBolt, false,, "boundary")) ((bool, fixedNormal, false,, "boundary")) ((Vector3r, boundaryNormal, Vector3r::Zero(),,"normal direction of boundary")) ((bool, AabbMinMax, false,, "aabb")) ((Vector3r, minAabb, Vector3r::Zero(),,"min from box centre")) ((Vector3r, maxAabb, Vector3r::Zero(),,"max frin box centre")) ((Vector3r, minAabbRotated, Vector3r::Zero(),,"min from box centre")) ((Vector3r, maxAabbRotated, Vector3r::Zero(),,"max frin box centre")) ((Vector3r, halfSize, Vector3r::Zero(),,"max frin box centre")) ((vector , node, ,, "nodes ")) ((Real, gridVol, ,, "nodes ")) ((Quaternionr , oriAabb, Quaternionr::Identity(),, "r ")) ((Real , r, 0.1,, "r ")) ((Real , R, 1.0,, "R ")) ((Real , k, 0.1,, "k ")) ((Real , volume, 0.1,, "k ")) ((int, id, -1,, " for graphics")) ((bool, erase, false,, " for graphics")) ((vector, intactRock, false,, " for graphics")) ((vector, isBoundaryPlane, ,, "whether it is a boundary")) ((vector, hwater, ,, "height of pore water")) ((vector, JRC, ,, "rock joint")) ((vector, JCS, ,, "rock joint")) ((vector, asperity, ,, "rock joint")) ((vector, sigmaC, ,,"rock joint")) ((vector, phi_b, ,, "rock joint")) ((vector, phi_r, ,, "rock joint")) ((vector, cohesion, ,, "rock joint")) ((vector, tension, ,, "rock joint")) ((vector, lambda0, ,, "rock joint")) ((vector, heatCapacity, ,, "rock joint")) ((vector, rFactor, ,, "individual factors for r")) ((vector, vertices,,,"vertices")) //((Eigen::MatrixXd , Amatrix, ,, "a ")) //((Eigen::MatrixXd , Dmatrix, ,, "b ")) ((double, waterVolume, ,, "water")) ((vector ,verticesCD, ,, "vertices ")) ((vector , a, ,, "a ")) ((vector , b, ,, "b ")) ((vector , c, ,, "c ")) ((vector , d, ,, "d ")) ((vector , jointType, ,, "jointType")) , createIndex(); /*ctor*/ #if 0 for (int i=0; i #include void PotentialBlock2AABB::go(const shared_ptr& cm, shared_ptr& bv, const Se3r& se3, const Body*){ PotentialBlock* pp = static_cast(cm.get()); if(!bv){ bv=shared_ptr(new Aabb); } Aabb* aabb = static_cast(bv.get()); Matrix3r r = se3.orientation.toRotationMatrix(); if(pp->AabbMinMax == false){ Real distFromCentre = 1.05*pp->R; // std::max(maxD, pp->R); halfSize = Vector3r(distFromCentre,distFromCentre,distFromCentre); aabb->min = se3.position-halfSize; aabb->max = se3.position+halfSize; return; }else{ Matrix3r r=se3.orientation.toRotationMatrix(); Vector3r halfSizeMin(Vector3r::Zero());Vector3r halfSizeMax(Vector3r::Zero()); if(pp->vertices.size() ==0){ //pp->vertices.clear(); pp->vertices.push_back(Vector3r(pp->maxAabbRotated[0],pp->maxAabbRotated[1],pp->maxAabbRotated[2])); pp->vertices.push_back(Vector3r(pp->maxAabbRotated[0],pp->maxAabbRotated[1],-pp->minAabbRotated[2])); pp->vertices.push_back(Vector3r(-pp->minAabbRotated[0],-pp->minAabbRotated[1],pp->maxAabbRotated[2])); pp->vertices.push_back(Vector3r(-pp->minAabbRotated[0],-pp->minAabbRotated[1],-pp->minAabbRotated[2])); pp->vertices.push_back(Vector3r(-pp->minAabbRotated[0],pp->maxAabbRotated[1],pp->maxAabbRotated[2])); pp->vertices.push_back(Vector3r(-pp->minAabbRotated[0],pp->maxAabbRotated[1],-pp->minAabbRotated[2])); pp->vertices.push_back(Vector3r(pp->maxAabbRotated[0],-pp->minAabbRotated[1],pp->maxAabbRotated[2])); pp->vertices.push_back(Vector3r(pp->maxAabbRotated[0],-pp->minAabbRotated[1],-pp->minAabbRotated[2])); } Vector3r aabbMin(0,0,0); Vector3r aabbMax(0,0,0); for (int i=0; i<8; i++){ Vector3r vertex = r*(pp->oriAabb.conjugate()*pp->vertices[i]); if(vertex.x() < aabbMin.x()){ aabbMin.x() = vertex.x(); } if(vertex.y() < aabbMin.y()){ aabbMin.y() = vertex.y(); } if(vertex.z() < aabbMin.z()){ aabbMin.z() = vertex.z(); } if(vertex.x() > aabbMax.x()){ aabbMax.x() = vertex.x(); } if(vertex.y() > aabbMax.y()){ aabbMax.y() = vertex.y(); } if(vertex.z() > aabbMax.z()){ aabbMax.z() = vertex.z(); } } aabb->min= se3.position + 1.05*aabbMin; aabb->max = se3.position + 1.05*aabbMax; halfSizeMin = -1.0*aabbMin; halfSizeMax = 1.0*aabbMax; pp->halfSize = 1.1*Vector3r(std::max(halfSizeMin.x(),halfSizeMax.x()),std::max(halfSizeMin.y(),halfSizeMax.y()),std::max(halfSizeMin.z(),halfSizeMax.z())); return; } } YADE_PLUGIN((PotentialBlock2AABB)); #endif // YADE_POTENTIAL_BLOCKS trunk-2017.01a/pkg/dem/PotentialBlock2AABB.hpp000077500000000000000000000021731304022710500206310ustar00rootroot00000000000000/*CWBoon 2015 */ #ifdef YADE_POTENTIAL_BLOCKS #pragma once #include #include class PotentialBlock2AABB : public BoundFunctor { public : void go(const shared_ptr& cm, shared_ptr& bv, const Se3r&, const Body*); FUNCTOR1D(PotentialBlock); //REGISTER_ATTRIBUTES(BoundFunctor,(aabbEnlargeFactor)); YADE_CLASS_BASE_DOC_ATTRS(PotentialBlock2AABB,BoundFunctor,"Functor creating :yref:`Aabb` from :yref:`Sphere`.", ((Real,aabbEnlargeFactor,((void)"deactivated",-1),,"Relative enlargement of the bounding box; deactivated if negative.\n\n.. note::\n\tThis attribute is used to create distant interaction, but is only meaningful with an :yref:`InteractionGeometryFunctor` which will not simply discard such interactions: :yref:`Ig2_Sphere_Sphere_Dem3DofGeom::distFactor` / :yref:`Ig2_Sphere_Sphere_ScGeom::interactionDetectionFactor` should have the same value as :yref:`aabbEnlargeFactor`.")) ((Vector3r, halfSize, Vector3r::Zero(),,"halfSize")) ); }; REGISTER_SERIALIZABLE(PotentialBlock2AABB); #endif // YADE_POTENTIAL_BLOCKS trunk-2017.01a/pkg/dem/PotentialParticle.cpp000066400000000000000000000004111304022710500206330ustar00rootroot00000000000000/*CWBoon 2015 */ #ifdef YADE_POTENTIAL_PARTICLES //! To implement potential particles (Houlsby 2009) using sphere #include "PotentialParticle.hpp" YADE_PLUGIN((PotentialParticle)); PotentialParticle::~PotentialParticle() { } #endif // YADE_POTENTIAL_PARTICLES trunk-2017.01a/pkg/dem/PotentialParticle.hpp000066400000000000000000000040461304022710500206500ustar00rootroot00000000000000/*CWBoon 2015 */ #pragma once #ifdef YADE_POTENTIAL_PARTICLES #include #include #include #include #include #include namespace yade { class PotentialParticle : public Shape { public: virtual ~PotentialParticle (); YADE_CLASS_BASE_DOC_ATTRS_CTOR(PotentialParticle,Shape,"EXPERIMENTAL. Geometry of PotentialParticle.", ((int, id, 1,, "idNo")) ((bool, isBoundary, false,, "boundary")) ((bool, fixedNormal, false,, "use fixed normal")) ((Vector3r, boundaryNormal, Vector3r::Zero(),,"normal direction of boundary")) ((bool, AabbMinMax, false,, "aabb")) ((Vector3r, minAabb, Vector3r::Zero(),,"min from box centre")) ((Vector3r, maxAabb, Vector3r::Zero(),,"max from box centre")) ((Vector3r, minAabbRotated, Vector3r::Zero(),,"min from box centre")) ((Vector3r, maxAabbRotated, Vector3r::Zero(),,"max from box centre")) ((Vector3r, halfSize, Vector3r::Zero(),,"max from box centre")) ((Quaternionr , oriAabb, Quaternionr::Identity(),, "r ")) ((Real , r, 0.1,, "r ")) ((Real , R, 1.0,, "R ")) ((Real , k, 0.1,, "k ")) ((vector, vertices,,,"vertices")) ((vector , isBoundaryPlane, ,, "whether it is a boundaryPlane ")) ((vector , a, ,, "a ")) ((vector , b, ,, "b ")) ((vector , c, ,, "c ")) ((vector , d, ,, "d ")) , createIndex(); /*ctor*/ #if 0 for (int i=0; i #include void PotentialParticle2AABB::go(const shared_ptr& cm, shared_ptr& bv, const Se3r& se3, const Body*) { PotentialParticle* pp = static_cast(cm.get()); if(!bv) { bv=shared_ptr(new Aabb); } Aabb* aabb = static_cast(bv.get()); if(pp->AabbMinMax == false) { Real distFromCentre = 1.05*pp->R; // std::max(maxD, pp->R); halfSize = Vector3r(distFromCentre,distFromCentre,distFromCentre); aabb->min = se3.position-halfSize; aabb->max = se3.position+halfSize; return; } else { Matrix3r r=se3.orientation.toRotationMatrix(); Vector3r halfSizeMin(Vector3r::Zero()); Vector3r halfSizeMax(Vector3r::Zero()); if(pp->vertices.size() ==0) { //pp->vertices.clear(); pp->vertices.push_back(Vector3r(pp->maxAabbRotated[0],pp->maxAabbRotated[1],pp->maxAabbRotated[2])); pp->vertices.push_back(Vector3r(pp->maxAabbRotated[0],pp->maxAabbRotated[1],-pp->minAabbRotated[2])); pp->vertices.push_back(Vector3r(-pp->minAabbRotated[0],-pp->minAabbRotated[1],pp->maxAabbRotated[2])); pp->vertices.push_back(Vector3r(-pp->minAabbRotated[0],-pp->minAabbRotated[1],-pp->minAabbRotated[2])); pp->vertices.push_back(Vector3r(-pp->minAabbRotated[0],pp->maxAabbRotated[1],pp->maxAabbRotated[2])); pp->vertices.push_back(Vector3r(-pp->minAabbRotated[0],pp->maxAabbRotated[1],-pp->minAabbRotated[2])); pp->vertices.push_back(Vector3r(pp->maxAabbRotated[0],-pp->minAabbRotated[1],pp->maxAabbRotated[2])); pp->vertices.push_back(Vector3r(pp->maxAabbRotated[0],-pp->minAabbRotated[1],-pp->minAabbRotated[2])); } Vector3r aabbMin(0,0,0); Vector3r aabbMax(0,0,0); for (int i=0; i<8; i++) { Vector3r vertex = r*(pp->oriAabb.conjugate()*pp->vertices[i]); if(vertex.x() < aabbMin.x()) { aabbMin.x() = vertex.x(); } if(vertex.y() < aabbMin.y()) { aabbMin.y() = vertex.y(); } if(vertex.z() < aabbMin.z()) { aabbMin.z() = vertex.z(); } if(vertex.x() > aabbMax.x()) { aabbMax.x() = vertex.x(); } if(vertex.y() > aabbMax.y()) { aabbMax.y() = vertex.y(); } if(vertex.z() > aabbMax.z()) { aabbMax.z() = vertex.z(); } } aabb->min= se3.position + 1.05*aabbMin; aabb->max = se3.position + 1.05*aabbMax; halfSizeMin = -1.0*aabbMin; halfSizeMax = 1.0*aabbMax; return; } } YADE_PLUGIN((PotentialParticle2AABB)); #endif // YADE_POTENTIAL_PARTICLES trunk-2017.01a/pkg/dem/PotentialParticle2AABB.hpp000066400000000000000000000013741304022710500213410ustar00rootroot00000000000000/*CWBoon 2015 */ #pragma once #ifdef YADE_POTENTIAL_PARTICLES #include #include class PotentialParticle2AABB : public BoundFunctor { public : void go(const shared_ptr& cm, shared_ptr& bv, const Se3r&, const Body*); FUNCTOR1D(PotentialParticle); //REGISTER_ATTRIBUTES(BoundFunctor,(aabbEnlargeFactor)); YADE_CLASS_BASE_DOC_ATTRS(PotentialParticle2AABB,BoundFunctor,"EXPERIMENTAL. Functor creating :yref:`Aabb` from :yref:`PotentialParticle`.", ((Real,aabbEnlargeFactor,((void)"deactivated",-1),,"see :yref:`Sphere2AABB`.")) ((Vector3r, halfSize, Vector3r::Zero(),,"halfSize")) ); }; REGISTER_SERIALIZABLE(PotentialParticle2AABB); #endif // YADE_POTENTIAL_PARTICLES trunk-2017.01a/pkg/dem/RockBolt.cpp000077500000000000000000000532271304022710500167470ustar00rootroot00000000000000/*CWBoon 2016 */ /* Please cite: */ /* CW Boon, GT Houlsby, S Utili (2015). Designing Tunnel Support in Jointed Rock Masses Via the DEM. Rock Mechanics and Rock Engineering, 48 (2), 603-632. */ #ifdef YADE_POTENTIAL_BLOCKS #include "RockBolt.hpp" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include void RockBolt::action(){ if (openingCreated == true && installed == false){ vector distanceFrOpening; FOREACH(const shared_ptr& b, *scene->bodies){ if (!b) continue; if (b->isClump() == true) continue; PotentialBlock* pb=static_cast(b->shape.get()); if(!pb) continue; if(pb->isBoundary == true || pb->erase== true || pb->isLining==true){continue;} State* state1 = b->state.get(); Vector3r intersectionPt(0,0,0); if ( installBolts(pb, state1, startingPoint, boltDirection, boltLength, intersectionPt )){ blockIDs.push_back(b->id); pb->isBolt = true; distanceFrOpening.push_back((intersectionPt-startingPoint).norm()); } } /* sort blocks according to distance from the centre */ int totalBlocks = blockIDs.size(); for (int i=0; i 0 && distanceFrOpening[ihole-1] > distance){ distanceFrOpening[ihole] = distanceFrOpening[ihole-1]; blockIDs[ihole] = blockIDs[ihole-1]; ihole = ihole-1; } distanceFrOpening[ihole] = distance; blockIDs[ihole] = blockID; } Vector3r jointIntersection (0,0,0); for (int j=0; jstate.get(); Shape* shape1 = Body::byId(blockIDs[j],scene)->shape.get(); PotentialBlock *pb=static_cast(shape1); int totalPlanes = pb->a.size(); int intersectNo = 0; vector tempCoord; vector distance; for (int i=0; iori*Vector3r(pb->a[i], pb->b[i], pb->c[i]); double planeD = plane.dot(state1->pos) + pb->d[i] +pb->r; if ( intersectPlane(pb, state1,startingPoint,boltDirection, boltLength, jointIntersection, plane, planeD)){ double sign = plane.dot(boltDirection); jointIntersection = jointIntersection - Mathr::Sign(sign)*halfActiveLength*boltDirection; distance.push_back(jointIntersection.norm() ); jointIntersection = state1->ori.conjugate()*(jointIntersection-state1->pos); intersectNo++; if(intersectNo >2){std::cout<<"intersectNo > 2: "<state.get(); endPoint = state1 ->ori.conjugate()*(endPoint-state1->pos); if(useMidPoint == false){ localCoordinates.push_back(tempCoord[0]); }else{ localCoordinates.push_back(0.5*(endPoint+tempCoord[0])); } localCoordinates.push_back(endPoint); }else{ if(useMidPoint == false){ if(distance[0] < distance[1] ){ localCoordinates.push_back(tempCoord[0]);localCoordinates.push_back(tempCoord[1]); }else{ localCoordinates.push_back(tempCoord[1]);localCoordinates.push_back(tempCoord[0]); } }else{ Vector3r midPoint = 0.5*(tempCoord[0] + tempCoord[1]); if(j!=0){ localCoordinates.push_back(midPoint); localCoordinates.push_back(midPoint); }else{ if(distance[0] < distance[1] ){ localCoordinates.push_back(tempCoord[0]);localCoordinates.push_back(midPoint); }else{ localCoordinates.push_back(tempCoord[1]);localCoordinates.push_back(midPoint); } } } } tempCoord.clear(); distance.clear(); //std::cout<<"j: "< tempCoord = localCoordinates; localCoordinates.clear(); State* stateB = Body::byId(blockIDs[0],scene)->state.get(); Vector3r startPt = stateB->ori.conjugate()*(startingPoint-stateB->pos); localCoordinates.push_back(startPt); for (int i=0; istate.get(); endPoint = stateA->ori.conjugate()*(endPoint-stateA->pos); localCoordinates.push_back(endPoint); } #endif installed = true; distanceFrOpening.clear(); } if (installed == true && blockIDs.size()>=2){ averageForce = 0.0; maxForce = 0.0; int blockNo = blockIDs.size(); for (int j=1; jstate.get(); State* state2 = Body::byId(blockIDs[j],scene)->state.get(); Shape* shape1 = Body::byId(blockIDs[j-1],scene)->shape.get(); Shape* shape2 = Body::byId(blockIDs[j],scene)->shape.get(); PotentialBlock *s1=static_cast(shape1); PotentialBlock *s2=static_cast(shape2); Vector3r nodeDistance = getNodeDistance(s1,state1,s2,state2,localCoordinates[2*j-1],localCoordinates[2*j]); /* 2 minus 1, from 1 to 2 */ if (initialLength.size() < blockNo-1 ){ /*not initialized */ initialLength.push_back(nodeDistance.norm()*Mathr::Sign(nodeDistance.dot(boltDirection) )); /* negative if there is overlap */ initialDirection.push_back(nodeDistance); forces.push_back(0.0); axialForces.push_back(0.0); shearForces.push_back(0.0);ruptured.push_back(false); nodeDistanceVec.push_back(nodeDistance); nodePosition.push_back(Vector3r(0,0,0)); distanceFrCentre.push_back(0.0); }else{ if (resetLengthInit == true){ initialLength[j-1] =nodeDistance.norm()*Mathr::Sign(nodeDistance.dot(boltDirection) ); resetLengthInit = false; } Vector3r direction = nodeDistance; direction.normalize(); double dirSign = 1.0; nodeDistanceVec[j-1] =nodeDistance; //if (initialDirection[j-1].norm()>pow(10,-11) ){ // dirSign = direction.dot(initialDirection[j-1]); //}else{ dirSign = direction.dot(boltDirection); //FIXME assume special case does not happen, i.e., activeLength is long enough //} Vector3r axialForce = (normalStiffness*(Mathr::Sign(dirSign)*nodeDistance.norm() - initialLength[j-1])+preTension)*(Mathr::Sign(dirSign)*direction);/* the last term makes sure tension is always pointing in the direction of boltdirection */ //Vector3r axialForce = (axialStiffness/initialLength[j-1]*(Mathr::Sign(dirSign)*nodeDistance.norm() - initialLength[j-1])+preTension)*(Mathr::Sign(dirSign)*direction);/* the last term makes sure tension is always pointing in the direction of boltdirection */ Vector3r shearDir = boltDirection.cross(Vector3r(0,1,0)); shearDir.normalize(); Vector3r shearForce = shearStiffness*(nodeDistance.dot(shearDir))*shearDir; if(axialForce.norm()>axialMax || shearForce.norm()>shearMax || ruptured[j-1] == true){ axialForce = Vector3r(0,0,0); shearForce = Vector3r(0,0,0); ruptured[j-1]= true; } axialForces[j-1] = axialForce.norm(); shearForces[j-1] = shearForce.norm(); forces[j-1] = (axialForce +shearForce).norm(); //*Mathr::Sign(dirSign); averageForce += forces[j-1]; maxForce = std::max(maxForce,forces[j-1]); Vector3r totalForce = axialForce + shearForce; Vector3r c1x = state1->ori*localCoordinates[2*j-1]+0.5*nodeDistance; nodePosition[j-1] = state1->pos + c1x; distanceFrCentre[j-1]=nodePosition[j-1].dot(boltDirection); if(j==1){ displacements=(state1->pos+state1->ori*localCoordinates[0]).dot(boltDirection); } Vector3r c2x = state2->ori*localCoordinates[2*j]-0.5*nodeDistance; scene->forces.addTorque(blockIDs[j-1],c1x.cross(totalForce)); scene->forces.addTorque(blockIDs[j],-c2x.cross(totalForce)); scene->forces.addForce(blockIDs[j-1],totalForce ); scene->forces.addForce(blockIDs[j],-totalForce ); } } averageForce = averageForce/static_cast(blockNo-1); } if ((scene->iter-vtkRefTimeStep)%vtkIteratorInterval == 0 && installed == true && blockIDs.size()>=2){ vtkRefTimeStep = scene->iter; vtkSmartPointer appendFilter = vtkSmartPointer::New(); int blockNo = blockIDs.size(); /// BOLT FORCE // vtkSmartPointer boltNodalPoints = vtkSmartPointer::New(); vtkSmartPointer boltNodalPointsCells = vtkSmartPointer::New(); vtkSmartPointer boltNode = vtkSmartPointer::New(); vtkSmartPointer boltNodeCells = vtkSmartPointer::New(); vtkSmartPointer boltNodalForce = vtkSmartPointer::New(); boltNodalForce->SetNumberOfComponents(3); boltNodalForce->SetName("Bolt Force"); //Linear velocity in Vector3 form vtkSmartPointer boltAxialForce = vtkSmartPointer::New(); boltAxialForce->SetNumberOfComponents(3); boltAxialForce->SetName("AxialForce"); //Linear velocity in Vector3 form vtkSmartPointer boltShearForce = vtkSmartPointer::New(); boltShearForce->SetNumberOfComponents(3); boltShearForce->SetName("Shear Force"); //Linear velocity in Vector3 form //#if 0; for (int i=0; i state.get(); Vector3r globalPoint1 = state1->ori*localCoordinates[2*i]+state1->pos; Vector3r globalPoint2 = state1->ori*localCoordinates[2*i+1]+state1->pos; vtkSmartPointer lineSource = vtkSmartPointer::New(); double p0[3] = {globalPoint1[0], globalPoint1[1], globalPoint1[2]}; double p1[3] = {globalPoint2[0], globalPoint2[1], globalPoint2[2]}; lineSource->SetPoint1(p0); lineSource->SetPoint2(p1); appendFilter->AddInputConnection(lineSource-> GetOutputPort()); vtkIdType pid2[1]; pid2[0]= boltNodalPoints->InsertNextPoint(globalPoint1[0], globalPoint1[1], globalPoint1[2]); boltNodalPointsCells->InsertNextCell(1,pid2); pid2[0]= boltNodalPoints->InsertNextPoint(globalPoint2[0], globalPoint2[1], globalPoint2[2]); boltNodalPointsCells->InsertNextCell(1,pid2); if(i < blockNo-1){ /* draw a line between joints*/ State* state2 = Body::byId(blockIDs[i+1],scene)->state.get(); Vector3r globalPoint3 = state2->ori*localCoordinates[2*i+2]+state2->pos; vtkSmartPointer lineSourceJoint = vtkSmartPointer::New(); double p2[3] = {globalPoint2[0], globalPoint2[1], globalPoint2[2]}; double p3[3] = {globalPoint3[0], globalPoint3[1], globalPoint3[2]}; lineSourceJoint->SetPoint1(p2); lineSourceJoint->SetPoint2(p3); appendFilter->AddInputConnection(lineSourceJoint-> GetOutputPort()); /* try to draw forces */ vtkIdType pid[1]; Vector3r midPoint = 0.5*(globalPoint2+globalPoint3); pid[0] = boltNode->InsertNextPoint( midPoint[0], midPoint[1], midPoint[2]); boltNodeCells->InsertNextCell(1,pid); Vector3r plotDirection = boltDirection.cross(Vector3r(0,1,0)); if(plotDirection.dot(Vector3r(1,0,0)) <0.0){ plotDirection = -plotDirection; } plotDirection.normalize(); Vector3r nodalForce = forces[i]*plotDirection; float f[3]={nodalForce[0],nodalForce[1],nodalForce[2]}; boltNodalForce->InsertNextTupleValue(f); Vector3r axialForce = axialForces[i]*plotDirection; float fa[3]={axialForce[0],axialForce[1],axialForce[2]}; boltAxialForce->InsertNextTupleValue(fa); Vector3r shearForce = shearForces[i]*plotDirection; float fs[3]={shearForce[0],shearForce[1],shearForce[2]}; boltShearForce->InsertNextTupleValue(fs); } //lineSource->Update(); } //#endif vtkSmartPointer pbUgCP2 = vtkSmartPointer::New(); pbUgCP2->SetPoints(boltNodalPoints); pbUgCP2->SetCells(VTK_VERTEX, boltNodalPointsCells); vtkSmartPointer writerC = vtkSmartPointer::New(); writerC->SetDataModeToAscii(); string fileBoltC=fileName+"boltNodalPoints"+name+"."+std::to_string(scene->iter)+".vtu"; writerC->SetFileName(fileBoltC.c_str()); writerC->SetInputData(pbUgCP2); writerC->Write(); vtkSmartPointer pbUgCP = vtkSmartPointer::New(); pbUgCP->SetPoints(boltNode); pbUgCP->SetCells(VTK_VERTEX, boltNodeCells); pbUgCP->GetPointData()->AddArray(boltNodalForce); pbUgCP->GetPointData()->AddArray(boltAxialForce); pbUgCP->GetPointData()->AddArray(boltShearForce); vtkSmartPointer writerB = vtkSmartPointer::New(); writerB->SetDataModeToAscii(); string fileBolt=fileName+"boltNodeForce"+name+"."+std::to_string(scene->iter)+".vtu"; writerB->SetFileName(fileBolt.c_str()); writerB->SetInputData(pbUgCP); writerB->Write(); vtkSmartPointer writer = vtkXMLPolyDataWriter::New(); writer->SetDataModeToAscii(); string fn=fileName+"-bolt"+name+"."+std::to_string(scene->iter)+".vtp"; writer->SetFileName(fn.c_str()); writer->SetInputConnection(appendFilter->GetOutputPort()); writer->Write(); } } Vector3r RockBolt::getNodeDistance(const PotentialBlock* cm1,const State* state1,const PotentialBlock* cm2,const State* state2, const Vector3r localPt1, const Vector3r localPt2){ Vector3r nodeDist = Vector3r(0,0,0.0); Vector3r global1 = state1->ori*localPt1 + state1->pos; Vector3r global2 = state2->ori*localPt2 + state2->pos; return (global2-global1); } double RockBolt::evaluateFNoSphereVol(const PotentialBlock* s1,const State* state1, const Vector3r newTrial){ Vector3r tempP1 = newTrial - state1->pos; /* Direction cosines */ //state1.ori.normalize(); Vector3r localP1 = state1->ori.conjugate()*tempP1; Real x = localP1.x(); Real y = localP1.y(); Real z = localP1.z(); int planeNo = s1->a.size(); Real r = s1->r; int insideCount = 0; for (int i=0; ia[i]*x + s1->b[i]*y + s1->c[i]*z - s1->d[i]-1.0002*r; //-pow(10,-10); if (Mathr::Sign(plane)*1.0<0.0){ insideCount++; } } /* Complete potential particle */ Real f = 1.0; if (insideCount == planeNo){ f = -1.0;} return f; } bool RockBolt::installBolts(const PotentialBlock* s1,const State* state1,const Vector3r startingPt,const Vector3r direction, const double length, Vector3r& intersectionPt){ Vector3r endPt = startingPt + length*direction; // PotentialBlock *s1=static_cast(cm1.get()); int planeNoA = s1->a.size(); /* line equality */ // x = x0 + t*dirX // y = y0 + t*dirY // z = z0 + t*dirZ /* linear inequality for blocks */ // Ax - d < 0 /* Variables to keep things neat */ int NUMCON = 3 /* equality */ + planeNoA /*block inequality */; int NUMVAR = 3/*3D */ + 1 /*t */+ 1 /* s */; double s = 0.0; bool converge = true; Matrix3r Q1 = (state1->ori.conjugate()).toRotationMatrix(); Eigen::MatrixXd A1 = Eigen::MatrixXd::Zero(planeNoA,3); for (int i=0; i < planeNoA; i++){ A1(i,0) = s1->a[i]; A1(i,1) = s1->b[i]; A1(i,2) = s1->c[i]; } Eigen::MatrixXd AQ1 = A1*Q1; Eigen::MatrixXd pos1(3,1); pos1(0,0) = state1->pos.x(); pos1(1,0) = state1->pos.y(); pos1(2,0) = state1->pos.z(); Eigen::MatrixXd Q1pos1 = AQ1*pos1; ClpSimplex model2; model2.setOptimizationDirection(1); // Create space for 3 columns and 10000 rows int numberRows = NUMCON; int numberColumns = NUMVAR; // This is fully dense - but would not normally be so // Arrays will be set to default values model2.resize(0, numberColumns); model2.setObjectiveCoefficient(0,0.0); model2.setObjectiveCoefficient(1,0.0); model2.setObjectiveCoefficient(2,0.0); model2.setObjectiveCoefficient(3,0.0); model2.setObjectiveCoefficient(4,1.0); for (int k = 0; k < 3; k++){ model2.setColumnLower(k,-COIN_DBL_MAX); model2.setColumnUpper(k,COIN_DBL_MAX); } model2.setColumnLower(3,openingRad); model2.setColumnUpper(3,length); model2.setColumnLower(4,-COIN_DBL_MAX); model2.setColumnUpper(4,COIN_DBL_MAX); // Rows double rowLower[numberRows]; double rowUpper[numberRows]; rowLower[0] = startingPt.x(); rowLower[1] = startingPt.y(); rowLower[2] = startingPt.z(); rowUpper[0] = startingPt.x(); rowUpper[1] = startingPt.y(); rowUpper[2] = startingPt.z(); for (int k = 0; k < planeNoA; k++){ rowLower[3+k]= -COIN_DBL_MAX; rowUpper[3+k] = s1->d[k] + s1->r + Q1pos1(k,0); } int row1Index[] = {0,3}; double row1Value[] = {1.0, -1.0*direction.x()}; model2.addRow(2,row1Index,row1Value,rowLower[0],rowUpper[0]); int row2Index[] = {1,3}; double row2Value[] = {1.0, -1.0*direction.y()}; model2.addRow(2,row2Index,row2Value,rowLower[1],rowUpper[1]); int row3Index[] = {2,3}; double row3Value[] = {1.0, -1.0*direction.z()}; model2.addRow(2,row3Index,row3Value,rowLower[2],rowUpper[2]); for (int i=0; iori.conjugate()*(temp-state1->pos); s = columnPrimal[4]; int convergeSuccess = model2.status(); if(s>-pow(10,-8) || convergeSuccess !=0){ return false; }else{ return true; } } bool RockBolt::intersectPlane(const PotentialBlock* s1,const State* state1,const Vector3r startingPt,const Vector3r direction, const double length, Vector3r& intersectionPt, const Vector3r plane, const double planeD){ bool feasible = true; Vector3r endPt = startingPt + length*direction; // PotentialBlock *s1=static_cast(cm1.get()); int planeNoA = s1->a.size(); /* Variables to keep things neat */ int NUMCON = 3 /* equality */ + 1 /*planeEquality */; int NUMVAR = 3/*3D */ + 1 /*t */; double t = 0.0; bool converge = true; /* line equality */ // x = x0 + t*dirX // y = y0 + t*dirY // z = z0 + t*dirZ /* linear equality for blocks */ // Ax - d = 0 /* LINEAR CONSTRAINTS */ ClpSimplex model2; model2.setOptimizationDirection(1); // Create space for 3 columns and 10000 rows int numberRows = NUMCON; int numberColumns = NUMVAR; // This is fully dense - but would not normally be so // Arrays will be set to default values model2.resize(0, numberColumns); model2.setObjectiveCoefficient(0,0.0); model2.setObjectiveCoefficient(1,0.0); model2.setObjectiveCoefficient(2,0.0); model2.setObjectiveCoefficient(3,1.0); for (int k = 0; k < 4; k++){ model2.setColumnLower(k,-COIN_DBL_MAX); model2.setColumnUpper(k,COIN_DBL_MAX); } // Rows double rowLower[numberRows]; double rowUpper[numberRows]; rowLower[0] = startingPt.x(); rowLower[1] = startingPt.y(); rowLower[2] = startingPt.z(); rowLower[3] = planeD; rowUpper[0] = startingPt.x(); rowUpper[1] = startingPt.y(); rowUpper[2] = startingPt.z(); rowUpper[3] = planeD; int row1Index[] = {0,3}; double row1Value[] = {1.0, -1.0*direction.x()}; model2.addRow(2,row1Index,row1Value,rowLower[0],rowUpper[0]); int row2Index[] = {1,3}; double row2Value[] = {1.0, -1.0*direction.y()}; model2.addRow(2,row2Index,row2Value,rowLower[1],rowUpper[1]); int row3Index[] = {2,3}; double row3Value[] = {1.0, -1.0*direction.z()}; model2.addRow(2,row3Index,row3Value,rowLower[2],rowUpper[2]); int row4Index[] = {0,1,2}; double row4Value[] = {plane.x(),plane.y(),plane.z()}; model2.addRow(3,row4Index,row4Value,rowLower[3],rowUpper[3]); model2.scaling(0); model2.setLogLevel(0); model2.primal(); double * columnPrimal = model2.primalColumnSolution(); Vector3r temp = Vector3r(columnPrimal[0],columnPrimal[1],columnPrimal[2]); intersectionPt = temp; //state1->ori.conjugate()*(temp-state1->pos); t = columnPrimal[3]; double f = evaluateFNoSphereVol(s1,state1,intersectionPt); //std::cout<<"t: "<1.001*length || t< 0.0 || f> 0.0|| convergeSuccess !=0){ return false; }else{ return true; } } YADE_PLUGIN((RockBolt)); #endif // YADE_POTENTIAL_BLOCKS trunk-2017.01a/pkg/dem/RockBolt.hpp000077500000000000000000000105651304022710500167520ustar00rootroot00000000000000/*CWBoon 2016 */ /* Please cite: */ /* CW Boon, GT Houlsby, S Utili (2015). Designing Tunnel Support in Jointed Rock Masses Via the DEM. Rock Mechanics and Rock Engineering, 48 (2), 603-632. */ #ifdef YADE_POTENTIAL_BLOCKS #pragma once #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include //#include "/home/boon/coin-Clp/Clp/src/ClpSimplex.hpp" //#include "/home/boon/coin-Clp/CoinUtils/src/CoinHelperFunctions.hpp" //#include "/home/boon/coin-Clp/CoinUtils/src/CoinTime.hpp" //#include "/home/boon/coin-Clp/CoinUtils/src/CoinBuild.hpp" //#include "/home/boon/coin-Clp/CoinUtils/src/CoinModel.hpp" class RockBolt: public PeriodicEngine{ public: #if 0 struct Bolts{ Bolts(Vector3r pt1, Vector3r pt2){startingPoint = pt1; endPoint=pt2; } Vector3r startingPoint; Vector3r endPoint; /* variables stored in sequence starting from the block closest to the opening */ vector blockIDs; /*blocks intersected */ vector localCoordinates; /*local coordinates inside blocks */ vector initialLength; }; vector bolt; #endif Vector3r getNodeDistance(const PotentialBlock* cm1,const State* state1,const PotentialBlock* cm2,const State* state2, const Vector3r localPt1, const Vector3r localPt2); bool installBolts(const PotentialBlock* cm1,const State* state1,const Vector3r startingPt,const Vector3r direction, const double length, Vector3r& intersectionPt); double evaluateFNoSphereVol(const PotentialBlock* s1,const State* state1, const Vector3r newTrial); bool intersectPlane(const PotentialBlock* s1,const State* state1,const Vector3r startingPt,const Vector3r direction, const double length, Vector3r& intersectionPt, const Vector3r plane, const double planeD); virtual void action(void); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(RockBolt,PeriodicEngine,"Engine recording potential blocks as surfaces into files with given periodicity.", ((double,normalStiffness,0.0 ,,"EA/L")) ((double,shearStiffness,0.0 ,,"stiffness")) ((double,axialStiffness,0.0 ,,"EA")) ((bool,useMidPoint,false ,,"large length")) ((double,halfActiveLength,0.02 ,,"stiffness")) ((bool,resetLengthInit,false ,,"reset length for pretension")) ((Vector3r,startingPoint,Vector3r(0,0,0) ,,"startingPt")) ((double,boltLength,0.0 ,,"startingPt")) ((Vector3r,boltDirection,Vector3r(0,0,0) ,,"direction")) ((vector,blockIDs, ,,"ids")) ((double,displacements, ,,"ids")) ((vector,localCoordinates, ,,"local coordinates of intersection")) ((vector,initialLength, ,,"initial length")) ((vector,initialDirection, ,,"initial length")) ((vector,nodeDistanceVec, ,,"nodeDistance")) ((vector,nodePosition, ,,"nodePosition")) ((vector,distanceFrCentre, ,,"nodePosition")) ((vector,forces, ,,"force")) ((vector,axialForces, ,,"force")) ((vector,shearForces, ,,"force")) ((double,openingRad,5.0 ,,"estimated opening radius")) ((double,preTension,0.0 ,,"prestressed tension")) ((double,averageForce,0.0 ,,"averageForce")) ((double,maxForce,0.0 ,,"maxForce")) ((bool,installed,false ,,"installed?")) ((bool,openingCreated,false ,,"opening created?")) ((vector,ruptured, ,,"ruptured")) ((Real,axialMax,1000000000 ,,"maximum axial force")) ((Real,shearMax,1000000000 ,,"maximum shear force")) ((int,vtkIteratorInterval,10000 ,,"how often to print vtk")) ((int,vtkRefTimeStep,1 ,,"first timestep to print vtk")) ((string,fileName,,,"File prefix to save to")) ((string,name,,,"File prefix to save to")) , , ); }; REGISTER_SERIALIZABLE(RockBolt); #endif // YADE_POTENTIAL_BLOCKS trunk-2017.01a/pkg/dem/RockLiningGlobal.cpp000077500000000000000000000662571304022710500204170ustar00rootroot00000000000000/*CWBoon 2016 */ /* Please cite: */ /* CW Boon, GT Houlsby, S Utili (2015). Designing Tunnel Support in Jointed Rock Masses Via the DEM. Rock Mechanics and Rock Engineering, 48 (2), 603-632. */ #ifdef YADE_POTENTIAL_BLOCKS #include "RockLiningGlobal.hpp" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include void RockLiningGlobal::action(){ const double PI = 3.14159; if (openingCreated == true && installed == false){ double angleInterval = 2.0*PI/static_cast(totalNodes); for (int n=0; n distanceFrOpening; vector IDs; double outerRadius = openingRad + 1.0; FOREACH(const shared_ptr& b, *scene->bodies){ if (!b) continue; if (b->isClump() == true) continue; PotentialBlock* pb=static_cast(b->shape.get()); if(!pb) continue; if(pb->isBoundary == true || pb->erase== true || pb->isLining==true){continue;} State* state1 = b->state.get(); Vector3r intersectionPt(0,0,0); if ( installLining(pb, state1, startingPoint, searchDir, outerRadius, intersectionPt )){ IDs.push_back(b->id); distanceFrOpening.push_back((intersectionPt-startingPoint).norm()); //std::cout<<"currentAngle: "<id: "<id<<", dist: "<<(intersectionPt-startingPoint).norm()<state.get(); Shape* shape1 = Body::byId(closestID,scene)->shape.get(); PotentialBlock *pb=static_cast(shape1); int totalPlanes = pb->a.size(); int intersectNo = 0; Vector3r nodeLocalPos(0,0,0); Vector3r nodeGlobalPos(0,0,0); //std::cout<<"totalPlanes: "<ori*Vector3r(pb->a[i], pb->b[i], pb->c[i]); double planeD = plane.dot(state1->pos) + pb->d[i] +pb->r; if ( intersectPlane(pb, state1,startingPoint,searchDir, outerRadius, jointIntersection, plane, planeD)){ double distance = jointIntersection.norm(); if (distance < closestPlaneDist){ closestPlaneDist = distance; nodeLocalPos = state1->ori.conjugate()*(jointIntersection-state1->pos); nodeGlobalPos=jointIntersection; } } } if(nodeGlobalPos.norm() > 1.03*openingRad){ nodeGlobalPos=1.03*openingRad*searchDir;} //if(nodeGlobalPos.norm() < 0.98*openingRad){ continue;} //initOverlap = interfaceTension/interfaceStiffness; nodeGlobalPos = nodeGlobalPos + searchDir*initOverlap; localCoordinates.push_back(nodeLocalPos); refPos.push_back(nodeGlobalPos); int nodeID = insertNode(nodeGlobalPos, lumpedMass, contactLength); blockIDs.push_back(nodeID); //(nodeID); //(closestID); refOri.push_back(Quaternionr::Identity()); //(state1->ori); installed = true; axialForces.push_back(0.0); shearForces.push_back(0.0); moment.push_back(0.0); sigmaMax.push_back(0.0); sigmaMin.push_back(0.0); displacement.push_back(0.0); radialDisplacement.push_back(0.0); } totalNodes=blockIDs.size(); /* Assembling global stiffness matrix */ for (int n=0; n=2){ double displacementMatrix[totalNodes*3]; memset(displacementMatrix,0.0,sizeof(displacementMatrix)); //averageForce = 0.0; maxForce = 0.0; int blockNo = blockIDs.size(); for (int j=0; jstate.get(); State* state2 = Body::byId(blockIDs[nextNode],scene)->state.get(); Quaternionr qA = (state1->ori); double thetaA = 2.0 *acos(qA.w()); if(qA.y() < 0.0){ thetaA = -thetaA ; } Quaternionr qB = (state2->ori); double thetaB = 2.0 *acos(qB.w()); if(qB.y() < 0.0){ thetaB = -thetaB ; } double deformedAngle = refAngle[j];// - thetaA; double temperatureForce = expansionFactor*lengthNode[j]*EA; Vector3r tempForceGlobal = Vector3r(temperatureForce*cos(refAngle[j] ) , 0.0,-temperatureForce*sin(refAngle[j] ) ) ; //Ttranspose Vector3r globalDispA = state1->pos - refPos[j]; double localXa = globalDispA.x()*cos(deformedAngle) + globalDispA.z()*sin(deformedAngle); double localYa = -globalDispA.x()*sin(deformedAngle) + globalDispA.z()*cos(deformedAngle); Vector3r globalDispB = state2->pos - refPos[nextNode]; double localXb = globalDispB.x()*cos(deformedAngle) + globalDispB.z()*sin(deformedAngle); double localYb = -globalDispB.x()*sin(deformedAngle) + globalDispB.z()*cos(deformedAngle); axialForces[j] = EA/lengthNode[j] * (localXa-localXb); shearForces[j] = 12.0*EI/(pow(lengthNode[j],3))*(localYa-localYb) - 6.0*EI/(pow(lengthNode[j],2))*(thetaA+thetaB); moment[j] = -6.0*EI/(pow(lengthNode[j],2))*(localYa-localYb) + 2.0*EI/lengthNode[j]*(2.0*thetaA+thetaB); double globalForceX = axialForces[j]*cos(deformedAngle) - shearForces[j]*sin(deformedAngle); double globalForceZ = axialForces[j]*sin(deformedAngle) + shearForces[j]*cos(deformedAngle); Vector3r totalForceA = Vector3r(globalForceX, 0.0, globalForceZ); Vector3r torqueA = moment[j]*Vector3r(0,1,0); double axialForcesB = EA/lengthNode[j] * (localXb-localXa); double shearForcesB = -12.0*EI/(pow(lengthNode[j],3))*(localYa-localYb) + 6.0*EI/(pow(lengthNode[j],2))*(thetaA+thetaB); double momentB = -6.0*EI/(pow(lengthNode[j],2))*(localYa-localYb) + 2.0*EI/lengthNode[j]*(thetaA+2.0*thetaB); double globalForceXb = axialForcesB*cos(deformedAngle) - shearForcesB*sin(deformedAngle); double globalForceZb = axialForcesB*sin(deformedAngle) + shearForcesB*cos(deformedAngle); Vector3r totalForceB = Vector3r(globalForceXb, 0.0, globalForceZb); Vector3r torqueB = momentB*Vector3r(0,1,0); double area = liningThickness*1.0; sigmaMax[j] = axialForces[j]/area + fabs(moment[j])*(2.0*liningThickness)/Inertia; sigmaMin[j] = axialForces[j]/area - fabs(moment[j])*(2.0*liningThickness)/Inertia; double displacementSign = (state1->pos - refPos[j]).dot(refPos[j]); displacement[j] = Mathr::Sign(displacementSign)*(state1->pos - refPos[j]).norm(); Vector3r dir = refPos[j]; dir.normalize(); radialDisplacement[j] = (state1->pos-refPos[j]).dot(dir); scene->forces.addTorque(blockIDs[j],-torqueA); scene->forces.addForce(blockIDs[j],-totalForceA); scene->forces.addTorque(blockIDs[nextNode],-torqueB); scene->forces.addForce(blockIDs[nextNode],-totalForceB); } //std::cout<<"end of rock llining global"<iter-vtkRefTimeStep)%vtkIteratorInterval == 0 && installed == true && blockIDs.size()>=2){ vtkRefTimeStep = scene->iter; vtkSmartPointer appendFilter = vtkSmartPointer::New(); int blockNo = blockIDs.size(); /// lining FORCE // vtkSmartPointer liningNode = vtkSmartPointer::New(); vtkSmartPointer liningNodeCells = vtkSmartPointer::New(); vtkSmartPointer liningNodalMoment = vtkSmartPointer::New(); liningNodalMoment->SetNumberOfComponents(3); liningNodalMoment->SetName("lining Moment"); //Linear velocity in Vector3 form vtkSmartPointer liningAxialForce = vtkSmartPointer::New(); liningAxialForce->SetNumberOfComponents(3); liningAxialForce->SetName("AxialForce"); //Linear velocity in Vector3 form vtkSmartPointer liningShearForce = vtkSmartPointer::New(); liningShearForce->SetNumberOfComponents(3); liningShearForce->SetName("Shear Force"); //Linear velocity in Vector3 form //#if 0 for (int i=0; i state.get(); State* state2 = Body::byId(blockIDs[nextID],scene)->state.get(); Vector3r globalPoint1 = state1->pos+state1->ori*localCoordinates[i]; Vector3r globalPoint2 = state2->pos+state2->ori*localCoordinates[nextID]; vtkSmartPointer lineSource = vtkSmartPointer::New(); double p0[3] = {globalPoint1[0], globalPoint1[1], globalPoint1[2]}; double p1[3] = {globalPoint2[0], globalPoint2[1], globalPoint2[2]}; lineSource->SetPoint1(p0); lineSource->SetPoint2(p1); appendFilter->AddInputConnection(lineSource-> GetOutputPort()); //#if 0 /* try to draw forces */ vtkIdType pid[1]; Vector3r midPoint = 0.5*(globalPoint1+globalPoint2); pid[0] = liningNode->InsertNextPoint( midPoint[0], midPoint[1], midPoint[2]); liningNodeCells->InsertNextCell(1,pid); Vector3r plotDirection = -midPoint; //local z-direction is pointing into the tunnel (positive), and clockwise moment is positive (outer lining is subject to compression) plotDirection.normalize(); Vector3r nodalMoment = moment[i]*plotDirection; float m[3]={nodalMoment[0],nodalMoment[1],nodalMoment[2]}; Vector3r axialForce = axialForces[i]*plotDirection; //axialForce tension is negative (plotdirection is pointing inwards), tension is pointing outwards float fa[3]={axialForce[0],axialForce[1],axialForce[2]}; Vector3r shearForce = shearForces[i]*plotDirection; float fs[3]={shearForce[0],shearForce[1],shearForce[2]}; //#endif if(blockIDs[i] == blockIDs[nextID] ){ m={0,0,0}; fa = {0,0,0}; fs = {0,0,0}; } if (Body::byId(blockIDs[i],scene)->isClumpMember()==true && Body::byId(blockIDs[nextID],scene)->isClumpMember()==true ){ if (Body::byId(blockIDs[i],scene)->clumpId == Body::byId(blockIDs[nextID],scene)->clumpId){ m={0,0,0}; fa = {0,0,0}; fs = {0,0,0}; } } liningNodalMoment->InsertNextTupleValue(m); liningAxialForce->InsertNextTupleValue(fa); liningShearForce->InsertNextTupleValue(fs); //lineSource->Update(); } //#endif //#if 0 vtkSmartPointer pbUgCP = vtkSmartPointer::New(); pbUgCP->SetPoints(liningNode); pbUgCP->SetCells(VTK_VERTEX, liningNodeCells); pbUgCP->GetPointData()->AddArray(liningNodalMoment); pbUgCP->GetPointData()->AddArray(liningAxialForce); pbUgCP->GetPointData()->AddArray(liningShearForce); vtkSmartPointer writerB = vtkSmartPointer::New(); writerB->SetDataModeToAscii(); string filelining=fileName+"liningNodeForce"+name+"."+std::to_string(scene->iter)+".vtu"; writerB->SetFileName(filelining.c_str()); writerB->SetInput(pbUgCP); writerB->Write(); vtkSmartPointer writer = vtkXMLPolyDataWriter::New(); writer->SetDataModeToAscii(); string fn=fileName+"-lining"+name+"."+std::to_string(scene->iter)+".vtp"; writer->SetFileName(fn.c_str()); writer->SetInputConnection(appendFilter->GetOutputPort()); writer->Write(); //#endif } #endif //#if 0 if ((scene->iter-vtkRefTimeStep)%vtkIteratorInterval == 0 && installed == true && blockIDs.size()>=2){ vtkRefTimeStep = scene->iter; vtkSmartPointer appendFilter = vtkSmartPointer::New(); int blockNo = blockIDs.size(); /// lining FORCE // vtkSmartPointer liningNode = vtkSmartPointer::New(); vtkSmartPointer liningNodeCells = vtkSmartPointer::New(); vtkSmartPointer liningNodalMoment = vtkSmartPointer::New(); liningNodalMoment->SetNumberOfComponents(3); liningNodalMoment->SetName("lining Moment"); //Linear velocity in Vector3 form vtkSmartPointer liningAxialForce = vtkSmartPointer::New(); liningAxialForce->SetNumberOfComponents(3); liningAxialForce->SetName("AxialForce"); //Linear velocity in Vector3 form vtkSmartPointer liningShearForce = vtkSmartPointer::New(); liningShearForce->SetNumberOfComponents(3); liningShearForce->SetName("Shear Force"); //Linear velocity in Vector3 form vtkSmartPointer liningNormalPressure = vtkSmartPointer::New(); liningNormalPressure->SetNumberOfComponents(3); liningNormalPressure->SetName("Normal Pressure"); //Linear velocity in Vector3 form vtkSmartPointer liningNormalPressureIdeal = vtkSmartPointer::New(); liningNormalPressureIdeal->SetNumberOfComponents(3); liningNormalPressureIdeal->SetName("Normal Pressure Magnitude"); vtkSmartPointer liningTotalPressure = vtkSmartPointer::New(); liningTotalPressure->SetNumberOfComponents(3); liningTotalPressure->SetName("Total Pressure"); //Linear velocity in Vector3 form //#if 0 for (int i=0; i state.get(); State* state2 = Body::byId(blockIDs[nextID],scene)->state.get(); PotentialBlock* pb=static_cast(Body::byId(blockIDs[i],scene)->shape.get()); Vector3r globalPoint1 = state1->pos; Vector3r globalPoint2 = state2->pos; vtkSmartPointer lineSource = vtkSmartPointer::New(); double p0[3] = {globalPoint1[0], globalPoint1[1], globalPoint1[2]}; double p1[3] = {globalPoint2[0], globalPoint2[1], globalPoint2[2]}; lineSource->SetPoint1(p0); lineSource->SetPoint2(p1); appendFilter->AddInputConnection(lineSource-> GetOutputPort()); //#if 0 /* try to draw forces */ vtkIdType pid[1]; Vector3r midPoint = globalPoint1; // 0.5*(globalPoint1+globalPoint2); pid[0] = liningNode->InsertNextPoint( midPoint[0], midPoint[1], midPoint[2]); liningNodeCells->InsertNextCell(1,pid); Vector3r plotDirection = midPoint; plotDirection.normalize(); Vector3r nodalMoment = moment[i]*plotDirection; float m[3]={nodalMoment[0],nodalMoment[1],nodalMoment[2]}; liningNodalMoment->InsertNextTupleValue(m); Vector3r axialForce = -axialForces[i]*plotDirection; float fa[3]={axialForce[0],axialForce[1],axialForce[2]}; liningAxialForce->InsertNextTupleValue(fa); Vector3r shearForce = shearForces[i]*plotDirection; float fs[3]={shearForce[0],shearForce[1],shearForce[2]}; liningShearForce->InsertNextTupleValue(fs); Vector3r normalP = pb->liningNormalPressure; Vector3r totalP = pb->liningTotalPressure; float pN[3] = {normalP[0], normalP[1],normalP[2]}; float pT[3] = {totalP[0], totalP[1], totalP[2]}; liningNormalPressure->InsertNextTupleValue(pN); liningTotalPressure->InsertNextTupleValue(pT); Vector3r normalPideal=-1.0*(normalP.norm())*plotDirection; float pNi[3] = {normalPideal[0], normalPideal[1],normalPideal[2]}; liningNormalPressureIdeal->InsertNextTupleValue(pNi); //#endif //lineSource->Update(); } //#endif //#if 0 vtkSmartPointer pbUgCP = vtkSmartPointer::New(); pbUgCP->SetPoints(liningNode); pbUgCP->SetCells(VTK_VERTEX, liningNodeCells); pbUgCP->GetPointData()->AddArray(liningNodalMoment); pbUgCP->GetPointData()->AddArray(liningAxialForce); pbUgCP->GetPointData()->AddArray(liningShearForce); pbUgCP->GetPointData()->AddArray(liningNormalPressure); pbUgCP->GetPointData()->AddArray(liningNormalPressureIdeal); pbUgCP->GetPointData()->AddArray(liningTotalPressure); vtkSmartPointer writerB = vtkSmartPointer::New(); writerB->SetDataModeToAscii(); string filelining=fileName+"liningNodeForce"+name+"."+std::to_string(scene->iter)+".vtu"; writerB->SetFileName(filelining.c_str()); writerB->SetInputData(pbUgCP); writerB->Write(); vtkSmartPointer writer = vtkXMLPolyDataWriter::New(); writer->SetDataModeToAscii(); string fn=fileName+"-lining"+name+"."+std::to_string(scene->iter)+".vtp"; writer->SetFileName(fn.c_str()); writer->SetInputConnection(appendFilter->GetOutputPort()); writer->Write(); //#endif } //#endif } int RockLiningGlobal::insertNode(Vector3r pos, double mass, double intervalLength){ shared_ptr& bodies = scene->bodies; //std::cout<<"pos: "< body(new Body()); /* new body */ shared_ptr pBlock(new PotentialBlock); shared_ptr aabb(new Aabb); shared_ptr mat(new FrictMat); pBlock->isLining = true; /* Shape object, variables not added: node, gridVol,vertices */ pBlock->AabbMinMax = false; pBlock->R = 1.0; pBlock->liningLength = intervalLength; pBlock->liningStiffness = interfaceStiffness; pBlock->liningFriction = interfaceFriction; pBlock->cohesion.push_back(interfaceCohesion); pBlock->tension.push_back(interfaceTension); pBlock->liningTensionGap = interfaceTension/interfaceStiffness; const int body_size= bodies->size(); int newID = body_size; pBlock->id = newID; aabb->color = Vector3r(0,1,0); body->state->ori = Quaternionr::Identity(); body->state->pos = pos; mat->frictionAngle = interfaceFriction/180.0*3.14159; body->setDynamic(true); body->state->mass = mass; body->state->inertia = 1.0/12.0*body->state->mass*(liningThickness*liningThickness + intervalLength*intervalLength)*Vector3r(1,1,1); //std::cout<<"mass: "<state->inertia<shape = pBlock; body->bound = aabb; body->material = mat; // std::cout<<"pos: "<insert(body); //std::cout<<"after insert"<ori*localPt1 + state1->pos; Vector3r global2 = state2->ori*localPt2 + state2->pos; return (global2-global1); } double RockLiningGlobal::evaluateFNoSphereVol(const PotentialBlock* s1,const State* state1, const Vector3r newTrial){ Vector3r tempP1 = newTrial - state1->pos; /* Direction cosines */ //state1.ori.normalize(); Vector3r localP1 = state1->ori.conjugate()*tempP1; Real x = localP1.x(); Real y = localP1.y(); Real z = localP1.z(); int planeNo = s1->a.size(); Real r = s1->r; int insideCount = 0; for (int i=0; ia[i]*x + s1->b[i]*y + s1->c[i]*z - s1->d[i]-1.0002*r; //-pow(10,-10); if (Mathr::Sign(plane)*1.0<0.0){ insideCount++; } } /* Complete potential particle */ Real f = 1.0; if (insideCount == planeNo){ f = -1.0;} return f; } bool RockLiningGlobal::installLining(const PotentialBlock* s1,const State* state1,const Vector3r startingPt,const Vector3r direction, const double length, Vector3r& intersectionPt){ Vector3r endPt = startingPt + length*direction; // PotentialBlock *s1=static_cast(cm1.get()); int planeNoA = s1->a.size(); /* line equality */ // x = x0 + t*dirX // y = y0 + t*dirY // z = z0 + t*dirZ /* linear inequality for blocks */ // Ax - d < 0 /* Variables to keep things neat */ int NUMCON = 3 /* equality */ + planeNoA /*block inequality */; int NUMVAR = 3/*3D */ + 1 /*t */+ 1 /* s */; double s = 0.0; bool converge = true; Matrix3r Q1 = (state1->ori.conjugate()).toRotationMatrix(); Eigen::MatrixXd A1 = Eigen::MatrixXd::Zero(planeNoA,3); for (int i=0; i < planeNoA; i++){ A1(i,0) = s1->a[i]; A1(i,1) = s1->b[i]; A1(i,2) = s1->c[i]; } Eigen::MatrixXd AQ1 = A1*Q1; Eigen::MatrixXd pos1(3,1); pos1(0,0) = state1->pos.x(); pos1(1,0) = state1->pos.y(); pos1(2,0) = state1->pos.z(); Eigen::MatrixXd Q1pos1 = AQ1*pos1; ClpSimplex model2; model2.setOptimizationDirection(1); // Create space for 3 columns and 10000 rows int numberRows = NUMCON; int numberColumns = NUMVAR; // This is fully dense - but would not normally be so // Arrays will be set to default values model2.resize(0, numberColumns); model2.setObjectiveCoefficient(0,0.0); model2.setObjectiveCoefficient(1,0.0); model2.setObjectiveCoefficient(2,0.0); model2.setObjectiveCoefficient(3,0.0); model2.setObjectiveCoefficient(4,1.0); for (int k = 0; k < 3; k++){ model2.setColumnLower(k,-COIN_DBL_MAX); model2.setColumnUpper(k,COIN_DBL_MAX); } model2.setColumnLower(3,openingRad); model2.setColumnUpper(3,length); model2.setColumnLower(4,-COIN_DBL_MAX); model2.setColumnUpper(4,COIN_DBL_MAX); // Rows double rowLower[numberRows]; double rowUpper[numberRows]; rowLower[0] = startingPt.x(); rowLower[1] = startingPt.y(); rowLower[2] = startingPt.z(); rowUpper[0] = startingPt.x(); rowUpper[1] = startingPt.y(); rowUpper[2] = startingPt.z(); for (int k = 0; k < planeNoA; k++){ rowLower[3+k]= -COIN_DBL_MAX; rowUpper[3+k] = s1->d[k] + s1->r + Q1pos1(k,0); } int row1Index[] = {0,3}; double row1Value[] = {1.0, -1.0*direction.x()}; model2.addRow(2,row1Index,row1Value,rowLower[0],rowUpper[0]); int row2Index[] = {1,3}; double row2Value[] = {1.0, -1.0*direction.y()}; model2.addRow(2,row2Index,row2Value,rowLower[1],rowUpper[1]); int row3Index[] = {2,3}; double row3Value[] = {1.0, -1.0*direction.z()}; model2.addRow(2,row3Index,row3Value,rowLower[2],rowUpper[2]); for (int i=0; iori.conjugate()*(temp-state1->pos); s = columnPrimal[4]; int convergeSuccess = model2.status(); if(s>-pow(10,-8) || convergeSuccess !=0){ return false; }else{ return true; } } bool RockLiningGlobal::intersectPlane(const PotentialBlock* s1,const State* state1,const Vector3r startingPt,const Vector3r direction, const double length, Vector3r& intersectionPt, const Vector3r plane, const double planeD){ bool feasible = true; Vector3r endPt = startingPt + length*direction; // PotentialBlock *s1=static_cast(cm1.get()); int planeNoA = s1->a.size(); /* Variables to keep things neat */ int NUMCON = 3 /* equality */ + 1 /*planeEquality */; int NUMVAR = 3/*3D */ + 1 /*t */; double t = 0.0; bool converge = true; /* line equality */ // x = x0 + t*dirX // y = y0 + t*dirY // z = z0 + t*dirZ /* linear equality for blocks */ // Ax - d = 0 /* LINEAR CONSTRAINTS */ ClpSimplex model2; model2.setOptimizationDirection(1); // Create space for 3 columns and 10000 rows int numberRows = NUMCON; int numberColumns = NUMVAR; // This is fully dense - but would not normally be so // Arrays will be set to default values model2.resize(0, numberColumns); model2.setObjectiveCoefficient(0,0.0); model2.setObjectiveCoefficient(1,0.0); model2.setObjectiveCoefficient(2,0.0); model2.setObjectiveCoefficient(3,1.0); for (int k = 0; k < 4; k++){ model2.setColumnLower(k,-COIN_DBL_MAX); model2.setColumnUpper(k,COIN_DBL_MAX); } // Rows double rowLower[numberRows]; double rowUpper[numberRows]; rowLower[0] = startingPt.x(); rowLower[1] = startingPt.y(); rowLower[2] = startingPt.z(); rowLower[3] = planeD; rowUpper[0] = startingPt.x(); rowUpper[1] = startingPt.y(); rowUpper[2] = startingPt.z(); rowUpper[3] = planeD; int row1Index[] = {0,3}; double row1Value[] = {1.0, -1.0*direction.x()}; model2.addRow(2,row1Index,row1Value,rowLower[0],rowUpper[0]); int row2Index[] = {1,3}; double row2Value[] = {1.0, -1.0*direction.y()}; model2.addRow(2,row2Index,row2Value,rowLower[1],rowUpper[1]); int row3Index[] = {2,3}; double row3Value[] = {1.0, -1.0*direction.z()}; model2.addRow(2,row3Index,row3Value,rowLower[2],rowUpper[2]); int row4Index[] = {0,1,2}; double row4Value[] = {plane.x(),plane.y(),plane.z()}; model2.addRow(3,row4Index,row4Value,rowLower[3],rowUpper[3]); model2.scaling(0); model2.setLogLevel(0); model2.primal(); double * columnPrimal = model2.primalColumnSolution(); Vector3r temp = Vector3r(columnPrimal[0],columnPrimal[1],columnPrimal[2]); intersectionPt = temp; //state1->ori.conjugate()*(temp-state1->pos); t = columnPrimal[3]; int convergeSuccess = model2.status(); double f = evaluateFNoSphereVol(s1,state1,intersectionPt); //std::cout<<"t: "<1.001*length || t< 0.0 || f> 0.0|| convergeSuccess !=0){ return false; }else{ return true; } } YADE_PLUGIN((RockLiningGlobal)); #endif // YADE_POTENTIAL_BLOCKS trunk-2017.01a/pkg/dem/RockLiningGlobal.hpp000077500000000000000000000153201304022710500204050ustar00rootroot00000000000000/*CWBoon 2016 */ /* Please cite: */ /* CW Boon, GT Houlsby, S Utili (2015). Designing Tunnel Support in Jointed Rock Masses Via the DEM. Rock Mechanics and Rock Engineering, 48 (2), 603-632. */ #ifdef YADE_POTENTIAL_BLOCKS #pragma once #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include //#include "/home/boon/coin-Clp/Clp/src/ClpSimplex.hpp" //#include "/home/boon/coin-Clp/CoinUtils/src/CoinHelperFunctions.hpp" //#include "/home/boon/coin-Clp/CoinUtils/src/CoinTime.hpp" //#include "/home/boon/coin-Clp/CoinUtils/src/CoinBuild.hpp" //#include "/home/boon/coin-Clp/CoinUtils/src/CoinModel.hpp" class RockLiningGlobal: public PeriodicEngine{ protected: double stiffnessMatrix[36]; //double * globalStiffnessMatrix; double globalStiffnessMatrix[3*3*200*200]; public: #if 0 struct Bolts{ Bolts(Vector3r pt1, Vector3r pt2){startingPoint = pt1; endPoint=pt2; } Vector3r startingPoint; Vector3r endPoint; /* variables stored in sequence starting from the block closest to the opening */ vector blockIDs; /*blocks intersected */ vector localCoordinates; /*local coordinates inside blocks */ vector initialLength; }; vector bolt; #endif Vector3r getNodeDistance(const PotentialBlock* cm1,const State* state1,const PotentialBlock* cm2,const State* state2, const Vector3r localPt1, const Vector3r localPt2); bool installLining(const PotentialBlock* cm1,const State* state1,const Vector3r startingPt,const Vector3r direction, const double length, Vector3r& intersectionPt); int insertNode(Vector3r pos, double mass, double intervalLength); double evaluateFNoSphereVol(const PotentialBlock* s1,const State* state1, const Vector3r newTrial); bool intersectPlane(const PotentialBlock* s1,const State* state1,const Vector3r startingPt,const Vector3r direction, const double length, Vector3r& intersectionPt, const Vector3r plane, const double planeD); virtual void action(void); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(RockLiningGlobal,PeriodicEngine,"Engine recording potential blocks as surfaces into files with given periodicity.", ((bool,assembledKglobal,false ,,"global stiffness matrix")) ((double,density,0.0 ,,"density")) ((double,lumpedMass,0.0 ,,"lumpedMass")) ((double,EA,0.0 ,,"EA")) ((double,EI,0.0 ,,"EI")) ((double,initOverlap,pow(10,-5),,"initialOverlap")) ((double,expansionFactor,pow(10,-5),,"alpha deltaT")) ((double,contactLength,1.0 ,,"contactLength")) ((vector, sigmaMax, ,,"sigma max")) ((vector, sigmaMin, ,,"sigma min")) ((double,ElasticModulus,0.0 ,,"E")) ((double,liningThickness,0.1 ,,"liningThickness")) ((double,Inertia,0.0 ,,"I")) ((vector,lengthNode, ,,"L")) ((vector,stickIDs, ,,"L")) ((double,Area,0.02 ,,"A")) ((double,interfaceStiffness,pow(10,8) ,,"L")) ((double,interfaceFriction,30.0 ,,"L")) ((double,interfaceCohesion,0.5*pow(10,6) ,,"L")) ((double,interfaceTension,0.8*pow(10,6) ,,"L")) ((int,totalNodes,0 ,,"L")) ((Vector3r,startingPoint,Vector3r(0,0,0) ,,"startingPt")) ((vector,blockIDs, ,,"ids")) ((vector,localCoordinates, ,,"local coordinates of intersection")) ((vector,refPos, ,,"initial u")) ((vector,refDir, ,,"initial v")) ((vector,refOri, ,,"initial theta")) ((vector,refAngle, ,,"initial theta")) ((vector,moment, ,,"moment")) ((vector,axialForces, ,,"force")) ((vector,shearForces, ,,"force")) ((vector,displacement, ,,"force")) ((vector,radialDisplacement, ,,"force")) ((double,openingRad,5.0 ,,"estimated opening radius")) ((bool,installed,false ,,"installed?")) ((bool,openingCreated,false ,,"opening created?")) ((vector,ruptured, ,,"ruptured")) ((Real,axialMax,1000000000 ,,"maximum axial force")) ((Real,shearMax,1000000000 ,,"maximum shear force")) ((int,vtkIteratorInterval,10000 ,,"how often to print vtk")) ((int,vtkRefTimeStep,1 ,,"first timestep to print vtk")) ((string,fileName,,,"File prefix to save to")) ((string,name,,,"File prefix to save to")) , //globalStiffnessMatrix = new double[totalNodes*3*totalNodes*3]; , ); }; REGISTER_SERIALIZABLE(RockLiningGlobal); #ifdef __cplusplus extern "C" { #endif /* LAPACK LU */ //int dgesv(int varNo, int varNo2, double *H, int varNo3, int *pivot, double* g, int varNo4, int info){ extern void dgesv_(const int *N, const int *nrhs, double *Hessian, const int *lda, int *ipiv, double *gradient, const int *ldb, int *info); // int ans; // dgesv_(&varNo, &varNo2, H, &varNo3, pivot,g, &varNo4, &ans); // return ans; //} /* LAPACK Cholesky */ extern void dpbsv_(const char *uplo, const int *n, const int *kd, const int *nrhs, double *AB, const int *ldab, double *B, const int *ldb, int *info); /* LAPACK QR */ extern void dgels_(const char *Trans, const int *m, const int *n, const int *nrhs, double *A, const int *lda, double *B, const int *ldb, const double *work, const int *lwork, int *info); /*BLAS */ extern void dgemm_(const char *transA, const char *transB, const int *m, const int *n, const int *k, const double *alpha, double *A, const int *lda, double *B, const int *ldb, const double *beta, double *C, const int *ldc); extern void dgemv_(const char *trans, const int *m, const int *n, const double *alpha, double *A, const int *lda, double *x, const int *incx, const double *beta, double *y, const int *incy); extern void dcopy_(const int *N, double *x, const int *incx, double *y, const int *incy); extern double ddot_(const int *N, double *x, const int *incx, double *y, const int *incy); extern void daxpy_(const int *N, const double *da, double *dx, const int *incx, double *dy, const int *incy); extern void dscal_(const int *N, const double *alpha, double *x, const int *incx); void dsyev_(const char *jobz, const char *uplo, const int *N, double *A, const int *lda, double *W, double *work, int *lwork, int *info); #ifdef __cplusplus }; #endif #endif // YADE_POTENTIAL_BLOCKS trunk-2017.01a/pkg/dem/RungeKuttaCashKarp54Integrator.cpp000066400000000000000000000024221304022710500231320ustar00rootroot00000000000000#ifdef YADE_ODEINT #include #include YADE_PLUGIN((RungeKuttaCashKarp54Integrator)); shared_ptr RungeKuttaCashKarp54Integrator_ctor_list(const boost::python::list& slaves){ shared_ptr instance(new RungeKuttaCashKarp54Integrator); instance->slaves_set(slaves); return instance; } void RungeKuttaCashKarp54Integrator::action() { Real dt=scene->dt; Real time=scene->time; error_checker_type rungekuttaerrorcontroller=error_checker_type(abs_err,rel_err,a_x,a_dxdt); controlled_stepper_type rungekuttastepper=controlled_stepper_type(rungekuttaerrorcontroller); stateVector currentstates=getCurrentStates(); resetstate.reserve(currentstates.size()); copy(currentstates.begin(),currentstates.end(),back_inserter(resetstate));//copy current state to resetstate this->timeresetvalue=time; //set reset time to the time just before the integration /*Try an adaptive integration*/ integrationsteps+=integrate_adaptive(rungekuttastepper,make_ode_wrapper( *((Integrator*)this) , &Integrator::system ),currentstates,time,time+dt, stepsize, observer(this)); scene->time=scene->time-dt;//Scene move next time step function already increments the time so we have to decrement it just before it. } #endif trunk-2017.01a/pkg/dem/RungeKuttaCashKarp54Integrator.hpp000066400000000000000000000034711304022710500231440ustar00rootroot00000000000000#ifdef YADE_ODEINT #pragma once #include #include #include typedef boost::numeric::odeint::runge_kutta_cash_karp54< stateVector > error_stepper_type; //Runge-Kutta 54 error stepper other steppers can also be used typedef boost::numeric::odeint::controlled_runge_kutta< error_stepper_type > controlled_stepper_type;//Controlled Runge Kutta stepper typedef boost::numeric::odeint::default_error_checker< error_stepper_type::value_type,error_stepper_type::algebra_type ,error_stepper_type::operations_type > error_checker_type; //Error checker type that is redefined for initialization using different tolerance values shared_ptr RungeKuttaCashKarp54Integrator_ctor_list(const boost::python::list& slaves); class RungeKuttaCashKarp54Integrator: public Integrator { public: error_checker_type rungekuttaerrorcontroller; controlled_stepper_type rungekuttastepper; void init() { rungekuttaerrorcontroller=error_checker_type(abs_err,rel_err,a_x,a_dxdt); rungekuttastepper=controlled_stepper_type(rungekuttaerrorcontroller); } virtual void action(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(RungeKuttaCashKarp54Integrator,Integrator,"RungeKuttaCashKarp54Integrator engine.", ((Real,abs_err,1e-6,,"Relative integration tolerance")) ((Real,rel_err,1e-6,,"Absolute integration tolerance")) ((Real,a_x,1.0,,"")) ((Real,a_dxdt,1.0,,"")) ((Real,stepsize,1e-6,,"It is not important for an adaptive integration but important for the observer for setting the found states after integration")) , /*ctor*/ init(); , .def("__init__",boost::python::make_constructor(RungeKuttaCashKarp54Integrator_ctor_list),"Construct from (possibly nested) list of slaves.") /*py*/ ); }; REGISTER_SERIALIZABLE(RungeKuttaCashKarp54Integrator); #endif trunk-2017.01a/pkg/dem/STLImporter.cpp000066400000000000000000000032561304022710500174060ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2008 by Sergei Dorofeenko * * sega@users.berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include"STLImporter.hpp" #include CREATE_LOGGER(STLImporter); vector > STLImporter::import(const char* filename) { vector tr; vector > imported; // Load geometry vector vtmp, ntmp; vector etmp, ftmp; STLReader reader; reader.tolerance=Mathr::ZERO_TOLERANCE; if(!reader.open(filename, back_inserter(vtmp), back_inserter(etmp), back_inserter(ftmp), back_inserter(ntmp))) { LOG_ERROR("Can't open file: " << filename); return imported; // zero size } for(int i=0,e=ftmp.size(); i iFacet(new Facet); iFacet->color = Vector3r(0.8,0.3,0.3); for (int j=0; j<3; ++j) { iFacet->vertices[j]=v[j]-icc; } iFacet->postLoad(*iFacet); shared_ptr b(new Body); b->state->pos=b->state->refPos=icc; b->state->ori=b->state->refOri=Quaternionr::Identity(); b->shape = iFacet; imported.push_back(b); } return imported; } trunk-2017.01a/pkg/dem/STLImporter.hpp000066400000000000000000000156541304022710500174200ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2008 by Sergei Dorofeenko * * sega@users.berlios.de * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include class STLImporter { public: vector > import(const char*); DECLARE_LOGGER; }; template std::pair minmax(const T &a, const T &b) { return (a(a,b) : std::pair(b,a); } class STLReader { public: // if it is binary there are 80 char of comment, the number fn of faces and then exactly fn*4*3 bytes. enum {STL_LABEL_SIZE=80}; template bool open(const char* filename, OutV vertices, OutE edges, OutF facets, OutN normals); float tolerance; protected: template bool open_binary(const char* filename, OutV vertices, OutE edges, OutF facets, OutN normals); template bool open_ascii(const char* filename, OutV vertices, OutE edges, OutF facets, OutN normals); struct Vrtx { float pos[3]; Vrtx(){} Vrtx(float x, float y, float z) {pos[0]=x; pos[1]=y; pos[2]=z;} bool operator< (const Vrtx& v) const { return memcmp(pos, v.pos,3*sizeof(float)) < 0; } float operator[](int id) const { return pos[id]; } float& operator[](int id) { return pos[id]; } }; class IsDifferent { float tolerance; public: IsDifferent(float _tolerance): tolerance(_tolerance){} bool operator() (const Vrtx& v1, const Vrtx& v2) { if ( std::abs(v1[0]-v2[0]) bool STLReader::open(const char* filename, OutV vertices, OutE edges, OutF facets, OutN normals) { FILE *fp; bool binary=false; fp = fopen(filename, "r"); if(fp == NULL) return false; /* Find size of file */ fseek(fp, 0, SEEK_END); int file_size = ftell(fp); int facenum; /* Check for binary or ASCII file */ fseek(fp, STL_LABEL_SIZE, SEEK_SET); size_t res=fread(&facenum, sizeof(int), 1, fp); int expected_file_size=STL_LABEL_SIZE + 4 + (sizeof(short)+4*sizeof(float) )*facenum ; if(file_size == expected_file_size) binary = true; unsigned char tmpbuf[128]; res=fread(tmpbuf,sizeof(tmpbuf),1,fp); if (res) { for(size_t i = 0; i < sizeof(tmpbuf); i++) { if(tmpbuf[i] > 127) { binary=true; break; } } } // Now we know if the stl file is ascii or binary. fclose(fp); if(binary) return open_binary(filename,vertices,edges,facets,normals); else return open_ascii(filename,vertices,edges,facets,normals); } template bool STLReader::open_ascii(const char* filename, OutV vertices, OutE edges, OutF facets, OutN normals) { FILE *fp; fp = fopen(filename, "r"); if(fp == NULL) return false; /* Skip the first line of the file */ while(getc(fp) != '\n'); vector vcs; set > egs; /* Read a single facet from an ASCII .STL file */ int r=0; //just to escape "warning: ignoring return value of 'int fscanf(FILE*, const char*, ...)'," while(!feof(fp)) { float n[3]; Vrtx v[3]; r=fscanf(fp, "%*s %*s %f %f %f\n", &n[0], &n[1], &n[2]); r+=fscanf(fp, "%*s %*s"); r+=fscanf(fp, "%*s %f %f %f\n", &v[0][0], &v[0][1], &v[0][2]); r+=fscanf(fp, "%*s %f %f %f\n", &v[1][0], &v[1][1], &v[1][2]); r+=fscanf(fp, "%*s %f %f %f\n", &v[2][0], &v[2][1], &v[2][2]); r+=fscanf(fp, "%*s"); // end loop r+=fscanf(fp, "%*s"); // end facet if(feof(fp)) break; int vid[3]; for(int i=0;i<3;++i) { (normals++) = n[i]; bool is_different=true; IsDifferent isd(tolerance); int j=0; for(int ej=vcs.size(); j::iterator it=vcs.begin(),end=vcs.end(); it!=end; ++it) { (vertices++) = (*it)[0]; (vertices++) = (*it)[1]; (vertices++) = (*it)[2]; } for(set >::iterator it=egs.begin(),end=egs.end(); it!=end; ++it) { (edges++) = it->first; (edges++) = it->second; } return (r>0); } template bool STLReader::open_binary(const char* filename, OutV vertices, OutE edges, OutF facets, OutN normals) { FILE *fp; fp = fopen(filename, "rb"); if (fp == NULL) { return false; } int facenum; fseek(fp, STL_LABEL_SIZE, SEEK_SET); int res=fread(&facenum, sizeof(int), 1, fp); vector vcs; set > egs; if (res) { // For each triangle read the normal, the three coords and a short set to zero for(int i=0;i::iterator it=vcs.begin(),end=vcs.end(); it!=end; ++it) { (vertices++) = (*it)[0]; (vertices++) = (*it)[1]; (vertices++) = (*it)[2]; } for(set >::iterator it=egs.begin(),end=egs.end(); it!=end; ++it) { (edges++) = it->first; (edges++) = it->second; } return true; } trunk-2017.01a/pkg/dem/SampleCapillaryPressureEngine.cpp000066400000000000000000000050621304022710500231600ustar00rootroot00000000000000#ifdef DEPREC_CODE /************************************************************************* * Copyright (C) 2006 by Luc Scholtes * * luc.scholtes@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "SampleCapillaryPressureEngine.hpp" #include #include #include #include #include YADE_PLUGIN((SampleCapillaryPressureEngine)); CREATE_LOGGER(SampleCapillaryPressureEngine); SampleCapillaryPressureEngine::~SampleCapillaryPressureEngine() { } void SampleCapillaryPressureEngine::updateParameters() { UnbalancedForce = ComputeUnbalancedForce(scene); if (!Phase1 && UnbalancedForce<=StabilityCriterion && !pressureVariationActivated) { internalCompaction = false; Phase1 = true; } if ( Phase1 && UnbalancedForce<=StabilityCriterion && !pressureVariationActivated) { Real S = meanStress; cerr << "Smoy = " << meanStress << endl; if ((S > (sigma_iso - (sigma_iso*SigmaPrecision))) && (S < (sigma_iso + (sigma_iso*SigmaPrecision)))) { string fileName = "../data/" + Phase1End + "_" + boost::lexical_cast(scene->iter) + ".xml"; cerr << "saving snapshot: " << fileName << " ..."; Omega::instance().saveSimulation(fileName); pressureVariationActivated = true; } } } void SampleCapillaryPressureEngine::action() { updateParameters(); TriaxialStressController::action(); if (pressureVariationActivated) { if (scene->iter % 100 == 0) cerr << "pressure variation!!" << endl; if ((Pressure>=0) && (Pressure<=1000000000)) Pressure += PressureVariation; capillaryCohesiveLaw->capillaryPressure = Pressure; capillaryCohesiveLaw->fusionDetection = fusionDetection; capillaryCohesiveLaw->binaryFusion = binaryFusion; } else { capillaryCohesiveLaw->capillaryPressure = Pressure; capillaryCohesiveLaw->fusionDetection = fusionDetection; capillaryCohesiveLaw->binaryFusion = binaryFusion;} if (scene->iter % 100 == 0) cerr << "capillary pressure = " << Pressure << endl; capillaryCohesiveLaw->scene=scene;; capillaryCohesiveLaw->action(); UnbalancedForce = ComputeUnbalancedForce(scene); } #endif //DEPREC CODE trunk-2017.01a/pkg/dem/SampleCapillaryPressureEngine.hpp000066400000000000000000000052631304022710500231700ustar00rootroot00000000000000#ifdef DEPREC_CODE /************************************************************************* * Copyright (C) 2006 by Luc Scholtes * * luc.scholtes@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifndef SAMPLE_CAPILLARY_PRESSURE_ENGINE_HPP #define SAMPLE_CAPILLARY_PRESSURE_ENGINE_HPP #include #include #include #include /*! \brief Isotropic compression + suction variation test */ class Law2_ScGeom_CapillaryPhys_Capillarity; class SampleCapillaryPressureEngine : public TriaxialStressController { public : //! is isotropicInternalCompactionFinished? bool Phase1; std::string Phase1End; //! is this the beginning of the simulation, after reading the scene? bool firstRun; shared_ptr capillaryCohesiveLaw; //Law2_ScGeom_CapillaryPhys_Capillarity* capillaryCohesiveLaw; // which one is right? virtual ~SampleCapillaryPressureEngine(); void updateParameters(); virtual void action(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(SampleCapillaryPressureEngine,TriaxialStressController,"It produces the isotropic compaction of an assembly and allows one to controlled the capillary pressure inside (uses Law2_ScGeom_CapillaryPhys_Capillarity).", ((Real,Pressure,0,,"Value of the capillary pressure Uc=Ugas-Uliquid (see Law2_ScGeom_CapillaryPhys_Capillarity). [Pa]")) ((bool,pressureVariationActivated,1,,"Is the capillary pressure varying?")) ((bool,fusionDetection,1,,"Is the detection of menisci overlapping activated?")) ((bool,binaryFusion,1,,"If yes, capillary force are set to 0 when, at least, 1 overlap is detected for a meniscus. If no, capillary force is divided by the number of overlaps.")) ((Real,PressureVariation,0,,"Variation of the capillary pressure (each iteration). [Pa]")) ((Real,UnbalancedForce,1,,"mean resultant forces divided by mean contact force")) ((Real,StabilityCriterion,0.01,,"tolerance in terms of :yref:`TriaxialCompressionEngine::UnbalancedForce` to consider the packing as stable")) ((Real,SigmaPrecision,0.001,,"tolerance in terms of mean stress to consider the packing as stable")), Phase1=false; Phase1End = "Compacted"; firstRun=true; ,) DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(SampleCapillaryPressureEngine); #endif // SAMPLECAPILLARYPRESSUREENGINE_HPP #endif //DEPREC CODE trunk-2017.01a/pkg/dem/ScGeom.cpp000066400000000000000000000176701304022710500164040ustar00rootroot00000000000000// © 2004 Olivier Galizzi // © 2004 Janek Kozicki // © 2008 Václav Šmilauer // © 2006 Bruno Chareyre #include #include #include YADE_PLUGIN((ScGeom)(ScGeom6D)(ChCylGeom6D)); ScGeom::~ScGeom(){}; ScGeom6D::~ScGeom6D(){}; ChCylGeom6D::~ChCylGeom6D(){}; Vector3r& ScGeom::rotate(Vector3r& shearForce) const { // approximated rotations shearForce -= shearForce.cross(orthonormal_axis); shearForce -= shearForce.cross(twist_axis); //NOTE : make sure it is in the tangent plane? It's never been done before. Is it not adding rounding errors at the same time in fact?... //shearForce -= normal.dot(shearForce)*normal; return shearForce; } Vector3r& ScGeom::rotateNonSpherical(Vector3r& shearForce) const { //FIXME // approximated rotations shearForce -= shearForce.cross(orthonormal_axis); //shearForce -= shearForce.cross(twist_axis); //NOTE : make sure it is in the tangent plane? It's never been done before. Is it not adding rounding errors at the same time in fact?... //shearForce -= normal.dot(shearForce)*normal; if(std::isnan(shearForce.norm())){ std::cout<<"orthonormal_axis: "<& c, const Vector3r& currentNormal, bool isNew, const Vector3r& shift2, bool avoidGranularRatcheting){ if(!isNew) { orthonormal_axis = normal.cross(currentNormal); Real angle = scene->dt*0.5*normal.dot(rbp1.angVel + rbp2.angVel); twist_axis = angle*normal;} else twist_axis=orthonormal_axis=Vector3r::Zero(); //Update contact normal normal=currentNormal; //Precompute shear increment Vector3r relativeVelocity=getIncidentVel(&rbp1,&rbp2,scene->dt,shift2,scene->isPeriodic ? scene->cell->intrShiftVel(c->cellDist) : Vector3r::Zero(),avoidGranularRatcheting); //keep the shear part only relativeVelocity = relativeVelocity-normal.dot(relativeVelocity)*normal; shearInc = relativeVelocity*scene->dt; } Vector3r ScGeom::getIncidentVel(const State* rbp1, const State* rbp2, Real dt, const Vector3r& shift2, const Vector3r& shiftVel, bool avoidGranularRatcheting){ if(avoidGranularRatcheting){ /* B.C. Comment : Short explanation of what we want to avoid : Numerical ratcheting is best understood considering a small elastic cycle at a contact between two grains : assuming b1 is fixed, impose this displacement to b2 : 1. translation "dx" in the normal direction 2. rotation "a" 3. translation "-dx" (back to initial position) 4. rotation "-a" (back to initial orientation) If the branch vector used to define the relative shear in rotation×branch is not constant (typically if it is defined from the vector center→contactPoint), then the shear displacement at the end of this cycle is not zero: rotations *a* and *-a* are multiplied by branches of different lengths. It results in a finite contact force at the end of the cycle even though the positions and orientations are unchanged, in total contradiction with the elastic nature of the problem. It could also be seen as an *inconsistent energy creation or loss*. Given that DEM simulations tend to generate oscillations around equilibrium (damped mass-spring), it can have a significant impact on the evolution of the packings, resulting for instance in slow creep in iterations under constant load. The solution adopted here to avoid ratcheting is as proposed by McNamara and co-workers. They analyzed the ratcheting problem in detail - even though they comment on the basis of a cycle that differs from the one shown above. One will find interesting discussions in e.g. DOI 10.1103/PhysRevE.77.031304, even though solution it suggests is not fully applied here (equations of motion are not incorporating alpha, in contradiction with what is suggested by McNamara et al.). */ // For sphere-facet contact this will give an erroneous value of relative velocity... Real alpha = (radius1+radius2)/(radius1+radius2-penetrationDepth); Vector3r relativeVelocity = (rbp2->vel-rbp1->vel)*alpha + rbp2->angVel.cross(-radius2*normal) - rbp1->angVel.cross(radius1*normal); relativeVelocity+=alpha*shiftVel; return relativeVelocity; } else { // It is correct for sphere-sphere and sphere-facet contact Vector3r c1x = (contactPoint - rbp1->pos); Vector3r c2x = (contactPoint - rbp2->pos + shift2); Vector3r relativeVelocity = (rbp2->vel+rbp2->angVel.cross(c2x)) - (rbp1->vel+rbp1->angVel.cross(c1x)); relativeVelocity+=shiftVel; return relativeVelocity;} } Vector3r ScGeom::getIncidentVel(const State* rbp1, const State* rbp2, Real dt, bool avoidGranularRatcheting){ //Just pass null shift to the periodic version return getIncidentVel(rbp1,rbp2,dt,Vector3r::Zero(),Vector3r::Zero(),avoidGranularRatcheting); } Vector3r ScGeom::getIncidentVel_py(shared_ptr i, bool avoidGranularRatcheting){ if(i->geom.get()!=this) throw invalid_argument("ScGeom object is not the same as Interaction.geom."); Scene* scene=Omega::instance().getScene().get(); return getIncidentVel(Body::byId(i->getId1(),scene)->state.get(),Body::byId(i->getId2(),scene)->state.get(), scene->dt, scene->isPeriodic ? scene->cell->intrShiftPos(i->cellDist): Vector3r::Zero(), // shift2 scene->isPeriodic ? scene->cell->intrShiftVel(i->cellDist): Vector3r::Zero(), // shiftVel avoidGranularRatcheting); } Vector3r ScGeom::getRelAngVel(const State* rbp1, const State* rbp2, Real dt){ Vector3r relAngVel = (rbp2->angVel-rbp1->angVel); return relAngVel; } Vector3r ScGeom::getRelAngVel_py(shared_ptr i){ if(i->geom.get()!=this) throw invalid_argument("ScGeom object is not the same as Interaction.geom."); Scene* scene=Omega::instance().getScene().get(); return getRelAngVel(Body::byId(i->getId1(),scene)->state.get(),Body::byId(i->getId2(),scene)->state.get(),scene->dt); } //!Precompute relative rotations (and precompute ScGeom3D) void ScGeom6D::precomputeRotations(const State& rbp1, const State& rbp2, bool isNew, bool creep){ if (isNew) { initRotations(rbp1,rbp2); } else { Quaternionr delta((rbp1.ori * (initialOrientation1.conjugate())) * (initialOrientation2 * (rbp2.ori.conjugate()))); delta.normalize(); if (creep) delta = delta * twistCreep; AngleAxisr aa(delta); // axis of rotation - this is the Moment direction UNIT vector; // angle represents the power of resistant ELASTIC moment //Eigen::AngleAxisr(q) returns nan's when q close to identity, next tline fixes the pb. // add -DYADE_SCGEOM_DEBUG to CXXFLAGS to enable this piece or just do // #define YADE_SCGEOM_DEBUG //(but do not commit with that enabled in the code) #ifdef YADE_SCGEOM_DEBUG if (std::isnan(aa.angle())) { cerr<<"NaN angle found in angleAxisr(q), for quaternion "< Mathr::PI) aa.angle() -= Mathr::TWO_PI; // angle is between 0 and 2*pi, but should be between -pi and pi twist = (aa.angle() * aa.axis().dot(normal)); bending = Vector3r(aa.angle()*aa.axis() - twist*normal); } } void ScGeom6D::initRotations(const State& state1, const State& state2) { initialOrientation1 = state1.ori; initialOrientation2 = state2.ori; twist=0; bending=Vector3r::Zero(); twistCreep=Quaternionr(1.0,0.0,0.0,0.0); } trunk-2017.01a/pkg/dem/ScGeom.hpp000066400000000000000000000160541304022710500164040ustar00rootroot00000000000000// © 2004 Olivier Galizzi // © 2008 Václav Šmilauer // © 2006 Bruno Chareyre #pragma once #include #include #include #include #include /*! Class representing geometry of two bodies in contact. * * The code under SCG_SHEAR is experimental and is used only if ElasticContactLaw::useShear is explicitly true */ #define SCG_SHEAR class ScGeom: public GenericSpheresContact { private: //cached values Vector3r twist_axis;//rotation vector around normal Vector3r orthonormal_axis;//rotation vector in contact plane public: // inherited from GenericSpheresContact: Vector3r& normal; Real &radius1, &radius2; virtual ~ScGeom(); inline ScGeom& operator= (const ScGeom& source){ normal=source.normal; contactPoint=source.contactPoint; twist_axis=source.twist_axis; orthonormal_axis=source.orthonormal_axis; radius1=source.radius1; radius2=source.radius2; penetrationDepth=source.penetrationDepth; shearInc=source.shearInc; return *this;} //!precompute values of shear increment and interaction rotation data. Update contact normal to the currentNormal value. Precondition : the value of normal is not updated outside (and before) this function. void precompute(const State& rbp1, const State& rbp2, const Scene* scene, const shared_ptr& c, const Vector3r& currentNormal, bool isNew, const Vector3r& shift2, bool avoidGranularRatcheting=true); //! Rotates a "shear" vector to keep track of contact orientation. Returns reference of the updated vector. Vector3r& rotate(Vector3r& tangentVector) const; Vector3r& rotateNonSpherical(Vector3r& tangentVector) const; //FIXME const Vector3r& shearIncrement() const {return shearInc;} // Add method which returns the relative velocity (then, inside the contact law, this can be split into shear and normal component). Handle periodicity. Vector3r getIncidentVel(const State* rbp1, const State* rbp2, Real dt, const Vector3r& shiftVel, const Vector3r& shift2, bool avoidGranularRatcheting=true); // Implement another version of getIncidentVel which does not handle periodicity. Vector3r getIncidentVel(const State* rbp1, const State* rbp2, Real dt, bool avoidGranularRatcheting=true); // Add function to get the relative angular velocity (useful to determine bending moment at the contact level) Vector3r getRelAngVel(const State* rbp1, const State* rbp2, Real dt); // convenience version to be called from python Vector3r getIncidentVel_py(shared_ptr i, bool avoidGranularRatcheting); Vector3r getRelAngVel_py(shared_ptr i); YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(ScGeom,GenericSpheresContact,"Class representing :yref:`geometry` of a contact point between two :yref:`bodies`. It is more general than sphere-sphere contact even though it is primarily focused on spheres interactions (reason for the 'Sc' namming); it is also used for representing contacts of a :yref:`Sphere` with non-spherical bodies (:yref:`Facet`, :yref:`Plane`, :yref:`Box`, :yref:`ChainedCylinder`), or between two non-spherical bodies (:yref:`ChainedCylinder`). The contact has 3 DOFs (normal and 2×shear) and uses incremental algorithm for updating shear.\n\nWe use symbols $\\vec{x}$, $\\vec{v}$, $\\vec{\\omega}$ respectively for position, linear and angular velocities (all in global coordinates) and $r$ for particles radii; subscripted with 1 or 2 to distinguish 2 spheres in contact. Then we define branch length and unit contact normal\n\n.. math::\n\n\tl=||\\vec{x}_2-\\vec{x}_1||, \\vec{n}=\\frac{\\vec{x}_2-\\vec{x}_1}{||\\vec{x}_2-\\vec{x}_1||}\n\nThe relative velocity of the spheres is then\n\n.. math::\n\n\t\\vec{v}_{12}=\\frac{r_1+r_2}{l}(\\vec{v}_2-\\vec{v}_1) -(r_2 \\vec{\\omega}_2 + r_1\\vec{\\omega}_1)\\times\\vec{n}\n\nwhere the fraction multiplying translational velocities is to make the definition objective and avoid ratcheting effects (see :yref:`Ig2_Sphere_Sphere_ScGeom.avoidGranularRatcheting`). The shear component is\n\n.. math::\n\n\t\\vec{v}_{12}^s=\\vec{v}_{12}-(\\vec{n}\\cdot\\vec{v}_{12})\\vec{n}.\n\nTangential displacement increment over last step then reads\n\n.. math::\n\n\t\\Delta\\vec{x}_{12}^s=\\Delta t \\vec{v}_{12}^s.", ((Real,penetrationDepth,NaN,(Attr::noSave|Attr::readonly),"Penetration distance of spheres (positive if overlapping)")) ((Vector3r,shearInc,Vector3r::Zero(),(Attr::noSave|Attr::readonly),"Shear displacement increment in the last step")) , /* extra initializers */ ((radius1,GenericSpheresContact::refR1)) ((radius2,GenericSpheresContact::refR2)), /* ctor */ createIndex(); twist_axis=orthonormal_axis=Vector3r::Zero();, /* py */ .def("incidentVel",&ScGeom::getIncidentVel_py,(boost::python::arg("i"),boost::python::arg("avoidGranularRatcheting")=true),"Return incident velocity of the interaction (see also :yref:`Ig2_Sphere_Sphere_ScGeom.avoidGranularRatcheting` for explanation of the ratcheting argument).") .def("relAngVel",&ScGeom::getRelAngVel_py,(boost::python::arg("i")),"Return relative angular velocity of the interaction.") ); REGISTER_CLASS_INDEX(ScGeom,GenericSpheresContact); }; REGISTER_SERIALIZABLE(ScGeom); class ScGeom6D: public ScGeom { public: virtual ~ScGeom6D(); const Real& getTwist() const {return twist;} const Vector3r& getBending() const {return bending;} void precomputeRotations(const State& rbp1, const State& rbp2, bool isNew, bool creep=false); void initRotations(const State& rbp1, const State& rbp2); YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(ScGeom6D,ScGeom,"Class representing :yref:`geometry` of two :yref:`bodies` in contact. The contact has 6 DOFs (normal, 2×shear, twist, 2xbending) and uses :yref:`ScGeom` incremental algorithm for updating shear.", ((Quaternionr,initialOrientation1,Quaternionr(1.0,0.0,0.0,0.0),(Attr::readonly),"Orientation of body 1 one at initialisation time |yupdate|")) ((Quaternionr,initialOrientation2,Quaternionr(1.0,0.0,0.0,0.0),(Attr::readonly),"Orientation of body 2 one at initialisation time |yupdate|")) ((Quaternionr,twistCreep,Quaternionr(1.0,0.0,0.0,0.0),(Attr::readonly),"Stored creep, substracted from total relative rotation for computation of elastic moment |yupdate|")) ((Real,twist,0,(Attr::readonly),"Elastic twist angle (around :yref:`normal axis`) of the contact.")) ((Vector3r,bending,Vector3r::Zero(),(Attr::readonly),"Bending at contact as a vector defining axis of rotation and angle (angle=norm).")) , /* extra initializers */, /* ctor */ createIndex();, /* py */ ); REGISTER_CLASS_INDEX(ScGeom6D,ScGeom); }; REGISTER_SERIALIZABLE(ScGeom6D); class ChCylGeom6D: public ScGeom6D { public: virtual ~ChCylGeom6D(); State fictiousState1; State fictiousState2; Real relPos1, relPos2; YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(ChCylGeom6D,ScGeom6D,"Test", /*attributes*/ , /* extra initializers */, /* ctor */ createIndex();, /* py */ ); REGISTER_CLASS_INDEX(ChCylGeom6D,ScGeom6D); }; REGISTER_SERIALIZABLE(ChCylGeom6D); trunk-2017.01a/pkg/dem/Shop.hpp000066400000000000000000000173341304022710500161420ustar00rootroot00000000000000// 2007 © Václav Šmilauer #pragma once #include #include "lib/base/Math.hpp" #include "lib/base/Logging.hpp" #include "core/Body.hpp" #include class Scene; class Body; class SimpleViscoelasticBodyParameters; class ViscElMat; class FrictMat; class Interaction; using boost::shared_ptr; namespace py = boost::python; /*! Miscillaneous utility functions which are believed to be generally useful. * * All data members are methods are static, no instance of Shop is created. It is not serializable either. */ class Shop{ public: DECLARE_LOGGER; //! create default sphere, along with its bound etc. static shared_ptr sphere(Vector3r center, Real radius, shared_ptr mat); //! create default box with everything needed static shared_ptr box(Vector3r center, Vector3r extents, shared_ptr mat); //! create default tetrahedron static shared_ptr tetra(Vector3r v[4], shared_ptr mat); //! return instance of default FrictMat static shared_ptr defaultGranularMat(); //! Return vector of pairs (center,radius) loaded from a file with numbers inside static vector > loadSpheresFromFile(const string& fname,Vector3r& minXYZ, Vector3r& maxXYZ, Vector3r* cellSize=NULL); //! Save spheres in the current simulation into a text file static void saveSpheresToFile(string fileName); //! Compute the total volume of spheres static Real getSpheresVolume(const shared_ptr& rb=shared_ptr(), int mask=-1); //! Compute the total mass of spheres static Real getSpheresMass(const shared_ptr& rb=shared_ptr(), int mask=-1); //! Compute porosity; volume must be given for aperiodic simulations static Real getPorosity(const shared_ptr& rb=shared_ptr(),Real volume=-1); //! Compute porosity by dividing given volume into a grid of voxels; static Real getVoxelPorosity(const shared_ptr& rb=shared_ptr(),int resolution=500,Vector3r start=Vector3r(0,0,0),Vector3r end=Vector3r(0,0,0)); //! Estimate timestep based on P-wave propagation speed static Real PWaveTimeStep(const shared_ptr rb=shared_ptr()); //! Estimate timestep based on Rayleigh-wave propagation speed static Real RayleighWaveTimeStep(const shared_ptr rb=shared_ptr()); //! return 2d coordinates of a 3d point within plane defined by rotation axis and inclination of spiral, wrapped to the 0th period static boost::tuple spiralProject(const Vector3r& pt, Real dH_dTheta, int axis=2, Real periodStart=std::numeric_limits::quiet_NaN(), Real theta0=0); //! Calculate inscribed circle center of trianlge static Vector3r inscribedCircleCenter(const Vector3r& v0, const Vector3r& v1, const Vector3r& v2); /// Get viscoelastic parameters kn,cn,ks,cs from analytical solution of /// a problem of interaction of pair spheres with mass 1, collision /// time tc and restitution coefficients en,es. static void getViscoelasticFromSpheresInteraction(Real tc, Real en, Real es, shared_ptr b); //! Get unbalanced force of the whole simulation static Real unbalancedForce(bool useMaxForce=false, Scene* _rb=NULL); static Real kineticEnergy(Scene* _rb=NULL, Body::id_t* maxId=NULL); //! get total momentum of current simulation static Vector3r momentum(); //! get total angular momentum of current simulation static Vector3r angularMomentum(Vector3r origin = Vector3r::Zero()); static Vector3r totalForceInVolume(Real& avgIsoStiffness, Scene *_rb=NULL); //! create transientInteraction between 2 bodies, using existing Dispatcher in Omega static shared_ptr createExplicitInteraction(Body::id_t id1, Body::id_t id2, bool force); //! apply force on contact point on both bodies (reversed on body 2) static void applyForceAtContactPoint(const Vector3r& force, const Vector3r& contPt, Body::id_t id1, const Vector3r& pos1, Body::id_t id2, const Vector3r& pos2, Scene* scene); //! map scalar variable to 1d colorscale static Vector3r scalarOnColorScale(Real x, Real xmin=0., Real xmax=1.); //! wrap floating number periodically to the given range static Real periodicWrap(Real x, Real x0, Real x1, long* period=NULL); //! Flip cell shear without affecting interactions; if flip is zeros, it will be computed such that abs of shear strain is minimal for each shear component //! Diagonal terms of flip are meaningless and ignored. static Matrix3r flipCell(const Matrix3r& flip=Matrix3r::Zero()); //! Class for storing stresses, affected on bodies, obtained from Interactions struct bodyState{ Vector3r normStress, shearStress; bodyState (){ normStress = Vector3r(0.0,0.0,0.0); shearStress = Vector3r(0.0,0.0,0.0); } }; //! Function of getting stresses for each body static void getStressForEachBody(vector&); //! Define the exact average stress in each particle from contour integral ("LW" stands for Love-Weber, since this is what the contour integral gives). static void getStressLWForEachBody(vector& bStresses); static py::list getStressLWForEachBody(); //! Function to compute overall ("macroscopic") stress. static Matrix3r getStress(Real volume=0); static Matrix3r getCapillaryStress(Real volume=0, bool mindlin=false); static Matrix3r stressTensorOfPeriodicCell() { LOG_WARN("Shop::stressTensorOfPeriodicCelli is DEPRECATED: use getStress instead"); return Shop::getStress(); } //! Compute the stress tensor in each defined cell, return a stress tensor depth profile static py::tuple getStressProfile(Real volume, int nCell, Real dz, Real zRef, vector vPartAverageX, vector vPartAverageY, vector vPartAverageZ); //! Compute average depth profile of particle velocity (x,y,z) and solid volume fraction static py::tuple getDepthProfiles(Real vCell, int nCell, Real dz, Real zRef,bool activateCond=false, Real radiusPy=0); //! Compute overall ("macroscopic") stress of periodic cell, returning 2 tensors //! (contribution of normal and shear forces) static py::tuple normalShearStressTensors(bool compressionPositive=false, bool splitNormalTensor=false, Real thresholdForce=NaN); //! Function to compute fabric tensor static void fabricTensor(Real& Fmean, Matrix3r& fabric, Matrix3r& fabricStrong, Matrix3r& fabricWeak, Real cutoff=0.0, bool splitTensor=false, Real thresholdForce=NaN); static py::tuple fabricTensor(Real cutoff=0.0, bool splitTensor=false, Real thresholdForce=NaN); //! Function to set translational and rotational velocities of all bodies to zero static void calm(const shared_ptr& rb=shared_ptr(), int mask=-1); //! Get a list of body-ids, which contacts the given body; static py::list getBodyIdsContacts(Body::id_t bodyID=-1); //! Set material and contact friction to the given value, non-dynamic bodies are not affected static void setContactFriction(Real angleRad); //! Homothetic change of sizes of spheres and clumps static void growParticles(Real multiplier, bool updateMass, bool dynamicOnly); //! Change of size of a single sphere or a clump // DEPREC, update wrt growParticles() static void growParticle(Body::id_t bodyID, Real multiplier, bool updateMass); /* \todo implement groupMask */ static py::tuple aabbExtrema(Real cutoff=0.0, bool centers=false); //! evaluation of 2D quantities static Real getSpheresVolume2D(const shared_ptr& rb=shared_ptr(), int mask=-1); static Real getVoidRatio2D(const shared_ptr& rb=shared_ptr(),Real zlen=1); //! get stress tensor and tangent operator tensor for FEMxDEM coupling. By Ning Guo static py::tuple getStressAndTangent(Real volume=0, bool symmetry=true); }; trunk-2017.01a/pkg/dem/Shop_01.cpp000066400000000000000000000437501304022710500164360ustar00rootroot00000000000000// 2007 © Václav Šmilauer #include"Shop.hpp" #include #include"core/Scene.hpp" #include"core/Body.hpp" #include"core/Interaction.hpp" #include"pkg/common/Aabb.hpp" #include"core/Clump.hpp" #include"pkg/common/InsertionSortCollider.hpp" #include"pkg/common/Box.hpp" #include"pkg/common/Sphere.hpp" #include"pkg/common/ElastMat.hpp" #include"pkg/dem/ViscoelasticPM.hpp" #include"pkg/dem/CapillaryPhys.hpp" #include"pkg/common/Bo1_Aabb.hpp" #include"pkg/dem/NewtonIntegrator.hpp" #include"pkg/dem/Ig2_Sphere_Sphere_ScGeom.hpp" #include"pkg/dem/Ig2_Box_Sphere_ScGeom.hpp" #include"pkg/dem/FrictPhys.hpp" #include"pkg/common/ForceResetter.hpp" #include"pkg/common/Dispatching.hpp" #include"pkg/common/InteractionLoop.hpp" #include"pkg/common/GravityEngines.hpp" #include"pkg/dem/GlobalStiffnessTimeStepper.hpp" #include"pkg/dem/ElasticContactLaw.hpp" #include"pkg/dem/ScGeom.hpp" #include"pkg/dem/FrictPhys.hpp" #include"pkg/common/Grid.hpp" #include"pkg/dem/Tetra.hpp" #ifdef YADE_OPENGL #include"pkg/common/Gl1_NormPhys.hpp" #endif #include #include "py/_utils.hpp" CREATE_LOGGER(Shop); /*! Flip periodic cell by given number of cells. Still broken, some interactions are missed. Should be checked. */ Matrix3r Shop::flipCell(const Matrix3r& _flip){ Scene* scene=Omega::instance().getScene().get(); const shared_ptr& cell(scene->cell); const Matrix3r& trsf(cell->trsf); Vector3r size=cell->getSize(); Matrix3r flip; if(_flip==Matrix3r::Zero()){ bool hasNonzero=false; for(int i=0; i<3; i++) for(int j=0; j<3; j++) { if(i==j){ flip(i,j)=0; continue; } flip(i,j)=-floor(.5+trsf(i,j)/(size[j]/size[i])); if(flip(i,j)!=0) hasNonzero=true; } if(!hasNonzero) {LOG_TRACE("No flip necessary."); return Matrix3r::Zero();} LOG_DEBUG("Computed flip matrix: upper "< oldCells; oldCells.resize(scene->bodies->size()); FOREACH(const shared_ptr& b, *scene->bodies){ if(!b) continue; cell->wrapShearedPt(b->state->pos,oldCells[b->getId()]); } // change cell trsf here Matrix3r trsfInc; for(int i=0; i<3; i++) for(int j=0; j<3; j++){ if(i==j) { if(flip(i,j)!=0) LOG_WARN("Non-zero diagonal term at ["<trsf+=trsfInc; cell->postLoad(*cell); // new cell coords of bodies vector newCells; newCells.resize(scene->bodies->size()); FOREACH(const shared_ptr& b, *scene->bodies){ if(!b) continue; cell->wrapShearedPt(b->state->pos,newCells[b->getId()]); } // remove all potential interactions scene->interactions->eraseNonReal(); // adjust Interaction::cellDist for real interactions; FOREACH(const shared_ptr& i, *scene->interactions){ Body::id_t id1=i->getId1(),id2=i->getId2(); // this must be the same for both old and new interaction: cell2-cell1+cellDist // c₂-c₁+c₁₂=k; c'₂+c₁'+c₁₂'=k (new cell coords have ') // c₁₂'=(c₂-c₁+c₁₂)-(c₂'-c₁') i->cellDist=(oldCells[id2]-oldCells[id1]+i->cellDist)-(newCells[id2]-newCells[id1]); } // force reinitialization of the collider bool colliderFound=false; FOREACH(const shared_ptr& e, scene->engines){ Collider* c=dynamic_cast(e.get()); if(c){ colliderFound=true; c->invalidatePersistentData(); } } if(!colliderFound) LOG_WARN("No collider found while flipping cell; continuing simulation might give garbage results."); return flip; } /* Apply force on contact point to 2 bodies; the force is oriented as it applies on the first body and is reversed on the second. */ void Shop::applyForceAtContactPoint(const Vector3r& force, const Vector3r& contPt, Body::id_t id1, const Vector3r& pos1, Body::id_t id2, const Vector3r& pos2, Scene* scene){ scene->forces.addForce(id1,force); scene->forces.addForce(id2,-force); scene->forces.addTorque(id1,(contPt-pos1).cross(force)); scene->forces.addTorque(id2,-(contPt-pos2).cross(force)); } /*! Compute sum of forces in the whole simulation and averages stiffness. Designed for being used with periodic cell, where diving the resulting components by areas of the cell will give average stress in that direction. Requires all .isReal() interaction to have phys deriving from NormShearPhys. */ Vector3r Shop::totalForceInVolume(Real& avgIsoStiffness, Scene* _rb){ Scene* rb=_rb ? _rb : Omega::instance().getScene().get(); Vector3r force(Vector3r::Zero()); Real stiff=0; long n=0; FOREACH(const shared_ptr&I, *rb->interactions){ if(!I->isReal()) continue; NormShearPhys* nsi=YADE_CAST(I->phys.get()); force+=Vector3r(std::abs(nsi->normalForce[0]+nsi->shearForce[0]),std::abs(nsi->normalForce[1]+nsi->shearForce[1]),std::abs(nsi->normalForce[2]+nsi->shearForce[2])); stiff+=(1/3.)*nsi->kn+(2/3.)*nsi->ks; // count kn in one direction and ks in the other two n++; } avgIsoStiffness= n>0 ? (1./n)*stiff : -1; return force; } Real Shop::unbalancedForce(bool useMaxForce, Scene* _rb){ Scene* rb=_rb ? _rb : Omega::instance().getScene().get(); rb->forces.sync(); shared_ptr newton; Vector3r gravity = Vector3r::Zero(); FOREACH(shared_ptr& e, rb->engines){ newton=YADE_PTR_DYN_CAST(e); if(newton) {gravity=newton->gravity; break;} } // get maximum force on a body and sum of all forces (for averaging) Real sumF=0,maxF=0,currF; int nb=0; FOREACH(const shared_ptr& b, *rb->bodies){ if(!b || b->isClumpMember() || !b->isDynamic()) continue; currF=(rb->forces.getForce(b->id)+b->state->mass*gravity).norm(); if(b->isClump() && currF==0){ // this should not happen unless the function is called by an engine whose position in the loop is before Newton (with the exception of bodies which really have null force), because clumps forces are updated in Newton. Typical triaxial loops are using such ordering unfortunately (triaxEngine before Newton). So, here we make sure that they will get correct unbalance. In the future, it is better for optimality to check unbalancedF inside scripts at the end of loops, so that this "if" is never active. Vector3r f(rb->forces.getForce(b->id)),m(Vector3r::Zero()); b->shape->cast().addForceTorqueFromMembers(b->state.get(),rb,f,m); currF=(f+b->state->mass*gravity).norm(); } maxF=max(currF,maxF); sumF+=currF; nb++; } Real meanF=sumF/nb; // get mean force on interactions sumF=0; nb=0; FOREACH(const shared_ptr& I, *rb->interactions){ if(!I->isReal()) continue; shared_ptr nsi=YADE_PTR_CAST(I->phys); assert(nsi); sumF+=(nsi->normalForce+nsi->shearForce).norm(); nb++; } sumF/=nb; return (useMaxForce?maxF:meanF)/(sumF); } Real Shop::kineticEnergy(Scene* _scene, Body::id_t* maxId){ Scene* scene=_scene ? _scene : Omega::instance().getScene().get(); Real ret=0.; Real maxE=0; if(maxId) *maxId=Body::ID_NONE; Vector3r spin = scene->cell->getSpin(); FOREACH(const shared_ptr& b, *scene->bodies){ if(!b || !b->isDynamic()) continue; const State* state(b->state.get()); // ½(mv²+ωIω) Real E=0; if(scene->isPeriodic){ /* Only take in account the fluctuation velocity, not the mean velocity of homothetic resize. */ E=.5*state->mass*scene->cell->bodyFluctuationVel(state->pos-state->vel*scene->dt,state->vel,scene->cell->velGrad).squaredNorm(); } else { E=.5*(state->mass*state->vel.squaredNorm()); } Vector3r angVel = state->angVel; if (scene->isPeriodic) angVel=angVel-spin; if(b->isAspherical()){ Matrix3r T(state->ori); // the tensorial expression http://en.wikipedia.org/wiki/Moment_of_inertia#Moment_of_inertia_tensor // inertia tensor rotation from http://www.kwon3d.com/theory/moi/triten.html Matrix3r mI; mI<inertia[0],0,0, 0,state->inertia[1],0, 0,0,state->inertia[2]; //E+=.5*state->angVel.transpose().dot((T.transpose()*mI*T)*state->angVel); E+=.5*angVel.transpose().dot((T*mI*T.transpose())*angVel); } else { E+=0.5*angVel.dot(state->inertia.cwiseProduct(angVel)); } if(maxId && E>maxE) { *maxId=b->getId(); maxE=E; } ret+=E; } return ret; } Vector3r Shop::momentum() { Vector3r ret = Vector3r::Zero(); Scene* scene=Omega::instance().getScene().get(); FOREACH(const shared_ptr b, *scene->bodies){ ret += b->state->mass * b->state->vel; } return ret; } Vector3r Shop::angularMomentum(Vector3r origin) { Vector3r ret = Vector3r::Zero(); Scene* scene=Omega::instance().getScene().get(); Matrix3r T,Iloc; FOREACH(const shared_ptr b, *scene->bodies){ ret += (b->state->pos-origin).cross(b->state->mass * b->state->vel); ret += b->state->angMom; } return ret; } shared_ptr Shop::defaultGranularMat(){ shared_ptr mat(new FrictMat); mat->density=2e3; mat->young=30e9; mat->poisson=.3; mat->frictionAngle=.5236; //30˚ return mat; } /*! Create body - sphere. */ shared_ptr Shop::sphere(Vector3r center, Real radius, shared_ptr mat){ shared_ptr body(new Body); body->material=mat ? mat : boost::static_pointer_cast(defaultGranularMat()); body->state->pos=center; body->state->mass=4.0/3.0*Mathr::PI*radius*radius*radius*body->material->density; body->state->inertia=Vector3r(2.0/5.0*body->state->mass*radius*radius,2.0/5.0*body->state->mass*radius*radius,2.0/5.0*body->state->mass*radius*radius); body->bound=shared_ptr(new Aabb); body->shape=shared_ptr(new Sphere(radius)); return body; } /*! Create body - box. */ shared_ptr Shop::box(Vector3r center, Vector3r extents, shared_ptr mat){ shared_ptr body(new Body); body->material=mat ? mat : boost::static_pointer_cast(defaultGranularMat()); body->state->pos=center; Real mass=8.0*extents[0]*extents[1]*extents[2]*body->material->density; body->state->mass=mass; body->state->inertia=Vector3r(mass*(4*extents[1]*extents[1]+4*extents[2]*extents[2])/12.,mass*(4*extents[0]*extents[0]+4*extents[2]*extents[2])/12.,mass*(4*extents[0]*extents[0]+4*extents[1]*extents[1])/12.); body->bound=shared_ptr(new Aabb); body->shape=shared_ptr(new Box(extents)); return body; } /*! Create body - tetrahedron. */ shared_ptr Shop::tetra(Vector3r v_global[4], shared_ptr mat){ shared_ptr body(new Body); body->material=mat ? mat : boost::static_pointer_cast(defaultGranularMat()); Vector3r centroid=(v_global[0]+v_global[1]+v_global[2]+v_global[3])*.25; Vector3r v[4]; for(int i=0; i<4; i++) v[i]=v_global[i]-centroid; body->state->pos=centroid; body->state->mass=body->material->density*TetrahedronVolume(v); // inertia will be calculated below, by TetrahedronWithLocalAxesPrincipal body->bound=shared_ptr(new Aabb); body->shape=shared_ptr(new Tetra(v[0],v[1],v[2],v[3])); // make local axes coincident with principal axes TetrahedronWithLocalAxesPrincipal(body); return body; } void Shop::saveSpheresToFile(string fname){ const shared_ptr& scene=Omega::instance().getScene(); ofstream f(fname.c_str()); if(!f.good()) throw runtime_error("Unable to open file `"+fname+"'"); FOREACH(shared_ptr b, *scene->bodies){ if (!b->isDynamic()) continue; shared_ptr intSph=YADE_PTR_DYN_CAST(b->shape); if(!intSph) continue; const Vector3r& pos=b->state->pos; f<radius<& _scene, int mask){ const shared_ptr scene=(_scene?_scene:Omega::instance().getScene()); Real vol=0; FOREACH(shared_ptr b, *scene->bodies){ if (!b) continue; Sphere* s=dynamic_cast(b->shape.get()); if((!s) or ((mask>0) and ((b->groupMask & mask)==0))) continue; vol += (4/3.)*Mathr::PI*pow(s->radius,3); } return vol; } Real Shop::getSpheresMass(const shared_ptr& _scene, int mask){ const shared_ptr scene=(_scene?_scene:Omega::instance().getScene()); Real mass=0; FOREACH(shared_ptr b, *scene->bodies){ if (!b) continue; Sphere* s=dynamic_cast(b->shape.get()); if((!s) or ((mask>0) and ((b->groupMask & mask)==0))) continue; mass += b->state->mass; } return mass; } Real Shop::getPorosity(const shared_ptr& _scene, Real _volume){ const shared_ptr scene=(_scene?_scene:Omega::instance().getScene()); Real V; if(!scene->isPeriodic){ if(_volume<=0){// throw std::invalid_argument("utils.porosity must be given (positive) *volume* for aperiodic simulations."); py::tuple extrema = aabbExtrema(); V = py::extract( (extrema[1][0] - extrema[0][0])*(extrema[1][1] - extrema[0][1])*(extrema[1][2] - extrema[0][2]) ); } else V=_volume; } else { V=scene->cell->getVolume(); } Real Vs=Shop::getSpheresVolume(); return (V-Vs)/V; } Real Shop::getVoxelPorosity(const shared_ptr& _scene, int _resolution, Vector3r _start,Vector3r _end){ const shared_ptr scene=(_scene?_scene:Omega::instance().getScene()); if(_start==_end) throw std::invalid_argument("utils.voxelPorosity: cannot calculate porosity when start==end of the volume box."); if(_resolution<50) throw std::invalid_argument("utils.voxelPorosity: it doesn't make sense to calculate porosity with voxel resolution below 50."); // prepare the gird, it eats a lot of memory. // I am not optimizing for using bits. A single byte for each cell is used. std::vector > > grid; int S(_resolution); grid.resize(S); for(int i=0 ; i bi, *scene->bodies){ if((bi)->isClump()) continue; const shared_ptr& b = bi; if ( b->isDynamic() || b->isClumpMember() ) { const shared_ptr& sphere = YADE_PTR_CAST ( b->shape ); Real r = sphere->radius; Real rr = r*r; Vector3r pos = b->state->se3.position; // we got sphere with radius r, at position pos. // and a box of size S, scaled to 'size' // mark cells that are iniside a sphere int ii(0),II(S),jj(0),JJ(S),kk(0),KK(S); // make sure to loop only in AABB of that sphere. No need to waste cycles outside of it. ii = std::max((int)((Real)(pos[0]-start[0]-r)*(Real)(S)/(Real)(size[0]))-1,0); II = std::min(ii+(int)((Real)(2.0*r)*(Real)(S)/(Real)(size[0]))+3,S); jj = std::max((int)((Real)(pos[1]-start[1]-r)*(Real)(S)/(Real)(size[1]))-1,0); JJ = std::min(jj+(int)((Real)(2.0*r)*(Real)(S)/(Real)(size[1]))+3,S); kk = std::max((int)((Real)(pos[2]-start[2]-r)*(Real)(S)/(Real)(size[2]))-1,0); KK = std::min(kk+(int)((Real)(2.0*r)*(Real)(S)/(Real)(size[2]))+3,S); for(int i=ii ; i > Shop::loadSpheresFromFile(const string& fname, Vector3r& minXYZ, Vector3r& maxXYZ, Vector3r* cellSize){ if(!boost::filesystem::exists(fname)) { throw std::invalid_argument(string("File with spheres `")+fname+"' doesn't exist."); } vector > spheres; ifstream sphereFile(fname.c_str()); if(!sphereFile.good()) throw std::runtime_error("File with spheres `"+fname+"' couldn't be opened."); Vector3r C; Real r=0; int clumpId=-1; string line; size_t lineNo=0; while(std::getline(sphereFile, line, '\n')){ lineNo++; boost::tokenizer > toks(line,boost::char_separator(" \t")); vector tokens; FOREACH(const string& s, toks) tokens.push_back(s); if(tokens.empty()) continue; if(tokens[0]=="##PERIODIC::"){ if(tokens.size()!=4) throw std::invalid_argument(("Spheres file "+fname+":"+boost::lexical_cast(lineNo)+" contains ##PERIODIC::, but the line is malformed.").c_str()); if(cellSize){ *cellSize=Vector3r(boost::lexical_cast(tokens[1]),boost::lexical_cast(tokens[2]),boost::lexical_cast(tokens[3])); } continue; } if(tokens.size()!=5 and tokens.size()!=4) throw std::invalid_argument(("Line "+boost::lexical_cast(lineNo)+" in the spheres file "+fname+" has "+boost::lexical_cast(tokens.size())+" columns (must be 4 or 5).").c_str()); C=Vector3r(boost::lexical_cast(tokens[0]),boost::lexical_cast(tokens[1]),boost::lexical_cast(tokens[2])); r=boost::lexical_cast(tokens[3]); for(int j=0; j<3; j++) { minXYZ[j]=(spheres.size()>0?min(C[j]-r,minXYZ[j]):C[j]-r); maxXYZ[j]=(spheres.size()>0?max(C[j]+r,maxXYZ[j]):C[j]+r);} if(tokens.size()==5)clumpId=boost::lexical_cast(tokens[4]); spheres.push_back(boost::tuple(C,r,clumpId)); } return spheres; } Real Shop::PWaveTimeStep(const shared_ptr _rb){ shared_ptr rb=(_rb?_rb:Omega::instance().getScene()); Real dt=std::numeric_limits::infinity(); FOREACH(const shared_ptr& b, *rb->bodies){ if(!b || !b->material || !b->shape) continue; shared_ptr ebp=YADE_PTR_DYN_CAST(b->material); shared_ptr s=YADE_PTR_DYN_CAST(b->shape); if(!ebp || !s) continue; Real density=b->state->mass/((4/3.)*Mathr::PI*pow(s->radius,3)); dt=min(dt,s->radius/sqrt(ebp->young/density)); } if (dt==std::numeric_limits::infinity()) { dt = 1.0; LOG_WARN("PWaveTimeStep has not found any suitable spherical body to calculate dt. dt is set to 1.0"); } return dt; } trunk-2017.01a/pkg/dem/Shop_02.cpp000066400000000000000000001072421304022710500164340ustar00rootroot00000000000000// 2007 © Václav Šmilauer #include"Shop.hpp" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #ifdef YADE_OPENGL #include #endif CREATE_LOGGER(Shop); /*! Flip periodic cell by given number of cells. Still broken, some interactions are missed. Should be checked. */ /* Detremination of time step as according to Rayleigh wave speed of force propagation (see Thornton 2000, ref. MillerPursey_1955) */ Real Shop::RayleighWaveTimeStep(const shared_ptr _rb){ shared_ptr rb=(_rb?_rb:Omega::instance().getScene()); Real dt=std::numeric_limits::infinity(); FOREACH(const shared_ptr& b, *rb->bodies){ if(!b || !b->material || !b->shape) continue; shared_ptr ebp=YADE_PTR_DYN_CAST(b->material); shared_ptr s=YADE_PTR_DYN_CAST(b->shape); if(!ebp || !s) continue; Real density=b->state->mass/((4/3.)*Mathr::PI*pow(s->radius,3)); Real ShearModulus=ebp->young/(2.*(1+ebp->poisson)); Real lambda=0.1631*ebp->poisson+0.876605; dt=min(dt,Mathr::PI*s->radius/lambda*sqrt(density/ShearModulus)); } return dt; } /* Project 3d point into 2d using spiral projection along given axis; * the returned tuple is * * (height relative to the spiral, distance from axis, theta ) * * dH_dTheta is the inclination of the spiral (height increase per radian), * theta0 is the angle for zero height (by given axis). */ boost::tuple Shop::spiralProject(const Vector3r& pt, Real dH_dTheta, int axis, Real periodStart, Real theta0){ int ax1=(axis+1)%3,ax2=(axis+2)%3; Real r=sqrt(pow(pt[ax1],2)+pow(pt[ax2],2)); Real theta; if(r>Mathr::ZERO_TOLERANCE){ theta=acos(pt[ax1]/r); if(pt[ax2]<0) theta=Mathr::TWO_PI-theta; } else theta=0; Real hRef=dH_dTheta*(theta-theta0); long period; if(std::isnan(periodStart)){ Real h=Shop::periodicWrap(pt[axis]-hRef,hRef-Mathr::PI*dH_dTheta,hRef+Mathr::PI*dH_dTheta,&period); return boost::make_tuple(r,h,theta); } else{ // Real hPeriodStart=(periodStart-theta0)*dH_dTheta; //Real h=Shop::periodicWrap(pt[axis]-hRef,hPeriodStart,hPeriodStart+2*Mathr::PI*dH_dTheta,&period); theta=Shop::periodicWrap(theta,periodStart,periodStart+2*Mathr::PI,&period); Real h=pt[axis]-hRef+period*2*Mathr::PI*dH_dTheta; return boost::make_tuple(r,h,theta); } } shared_ptr Shop::createExplicitInteraction(Body::id_t id1, Body::id_t id2, bool force){ IGeomDispatcher* geomMeta=NULL; IPhysDispatcher* physMeta=NULL; shared_ptr rb=Omega::instance().getScene(); if(rb->interactions->find(Body::id_t(id1),Body::id_t(id2))!=0) throw runtime_error(string("Interaction #")+boost::lexical_cast(id1)+"+#"+boost::lexical_cast(id2)+" already exists."); FOREACH(const shared_ptr& e, rb->engines){ if(!geomMeta) { geomMeta=dynamic_cast(e.get()); if(geomMeta) continue; } if(!physMeta) { physMeta=dynamic_cast(e.get()); if(physMeta) continue; } InteractionLoop* id(dynamic_cast(e.get())); if(id){ geomMeta=id->geomDispatcher.get(); physMeta=id->physDispatcher.get(); } if(geomMeta&&physMeta){break;} } if(!geomMeta) throw runtime_error("No IGeomDispatcher in engines or inside InteractionLoop."); if(!physMeta) throw runtime_error("No IPhysDispatcher in engines or inside InteractionLoop."); shared_ptr b1=Body::byId(id1,rb), b2=Body::byId(id2,rb); if(!b1) throw runtime_error(("No body #"+boost::lexical_cast(id1)).c_str()); if(!b2) throw runtime_error(("No body #"+boost::lexical_cast(id2)).c_str()); shared_ptr i=geomMeta->explicitAction(b1,b2,/*force*/force); assert(force && i); if(!i) return i; physMeta->explicitAction(b1->material,b2->material,i); i->iterMadeReal=rb->iter; rb->interactions->insert(i); return i; } Vector3r Shop::inscribedCircleCenter(const Vector3r& v0, const Vector3r& v1, const Vector3r& v2) { return v0+((v2-v0)*(v1-v0).norm()+(v1-v0)*(v2-v0).norm())/((v1-v0).norm()+(v2-v1).norm()+(v0-v2).norm()); } void Shop::getViscoelasticFromSpheresInteraction( Real tc, Real en, Real es, shared_ptr b) { throw runtime_error("Setting parameters in ViscoElastic model is changed. You do not need to use getViscoelasticFromSpheresInteraction function any more, because this functino is deprecated. You need to set the parameters tc, en and es directly in material properties. Please, update your scripts. How to do it you can see in the following commit https://github.com/yade/trunk/commit/1987c2febdb8a6ce2d27f2dc1bb29df0dc5f686e"); } /* This function is copied almost verbatim from scientific python, module Visualization, class ColorScale * */ Vector3r Shop::scalarOnColorScale(Real x, Real xmin, Real xmax){ Real xnorm=min((Real)1.,max((x-xmin)/(xmax-xmin),(Real)0.)); if(xnorm<.25) return Vector3r(0,4.*xnorm,1); if(xnorm<.5) return Vector3r(0,1,1.-4.*(xnorm-.25)); if(xnorm<.75) return Vector3r(4*(xnorm-.5),1.,0); return Vector3r(1,1-4*(xnorm-.75),0); } /* Wrap floating point number into interval (x0,x1〉such that it is shifted * by integral number of the interval range. If given, *period will hold * this number. The wrapped value is returned. */ Real Shop::periodicWrap(Real x, Real x0, Real x1, long* period){ Real xNorm=(x-x0)/(x1-x0); Real xxNorm=xNorm-floor(xNorm); if(period) *period=(long)floor(xNorm); return x0+xxNorm*(x1-x0); } void Shop::getStressForEachBody(vector& bodyStates){ const shared_ptr& scene=Omega::instance().getScene(); bodyStates.resize(scene->bodies->size()); FOREACH(const shared_ptr& I, *scene->interactions){ Vector3r normalStress,shearStress; if(!I->isReal()) continue; const FrictPhys* physFP = YADE_CAST(I->phys.get()); ScGeom* geomScG=YADE_CAST(I->geom.get()); const Body::id_t id1=I->getId1(), id2=I->getId2(); if((physFP) and (geomScG)){ Real minRad=(geomScG->radius1<=0?geomScG->radius2:(geomScG->radius2<=0?geomScG->radius1:min(geomScG->radius1,geomScG->radius2))); Real crossSection=Mathr::PI*pow(minRad,2); normalStress=((1./crossSection)*geomScG->normal.dot(physFP->normalForce))*geomScG->normal; for(int i=0; i<3; i++){ int ix1=(i+1)%3,ix2=(i+2)%3; shearStress[i]=geomScG->normal[ix1]*physFP->shearForce[ix1]+geomScG->normal[ix2]*physFP->shearForce[ix2]; shearStress[i]/=crossSection; } bodyStates[id1].normStress+=normalStress; bodyStates[id2].normStress+=normalStress; bodyStates[id1].shearStress+=shearStress; bodyStates[id2].shearStress+=shearStress; } } } /* Return the stress tensor decomposed in 2 contributions, from normal and shear forces. The formulation follows the [Thornton2000]_ article "Numerical simulations of deviatoric shear deformation of granular media", eq (3) and (4) */ py::tuple Shop::normalShearStressTensors(bool compressionPositive, bool splitNormalTensor, Real thresholdForce){ //*** Stress tensor split into shear and normal contribution ***/ Scene* scene=Omega::instance().getScene().get(); if (!scene->isPeriodic){ throw runtime_error("Can't compute stress of periodic cell in aperiodic simulation."); } Matrix3r sigN(Matrix3r::Zero()),sigT(Matrix3r::Zero()); //const Matrix3r& cellHsize(scene->cell->Hsize); //Disabled because of warning. FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; GenericSpheresContact* geom=YADE_CAST(I->geom.get()); NormShearPhys* phys=YADE_CAST(I->phys.get()); const Vector3r& n=geom->normal; // if compression has positive sign, we need to change sign for both normal and shear force // make copy to Fs since shearForce is used at multiple places (less efficient, but avoids confusion) Vector3r Fs=(compressionPositive?-1:1)*phys->shearForce; Real N=(compressionPositive?-1:1)*phys->normalForce.dot(n), T=Fs.norm(); bool hasShear=(T>0); Vector3r t; if(hasShear) t=Fs/T; // Real R=(Body::byId(I->getId2(),scene)->state->pos+cellHsize*I->cellDist.cast()-Body::byId(I->getId1(),scene)->state->pos).norm(); Real R=.5*(geom->refR1+geom->refR2); for(int i=0; i<3; i++) for(int j=i; j<3; j++){ sigN(i,j)+=R*N*n[i]*n[j]; if(hasShear) sigT(i,j)+=R*T*n[i]*t[j]; } } Real vol=scene->cell->getVolume(); sigN*=2/vol; sigT*=2/vol; // fill terms under the diagonal sigN(1,0)=sigN(0,1); sigN(2,0)=sigN(0,2); sigN(2,1)=sigN(1,2); sigT(1,0)=sigT(0,1); sigT(2,0)=sigT(0,2); sigT(2,1)=sigT(1,2); // *** Normal stress tensor split into two parts according to subnetworks of strong and weak forces (or other distinction if a threshold value for the force is assigned) ***/ Real Fmean(0); Matrix3r f, fs, fw; fabricTensor(Fmean,f,fs,fw); // 0,false,NaN for cutoff, split and thresholdForce as default arguments Matrix3r sigNStrong(Matrix3r::Zero()), sigNWeak(Matrix3r::Zero()); FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; GenericSpheresContact* geom=YADE_CAST(I->geom.get()); NormShearPhys* phys=YADE_CAST(I->phys.get()); const Vector3r& n=geom->normal; Real N=(compressionPositive?-1:1)*phys->normalForce.dot(n); // Real R=(Body::byId(I->getId2(),scene)->state->pos+cellHsize*I->cellDist.cast()-Body::byId(I->getId1(),scene)->state->pos).norm(); Real R=.5*(geom->refR1+geom->refR2); Real Fsplit=(!std::isnan(thresholdForce))?thresholdForce:Fmean; if (compressionPositive?(NFsplit)){ for(int i=0; i<3; i++) for(int j=i; j<3; j++){ sigNStrong(i,j)+=R*N*n[i]*n[j];} } else{ for(int i=0; i<3; i++) for(int j=i; j<3; j++){ sigNWeak(i,j)+=R*N*n[i]*n[j];} } } sigNStrong*=2/vol; sigNWeak*=2/vol; // fill terms under the diagonal sigNStrong(1,0)=sigNStrong(0,1); sigNStrong(2,0)=sigNStrong(0,2); sigNStrong(2,1)=sigNStrong(1,2); sigNWeak(1,0)=sigNWeak(0,1); sigNWeak(2,0)=sigNWeak(0,2); sigNWeak(2,1)=sigNWeak(1,2); /// tensile forces are taken as positive! if (splitNormalTensor){return py::make_tuple(sigNStrong,sigNWeak);} // return strong-weak or tensile-compressive parts of the stress tensor (only normal part) return py::make_tuple(sigN,sigT); // return normal and shear components } /* Return the fabric tensor as according to [Satake1982]. */ /* as side-effect, set Gl1_NormShear::strongWeakThresholdForce */ void Shop::fabricTensor(Real& Fmean, Matrix3r& fabric, Matrix3r& fabricStrong, Matrix3r& fabricWeak, Real cutoff, bool splitTensor, Real thresholdForce){ Scene* scene=Omega::instance().getScene().get(); // *** Fabric tensor ***/ fabric=Matrix3r::Zero(); int count=0; // number of interactions py::tuple aabb = Shop::aabbExtrema(cutoff); Vector3r bbMin = py::extract(aabb[0]), bbMax = py::extract(aabb[1]); Vector3r cp; Fmean=0; // initialize average contact force for split = 1 fabric measurements // interactions loop to compute the fabric tensor returned when split = 0, and also measures average force for subsequent computations for split = 1: FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; GenericSpheresContact* geom=YADE_CAST(I->geom.get()); cp = geom->contactPoint; if( !(cp[0]>=bbMin[0] && cp[0]<=bbMax[0] && cp[1]>=bbMin[1] && cp[1]<=bbMax[1] && cp[2]>=bbMin[2] && cp[2]<=bbMax[2]) ) continue; // possible to use isInBB() from _utils.cpp ? (NB: would exclude the contact points exactly along the BB) const Vector3r& n=geom->normal; for(int i=0; i<3; i++) for(int j=i; j<3; j++){ fabric(i,j)+=n[i]*n[j]; } NormShearPhys* phys=YADE_CAST(I->phys.get()); Real f=-phys->normalForce.dot(n); // will be < 0 in compression Fmean+=f; count++; } Fmean/=count; // fill terms under the diagonal fabric(1,0)=fabric(0,1); fabric(2,0)=fabric(0,2); fabric(2,1)=fabric(1,2); fabric/=count; #ifdef YADE_OPENGL Gl1_NormPhys::maxWeakFn=Fmean; #endif // *** Weak and strong fabric tensors ***/ // evaluate two different parts of the fabric tensor // making distinction between strong and weak network of contact forces fabricStrong=Matrix3r::Zero(); fabricWeak=Matrix3r::Zero(); int nStrong(0), nWeak(0); // number of strong and weak contacts respectively if (!splitTensor & !std::isnan(thresholdForce)) {LOG_WARN("The bool splitTensor should be set to True if you specified a threshold value for the contact force, otherwise the function will return only the fabric tensor and not the two separate contributions.");} FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; GenericSpheresContact* geom=YADE_CAST(I->geom.get()); cp = geom->contactPoint; if( !(cp[0]>=bbMin[0] && cp[0]<=bbMax[0] && cp[1]>=bbMin[1] && cp[1]<=bbMax[1] && cp[2]>=bbMin[2] && cp[2]<=bbMax[2]) ) continue; // see above for idea about isInBB() from _utils.cpp NormShearPhys* phys=YADE_CAST(I->phys.get()); const Vector3r& n=geom->normal; Real f=-phys->normalForce.dot(n); // slipt the tensor according to the mean contact force or a threshold value if this is given Real Fsplit=(!std::isnan(thresholdForce))?thresholdForce:Fmean; if (fisPeriodic ) { py::tuple extrema = Shop::aabbExtrema(); volumeNonPeri = py::extract( (extrema[1][0] - extrema[0][0])*(extrema[1][1] - extrema[0][1])*(extrema[1][2] - extrema[0][2]) ); } if (volume==0) volume = scene->isPeriodic?scene->cell->hSize.determinant():volumeNonPeri; Matrix3r stressTensor = Matrix3r::Zero(); const bool isPeriodic = scene->isPeriodic; FOREACH(const shared_ptr&I, *scene->interactions){ if (!I->isReal()) continue; shared_ptr b1 = Body::byId(I->getId1(),scene); shared_ptr b2 = Body::byId(I->getId2(),scene); if (b1->shape->getClassIndex()==GridNode::getClassIndexStatic()) continue; //no need to check b2 because a GridNode can only be in interaction with an oher GridNode. NormShearPhys* nsi=YADE_CAST ( I->phys.get() ); Vector3r branch=b1->state->pos -b2->state->pos; if (isPeriodic) branch-= scene->cell->hSize*I->cellDist.cast(); stressTensor += (nsi->normalForce+nsi->shearForce)*branch.transpose(); } return stressTensor/volume; } py::tuple Shop::getStressProfile(Real volume, int nCell, Real dz, Real zRef, vector vPartAverageX, vector vPartAverageY, vector vPartAverageZ){ int minZ=0; int maxZ=0; Real minPosZ=0.; Real maxPosZ=0.; Scene* scene=Omega::instance().getScene().get(); vector stressTensorProfile(nCell,Matrix3r::Zero()); vector kineticStressTensorProfile(nCell,Matrix3r::Zero()); vector granularTemperatureProfile(nCell,0.0); vector numPart(nCell,0.0); const bool isPeriodic = scene->isPeriodic; // //Dynamic contribution to the stress tensor // FOREACH(const shared_ptr& b,*Omega::instance().getScene()->bodies){ int Np = floor((b->state->pos[2]-zRef)/dz); //Define the layer number with 0 corresponding to zRef if ((Np>=0)&&(Npstate->vel - Vector3r(vPartAverageX[Np],vPartAverageY[Np],vPartAverageZ[Np]); //Classical dynamical expression of the stress tensor stressTensorProfile[Np]+= -1/volume*b->state->mass*vFluct*vFluct.transpose(); kineticStressTensorProfile[Np]+= -1/volume*b->state->mass*vFluct*vFluct.transpose(); granularTemperatureProfile[Np] += 1/3.*(pow(vFluct[0],2) + pow(vFluct[1],2) + pow(vFluct[2],2)); numPart[Np]+=1.; } } for(int n=0;n0) granularTemperatureProfile[n]/=numPart[n]; } // //Love Weber contribution (same as getStress(), but with different layers) // FOREACH(const shared_ptr&I, *scene->interactions){ // loop over the interactions if (!I->isReal()) continue; shared_ptr b1 = Body::byId(I->getId1(),scene); shared_ptr b2 = Body::byId(I->getId2(),scene); if ((b1->state->blockedDOFs!=State::DOF_ALL)||(b2->state->blockedDOFs!=State::DOF_ALL)){// to remove annoying contribution from the fixed particles //Layers in which the particle center is contained int Np1 = floor((b1->state->pos[2] - zRef)/dz); int Np2 = floor((b2->state->pos[2] - zRef)/dz); //Vector between the two centers, from 2 to 1 Vector3r branch = b1->state->pos -b2->state->pos; if (isPeriodic) branch -= scene->cell->hSize*I->cellDist.cast();//to handle periodicity //Contact vector (from 1 to 2) NormShearPhys* nsi=YADE_CAST ( I->phys.get() ); Vector3r fContact = nsi->normalForce + nsi->shearForce; //The contribution to the stress tensor is taken such that only the part of the branch vector //inside the cell is taken into account //If the whole vector is in the cell, add the whole contribution to the cell if (Np1==Np2){ if ((Np1>=0) && (Np1Np2){ minZ = Np2; minPosZ = b2->state->pos[2]-zRef; maxZ = Np1; maxPosZ = b1->state->pos[2]-zRef; } else if (Np2>Np1) { minZ = Np1; minPosZ = b1->state->pos[2]-zRef; maxZ = Np2; maxPosZ = b2->state->pos[2]-zRef; } Real branchS_x = pow(branch[0],2.0); Real branchS_y = pow(branch[1],2.0); Real branchS_z = pow(branch[2],2.0); //Normalize the branch vector branch/=sqrt(branchS_x + branchS_y+branchS_z); //Loop over the cell containing the branch vector int numLayer = minZ; while (numLayer<=maxZ){ if ((numLayer>= 0)&&(numLayer velAverageX(nCell,0.0); vector velAverageY(nCell,0.0); vector velAverageZ(nCell,0.0); vector phiAverage(nCell,0.0); //Loop over the particles FOREACH(const shared_ptr& b, *Omega::instance().getScene()->bodies){ shared_ptr s=YADE_PTR_DYN_CAST(b->shape); if(!s) continue; if (activateCond==true){ const Sphere* sphere = dynamic_cast(b->shape.get()); if (sphere->radius!=radiusPy) continue; } //select diameters asked const Real zPos = b->state->pos[2]-zRef; int Np = floor(zPos/dz); //Define the layer number with 0 corresponding to zRef. Let the z position wrt to zero, that way all z altitude are positive. (otherwise problem with volPart evaluation) minZ= floor((zPos-s->radius)/dz); maxZ= floor((zPos+s->radius)/dz); deltaCenter = zPos - Np*dz; // Loop over the cell in which the particle is contained numLayer = minZ; while (numLayer<=maxZ){ if ((numLayer>=0)&&(numLayerradius) zInf = -s->radius; if (zSup>s->radius) zSup = s->radius; //Analytical formulation of the volume of a slice of sphere volPart = Mathr::PI*pow(s->radius,2)*(zSup - zInf +(pow(zInf,3)-pow(zSup,3))/(3*pow(s->radius,2))); phiAverage[numLayer]+=volPart; velAverageX[numLayer]+=volPart*b->state->vel[0]; velAverageY[numLayer]+=volPart*b->state->vel[1]; velAverageZ[numLayer]+=volPart*b->state->vel[2]; } numLayer+=1; } } //Normalized the weighted velocity by the volume of particles contained inside the cell for(int n=0;nisPeriodic?scene->cell->hSize.determinant():1; Matrix3r stressTensor = Matrix3r::Zero(); const bool isPeriodic = scene->isPeriodic; FOREACH(const shared_ptr&I, *scene->interactions){ if (!I->isReal()) continue; shared_ptr b1 = Body::byId(I->getId1(),scene); shared_ptr b2 = Body::byId(I->getId2(),scene); Vector3r fCap = mindlin? YADE_CAST (I->phys.get())->fCap : YADE_CAST (I->phys.get())->fCap; Vector3r branch=b1->state->pos -b2->state->pos; if (isPeriodic) branch-= scene->cell->hSize*I->cellDist.cast(); stressTensor += fCap*branch.transpose(); } return stressTensor/volume; } void Shop::getStressLWForEachBody(vector& bStresses){ const shared_ptr& scene=Omega::instance().getScene(); bStresses.resize(scene->bodies->size()); for (size_t k=0;kbodies->size();k++) bStresses[k]=Matrix3r::Zero(); FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; GenericSpheresContact* geom=YADE_CAST(I->geom.get()); NormShearPhys* phys=YADE_CAST(I->phys.get()); Vector3r f=phys->normalForce+phys->shearForce; //Sum f_i*l_j/V for each contact of each particle bStresses[I->getId1()]-=(3.0/(4.0*Mathr::PI*pow(geom->refR1,3)))*f*((geom->contactPoint-Body::byId(I->getId1(),scene)->state->pos).transpose()); if (!scene->isPeriodic) bStresses[I->getId2()]+=(3.0/(4.0*Mathr::PI*pow(geom->refR2,3)))*f*((geom->contactPoint- (Body::byId(I->getId2(),scene)->state->pos)).transpose()); else bStresses[I->getId2()]+=(3.0/(4.0*Mathr::PI*pow(geom->refR2,3)))*f* ((geom->contactPoint- (Body::byId(I->getId2(),scene)->state->pos + (scene->cell->hSize*I->cellDist.cast()))).transpose()); } } py::list Shop::getStressLWForEachBody(){ py::list ret; vector bStresses; getStressLWForEachBody(bStresses); FOREACH(const Matrix3r& m, bStresses) ret.append(m); return ret; // return py::make_tuple(bStresses); } void Shop::calm(const shared_ptr& _scene, int mask){ const shared_ptr scene=(_scene?_scene:Omega::instance().getScene()); FOREACH(shared_ptr b, *scene->bodies){ if (!b || !b->isDynamic()) continue; if(((mask>0) and ((b->groupMask & mask)==0))) continue; b->state->vel=Vector3r::Zero(); b->state->angVel=Vector3r::Zero(); b->state->angMom=Vector3r::Zero(); } } py::list Shop::getBodyIdsContacts(Body::id_t bodyID) { py::list ret; if (bodyID < 0) { throw std::logic_error("BodyID should be a positive value!"); } const shared_ptr& scene=Omega::instance().getScene(); const shared_ptr& b = Body::byId(bodyID,scene); for(Body::MapId2IntrT::iterator it=b->intrs.begin(),end=b->intrs.end(); it!=end; ++it) { ret.append((*it).first); } return ret; } void Shop::setContactFriction(Real angleRad){ Scene* scene = Omega::instance().getScene().get(); shared_ptr& bodies = scene->bodies; FOREACH(const shared_ptr& b,*scene->bodies){ if(b->isClump()) continue; if (b->isDynamic()) YADE_PTR_CAST (b->material)->frictionAngle = angleRad; } FOREACH(const shared_ptr& ii, *scene->interactions){ if (!ii->isReal()) continue; const shared_ptr& sdec1 = YADE_PTR_CAST((*bodies)[(Body::id_t) ((ii)->getId1())]->material); const shared_ptr& sdec2 = YADE_PTR_CAST((*bodies)[(Body::id_t) ((ii)->getId2())]->material); //FIXME - why dynamic_cast fails here? FrictPhys* contactPhysics = YADE_CAST((ii)->phys.get()); const Real& fa = sdec1->frictionAngle; const Real& fb = sdec2->frictionAngle; contactPhysics->tangensOfFrictionAngle = std::tan(std::min(fa,fb)); } } void Shop::growParticles(Real multiplier, bool updateMass, bool dynamicOnly) { Scene* scene = Omega::instance().getScene().get(); const int sphereIdx = Sphere::getClassIndexStatic(); FOREACH(const shared_ptr& b,*scene->bodies){ if (dynamicOnly && !b->isDynamic()) continue; //We grow only spheres and clumps if(b->isClump() or sphereIdx == b->shape->getClassIndex()){ if (updateMass) {b->state->mass*=pow(multiplier,3); b->state->inertia*=pow(multiplier,5);} // for clumps we updated inertia, nothing else to do if (b->isClump()) continue; // for spheres, we update radius (YADE_CAST (b->shape.get()))->radius *= multiplier; // and if they are clump members,clump volume variation with homothetic displacement of all members if (b->isClumpMember()) b->state->pos += (multiplier-1) * (b->state->pos - Body::byId(b->clumpId, scene)->state->pos); } } FOREACH(const shared_ptr& ii, *scene->interactions){ int ci1=(*(scene->bodies))[ii->getId1()]->shape->getClassIndex(); int ci2=(*(scene->bodies))[ii->getId2()]->shape->getClassIndex(); if (ii->isReal()) { GenericSpheresContact* contact = YADE_CAST(ii->geom.get()); if ((!dynamicOnly || (*(scene->bodies))[ii->getId1()]->isDynamic()) && ci1==sphereIdx) contact->refR1 = YADE_CAST((* (scene->bodies))[ii->getId1()]->shape.get())->radius; if ((!dynamicOnly || (*(scene->bodies))[ii->getId2()]->isDynamic()) && ci2==sphereIdx) contact->refR2 = YADE_CAST((* (scene->bodies))[ii->getId2()]->shape.get())->radius; const shared_ptr& contactPhysics = YADE_PTR_CAST(ii->phys); contactPhysics->kn*=multiplier; contactPhysics->ks*=multiplier; } } } void Shop::growParticle(Body::id_t bodyID, Real multiplier, bool updateMass) { const shared_ptr& b = Body::byId(bodyID); Real& rad = YADE_CAST(b->shape.get())->radius; rad *= multiplier; if (updateMass) {b->state->mass*=pow(multiplier,3); b->state->inertia*=pow(multiplier,5);} for(Body::MapId2IntrT::iterator it=b->intrs.begin(),end=b->intrs.end(); it!=end; ++it) { //Iterate over all bodie's interactions if(!(*it).second->isReal()) continue; GenericSpheresContact* contact = YADE_CAST((*it).second->geom.get()); if (bodyID==it->second->getId1()) contact->refR1 = rad; else contact->refR2 = rad; } } py::tuple Shop::aabbExtrema(Real cutoff, bool centers){ if(cutoff<0. || cutoff>1.) throw invalid_argument("Cutoff must be >=0 and <=1."); Real inf=std::numeric_limits::infinity(); Vector3r minimum(inf,inf,inf),maximum(-inf,-inf,-inf); FOREACH(const shared_ptr& b, *Omega::instance().getScene()->bodies){ shared_ptr s=YADE_PTR_DYN_CAST(b->shape); if(!s) continue; Vector3r rrr(s->radius,s->radius,s->radius); minimum=minimum.cwiseMin(b->state->pos-(centers?Vector3r::Zero():rrr)); maximum=maximum.cwiseMax(b->state->pos+(centers?Vector3r::Zero():rrr)); } Vector3r dim=maximum-minimum; return py::make_tuple(Vector3r(minimum+.5*cutoff*dim),Vector3r(maximum-.5*cutoff*dim)); } /*! Added function for 2D calculation: sphere volume. Optional. By Ning Guo */ Real Shop::getSpheresVolume2D(const shared_ptr& _scene, int mask){ const shared_ptr scene=(_scene?_scene:Omega::instance().getScene()); Real vol=0; FOREACH(shared_ptr b, *scene->bodies){ if (!b) continue; Sphere* s=dynamic_cast(b->shape.get()); if((!s) or ((mask>0) and ((b->groupMask & mask)==0))) continue; vol += Mathr::PI*pow(s->radius,2); } return vol; } /*! Added function for 2D calculation: void ratio. Optional. By Ning Guo */ Real Shop::getVoidRatio2D(const shared_ptr& _scene, Real _zlen){ const shared_ptr scene=(_scene?_scene:Omega::instance().getScene()); Real V; if(!scene->isPeriodic){ throw std::invalid_argument("utils.voidratio2D applies only to aperiodic simulations."); } else { V=scene->cell->getVolume()/_zlen; } Real Vs=Shop::getSpheresVolume2D(); return (V-Vs)/Vs; } /*! Added function to get stress tensor and tangent operator tensor. By Ning Guo */ py::tuple Shop::getStressAndTangent(Real volume, bool symmetry){ Scene* scene=Omega::instance().getScene().get(); if (volume==0) volume = scene->isPeriodic?scene->cell->hSize.determinant():1; Matrix3r stress = Matrix3r::Zero(); Matrix6r tangent = Matrix6r::Zero(); const bool isPeriodic = scene->isPeriodic; FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; shared_ptr b1 = Body::byId(I->getId1(),scene); shared_ptr b2 = Body::byId(I->getId2(),scene); Vector3r pos1 = Vector3r::Zero(); Vector3r pos2 = Vector3r::Zero(); if(b1->isClumpMember()) { pos1 = Body::byId(b1->clumpId,scene)->state->pos; } else { pos1 = b1->state->pos; } if(b2->isClumpMember()) { pos2 = Body::byId(b2->clumpId,scene)->state->pos; } else { pos2 = b2->state->pos; } Vector3r branch=pos1 - pos2; if (isPeriodic) branch -= scene->cell->hSize*I->cellDist.cast(); NormShearPhys* nsi=YADE_CAST(I->phys.get()); Real kN=nsi->kn; Real kT=nsi->ks; GenericSpheresContact* geom=YADE_CAST(I->geom.get()); const Vector3r& n=geom->normal; const Vector3r& fT=nsi->shearForce; const Vector3r& fTotal=nsi->normalForce+nsi->shearForce; Real T=fT.norm(); bool hasShear=(T>0); Vector3r t(Vector3r::Zero()); if(hasShear) t=fT/T; stress += fTotal*branch.transpose(); tangent(0,0) += kN*n[0]*branch[0]*n[0]*branch[0]+kT*t[0]*branch[0]*t[0]*branch[0]; tangent(0,1) += kN*n[0]*branch[0]*n[1]*branch[1]+kT*t[0]*branch[0]*t[1]*branch[1]; tangent(0,2) += kN*n[0]*branch[0]*n[2]*branch[2]+kT*t[0]*branch[0]*t[2]*branch[2]; tangent(0,3) += kN*n[0]*branch[0]*(n[1]*branch[2]+n[2]*branch[1])*0.5+kT*t[0]*branch[0]*(t[1]*branch[2]+t[2]*branch[1])*0.5; tangent(0,4) += kN*n[0]*branch[0]*(n[0]*branch[2]+n[2]*branch[0])*0.5+kT*t[0]*branch[0]*(t[0]*branch[2]+t[2]*branch[0])*0.5; tangent(0,5) += kN*n[0]*branch[0]*(n[0]*branch[1]+n[1]*branch[0])*0.5+kT*t[0]*branch[0]*(t[0]*branch[1]+t[1]*branch[0])*0.5; tangent(1,1) += kN*n[1]*branch[1]*n[1]*branch[1]+kT*t[1]*branch[1]*t[1]*branch[1]; tangent(1,2) += kN*n[1]*branch[1]*n[2]*branch[2]+kT*t[1]*branch[1]*t[2]*branch[2]; tangent(1,3) += kN*n[1]*branch[1]*(n[1]*branch[2]+n[2]*branch[1])*0.5+kT*t[1]*branch[1]*(t[1]*branch[2]+t[2]*branch[1])*0.5; tangent(1,4) += kN*n[1]*branch[1]*(n[0]*branch[2]+n[2]*branch[0])*0.5+kT*t[1]*branch[1]*(t[0]*branch[2]+t[2]*branch[0])*0.5; tangent(1,5) += kN*n[1]*branch[1]*(n[0]*branch[1]+n[1]*branch[0])*0.5+kT*t[1]*branch[1]*(t[0]*branch[1]+t[1]*branch[0])*0.5; tangent(2,2) += kN*n[2]*branch[2]*n[2]*branch[2]+kT*t[2]*branch[2]*t[2]*branch[2]; tangent(2,3) += kN*n[2]*branch[2]*(n[1]*branch[2]+n[2]*branch[1])*0.5+kT*t[2]*branch[2]*(t[1]*branch[2]+t[2]*branch[1])*0.5; tangent(2,4) += kN*n[2]*branch[2]*(n[0]*branch[2]+n[2]*branch[0])*0.5+kT*t[2]*branch[2]*(t[0]*branch[2]+t[2]*branch[0])*0.5; tangent(2,5) += kN*n[2]*branch[2]*(n[0]*branch[1]+n[1]*branch[0])*0.5+kT*t[2]*branch[2]*(t[0]*branch[1]+t[1]*branch[0])*0.5; tangent(3,3) += kN*(n[1]*branch[2]*n[1]*branch[2]+n[1]*branch[2]*n[2]*branch[1]*2+n[2]*branch[1]*n[2]*branch[1])*0.25+kT*(t[1]*branch[2]*t[1]*branch[2]+t[1]*branch[2]*t[2]*branch[1]*2+t[2]*branch[1]*t[2]*branch[1])*0.25; tangent(3,4) += kN*(n[1]*branch[2]*n[0]*branch[2]+n[1]*branch[2]*n[2]*branch[0]+n[2]*branch[1]*n[0]*branch[2]+n[2]*branch[1]*n[2]*branch[0])*0.25+kT*(t[1]*branch[2]*t[0]*branch[2]+t[1]*branch[2]*t[2]*branch[0]+t[2]*branch[1]*t[0]*branch[2]+t[2]*branch[1]*t[2]*branch[0])*0.25; tangent(3,5) += kN*(n[1]*branch[2]*n[0]*branch[1]+n[1]*branch[2]*n[1]*branch[0]+n[2]*branch[1]*n[0]*branch[1]+n[2]*branch[1]*n[1]*branch[0])*0.25+kT*(t[1]*branch[2]*t[0]*branch[1]+t[1]*branch[2]*t[1]*branch[0]+t[2]*branch[1]*t[0]*branch[1]+t[2]*branch[1]*t[1]*branch[0])*0.25; tangent(4,4) += kN*(n[0]*branch[2]*n[0]*branch[2]+n[0]*branch[2]*n[2]*branch[0]*2+n[2]*branch[0]*n[2]*branch[0])*0.25+kT*(t[0]*branch[2]*t[0]*branch[2]+t[0]*branch[2]*t[2]*branch[0]*2+t[2]*branch[0]*t[2]*branch[0])*0.25; tangent(4,5) += kN*(n[0]*branch[2]*n[0]*branch[1]+n[0]*branch[2]*n[1]*branch[0]+n[2]*branch[0]*n[0]*branch[1]+n[2]*branch[0]*n[1]*branch[0])*0.25+kT*(t[0]*branch[2]*t[0]*branch[1]+t[0]*branch[2]*t[1]*branch[0]+t[2]*branch[0]*t[0]*branch[1]+t[2]*branch[0]*t[1]*branch[0])*0.25; tangent(5,5) += kN*(n[0]*branch[1]*n[0]*branch[1]+n[0]*branch[1]*n[1]*branch[0]*2+n[1]*branch[0]*n[1]*branch[0])*0.25+kT*(t[0]*branch[1]*t[0]*branch[1]+t[0]*branch[1]*t[1]*branch[0]*2+t[1]*branch[0]*t[1]*branch[0])*0.25; } stress/=volume; tangent/=volume; return py::make_tuple(stress,tangent); } trunk-2017.01a/pkg/dem/SimpleShear.cpp000066400000000000000000000263541304022710500174420ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2008 by Jerome Duriez * * duriez@geo.hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "SimpleShear.hpp" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include YADE_PLUGIN((SimpleShear)) CREATE_LOGGER(SimpleShear); SimpleShear::~SimpleShear () { } bool SimpleShear::generate(std::string& message) { scene = shared_ptr(new Scene); createActors(scene); // Box walls shared_ptr w1; // The left one : createBox(w1,Vector3r(-thickness/2.0,(height)/2.0,0),Vector3r(thickness/2.0,5*(height/2.0+thickness),width/2.0)); scene->bodies->insert(w1); shared_ptr w2; // The lower one : createBox(w2,Vector3r(length/2.0,-thickness/2.0,0),Vector3r(length/2.0,thickness/2.0,width/2.0)); YADE_PTR_CAST (w2->material)->frictionAngle = sphereFrictionDeg * Mathr::PI/180.0; // so that we have phi(spheres-inferior wall)=phi(sphere-sphere) scene->bodies->insert(w2); shared_ptr w3; // The right one createBox(w3,Vector3r(length+thickness/2.0,height/2.0,0),Vector3r(thickness/2.0,5*(height/2.0+thickness),width/2.0)); scene->bodies->insert(w3); shared_ptr w4; // The upper one createBox(w4,Vector3r(length/2.0,height+thickness/2.0,0),Vector3r(length/2.0,thickness/2.0,width/2.0)); YADE_PTR_CAST (w4->material)->frictionAngle = sphereFrictionDeg * Mathr::PI/180.0; // so that we have phi(spheres-superior wall)=phi(sphere-sphere) scene->bodies->insert(w4); // To close the front and the back of the box shared_ptr w5; // behind createBox(w5,Vector3r(length/2.0,height/2.0,-width/2.0-thickness/2.0), Vector3r(2.5*length/2.0,height/2.0+thickness,thickness/2.0)); scene->bodies->insert(w5); shared_ptr w6; // the front createBox(w6,Vector3r(length/2.0,height/2.0,width/2.0+thickness/2.0), Vector3r(2.5*length/2.0,height/2.0+thickness,thickness/2.0)); scene->bodies->insert(w6); // the list which will contain the positions of centers and the radii of the created spheres vector sphere_list; // to use the TriaxialTest method : string out=GenerateCloud(sphere_list,Vector3r(0,0,-width/2.0),Vector3r(length,height,width/2.0),1000,0.3,0.7);// tries to generate a sample of 1000 spheres, with a required porosity of 0.7 cout << out << endl; // to use a text file : // std::pair res=ImportCloud(sphere_list,filename); vector::iterator it = sphere_list.begin(); vector::iterator it_end = sphere_list.end(); shared_ptr body; for (;it!=it_end; ++it) { createSphere(body,it->first,it->second); scene->bodies->insert(body); } return true; } void SimpleShear::createSphere(shared_ptr& body, Vector3r position, Real radius) { body = shared_ptr(new Body); body->groupMask=1; shared_ptr mat(new NormalInelasticMat); shared_ptr aabb(new Aabb); shared_ptr iSphere(new Sphere); body->state->pos =position; body->state->ori =Quaternionr::Identity(); body->state->vel =Vector3r(0,0,0); body->state->angVel =Vector3r(0,0,0); Real masse =4.0/3.0*Mathr::PI*radius*radius*radius*density; body->state->mass =masse; body->state->inertia = Vector3r(2.0/5.0*masse*radius*radius,2.0/5.0*masse*radius*radius,2.0/5.0*masse*radius*radius); mat->young = sphereYoungModulus; mat->poisson = spherePoissonRatio; mat->frictionAngle = sphereFrictionDeg * Mathr::PI/180.0; body->material = mat; aabb->color = Vector3r(0,1,0); iSphere->radius = radius; iSphere->color = ((int)(floor(8*position.x()/length)))%2?Vector3r(0.7,0.7,0.7):Vector3r(0.45,0.45,0.45);// so that we have eight different colour bands body->shape = iSphere; body->bound = aabb; } void SimpleShear::createBox(shared_ptr& body, Vector3r position, Vector3r extents) { body = shared_ptr(new Body); body->groupMask=1; shared_ptr mat(new NormalInelasticMat); shared_ptr aabb(new Aabb); // shared_ptr gBox(new BoxModel); shared_ptr iBox(new Box); iBox->wire = true; body->setDynamic(false); body->state->angVel = Vector3r(0,0,0); body->state->vel = Vector3r(0,0,0); // NB : mass and inertia not defined because not used, since Box are not dynamics body->state->pos = position; body->state->ori = Quaternionr::Identity(); mat->young = boxYoungModulus; mat->poisson = boxPoissonRatio; mat->frictionAngle = 0.0; //default value, modified after for w2 and w4 to have good values of phi(sphere-walls) body->material = mat; aabb->color = Vector3r(1,0,0); /* gBox->extents = extents; gBox->color = Vector3r(1,0,0); gBox->wire = true; gBox->shadowCaster = false;*/ iBox->extents = extents; iBox->color = Vector3r(1,0,0); body->bound = aabb; body->shape = iBox; // body->geometricalModel = gBox; } void SimpleShear::createActors(shared_ptr& scene) { shared_ptr interactionGeometryDispatcher(new IGeomDispatcher); interactionGeometryDispatcher->add(new Ig2_Sphere_Sphere_ScGeom6D); interactionGeometryDispatcher->add(new Ig2_Box_Sphere_ScGeom6D); shared_ptr interactionPhysicsDispatcher(new IPhysDispatcher); shared_ptr CL1Rel(new Ip2_2xNormalInelasticMat_NormalInelasticityPhys); interactionPhysicsDispatcher->add(CL1Rel); shared_ptr collider(new InsertionSortCollider); collider->boundDispatcher->add(new Bo1_Sphere_Aabb); collider->boundDispatcher->add(new Bo1_Box_Aabb); shared_ptr gravityCondition(new GravityEngine); gravityCondition->gravity = gravity; shared_ptr globalStiffnessTimeStepper(new GlobalStiffnessTimeStepper); globalStiffnessTimeStepper->timeStepUpdateInterval = timeStepUpdateInterval; globalStiffnessTimeStepper->defaultDt=3e-6; shared_ptr kinemEngine (new KinemCTDEngine); kinemEngine->compSpeed = 10.0; kinemEngine->targetSigma=2000.0; shared_ptr ids(new InteractionLoop); ids->geomDispatcher=interactionGeometryDispatcher; ids->physDispatcher=interactionPhysicsDispatcher; ids->lawDispatcher=shared_ptr(new LawDispatcher); shared_ptr ldc(new Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity); ids->lawDispatcher->add(ldc); scene->engines.clear(); scene->engines.push_back(shared_ptr(new ForceResetter)); scene->engines.push_back(globalStiffnessTimeStepper); scene->engines.push_back(collider); scene->engines.push_back(ids); if(gravApplied) scene->engines.push_back(gravityCondition); scene->engines.push_back(shared_ptr (new NewtonIntegrator)); scene->engines.push_back(kinemEngine); } string SimpleShear::GenerateCloud(vector& sphere_list,Vector3r lowerCorner,Vector3r upperCorner,long number,Real rad_std_dev, Real porosity) { sphere_list.clear(); long tries = 1000; //nb max of tries for positionning the next sphere Vector3r dimensions = upperCorner - lowerCorner; Real mean_radius = pow(dimensions.x()*dimensions.y()*dimensions.z()*(1-porosity)/(4.0/3.0*Mathr::PI*number),1.0/3.0); cerr << " mean radius " << mean_radius << endl;; // std::cerr << "generating aggregates ... "; long t, i; for (i=0; i (sphere_list[j].first-s.first).squaredNorm()) overlap=true; if (!overlap) { sphere_list.push_back(s); // cout << "j'ai bien rajoute une sphere dans la liste" << endl; break; } } if (t==tries) { string str1="Generated a sample with " + boost::lexical_cast(i) + " spheres inside box of dimensions: (" + boost::lexical_cast(dimensions[0]) + "," + boost::lexical_cast(dimensions[1]) + "," + boost::lexical_cast(dimensions[2]) + ").\n"; return str1 + "More than " + boost::lexical_cast(tries) + " tries while generating sphere number " + boost::lexical_cast(i+1) + "/" + boost::lexical_cast(number) + "."; } } return "Generated a sample with " + boost::lexical_cast(number) + " spheres inside box of dimensions: (" + boost::lexical_cast(dimensions[0]) + "," + boost::lexical_cast(dimensions[1]) + "," + boost::lexical_cast(dimensions[2]) + ")."; } std::pair SimpleShear::ImportCloud(vector& sphere_list,string importFilename) { sphere_list.clear(); int nombre=0; if(importFilename.size() != 0 && boost::filesystem::exists(importFilename) ) { ifstream loadFile(importFilename.c_str()); // cree l'objet loadFile de la classe ifstream qui va permettre de lire ce qu'il y a dans importFilename // Real zJF; // while( !loadFile.eof() ) // tant qu'on n'est pas a la fin du fichier // { // BasicSphere s; // l'elt de la liste sphere_list (= la sphere) que l'on va lire maintenant // loadFile >> s.first.X();// le X de la position de son centre // loadFile >> zJF; // s.first.Z()=zJF - width/2.0;// le Z de la position de son centre // loadFile >> s.first.Y();// le Y de la position de son centre // loadFile >> s.second; // son rayon // sphere_list.push_back(s); // nombre++; // } Real it; while( !loadFile.eof() ) // tant qu'on n'est pas a la fin du fichier { BasicSphere s; // l'elt de la liste sphere_list (= la sphere) que l'on va lire maintenant loadFile >> it; loadFile >> s.second; // son rayon loadFile >> s.first.x(); loadFile >> s.first.y();// le y de la position de son centre loadFile >> s.first.z();// le z de la position de son centre sphere_list.push_back(s); nombre++; } return std::make_pair(std::string("Echantillon correctement genere : " + boost::lexical_cast(nombre) + " billes"),true); } else { cerr << "Cannot find input file" << endl; return std::make_pair("Cannot find input file",false); } } trunk-2017.01a/pkg/dem/SimpleShear.hpp000066400000000000000000000077371304022710500174530ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2008 by Jerome Duriez * * duriez@geo.hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include typedef pair BasicSphere; //! make a list of spheres non-overlapping sphere class SimpleShear : public FileGenerator { void createBox(shared_ptr& body, Vector3r position, Vector3r extents); void createSphere(shared_ptr& body, Vector3r position, Real radius); void createActors(shared_ptr& scene); //method to create a list (containing the positions of centers and radii) of n non interpenetrating spheres, occupying a rectangle with a given (rather high) porosity (issued from TriaxialTest) : string GenerateCloud(vector& sphere_list,Vector3r lowerCorner,Vector3r upperCorner,long number,Real rad_std_dev, Real porosity); // to create the same list but by reading a text file containing the information : std::pair ImportCloud(vector& sphere_list,string importFilename); public : ~SimpleShear (); bool generate(std::string& message); YADE_CLASS_BASE_DOC_ATTRS(SimpleShear,FileGenerator,"Preprocessor for creating a numerical model of a simple shear box.\n\n\t- Boxes (6) constitute the different sides of the box itself\n \t- Spheres are contained in the box. The sample is generated by default via the same method used in TriaxialTest Preprocesor (=> see in source function GenerateCloud). But import of a list of spheres from a text file can be also performed after few changes in the source code.\n \n \t Launching this preprocessor will carry out an oedometric compression, until a value of normal stress equal to 2 MPa (and stable). But with others Engines :yref:`KinemCNDEngine`, :yref:`KinemCNSEngine` and :yref:`KinemCNLEngine`, respectively constant normal displacement, constant normal rigidity and constant normal stress paths can be carried out for such simple shear boxes.\n \n \tNB about micro-parameters : their default values correspond to those used in [Duriez2009a]_ and [Duriez2011]_ to simulate infilled rock joints.", /* ((string,filename,"../porosite0_44.txt",,"file with the list of spheres centers and radii"))*/ ((Real,thickness,0.001,,"thickness of the boxes constituting the shear box [$m$]")) ((Real,length,0.1,,"initial length (along x-axis) of the shear box [$m$]")) ((Real,height,0.02,,"initial height (along y-axis) of the shear box [$m$]")) ((Real,width,0.04,,"initial width (along z-axis) of the shear box [$m$]")) ((Real,density,2600,,"density of the spheres [$kg/m^3$]")) ((Real,sphereYoungModulus,4.0e9,,"value of :yref:`ElastMat::young` for the spheres [$Pa$]")) ((Real,spherePoissonRatio,0.04,,"value of :yref:`ElastMat::poisson` for the spheres [-]")) ((Real,sphereFrictionDeg,37,,"value of :yref:`ElastMat::poisson` for the spheres [$^\\circ$] (the necessary conversion in $rad$ is done automatically)")) ((Real,boxYoungModulus,4.0e9,,"value of :yref:`ElastMat::young` for the boxes [$Pa$]")) ((Real,boxPoissonRatio,0.04,,"value of :yref:`ElastMat::poisson` for the spheres [-]")) ((bool,gravApplied,false,,"depending on this, :yref:`GravityEngine` is added or not to the scene to take into account the weight of particles")) ((Vector3r,gravity,Vector3r(0,-9.81,0),,"vector corresponding to used gravity (if :yref:`gravApplied`) [$m/s^2$]")) ((int,timeStepUpdateInterval,50,,"value of :yref:`TimeStepper::timeStepUpdateInterval` for the :yref:`TimeStepper` used here")) ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(SimpleShear); trunk-2017.01a/pkg/dem/SnapshotEngine.cpp000066400000000000000000000032351304022710500201440ustar00rootroot00000000000000#ifdef YADE_OPENGL #include"SnapshotEngine.hpp" YADE_PLUGIN((SnapshotEngine)); CREATE_LOGGER(SnapshotEngine); void SnapshotEngine::action(){ if(!OpenGLManager::self) throw logic_error("No OpenGLManager instance?!"); if(OpenGLManager::self->views.size()==0){ int viewNo=OpenGLManager::self->waitForNewView(deadTimeout); if(viewNo<0){ if(!ignoreErrors) throw runtime_error("SnapshotEngine: Timeout waiting for new 3d view."); else { LOG_WARN("Making myself Engine::dead, as I can not live without a 3d view (timeout)."); dead=true; return; } } } const shared_ptr& glv=OpenGLManager::self->views[0]; ostringstream fss; fss<setSnapshotFormat(QString(format.c_str())); glv->nextFrameSnapshotFilename=fss.str(); // wait for the renderer to save the frame (will happen at next postDraw) timespec t1,t2; t1.tv_sec=0; t1.tv_nsec=10000000; /* 10 ms */ long waiting=0; while(!glv->nextFrameSnapshotFilename.empty()){ nanosleep(&t1,&t2); waiting++; if(((waiting) % 1000)==0) LOG_WARN("Already waiting "<deadTimeout){ if(ignoreErrors){ LOG_WARN("Timeout waiting for snapshot to be saved, making byself Engine::dead"); dead=true; return; } else throw runtime_error("SnapshotEngine: Timeout waiting for snapshot to be saved."); } } snapshots.push_back(fss.str()); usleep((long)(msecSleep*1000)); //if(!plot.empty()){ pyRunString("import yade.plot; yade.plot.addImgData("+plot+"='"+fss.str()+"')"); } } #endif /* YADE_OPENGL */ trunk-2017.01a/pkg/dem/SnapshotEngine.hpp000066400000000000000000000032071304022710500201500ustar00rootroot00000000000000#pragma once #include #include #include #ifdef YADE_QT5 #include #elif YADE_QT4 #include #endif class SnapshotEngine: public PeriodicEngine { public: virtual void action(); YADE_CLASS_BASE_DOC_ATTRS(SnapshotEngine,PeriodicEngine,"Periodically save snapshots of GLView(s) as .png files. Files are named *fileBase* + *counter* + '.png' (counter is left-padded by 0s, i.e. snap00004.png).", ((string,format,"PNG",,"Format of snapshots (one of JPEG, PNG, EPS, PS, PPM, BMP) `QGLViewer documentation `_. File extension will be lowercased *format*. Validity of format is not checked.")) ((string,fileBase,"",,"Basename for snapshots")) ((int,counter,0,,"Number that will be appended to fileBase when the next snapshot is saved (incremented at every save). |yupdate|")) ((bool,ignoreErrors,true,,"Only report errors instead of throwing exceptions, in case of timeouts.")) ((vector,snapshots,,,"Files that have been created so far")) ((int,msecSleep,0,,"number of msec to sleep after snapshot (to prevent 3d hw problems) [ms]")) ((Real,deadTimeout,3,,"Timeout for 3d operations (opening new view, saving snapshot); after timing out, throw exception (or only report error if *ignoreErrors*) and make myself :yref:`dead`. [s]")) ((string,plot,,,"Name of field in :yref:`yade.plot.imgData` to which taken snapshots will be appended automatically.")) ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(SnapshotEngine); trunk-2017.01a/pkg/dem/SpherePack.cpp000066400000000000000000000533061304022710500172500ustar00rootroot00000000000000// © 2009 Václav Šmilauer #include #include #include #include #include #include #include #include #include // not a serializable in the sense of YADE_PLUGIN CREATE_LOGGER(SpherePack); namespace py=boost::python; void SpherePack::fromList(const py::list& l){ pack.clear(); size_t len=py::len(l); for(size_t i=0; i(l[i]); py::extract vec(t[0]); if(vec.check()) { pack.push_back(Sph(vec(),py::extract(t[1]),(py::len(t)>2?py::extract(t[2]):-1))); continue; } PyErr_SetString(PyExc_TypeError, "List elements must be (Vector3, float) or (Vector3, float, int)!"); py::throw_error_already_set(); } }; void SpherePack::fromLists(const vector& centers, const vector& radii){ pack.clear(); if(centers.size()!=radii.size()) throw std::invalid_argument(("The same number of centers and radii must be given (is "+boost::lexical_cast(centers.size())+", "+boost::lexical_cast(radii.size())+")").c_str()); size_t l=centers.size(); for(size_t i=0; i tupleVector3rRealInt; vector ss; Vector3r mn,mx; ss=Shop::loadSpheresFromFile(file,mn,mx,&cellSize); pack.clear(); FOREACH(const tupleVector3rRealInt& s, ss) pack.push_back(Sph(boost::get<0>(s),boost::get<1>(s),boost::get<2>(s))); } void SpherePack::toFile(const string fname) const { ofstream f(fname.c_str()); if(!f.good()) throw runtime_error("Unable to open file `"+fname+"'"); if(cellSize!=Vector3r::Zero()){ f<<"##PERIODIC:: "<=0) throw std::invalid_argument("SpherePack with clumps cannot be (currently) exported to a text file."); f<& b, *scene->bodies){ if(!b) continue; shared_ptr intSph=YADE_PTR_DYN_CAST(b->shape); if(!intSph) continue; pack.push_back(Sph(b->state->pos,intSph->radius,(b->isClumpMember()?b->clumpId:-1))); } if(scene->isPeriodic) { cellSize=scene->cell->getSize(); isPeriodic = true; } } long SpherePack::makeCloud(Vector3r mn, Vector3r mx, Real rMean, Real rRelFuzz, int num, bool periodic, Real porosity, const vector& psdSizes, const vector& psdCumm, bool distributeMass, int seed, Matrix3r hSize){ isPeriodic = periodic; static boost::minstd_rand randGen(seed!=0?seed:(int)TimingInfo::getNow(/* get the number even if timing is disabled globally */ true)); static boost::variate_generator > rnd(randGen, boost::uniform_real(0,1)); vector psdRadii; // holds plain radii (rather than diameters), scaled down in some situations to get the target number vector psdCumm2; // psdCumm but dimensionally transformed to match mass distribution Vector3r size=mx-mn; bool hSizeFound =(hSize!=Matrix3r::Zero());//is hSize passed to the function? if (!hSizeFound) {hSize=size.asDiagonal();} if (hSizeFound && !periodic) LOG_WARN("hSize can be defined only for periodic cells."); Real volume=hSize.determinant(); Matrix3r invHsize =hSize.inverse(); Real area=std::abs(size[0]*size[2]+size[0]*size[1]+size[1]*size[2]);//2 terms will be null if one coordinate is 0, the other is the area if (!volume) { if (hSizeFound) throw invalid_argument("The period defined by hSize has null length in at least one direction, this is not supported. Define flat boxes via min-max and keep hSize undefined if you want a 2D packing."); else LOG_WARN("The volume of the min-max box is null, we will assume that the packing is 2D. If it is not what you want then you defined wrong input values; check that min and max corners are defined correctly.");} int mode=-1; bool err=false; // determine the way we generate radii if(porosity<=0) {LOG_WARN("porosity must be >0, changing it for you. It will be ineffective if rMean>0."); porosity=0.5;} //If rMean is not defined, then in will be defined in RDIST_NUM if(rMean>0) mode=RDIST_RMEAN; else if(num>0 && psdSizes.size()==0) { mode=RDIST_NUM; // the term (1+rRelFuzz²) comes from the mean volume for uniform distribution : Vmean = 4/3*pi*Rmean*(1+rRelFuzz²) if (volume) rMean=pow(volume*(1-porosity)/(Mathr::PI*(4/3.)*(1+rRelFuzz*rRelFuzz)*num),1/3.); else {//The volume is null, we will generate a 2D packing with the following rMean if (!area) throw invalid_argument("The box defined has null volume AND null surface. Define at least maxCorner of the box, or hSize if periodic."); rMean=pow(area*(1-porosity)/(Mathr::PI*(1+rRelFuzz*rRelFuzz)*num),0.5);} } // transform sizes and cummulated fractions values in something convenient for the generation process if(psdSizes.size()>0){ err=(mode>=0); mode=RDIST_PSD; if(psdSizes.size()!=psdCumm.size()) throw invalid_argument(("SpherePack.makeCloud: psdSizes and psdCumm must have same dimensions ("+boost::lexical_cast(psdSizes.size())+"!="+boost::lexical_cast(psdCumm.size())).c_str()); if(psdSizes.size()<=1) throw invalid_argument("SpherePack.makeCloud: psdSizes must have at least 2 items"); if((*psdCumm.begin())!=0. && (*psdCumm.rbegin())!=1.) throw invalid_argument("SpherePack.makeCloud: first and last items of psdCumm *must* be exactly 0 and 1."); psdRadii.reserve(psdSizes.size()); for(size_t i=0; i0 && (psdSizes[i-1]>psdSizes[i] || psdCumm[i-1]>psdCumm[i])) throw invalid_argument("SpherePack:makeCloud: psdSizes and psdCumm must be both non-decreasing."); } // check the consistency between sizes, num, and poro if all three are imposed. If target number will not fit in (1-poro)*volume, scale down particles sizes if (num>1){ appliedPsdScaling=1; if(distributeMass) { if (psdCumm2[psdSizes.size()-1]1) appliedPsdScaling=pow(volumeRatio,-1./3.); } if (appliedPsdScaling<1) for(size_t i=0; i0), generate radii the deterministic way, in decreasing order, else radii are stochastic since we don't know what the final number will be if (num>0) rand = ((Real)num-(Real)i+0.5)/((Real)num+1.); else rand = rnd(); int t; switch(mode){ case RDIST_RMEAN: //FIXME : r is never defined, it will be zero at first iteration, but it will have values in the next ones. //I don't understand why it apparently works. Some magic? case RDIST_NUM: if(distributeMass) r=pow3Interp(rand,rMean*(1-rRelFuzz),rMean*(1+rRelFuzz)); else r=rMean*(2*(rand-.5)*rRelFuzz+1); // uniform distribution in rMean*(1±rRelFuzz) break; case RDIST_PSD: if(distributeMass){ int piece=psdGetPiece(rand,psdCumm2,norm); r=pow3Interp(norm,psdRadii[piece],psdRadii[piece+1]); } else { int piece=psdGetPiece(rand,psdCumm,norm); r=psdRadii[piece]+norm*(psdRadii[piece+1]-psdRadii[piece]);} } // try to put the sphere into a free spot for(t=0; t=(pack[j].c-c).squaredNorm()) { overlap=true; break; } } } else { for(size_t j=0; j= dr.squaredNorm()) { overlap=true; break; } } } if(!overlap) { pack.push_back(Sph(c,r)); break; } } if (t==maxTry) { if(num>0) { if (mode!=RDIST_RMEAN) { //if rMean is not imposed, then we call makeCloud recursively, //scaling the PSD down until the target num is obtained Real nextPoro = porosity+(1-porosity)/10.; LOG_WARN("Exceeded "<& cumm, Real& norm){ int sz=cumm.size(); int i=0; while(i& radii, const vector& passing, int numSph, bool periodic, Real cloudPorosity, int seed){ //deprecated (https://bugs.launchpad.net/yade/+bug/1024443) LOG_ERROR("particleSD2() has been removed. Please use makeCloud() instead."); return 1; }; // Discrete particle size distribution long SpherePack::particleSD(Vector3r mn, Vector3r mx, Real rMean, bool periodic, string name, int numSph, const vector& radii, const vector& passing, bool passingIsNotPercentageButCount, int seed){ //deprecated (https://bugs.launchpad.net/yade/+bug/1024443) LOG_ERROR("particleSD() has been removed. Please use makeCloud() instead."); return 1; } long SpherePack::particleSD_2d(Vector2r mn, Vector2r mx, Real rMean, bool periodic, string name, int numSph, const vector& radii, const vector& passing, bool passingIsNotPercentageButCount, int seed){ //deprecated (https://bugs.launchpad.net/yade/+bug/1024443) LOG_ERROR("particleSD_2d() has been removed. Please use makeCloud() instead."); return 1; } long SpherePack::makeClumpCloud(const Vector3r& mn, const Vector3r& mx, const vector >& _clumps, bool periodic, int num, int seed){ // recenter given clumps and compute their margins vector clumps; /* vector margins; */ Vector3r boxMargins(Vector3r::Zero()); Real maxR=0; vector boundRad; // squared radii of bounding sphere for each clump FOREACH(const shared_ptr& c, _clumps){ SpherePack c2(*c); c2.translate(c2.midPt()); //recenter clumps.push_back(c2); Real r=0; FOREACH(const Sph& s, c2.pack) r=max(r,s.c.norm()+s.r); boundRad.push_back(r); Vector3r cMn,cMx; c2.aabb(cMn,cMx); // centered at zero now, this gives margin //margins.push_back(periodic?cMx:Vector3r::Zero()); //boxMargins=boxMargins.cwise().max(cMx); FOREACH(const Sph& s, c2.pack) maxR=max(maxR,s.r); // keep track of maximum sphere radius } std::list clumpInfos; Vector3r size=mx-mn; if(periodic)(cellSize=size); const int maxTry=200; int nGen=0; // number of clumps generated // random point coordinate generator, with non-zero margins if aperiodic static boost::minstd_rand randGen(seed!=0?seed:(int)TimingInfo::getNow(/* get the number even if timing is disabled globally */ true)); static boost::variate_generator > rnd(randGen, boost::uniform_real(0,1)); while(nGen(s.c-cInfo.center).squaredNorm()){ detailedCheck=true; break; }} // check sphere-by-sphere, since bounding spheres did overlap if(detailedCheck){ FOREACH(const Sph& s, C.pack) for(int id=cInfo.minId; id<=cInfo.maxId; id++) if((s.c-pack[id].c).squaredNorm()periPtDistSq(s.c,cInfo.center)){ detailedCheck=true; break; } // check sphere-by-sphere if(detailedCheck){ FOREACH(const Sph& s, C.pack) for(int id=cInfo.minId; id<=cInfo.maxId; id++) if(periPtDistSq(s.c,pack[id].c)=(c-pack[j].c).squaredNorm()) goto overlap; // check that we are not over the box boundary // this could be handled by adjusting the position random interval (by taking off the smallest radius in the clump) // but usually the margin band is relatively small and this does not make the code as hairy if((c+r*Vector3r::Ones()).cwise().max(mx)!=mx || (c-r*Vector3r::Ones()).cwise().min(mn)!=mn) goto overlap; } } }else{ for(size_t i=0; i= dr.squaredNorm()) goto overlap; } } } #endif // add the clump, if no collisions /*number clumps consecutively*/ ci.clumpId=nGen; ci.center=pos; ci.rad=rad; ci.minId=pack.size(); ci.maxId=pack.size()+C.pack.size(); FOREACH(const Sph& s, C.pack){ pack.push_back(Sph(s.c,s.r,ci.clumpId)); } clumpInfos.push_back(ci); nGen++; //cerr<<"O"; break; // break away from the try-loop overlap: //cerr<<"."; if(tries++==maxTry){ // last loop if(num>0) LOG_WARN("Exceeded "<=0) return true; } return false; } py::tuple SpherePack::getClumps() const{ std::map clumps; py::list standalone; size_t packSize=pack.size(); for(size_t i=0; i intListPair; FOREACH(const intListPair& c, clumps) clumpList.append(c.second); return py::make_tuple(standalone,clumpList); } trunk-2017.01a/pkg/dem/SpherePack.hpp000066400000000000000000000143671304022710500172610ustar00rootroot00000000000000// © 2009 Václav Šmilauer #pragma once #include #include /*! Class representing geometry of spherical packing, with some utility functions. */ class SpherePack{ // return coordinate wrapped to x0…x1, relative to x0; don't care about period // copied from PeriodicInsertionSortCollider Real cellWrapRel(const Real x, const Real x0, const Real x1){ Real xNorm=(x-x0)/(x1-x0); return (xNorm-floor(xNorm))*(x1-x0); } Real periPtDistSq(const Vector3r& p1, const Vector3r& p2){ Vector3r dr; for(int ax=0; ax<3; ax++) dr[ax]=min(cellWrapRel(p1[ax],p2[ax],p2[ax]+cellSize[ax]),cellWrapRel(p2[ax],p1[ax],p1[ax]+cellSize[ax])); return dr.squaredNorm(); } struct ClumpInfo{ int clumpId; Vector3r center; Real rad; int minId, maxId; }; public: enum {RDIST_RMEAN, RDIST_NUM, RDIST_PSD}; struct Sph{ Vector3r c; Real r; int clumpId; Sph(const Vector3r& _c, Real _r, int _clumpId=-1): c(_c), r(_r), clumpId(_clumpId) {}; boost::python::tuple asTuple() const { if(clumpId<0) return boost::python::make_tuple(c,r); return boost::python::make_tuple(c,r,clumpId); } boost::python::tuple asTupleNoClump() const { return boost::python::make_tuple(c,r); } }; std::vector pack; Vector3r cellSize; Real appliedPsdScaling;//a scaling factor that can be applied on size distribution bool isPeriodic; SpherePack(): cellSize(Vector3r::Zero()), appliedPsdScaling(1.), isPeriodic(0) {}; SpherePack(const boost::python::list& l):cellSize(Vector3r::Zero()){ fromList(l); } // add single sphere void add(const Vector3r& c, Real r){ pack.push_back(Sph(c,r)); } // I/O void fromList(const boost::python::list& l); void fromLists(const vector& centers, const vector& radii); // used as ctor in python boost::python::list toList() const; void fromFile(const string file); void toFile(const string file) const; void fromSimulation(); // random generation; if num<0, insert as many spheres as possible; if porosity>0, recompute meanRadius (porosity>0.65 recommended) and try generating this porosity with num spheres. long makeCloud(Vector3r min, Vector3r max, Real rMean=-1, Real rFuzz=0, int num=-1, bool periodic=false, Real porosity=-1, const vector& psdSizes=vector(), const vector& psdCumm=vector(), bool distributeMass=false, int seed=0, Matrix3r hSize=Matrix3r::Zero()); // return number of piece for x in piecewise function defined by cumm with non-decreasing elements ∈(0,1) // norm holds normalized coordinate withing the piece int psdGetPiece(Real x, const vector& cumm, Real& norm); // function to generate the packing based on a given psd long particleSD(Vector3r min, Vector3r max, Real rMean, bool periodic=false, string name="", int numSph=400, const vector& radii=vector(), const vector& passing=vector(),bool passingIsNotPercentageButCount=false, int seed=0); long particleSD_2d(Vector2r min, Vector2r max, Real rMean, bool periodic=false, string name="", int numSph=400, const vector& radii=vector(), const vector& passing=vector(),bool passingIsNotPercentageButCount=false, int seed=0); long particleSD2(const vector& radii, const vector& passing, int numSph, bool periodic=false, Real cloudPorosity=.8, int seed=0); // interpolate a variable with power distribution (exponent -3) between two margin values, given uniformly distributed x∈(0,1) Real pow3Interp(Real x,Real a,Real b){ return pow(x*(pow(b,-2)-pow(a,-2))+pow(a,-2),-1./2); } // generate packing of clumps, selected with equal probability // periodic boundary is supported long makeClumpCloud(const Vector3r& mn, const Vector3r& mx, const vector >& clumps, bool periodic=false, int num=-1, int seed=0); // periodic repetition void cellRepeat(Vector3i count); void cellFill(Vector3r volume); // spatial characteristics Vector3r dim() const {Vector3r mn,mx; aabb(mn,mx); return mx-mn;} boost::python::tuple aabb_py() const { Vector3r mn,mx; aabb(mn,mx); return boost::python::make_tuple(mn,mx); } void aabb(Vector3r& mn, Vector3r& mx) const { Real inf=std::numeric_limits::infinity(); mn=Vector3r(inf,inf,inf); mx=Vector3r(-inf,-inf,-inf); FOREACH(const Sph& s, pack){ Vector3r r(s.r,s.r,s.r); mn=mn.cwiseMin(s.c-r); mx=mx.cwiseMax(s.c+r); } } Vector3r midPt() const {Vector3r mn,mx; aabb(mn,mx); return .5*(mn+mx);} Real relDensity() const { Real sphVol=0; Vector3r dd=dim(); FOREACH(const Sph& s, pack) sphVol+=pow(s.r,3); sphVol*=(4/3.)*Mathr::PI; return sphVol/(dd[0]*dd[1]*dd[2]); } boost::python::tuple psd(int bins=10, bool mass=false) const; bool hasClumps() const; boost::python::tuple getClumps() const; // transformations void translate(const Vector3r& shift){ FOREACH(Sph& s, pack) s.c+=shift; } void rotate(const Vector3r& axis, Real angle){ if(cellSize!=Vector3r::Zero()) { LOG_WARN("Periodicity reset when rotating periodic packing (non-zero cellSize="<=pack.size()) throw runtime_error("Index "+boost::lexical_cast(idx)+" out of range 0.."+boost::lexical_cast(pack.size()-1)); return pack[idx].asTuple(); } struct _iterator{ const SpherePack& sPack; size_t pos; _iterator(const SpherePack& _sPack): sPack(_sPack), pos(0){} _iterator iter(){ return *this;} boost::python::tuple next(){ if(pos==sPack.pack.size()){ PyErr_SetNone(PyExc_StopIteration); boost::python::throw_error_already_set(); } return sPack.pack[pos++].asTupleNoClump(); } }; SpherePack::_iterator getIterator() const{ return SpherePack::_iterator(*this);}; DECLARE_LOGGER; }; trunk-2017.01a/pkg/dem/SpheresFactory.cpp000066400000000000000000000210611304022710500201550ustar00rootroot00000000000000 #include #include #include #include #include YADE_PLUGIN((SpheresFactory)(CircularFactory)(BoxFactory)); CREATE_LOGGER(SpheresFactory); CREATE_LOGGER(CircularFactory); CREATE_LOGGER(BoxFactory); // initialize random number generator with time seed static boost::minstd_rand randGen(TimingInfo::getNow(/* get the number even if timing is disabled globally */ true)); static boost::variate_generator > randomUnit(randGen, boost::uniform_real(0,1)); void SpheresFactory::pickRandomPosition(Vector3r&,Real){ LOG_FATAL("Engine "<& e, scene->engines){ collider=YADE_PTR_DYN_CAST(e); if(collider) break; } if(!collider) throw runtime_error("SpheresFactory: No Collider instance found in engines (needed for collision detection)."); } goalMass+=massFlowRate*scene->dt; // totalMass that we want to attain in the current step if ((PSDcum.size()>0) and (!PSDuse)) { //Defined, that we will use PSD if ((PSDcum.size() != PSDsizes.size()) and (exactDiam)) { //The number of elements in both arrays should be the same LOG_ERROR("PSDcum and PSDsizes should have an equal number of elements, if exactDiam=True."); throw std::logic_error("PSDcum and PSDsizes should have an equal number of elements, if exactDiam=True."); } else if ((PSDcum.size() != (PSDsizes.size()-1)) and (not(exactDiam))) {//The number of elements in PSDsizes should be on 1 more, than in PSDcum LOG_ERROR("PSDsizes should have a number of elements on 1 more, than PSDcum, if exactDiam=False"); throw std::logic_error("PSDsizes should have a number of elements on 1 more, than PSDcum, if exactDiam=False"); } //Check the correctness of inputted data PSDcum for (unsigned int i=1; i 0; Setting maxMass=-1)"); maxMass = -1; } vector< SpherCoord > justCreatedBodies; // pick random initial velocity Vector3r initVel; if (normalVel.norm()>0) { normalVel.normalize(); initVel = normalVel; } else { initVel = normal; } initVel*=(vMin+randomUnit()*(vMax-vMin)); // TODO: compute from vMin, vMax, vAngle, normal; while(totalMass collidingParticles=collider->probeBoundingVolume(b); //Check, whether newly created sphere collides with existing bodies bool collideWithNewBodies = false; if (justCreatedBodies.size()>0) { //Check, whether newly created sphere collides with bodies from this scope for (unsigned int ii = 0; ii < justCreatedBodies.size(); ii++) { if ((justCreatedBodies.at(ii).c-c).norm() < (justCreatedBodies.at(ii).r+r)) { //Bodies intersect collideWithNewBodies = true; break; } } } if(collidingParticles.size()==0 and not(collideWithNewBodies)) break; #ifdef YADE_DEBUG FOREACH(const Body::id_t& id, collidingParticles) LOG_TRACE(scene->iter<<":"<=0 ? materialId : scene->materials.size()+materialId); if(mId<0 || (size_t) mId>=scene->materials.size()) throw std::invalid_argument(("SpheresFactory: invalid material id "+boost::lexical_cast(materialId)).c_str()); const shared_ptr& material=scene->materials[mId]; shared_ptr b(new Body); shared_ptr sphere(new Sphere); shared_ptr state(material->newAssocState()); sphere->radius=r; state->pos=state->refPos=c; if (color[0]>=0 and color[1]>=0 and color[2]>=0){ sphere->color = color; } state->vel=initVel; Real vol=(4/3.)*Mathr::PI*pow(r,3); state->mass=vol*material->density; state->inertia=(2./5.)*vol*r*r*material->density*Vector3r::Ones(); state->blockedDOFs_vec_set(blockedDOFs); b->shape=sphere; b->state=state; b->material=material; if (mask>0) {b->groupMask=mask;} // insert particle in the simulation scene->bodies->insert(b); ids.push_back(b->getId()); // increment total mass, volume and numparticles we've spit out totalMass+=state->mass; totalVolume+= vol; numParticles++; justCreatedBodies.push_back(SpherCoord(c, r)); if (PSDuse) { //Add newly created "material" into the bin Real summMaterial = 0.0; if (PSDcalculateMass) { PSDCurMean[maxdiffID]=PSDCurMean[maxdiffID]+state->mass; summMaterial = totalMass;} else { PSDCurMean[maxdiffID]=PSDCurMean[maxdiffID]+1; summMaterial = numParticles;} for (unsigned int k=0; k #include #include class SpheresFactory: public GlobalEngine { shared_ptr collider; protected: // Pick random position of a sphere. Should be override in derived engine. virtual void pickRandomPosition(Vector3r&/*picked position*/, Real/*sphere's radius*/); vector PSDCurMean; //Current value of material in each bin vector PSDCurProc; //Current value of material in each bin, in procents vector PSDNeedProc; //Need value of procent in each bin bool PSDuse; //PSD or not public: virtual void action(); struct SpherCoord{ Vector3r c; Real r; SpherCoord(const Vector3r& _c, Real _r){ c=_c; r=_r;} }; DECLARE_LOGGER; YADE_CLASS_BASE_DOC_ATTRS_CTOR(SpheresFactory,GlobalEngine,"Engine for spitting spheres based on mass flow rate, particle size distribution etc. Initial velocity of particles is given by *vMin*, *vMax*, the *massFlowRate* determines how many particles to generate at each step. When *goalMass* is attained or positive *maxParticles* is reached, the engine does not produce particles anymore. Geometry of the region should be defined in a derived engine by overridden SpheresFactory::pickRandomPosition(). \n\nA sample script for this engine is in :ysrc:`scripts/spheresFactory.py`.", ((Real,massFlowRate,NaN,,"Mass flow rate [kg/s]")) ((Real,rMin,NaN,,"Minimum radius of generated spheres (uniform distribution)")) ((Real,rMax,NaN,,"Maximum radius of generated spheres (uniform distribution)")) ((Real,vMin,NaN,,"Minimum velocity norm of generated spheres (uniform distribution)")) ((Real,vMax,NaN,,"Maximum velocity norm of generated spheres (uniform distribution)")) ((Real,vAngle,NaN,,"Maximum angle by which the initial sphere velocity deviates from the normal.")) ((Vector3r,normal,Vector3r(NaN,NaN,NaN),,"Orientation of the region's geometry, direction of particle's velocites if normalVel is not set.")) ((Vector3r,normalVel,Vector3r(NaN,NaN,NaN),,"Direction of particle's velocites.")) ((int,materialId,-1,,"Shared material id to use for newly created spheres (can be negative to count from the end)")) ((int,mask,-1,,"groupMask to apply for newly created spheres ")) ((Vector3r,color,Vector3r(-1,-1,-1),,"Use the color for newly created particles, if specified")) ((vector,ids,,,"ids of created bodies")) ((Real,totalMass,0,,"Mass of spheres that was produced so far. |yupdate|")) ((Real,totalVolume,0,,"Volume of spheres that was produced so far. |yupdate|")) ((Real,goalMass,0,,"Total mass that should be attained at the end of the current step. |yupdate|")) ((int,maxParticles,100,,"The number of particles at which to stop generating new ones regardless of massFlowRate. if maxParticles=-1 - this parameter is ignored .")) ((Real,maxMass,-1,,"Maximal mass at which to stop generating new particles regardless of massFlowRate. if maxMass=-1 - this parameter is ignored.")) ((int,numParticles,0,,"Cummulative number of particles produces so far |yupdate|")) ((int,maxAttempt,5000 ,,"Maximum number of attempts to position a new sphere randomly.")) ((bool,silent,false ,,"If true no complain about excessing maxAttempt but disable the factory (by set massFlowRate=0).")) ((std::string,blockedDOFs,"" ,,"Blocked degress of freedom")) ((vector,PSDsizes,,,"PSD-dispersion, sizes of cells, Diameter [m]")) ((vector,PSDcum,,,"PSD-dispersion, cumulative procent meanings [-]")) ((bool,PSDcalculateMass,true,,"PSD-Input is in mass (true), otherwise the number of particles will be considered.")) ((bool,stopIfFailed,true,,"If true, the SpheresFactory stops (sets massFlowRate=0), when maximal number of attempts to insert particle exceed.")) ((bool,exactDiam,true,,"If true, the particles only with the defined in PSDsizes diameters will be created. Otherwise the diameter will be randomly chosen in the range [PSDsizes[i-1]:PSDsizes[i]], in this case the length of PSDsizes should be more on 1, than the length of PSDcum.")), PSDuse=false; ); }; REGISTER_SERIALIZABLE(SpheresFactory); class CircularFactory: public SpheresFactory { protected: virtual void pickRandomPosition(Vector3r&, Real); public: virtual ~CircularFactory(){}; DECLARE_LOGGER; YADE_CLASS_BASE_DOC_ATTRS(CircularFactory,SpheresFactory,"Circular geometry of the SpheresFactory region. It can be disk (given by radius and center), or cylinder (given by radius, length and center).", ((Real,radius,NaN,,"Radius of the region")) ((Real,length,0,,"Length of the cylindrical region (0 by default)")) ((Vector3r,center,Vector3r(NaN,NaN,NaN),,"Center of the region")) ); }; REGISTER_SERIALIZABLE(CircularFactory); class BoxFactory: public SpheresFactory { protected: virtual void pickRandomPosition(Vector3r&, Real); public: virtual ~BoxFactory(){}; DECLARE_LOGGER; YADE_CLASS_BASE_DOC_ATTRS(BoxFactory,SpheresFactory,"Box geometry of the SpheresFactory region, given by extents and center", ((Vector3r,extents,Vector3r(NaN,NaN,NaN),,"Extents of the region")) ((Vector3r,center,Vector3r(NaN,NaN,NaN),,"Center of the region")) ); }; REGISTER_SERIALIZABLE(BoxFactory); trunk-2017.01a/pkg/dem/TesselationWrapper.cpp000066400000000000000000000356321304022710500210600ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2008 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef YADE_CGAL #include #include "TesselationWrapper.hpp" #include #include #include YADE_PLUGIN((TesselationWrapper)); CREATE_LOGGER(TesselationWrapper); // helper macro do assign Matrix3r values to subarrays #define MATRIX3R_TO_NUMPY(mat,arr) arr[0]=mat(0,0);arr[1]=mat(0,1);arr[2]=mat(0,2);arr[3]=mat(1,0);arr[4]=mat(1,1);arr[5]=mat(1,2);arr[6]=mat(2,0);arr[7]=mat(2,1);arr[8]=mat(2,2); //spatial sort traits to use with a pair of CGAL::sphere pointers and integer. //template struct RTraits_for_spatial_sort : public CGT::SimpleTriangulationTypes::RTriangulation::Geom_traits { //typedef typename _Triangulation::Geom_traits Gt; typedef CGT::SimpleTriangulationTypes::RTriangulation::Geom_traits Gt; typedef std::pair Point_3; struct Less_x_3 { bool operator()(const Point_3& p,const Point_3& q) const { return Gt::Less_x_3()(* (p.first),* (q.first)); } }; struct Less_y_3 { bool operator()(const Point_3& p,const Point_3& q) const { return Gt::Less_y_3()(* (p.first),* (q.first)); } }; struct Less_z_3 { bool operator()(const Point_3& p,const Point_3& q) const { return Gt::Less_z_3()(* (p.first),* (q.first)); } }; Less_x_3 less_x_3_object() const {return Less_x_3();} Less_y_3 less_y_3_object() const {return Less_y_3();} Less_z_3 less_z_3_object() const {return Less_z_3();} }; //function inserting points into a triangulation (where YADE::Sphere is converted to CGT::Sphere) //and setting the info field to the bodies id. //Possible improvements : use bodies pointers to avoid one copy, use aabb's lists to replace the shuffle/sort part // template void build_triangulation_with_ids(const shared_ptr& bodies, TesselationWrapper &TW, bool reset=true) { if (reset) TW.clear(); typedef SimpleTesselation::RTriangulation RTriangulation; SimpleTesselation& Tes = *(TW.Tes); RTriangulation& T = Tes.Triangulation(); std::vector spheres; std::vector > pointsPtrs; spheres.reserve(bodies->size()); pointsPtrs.reserve(bodies->size()); BodyContainer::iterator biBegin = bodies->begin(); BodyContainer::iterator biEnd = bodies->end(); BodyContainer::iterator bi = biBegin; Body::id_t Ng = 0; Body::id_t& MaxId=Tes.maxId; TW.mean_radius = 0; int nonSpheres =0; shared_ptr sph (new Sphere); int Sph_Index = sph->getClassIndexStatic(); Scene* scene = Omega::instance().getScene().get(); for (; bi!=biEnd ; ++bi) { if ( (*bi)->shape->getClassIndex() == Sph_Index ) { const Sphere* s = YADE_CAST ((*bi)->shape.get()); //FIXME: is the scene periodicity verification useful in the next line ? Tesselation seems to work in both periodic and non-periodic conditions with "scene->cell->wrapShearedPt((*bi)->state->pos)". I keep the verification to be consistent with all other uses of "wrapShearedPt" function. const Vector3r& pos = scene->isPeriodic ? scene->cell->wrapShearedPt((*bi)->state->pos) : (*bi)->state->pos; const Real rad = s->radius; CGT::Sphere sp(CGT::Point(pos[0],pos[1],pos[2]),rad*rad); spheres.push_back(sp); pointsPtrs.push_back(std::make_pair(&(spheres[Ng]/*.point()*/),(*bi)->getId())); TW.Pmin = CGT::Point(min(TW.Pmin.x(),pos.x()-rad),min(TW.Pmin.y(), pos.y()-rad),min(TW.Pmin.z(), pos.z()-rad)); TW.Pmax = CGT::Point(max(TW.Pmax.x(),pos.x()+rad),max(TW.Pmax.y(),pos.y()+rad),max(TW.Pmax.z(),pos.z()+rad)); Ng++; TW.mean_radius += rad; MaxId = max(MaxId,(*bi)->getId()); } else ++nonSpheres; } TW.mean_radius /= Ng; TW.rad_divided = true; spheres.resize(Ng); pointsPtrs.resize(Ng); Tes.vertexHandles.resize(MaxId+1+max(0,6-nonSpheres),NULL);//+6 extra slots max for adding boundaries latter Tes.redirected = 1; std::random_shuffle(pointsPtrs.begin(), pointsPtrs.end()); spatial_sort(pointsPtrs.begin(),pointsPtrs.end(), RTraits_for_spatial_sort()/*, CGT::RTriangulation::Weighted_point*/); RTriangulation::Cell_handle hint; TW.n_spheres = 0; for (std::vector >::const_iterator p = pointsPtrs.begin();p != pointsPtrs.end(); ++p) { RTriangulation::Locate_type lt; RTriangulation::Cell_handle c; int li, lj; c = T.locate(* (p->first), lt, li, lj, hint); RTriangulation::Vertex_handle v = T.insert(*(p->first),lt,c,li,lj); if (v==RTriangulation::Vertex_handle()) hint=c; else { v->info().setId((const unsigned int) p->second); //Vh->info().isFictious = false;//false is the default Tes.maxId = std::max(Tes.maxId,(int) p->second); Tes.vertexHandles[p->second]=v; hint=v->cell(); ++TW.n_spheres; } } //cerr << " loaded : " << Ng<<", triangulated : "<Max_id() >= id) ? Tes->Volume(id) : -1;} bool TesselationWrapper::insert(double x, double y, double z, double rad, unsigned int id) { checkMinMax(x,y,z,rad); mean_radius += rad; ++n_spheres; return (Tes->insert(x,y,z,rad,id)!=NULL); } void TesselationWrapper::checkMinMax(double x, double y, double z, double rad) { using std::min; using std::max; Pmin = CGT::Point(min(Pmin.x(), x-rad), min(Pmin.y(), y-rad), min(Pmin.z(), z-rad)); Pmax = CGT::Point(max(Pmax.x(), x+rad), max(Pmax.y(), y+rad), max(Pmax.z(), z+rad)); } bool TesselationWrapper::move(double x, double y, double z, double rad, unsigned int id) { checkMinMax(x,y,z,rad); if (Tes->move(x,y,z,rad,id)!=NULL) return true; else { std::cerr << "Tes->move(x,y,z,rad,id)==NULL" << std::endl; return false; } } void TesselationWrapper::computeTesselation(void) { if (!rad_divided) { mean_radius /= n_spheres; rad_divided = true; } Tes->compute(); } void TesselationWrapper::computeTesselation(double pminx, double pmaxx, double pminy, double pmaxy, double pminz, double pmaxz) { addBoundingPlanes(pminx, pmaxx, pminy, pmaxy, pminz, pmaxz); computeTesselation(); } void TesselationWrapper::computeVolumes(void) { if (!bounded) addBoundingPlanes(); computeTesselation(); Tes->computeVolumes(); } unsigned int TesselationWrapper::NumberOfFacets(bool initIters) { if (initIters) InitIter(); return Tes->Triangulation().number_of_finite_edges(); } void TesselationWrapper::InitIter(void) { facet_begin = Tes->Triangulation().finite_edges_begin(); facet_end = Tes->Triangulation().finite_edges_end(); facet_it = facet_begin; } bool TesselationWrapper::nextFacet(std::pair& facet) { if (facet_end==facet_it) return false; facet.first = facet_it->first->vertex(facet_it->second)->info().id(); facet.second = facet_it->first->vertex((facet_it)->third)->info().id(); ++facet_it; return true; } void TesselationWrapper::addBoundingPlanes(double pminx, double pmaxx, double pminy, double pmaxy, double pminz, double pmaxz) { if (!bounded) { if (!rad_divided) { mean_radius /= n_spheres; rad_divided = true; } // Insert the 6 additional vertices in the right place (usually they will be ids 0 to 5 when walls/facets/boxes are used, but not always) // append them at the end if the initial list is full int freeIds [6]; int i=0; for (int k=0; k<6; k++) { while (Tes->vertexHandles[i]!=NULL) ++i; freeIds[k] = i;} // now insert Tes->vertexHandles[freeIds[0]]=Tes->insert(0.5*(pminx+pmaxx),pminy-far*(pmaxx-pminx),0.5*(pmaxz+pminz),far*(pmaxx-pminx)+thickness,freeIds[0],true); Tes->vertexHandles[freeIds[1]]=Tes->insert(0.5*(pminx+pmaxx), pmaxy+far*(pmaxx-pminx),0.5*(pmaxz+pminz),far*(pmaxx-pminx)+thickness, freeIds[1], true); Tes->vertexHandles[freeIds[2]]=Tes->insert(pminx-far*(pmaxy-pminy), 0.5*(pmaxy+pminy), 0.5*(pmaxz+pminz), far*(pmaxy-pminy)+thickness, freeIds[2], true); Tes->vertexHandles[freeIds[3]]=Tes->insert(pmaxx+far*(pmaxy-pminy), 0.5*(pmaxy+pminy), 0.5*(pmaxz+pminz), far*(pmaxy-pminy)+thickness, freeIds[3], true); Tes->vertexHandles[freeIds[4]]=Tes->insert(0.5*(pminx+pmaxx), 0.5*(pmaxy+pminy), pminz-far*(pmaxy-pminy), far*(pmaxy-pminy)+thickness, freeIds[4], true); Tes->vertexHandles[freeIds[5]]=Tes->insert(0.5*(pminx+pmaxx), 0.5*(pmaxy+pminy), pmaxz+far*(pmaxy-pminy), far*(pmaxy-pminy)+thickness, freeIds[5], true); bounded = true; } } void TesselationWrapper::addBoundingPlanes(void) {addBoundingPlanes(Pmin.x(),Pmax.x(),Pmin.y(),Pmax.y(),Pmin.z(),Pmax.z());} // { // if (!bounded) { // if (!rad_divided) { // mean_radius /= n_spheres; // rad_divided = true; // } // double FAR = 10000; // //Add big bounding spheres with isFictious=true // Tes->vertexHandles[0]=Tes->insert(0.5*(Pmin.x()+Pmax.x()),Pmin.y()-FAR*(Pmax.x()-Pmin.x()),0.5*(Pmax.z()+Pmin.z()),FAR*(Pmax.x()-Pmin.x()), 0, true); // Tes->vertexHandles[1]=Tes->insert(0.5*(Pmin.x()+Pmax.x()),Pmax.y()+FAR*(Pmax.x()-Pmin.x()),0.5*(Pmax.z()+Pmin.z()),FAR*(Pmax.x()-Pmin.x()), 1, true); // Tes->vertexHandles[2]=Tes->insert(Pmin.x()-FAR*(Pmax.y()-Pmin.y()),0.5*(Pmax.y()+Pmin.y()),0.5*(Pmax.z()+Pmin.z()),FAR*(Pmax.y()-Pmin.y()),2, true); // Tes->vertexHandles[3]=Tes->insert(Pmax.x()+FAR*(Pmax.y()-Pmin.y()),0.5*(Pmax.y()+Pmin.y()),0.5*(Pmax.z()+Pmin.z()),FAR*(Pmax.y()-Pmin.y()),3,true); // Tes->vertexHandles[4]=Tes->insert(0.5*(Pmin.x()+Pmax.x()),0.5*(Pmax.y()+Pmin.y()),Pmin.z()-FAR*(Pmax.y()-Pmin.y()),FAR*(Pmax.y()-Pmin.y()),4,true); // Tes->vertexHandles[5]=Tes->insert(0.5*(Pmin.x()+Pmax.x()),0.5*(Pmax.y()+Pmin.y()),Pmax.z()+FAR*(Pmax.y()-Pmin.y()),FAR*(Pmax.y()-Pmin.y()),5, true); // bounded = true; // } // } void TesselationWrapper::RemoveBoundingPlanes(void) { Tes->remove(0); Tes->remove(1); Tes->remove(2); Tes->remove(3); Tes->remove(4); Tes->remove(5); Pmin = CGT::Point(inf, inf, inf); Pmax = CGT::Point(-inf, -inf, -inf); mean_radius = 0; rad_divided = false; bounded = false; } void TesselationWrapper::setState (bool state){ mma.setState(state ? 2 : 1);} void TesselationWrapper::loadState (string filename, bool stateNumber, bool bz2){ CGT::TriaxialState& TS = stateNumber? *(mma.analyser->TS1) :*( mma.analyser->TS0); TS.from_file(filename.c_str(),bz2); } void TesselationWrapper::saveState (string filename, bool stateNumber, bool bz2){ CGT::TriaxialState& TS = stateNumber? *(mma.analyser->TS1) :*( mma.analyser->TS0); TS.to_file(filename.c_str(),bz2); } void TesselationWrapper::defToVtkFromStates (string inputFile1, string inputFile2, string outputFile, bool bz2){ mma.analyser->DefToFile(inputFile1.c_str(),inputFile2.c_str(),outputFile.c_str(),bz2); } void createSphere(shared_ptr& body, Vector3r position, Real radius, bool big, bool dynamic ) { body = shared_ptr(new Body); body->groupMask=2; shared_ptr iSphere(new Sphere); body->state->blockedDOFs=State::DOF_NONE; body->state->pos=position; iSphere->radius = radius; body->shape = iSphere; } void TesselationWrapper::defToVtkFromPositions (string inputFile1, string inputFile2, string outputFile, bool bz2){ SpherePack sp1, sp2; sp1.fromFile(inputFile1); sp2.fromFile(inputFile2); size_t imax=sp1.pack.size(); if (imax!=sp2.pack.size()) LOG_ERROR("The files have different numbers of spheres"); shared_ptr body; scene->bodies->clear(); for(size_t i=0; ibodies->insert(body); } mma.setState(1); scene->bodies->clear(); for(size_t i=0; ibodies->insert(body); } mma.setState(2); mma.analyser->DefToFile(outputFile.c_str()); } void TesselationWrapper::defToVtk (string outputFile){ mma.analyser->DefToFile(outputFile.c_str()); } boost::python::dict TesselationWrapper::getVolPoroDef(bool deformation) { delete Tes; CGT::TriaxialState* ts; if (deformation){//use the final state to compute volumes /*const vector& def =*/ mma.analyser->computeParticlesDeformation(); Tes = &mma.analyser->TS1->tesselation(); ts = mma.analyser->TS1; } else { Tes = &mma.analyser->TS0->tesselation();//no reason to use the final state if we don't want to compute deformations, keep using the initial ts = mma.analyser->TS0;} RTriangulation& Tri = Tes->Triangulation(); Pmin=ts->box.base; Pmax=ts->box.sommet; //if (!scene->isPeriodic) addBoundingPlanes(); computeVolumes(); int bodiesDim = Tes->Max_id() + 1; //=scene->bodies->size(); cerr<<"bodiesDim="< id(dim1); numpy_boost vol(dim1); numpy_boost poro(dim1); numpy_boost def(dim2); //FOREACH(const shared_ptr& b, *scene->bodies){ for (RTriangulation::Finite_vertices_iterator V_it = Tri.finite_vertices_begin(); V_it != Tri.finite_vertices_end(); V_it++) { //id[]=V_it->info().id() //if(!b) continue; const Body::id_t id = V_it->info().id(); Real sphereVol = 4.188790 * std::pow ( ( V_it->point().weight() ),1.5 );// 4/3*PI*R³ = 4.188...*R³ vol[id]=V_it->info().v(); poro[id]=(V_it->info().v() - sphereVol)/V_it->info().v(); if (deformation) MATRIX3R_TO_NUMPY(mma.analyser->ParticleDeformation[id],def[id]); //cerr << V_it->info().v()<<" "< #include #include #include #include #include /*! \class TesselationWrapper * \brief Handle the triangulation of spheres in a scene, build tesselation on request, and give access to computed quantities : currently volume and porosity of each Voronoï sphere. * More accessors in course of implementation. Feel free to suggest new ones. * * Example usage script : * *tt=TriaxialTest() *tt.generate("test.xml") *O.load("test.xml") *O.run(100) //for unknown reasons, this procedure crashes at iteration 0 *TW=TesselationWrapper() *TW.triangulate() //compute regular Delaunay triangulation, don't construct tesselation *TW.computeVolumes() //will silently tesselate the packing *TW.volume(10) //get volume associated to sphere of id 10 * */ class TesselationWrapper : public GlobalEngine{ public: typedef CGT::_Tesselation Tesselation; typedef Tesselation::RTriangulation RTriangulation; typedef Tesselation::VertexInfo VertexInfo; typedef Tesselation::CellInfo CellInfo; typedef RTriangulation::Finite_edges_iterator FiniteEdgesIterator; Tesselation* Tes; double mean_radius, inf; bool rad_divided; bool bounded; CGT::Point Pmin; CGT::Point Pmax; ~TesselationWrapper(); /// Insert a sphere, "id" will be used by some getters to retrieve spheres bool insert(double x, double y, double z, double rad, unsigned int id); /// A faster version of insert, inserting all spheres in scene (first erasing current triangulation if reset=true) void insertSceneSpheres(bool reset=true); /// Move one sphere to the new position (x,y,z) and maintain triangulation (invalidates the tesselation) bool move (double x, double y, double z, double rad, unsigned int id); void checkMinMax(double x, double y, double z, double rad);//for experimentation purpose /// Reset the triangulation void clear(void); void clear2(void); /// Add axis aligned bounding planes (modelised as spheres with (almost) infinite radius) void addBoundingPlanes (void); /// Force boudaries at positions not equal to precomputed ones void addBoundingPlanes(double pminx, double pmaxx, double pminy, double pmaxy, double pminz, double pmaxz); void RemoveBoundingPlanes (void); ///compute voronoi centers then stop (don't compute anything else) void computeTesselation (void); void computeTesselation( double pminx, double pmaxx, double pminy, double pmaxy, double pminz, double pmaxz); ///compute Voronoi vertices + volumes of all cells ///use computeTesselation to force update, e.g. after spheres positions have been updated void computeVolumes (void); void computeDeformations (void) {mma.analyser->computeParticlesDeformation();} ///Get volume of the sphere inserted with indentifier "id"" double Volume (unsigned int id); double deformation (unsigned int id,unsigned int i,unsigned int j) { if (!mma.analyser->ParticleDeformation.size()) {LOG_ERROR("compute deformations first"); return 0;} if (mma.analyser->ParticleDeformation.size()3 || j<1 || j>3) {LOG_ERROR("tensor index must be between 1 and 3"); return 0;} return mma.analyser->ParticleDeformation[id](i,j);} /// number of facets in the tesselation (finite branches of the triangulation) unsigned int NumberOfFacets(bool initIters=false); /// set first and last facets, set facet_it = facet_begin void InitIter(void); /// set facet = next pair (body1->id,body2->id), returns facet_it==facet_end bool nextFacet (std::pair& facet); /// make the current state the initial (0) or final (1) configuration for the definition of displacement increments, use only state=0 if you just want to get only volmumes and porosity void setState (bool state=0); void loadState (string fileName, bool stateNumber=0, bool bz2=false); void saveState (string fileName, bool stateNumber=0, bool bz2=false); /// read two state files and write per-particle deformation to a vtk file. The second variant uses existing states. void defToVtkFromStates (string inputFile1, string inputFile2, string outputFile="def.vtk", bool bz2=false); void defToVtkFromPositions (string inputFile1, string inputFile2, string outputFile="def.vtk", bool bz2=false); void defToVtk (string outputFile="def.vtk"); /// return python array containing voronoi volumes, per-particle porosity, and optionaly per-particle deformation, if states 0 and 1 have been assigned boost::python::dict getVolPoroDef(bool deformation);//FIXME ; unexplained crash for now public: /// edge iterators are used for returning tesselation "facets", i.e. spheres with a common branch in the triangulation, convert CGAL::edge to int pair (b1->id, b2->id) FiniteEdgesIterator facet_begin; FiniteEdgesIterator facet_end; FiniteEdgesIterator facet_it; MicroMacroAnalyser mma; YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(TesselationWrapper,GlobalEngine,"Handle the triangulation of spheres in a scene, build tesselation on request, and give access to computed quantities (see also the `dedicated section in user manual `_). The calculation of microstrain is explained in [Catalano2014a]_ \n\nSee example usage in script example/tesselationWrapper/tesselationWrapper.py.\n\nBelow is an output of the :yref:`defToVtk` function visualized with paraview (in this case Yade's TesselationWrapper was used to process experimental data obtained on sand by Edward Ando at Grenoble University, 3SR lab.)\n\n.. figure:: fig/localstrain.*", ((unsigned int,n_spheres,0,,"|ycomp|")) ((Real,far,10000.,,"Defines the radius of the large virtual spheres used to define nearly flat boundaries around the assembly. The radius will be the (scene's) bounding box size multiplied by 'far'. Higher values will minimize the error theoretically (since the infinite sphere really defines a plane), but it may increase numerical errors at some point. The default should give a resonable compromize.")) ,/*ctor*/ Tes = new Tesselation; clear(); facet_begin = Tes->Triangulation().finite_edges_begin(); facet_end = Tes->Triangulation().finite_edges_end(); facet_it = Tes->Triangulation().finite_edges_begin(); inf=1e10; mma.analyser->SetConsecutive(false); ,/*py*/ .def("triangulate",&TesselationWrapper::insertSceneSpheres,(boost::python::arg("reset")=true),"triangulate spheres of the packing") .def("setState",&TesselationWrapper::setState,(boost::python::arg("state")=0),"Make the current state of the simulation the initial (0) or final (1) configuration for the definition of displacement increments, use only state=0 if you just want to get volmumes and porosity.") .def("loadState",&TesselationWrapper::loadState,(boost::python::arg("inputFile")="state",boost::python::arg("state")=0,boost::python::arg("bz2")=true),"Load a file with positions to define state 0 or 1.") .def("saveState",&TesselationWrapper::saveState,(boost::python::arg("outputFile")="state",boost::python::arg("state")=0,boost::python::arg("bz2")=true),"Save a file with positions, can be later reloaded in order to define state 0 or 1.") .def("volume",&TesselationWrapper::Volume,(boost::python::arg("id")=0),"Returns the volume of Voronoi's cell of a sphere.") .def("defToVtk",&TesselationWrapper::defToVtk,(boost::python::arg("outputFile")="def.vtk"),"Write local deformations in vtk format from states 0 and 1.") .def("defToVtkFromStates",&TesselationWrapper::defToVtkFromStates,(boost::python::arg("input1")="state1",boost::python::arg("input2")="state2",boost::python::arg("outputFile")="def.vtk",boost::python::arg("bz2")=true),"Write local deformations in vtk format from state files (since the file format is very special, consider using defToVtkFromPositions if the input files were not generated by TesselationWrapper).") .def("defToVtkFromPositions",&TesselationWrapper::defToVtkFromPositions,(boost::python::arg("input1")="pos1",boost::python::arg("input2")="pos2",boost::python::arg("outputFile")="def.vtk",boost::python::arg("bz2")=false),"Write local deformations in vtk format from positions files (one sphere per line, with x,y,z,rad separated by spaces).") .def("computeVolumes",&TesselationWrapper::computeVolumes,"compute volumes of all Voronoi's cells.") .def("getVolPoroDef",&TesselationWrapper::getVolPoroDef,(boost::python::arg("deformation")=false),"Return a table with per-sphere computed quantities. Include deformations on the increment defined by states 0 and 1 if deformation=True (make sure to define states 0 and 1 consistently).") .def("computeDeformations",&TesselationWrapper::computeDeformations,"compute per-particle deformation. Get it with :yref:`TesselationWrapper::deformation` (id,i,j).") .def("deformation",&TesselationWrapper::deformation,(boost::python::arg("id"),boost::python::arg("i"),boost::python::arg("j")),"Get particle deformation") ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(TesselationWrapper); //} // namespace CGT #endif /* YADE_CGAL */ trunk-2017.01a/pkg/dem/Tetra.cpp000066400000000000000000001306351304022710500163030ustar00rootroot00000000000000// © 2007 Václav Šmilauer // © 2013 Jan Stránský #include"Tetra.hpp" #include #include #include #include #include #include #ifdef YADE_CGAL #include #endif YADE_PLUGIN(/* self-contained in hpp: */ (Tetra) (TTetraGeom) (TTetraSimpleGeom) (Bo1_Tetra_Aabb) /* some code in cpp (this file): */ (TetraVolumetricLaw) (Ig2_Tetra_Tetra_TTetraGeom) #ifdef YADE_CGAL (Ig2_Tetra_Tetra_TTetraSimpleGeom) (Law2_TTetraSimpleGeom_NormPhys_Simple) #endif #ifdef YADE_OPENGL (Gl1_Tetra) #endif ); Tetra::~Tetra(){} TTetraGeom::~TTetraGeom(){} TTetraSimpleGeom::~TTetraSimpleGeom(){} void Bo1_Tetra_Aabb::go(const shared_ptr& ig, shared_ptr& bv, const Se3r& se3, const Body*){ Tetra* t=static_cast(ig.get()); if(!bv){ bv=shared_ptr(new Aabb); } Aabb* aabb=static_cast(bv.get()); //Quaternionr invRot=se3.orientation.conjugate(); //The variable set but not used Vector3r v_g[4]; for(int i=0; i<4; i++) v_g[i]=se3.orientation*t->v[i]; // vertices in global coordinates #define __VOP(op,ix) op(v_g[0][ix],op(v_g[1][ix],op(v_g[2][ix],v_g[3][ix]))) aabb->min=se3.position+Vector3r(__VOP(std::min,0),__VOP(std::min,1),__VOP(std::min,2)); aabb->max=se3.position+Vector3r(__VOP(std::max,0),__VOP(std::max,1),__VOP(std::max,2)); #undef __VOP } #ifdef YADE_CGAL const int Ig2_Tetra_Tetra_TTetraSimpleGeom::psMap[4][3] = { // segments of point {0,2,3}, {0,1,4}, {1,2,5}, {3,4,5} }; const int Ig2_Tetra_Tetra_TTetraSimpleGeom::ptMap[4][3] = { // triangles of point {0,1,3}, {0,1,2}, {1,2,3}, {0,2,3} }; const int Ig2_Tetra_Tetra_TTetraSimpleGeom::stMap[6][2] = { // triangles of segments {0,1}, {1,2}, {1,3}, {0,3}, {0,2}, {2,3} }; const int Ig2_Tetra_Tetra_TTetraSimpleGeom::ppsMap[4][4] = { // point-point pair to segment {-1, 0, 2, 3}, { 0,-1, 1, 4}, { 2, 1,-1, 5}, { 3, 4, 5,-1} }; const int Ig2_Tetra_Tetra_TTetraSimpleGeom::tsMap[4][3] = { // segmnts of triangle {0,3,4}, {0,1,2}, {1,4,5}, {2,3,5} }; const int Ig2_Tetra_Tetra_TTetraSimpleGeom::sstMap[6][6] = { // segment-segment pair to triangle {-1, 1, 1, 0, 0,-1}, { 1,-1, 1,-1, 2, 2}, { 1, 1,-1, 3,-1, 3}, { 0,-1, 3,-1, 0, 3}, { 0, 2,-1, 0,-1, 2}, {-1, 2, 3, 3, 2,-1} }; bool Ig2_Tetra_Tetra_TTetraSimpleGeom::checkVertexToTriangleCase( const Triangle tA[4], const Point pB[4], const Segment sB[6], Vector3r& normal, Vector3r& contactPoint, Real& penetrationVolume) { for (int i=0; i<4; i++) { // loop over triangles 1 const Triangle& t = tA[i]; // choose triangle 1 for (int j=0; j<4; j++) { // loop over vertices 2 const Point& p = pB[j]; // choose vertex 2 // choose edges posessing p const Segment& sa = sB[psMap[j][0]]; const Segment& sb = sB[psMap[j][1]]; const Segment& sc = sB[psMap[j][2]]; if ( !(do_intersect(t,sa) && do_intersect(t,sb) && do_intersect(t,sc)) ) { continue; }// if all edges intersect with t // evaluate the points CGAL::Object oa = intersection(t,sa); const Point* pa = CGAL::object_cast(&oa); CGAL::Object ob = intersection(t,sb); const Point* pb = CGAL::object_cast(&ob); CGAL::Object oc = intersection(t,sc); const Point* pc = CGAL::object_cast(&oc); if ( !(pa && pb && pc) ) { continue; } // check that the intrsection really exists Vector_3 n = CGAL::normal(t[0],t[1],t[2]); // normal of triangle for (int k=0; k<3; k++) { normal[k] = n[k]; // sets normal of contact = nornal of triangle // contact point is center of mass of overlaping tetrahedron contactPoint[k] = .25*(p[k]+pa->operator[](k)+pb->operator[](k)+pc->operator[](k)); } normal.normalize(); const Point* v[4] = {&p,pa,pb,pc}; penetrationVolume = TetrahedronVolume(v); Real vol = TetrahedronVolume(pB); if (penetrationVolume > .5*vol) { penetrationVolume = vol-penetrationVolume; } return true; } } return false; } bool Ig2_Tetra_Tetra_TTetraSimpleGeom::checkEdgeToEdgeCase( const Segment sA[6], const Segment sB[6], const Triangle tA[4], const Triangle tB[4], Vector3r& normal, Vector3r& contactPoint, Real& penetrationVolume) { for (int i=0; i<6; i++) { const Segment& sa = sA[i]; const Triangle& ta0 = tA[stMap[i][0]]; const Triangle& ta1 = tA[stMap[i][1]]; for (int j=0; j<6; j++) { const Segment sb = sB[j]; if ( !(do_intersect(sb,ta0) && do_intersect(sb,ta1) ) ) { continue; } const Triangle tb0 = tB[stMap[j][0]]; const Triangle tb1 = tB[stMap[j][1]]; if ( !(do_intersect(sa,tb0) && do_intersect(sa,tb1) ) ) { continue; } CGAL::Object osb1 = intersection(sb,ta0); CGAL::Object osb2 = intersection(sb,ta1); CGAL::Object osa1 = intersection(sa,tb0); CGAL::Object osa2 = intersection(sa,tb1); const Point* psb1 = CGAL::object_cast(&osb1); const Point* psb2 = CGAL::object_cast(&osb2); const Point* psa1 = CGAL::object_cast(&osa1); const Point* psa2 = CGAL::object_cast(&osa2); if ( !(psb1 && psb2 && psa1 && psa2) ) { continue; } Vector_3 n = CGAL::cross_product(sa.to_vector(),sb.to_vector()); Vector3r nApprox; for (int k=0; k<3; k++) { normal[k] = n[k]; #define OP(p) p->operator[](k) nApprox[k] = .5*(OP(psa1)+OP(psa2)) - .5*(OP(psb1)+OP(psb2)); contactPoint[k] = .25*(OP(psa1)+OP(psa2)+OP(psb1)+OP(psb2)); #undef OP } if ( nApprox.dot(normal) < 0 ) { normal *= (Real)-1.; } normal.normalize(); const Point* p[4] = {psb1,psb2,psa1,psa2}; penetrationVolume = TetrahedronVolume(p); return true; } } return false; } bool Ig2_Tetra_Tetra_TTetraSimpleGeom::checkEdgeToTriangleCase1( // edge smaller than triangle const Triangle tA[4], const Segment sB[6], const Point pB[6], Vector3r& normal, Vector3r& contactPoint, Real& penetrationVolume) { for (int i=0; i<4; i++) { const Triangle& ta = tA[i]; int ni = 0; for (int j=0; j<6; j++) { const Segment& s = sB[j]; if ( do_intersect(ta,s) ) { ni++; } } if ( ni != 4 ) { continue; } Vector_3 n = CGAL::normal(ta[0],ta[1],ta[2]); for (int j=0; j<3; j++) { const Point& p1 = pB[j]; if ( Vector_3(ta[0],p1)*n > 0.) { continue; } const Segment& s10 = sB[psMap[j][0]]; const Segment& s11 = sB[psMap[j][1]]; const Segment& s12 = sB[psMap[j][2]]; bool b10 = do_intersect(ta,s10); bool b11 = do_intersect(ta,s11); bool b12 = do_intersect(ta,s12); if ( !((b10 && b11) || (b11 && b12) || (b12 && b10) ) ) { continue; } for (int k=j+1; k<4; k++) { const Point& p2 = pB[k]; if ( Vector_3(ta[0],p2)*n > 0. ) { continue; } const Segment& s20 = sB[psMap[k][0]]; const Segment& s21 = sB[psMap[k][1]]; const Segment& s22 = sB[psMap[k][2]]; bool b20 = do_intersect(ta,s20); bool b21 = do_intersect(ta,s21); bool b22 = do_intersect(ta,s22); if ( !((b20 && b21) || (b21 && b22) || (b22 && b20) ) ) { continue; } int l,m; for (l=0; l<3; l++) { if (l!=j && l!=k) { break; } } for (m=l+1; m<4; m++) { if (m!=j && m!=k) { break; } } const Segment& s13 = sB[ppsMap[j][l]]; const Segment& s14 = sB[ppsMap[j][m]]; const Segment& s23 = sB[ppsMap[k][l]]; const Segment& s24 = sB[ppsMap[k][m]]; CGAL::Object o13 = intersection(ta,s13); CGAL::Object o14 = intersection(ta,s14); CGAL::Object o23 = intersection(ta,s23); CGAL::Object o24 = intersection(ta,s24); const Point* ps13 = CGAL::object_cast(&o13); const Point* ps14 = CGAL::object_cast(&o14); const Point* ps23 = CGAL::object_cast(&o23); const Point* ps24 = CGAL::object_cast(&o24); if ( !(ps13 && ps14 && ps23 && ps24) ) { continue; } const Point* pp1[4] = {&p1,&p2,ps13,ps14}; const Point* pp2[4] = {&p2,ps23,ps24,ps14}; const Point* pp3[4] = {&p2,ps23,ps13,ps14}; Real v1 = TetrahedronVolume(pp1); Real v2 = TetrahedronVolume(pp2); Real v3 = TetrahedronVolume(pp3); Vector3r cg1,cg2,cg3; for (l=0; l<3; l++) { normal[l] = n[l]; #define OP(p) p->operator[](l) cg1[l] = .25*(p1[l]+p2[l]+OP(ps13)+OP(ps14)); cg2[l] = .25*(p2[l]+OP(ps23)+OP(ps24)+OP(ps14)); cg3[l] = .25*(p2[l]+OP(ps23)+OP(ps13)+OP(ps14)); #undef OP } penetrationVolume = v1 + v2 + v3; contactPoint = (v1*cg1 + v2*cg2 + v3*cg3) / penetrationVolume; normal.normalize(); return true; } } } return false; } bool Ig2_Tetra_Tetra_TTetraSimpleGeom::checkEdgeToTriangleCase2( // edge larger than triangle const Triangle tA[4], const Triangle tB[4], const Segment sA[6], const Segment sB[6], Vector3r& normal, Vector3r& contactPoint, Real& penetrationVolume) { for (int i=0; i<6; i++) { const Segment& sb = sB[i]; int ni = 0; for (int j=0; j<4; j++) { const Triangle& t = tA[j]; if ( do_intersect(t,sb) ) { ni++; } } if ( ni != 2 ) { continue; } for (int j=0; j<3; j++) { const Triangle& ta1 = tA[j]; if ( !(do_intersect(ta1,sb) ) ) { continue; } for (int k=j+1; k<4; k++) { const Triangle& ta2 = tA[k]; if ( !(do_intersect(ta2,sb) ) ) { continue; } const Triangle& tb1 = tB[stMap[i][0]]; const Triangle& tb2 = tB[stMap[i][1]]; const Segment& sa1a = sA[tsMap[j][0]]; const Segment& sa1b = sA[tsMap[j][1]]; const Segment& sa1c = sA[tsMap[j][2]]; bool b1a = do_intersect(sa1a,tb1) && do_intersect(sa1a,tb2); bool b1b = do_intersect(sa1b,tb1) && do_intersect(sa1b,tb2); bool b1c = do_intersect(sa1c,tb1) && do_intersect(sa1c,tb2); if ( !(b1a || b1b || b1c) ) { continue; } const Segment& sa2a = sA[tsMap[k][0]]; const Segment& sa2b = sA[tsMap[k][1]]; const Segment& sa2c = sA[tsMap[k][2]]; bool b2a = do_intersect(sa2a,tb1) && do_intersect(sa2a,tb2); bool b2b = do_intersect(sa2b,tb1) && do_intersect(sa2b,tb2); bool b2c = do_intersect(sa2c,tb1) && do_intersect(sa2c,tb2); if ( !(b2a || b2b || b2c) ) { continue; } int l = b1a? tsMap[j][0] : b1b? tsMap[j][1] : tsMap[j][2]; int m = b2a? tsMap[k][0] : b2b? tsMap[k][1] : tsMap[k][2]; if (sstMap[l][m] == -1) { continue; } const Segment& sa1 = sA[l]; const Segment& sa2 = sA[m]; const Triangle& taN = tA[sstMap[l][m]]; CGAL::Object o1 = intersection(sb,ta1); CGAL::Object o2 = intersection(sb,ta2); CGAL::Object o11 = intersection(sa1,tb1); CGAL::Object o12 = intersection(sa1,tb2); CGAL::Object o21 = intersection(sa2,tb1); CGAL::Object o22 = intersection(sa2,tb2); const Point* p1 = CGAL::object_cast(&o1); const Point* p2 = CGAL::object_cast(&o2); const Point* p11 = CGAL::object_cast(&o11); const Point* p12 = CGAL::object_cast(&o12); const Point* p21 = CGAL::object_cast(&o21); const Point* p22 = CGAL::object_cast(&o22); if ( !(p1 && p2 && p11 && p12 && p21 && p22) ) { continue; } const Point* pp1[4] = {p1,p2,p11,p12}; const Point* pp2[4] = {p2,p21,p22,p12}; const Point* pp3[4] = {p2,p21,p11,p12}; Real v1 = TetrahedronVolume(pp1); Real v2 = TetrahedronVolume(pp2); Real v3 = TetrahedronVolume(pp3); Vector3r cg1,cg2,cg3; Vector_3 n = CGAL::normal(taN[0],taN[1],taN[2]); for (int l=0; l<3; l++) { normal[l] = n[l]; #define OP(p) p->operator[](l) cg1[l] = .25*(OP(p1)+OP(p2)+OP(p11)+OP(p12)); cg2[l] = .25*(OP(p2)+OP(p21)+OP(p22)+OP(p12)); cg3[l] = .25*(OP(p2)+OP(p21)+OP(p11)+OP(p12)); #undef OP } penetrationVolume = v1 + v2 + v3; contactPoint = (v1*cg1 + v2*cg2 + v3*cg3) / penetrationVolume; normal.normalize(); return true; } } } return false; } bool Ig2_Tetra_Tetra_TTetraSimpleGeom::checkVertexToEdgeCase( const Point pA[4], const Segment sA[6], const Triangle tA[4], const Segment sB[6], const Triangle tB[4], Vector3r& normal, Vector3r& contactPoint, Real& penetrationVolume) { for (int i=0; i<4; i++) { const Point& pa = pA[i]; if ( Vector_3(tB[0][0],pa)*CGAL::normal(tB[0][0],tB[0][1],tB[0][2]) > 0. ) { continue; } if ( Vector_3(tB[1][0],pa)*CGAL::normal(tB[1][0],tB[1][1],tB[1][2]) > 0. ) { continue; } if ( Vector_3(tB[2][0],pa)*CGAL::normal(tB[2][0],tB[2][1],tB[2][2]) > 0. ) { continue; } if ( Vector_3(tB[3][0],pa)*CGAL::normal(tB[3][0],tB[3][1],tB[3][2]) > 0. ) { continue; } const Segment& sa1 = sA[psMap[i][0]]; const Segment& sa2 = sA[psMap[i][1]]; const Segment& sa3 = sA[psMap[i][2]]; for (int j=0; j<6; j++) { const Segment& sb = sB[j]; const Triangle& tb1 = tB[stMap[j][0]]; const Triangle& tb2 = tB[stMap[j][1]]; const Triangle& ta1 = tA[ptMap[i][0]]; const Triangle& ta2 = tA[ptMap[i][1]]; const Triangle& ta3 = tA[ptMap[i][2]]; bool bsa1tb1 = do_intersect(sa1,tb1); bool bsa1tb2 = do_intersect(sa1,tb2); bool bsa2tb1 = do_intersect(sa2,tb1); bool bsa2tb2 = do_intersect(sa2,tb2); bool bsa3tb1 = do_intersect(sa3,tb1); bool bsa3tb2 = do_intersect(sa3,tb2); bool bsbta1 = do_intersect(sb,ta1); bool bsbta2 = do_intersect(sb,ta2); bool bsbta3 = do_intersect(sb,ta3); if ( !( (bsa1tb1 || bsa1tb2) && (bsa2tb1 || bsa2tb2) && (bsa3tb1 || bsa3tb2) && ((bsbta1 && bsbta2) || (bsbta2 && bsbta3) || (bsbta3 && bsbta1)) ) ) { continue; } CGAL::Object oa1 = intersection(sa1,bsa1tb1? tb1 : tb2); CGAL::Object oa2 = intersection(sa2,bsa2tb1? tb1 : tb2); CGAL::Object oa3 = intersection(sa3,bsa3tb1? tb1 : tb2); CGAL::Object ob1 = intersection(sb, (bsbta1 && bsbta2)? ta1 : (bsbta2 && bsbta3)? ta2 : ta3); CGAL::Object ob2 = intersection(sb, (bsbta1 && bsbta2)? ta2 : (bsbta2 && bsbta3)? ta3 : ta1); const Point* pa1 = CGAL::object_cast(&oa1); const Point* pa2 = CGAL::object_cast(&oa2); const Point* pa3 = CGAL::object_cast(&oa3); const Point* pb1 = CGAL::object_cast(&ob1); const Point* pb2 = CGAL::object_cast(&ob2); if ( !(pa1 && pa2 && pa3 && pb1 && pb2) ) { continue; } Segment sa(*pa1,*pa2); Real d1 = sqrt(CGAL::squared_distance(sa,*pb1)); Real d2 = sqrt(CGAL::squared_distance(sa,*pb2)); const Point* ppb1 = d1operator[](l) cg1[l] = .25*(pa[l]+OP(pa1)+OP(pa2)+OP(pa3)); cg2[l] = .25*(OP(pa1)+OP(pa2)+OP(pa3)+OP(ppb2)); cg3[l] = .25*(OP(pa1)+OP(pa2)+OP(ppb1)+OP(ppb2)); #undef OP } penetrationVolume = v1 + v2 + v3; contactPoint = (v1*cg1 + v2*cg2 + v3*cg3) / penetrationVolume; normal.normalize(); return true; } } return false; } bool Ig2_Tetra_Tetra_TTetraSimpleGeom::checkVertexToVertexCase( const Point pA[4], const Point pB[4], const Segment sA[6], const Triangle tA[4], const Triangle tB[4], Vector3r& normal, Vector3r& contactPoint, Real& penetrationVolume) { for (int i=0; i<4; i++) { const Point& pa = pA[i]; if ( Vector_3(tB[0][0],pa)*CGAL::normal(tB[0][0],tB[0][1],tB[0][2]) > 0. ) { continue; } if ( Vector_3(tB[1][0],pa)*CGAL::normal(tB[1][0],tB[1][1],tB[1][2]) > 0. ) { continue; } if ( Vector_3(tB[2][0],pa)*CGAL::normal(tB[2][0],tB[2][1],tB[2][2]) > 0. ) { continue; } if ( Vector_3(tB[3][0],pa)*CGAL::normal(tB[3][0],tB[3][1],tB[3][2]) > 0. ) { continue; } const Segment& sa1 = sA[psMap[i][0]]; const Segment& sa2 = sA[psMap[i][1]]; const Segment& sa3 = sA[psMap[i][2]]; for (int j=0; j<4; j++) { const Point& pb = pB[j]; if ( Vector_3(tA[0][0],pb)*CGAL::normal(tA[0][0],tA[0][1],tA[0][2]) > 0. ) { continue; } if ( Vector_3(tA[1][0],pb)*CGAL::normal(tA[1][0],tA[1][1],tA[1][2]) > 0. ) { continue; } if ( Vector_3(tA[2][0],pb)*CGAL::normal(tA[2][0],tA[2][1],tA[2][2]) > 0. ) { continue; } if ( Vector_3(tA[3][0],pb)*CGAL::normal(tA[3][0],tB[3][1],tB[3][2]) > 0. ) { continue; } const Triangle& tb1 = tB[ptMap[j][0]]; const Triangle& tb2 = tB[ptMap[j][1]]; const Triangle& tb3 = tB[ptMap[j][2]]; bool b11 = do_intersect(sa1,tb1); bool b12 = do_intersect(sa1,tb2); bool b13 = do_intersect(sa1,tb3); bool b21 = do_intersect(sa2,tb1); bool b22 = do_intersect(sa2,tb2); bool b23 = do_intersect(sa2,tb3); bool b31 = do_intersect(sa3,tb1); bool b32 = do_intersect(sa3,tb2); bool b33 = do_intersect(sa3,tb3); if ( !(b11 || b12 || b13) && (b21 || b22 || b23) && (b31 || b32 || b33) ) { continue; } CGAL::Object o1 = intersection(sa1, b11? tb1: b12? tb2 : tb3); CGAL::Object o2 = intersection(sa2, b21? tb1: b22? tb2 : tb3); CGAL::Object o3 = intersection(sa3, b31? tb1: b32? tb2 : tb3); const Point* p1 = CGAL::object_cast(&o1); const Point* p2 = CGAL::object_cast(&o2); const Point* p3 = CGAL::object_cast(&o3); if ( !(p1 && p2 && p3) ) { continue; } const Point* pp1[4] = {&pa,p1,p2,p3}; const Point* pp2[4] = {&pb,p2,p3,p3}; Real v1 = TetrahedronVolume(pp1); Real v2 = TetrahedronVolume(pp2); Vector3r cg1,cg2; Vector_3 n(pa,pb); for (int l=0; l<3; l++) { normal[l] = n[l]; #define OP(p) p->operator[](l) cg1[l] = .25*(pa[l]+OP(p1)+OP(p2)+OP(p3)); cg2[l] = .25*(pb[l]+OP(p1)+OP(p2)+OP(p3)); #undef OP } penetrationVolume = v1 + v2; contactPoint = (v1*cg1 + v2*cg2) / penetrationVolume; normal.normalize(); return true; } } return false; } bool Ig2_Tetra_Tetra_TTetraSimpleGeom::go( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& interaction) { const Se3r& se31=state1.se3; const Se3r& se32=state2.se3; Tetra* shape1 = static_cast(cm1.get()); Tetra* shape2 = static_cast(cm2.get()); Point p1[4], p2[4]; Vector3r vTemp; // vertices in global coordinates for (int i=0; i<4; i++) { vTemp = se31.position + se31.orientation*shape1->v[i]; p1[i] = Point(vTemp[0],vTemp[1],vTemp[2]); vTemp = se32.position + se32.orientation*shape2->v[i] + shift2; p2[i] = Point(vTemp[0],vTemp[1],vTemp[2]); } // Faces (CGAL triangles) of each tetra #define T(p,i,j,k) Triangle(p[i],p[j],p[k]) const Triangle t1[4] = {T(p1,0,1,3),T(p1,0,2,1),T(p1,1,2,3),T(p1,0,3,2)}; const Triangle t2[4] = {T(p2,0,1,3),T(p2,0,2,1),T(p2,1,2,3),T(p2,0,3,2)}; #undef T // Edges (CGAL segments) of each tetra #define S(p,i,j) Segment(p[i],p[j]) const Segment s1[6] = {S(p1,0,1),S(p1,1,2),S(p1,0,2),S(p1,0,3),S(p1,1,3),S(p1,2,3)}; const Segment s2[6] = {S(p2,0,1),S(p2,1,2),S(p2,0,2),S(p2,0,3),S(p2,1,3),S(p2,2,3)}; #undef S Vector3r n; Vector3r cp; Real V; int flag; # define SET_GEOM_AND_RETURN_TRUE \ shared_ptr geom; \ if (!interaction->geom) geom=shared_ptr(new TTetraSimpleGeom()); \ else geom=YADE_PTR_CAST(interaction->geom); \ interaction->geom=geom; \ geom->normal = n; \ geom->contactPoint = cp; \ geom->penetrationVolume = V; \ geom->flag = flag; \ return true; if (checkVertexToTriangleCase(t1,p2,s2,n,cp,V)) { flag = 1; SET_GEOM_AND_RETURN_TRUE } if (checkVertexToTriangleCase(t2,p1,s1,n,cp,V)) { n *= -1.; flag = 2; SET_GEOM_AND_RETURN_TRUE } if (checkEdgeToEdgeCase(s1,s2,t1,t2,n,cp,V)) { flag = 3; SET_GEOM_AND_RETURN_TRUE } if (checkEdgeToTriangleCase1(t1,s2,p2,n,cp,V)) { flag = 4; SET_GEOM_AND_RETURN_TRUE } if (checkEdgeToTriangleCase1(t2,s1,p1,n,cp,V)) { n *= -1.; flag = 5; SET_GEOM_AND_RETURN_TRUE } if (checkEdgeToTriangleCase2(t1,t2,s1,s2,n,cp,V)) { flag = 6; SET_GEOM_AND_RETURN_TRUE } if (checkEdgeToTriangleCase2(t2,t1,s2,s1,n,cp,V)) { n *= -1.; flag = 7; SET_GEOM_AND_RETURN_TRUE } if (checkVertexToEdgeCase(p1,s1,t1,s2,t2,n,cp,V)) { n *= -1.; flag = 8; SET_GEOM_AND_RETURN_TRUE } if (checkVertexToEdgeCase(p2,s2,t2,s1,t1,n,cp,V)) { flag = 9; SET_GEOM_AND_RETURN_TRUE } #undef SET_GEOM_AND_RETURN_TRUE if (interaction->geom) { TTetraSimpleGeom* geom = static_cast(interaction->geom.get()); geom->penetrationVolume = (Real)-1.; geom->flag = 0; return true; } return false; } #endif CREATE_LOGGER(Ig2_Tetra_Tetra_TTetraGeom); /*! Calculate configuration of Tetra - Tetra intersection. * * Wildmagick's functions are used here: intersection is returned as a set of tetrahedra (may be empty, inwhich case there is no real intersection). * Then we calcualte volumetric proeprties of this intersection volume: inertia, centroid, volume. * * Contact normal (the direction in which repulsive force will act) coincides with the direction of least inertia, * since that is the gradient that maximizes the drop of elastic deformation energy and will reach minimum fastest. * * Equivalent cross section of the penetrating volume (as if it were a cuboid with the same inertia) and equivalent penetration depth are calculated; * Equivalent solid size in the dimension of normal serves as reference for strain calculation and is different for solids A and B. * * Strain will be then approximated by equivalentPenetrationDepth/.5*(maxPenetrationDepthA+maxPenetrationDepthB) (the average of A and B) * * All the relevant results are fed into TTetraGeom which is passed to TetraVolumetricLaw later that makes actual use of all this. * * @todo thoroughly test this for numerical correctness. * */ bool Ig2_Tetra_Tetra_TTetraGeom::go(const shared_ptr& cm1,const shared_ptr& cm2,const State& state1,const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& interaction){ const Se3r& se31=state1.se3; const Se3r& se32=state2.se3; Tetra* A = static_cast(cm1.get()); Tetra* B = static_cast(cm2.get()); //return false; shared_ptr bang; // depending whether it's a new interaction: create new one, or use the existing one. if (!interaction->geom) bang=shared_ptr(new TTetraGeom()); else bang=YADE_PTR_CAST(interaction->geom); interaction->geom=bang; // use wildmagick's intersection routine? #if 0 // transform to global coordinates, build Tetrahedron3r objects to make wm3 happy Tetrahedron3r tA(se31.orientation*A->v[0]+se31.position,se31.orientation*A->v[1]+se31.position,se31.orientation*A->v[2]+se31.position,se31.orientation*A->v[3]+se31.position); Tetrahedron3r tB(se32.orientation*B->v[0]+se32.position,se32.orientation*B->v[1]+se32.position,se32.orientation*B->v[2]+se32.position,se32.orientation*B->v[3]+se32.position); IntrTetrahedron3Tetrahedron3r iAB(tA,tB); bool found=iAB.Find(); //calculates the intersection volume as a composition of 0 or more tetrahedra if(!found) return false; // no intersecting volume Real V(0); // volume of intersection (cummulative) Vector3r Sg(0,0,0); // static moment of intersection vector > tAB; Wm3::TArray iABinfo(iAB.GetIntersection()); // retrieve the array of 4hedra for(int i=0; i t; t.push_back(v0); t.push_back(v1); t.push_back(v2); t.push_back(v3); tAB.push_back(t); #undef v0 #undef v1 #undef v2 #undef v3 } #endif // transform to global coordinates, build Tetra objects Tetra tA(se31.orientation*A->v[0]+se31.position,se31.orientation*A->v[1]+se31.position,se31.orientation*A->v[2]+se31.position,se31.orientation*A->v[3]+se31.position); Tetra tB(se32.orientation*B->v[0]+se32.position+shift2,se32.orientation*B->v[1]+se32.position+shift2,se32.orientation*B->v[2]+se32.position+shift2,se32.orientation*B->v[3]+se32.position+shift2); // calculate intersection #if 0 tB=Tetra(Vector3r(0,0,0),Vector3r(1.5,1,1),Vector3r(0.5,1,1),Vector3r(1,1,.5)); tA=Tetra(Vector3r(0,0,0),Vector3r(1,0,0),Vector3r(0,1,0),Vector3r(0,0,1)); #endif list tAB=Tetra2TetraIntersection(tA,tB); if (!interaction->isReal() && !force) { if(tAB.size()==0) { /* LOG_DEBUG("No intersection."); */ return false;} //no intersecting volume } Real V(0); // volume of intersection (cummulative) Vector3r Sg(0,0,0); // static moment of intersection Vector3r tt[4]; for(int i=0; i<4; i++) tt[i]=tA.v[i]; for(list::iterator II=tAB.begin(); II!=tAB.end(); II++){ Real dV=TetrahedronVolume(II->v); V+=dV; Sg+=dV*(II->v[0]+II->v[1]+II->v[2]+II->v[3])*.25; } Vector3r centroid=Sg/V; Matrix3r I(Matrix3r::Zero()); // inertia tensor for the composition; zero matrix initially // I is purely geometrical (as if with unit density) // get total Vector3r dist; for(list::iterator II=tAB.begin(); II!=tAB.end(); II++){ II->v[0]-=centroid; II->v[1]-=centroid; II->v[2]-=centroid; II->v[3]-=centroid; dist=(II->v[0]+II->v[1]+II->v[2]+II->v[3])*.25-centroid; /* use parallel axis theorem */ Matrix3r distSq(Matrix3r::Zero()); distSq(0,0)=dist[0]*dist[0]; distSq(1,1)=dist[1]*dist[1]; distSq(2,2)=dist[2]*dist[2]; // could be done more intelligently with eigen I+=TetrahedronInertiaTensor(II->v)+TetrahedronVolume(II->v)*distSq; } /* Now, we have the collision volumetrically described by intersection volume (V), its inertia tensor (I) and centroid (centroid; contact point). * The inertia tensor is in global coordinates; by eigendecomposition, we find principal axes, which will give us * 1. normal, the direction of the lest inertia; this is the gradient of penetration energy * it may have either direction mathematically, but since 4hedra are convex, * normal will be always the direction pointing more towards the centroid of the other 4hedron * 2. tangent?! hopefully not needed at all. */ Matrix3r Ip, R; // principal moments of inertia, rotation matrix /* should check convergence*/ matrixEigenDecomposition(I,R,Ip); // according to the documentation in Wm3 header, diagonal entries are in ascending order: d0<=d1<=d2; // but keep it algorithmic for now and just assert that. int ix=(Ip(0,0)v[0]+B->v[1]+B->v[2]+B->v[3])*.25)+se31.position; // reverse direction if projection of the (contact_point-centroid_of_B) vector onto the normal is negative (i.e. the normal points more towards A) if((Bcent-centroid).dot(normal)<0) normal*=-1; /* now estimate the area of the solid that is perpendicular to the normal. This will be needed to estimate elastic force based on Young's modulus. * Suppose we have cuboid, with edges of lengths x,y,z in the direction of respective axes. * It's inertia are Ix=(V/12)*(y^2+z^2), Iy=(V/12)*(x^2+z^2), Iz=(V/12)*(x^2+y^2) and suppose Iz is maximal; Ix, Iy and Iz are known (from decomposition above). * Then the area perpendicular to z (normal direction) is given by x*y=V/z, where V is known. * Ix+Iy-Iz=(V/12)*(y^2+z^2+x^2+z^2-x^2-y^2)=(V*z^2)/6, z=√(6*(Ix+Iy-Iz)/V) * Az=V/z=√(V^3/(6*(Ix+Iy-Iz))). * * In our case, the greatest inertia is along ixxx, the other coordinates are ixx and ix. equivalentPenetrationDepth means what was z. */ Real equivalentPenetrationDepth=sqrt(6.*(Ip(ix,ix)+Ip(ixx,ixx)-Ip(ixxx,ixxx))/V); Real equivalentCrossSection=V/equivalentPenetrationDepth; TRVAR3(V,equivalentPenetrationDepth,equivalentCrossSection); /* Now rotate the whole inertia tensors of A and B and estimate maxPenetrationDepth -- the length of the body in the direction of the contact normal. * This will be used to calculate relative deformation, which is needed for elastic response. */ const State* physA=Body::byId(interaction->getId1())->state.get(); const State* physB=Body::byId(interaction->getId2())->state.get(); // WARNING: Matrix3r(Vector3r(...)) is compiled, but gives zero matrix??!! Use explicitly constructor from diagonal entries //Matrix3r IA(physA->inertia[0],physA->inertia[1],physA->inertia[2]); Matrix3r IB(physB->inertia[0],physB->inertia[1],physB->inertia[2]); Matrix3r IA=Matrix3r::Zero(), IB=Matrix3r::Zero(); for(int i=0; i<3; i++){ IA(i,i)=physA->inertia[i]; IB(i,i)=physB->inertia[i]; } // see Clump::inertiaTensorRotate for references IA=R.transpose()*IA*R; IB=R.transpose()*IB*R; Real maxPenetrationDepthA=sqrt(6*(IA(ix,ix)+IA(ixx,ixx)-IA(ixxx,ixxx))/V); Real maxPenetrationDepthB=sqrt(6*(IB(ix,ix)+IB(ixx,ixx)-IB(ixxx,ixxx))/V); TRVAR2(maxPenetrationDepthA,maxPenetrationDepthB); //normal = se32.position - se31.position; normal.normalize(); /* store calculated stuff in bang; some is redundant */ bang->normal=normal; bang->equivalentCrossSection=equivalentCrossSection; bang->contactPoint=centroid; bang->penetrationVolume=V; bang->equivalentPenetrationDepth=equivalentPenetrationDepth; bang->maxPenetrationDepthA=maxPenetrationDepthA; bang->maxPenetrationDepthB=maxPenetrationDepthB; return true; } /*! Calculate intersection o Tetrahedron A and B as union of set (std::list) of 4hedra. * * intersecting tetrahedra A and B * S=intersection set (4hedra) * S={A} * for face in B_faces: * for t in S: [ S is mutable, but if list, iterators remain valid? ] * tmp = clip t by face // may return multiple 4hedra or none * replace t by tmp (possibly none) in S * return S * */ list Ig2_Tetra_Tetra_TTetraGeom::Tetra2TetraIntersection(const Tetra& A, const Tetra& B){ // list of 4hedra to split; initially A list ret; ret.push_back(A); /* I is vertex index at B; * clipping face is [i i1 i2], normal points away from i3 */ int i,i1,i2,i3; Vector3r normal; /* LOG_TRACE("===========================================================================================") LOG_TRACE("===========================================================================================") LOG_TRACE(ret.size()); LOG_TRACE("DUMP A and B:"); A.dump(); B.dump(); */ for(i=0; i<4; i++){ i1=(i+1)%4; i2=(i+2)%4; i3=(i+3)%4; const Vector3r& P(B.v[i]); // reference point on the plane normal=(B.v[i1]-P).cross(B.v[i2]-P); normal.normalize(); // normal if((B.v[i3]-P).dot(normal)>0) normal*=-1; // outer normal for(list::iterator I=ret.begin(); I!=ret.end(); /* I++ */ ){ list splitDecomposition=TetraClipByPlane(*I,P,normal); // replace current list element by the result of decomposition; // I points after the erased one, so decomposed 4hedra will not be touched in this iteration, just as we want. // Since it will be incremented by I++ at the end of the cycle, compensate for that by I--; I=ret.erase(I); ret.insert(I,splitDecomposition.begin(),splitDecomposition.end()); /* I--; */ /* LOG_TRACE("DUMP current tetrahedron list:"); for(list::iterator I=ret.begin(); I!=ret.end(); I++) (*I).dump();*/ } } //exit(0); return ret; } /*! Clip Tetra T by plane give by point P and outer normal n. * * Algorithm: * * clip t by face * sort points of t into positive, negative, zero (face normal n points outside) * -: inside; +: outside; 0: on face * homogeneous cases (no split): * ++++, +++0, ++00, +000 : * 0Δ full clip (everything outside), nothing left; return ∅ * ----, ---0, --00, -000 : * 1Δ all inside, return identity * split (at least one - and one +) * -+++ * 1Δ [A AB AC AD] * -++0 * 1Δ [A AB AC D] * -+00: * 1Δ [A AB C D] * --++: * 3Δ [A AC AD B BC BD] ⇒ (e.g.) [A AC AD B] [B BC BD AD] [B AD AC BC] * --+0: * 2Δ [A B AC BC D] ⇒ (e.g.) [A AC BC D] [B BC A D] * ---+: * 3Δ tetrahedrize [A B C AD BD CD] * * http://members.tripod.com/~Paul_Kirby/vector/Vplanelineint.html */ list Ig2_Tetra_Tetra_TTetraGeom::TetraClipByPlane(const Tetra& T, const Vector3r& P, const Vector3r& normal){ list ret; // scaling factor for Mathr::EPSILON: average edge length Real scaledEPSILON=Mathr::EPSILON*(1/6.)*((T.v[1]-T.v[0])+(T.v[2]-T.v[0])+(T.v[3]-T.v[0])+(T.v[2]-T.v[1])+(T.v[3]-T.v[1])+(T.v[3]-T.v[2])).norm(); vector pos, neg, zer; Real dist[4]; for(size_t i=0; i<4; i++){ dist[i]=(T.v[i]-P).dot(normal); if(dist[i]>scaledEPSILON) pos.push_back(i); else if(dist[i]<-scaledEPSILON) neg.push_back(i); else zer.push_back(i); } /* LOG_TRACE("dist[i]=["<& I, *scene->interactions){ // normally, we would test isReal(), but TetraVolumetricLaw doesn't use phys at all if (!I->geom) continue; // Ig2_Tetra_Tetra_TTetraGeom::go returned false for this interaction, skip it const shared_ptr& contactGeom(YADE_PTR_DYN_CAST(I->geom)); if(!contactGeom) continue; const Body::id_t idA=I->getId1(), idB=I->getId2(); const shared_ptr& A=Body::byId(idA), B=Body::byId(idB); const shared_ptr& physA(YADE_PTR_DYN_CAST(A->material)); const shared_ptr& physB(YADE_PTR_DYN_CAST(B->material)); /* Cross-section is volumetrically equivalent to the penetration configuration */ Real averageStrain=contactGeom->equivalentPenetrationDepth/(.5*(contactGeom->maxPenetrationDepthA+contactGeom->maxPenetrationDepthB)); /* Do not use NormPhys::kn (as calculated by ElasticBodySimpleRelationship). * NormPhys::kn is not Young's modulus, it is calculated by MacroMicroElasticRelationships. So perhaps * a new IPhysFunctor will be needed that will just pass the average Young's modulus here? * For now, just go back to Young's moduli directly here. */ Real young=.5*(physA->young+physB->young); TRVAR3(young,averageStrain,contactGeom->equivalentCrossSection); // F=σA=εEA // this is unused; should it?: contactPhys->kn Vector3r F=contactGeom->normal*averageStrain*young*contactGeom->equivalentCrossSection; scene->forces.addForce (idA,-F); scene->forces.addForce (idB, F); scene->forces.addTorque(idA,-(A->state->pos-contactGeom->contactPoint).cross(F)); scene->forces.addTorque(idB, (B->state->pos-contactGeom->contactPoint).cross(F)); } } #ifdef YADE_OPENGL #include bool Gl1_Tetra::wire; void Gl1_Tetra::go(const shared_ptr& cm, const shared_ptr&,bool wire2,const GLViewInfo&) { glMaterialv(GL_FRONT,GL_AMBIENT_AND_DIFFUSE,Vector3r(cm->color[0],cm->color[1],cm->color[2])); glColor3v(cm->color); Tetra* t=static_cast(cm.get()); if (wire && wire2) { // wireframe, as for Tetrahedron glDisable(GL_LIGHTING); glBegin(GL_LINES); glOneWire(t, 0, 1); glOneWire(t, 0, 2); glOneWire(t, 0, 3); glOneWire(t, 1, 2); glOneWire(t, 1, 3); glOneWire(t, 2, 3); glEnd(); } else { glDisable(GL_CULL_FACE); glEnable(GL_LIGHTING); glBegin(GL_TRIANGLES); glOneFace (t, 0,2,1); glOneFace (t, 0,1,3); glOneFace (t, 1,2,3); glOneFace (t, 0,3,2); glEnd(); } } #endif /*! Calculates tetrahedron inertia relative to the origin (0,0,0), with unit density (scales linearly). See article F. Tonon, "Explicit Exact Formulas for the 3-D Tetrahedron Inertia Tensor in Terms of its Vertex Coordinates", http://www.scipub.org/fulltext/jms2/jms2118-11.pdf Numerical example to check: vertices: (8.33220, 11.86875, 0.93355) (0.75523 ,5.00000, 16.37072) (52.61236, 5.00000, 5.38580) (2.00000, 5.00000, 3.00000) centroid: (15.92492, 0.78281, 3.72962) intertia/density WRT centroid: a/μ = 43520.33257 m⁵ b/μ = 194711.28938 m⁵ c/μ = 191168.76173 m⁵ a’/μ= 4417.66150 m⁵ b’/μ=-46343.16662 m⁵ c’/μ= 11996.20119 m⁵ The numerical testcase (in TetraTestGen::generate) is exact as in the article for inertia (as well as centroid): 43520.3 194711 191169 4417.66 -46343.2 11996.2 */ //Matrix3r TetrahedronInertiaTensor(const Vector3r v[4]){ Matrix3r TetrahedronInertiaTensor(const vector& v){ #define x1 v[0][0] #define y1 v[0][1] #define z1 v[0][2] #define x2 v[1][0] #define y2 v[1][1] #define z2 v[1][2] #define x3 v[2][0] #define y3 v[2][1] #define z3 v[2][2] #define x4 v[3][0] #define y4 v[3][1] #define z4 v[3][2] // FIXME - C array assert(v.size()==4); // Jacobian of transformation to the reference 4hedron double detJ=(x2-x1)*(y3-y1)*(z4-z1)+(x3-x1)*(y4-y1)*(z2-z1)+(x4-x1)*(y2-y1)*(z3-z1) -(x2-x1)*(y4-y1)*(z3-z1)-(x3-x1)*(y2-y1)*(z4-z1)-(x4-x1)*(y3-y1)*(z2-z1); detJ=std::abs(detJ); double a=detJ*(y1*y1+y1*y2+y2*y2+y1*y3+y2*y3+ y3*y3+y1*y4+y2*y4+y3*y4+y4*y4+z1*z1+z1*z2+ z2*z2+z1*z3+z2*z3+z3*z3+z1*z4+z2*z4+z3*z4+z4*z4)/60.; double b=detJ*(x1*x1+x1*x2+x2*x2+x1*x3+x2*x3+x3*x3+ x1*x4+x2*x4+x3*x4+x4*x4+z1*z1+z1*z2+z2*z2+z1*z3+ z2*z3+z3*z3+z1*z4+z2*z4+z3*z4+z4*z4)/60.; double c=detJ*(x1*x1+x1*x2+x2*x2+x1*x3+x2*x3+x3*x3+x1*x4+ x2*x4+x3*x4+x4*x4+y1*y1+y1*y2+y2*y2+y1*y3+ y2*y3+y3*y3+y1*y4+y2*y4+y3*y4+y4*y4)/60.; // a' in the article etc. double a__=detJ*(2*y1*z1+y2*z1+y3*z1+y4*z1+y1*z2+ 2*y2*z2+y3*z2+y4*z2+y1*z3+y2*z3+2*y3*z3+ y4*z3+y1*z4+y2*z4+y3*z4+2*y4*z4)/120.; double b__=detJ*(2*x1*z1+x2*z1+x3*z1+x4*z1+x1*z2+ 2*x2*z2+x3*z2+x4*z2+x1*z3+x2*z3+2*x3*z3+ x4*z3+x1*z4+x2*z4+x3*z4+2*x4*z4)/120.; double c__=detJ*(2*x1*y1+x2*y1+x3*y1+x4*y1+x1*y2+ 2*x2*y2+x3*y2+x4*y2+x1*y3+x2*y3+2*x3*y3+ x4*y3+x1*y4+x2*y4+x3*y4+2*x4*y4)/120.; Matrix3r ret; ret<< a , -b__, -c__, -b__, b , -a__, -c__, -a__, c ; return ret; #undef x1 #undef y1 #undef z1 #undef x2 #undef y2 #undef z2 #undef x3 #undef y3 #undef z3 #undef x4 #undef y4 #undef z4 } /*! Caluclate tetrahedron's central inertia tensor */ //Matrix3r TetrahedronCentralInertiaTensor(const Vector3r v[4]){ Matrix3r TetrahedronCentralInertiaTensor(const vector& v){ assert(v.size()==4); vector vv; // Vector3r vv[4]; Vector3r cg=(v[0]+v[1]+v[2]+v[3])*.25; // vv[0]=v[0]-cg; // vv[1]=v[1]-cg; // vv[2]=v[2]-cg; // vv[3]=v[3]-cg; vv.push_back(v[0]-cg); vv.push_back(v[1]-cg); vv.push_back(v[2]-cg); vv.push_back(v[3]-cg); return TetrahedronInertiaTensor(vv); } /*! Rotate and translate terahedron body so that its local axes are principal, keeping global position by updating vertex positions as well. * Updates all body parameters as need. * * @returns rotation that was done as Wm3::Quaternionr. * @todo check for geometrical correctness... * */ Quaternionr TetrahedronWithLocalAxesPrincipal(shared_ptr& tetraBody){ //const shared_ptr& rbp(YADE_PTR_CAST(tetraBody->physicalParameters)); State* rbp=tetraBody->state.get(); const shared_ptr& tMold(YADE_PTR_DYN_CAST(tetraBody->shape)); #define v0 tMold->v[0] #define v1 tMold->v[1] #define v2 tMold->v[2] #define v3 tMold->v[3] // adjust position (origin to centroid) Vector3r cg=(v0+v1+v2+v3)*.25; v0-=cg; v1-=cg; v2-=cg; v3-=cg; //tMold->v[0]=v0; tMold->v[1]=v1; tMold->v[2]=v2; tMold->v[3]=v3; rbp->se3.position+=cg; // adjust orientation (local axes to principal axes) Matrix3r I_old=TetrahedronInertiaTensor(tMold->v); //≡TetrahedronCentralInertiaTensor Matrix3r I_rot(Matrix3r::Zero()), I_new(Matrix3r::Zero()); matrixEigenDecomposition(I_old,I_rot,I_new); Quaternionr I_Qrot(I_rot); //! @fixme from right to left: rotate by I_rot, then add original rotation (?!!) rbp->se3.orientation=rbp->se3.orientation*I_Qrot; for(size_t i=0; i<4; i++){ tMold->v[i]=I_Qrot.conjugate()*tMold->v[i]; } // set inertia rbp->inertia=Vector3r(I_new(0,0),I_new(1,1),I_new(2,2)); return I_Qrot; #undef v0 #undef v1 #undef v2 #undef v3 } Real TetrahedronSignedVolume(const Vector3r v[4]) { return (Vector3r(v[3])-Vector3r(v[0])).dot((Vector3r(v[3])-Vector3r(v[1])).cross(Vector3r(v[3])-Vector3r(v[2])))/6.; } Real TetrahedronVolume(const Vector3r v[4]) { return std::abs(TetrahedronSignedVolume(v)); } Real TetrahedronSignedVolume(const vector& v) { return Vector3r(v[1]-v[0]).dot(Vector3r(v[2]-v[0]).cross(v[3]-v[0]))/6.; } Real TetrahedronVolume(const vector& v) { return std::abs(TetrahedronSignedVolume(v)); } #ifdef YADE_CGAL Real TetrahedronVolume(const CGAL::Point_3 >* v[4]) { Vector3r vv[4]; for (int i=0; i<4; i++) { for (int j=0; j<3; j++) { vv[i][j] = v[i]->operator[](j); } } return TetrahedronVolume(vv); } Real TetrahedronVolume(const CGAL::Point_3 > v[4]) { Vector3r vv[4]; for (int i=0; i<4; i++) { for (int j=0; j<3; j++) { vv[i][j] = v[i][j]; } } return TetrahedronVolume(vv); } #endif #ifdef YADE_CGAL bool Law2_TTetraSimpleGeom_NormPhys_Simple::go(shared_ptr& ig, shared_ptr& ip, Interaction* contact){ int id1 = contact->getId1(), id2 = contact->getId2(); TTetraSimpleGeom* geom= static_cast(ig.get()); NormPhys* phys = static_cast(ip.get()); if ( geom->flag == 0 || geom->penetrationVolume <= 0. ) { return false; } Real& un=geom->penetrationVolume; phys->normalForce=phys->kn*std::max(un,(Real) 0)*geom->normal; State* de1 = Body::byId(id1,scene)->state.get(); State* de2 = Body::byId(id2,scene)->state.get(); applyForceAtContactPoint(-phys->normalForce, geom->contactPoint, id1, de1->se3.position, id2, de2->se3.position); // TODO periodic return true; } #endif trunk-2017.01a/pkg/dem/Tetra.hpp000066400000000000000000000211731304022710500163040ustar00rootroot00000000000000// © 2007 Václav Šmilauer // © 2013 Jan Stránský #pragma once #include #include #include #include #include #include #ifdef YADE_CGAL #include //#include #endif /* Our mold of tetrahedron: just 4 vertices. * * Self-contained. */ class Tetra: public Shape{ public: Tetra(Vector3r v0, Vector3r v1, Vector3r v2, Vector3r v3) { createIndex(); v.resize(4); v[0]=v0; v[1]=v1; v[2]=v2; v[3]=v3; } virtual ~Tetra(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(Tetra,Shape,"Tetrahedron geometry.", ((std::vector,v,std::vector(4),,"Tetrahedron vertices (in local coordinate system).")), /*ctor*/createIndex(); ); REGISTER_CLASS_INDEX(Tetra,Shape); }; REGISTER_SERIALIZABLE(Tetra); /*! Collision configuration for Tetra and something. * This is expressed as penetration volume properties: centroid, volume, orientation of principal axes, inertia. * * Self-contained. */ class TTetraGeom: public IGeom{ public: virtual ~TTetraGeom(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(TTetraGeom,IGeom,"Geometry of interaction between 2 :yref:`tetrahedra`, including volumetric characteristics", ((Real,penetrationVolume,NaN,,"Volume of overlap [m³]")) ((Real,equivalentCrossSection,NaN,,"Cross-section of the overlap (perpendicular to the axis of least inertia")) ((Real,maxPenetrationDepthA,NaN,,"??")) ((Real,maxPenetrationDepthB,NaN,,"??")) ((Real,equivalentPenetrationDepth,NaN,,"??")) ((Vector3r,contactPoint,,,"Contact point (global coords)")) ((Vector3r,normal,,,"Normal of the interaction, directed in the sense of least inertia of the overlap volume")), createIndex(); ); REGISTER_CLASS_INDEX(TTetraGeom,IGeom); }; REGISTER_SERIALIZABLE(TTetraGeom); class TTetraSimpleGeom: public IGeom{ public: virtual ~TTetraSimpleGeom(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(TTetraSimpleGeom,IGeom,"EXPERIMENTAL. Geometry of interaction between 2 :yref:`tetrahedra`", ((Real,penetrationVolume,NaN,,"Volume of overlap [m³]")) ((Vector3r,contactPoint,,,"Contact point (global coords)")) ((Vector3r,normal,,,"Normal of the interaction TODO")) ((int,flag,0,,"TODO")), createIndex(); ); REGISTER_CLASS_INDEX(TTetraSimpleGeom,IGeom); }; REGISTER_SERIALIZABLE(TTetraSimpleGeom); /*! Creates Aabb from Tetra. * * Self-contained. */ class Bo1_Tetra_Aabb: public BoundFunctor{ public: void go(const shared_ptr& ig, shared_ptr& bv, const Se3r& se3, const Body*); FUNCTOR1D(Tetra); YADE_CLASS_BASE_DOC(Bo1_Tetra_Aabb,BoundFunctor,"Create/update :yref:`Aabb` of a :yref:`Tetra`"); }; REGISTER_SERIALIZABLE(Bo1_Tetra_Aabb); #ifdef YADE_OPENGL #include /*! Draw Tetra using OpenGL */ class Gl1_Tetra: public GlShapeFunctor{ public: virtual void go(const shared_ptr&, const shared_ptr&,bool,const GLViewInfo&); YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_Tetra,GlShapeFunctor,"Renders :yref:`Tetra` object", ((bool,wire,true,,"TODO")) ); RENDERS(Tetra); }; REGISTER_SERIALIZABLE(Gl1_Tetra); #endif /*! Calculate physical response based on penetration configuration given by TTetraGeom. */ class TetraVolumetricLaw: public GlobalEngine { public: void action(); DECLARE_LOGGER; YADE_CLASS_BASE_DOC(TetraVolumetricLaw,GlobalEngine,"Calculate physical response of 2 :yref:`tetrahedra` in interaction, based on penetration configuration given by :yref:`TTetraGeom`."); }; REGISTER_SERIALIZABLE(TetraVolumetricLaw); /*! @fixme implement Tetra2BoxBang by representing box as 6 tetrahedra. */ /*! Create TTetraGeom (collision geometry) from colliding Tetra's. */ class Ig2_Tetra_Tetra_TTetraGeom: public IGeomFunctor { public: virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c){ throw std::logic_error("Ig2_Tetra_Tetra_TTetraGeom::goReverse called, but the functor is symmetric."); } FUNCTOR2D(Tetra,Tetra); DEFINE_FUNCTOR_ORDER_2D(Tetra,Tetra); YADE_CLASS_BASE_DOC(Ig2_Tetra_Tetra_TTetraGeom,IGeomFunctor,"Create/update geometry of collision between 2 :yref:`tetrahedra` (:yref:`TTetraGeom` instance)"); DECLARE_LOGGER; private: std::list Tetra2TetraIntersection(const Tetra& A, const Tetra& B); std::list TetraClipByPlane(const Tetra& T, const Vector3r& P, const Vector3r& n); //! Intersection of line given by points A, B and plane given by P and its normal. Vector3r PtPtPlaneIntr(const Vector3r& A, const Vector3r& B, const Vector3r& P, const Vector3r& normal){const double t=(P-A).dot(normal) / (B-A).dot(normal); return A+t*(B-A); } }; REGISTER_SERIALIZABLE(Ig2_Tetra_Tetra_TTetraGeom); #ifdef YADE_CGAL class Ig2_Tetra_Tetra_TTetraSimpleGeom: public IGeomFunctor { protected: typedef CGAL::Cartesian K; typedef K::Point_3 Point; typedef CGAL::Tetrahedron_3 CGALTetra; typedef CGAL::Segment_3 Segment; typedef CGAL::Triangle_3 Triangle; typedef CGAL::Vector_3 Vector_3; bool checkVertexToTriangleCase(const Triangle tA[4], const Point pB[4], const Segment sB[6], Vector3r& normal, Vector3r& contactPoint, Real& penetrationVolume); bool checkEdgeToEdgeCase(const Segment sA[6], const Segment sB[6], const Triangle tA[4], const Triangle tB[4], Vector3r& normal, Vector3r& contactPoint, Real& penetrationVolume); bool checkEdgeToTriangleCase1(const Triangle tA[4], const Segment sB[6], const Point pB[4], Vector3r& normal, Vector3r& contactPoint, Real& penetrationVolume); bool checkEdgeToTriangleCase2(const Triangle tA[4], const Triangle tB[4], const Segment sA[6], const Segment sB[6], Vector3r& normal, Vector3r& contactPoint, Real& penetrationVolume); bool checkVertexToEdgeCase(const Point pA[4], const Segment sA[6], const Triangle tA[4], const Segment sB[6], const Triangle tB[4], Vector3r& normal, Vector3r& contactPoint, Real& penetrationVolume); bool checkVertexToVertexCase(const Point pA[4], const Point pB[4], const Segment sA[6], const Triangle tA[4], const Triangle tB[4], Vector3r& normal, Vector3r& contactPoint, Real& penetrationVolume); static const int psMap[4][3]; static const int ptMap[4][3]; static const int stMap[6][2]; static const int tsMap[4][3]; static const int ppsMap[4][4]; static const int sstMap[6][6]; public: virtual bool go(const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c); virtual bool goReverse( const shared_ptr& cm1, const shared_ptr& cm2, const State& state1, const State& state2, const Vector3r& shift2, const bool& force, const shared_ptr& c){ throw std::logic_error("Ig2_Tetra_Tetra_TTetraSimpleGeom::goReverse called, but the functor is symmetric."); } FUNCTOR2D(Tetra,Tetra); DEFINE_FUNCTOR_ORDER_2D(Tetra,Tetra); YADE_CLASS_BASE_DOC(Ig2_Tetra_Tetra_TTetraSimpleGeom,IGeomFunctor,"EXPERIMANTAL. Create/update geometry of collision between 2 :yref:`tetrahedra` (:yref:`TTetraSimpleGeom` instance)"); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Ig2_Tetra_Tetra_TTetraSimpleGeom); class Law2_TTetraSimpleGeom_NormPhys_Simple: public LawFunctor{ public: virtual bool go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I); YADE_CLASS_BASE_DOC(Law2_TTetraSimpleGeom_NormPhys_Simple,LawFunctor,"EXPERIMENTAL. TODO"); FUNCTOR2D(TTetraSimpleGeom,NormPhys); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_TTetraSimpleGeom_NormPhys_Simple); #endif // Miscillaneous functions //! Tetrahedron's volume. /// http://en.wikipedia.org/wiki/Tetrahedron#Surface_area_and_volume Real TetrahedronSignedVolume(const Vector3r v[4]); Real TetrahedronVolume(const Vector3r v[4]); Real TetrahedronSignedVolume(const vector& v); Real TetrahedronVolume(const vector& v); #ifdef YADE_CGAL Real TetrahedronVolume(const CGAL::Point_3 >* v[4]); Real TetrahedronVolume(const CGAL::Point_3 > v[4]); #endif Matrix3r TetrahedronInertiaTensor(const vector& v); //Matrix3r TetrahedronInertiaTensor(const Vector3r v[4]); Matrix3r TetrahedronCentralInertiaTensor(const vector& v); //Matrix3r TetrahedronCentralInertiaTensor(const Vector3r v[4]); Quaternionr TetrahedronWithLocalAxesPrincipal(shared_ptr& tetraBody); trunk-2017.01a/pkg/dem/ThreeDTriaxialEngine.cpp000066400000000000000000000120441304022710500212140ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2009 by Luc Sibille * * luc.sibille@univ-nantes.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "ThreeDTriaxialEngine.hpp" #include #include #include #include #include #include #include #include #include class Ip2_CohFrictMat_CohFrictMat_CohFrictPhys; CREATE_LOGGER(ThreeDTriaxialEngine); YADE_PLUGIN((ThreeDTriaxialEngine)); ThreeDTriaxialEngine::~ThreeDTriaxialEngine() { } void ThreeDTriaxialEngine::action() { static int warn = 0; if (!warn++) LOG_WARN ("This engine is deprecated, please switch to TriaxialStressController if you expect long term support.") if ( firstRun ) { LOG_INFO ( "First run, will initialize!" ); if (updateFrictionAngle) setContactProperties(frictionAngleDegree); height0 = height; depth0 = depth; width0 = width; if (stressControl_1){ wall_right_activated=true; wall_left_activated=true; //are the right walls for direction 1? } else { wall_right_activated=false; wall_left_activated=false; } if (stressControl_2){ wall_bottom_activated=true; wall_top_activated=true; } else { wall_bottom_activated=false; wall_top_activated=false; } if (stressControl_3){ wall_front_activated=true; wall_back_activated=true; //are the right walls for direction 3? } else { wall_front_activated=false; wall_back_activated=false; } //internalCompaction=false; //is needed to avoid a control for internal compaction by the TriaxialStressController engine // isAxisymetric=false; //is needed to avoid a stress control according the parameter sigma_iso (but according to sigma1, sigma2 and sigma3) firstRun=false; } const Real& dt = scene->dt; if(!stressControl_1) // control in strain if wanted { if ( currentStrainRate1 != strainRate1 ) currentStrainRate1 += ( strainRate1-currentStrainRate1 ) *(1-strainDamping); State* p_left=Body::byId(wall_left_id,scene)->state.get(); p_left->pos += 0.5*currentStrainRate1*width*translationAxisx*dt; State* p_right=Body::byId(wall_right_id,scene)->state.get(); p_right->pos -= 0.5*currentStrainRate1*width*translationAxisx*dt; } else { if ( currentStrainRate1 != strainRate1 ) currentStrainRate1 += ( strainRate1-currentStrainRate1 ) *(1-strainDamping); max_vel1 = 0.5*currentStrainRate1*width; } if(!stressControl_2) // control in strain if wanted { if ( currentStrainRate2 != strainRate2 ) currentStrainRate2 += ( strainRate2-currentStrainRate2 ) *(1-strainDamping); State* p_bottom=Body::byId(wall_bottom_id,scene)->state.get(); p_bottom->pos += 0.5*currentStrainRate2*height*translationAxisy*dt; State* p_top=Body::byId(wall_top_id,scene)->state.get(); p_top->pos -= 0.5*currentStrainRate2*height*translationAxisy*dt; } else { if ( currentStrainRate2 != strainRate2 ) currentStrainRate2 += ( strainRate2-currentStrainRate2 ) *(1-strainDamping); max_vel2 = 0.5*currentStrainRate2*height; } if(!stressControl_3) // control in strain if wanted { if ( currentStrainRate3 != strainRate3 ) currentStrainRate3 += ( strainRate3-currentStrainRate3 ) *(1-strainDamping); State* p_back=Body::byId(wall_back_id,scene)->state.get(); p_back->pos += 0.5*currentStrainRate3*depth*translationAxisz*dt; State* p_front=Body::byId(wall_front_id,scene)->state.get(); p_front->pos -= 0.5*currentStrainRate3*depth*translationAxisz*dt; } else { if ( currentStrainRate3 != strainRate3 ) currentStrainRate3 += ( strainRate3-currentStrainRate3 ) *(1-strainDamping); max_vel3 = 0.5*currentStrainRate3*depth; } TriaxialStressController::action(); // this function is called to perform the external stress control or the internal compaction } void ThreeDTriaxialEngine::setContactProperties(Real frictionDegree) { scene = Omega::instance().getScene().get(); shared_ptr& bodies = scene->bodies; FOREACH(const shared_ptr& b,*scene->bodies){ if (b->isDynamic()) YADE_PTR_CAST (b->material)->frictionAngle = frictionDegree * Mathr::PI/180.0; } FOREACH(const shared_ptr& ii, *scene->interactions){ if (!ii->isReal()) continue; const shared_ptr& sdec1 = YADE_PTR_CAST((*bodies)[(Body::id_t) ((ii)->getId1())]->material); const shared_ptr& sdec2 = YADE_PTR_CAST((*bodies)[(Body::id_t) ((ii)->getId2())]->material); //FIXME - why dynamic_cast fails here? FrictPhys* contactPhysics = YADE_CAST((ii)->phys.get()); Real fa = sdec1->frictionAngle; Real fb = sdec2->frictionAngle; contactPhysics->tangensOfFrictionAngle = std::tan(std::min(fa,fb)); } } trunk-2017.01a/pkg/dem/ThreeDTriaxialEngine.hpp000066400000000000000000000121301304022710500212150ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2009 by Luc Sibille * * luc.sibille@univ-nantes.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include /** \brief Class for controlling in stress or in strain with respect to each spatial direction a cubical assembly of particles. * * The engine perform a triaxial compression with a control in direction "i" in stress "if (stressControl_i)" else in strain. * For a stress control the imposed stress is specified by "sigma_i" with a "max_veli" depending on "strainRatei". To obtain the same strain rate in stress control than in strain control you need to set "wallDamping = 0.8". * For a strain control the imposed strain is specified by "strainRatei". * With this engine you can perform internal compaction by growing the size of particles by using TriaxialStressController::controlInternalStress . For that, just switch on 'internalCompaction=1' and fix sigma_iso=value of mean pressure that you want at the end of the internal compaction. * */ class ThreeDTriaxialEngine : public TriaxialStressController { public : // ThreeDTriaxialEngine(); virtual ~ThreeDTriaxialEngine(); Vector3r translationAxisy; Vector3r translationAxisx; Vector3r translationAxisz; //! is this the beginning of the simulation, after reading the scene? -> it is the first time that Yade passes trought the engine ThreeDTriaxialEngine bool firstRun; virtual void action(); ///Change physical properties of interactions and/or bodies in the middle of a simulation (change only friction for the moment, complete this function to set cohesion and others before compression test) void setContactProperties(Real frictionDegree); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY( ThreeDTriaxialEngine,TriaxialStressController, "The engine perform a triaxial compression with a control in direction 'i' in stress (if stressControl_i) else in strain.\n\n" "For a stress control the imposed stress is specified by 'sigma_i' with a 'max_veli' depending on 'strainRatei'. To obtain the same strain rate in stress control than in strain control you need to set 'wallDamping = 0.8'.\n" "For a strain control the imposed strain is specified by 'strainRatei'.\n" "With this engine you can also perform internal compaction by growing the size of particles by using ``TriaxialStressController::controlInternalStress``. For that, just switch on 'internalCompaction=1' and fix sigma_iso=value of mean pressure that you want at the end of the internal compaction.\n" "\n\n.. warning::\n\t This engine is deprecated, please switch to TriaxialStressController if you expect long term support." , ((Real, strainRate1,0,,"target strain rate in direction 1 (./s, >0 for compression)")) ((Real, currentStrainRate1,0,,"current strain rate in direction 1 - converging to :yref:`ThreeDTriaxialEngine::strainRate1` (./s)")) ((Real, strainRate2,0,,"target strain rate in direction 2 (./s, >0 for compression)")) ((Real, currentStrainRate2,0,,"current strain rate in direction 2 - converging to :yref:`ThreeDTriaxialEngine::strainRate2` (./s)")) ((Real, strainRate3,0,,"target strain rate in direction 3 (./s, >0 for compression)")) ((Real, currentStrainRate3,0,,"current strain rate in direction 3 - converging to :yref:`ThreeDTriaxialEngine::strainRate3` (./s)")) ((Real, UnbalancedForce,1,,"mean resultant forces divided by mean contact force")) ((Real, frictionAngleDegree,-1,,"Value of friction used in the simulation if (updateFrictionAngle)")) ((bool, updateFrictionAngle,false,,"Switch to activate the update of the intergranular frictionto the value :yref:`ThreeDTriaxialEngine::frictionAngleDegree`.")) ((bool, stressControl_1,true,,"Switch to choose a stress or a strain control in directions 1")) ((bool, stressControl_2,true,,"Switch to choose a stress or a strain control in directions 2")) ((bool, stressControl_3,true,,"Switch to choose a stress or a strain control in directions 3")) ((Real, strainDamping,0.9997,,"factor used for smoothing changes in effective strain rate. If target rate is TR, then (1-damping)*(TR-currentRate) will be added at each iteration. With damping=0, rate=target all the time. With damping=1, it doesn't change.")) ((std::string,Key,"",,"A string appended at the end of all files, use it to name simulations.")) , translationAxisy=Vector3r(0,1,0); translationAxisx=Vector3r(1,0,0); translationAxisz=Vector3r(0,0,1); firstRun=true; boxVolume=0; , .def("setContactProperties",&ThreeDTriaxialEngine::setContactProperties,"Assign a new friction angle (degrees) to dynamic bodies and relative interactions") ) DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(ThreeDTriaxialEngine); trunk-2017.01a/pkg/dem/TriaxialCompressionEngine.cpp000066400000000000000000000210551304022710500223440ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include "TriaxialCompressionEngine.hpp" #include #include #include #include #include #include #include #include #include class Ip2_CohFrictMat_CohFrictMat_CohFrictPhys; CREATE_LOGGER(TriaxialCompressionEngine); YADE_PLUGIN((TriaxialCompressionEngine)); TriaxialCompressionEngine::~TriaxialCompressionEngine() { } void TriaxialCompressionEngine::doStateTransition(stateNum nextState){ if ( /* currentState==STATE_UNINITIALIZED && */ nextState==STATE_ISO_COMPACTION){ sigma_iso=sigmaIsoCompaction; previousSigmaIso=sigma_iso; } else if(nextState==STATE_TRIAX_LOADING){ sigma_iso=sigmaLateralConfinement; previousSigmaIso=sigma_iso; internalCompaction = false; if (frictionAngleDegree>0) setContactProperties(frictionAngleDegree); height0 = height; depth0 = depth; width0 = width; //compressionActivated = true; wall_bottom_activated=false; wall_top_activated=false; if(currentState==STATE_ISO_UNLOADING && !noFiles){ LOG_INFO("Speres -> /tmp/unloaded.spheres"); Shop::saveSpheresToFile("/tmp/unloaded.spheres"); } if(!firstRun && !noFiles) saveSimulation=true; // saving snapshot .xml will actually be done in ::action Phase1End = "Unloaded"; } else if(currentState==STATE_ISO_COMPACTION && nextState==STATE_ISO_UNLOADING){ sigma_iso=sigmaLateralConfinement; sigmaIsoCompaction = sigmaLateralConfinement; previousSigmaIso=sigma_iso; internalCompaction=false; // unloading will not change grain sizes if (frictionAngleDegree>0) setContactProperties(frictionAngleDegree); if(!firstRun && !noFiles) saveSimulation=true; Phase1End = "Compacted"; } else if ((currentState==STATE_ISO_COMPACTION || currentState==STATE_ISO_UNLOADING) && nextState==STATE_LIMBO) { //urrentState==STATE_DIE_COMPACTION internalCompaction = false; if (frictionAngleDegree>0) setContactProperties(frictionAngleDegree); height0 = height; depth0 = depth; width0 = width; if(!noFiles) saveSimulation=true; // saving snapshot .xml will actually be done in ::action // stop simulation here, since nothing will happen from now on Phase1End = (currentState==STATE_ISO_COMPACTION ? "compacted" : "unloaded"); if(!noFiles) Shop::saveSpheresToFile("/tmp/limbo.spheres"); // Please keep this saving process intact, I'm tired of running 3 days simulations and getting nothing at the end! if(!firstRun && !noFiles) saveSimulation=true; // saving snapshot .xml will actually be done in ::action } else if( nextState==STATE_FIXED_POROSITY_COMPACTION){ internalCompaction = false; wall_bottom_activated=false; wall_top_activated=false; wall_front_activated=false; wall_back_activated=false; wall_right_activated=false; wall_left_activated=false; } else { LOG_ERROR("Undefined transition from "<iter % testEquilibriumInterval == 0 ) { updateParameters (); maxStress = max(maxStress,-stress[wall_top][1]); LOG_INFO("UnbalancedForce="<< UnbalancedForce<<", rel stress "<< std::abs ( ( meanStress-sigma_iso ) /sigma_iso )); } if ( saveSimulation ) { if(!noFiles){ string fileName = "./"+ Key + "_" + Phase1End + "_" + boost::lexical_cast ( scene->iter ) + "_" + boost::lexical_cast ( currentState ) + ".xml"; LOG_INFO ( "saving snapshot: "< ( scene->iter ) + "_" + boost::lexical_cast ( currentState ) +".spheres"; LOG_INFO ( "saving spheres: "<iter % 100 == 0 ) { LOG_INFO ("Triax Compression started"); } if (scene->iter % 100 == 0) LOG_DEBUG("Compression active."); const Real& dt = scene->dt; if (std::abs(epsilonMax) > std::abs(strain[1])) { if ( currentStrainRate != strainRate ) currentStrainRate += ( strainRate-currentStrainRate ) *0.0003; /* Move top and bottom wall according to strain rate */ State* p_bottom=Body::byId(wall_bottom_id,scene)->state.get(); p_bottom->pos += 0.5*currentStrainRate*height*translationAxis*dt; State* p_top=Body::byId(wall_top_id,scene)->state.get(); p_top->pos -= 0.5*currentStrainRate*height*translationAxis*dt; } } if ( currentState==STATE_FIXED_POROSITY_COMPACTION ) { if ( scene->iter % 100 == 0 ) LOG_INFO ("Compression started"); const Real& dt = scene->dt; State* p_bottom=Body::byId(wall_bottom_id,scene)->state.get(); State* p_top=Body::byId(wall_top_id,scene)->state.get(); State* p_left=Body::byId(wall_left_id,scene)->state.get(); State* p_right=Body::byId(wall_right_id,scene)->state.get(); State* p_front=Body::byId(wall_front_id,scene)->state.get(); State* p_back=Body::byId(wall_back_id,scene)->state.get(); /* Move top and bottom wall according to strain rate */ p_bottom->pos += 0.5*strainRate*height*translationAxis*dt; p_top->pos -= 0.5*strainRate*height*translationAxis*dt; p_back->pos += 0.5*strainRate*depth*translationAxisz*dt; p_front->pos -= 0.5*strainRate*depth*translationAxisz*dt; p_left->pos += 0.5*strainRate*width*translationAxisx*dt; p_right->pos -= 0.5*strainRate*width*translationAxisx*dt; } } void TriaxialCompressionEngine::setContactProperties(Real frictionDegree) { Shop::setContactFriction(frictionDegree*Mathr::PI/180.0); } trunk-2017.01a/pkg/dem/TriaxialCompressionEngine.hpp000066400000000000000000000247061304022710500223570ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include /** \brief Class for controlling optional initial isotropic compaction and subsequent triaxial test with constant lateral stress and constant axial strain rate. The algorithms used have been developed initialy for simulations reported in [Chareyre2002a] and [Chareyre2005]. They have been ported to Yade in a second step and used in e.g. [Kozicki2008],[Scholtes2009b],[Jerier2010b]. * * The engine is a state machine with the following states; transitions may be automatic, see below. The algorithms used have been developed initialy for simulations reported in [Chareyre2002a]_ and [Chareyre2005]_. They have been ported to Yade in a second step and used in e.g. [Kozicki2008]_,[Scholtes2009b]_,[Jerier2010b]. * * 1. STATE_ISO_COMPACTION: isotropic compaction (compression) until * the prescribed mean pressue sigmaIsoCompaction is reached and the packing is stable. * The compaction happens either by straining the walls (!internalCompaction) * or by growing size of grains (internalCompaction). * 2. STATE_ISO_UNLOADING: isotropic unloading from the previously reached state, until * the mean pressure sigmaLateralConfinement is reached (and stabilizes). * NOTE: this state will be skipped if sigmaLateralConfinement == sigmaIsoCompaction. * 3. STATE_TRIAX_LOADING: confined uniaxial compression: * constant sigmaLateralConfinement is kept at lateral walls (left, right, front, back), while * top and bottom walls load the packing in their axis (by straining), until the value of epsilonMax * (deformation along the loading axis) is reached. At this point, the simulation is stopped. * 4. STATE_FIXED_POROSITY_COMPACTION: isotropic compaction (compression) until * a chosen porosity value (parameter:fixedPorosity). The six walls move with a chosen translation speed * (parameter StrainRate). * 5. STATE_TRIAX_LIMBO: currently unused, since simulation is hard-stopped in the previous state. * * Transition from COMPACTION to UNLOADING is done automatically if autoUnload==true; * Transition from (UNLOADING to LOADING) or from (COMPACTION to LOADING: if UNLOADING is skipped) is * done automatically if autoCompressionActivation=true; * Both autoUnload and autoCompressionActivation are true by default. * * NOTE: This engine handles many different manipulations, including some save/reload with attributes modified manually in between. Please don't modify the algorithms, even if they look strange (especially test sequences) without notifying me and getting explicit approval. A typical situation is somebody generates a sample with !autoCompressionActivation and run : he wants a saved simulation at the end. He then reload the saved state, modify some parameters, set autoCompressionActivation=true, and run. He should get the compression test done. * */ class TriaxialCompressionEngine : public TriaxialStressController { private : std::string Phase1End;//used to name output files based on current state public : //TriaxialCompressionEngine(); virtual ~TriaxialCompressionEngine(); // FIXME: current serializer doesn't handle named enum types, this is workaround. #define stateNum int // should be "enum stateNum {...}" once this is fixed enum {STATE_UNINITIALIZED, STATE_ISO_COMPACTION, STATE_ISO_UNLOADING, STATE_TRIAX_LOADING, STATE_FIXED_POROSITY_COMPACTION, STATE_LIMBO}; void doStateTransition(stateNum nextState); #define _STATE_CASE(ST) case ST: return #ST string stateName(stateNum st){switch(st){ _STATE_CASE(STATE_UNINITIALIZED);_STATE_CASE(STATE_ISO_COMPACTION);_STATE_CASE(STATE_ISO_UNLOADING);_STATE_CASE(STATE_TRIAX_LOADING);_STATE_CASE(STATE_FIXED_POROSITY_COMPACTION);_STATE_CASE(STATE_LIMBO); default: return ""; } } #undef _STATE_CASE Vector3r translationAxisx; Vector3r translationAxisz; //! is isotropicInternalCompactionFinished? bool Phase1, saveSimulation, DieCompaction;//FIXME : document DieCompaction //! is this the beginning of the simulation, after reading the scene? bool firstRun; int FinalIterationPhase1, Iteration/*, testEquilibriumInterval*/;//FIXME : what is that? virtual void action(); void updateParameters(); ///Change physical properties of interactions and/or bodies in the middle of a simulation (change only friction for the moment, complete this function to set cohesion and others before compression test) void setContactProperties(Real frictionDegree); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY( TriaxialCompressionEngine,TriaxialStressController, "The engine is a state machine with the following states; transitions my be automatic, see below.\n\n" "#. STATE_ISO_COMPACTION: isotropic compaction (compression) until the prescribed mean pressue sigmaIsoCompaction is reached and the packing is stable. The compaction happens either by straining the walls (!internalCompaction) or by growing size of grains (internalCompaction).\n" "#. STATE_ISO_UNLOADING: isotropic unloading from the previously reached state, until the mean pressure sigmaLateralConfinement is reached (and stabilizes).\n\n\t.. note::\n\t\tthis state will be skipped if sigmaLateralConfinement == sigmaIsoCompaction.\n" "#. STATE_TRIAX_LOADING: confined uniaxial compression: constant sigmaLateralConfinement is kept at lateral walls (left, right, front, back), while top and bottom walls load the packing in their axis (by straining), until the value of epsilonMax (deformation along the loading axis) is reached. At this point, the simulation is stopped.\n" "#. STATE_FIXED_POROSITY_COMPACTION: isotropic compaction (compression) until a chosen porosity value (parameter:fixedPorosity). The six walls move with a chosen translation speed (parameter StrainRate).\n" "#. STATE_TRIAX_LIMBO: currently unused, since simulation is hard-stopped in the previous state.\n\n" "Transition from COMPACTION to UNLOADING is done automatically if autoUnload==true;\n\n Transition from (UNLOADING to LOADING) or from (COMPACTION to LOADING: if UNLOADING is skipped) is done automatically if autoCompressionActivation=true; Both autoUnload and autoCompressionActivation are true by default.\n\n" "\n\n.. note::\n\t Most of the algorithms used have been developed initialy for simulations reported in [Chareyre2002a]_ and [Chareyre2005]_. They have been ported to Yade in a second step and used in e.g. [Kozicki2008]_,[Scholtes2009b]_,[Jerier2010b]." "\n\n.. warning::\n\t This engine is deprecated, please switch to TriaxialStressController if you expect long term support." , ((int, warn, 0,,"counter used for sending a deprecation warning once")) ((Real,strainRate,0,,"target strain rate (./s, >0 for compression)")) ((Real,currentStrainRate,0,,"current strain rate - converging to :yref:`TriaxialCompressionEngine::strainRate` (./s)")) ((Real,UnbalancedForce,1,,"mean resultant forces divided by mean contact force")) ((Real,StabilityCriterion,0.001,,"tolerance in terms of :yref:`TriaxialCompressionEngine::UnbalancedForce` to consider the packing is stable")) ((Vector3r,translationAxis,TriaxialStressController::normal[wall_bottom],,"compression axis")) ((bool,autoCompressionActivation,true,,"Auto-switch from isotropic compaction (or unloading state if sigmaLateralConfinement #include #include #include #include #include #include #include CREATE_LOGGER(TriaxialStateRecorder); TriaxialStateRecorder::~TriaxialStateRecorder() {}; void TriaxialStateRecorder::action () { // at the beginning of the file; write column titles if(out.tellp()==0) out<<"iteration s11 s22 s33 e11 e22 e33 unb_force porosity kineticE"< >::iterator itFirst = scene->engines.begin(); vector >::iterator itLast = scene->engines.end(); for ( ;itFirst!=itLast; ++itFirst ){ if ( ( *itFirst )->getClassName() == "TriaxialCompressionEngine" || ( *itFirst )->getClassName() == "ThreeDTriaxialEngine" || ( *itFirst )->getClassName() == "TriaxialStressController"){ LOG_DEBUG ( "stress controller engine found" ); triaxialStressController = YADE_PTR_CAST ( *itFirst ); //triaxialCompressionEngine = shared_ptr (static_cast ( (*itFirst).get())); } } if ( !triaxialStressController ) LOG_ERROR ( "stress controller engine NOT found" ); } if ( ! ( scene->iter % triaxialStressController->computeStressStrainInterval == 0 ) ) triaxialStressController->computeStressStrain (); /// Compute porosity : Real Vs=0; Real V = ( triaxialStressController->height ) * ( triaxialStressController->width ) * ( triaxialStressController->depth ); BodyContainer::iterator bi = scene->bodies->begin(); BodyContainer::iterator biEnd = scene->bodies->end(); for ( ; bi!=biEnd; ++bi ){ if(!(*bi) || (*bi)->isClump()) continue; const shared_ptr& b = *bi; if ( b->isDynamic() ){ //Sorry, the next string was commented, because it gave a Warning "unused variable v". Anton Gladky //const Vector3r& v = b->state->vel; Vs += 1.3333333*Mathr::PI*pow ( YADE_PTR_CAST( b->shape)->radius, 3 );} } porosity = ( V - Vs ) /V; out << boost::lexical_cast ( scene->iter ) << " " << boost::lexical_cast ( triaxialStressController->stress[triaxialStressController->wall_right][0] ) << " " << boost::lexical_cast ( triaxialStressController->stress[triaxialStressController->wall_top][1] ) << " " << boost::lexical_cast ( triaxialStressController->stress[triaxialStressController->wall_front][2] ) << " " << boost::lexical_cast ( triaxialStressController->strain[0] ) << " " << boost::lexical_cast ( triaxialStressController->strain[1] ) << " " << boost::lexical_cast ( triaxialStressController->strain[2] ) << " " << boost::lexical_cast ( triaxialStressController->ComputeUnbalancedForce () ) << " " << boost::lexical_cast ( porosity ) << " " << boost::lexical_cast ( Shop::kineticEnergy() ) << endl; } YADE_PLUGIN((TriaxialStateRecorder)); trunk-2017.01a/pkg/dem/TriaxialStateRecorder.hpp000066400000000000000000000032341304022710500214670ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by luc Scholtes * * luc.scholtes@hmg.inpg.fr * * Copyright (C) 2008 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include /*! \brief Record the stress-strain state of a sample in simulations using TriaxialCompressionEngine The output is a text file where each line is a record, with the format IterationNumber sigma11 sigma22 sigma33 epsilon11 epsilon22 epsilon33 */ class TriaxialStressController; class TriaxialStateRecorder : public Recorder { private : shared_ptr triaxialStressController; public : virtual ~TriaxialStateRecorder (); virtual void action(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(TriaxialStateRecorder,Recorder,"Engine recording triaxial variables (see the variables list in the first line of the output file). This recorder needs :yref:`TriaxialCompressionEngine` or :yref:`ThreeDTriaxialEngine` present in the simulation).", ((Real,porosity,1,,"porosity of the packing [-]")), //Is it really needed to have this value as a serializable? initRun=true; ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(TriaxialStateRecorder); trunk-2017.01a/pkg/dem/TriaxialStressController.cpp000066400000000000000000000322441304022710500222460ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include"TriaxialStressController.hpp" #include #include #include #include #include #include #include #include #include #ifdef FLOW_ENGINE //#include #include "FlowEngine_FlowEngineT.hpp" #endif CREATE_LOGGER(TriaxialStressController); YADE_PLUGIN((TriaxialStressController)); TriaxialStressController::~TriaxialStressController(){} Vector3r TriaxialStressController::getStress(int boundId) {assert (boundId>=0 && boundId<=5); return stress[boundId];} Vector3r TriaxialStressController::getStrainRate() { return Vector3r ( (Body::byId(wall_right_id,scene)->state->vel[0]-Body::byId(wall_left_id,scene)->state->vel[0])/width, (Body::byId(wall_top_id,scene)->state->vel[1]-Body::byId(wall_bottom_id,scene)->state->vel[1])/height, (Body::byId(wall_front_id,scene)->state->vel[2]-Body::byId(wall_back_id,scene)->state->vel[2])/depth ); } void TriaxialStressController::updateStiffness() { Real fluidStiffness = 0.; #ifdef FLOW_ENGINE FOREACH(const shared_ptr e, Omega::instance().getScene()->engines) { if (e->getClassName() == "FlowEngine") { TemplateFlowEngine_FlowEngineT* flow = dynamic_cast*>(e.get()); if ( (flow->fluidBulkModulus > 0) && (!(flow->dead)) ) fluidStiffness = flow->fluidBulkModulus/porosity; } } #endif for (int i=0; i<6; ++i) stiffness[i] = 0; InteractionContainer::iterator ii = scene->interactions->begin(); InteractionContainer::iterator iiEnd = scene->interactions->end(); for( ; ii!=iiEnd ; ++ii ) if ((*ii)->isReal()) { const shared_ptr& contact = *ii; Real fn = (static_cast (contact->phys.get()))->normalForce.norm(); if (fn!=0) { int id1 = contact->getId1(), id2 = contact->getId2(); for (int index=0; index<6; ++index) if ( wall_id[index]==id1 || wall_id[index]==id2 ) { FrictPhys* currentContactPhysics = static_cast ( contact->phys.get() ); stiffness[index] += currentContactPhysics->kn; } } } if (fluidStiffness > 0) { stiffness[0] += fluidStiffness*width*depth/height; stiffness[1] += fluidStiffness*width*depth/height; stiffness[2] += fluidStiffness*height*depth/width; stiffness[3] += fluidStiffness*height*depth/width; stiffness[4] += fluidStiffness*width*height/depth; stiffness[5] += fluidStiffness*width*height/depth; } } void TriaxialStressController::controlExternalStress(int wall, Vector3r resultantForce, State* p, Real wall_max_vel) // controls walls such that Sum Forces from Sample on Wall = resultantForce { scene->forces.sync(); Real translation=normal[wall].dot(getForce(scene,wall_id[wall])-resultantForce); const bool log=false; if(log) LOG_DEBUG("wall="<se3.position += previousTranslation[wall]; externalWork += previousTranslation[wall].dot(getForce(scene,wall_id[wall])); // this is important is using VelocityBins. Otherwise the motion is never detected. Related to https://bugs.launchpad.net/yade/+bug/398089 p->vel=previousTranslation[wall]/scene->dt; //if(log)TRVAR2(previousTranslation,p->se3.position); } void TriaxialStressController::action() { // sync thread storage of ForceContainer scene->forces.sync(); if (first) {// sync boundaries ids in the table wall_id[wall_bottom] = wall_bottom_id; wall_id[wall_top] = wall_top_id; wall_id[wall_left] = wall_left_id; wall_id[wall_right] = wall_right_id; wall_id[wall_front] = wall_front_id; wall_id[wall_back] = wall_back_id;} if(thickness<0) thickness=2.0*YADE_PTR_CAST(Body::byId(wall_bottom_id,scene)->shape)->extents.y(); State* p_bottom=Body::byId(wall_bottom_id,scene)->state.get(); State* p_top=Body::byId(wall_top_id,scene)->state.get(); State* p_left=Body::byId(wall_left_id,scene)->state.get(); State* p_right=Body::byId(wall_right_id,scene)->state.get(); State* p_front=Body::byId(wall_front_id,scene)->state.get(); State* p_back=Body::byId(wall_back_id,scene)->state.get(); height = p_top->se3.position.y() - p_bottom->se3.position.y() - thickness; width = p_right->se3.position.x() - p_left->se3.position.x() - thickness; depth = p_front->se3.position.z() - p_back->se3.position.z() - thickness; boxVolume = height * width * depth; if ( (first) || (updatePorosity) ) { BodyContainer::iterator bi = scene->bodies->begin(); BodyContainer::iterator biEnd = scene->bodies->end(); particlesVolume = 0; for ( ; bi!=biEnd; ++bi ) { const shared_ptr& b = *bi; if (b->isClump()) { const shared_ptr& clump = YADE_PTR_CAST(b->shape); const shared_ptr& member = Body::byId(clump->members.begin()->first,scene); particlesVolume += b->state->mass / member->material->density; } else if (b->isDynamic() && !b->isClumpMember()) { const shared_ptr& sphere = YADE_PTR_CAST ( b->shape ); particlesVolume += 1.3333333*Mathr::PI*pow ( sphere->radius, 3 ); } } first = false; updatePorosity = false; } max_vel1=3 * width /(height+width+depth)*max_vel; max_vel2=3 * height /(height+width+depth)*max_vel; max_vel3 =3 * depth /(height+width+depth)*max_vel; porosity = ( boxVolume - particlesVolume ) /boxVolume; position_top = p_top->se3.position.y(); position_bottom = p_bottom->se3.position.y(); position_right = p_right->se3.position.x(); position_left = p_left->se3.position.x(); position_front = p_front->se3.position.z(); position_back = p_back->se3.position.z(); // must be done _after_ height, width, depth have been calculated //Update stiffness only if it has been computed by StiffnessCounter (see "stiffnessUpdateInterval") if (scene->iter % stiffnessUpdateInterval == 0 || scene->iter<100) updateStiffness(); bool isARadiusControlIteration = (scene->iter % radiusControlInterval == 0); if (scene->iter % computeStressStrainInterval == 0 || (internalCompaction && isARadiusControlIteration) ) computeStressStrain(); if (!internalCompaction) { Vector3r wallForce (0, goal2*width*depth, 0); if (wall_bottom_activated) { if (stressMask & 2) controlExternalStress(wall_bottom, wallForce, p_bottom, max_vel2); else { p_bottom->vel[1] += (-normal[wall_bottom][1]*0.5*goal2*height -p_bottom->vel[1])*(1-strainDamping); externalWork += p_bottom->vel.dot(getForce(scene,wall_bottom_id))*scene->dt;} } else p_bottom->vel=Vector3r::Zero(); if (wall_top_activated) { if (stressMask & 2) controlExternalStress(wall_top, -wallForce, p_top, max_vel2); else { p_top->vel[1] += (-normal[wall_top][1]*0.5*goal2*height -p_top->vel[1])*(1-strainDamping); externalWork += p_top->vel.dot(getForce(scene,wall_top_id))*scene->dt;} } else p_top->vel=Vector3r::Zero(); wallForce = Vector3r(goal1*height*depth, 0, 0); if (wall_left_activated) { if (stressMask & 1) controlExternalStress(wall_left, wallForce, p_left, max_vel1); else { p_left->vel[0] += (-normal[wall_left][0]*0.5*goal1*width -p_left->vel[0])*(1-strainDamping); externalWork += p_left->vel.dot(getForce(scene,wall_left_id))*scene->dt;} } else p_left->vel=Vector3r::Zero(); if (wall_right_activated) { if (stressMask & 1) controlExternalStress(wall_right, -wallForce, p_right, max_vel1); else { p_right->vel[0] += (-normal[wall_right][0]*0.5*goal1*width -p_right->vel[0])*(1-strainDamping); externalWork += p_right->vel.dot(getForce(scene,wall_right_id))*scene->dt;} } else p_right->vel=Vector3r::Zero(); wallForce = Vector3r(0, 0, goal3*height*width); if (wall_back_activated) { if (stressMask & 4) controlExternalStress(wall_back, wallForce, p_back, max_vel3); else { p_back->vel[2] += (-normal[wall_back][2]*0.5*goal3*depth -p_back->vel[2])*(1-strainDamping); externalWork += p_back->vel.dot(getForce(scene,wall_back_id))*scene->dt;} } else p_back->vel=Vector3r::Zero(); if (wall_front_activated) { if (stressMask & 4) controlExternalStress(wall_front, -wallForce, p_front, max_vel3); else { p_front->vel[2] += (-normal[wall_front][2]*0.5*goal3*depth -p_front->vel[2])*(1-strainDamping); externalWork += p_front->vel.dot(getForce(scene,wall_front_id))*scene->dt;} } else p_front->vel=Vector3r::Zero(); } else //if internal compaction { p_bottom->vel=Vector3r::Zero(); p_top->vel=Vector3r::Zero(); p_left->vel=Vector3r::Zero(); p_right->vel=Vector3r::Zero(); p_back->vel=Vector3r::Zero(); p_front->vel=Vector3r::Zero(); if (isARadiusControlIteration) { Real sigma_iso_ = bool(stressMask & 1)*goal1 + bool(stressMask & 2)*goal2 + bool(stressMask & 4)*goal3; sigma_iso_ /= bool(stressMask & 1) + bool(stressMask & 2) + bool(stressMask & 4); if (std::abs(sigma_iso_)<=std::abs(meanStress)) maxMultiplier = finalMaxMultiplier; if (meanStress==0) previousMultiplier = maxMultiplier; else { // previousMultiplier = 1+0.7*(sigma_iso-s)*(previousMultiplier-1.f)/(s-previousStress); // = (Dsigma/apparentModulus)*0.7 // previousMultiplier = std::max(2-maxMultiplier, std::min(previousMultiplier, maxMultiplier)); if (sigma_iso_ < 0) // compressive case: we have to increase radii if meanStress > sigma_iso_, considering that sigma_iso_ < 0. We end with the same expression as before sign change previousMultiplier = 1.+(sigma_iso_-meanStress)/sigma_iso_*(maxMultiplier-1.); // = (Dsigma/apparentModulus)*0.7 else // tensile case: we have to increase radii if meanStress > sigma_iso_ too. But here sigma_iso_ > 0 => another expression previousMultiplier = 1.+(meanStress-sigma_iso_)/sigma_iso_*(maxMultiplier-1.); // = (Dsigma/apparentModulus)*0.7 } previousStress = meanStress; //Real apparentModulus = (s-previousStress)/(previousMultiplier-1.f); controlInternalStress(previousMultiplier); } } } void TriaxialStressController::computeStressStrain() { scene->forces.sync(); State* p_bottom=Body::byId(wall_bottom_id,scene)->state.get(); State* p_top=Body::byId(wall_top_id,scene)->state.get(); State* p_left=Body::byId(wall_left_id,scene)->state.get(); State* p_right=Body::byId(wall_right_id,scene)->state.get(); State* p_front=Body::byId(wall_front_id,scene)->state.get(); State* p_back=Body::byId(wall_back_id,scene)->state.get(); height = p_top->se3.position.y() - p_bottom->se3.position.y() - thickness; width = p_right->se3.position.x() - p_left->se3.position.x() - thickness; depth = p_front->se3.position.z() - p_back->se3.position.z() - thickness; meanStress = 0; if (height0 == 0) height0 = height; if (width0 == 0) width0 = width; if (depth0 == 0) depth0 = depth; strain[0] = log(width/width0); // all strain values are positiv for extension strain[1] = log(height/height0); strain[2] = log(depth/depth0); volumetricStrain=strain[0]+strain[1]+strain[2]; Real invXSurface = 1.f/(height*depth); Real invYSurface = 1.f/(width*depth); Real invZSurface = 1.f/(width*height); force[wall_bottom]=getForce(scene,wall_id[wall_bottom]); stress[wall_bottom]=force[wall_bottom]*invYSurface; // all stress values are positiv for tension force[wall_top]= getForce(scene,wall_id[wall_top]); stress[wall_top]=-force[wall_top]*invYSurface; force[wall_left]= getForce(scene,wall_id[wall_left]); stress[wall_left]=force[wall_left]*invXSurface; force[wall_right]= getForce(scene,wall_id[wall_right]); stress[wall_right]= -force[wall_right]*invXSurface; force[wall_front]= getForce(scene,wall_id[wall_front]); stress[wall_front]=-force[wall_front]*invZSurface; force[wall_back]= getForce(scene,wall_id[wall_back]); stress[wall_back]= force[wall_back]*invZSurface; for (int i=0; i<6; i++) meanStress+=stress[i].dot(pow(-1.0,i)*normal[i]); // normal[i] is always inwards meanStress/=6.; // ( sXX(xLeft) + sXX(xRight) + sYY(yBottom) + sYY(yTop) + sZZ(zBack) + sZZ(zFront) ) / 6 } void TriaxialStressController::controlInternalStress ( Real multiplier ) { particlesVolume *= pow ( multiplier,3 ); Shop::growParticles(multiplier,true,true); } /*! \fn TriaxialStressController::ComputeUnbalancedForce( bool maxUnbalanced) */ Real TriaxialStressController::ComputeUnbalancedForce( bool maxUnbalanced) {return Shop::unbalancedForce(maxUnbalanced,scene);} trunk-2017.01a/pkg/dem/TriaxialStressController.hpp000066400000000000000000000251551304022710500222560ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include class Scene; class State; /*! \brief Controls the stress on the boundaries of a box and compute strain-like and stress-like quantities for the packing. The algorithms used have been developed initialy for simulations reported in [Chareyre2002a] and [Chareyre2005]. They have been ported to Yade in a second step and used in e.g. [Kozicki2008],[Scholtes2009b],[Jerier2010b]. */ class TriaxialStressController : public BoundaryController { private : bool first; inline const Vector3r getForce(Scene* rb, Body::id_t id){ return rb->forces.getForce(id); /* needs sync, which is done at the beginning of action */ } public : //! internal index values for retrieving walls enum {wall_left=0, wall_right, wall_bottom, wall_top, wall_back, wall_front}; //! real index values of walls in the Scene int wall_id [6]; //! Stores the value of the translation at the previous time step, stiffness, and normal boost::array previousTranslation; //! The value of stiffness (updated according to stiffnessUpdateInterval) vector stiffness; Vector3r strain; Vector3r normal [6]; //! The values of stresses Vector3r stress [6]; Vector3r force [6]; //! Value of particles volume (solid volume of clumps and spheres) Real particlesVolume; //! Value of box volume Real boxVolume; //! Sample porosity Real porosity; Real max_vel1; Real max_vel2; Real max_vel3; Real position_top; Real position_bottom; Real position_right; Real position_left; Real position_front; Real position_back; virtual ~TriaxialStressController(); virtual void action(); //! Regulate the stress applied on walls with flag wall_XXX_activated = true void controlExternalStress(int wall, Vector3r resultantForce, State* p, Real wall_max_vel); //! Regulate the mean stress by changing spheres size, WARNING : this function assumes that all dynamic bodies in the problem are spheres void controlInternalStress(Real multiplier); //! update the stiffness of boundary-packing interaction (sum of contacts stiffness on the boundary) void updateStiffness(); //! Compute stresses on walls as "Vector3r stress[6]", compute meanStress, strain[3] and mean strain void computeStressStrain(); //! Compute the mean/max unbalanced force in the assembly (normalized by mean contact force) Real ComputeUnbalancedForce(bool maxUnbalanced=false); ///! Getter for stress and rates in python Vector3r getStress(int boundId); Vector3r getStrainRate(); YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(TriaxialStressController,BoundaryController, "An engine maintaining constant stresses or constant strain rates on some boundaries of a parallepipedic packing. The stress/strain control is defined for each axis using :yref:`TriaxialStressController::stressMask` (a bitMask) and target values are defined by goal1,goal2, and goal3. The sign conventions of continuum mechanics are used for strains and stresses (positive traction)." "\n\n.. note::\n\t The algorithms used have been developed initialy for simulations reported in [Chareyre2002a]_ and [Chareyre2005]_. They have been ported to Yade in a second step and used in e.g. [Kozicki2008]_,[Scholtes2009b]_,[Jerier2010b]." , ((unsigned int,stiffnessUpdateInterval,10,,"target strain rate (./s)")) ((unsigned int,radiusControlInterval,10,,"")) ((unsigned int,computeStressStrainInterval,10,,"")) ((Real,stressDamping,0.25,,"wall damping coefficient for the stress control - wallDamping=0 implies a (theoretical) perfect control, wallDamping=1 means no movement")) ((Real,strainDamping,0.99,,"coefficient used for smoother transitions in the strain rate. The rate reaches the target value like $d^n$ reaches 0, where $d$ is the damping coefficient and $n$ is the number of steps")) ((Real,thickness,-1,,"thickness of boxes (needed by some functions)")) ((int,wall_bottom_id,2,,"id of boundary ; coordinate 1- (default value is ok if aabbWalls are appended BEFORE spheres.)")) ((int,wall_top_id,3,,"id of boundary ; coordinate 1+ (default value is ok if aabbWalls are appended BEFORE spheres.)")) ((int,wall_left_id,0,,"id of boundary ; coordinate 0- (default value is ok if aabbWalls are appended BEFORE spheres.)")) ((int,wall_right_id,1,,"id of boundary ; coordinate 0+ (default value is ok if aabbWalls are appended BEFORE spheres.)")) ((int,wall_front_id,5,,"id of boundary ; coordinate 2+ (default value is ok if aabbWalls are appended BEFORE spheres.)")) ((int,wall_back_id,4,,"id of boundary ; coordinate 2- (default value is ok if aabbWalls are appended BEFORE spheres.)")) ((bool,wall_bottom_activated,true,,"if true, this wall moves according to the target value (stress or strain rate).")) ((bool,wall_top_activated,true,,"if true, this wall moves according to the target value (stress or strain rate).")) ((bool,wall_left_activated,true,,"if true, this wall moves according to the target value (stress or strain rate).")) ((bool,wall_right_activated,true,,"if true, this wall moves according to the target value (stress or strain rate).")) ((bool,wall_front_activated,true,,"if true, this wall moves according to the target value (stress or strain rate).")) ((bool,wall_back_activated,true,,"if true, this wall moves according to the target value (stress or strain rate).")) ((Real,height,0,Attr::readonly,"size of the box (1-axis) |yupdate|")) ((Real,width,0,Attr::readonly,"size of the box (0-axis) |yupdate|")) ((Real,depth,0,Attr::readonly,"size of the box (2-axis) |yupdate|")) ((Real,height0,0,,"Reference size for strain definition. See :yref:`TriaxialStressController::height`")) ((Real,width0,0,,"Reference size for strain definition. See :yref:`TriaxialStressController::width`")) ((Real,depth0,0,,"Reference size for strain definition. See :yref:`TriaxialStressController::depth`")) ((Real,goal1,0,,"prescribed stress/strain rate on axis 1, as defined by :yref:`TriaxialStressController::stressMask`")) ((Real,goal2,0,,"prescribed stress/strain rate on axis 2, as defined by :yref:`TriaxialStressController::stressMask`")) ((Real,goal3,0,,"prescribed stress/strain rate on axis 3, as defined by :yref:`TriaxialStressController::stressMask`")) ((unsigned int,stressMask,7,,"Bitmask determining wether the imposed :yref:`TriaxialStressController::goal`s are stresses (0 for none, 7 for all, 1 for direction 1, 5 for directions 1 and 3, etc.")) ((Real,maxMultiplier,1.001,,"max multiplier of diameters during internal compaction (initial fast increase - :yref:`TriaxialStressController::finalMaxMultiplier` is used in a second stage)")) ((Real,finalMaxMultiplier,1.00001,,"max multiplier of diameters during internal compaction (secondary precise adjustment - :yref:`TriaxialStressController::maxMultiplier` is used in the initial stage)")) ((Real,max_vel,1,,"Maximum allowed walls velocity [m/s]. This value superseeds the one assigned by the stress controller if the later is higher. max_vel can be set to infinity in many cases, but sometimes helps stabilizing packings. Based on this value, different maxima are computed for each axis based on the dimensions of the sample, so that if each boundary moves at its maximum velocity, the strain rate will be isotropic (see e.g. :yref:`TriaxialStressController::max_vel1`).")) ((Real,previousStress,0,Attr::readonly,"|yupdate|")) ((Real,previousMultiplier,1,Attr::readonly,"|yupdate|")) ((bool,internalCompaction,true,,"Switch between 'external' (walls) and 'internal' (growth of particles) compaction.")) ((Real,meanStress,0,Attr::readonly,"Mean stress in the packing. |yupdate|")) ((Real,volumetricStrain,0,Attr::readonly,"Volumetric strain (see :yref:`TriaxialStressController::strain`). |yupdate|")) ((Real,externalWork,0,Attr::readonly,"Mechanical work associated to the boundary conditions, i.e. $\\int_{\\partial \\Omega} \\mat{T} \\cdot \\mat{u} ds$ with $\\mat{T}$ the surface traction and $\\mat{u}$ the displacement at the boundary. |yupdate|")) ((bool,updatePorosity,false,,"If true, :yref:`solid volume` will be updated once (will automatically reset to false after one calculation step) e.g. for porosity calculation purpose. Can be used when volume of particles changes during the simulation (e.g. when particles are erased or when clumps are created).")) , /* extra initializers */ , /* constructor */ strain = Vector3r::Zero(); first = true; stiffness.resize(6); previousTranslation.assign(Vector3r::Zero()); for (int i=0; i<6; ++i){normal[i]=stress[i]=force[i]=Vector3r::Zero();stiffness[i]=0;} normal[wall_bottom].y()=1; normal[wall_top].y()=-1; normal[wall_left].x()=1; normal[wall_right].x()=-1; normal[wall_front].z()=-1; normal[wall_back].z()=1; porosity=1; , .def_readonly("strain",&TriaxialStressController::strain,"Current strain in a vector (exx,eyy,ezz). The values reflect true (logarithmic) strain.") .def_readonly("strainRate",&TriaxialStressController::getStrainRate,"Current strain rate in a vector d/dt(exx,eyy,ezz).") .def_readonly("porosity",&TriaxialStressController::porosity,"Porosity of the packing. |yupdate|") .def_readonly("boxVolume",&TriaxialStressController::boxVolume,"Total packing volume.") .def_readonly("particlesVolume",&TriaxialStressController::particlesVolume,"Total volume of particles (clumps and spheres). |ycomp|") .def_readonly("spheresVolume",&TriaxialStressController::particlesVolume,"Shorthand for :yref:`TriaxialStressController::particlesVolume`") .def_readonly("max_vel1",&TriaxialStressController::max_vel1,"see :yref:`TriaxialStressController::max_vel` |ycomp|") .def_readonly("max_vel2",&TriaxialStressController::max_vel2,"see :yref:`TriaxialStressController::max_vel` |ycomp|") .def_readonly("max_vel3",&TriaxialStressController::max_vel3,"see :yref:`TriaxialStressController::max_vel` |ycomp|") .def("stress",&TriaxialStressController::getStress,(boost::python::arg("id")),"Returns the average stress on boundary 'id'. Here, 'id' refers to the internal numbering of boundaries, between 0 and 5.") ) DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(TriaxialStressController); trunk-2017.01a/pkg/dem/TriaxialTest.cpp000066400000000000000000000344701304022710500176410ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include // random #include #include #include #include #include //#include #include "TriaxialTest.hpp" CREATE_LOGGER(TriaxialTest); YADE_PLUGIN((TriaxialTest)); TriaxialTest::~TriaxialTest () {} bool TriaxialTest::generate(string& message) { message=""; if(biaxial2dTest && (8.0*(upperCorner[2]-lowerCorner[2]))>(upperCorner[0]-lowerCorner[0])){ message="Biaxial test can be generated only if Z size is more than 8 times smaller than X size"; return false;} if(facetWalls&&wallWalls){ LOG_WARN("Turning TriaxialTest::facetWalls off, since wallWalls were selected as well."); } shared_ptr body; /* if _mean_radius is not given (i.e. <=0), then calculate it from box size; * OTOH, if it is specified, scale the box preserving its ratio and lowerCorner so that the radius can be as requested */ Real porosity=.8; SpherePack sphere_pack; if(importFilename==""){ Vector3r dimensions=upperCorner-lowerCorner; Real volume=dimensions.x()*dimensions.y()*dimensions.z(); long num; if(radiusMean<=0) num=sphere_pack.makeCloud(lowerCorner,upperCorner,-1,radiusStdDev,numberOfGrains,false /*periodic?*/,porosity); else { bool fixedDims[3]; fixedDims[0]=fixedBoxDims.find('x')!=string::npos; fixedDims[1]=fixedBoxDims.find('y')!=string::npos; fixedDims[2]=fixedBoxDims.find('z')!=string::npos; int nScaled=(3-(int)fixedDims[0]+(int)fixedDims[1]+(int)fixedDims[2]); if(nScaled==0) throw std::invalid_argument("At most 2 (not 3) axes can have fixed dimensions in fixedBoxDims if scaling for given radiusMean."); Real boxScaleFactor=radiusMean*pow((4/3.)*Mathr::PI*numberOfGrains/(volume*(1-porosity)),1./nScaled); LOG_INFO("Mean radius value of "<(num) + " spheres inside box of dimensions: (" + boost::lexical_cast(upperCorner[0]-lowerCorner[0]) + "," + boost::lexical_cast(upperCorner[1]-lowerCorner[1]) + "," + boost::lexical_cast(upperCorner[2]-lowerCorner[2]) + ").";} else { if(radiusMean>0) LOG_WARN("radiusMean ignored, since importFilename specified."); sphere_pack.fromFile(importFilename); sphere_pack.aabb(lowerCorner,upperCorner);} // setup scene here, since radiusMean is now at its true value (if it was negative) scene = shared_ptr(new Scene); positionRootBody(scene); createActors(scene); if(thickness<0) thickness=radiusMean; if(facetWalls || wallWalls) thickness=0; if(!facetWalls && !wallWalls){ // bottom box Vector3r center = Vector3r((lowerCorner[0]+upperCorner[0])/2, lowerCorner[1]-thickness/2.0, (lowerCorner[2]+upperCorner[2])/2); Vector3r halfSize = Vector3r(wallOversizeFactor*std::abs(lowerCorner[0]-upperCorner[0])/2+thickness, thickness/2.0, wallOversizeFactor*std::abs(lowerCorner[2]-upperCorner[2])/2+thickness); createBox(body,center,halfSize,true); scene->bodies->insert(body); triaxialcompressionEngine->wall_bottom_id = body->getId(); // top box center = Vector3r((lowerCorner[0]+upperCorner[0])/2, upperCorner[1]+thickness/2.0, (lowerCorner[2]+upperCorner[2])/2); halfSize = Vector3r(wallOversizeFactor*std::abs(lowerCorner[0]-upperCorner[0])/2+thickness, thickness/2.0, wallOversizeFactor*std::abs(lowerCorner[2]-upperCorner[2])/2+thickness); createBox(body,center,halfSize,true); scene->bodies->insert(body); triaxialcompressionEngine->wall_top_id = body->getId(); // box 1 center = Vector3r(lowerCorner[0]-thickness/2.0, (lowerCorner[1]+upperCorner[1])/2, (lowerCorner[2]+upperCorner[2])/2); halfSize = Vector3r(thickness/2.0, wallOversizeFactor*std::abs(lowerCorner[1]-upperCorner[1])/2+thickness, wallOversizeFactor*std::abs(lowerCorner[2]-upperCorner[2])/2+thickness); createBox(body,center,halfSize,true); scene->bodies->insert(body); triaxialcompressionEngine->wall_left_id = body->getId(); // box 2 center = Vector3r(upperCorner[0]+thickness/2.0, (lowerCorner[1]+upperCorner[1])/2, (lowerCorner[2]+upperCorner[2])/2); halfSize = Vector3r(thickness/2.0, wallOversizeFactor*std::abs(lowerCorner[1]-upperCorner[1])/2+thickness, wallOversizeFactor*std::abs(lowerCorner[2]-upperCorner[2])/2+thickness); createBox(body,center,halfSize,true); scene->bodies->insert(body); triaxialcompressionEngine->wall_right_id = body->getId(); // box 3 center = Vector3r((lowerCorner[0]+upperCorner[0])/2, (lowerCorner[1]+upperCorner[1])/2, lowerCorner[2]-thickness/2.0); halfSize = Vector3r(wallOversizeFactor*std::abs(lowerCorner[0]-upperCorner[0])/2+thickness, wallOversizeFactor*std::abs(lowerCorner[1]-upperCorner[1])/2+thickness, thickness/2.0); createBox(body,center,halfSize,true); scene->bodies->insert(body); triaxialcompressionEngine->wall_back_id = body->getId(); // box 4 center = Vector3r((lowerCorner[0]+upperCorner[0])/2, (lowerCorner[1]+upperCorner[1])/2, upperCorner[2]+thickness/2.0); halfSize = Vector3r(wallOversizeFactor*std::abs(lowerCorner[0]-upperCorner[0])/2+thickness, wallOversizeFactor*std::abs(lowerCorner[1]-upperCorner[1])/2+thickness, thickness/2.0); createBox(body,center,halfSize,true); scene->bodies->insert(body); triaxialcompressionEngine->wall_front_id = body->getId(); } size_t imax=sphere_pack.pack.size(); for(size_t i=0; istate->blockedDOFs=State::DOF_Z; } scene->bodies->insert(body); } if(defaultDt<0){ defaultDt=Shop::PWaveTimeStep(scene); scene->dt=defaultDt; globalStiffnessTimeStepper->defaultDt=defaultDt; LOG_INFO("Computed default (PWave) timestep "<& body, Vector3r position, Real radius, bool big, bool dynamic ) { body = shared_ptr(new Body); body->groupMask=2; shared_ptr aabb(new Aabb); shared_ptr iSphere(new Sphere); body->state->blockedDOFs=State::DOF_NONE; body->state->mass = 4.0/3.0*Mathr::PI*radius*radius*radius*density; body->state->inertia = Vector3r(2.0/5.0*body->state->mass*radius*radius, 2.0/5.0*body->state->mass*radius*radius, 2.0/5.0*body->state->mass*radius*radius); body->state->pos=position; shared_ptr mat(new FrictMat); mat->young = sphereYoungModulus; mat->poisson = sphereKsDivKn; mat->frictionAngle = compactionFrictionDeg * Mathr::PI/180.0; aabb->color = Vector3r(0,1,0); iSphere->radius = radius; //iSphere->color = Vector3r(0.4,0.1,0.1); iSphere->color = Vector3r(Mathr::UnitRandom(),Mathr::UnitRandom(),Mathr::UnitRandom()); iSphere->color.normalize(); body->shape = iSphere; body->bound = aabb; body->material = mat; } void TriaxialTest::createBox(shared_ptr& body, Vector3r position, Vector3r extents, bool wire) { body = shared_ptr(new Body); body->groupMask=2; body->state->blockedDOFs=State::DOF_ALL; shared_ptr aabb(new Aabb); aabb->color = Vector3r(1,0,0); body->bound = aabb; body->state->pos=position; shared_ptr mat(new FrictMat); mat->young = sphereYoungModulus; mat->poisson = sphereKsDivKn; mat->frictionAngle = boxFrictionDeg * Mathr::PI/180.0; body->material=mat; if(!facetWalls && !wallWalls){ shared_ptr iBox(new Box); iBox->extents = extents; iBox->wire = wire; iBox->color = Vector3r(1,1,1); body->shape = iBox; } // guess the orientation int ax0 = extents[0]==0 ? 0 : (extents[1]==0 ? 1 : 2); int ax1=(ax0+1)%3, ax2=(ax0+2)%3; if(facetWalls){ Vector3r corner=position-extents; // "lower right" corner, with 90 degrees Vector3r side1(Vector3r::Zero()); side1[ax1]=4*extents[ax1]; Vector3r side2(Vector3r::Zero()); side2[ax2]=4*extents[ax2]; Vector3r v[3]; v[0]=corner; v[1]=corner+side1; v[2]=corner+side2; Vector3r cog=Shop::inscribedCircleCenter(v[0],v[1],v[2]); shared_ptr iFacet(new Facet); for(int i=0; i<3; i++){ iFacet->vertices[i]=v[i]-cog;} iFacet->color=Vector3r(1,1,1); body->shape=iFacet; } if(wallWalls){ shared_ptr wall(new Wall); wall->sense=0; // interact from both sides, since unspecified here wall->axis=ax0; body->shape=wall; } } void TriaxialTest::createActors(shared_ptr& scene) { shared_ptr interactionGeometryDispatcher(new IGeomDispatcher); interactionGeometryDispatcher->add(new Ig2_Sphere_Sphere_ScGeom); interactionGeometryDispatcher->add(new Ig2_Facet_Sphere_ScGeom); interactionGeometryDispatcher->add(new Ig2_Box_Sphere_ScGeom); shared_ptr interactionPhysicsDispatcher(new IPhysDispatcher); shared_ptr ss(new Ip2_FrictMat_FrictMat_FrictPhys); interactionPhysicsDispatcher->add(ss); shared_ptr gravityCondition(new GravityEngine); gravityCondition->gravity = gravity; globalStiffnessTimeStepper=shared_ptr(new GlobalStiffnessTimeStepper); globalStiffnessTimeStepper->timeStepUpdateInterval = timeStepUpdateInterval; globalStiffnessTimeStepper->defaultDt = defaultDt; // moving walls to regulate the stress applied + compress when the packing is dense an stable //cerr << "triaxialcompressionEngine = shared_ptr (new TriaxialCompressionEngine);" << std::endl; triaxialcompressionEngine = shared_ptr (new TriaxialCompressionEngine); //This prevent the deprecation warning. In fact this preprocessor in itself is becoming deprecated triaxialcompressionEngine->warn = 1; triaxialcompressionEngine-> stiffnessUpdateInterval = wallStiffnessUpdateInterval;// = stiffness update interval triaxialcompressionEngine-> radiusControlInterval = radiusControlInterval;// = stiffness update interval triaxialcompressionEngine-> sigmaIsoCompaction = sigmaIsoCompaction; triaxialcompressionEngine-> sigmaLateralConfinement = sigmaLateralConfinement; triaxialcompressionEngine->max_vel = maxWallVelocity; triaxialcompressionEngine-> thickness = thickness; triaxialcompressionEngine->strainRate = strainRate; triaxialcompressionEngine->StabilityCriterion = StabilityCriterion; triaxialcompressionEngine->autoCompressionActivation = autoCompressionActivation; triaxialcompressionEngine->autoUnload = autoUnload; triaxialcompressionEngine->autoStopSimulation = autoStopSimulation; triaxialcompressionEngine->internalCompaction = internalCompaction; triaxialcompressionEngine->maxMultiplier = maxMultiplier; triaxialcompressionEngine->finalMaxMultiplier = finalMaxMultiplier; triaxialcompressionEngine->Key = Key; triaxialcompressionEngine->noFiles=noFiles; triaxialcompressionEngine->frictionAngleDegree = sphereFrictionDeg; triaxialcompressionEngine->fixedPoroCompaction = false; triaxialcompressionEngine->fixedPorosity=1; // recording global stress if(recordIntervalIter>0 && !noFiles){ triaxialStateRecorder = shared_ptr(new TriaxialStateRecorder); triaxialStateRecorder-> file = WallStressRecordFile + Key; triaxialStateRecorder-> iterPeriod = recordIntervalIter; } scene->engines.clear(); scene->engines.push_back(shared_ptr(new ForceResetter)); shared_ptr collider(new InsertionSortCollider); scene->engines.push_back(collider); collider->verletDist=.5*radiusMean; collider->boundDispatcher->add(new Bo1_Sphere_Aabb); collider->boundDispatcher->add(new Bo1_Box_Aabb); collider->boundDispatcher->add(new Bo1_Facet_Aabb); collider->boundDispatcher->add(new Bo1_Wall_Aabb); shared_ptr ids(new InteractionLoop); ids->geomDispatcher=interactionGeometryDispatcher; ids->physDispatcher=interactionPhysicsDispatcher; ids->lawDispatcher=shared_ptr(new LawDispatcher); shared_ptr see(new Law2_ScGeom_FrictPhys_CundallStrack); ids->lawDispatcher->add(see); scene->engines.push_back(ids); scene->engines.push_back(globalStiffnessTimeStepper); scene->engines.push_back(triaxialcompressionEngine); if(recordIntervalIter>0 && !noFiles) scene->engines.push_back(triaxialStateRecorder); shared_ptr newton(new NewtonIntegrator); newton->damping=dampingForce; scene->engines.push_back(newton); } void TriaxialTest::positionRootBody(shared_ptr& scene) { } trunk-2017.01a/pkg/dem/TriaxialTest.hpp000066400000000000000000000224651304022710500176470ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2006 by Bruno Chareyre * * bruno.chareyre@hmg.inpg.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include class ForceRecorder; class AveragePositionRecorder; class VelocityRecorder; class TriaxialStressController; class TriaxialCompressionEngine; class TriaxialStateRecorder; class GlobalStiffnessTimeStepper; /*! \brief Isotropic compression + triaxial compression test TriaxialTest full documentation is here : http://yade-dem.org/wiki/TriaxialTest This preprocessor shows how to simulate a triaxial test in Yade. It is using the elastic-frictional contact law defined in ElasticContactLaw (similar procedures can be used for other contact laws). It is designed to : 1/ generate random loose packings and compress them under isotropic confining stress, either squeezing the packing between moving rigid boxes or expanding the particles while boxes are fixed (depending on flag "InternalCompaction"). 2/ simulate all sorts triaxial loading path (there is however a default loading path corresponding to constant lateral stress in 2 directions and constant strain rate on the third direction - this loading path is used when the flag AutoCompressionActivation = true, otherwise the simulation stops after isotropic compression) Essential engines : 1/ The TriaxialCompressionEngine is used for controlling the state of the sample and simulating loading paths. TriaxialCompressionEngine inherits from TriaxialStressController, which can compute stress- strain-like quantities in the packing and maintain a constant level of stress at each boundary. TriaxialCompressionEngine has few more members in order to impose constant strain rate and control the transition between isotropic compression and triaxial test. 2/ The class TriaxialStateRecorder is used to write to a file the history of stresses and strains. 3/ TriaxialTest is currently using GlobalStiffnessTimeStepper to compute an appropriate dt for the numerical scheme. The TriaxialTest is the only preprocessor using these classes in Yade because they have been developed AFTER most of preprocessor examples, BUT they can be used in principle in any situation and they have nothing specifically related to the triaxial test. @note TriaxialStressController::ComputeUnbalancedForce(...) returns a value that can be useful for evaluating the stability of the packing. It is defined as (mean force on particles)/(mean contact force), so that it tends to 0 in a stable packing. This parameter is checked by TriaxialCompressionEngine to switch from one stage of the simulation to the next one (e.g. stop isotropic confinment and start axial loading) @note Compaction is done (1) by moving rigid boxes or (2) by increasing the sizes of the particles (decided using the option "internalCompaction" : true => size increase). Both algorithm needs numerical parameters to prevent instabilities. For instance, with method (1) maxWallVelocity is the maximum wall velocity, with method (2) finalMaxMultiplier is the max value of the multiplier applied on sizes at each iteration (always something like 1.00001). */ class TriaxialTest : public FileGenerator { private : Vector3r gravity; Vector3r spheresColor; bool spheresRandomColor; shared_ptr triaxialcompressionEngine; shared_ptr triaxialstressController; shared_ptr triaxialStateRecorder; shared_ptr globalStiffnessTimeStepper; void createBox(shared_ptr& body, Vector3r position, Vector3r extents,bool wire); void createSphere(shared_ptr& body, Vector3r position, Real radius,bool big,bool dynamic); void createActors(shared_ptr& scene); void positionRootBody(shared_ptr& scene); typedef pair BasicSphere; public : ~TriaxialTest (); bool generate(string& message); YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY( TriaxialTest,FileGenerator,"Prepare a scene for triaxial tests. Full documentation in py/_extraDocs.py." , ((Vector3r,lowerCorner,Vector3r(0,0,0),,"Lower corner of the box.")) ((Vector3r,upperCorner,Vector3r(1,1,1),,"Upper corner of the box.")) ((string,importFilename,"",,"File with positions and sizes of spheres.")) ((string,Key,"",,"A code that is added to output filenames.")) ((string,fixedBoxDims,"",,"string that contains some subset (max. 2) of {'x','y','z'} ; contains axes will have box dimension hardcoded, even if box is scaled as mean_radius is prescribed: scaling will be applied on the rest.")) ((string,WallStressRecordFile,"./WallStresses"+Key,,"")) ((bool,internalCompaction,false,,"flag for choosing between moving boundaries or increasing particles sizes during the compaction stage.")) ((bool,biaxial2dTest,false,,"FIXME : what is that?")) ((bool,autoCompressionActivation,true,,"Do we just want to generate a stable packing under isotropic pressure (false) or do we want the triaxial loading to start automatically right after compaction stage (true)?")) ((bool,autoUnload,true,,"auto adjust the isotropic stress state from :yref:`TriaxialTest::sigmaIsoCompaction` to :yref:`TriaxialTest::sigmaLateralConfinement` if they have different values. See docs for :yref:`TriaxialCompressionEngine::autoUnload`")) ((bool,autoStopSimulation,false,,"freeze the simulation when conditions are reached (don't activate this if you want to be able to run/stop from Qt GUI)")) ((bool,noFiles,false,,"Do not create any files during run (.xml, .spheres, wall stress records)")) ((bool,facetWalls,false,,"Use facets for boundaries (not tested)")) ((bool,wallWalls,false,,"Use walls for boundaries (not tested)")) ((Real,thickness,0.001,,"thickness of boundaries. It is arbitrary and should have no effect")) ((Real,maxMultiplier,1.01,,"max multiplier of diameters during internal compaction (initial fast increase)")) ((Real,finalMaxMultiplier,1.001,,"max multiplier of diameters during internal compaction (secondary precise adjustment)")) ((Real,radiusStdDev,0.3,,"Normalized standard deviation of generated sizes.")) ((Real,radiusMean,-1,,"Mean radius. If negative (default), autocomputed to as a function of box size and :yref:`TriaxialTest::numberOfGrains`")) ((Real,sphereYoungModulus,15000000.0,,"Stiffness of spheres.")) ((Real,sphereKsDivKn,0.5,,"Ratio of shear vs. normal contact stiffness for spheres.")) ((Real,sphereFrictionDeg,18.0,,"Friction angle [°] of spheres assigned just before triaxial testing.")) ((Real,compactionFrictionDeg,sphereFrictionDeg,,"Friction angle [°] of spheres during compaction (different values result in different porosities)]. This value is overridden by :yref:`TriaxialTest::sphereFrictionDeg` before triaxial testing.")) ((Real,boxYoungModulus,15000000.0,,"Stiffness of boxes.")) ((Real,maxWallVelocity,10,,"max velocity of boundaries. Usually useless, but can help stabilizing the system in some cases.")) ((Real,boxKsDivKn,0.5,,"Ratio of shear vs. normal contact stiffness for boxes.")) ((Real,boxFrictionDeg,0.0,,"Friction angle [°] of boundaries contacts.")) ((Real,density,2600,,"density of spheres")) ((Real,strainRate,0.1,,"Strain rate in triaxial loading.")) ((Real,defaultDt,-1,,"Max time-step. Used as initial value if defined. Latter adjusted by the time stepper.")) ((Real,dampingForce,0.2,,"Coefficient of Cundal-Non-Viscous damping (applied on on the 3 components of forces)")) ((Real,dampingMomentum,0.2,,"Coefficient of Cundal-Non-Viscous damping (applied on on the 3 components of torques)")) ((Real,StabilityCriterion,0.01,,"Value of unbalanced force for which the system is considered stable. Used in conditionals to switch between loading stages.")) ((Real,wallOversizeFactor,1.3,,"Make boundaries larger than the packing to make sure spheres don't go out during deformation.")) ((Real,sigmaIsoCompaction,-50000,,"Confining stress during isotropic compaction (< 0 for real - compressive - compaction).")) ((Real,sigmaLateralConfinement,-50000,,"Lateral stress during triaxial loading (< 0 for classical compressive cases). An isotropic unloading is performed if the value is not equal to :yref:`TriaxialTest::sigmaIsoCompaction`.")) ((int,timeStepUpdateInterval,50,,"interval for :yref:`GlobalStiffnessTimeStepper`")) ((int,wallStiffnessUpdateInterval,10,,"interval for updating the stiffness of sample/boundaries contacts")) ((int,radiusControlInterval,10,,"interval between size changes when growing spheres.")) ((int,numberOfGrains,400,,"Number of generated spheres.")) ((int,recordIntervalIter,20,,"interval between file outputs")) , /* init */ , /* constructor */ spheresColor = Vector3r(0.8,0.3,0.3); spheresRandomColor = false; WallStressRecordFile = "./WallStresses"+Key; gravity = Vector3r(0,-9.81,0); , //.def("setContactProperties",&TriaxialCompressionEngine::setContactProperties,"Assign a new friction angle (degrees) to dynamic bodies and relative interactions") ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(TriaxialTest); trunk-2017.01a/pkg/dem/UnbalancedForceCallbacks.cpp000066400000000000000000000032131304022710500220260ustar00rootroot00000000000000#include #include #include #include #include YADE_PLUGIN((SumIntrForcesCb) #ifdef YADE_BODY_CALLBACK (SumBodyForcesCb) #endif ); IntrCallback::FuncPtr SumIntrForcesCb::stepInit(){ // if(scene->iter%100 != 0) return NULL; cerr<<"("<<(Real)force<<","<<(int)numIntr<<")"; // reset accumulators force.reset(); numIntr.reset(); // return function pointer return &SumIntrForcesCb::go; } void SumIntrForcesCb::go(IntrCallback* _self, Interaction* i){ SumIntrForcesCb* self=static_cast(_self); NormShearPhys* nsp=YADE_CAST(i->phys.get()); assert(nsp!=NULL); // only effective in debug mode Vector3r f=nsp->normalForce+nsp->shearForce; if(f==Vector3r::Zero()) return; self->numIntr+=1; self->force+=f.norm(); //cerr<<"[cb#"<getId1()<<"+"<getId2()<<"]"; } #ifdef YADE_BODY_CALLBACK BodyCallback::FuncPtr SumBodyForcesCb::stepInit(){ cerr<<"{"<<(Real)force<<","<<(int)numBodies<<",this="<forces)<<"}"; force.reset(); numBodies.reset(); // reset accumulators return &SumBodyForcesCb::go; } void SumBodyForcesCb::go(BodyCallback* _self, Body* b){ if(b->state->blockedDOFs==State::DOF_ALL) return; SumBodyForcesCb* self=static_cast(_self); #ifdef YADE_OPENMP cerr<<"["<id<<",scene="<scene<<"]"; #endif cerr<<"[force="<scene->forces.getForce(b->id)<<"]"; self->numBodies+=1; //self->scene->forces.sync(); self->force+=self->scene->forces.getForce(b->id).norm(); } #endif trunk-2017.01a/pkg/dem/UnbalancedForceCallbacks.hpp000066400000000000000000000020221304022710500220300ustar00rootroot00000000000000// 2010 © Václav Šmilauer #pragma once #include #include class SumIntrForcesCb: public IntrCallback{ public: OpenMPAccumulator numIntr; OpenMPAccumulator force; static void go(IntrCallback*,Interaction*); virtual IntrCallback::FuncPtr stepInit(); YADE_CLASS_BASE_DOC(SumIntrForcesCb,IntrCallback,"Callback summing magnitudes of forces over all interactions. :yref:`IPhys` of interactions must derive from :yref:`NormShearPhys` (responsability fo the user)."); }; REGISTER_SERIALIZABLE(SumIntrForcesCb); #ifdef YADE_BODY_CALLBACK class SumBodyForcesCb: public BodyCallback{ Scene* scene; public: OpenMPAccumulator numBodies; OpenMPAccumulator force; static void go(BodyCallback*,Body*); virtual BodyCallback::FuncPtr stepInit(); YADE_CLASS_BASE_DOC(SumBodyForcesCb,BodyCallback,"Callback summing magnitudes of resultant forces over :yref:`dynamic` bodies."); }; REGISTER_SERIALIZABLE(SumBodyForcesCb); #endif trunk-2017.01a/pkg/dem/UniaxialStrainer.cpp000066400000000000000000000155621304022710500205070ustar00rootroot00000000000000// 2008 © Václav Šmilauer #include"UniaxialStrainer.hpp" #include #include #include YADE_PLUGIN((UniaxialStrainer)); /************************ UniaxialStrainer **********************/ CREATE_LOGGER(UniaxialStrainer); void UniaxialStrainer::init(){ needsInit=false; assert(posIds.size()>0); assert(negIds.size()>0); posCoords.clear(); negCoords.clear(); FOREACH(Body::id_t id,posIds){ const shared_ptr& b=Body::byId(id,scene); posCoords.push_back(b->state->pos[axis]); if(blockDisplacements && blockRotations) b->state->blockedDOFs=State::DOF_ALL; else{ if(!blockDisplacements) b->state->blockedDOFs=State::axisDOF(axis); else b->state->blockedDOFs=State::DOF_XYZ; if(blockRotations) b->state->blockedDOFs|=State::DOF_RXRYRZ; } } FOREACH(Body::id_t id,negIds){ const shared_ptr& b=Body::byId(id,scene); negCoords.push_back(b->state->pos[axis]); if(blockDisplacements && blockRotations) b->state->blockedDOFs=State::DOF_ALL; else{ if(!blockDisplacements) b->state->blockedDOFs=State::axisDOF(axis); else b->state->blockedDOFs=State::DOF_XYZ; if(blockRotations) b->state->blockedDOFs|=State::DOF_RXRYRZ; } } assert(posIds.size()==posCoords.size() && negIds.size()==negCoords.size()); originalLength=axisCoord(posIds[0])-axisCoord(negIds[0]); LOG_DEBUG("Reference particles: positive #"<(originalLength)).c_str()); /* this happens is nan propagates from e.g. brefcom consitutive law in case 2 bodies have _exactly_ the same position * (the the normal strain is 0./0.=nan). That is an user's error, however and should not happen. */ if(std::isnan(originalLength)) throw logic_error("UniaxialStrainer: Initial length is NaN!"); assert(originalLength>0 && !std::isnan(originalLength)); assert(!std::isnan(strainRate) || !std::isnan(absSpeed)); if(!std::isnan(std::numeric_limits::quiet_NaN())){ throw runtime_error("UniaxialStrainer: NaN's are not properly supported (compiled with -ffast-math?), which is required."); } if(std::isnan(strainRate)){ strainRate=absSpeed/originalLength; LOG_INFO("Computed new strainRate "<=0 ? initAccelTime : scene->dt*(-initAccelTime); LOG_INFO("Strain speed will be "<dt<<" steps)."); } else { /* set speed such that it is linear on the strained axis; transversal speed is not set, which can perhaps create some problems. Note: all bodies in the simulation will have their speed set, since there is no way to tell which ones are part of the specimen and which are not. Speeds will be linearly interpolated beween axis positions p0,p1 and velocities v0,v1. */ initAccelTime_s=0; LOG_INFO("Strain speed will be "<(asymmetry)+" (should be -1,0,1)").c_str()); } assert(p1>p0); // set speeds for particles on the boundary FOREACH(const shared_ptr& b, *scene->bodies){ // skip bodies on the boundary, since those will have their positions updated directly if(std::find(posIds.begin(),posIds.end(),b->id)!=posIds.end() || std::find(negIds.begin(),negIds.end(),b->id)!=negIds.end()) { continue; } Real p=axisCoord(b->id); Real pNormalized=(p-p0)/(p1-p0); b->state->vel[axis]=pNormalized*(v1-v0)+v0; } } if(std::isnan(crossSectionArea)){ throw std::invalid_argument("UniaxialStrain.crossSectionArea must be specified."); } } void UniaxialStrainer::action(){ if(needsInit) init(); // postconditions for initParams assert(posIds.size()==posCoords.size() && negIds.size()==negCoords.size() && originalLength>0 && crossSectionArea>0); //nothing to do if(posIds.size()==0 || negIds.size()==0) return; // linearly increase strain to the desired value if(std::abs(currentStrainRate)time/initAccelTime_s)*strainRate; else currentStrainRate=strainRate; } else currentStrainRate=strainRate; // how much do we move (in total, symmetry handled below) Real dAX=currentStrainRate*originalLength*scene->dt; if(!std::isnan(stopStrain)){ Real axialLength=axisCoord(posIds[0])-axisCoord(negIds[0]); Real newStrain=(axialLength+dAX)/originalLength-1; if((newStrain*stopStrain>0) && std::abs(newStrain)>=stopStrain){ // same sign of newStrain and stopStrain && over the limit from below in abs values dAX=originalLength*(stopStrain+1)-axialLength; LOG_INFO("Reached stopStrain "<active=false; scene->stopAtIter=scene->iter+1+idleIterations; } } if(asymmetry==0) dAX*=.5; // apply half on both sides if straining symetrically if(asymmetry!=1){ for(size_t i=0; ipos is useless with curent velocity defined below, and use of NewtonIntegrator axisVel(negIds[i]) = -dAX/scene->dt; // update current position } } if(asymmetry!=-1){ for(size_t i=0; idt; } } Real axialLength=axisCoord(posIds[0])-axisCoord(negIds[0]); strain=axialLength/originalLength-1; // reverse if we're over the limit strain if(notYetReversed && limitStrain!=0 && ((currentStrainRate>0 && strain>limitStrain) || (currentStrainRate<0 && strainiter%stressUpdateInterval==0) { computeAxialForce(); avgStress=(sumPosForces+sumNegForces)/(2*crossSectionArea); // average nominal stress } } void UniaxialStrainer::computeAxialForce(){ sumPosForces=sumNegForces=0; scene->forces.sync(); FOREACH(Body::id_t id, negIds) sumNegForces+=scene->forces.getForce(id)[axis]; FOREACH(Body::id_t id, posIds) sumPosForces-=scene->forces.getForce(id)[axis]; } trunk-2017.01a/pkg/dem/UniaxialStrainer.hpp000066400000000000000000000075661304022710500205210ustar00rootroot00000000000000// 2008 © Václav Šmilauer #pragma once #include #include #include /*! Axial displacing two groups of bodies in the opposite direction with given strain rate. * * Takes two groups of body IDs (in posIds and negIds) and displaces them at each timestep in the direction given by axis∈{0,1,2} (for axes x,y,z respectively). These bodies automatically have Body::isDynamic==false. * * This engine should be run once forces on particles have been computed. */ class UniaxialStrainer: public BoundaryController { private: bool needsInit; void computeAxialForce(); Real axisCoord(Body::id_t id){ return Body::byId(id,scene)->state->pos[axis]; }; Real& axisVel(Body::id_t id){ return Body::byId(id,scene)->state->vel[axis]; }; void init(); public: virtual bool isActivated(){ return active; } Real sumPosForces,sumNegForces; Real initAccelTime_s /* value always in s, computed from initAccelTime */; /** coordinates of pos/neg bodies in the direction of axis */ vector posCoords,negCoords; virtual void action(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(UniaxialStrainer,BoundaryController,"Axial displacing two groups of bodies in the opposite direction with given strain rate.", ((Real,strainRate,NaN,,"Rate of strain, starting at 0, linearly raising to strainRate. [-]")) ((Real,absSpeed,NaN,,"alternatively, absolute speed of boundary motion can be specified; this is effective only at the beginning and if strainRate is not set; changing absSpeed directly during simulation wil have no effect. [ms⁻¹]")) ((Real,initAccelTime,-200,,"Time for strain reaching the requested value (linear interpolation). If negative, the time is dt*(-initAccelTime), where dt is the timestep at the first iteration. [s]")) ((Real,stopStrain,NaN,,"Strain at which we will pause simulation; inactive (nan) by default; must be reached from below (in absolute value)")) ((bool,active,true,,"Whether this engine is activated")) ((long,idleIterations,0,,"Number of iterations that will pass without straining activity after stopStrain has been reached")) ((Real,currentStrainRate,NaN,,"Current strain rate (update automatically). |yupdate|")) ((int,axis,2,,"The axis which is strained (0,1,2 for x,y,z)")) ((int,asymmetry,((void)"symmetric",0),,"If 0, straining is symmetric for negIds and posIds; for 1 (or -1), only posIds are strained and negIds don't move (or vice versa)")) ((vector,posIds,,,"Bodies on which strain will be applied (on the positive end along the axis)")) ((vector,negIds,,,"Bodies on which strain will be applied (on the negative end along the axis)")) ((Real,originalLength,NaN,,"Distance of reference bodies in the direction of axis before straining started (computed automatically) [m]")) ((Real,limitStrain,((void)"disabled",0),,"Invert the sense of straining (sharply, without transition) one this value of strain is reached. Not effective if 0.")) ((bool,notYetReversed,true,,"Flag whether the sense of straining has already been reversed (only used internally).")) ((Real,crossSectionArea,NaN,,"crossSection perpendicular to he strained axis; must be given explicitly [m²]")) ((Real,strain,0,,"Current strain value, elongation/originalLength |yupdate| [-]")) ((Real,avgStress,0,,"Current average stress |yupdate| [Pa]")) ((bool,blockDisplacements,false,,"Whether displacement of boundary bodies perpendicular to the strained axis are blocked or are free")) ((bool,blockRotations,false,,"Whether rotations of boundary bodies are blocked.")) ((bool,setSpeeds,false,,"should we set speeds at the beginning directly, instead of increasing strain rate progressively?")) ((int,stressUpdateInterval,10,,"How often to recompute stress on supports.")), /*ctor*/ needsInit=true; ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(UniaxialStrainer); trunk-2017.01a/pkg/dem/VTKRecorder.cpp000066400000000000000000001304361304022710500173550ustar00rootroot00000000000000#ifdef YADE_VTK #include"VTKRecorder.hpp" #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #ifdef YADE_VTK_MULTIBLOCK #include #include #endif #include #include #include #include #include #include #include #include #ifdef YADE_LIQMIGRATION #include #endif YADE_PLUGIN((VTKRecorder)); CREATE_LOGGER(VTKRecorder); #ifdef YADE_MASK_ARBITRARY #define GET_MASK(b) b->groupMask.to_ulong() #else #define GET_MASK(b) b->groupMask #endif #include #include #include void VTKRecorder::action(){ vector recActive(REC_SENTINEL,false); FOREACH(string& rec, recorders){ if(rec=="all"){ recActive[REC_SPHERES]=true; recActive[REC_VELOCITY]=true; recActive[REC_FACETS]=true; recActive[REC_BOXES]=true; recActive[REC_COLORS]=true; recActive[REC_MASS]=true; recActive[REC_INTR]=true; recActive[REC_ID]=true; recActive[REC_MASK]=true; recActive[REC_CLUMPID]=true; recActive[REC_MATERIALID]=true; recActive[REC_STRESS]=true; recActive[REC_FORCE]=true; recActive[REC_COORDNUMBER]=true; if (scene->isPeriodic) { recActive[REC_PERICELL]=true; } } else if(rec=="spheres") recActive[REC_SPHERES]=true; else if(rec=="velocity") recActive[REC_VELOCITY]=true; else if(rec=="facets") recActive[REC_FACETS]=true; else if(rec=="boxes") recActive[REC_BOXES]=true; else if(rec=="mass") recActive[REC_MASS]=true; else if((rec=="colors") || (rec=="color"))recActive[REC_COLORS]=true; else if(rec=="cpm") recActive[REC_CPM]=true; else if(rec=="wpm") recActive[REC_WPM]=true; else if(rec=="intr") recActive[REC_INTR]=true; else if((rec=="ids") || (rec=="id")) recActive[REC_ID]=true; else if(rec=="mask") recActive[REC_MASK]=true; else if((rec=="clumpids") || (rec=="clumpId")) recActive[REC_CLUMPID]=true; else if(rec=="materialId") recActive[REC_MATERIALID]=true; else if(rec=="stress") recActive[REC_STRESS]=true; else if(rec=="force") recActive[REC_FORCE]=true; else if(rec=="jcfpm") recActive[REC_JCFPM]=true; else if(rec=="cracks") recActive[REC_CRACKS]=true; else if(rec=="pericell" && scene->isPeriodic) recActive[REC_PERICELL]=true; else if(rec=="liquidcontrol") recActive[REC_LIQ]=true; else if(rec=="bstresses") recActive[REC_BSTRESS]=true; else if(rec=="coordNumber") recActive[REC_COORDNUMBER]=true; else LOG_ERROR("Unknown recorder named `"< spheresPos = vtkSmartPointer::New(); vtkSmartPointer spheresCells = vtkSmartPointer::New(); vtkSmartPointer radii = vtkSmartPointer::New(); radii->SetNumberOfComponents(1); radii->SetName("radii"); vtkSmartPointer spheresSigI = vtkSmartPointer::New(); spheresSigI->SetNumberOfComponents(1); spheresSigI->SetName("sigI"); vtkSmartPointer spheresSigII = vtkSmartPointer::New(); spheresSigII->SetNumberOfComponents(1); spheresSigII->SetName("sigII"); vtkSmartPointer spheresSigIII = vtkSmartPointer::New(); spheresSigIII->SetNumberOfComponents(1); spheresSigIII->SetName("sigIII"); vtkSmartPointer spheresDirI = vtkSmartPointer::New(); spheresDirI->SetNumberOfComponents(3); spheresDirI->SetName("dirI"); vtkSmartPointer spheresDirII = vtkSmartPointer::New(); spheresDirII->SetNumberOfComponents(3); spheresDirII->SetName("dirII"); vtkSmartPointer spheresDirIII = vtkSmartPointer::New(); spheresDirIII->SetNumberOfComponents(3); spheresDirIII->SetName("dirIII"); vtkSmartPointer spheresMass = vtkSmartPointer::New(); spheresMass->SetNumberOfComponents(1); spheresMass->SetName("mass"); vtkSmartPointer spheresId = vtkSmartPointer::New(); spheresId->SetNumberOfComponents(1); spheresId->SetName("id"); #ifdef YADE_SPH vtkSmartPointer spheresRhoSPH = vtkSmartPointer::New(); spheresRhoSPH->SetNumberOfComponents(1); spheresRhoSPH->SetName("SPH_Rho"); vtkSmartPointer spheresPressSPH = vtkSmartPointer::New(); spheresPressSPH->SetNumberOfComponents(1); spheresPressSPH->SetName("SPH_Press"); vtkSmartPointer spheresCoordNumbSPH = vtkSmartPointer::New(); spheresCoordNumbSPH->SetNumberOfComponents(1); spheresCoordNumbSPH->SetName("SPH_Neigh"); #endif #ifdef YADE_LIQMIGRATION vtkSmartPointer spheresLiqVol = vtkSmartPointer::New(); spheresLiqVol->SetNumberOfComponents(1); spheresLiqVol->SetName("Liq_Vol"); vtkSmartPointer spheresLiqVolIter = vtkSmartPointer::New(); spheresLiqVolIter->SetNumberOfComponents(1); spheresLiqVolIter->SetName("Liq_VolIter"); vtkSmartPointer spheresLiqVolTotal = vtkSmartPointer::New(); spheresLiqVolTotal->SetNumberOfComponents(1); spheresLiqVolTotal->SetName("Liq_VolTotal"); #endif vtkSmartPointer spheresMask = vtkSmartPointer::New(); spheresMask->SetNumberOfComponents(1); spheresMask->SetName("mask"); vtkSmartPointer spheresCoordNumb = vtkSmartPointer::New(); spheresCoordNumb->SetNumberOfComponents(1); spheresCoordNumb->SetName("coordNumber"); vtkSmartPointer clumpId = vtkSmartPointer::New(); clumpId->SetNumberOfComponents(1); clumpId->SetName("clumpId"); vtkSmartPointer spheresColors = vtkSmartPointer::New(); spheresColors->SetNumberOfComponents(3); spheresColors->SetName("color"); vtkSmartPointer spheresLinVelVec = vtkSmartPointer::New(); spheresLinVelVec->SetNumberOfComponents(3); spheresLinVelVec->SetName("linVelVec"); //Linear velocity in Vector3 form vtkSmartPointer spheresLinVelLen = vtkSmartPointer::New(); spheresLinVelLen->SetNumberOfComponents(1); spheresLinVelLen->SetName("linVelLen"); //Length (magnitude) of linear velocity vtkSmartPointer spheresAngVelVec = vtkSmartPointer::New(); spheresAngVelVec->SetNumberOfComponents(3); spheresAngVelVec->SetName("angVelVec"); //Angular velocity in Vector3 form vtkSmartPointer spheresAngVelLen = vtkSmartPointer::New(); spheresAngVelLen->SetNumberOfComponents(1); spheresAngVelLen->SetName("angVelLen"); //Length (magnitude) of angular velocity vtkSmartPointer spheresNormalStressVec = vtkSmartPointer::New(); spheresNormalStressVec->SetNumberOfComponents(3); spheresNormalStressVec->SetName("normalStress"); vtkSmartPointer spheresShearStressVec = vtkSmartPointer::New(); spheresShearStressVec->SetNumberOfComponents(3); spheresShearStressVec->SetName("shearStress"); vtkSmartPointer spheresNormalStressNorm = vtkSmartPointer::New(); spheresNormalStressNorm->SetNumberOfComponents(1); spheresNormalStressNorm->SetName("normalStressNorm"); vtkSmartPointer spheresMaterialId = vtkSmartPointer::New(); spheresMaterialId->SetNumberOfComponents(1); spheresMaterialId->SetName("materialId"); vtkSmartPointer spheresForceVec = vtkSmartPointer::New(); spheresForceVec->SetNumberOfComponents(3); spheresForceVec->SetName("forceVec"); vtkSmartPointer spheresForceLen = vtkSmartPointer::New(); spheresForceLen->SetNumberOfComponents(1); spheresForceLen->SetName("forceLen"); vtkSmartPointer spheresTorqueVec = vtkSmartPointer::New(); spheresTorqueVec->SetNumberOfComponents(3); spheresTorqueVec->SetName("torqueVec"); vtkSmartPointer spheresTorqueLen = vtkSmartPointer::New(); spheresTorqueLen->SetNumberOfComponents(1); spheresTorqueLen->SetName("torqueLen"); // facets vtkSmartPointer facetsPos = vtkSmartPointer::New(); vtkSmartPointer facetsCells = vtkSmartPointer::New(); vtkSmartPointer facetsColors = vtkSmartPointer::New(); facetsColors->SetNumberOfComponents(3); facetsColors->SetName("color"); vtkSmartPointer facetsStressVec = vtkSmartPointer::New(); facetsStressVec->SetNumberOfComponents(3); facetsStressVec->SetName("stressVec"); vtkSmartPointer facetsStressLen = vtkSmartPointer::New(); facetsStressLen->SetNumberOfComponents(1); facetsStressLen->SetName("stressLen"); vtkSmartPointer facetsMaterialId = vtkSmartPointer::New(); facetsMaterialId->SetNumberOfComponents(1); facetsMaterialId->SetName("materialId"); vtkSmartPointer facetsMask = vtkSmartPointer::New(); facetsMask->SetNumberOfComponents(1); facetsMask->SetName("mask"); vtkSmartPointer facetsForceVec = vtkSmartPointer::New(); facetsForceVec->SetNumberOfComponents(3); facetsForceVec->SetName("forceVec"); vtkSmartPointer facetsForceLen = vtkSmartPointer::New(); facetsForceLen->SetNumberOfComponents(1); facetsForceLen->SetName("forceLen"); vtkSmartPointer facetsTorqueVec = vtkSmartPointer::New(); facetsTorqueVec->SetNumberOfComponents(3); facetsTorqueVec->SetName("torqueVec"); vtkSmartPointer facetsTorqueLen = vtkSmartPointer::New(); facetsTorqueLen->SetNumberOfComponents(1); facetsTorqueLen->SetName("torqueLen"); vtkSmartPointer facetsCoordNumb = vtkSmartPointer::New(); facetsCoordNumb->SetNumberOfComponents(1); facetsCoordNumb->SetName("coordNumber"); // boxes vtkSmartPointer boxesPos = vtkSmartPointer::New(); vtkSmartPointer boxesCells = vtkSmartPointer::New(); vtkSmartPointer boxesColors = vtkSmartPointer::New(); boxesColors->SetNumberOfComponents(3); boxesColors->SetName("color"); vtkSmartPointer boxesStressVec = vtkSmartPointer::New(); boxesStressVec->SetNumberOfComponents(3); boxesStressVec->SetName("stressVec"); vtkSmartPointer boxesStressLen = vtkSmartPointer::New(); boxesStressLen->SetNumberOfComponents(1); boxesStressLen->SetName("stressLen"); vtkSmartPointer boxesMaterialId = vtkSmartPointer::New(); boxesMaterialId->SetNumberOfComponents(1); boxesMaterialId->SetName("materialId"); vtkSmartPointer boxesMask = vtkSmartPointer::New(); boxesMask->SetNumberOfComponents(1); boxesMask->SetName("mask"); vtkSmartPointer boxesForceVec = vtkSmartPointer::New(); boxesForceVec->SetNumberOfComponents(3); boxesForceVec->SetName("forceVec"); vtkSmartPointer boxesForceLen = vtkSmartPointer::New(); boxesForceLen->SetNumberOfComponents(1); boxesForceLen->SetName("forceLen"); vtkSmartPointer boxesTorqueVec = vtkSmartPointer::New(); boxesTorqueVec->SetNumberOfComponents(3); boxesTorqueVec->SetName("torqueVec"); vtkSmartPointer boxesTorqueLen = vtkSmartPointer::New(); boxesTorqueLen->SetNumberOfComponents(1); boxesTorqueLen->SetName("torqueLen"); // interactions vtkSmartPointer intrBodyPos = vtkSmartPointer::New(); vtkSmartPointer intrCells = vtkSmartPointer::New(); vtkSmartPointer intrForceN = vtkSmartPointer::New(); intrForceN->SetNumberOfComponents(1); intrForceN->SetName("forceN"); vtkSmartPointer intrAbsForceT = vtkSmartPointer::New(); intrAbsForceT->SetNumberOfComponents(3); intrAbsForceT->SetName("absForceT"); // pericell vtkSmartPointer pericellPoints = vtkSmartPointer::New(); vtkSmartPointer pericellHexa = vtkSmartPointer::New(); // extras for CPM if(recActive[REC_CPM]){ CpmStateUpdater csu; csu.update(scene); } vtkSmartPointer cpmDamage = vtkSmartPointer::New(); cpmDamage->SetNumberOfComponents(1); cpmDamage->SetName("cpmDamage"); vtkSmartPointer cpmStress = vtkSmartPointer::New(); cpmStress->SetNumberOfComponents(9); cpmStress->SetName("cpmStress"); // extras for JCFpm vtkSmartPointer damage = vtkSmartPointer::New(); damage->SetNumberOfComponents(1); damage->SetName("damage"); vtkSmartPointer damageRel = vtkSmartPointer::New(); damageRel->SetNumberOfComponents(1); damageRel->SetName("damageRel"); vtkSmartPointer intrIsCohesive = vtkSmartPointer::New(); intrIsCohesive->SetNumberOfComponents(1); intrIsCohesive->SetName("isCohesive"); vtkSmartPointer intrIsOnJoint = vtkSmartPointer::New(); intrIsOnJoint->SetNumberOfComponents(1); intrIsOnJoint->SetName("isOnJoint"); // extras for cracks vtkSmartPointer crackPos = vtkSmartPointer::New(); vtkSmartPointer crackCells = vtkSmartPointer::New(); vtkSmartPointer iter = vtkSmartPointer::New(); iter->SetNumberOfComponents(1); iter->SetName("iter"); vtkSmartPointer crackType = vtkSmartPointer::New(); crackType->SetNumberOfComponents(1); crackType->SetName("crackType"); vtkSmartPointer crackSize = vtkSmartPointer::New(); crackSize->SetNumberOfComponents(1); crackSize->SetName("crackSize"); vtkSmartPointer crackNorm = vtkSmartPointer::New(); crackNorm->SetNumberOfComponents(3); crackNorm->SetName("crackNorm"); #ifdef YADE_LIQMIGRATION vtkSmartPointer liqVol = vtkSmartPointer::New(); liqVol->SetNumberOfComponents(1); liqVol->SetName("liqVol"); vtkSmartPointer liqVolNorm = vtkSmartPointer::New(); liqVolNorm->SetNumberOfComponents(1); liqVolNorm->SetName("liqVolNorm"); #endif // extras for WireMatPM vtkSmartPointer wpmNormalForce = vtkSmartPointer::New(); wpmNormalForce->SetNumberOfComponents(1); wpmNormalForce->SetName("wpmNormalForce"); vtkSmartPointer wpmLimitFactor = vtkSmartPointer::New(); wpmLimitFactor->SetNumberOfComponents(1); wpmLimitFactor->SetName("wpmLimitFactor"); if(recActive[REC_INTR]){ // holds information about cell distance between spatial and displayed position of each particle vector wrapCellDist; if (scene->isPeriodic){ wrapCellDist.resize(scene->bodies->size()); } // save body positions, referenced by ids by vtkLine // map to keep real body ids and their number in a vector (intrBodyPos) boost::unordered_map bIdVector; Body::id_t curId = 0; FOREACH(const shared_ptr& b, *scene->bodies){ if (b) { if(!scene->isPeriodic) { intrBodyPos->InsertNextPoint(b->state->pos[0],b->state->pos[1],b->state->pos[2]); } else { Vector3r pos=scene->cell->wrapShearedPt(b->state->pos,wrapCellDist[b->id]); intrBodyPos->InsertNextPoint(pos[0],pos[1],pos[2]); } bIdVector.insert (std::pair(b->id,curId)); curId++; } } FOREACH(const shared_ptr& I, *scene->interactions){ if(!I->isReal()) continue; if(skipFacetIntr){ if(!(Body::byId(I->getId1()))) continue; if(!(Body::byId(I->getId2()))) continue; if(!(dynamic_cast(Body::byId(I->getId1())->shape.get()))) continue; if(!(dynamic_cast(Body::byId(I->getId2())->shape.get()))) continue; } const auto iterId1 = bIdVector.find (I->getId1()); const auto iterId2 = bIdVector.find (I->getId2()); if (iterId2 == bIdVector.end() || iterId2 == bIdVector.end()) continue; const auto setId1Line = iterId1->second; const auto setId2Line = iterId2->second; /* For the periodic boundary conditions, find out whether the interaction crosses the boundary of the periodic cell; if it does, display the interaction on both sides of the cell, with one of the points sticking out in each case. Since vtkLines must connect points with an ID assigned, we will create a new additional point for each point outside the cell. It might create some data redundancy, but let us suppose that the number of interactions crossing the cell boundary is low compared to total numer of interactions */ // how many times to add values defined on interactions, depending on how many times the interaction is saved int numAddValues=1; // aperiodic boundary, or interaction is inside the cell if(!scene->isPeriodic || (scene->isPeriodic && (I->cellDist==wrapCellDist[I->getId2()]-wrapCellDist[I->getId1()]))){ vtkSmartPointer line = vtkSmartPointer::New(); line->GetPointIds()->SetId(0,setId1Line); line->GetPointIds()->SetId(1,setId2Line); intrCells->InsertNextCell(line); } else { assert(scene->isPeriodic); // spatial positions of particles const Vector3r& p01(Body::byId(I->getId1())->state->pos); const Vector3r& p02(Body::byId(I->getId2())->state->pos); // create two line objects; each of them has one endpoint inside the cell and the other one sticks outside // A,B are the "fake" bodies outside the cell for id1 and id2 respectively, p1,p2 are the displayed points // distance in cell units for shifting A away from p1; negated value is shift of B away from p2 Vector3r ptA(p01+scene->cell->hSize*(wrapCellDist[I->getId2()]-I->cellDist).cast()); const vtkIdType idPtA=intrBodyPos->InsertNextPoint(ptA[0],ptA[1],ptA[2]); Vector3r ptB(p02+scene->cell->hSize*(wrapCellDist[I->getId1()]-I->cellDist).cast()); const vtkIdType idPtB=intrBodyPos->InsertNextPoint(ptB[0],ptB[1],ptB[2]); vtkSmartPointer line1B(vtkSmartPointer::New()); line1B->GetPointIds()->SetId(0,setId2Line); line1B->GetPointIds()->SetId(1,idPtB); vtkSmartPointer lineA2(vtkSmartPointer::New()); lineA2->GetPointIds()->SetId(0,idPtA); lineA2->GetPointIds()->SetId(1,setId2Line); numAddValues=2; } const NormShearPhys* phys = YADE_CAST(I->phys.get()); const GenericSpheresContact* geom = YADE_CAST(I->geom.get()); // gives _signed_ scalar of normal force, following the convention used in the respective constitutive law Real fn=phys->normalForce.dot(geom->normal); Real fs[3]={ (Real) std::abs(phys->shearForce[0]), (Real) std::abs(phys->shearForce[1]), (Real) std::abs(phys->shearForce[2])}; // add the value once for each interaction object that we created (might be 2 for the periodic boundary) for(int i=0; iInsertNextTupleValue(fs); if(recActive[REC_WPM]) { const WirePhys* wirephys = dynamic_cast(I->phys.get()); if (wirephys!=NULL && wirephys->isLinked) { wpmLimitFactor->InsertNextValue(wirephys->limitFactor); wpmNormalForce->InsertNextValue(fn); intrForceN->InsertNextValue(NaN); } else { intrForceN->InsertNextValue(fn); wpmNormalForce->InsertNextValue(NaN); wpmLimitFactor->InsertNextValue(NaN); } } else if (recActive[REC_JCFPM]){ const JCFpmPhys* jcfpmphys = YADE_CAST(I->phys.get()); intrIsCohesive->InsertNextValue(jcfpmphys->isCohesive); intrIsOnJoint->InsertNextValue(jcfpmphys->isOnJoint); intrForceN->InsertNextValue(fn); } else { intrForceN->InsertNextValue(fn); } #ifdef YADE_LIQMIGRATION if (recActive[REC_LIQ]) { const ViscElCapPhys* capphys = YADE_CAST(I->phys.get()); liqVol->InsertNextValue(capphys->Vb); liqVolNorm->InsertNextValue(capphys->Vb/capphys->Vmax); } #endif } } } //Additional Vector for storing forces vector bodyStates; if(recActive[REC_STRESS]) Shop::getStressForEachBody(bodyStates); vector bStresses; if (recActive[REC_BSTRESS]) { Shop::getStressLWForEachBody(bStresses); } FOREACH(const shared_ptr& b, *scene->bodies){ if (!b) continue; if(mask!=0 && !b->maskCompatible(mask)) continue; if (recActive[REC_SPHERES]){ const Sphere* sphere = dynamic_cast(b->shape.get()); if (sphere){ if(skipNondynamic && b->state->blockedDOFs==State::DOF_ALL) continue; vtkIdType pid[1]; Vector3r pos(scene->isPeriodic ? scene->cell->wrapShearedPt(b->state->pos) : b->state->pos); pid[0] = spheresPos->InsertNextPoint(pos[0], pos[1], pos[2]); spheresCells->InsertNextCell(1,pid); radii->InsertNextValue(sphere->radius); if (recActive[REC_BSTRESS]) { const Matrix3r& bStress = bStresses[b->getId()]; Eigen::SelfAdjointEigenSolver solver(bStress); // bStress is probably not symmetric (= self-adjoint for real matrices), but the solver hopefully works (considering only one half of bStress). And, moreover, existence of (real) eigenvalues is not sure for not symmetric bStress.. Matrix3r dirAll = solver.eigenvectors(); Vector3r eigenVal = solver.eigenvalues(); // cf http://eigen.tuxfamily.org/dox/classEigen_1_1SelfAdjointEigenSolver.html#a30caf3c3884a7f4a46b8ec94efd23c5e to be sure that eigenVal[i] * dirAll.col(i) = bStress * dirAll.col(i) int whereSigI(-1), whereSigII(-1), whereSigIII(-1); // all whereSig_i are in [0;2] : whereSigI = 2 => sigI=eigenVal[2] if ( eigenVal[0] > std::max(eigenVal[1],eigenVal[2]) ) { whereSigI = 0; if (eigenVal[1]>eigenVal[2]) { whereSigII=1; whereSigIII=2; } else { //eigenVal[0] > eigenVal[2] >= eigenVal[1] whereSigII = 2; whereSigIII=1; } } else { // max(lambda1,lambda2) >= lambda0 // lambda = eigenVal in the comments if (eigenVal[1]>=eigenVal[2]) {//max(lambda1,lambda2) = lambda1 : lambda 1 >= lambda2 whereSigI = 1; if (eigenVal[2]>=eigenVal[0]) {//lambda1 >= lambda2 >= lambda0 whereSigII=2; whereSigIII=0; } else { //lambda1 >= lambda0 > lambda2 whereSigII=0; whereSigIII=2; } } else { //max(lambda1,lambda2) = lambda2 : lambda2 > lambda1 whereSigI = 2; if (eigenVal[1] > eigenVal[0]) { whereSigII = 1; whereSigIII = 0; } else { whereSigIII = 1; whereSigII = 0; } } } spheresSigI->InsertNextValue(eigenVal[whereSigI]); spheresSigII->InsertNextValue(eigenVal[whereSigII]); spheresSigIII->InsertNextValue(eigenVal[whereSigIII]); Real dirI[3] { (Real) dirAll(0,whereSigI), (Real) dirAll(1,whereSigI), (Real) dirAll(2,whereSigI) }; spheresDirI->InsertNextTupleValue(dirI); Real dirII[3] { (Real) dirAll(0,whereSigII), (Real) dirAll(1,whereSigII), (Real) dirAll(2,whereSigII) }; spheresDirII->InsertNextTupleValue(dirII); Real dirIII[3] { (Real) dirAll(0,whereSigIII), (Real) dirAll(1,whereSigIII), (Real) dirAll(2,whereSigIII) }; spheresDirIII->InsertNextTupleValue(dirIII); } if (recActive[REC_ID]) spheresId->InsertNextValue(b->getId()); if (recActive[REC_MASK]) spheresMask->InsertNextValue(GET_MASK(b)); if (recActive[REC_MASS]) spheresMass->InsertNextValue(b->state->mass); if (recActive[REC_CLUMPID]) clumpId->InsertNextValue(b->clumpId); if (recActive[REC_COLORS]){ const Vector3r& color = sphere->color; Real c[3] = { (Real) color[0], (Real) color[1], (Real) color[2]}; spheresColors->InsertNextTupleValue(c); } if(recActive[REC_VELOCITY]){ const Vector3r& vel = b->state->vel; Real v[3] = { (Real) vel[0], (Real) vel[1], (Real) vel[2] }; spheresLinVelVec->InsertNextTupleValue(v); spheresLinVelLen->InsertNextValue(vel.norm()); const Vector3r& angVel = b->state->angVel; Real av[3] = { (Real) angVel[0], (Real) angVel[1], (Real) angVel[2] }; spheresAngVelVec->InsertNextTupleValue(av); spheresAngVelLen->InsertNextValue(angVel.norm()); } if(recActive[REC_STRESS]){ const Vector3r& stress = bodyStates[b->getId()].normStress; const Vector3r& shear = bodyStates[b->getId()].shearStress; Real n[3] = { (Real) stress[0], (Real) stress[1], (Real) stress[2] }; Real s[3] = { (Real) shear [0], (Real) shear [1], (Real) shear [2] }; spheresNormalStressVec->InsertNextTupleValue(n); spheresShearStressVec->InsertNextTupleValue(s); spheresNormalStressNorm->InsertNextValue(stress.norm()); } if(recActive[REC_FORCE]){ scene->forces.sync(); const Vector3r& f = scene->forces.getForce(b->getId()); const Vector3r& t = scene->forces.getTorque(b->getId()); Real ff[3] = { (Real) f[0], (Real) f[1], (Real) f[2] }; Real tt[3] = { (Real) t[0], (Real) t[1], (Real) t[2] }; Real fn = f.norm(); Real tn = t.norm(); spheresForceVec->InsertNextTupleValue(ff); spheresForceLen->InsertNextValue(fn); spheresTorqueVec->InsertNextTupleValue(tt); spheresTorqueLen->InsertNextValue(tn); } if (recActive[REC_CPM]){ cpmDamage->InsertNextValue(YADE_PTR_CAST(b->state)->normDmg); const Matrix3r& ss=YADE_PTR_CAST(b->state)->stress; //Real s[3]={ss[0],ss[1],ss[2]}; Real s[9]={ (Real) ss(0,0), (Real) ss(0,1), (Real) ss(0,2), (Real) ss(1,0), (Real) ss(1,1), (Real) ss(1,2), (Real) ss(2,0), (Real) ss(2,1), (Real) ss(2,2)}; cpmStress->InsertNextTupleValue(s); } if (recActive[REC_JCFPM]){ damage->InsertNextValue(YADE_PTR_CAST(b->state)->tensBreak + YADE_PTR_CAST(b->state)->shearBreak); damageRel->InsertNextValue(YADE_PTR_CAST(b->state)->tensBreakRel + YADE_PTR_CAST(b->state)->shearBreakRel); } if (recActive[REC_COORDNUMBER]){ spheresCoordNumb->InsertNextValue(b->coordNumber()); } #ifdef YADE_SPH spheresRhoSPH->InsertNextValue(b->state->rho); spheresPressSPH->InsertNextValue(b->state->press); spheresCoordNumbSPH->InsertNextValue(b->coordNumber()); #endif #ifdef YADE_LIQMIGRATION if (recActive[REC_LIQ]) { spheresLiqVol->InsertNextValue(b->state->Vf); const Real tmpVolIter = liqVolIterBody(b); spheresLiqVolIter->InsertNextValue(tmpVolIter); spheresLiqVolTotal->InsertNextValue(tmpVolIter + b->state->Vf); } #endif if (recActive[REC_MATERIALID]) spheresMaterialId->InsertNextValue(b->material->id); continue; } } if (recActive[REC_FACETS]){ const Facet* facet = dynamic_cast(b->shape.get()); if (facet){ Vector3r pos(scene->isPeriodic ? scene->cell->wrapShearedPt(b->state->pos) : b->state->pos); const vector& localPos = facet->vertices; Matrix3r facetAxisT=b->state->ori.toRotationMatrix(); vtkSmartPointer tri = vtkSmartPointer::New(); vtkIdType nbPoints=facetsPos->GetNumberOfPoints(); for (int i=0;i<3;++i){ Vector3r globalPos = pos + facetAxisT * localPos[i]; facetsPos->InsertNextPoint(globalPos[0], globalPos[1], globalPos[2]); tri->GetPointIds()->SetId(i,nbPoints+i); } facetsCells->InsertNextCell(tri); if (recActive[REC_COLORS]){ const Vector3r& color = facet->color; Real c[3] = { (Real) color[0], (Real) color[1], (Real) color[2]}; facetsColors->InsertNextTupleValue(c); } if(recActive[REC_STRESS]){ const Vector3r& stress = bodyStates[b->getId()].normStress+bodyStates[b->getId()].shearStress; Real s[3] = { (Real) stress[0], (Real) stress[1], (Real) stress[2] }; facetsStressVec->InsertNextTupleValue(s); facetsStressLen->InsertNextValue(stress.norm()); } if(recActive[REC_FORCE]){ scene->forces.sync(); const Vector3r& f = scene->forces.getForce(b->getId()); const Vector3r& t = scene->forces.getTorque(b->getId()); Real ff[3] = { (Real) f[0], (Real) f[1], (Real) f[2] }; Real tt[3] = { (Real) t[0], (Real) t[1], (Real) t[2] }; Real fn = f.norm(); Real tn = t.norm(); facetsForceVec->InsertNextTupleValue(ff); facetsForceLen->InsertNextValue(fn); facetsTorqueVec->InsertNextTupleValue(tt); facetsTorqueLen->InsertNextValue(tn); } if (recActive[REC_MATERIALID]) facetsMaterialId->InsertNextValue(b->material->id); if (recActive[REC_MASK]) facetsMask->InsertNextValue(GET_MASK(b)); if (recActive[REC_COORDNUMBER]){ facetsCoordNumb->InsertNextValue(b->coordNumber()); } continue; } } if (recActive[REC_BOXES]){ const Box* box = dynamic_cast(b->shape.get()); if (box){ Vector3r pos(scene->isPeriodic ? scene->cell->wrapShearedPt(b->state->pos) : b->state->pos); Quaternionr ori(b->state->ori); Vector3r ext(box->extents); vtkSmartPointer boxes = vtkSmartPointer::New(); Vector3r A = Vector3r(-ext[0], -ext[1], -ext[2]); Vector3r B = Vector3r(-ext[0], +ext[1], -ext[2]); Vector3r C = Vector3r(+ext[0], +ext[1], -ext[2]); Vector3r D = Vector3r(+ext[0], -ext[1], -ext[2]); Vector3r E = Vector3r(-ext[0], -ext[1], +ext[2]); Vector3r F = Vector3r(-ext[0], +ext[1], +ext[2]); Vector3r G = Vector3r(+ext[0], +ext[1], +ext[2]); Vector3r H = Vector3r(+ext[0], -ext[1], +ext[2]); A = pos + ori*A; B = pos + ori*B; C = pos + ori*C; D = pos + ori*D; E = pos + ori*E; F = pos + ori*F; G = pos + ori*G; H = pos + ori*H; addWallVTK(boxes, boxesPos, A, B, C, D); boxesCells->InsertNextCell(boxes); addWallVTK(boxes, boxesPos, E, H, G, F); boxesCells->InsertNextCell(boxes); addWallVTK(boxes, boxesPos, A, E, F, B); boxesCells->InsertNextCell(boxes); addWallVTK(boxes, boxesPos, G, H, D, C); boxesCells->InsertNextCell(boxes); addWallVTK(boxes, boxesPos, F, G, C, B); boxesCells->InsertNextCell(boxes); addWallVTK(boxes, boxesPos, D, H, E, A); boxesCells->InsertNextCell(boxes); for(int i=0; i<6; i++){ if (recActive[REC_COLORS]){ const Vector3r& color = box->color; Real c[3] = { (Real) color[0], (Real) color[1], (Real) color[2]}; boxesColors->InsertNextTupleValue(c); } if(recActive[REC_STRESS]){ const Vector3r& stress = bodyStates[b->getId()].normStress+bodyStates[b->getId()].shearStress; Real s[3] = { (Real) stress[0], (Real) stress[1], (Real) stress[2] }; boxesStressVec->InsertNextTupleValue(s); boxesStressLen->InsertNextValue(stress.norm()); } if(recActive[REC_FORCE]){ scene->forces.sync(); const Vector3r& f = scene->forces.getForce(b->getId()); const Vector3r& t = scene->forces.getTorque(b->getId()); Real ff[3] = { (Real) f[0], (Real) f[1], (Real) f[2] }; Real tt[3] = { (Real) t[0], (Real) t[1], (Real) t[2] }; Real fn = f.norm(); Real tn = t.norm(); boxesForceVec->InsertNextTupleValue(ff); boxesForceLen->InsertNextValue(fn); boxesTorqueVec->InsertNextTupleValue(tt); boxesTorqueLen->InsertNextValue(tn); } if (recActive[REC_MATERIALID]) boxesMaterialId->InsertNextValue(b->material->id); if (recActive[REC_MASK]) boxesMask->InsertNextValue(GET_MASK(b)); } continue; } } } if (recActive[REC_PERICELL]) { const Matrix3r& hSize = scene->cell->hSize; Vector3r v0 = hSize*Vector3r(0,0,1); Vector3r v1 = hSize*Vector3r(0,1,1); Vector3r v2 = hSize*Vector3r(1,1,1); Vector3r v3 = hSize*Vector3r(1,0,1); Vector3r v4 = hSize*Vector3r(0,0,0); Vector3r v5 = hSize*Vector3r(0,1,0); Vector3r v6 = hSize*Vector3r(1,1,0); Vector3r v7 = hSize*Vector3r(1,0,0); pericellPoints->InsertNextPoint(v0[0],v0[1],v0[2]); pericellPoints->InsertNextPoint(v1[0],v1[1],v1[2]); pericellPoints->InsertNextPoint(v2[0],v2[1],v2[2]); pericellPoints->InsertNextPoint(v3[0],v3[1],v3[2]); pericellPoints->InsertNextPoint(v4[0],v4[1],v4[2]); pericellPoints->InsertNextPoint(v5[0],v5[1],v5[2]); pericellPoints->InsertNextPoint(v6[0],v6[1],v6[2]); pericellPoints->InsertNextPoint(v7[0],v7[1],v7[2]); vtkSmartPointer h = vtkSmartPointer::New(); vtkIdList* l = h->GetPointIds(); for (int i=0; i<8; i++) { l->SetId(i,i); } pericellHexa->InsertNextCell(h); } vtkSmartPointer compressor; if(compress) compressor=vtkSmartPointer::New(); vtkSmartPointer spheresUg = vtkSmartPointer::New(); if (recActive[REC_SPHERES]){ spheresUg->SetPoints(spheresPos); spheresUg->SetCells(VTK_VERTEX, spheresCells); spheresUg->GetPointData()->AddArray(radii); if (recActive[REC_ID]) spheresUg->GetPointData()->AddArray(spheresId); if (recActive[REC_MASK]) spheresUg->GetPointData()->AddArray(spheresMask); if (recActive[REC_MASS]) spheresUg->GetPointData()->AddArray(spheresMass); if (recActive[REC_CLUMPID]) spheresUg->GetPointData()->AddArray(clumpId); if (recActive[REC_COLORS]) spheresUg->GetPointData()->AddArray(spheresColors); if (recActive[REC_VELOCITY]){ spheresUg->GetPointData()->AddArray(spheresLinVelVec); spheresUg->GetPointData()->AddArray(spheresAngVelVec); spheresUg->GetPointData()->AddArray(spheresLinVelLen); spheresUg->GetPointData()->AddArray(spheresAngVelLen); } #ifdef YADE_SPH spheresUg->GetPointData()->AddArray(spheresRhoSPH); spheresUg->GetPointData()->AddArray(spheresPressSPH); spheresUg->GetPointData()->AddArray(spheresCoordNumbSPH); #endif #ifdef YADE_LIQMIGRATION if (recActive[REC_LIQ]) { spheresUg->GetPointData()->AddArray(spheresLiqVol); spheresUg->GetPointData()->AddArray(spheresLiqVolIter); spheresUg->GetPointData()->AddArray(spheresLiqVolTotal); } #endif if (recActive[REC_STRESS]){ spheresUg->GetPointData()->AddArray(spheresNormalStressVec); spheresUg->GetPointData()->AddArray(spheresShearStressVec); spheresUg->GetPointData()->AddArray(spheresNormalStressNorm); } if (recActive[REC_FORCE]){ spheresUg->GetPointData()->AddArray(spheresForceVec); spheresUg->GetPointData()->AddArray(spheresForceLen); spheresUg->GetPointData()->AddArray(spheresTorqueVec); spheresUg->GetPointData()->AddArray(spheresTorqueLen); } if (recActive[REC_CPM]){ spheresUg->GetPointData()->AddArray(cpmDamage); spheresUg->GetPointData()->AddArray(cpmStress); } if (recActive[REC_JCFPM]) { spheresUg->GetPointData()->AddArray(damage); } if (recActive[REC_BSTRESS]) { spheresUg->GetPointData()->AddArray(spheresSigI); spheresUg->GetPointData()->AddArray(spheresSigII); spheresUg->GetPointData()->AddArray(spheresSigIII); spheresUg->GetPointData()->AddArray(spheresDirI); spheresUg->GetPointData()->AddArray(spheresDirII); spheresUg->GetPointData()->AddArray(spheresDirIII); } if (recActive[REC_MATERIALID]) spheresUg->GetPointData()->AddArray(spheresMaterialId); if (recActive[REC_COORDNUMBER]) spheresUg->GetCellData()->AddArray(spheresCoordNumb); #ifdef YADE_VTK_MULTIBLOCK if(!multiblock) #endif { vtkSmartPointer writer = vtkSmartPointer::New(); if(compress) writer->SetCompressor(compressor); if(ascii) writer->SetDataModeToAscii(); string fn=fileName+"spheres."+boost::lexical_cast(scene->iter)+".vtu"; writer->SetFileName(fn.c_str()); #ifdef YADE_VTK6 writer->SetInputData(spheresUg); #else writer->SetInput(spheresUg); #endif writer->Write(); } } vtkSmartPointer facetsUg = vtkSmartPointer::New(); if (recActive[REC_FACETS]){ facetsUg->SetPoints(facetsPos); facetsUg->SetCells(VTK_TRIANGLE, facetsCells); if (recActive[REC_COLORS]) facetsUg->GetCellData()->AddArray(facetsColors); if (recActive[REC_STRESS]){ facetsUg->GetCellData()->AddArray(facetsStressVec); facetsUg->GetCellData()->AddArray(facetsStressLen); } if (recActive[REC_FORCE]){ facetsUg->GetCellData()->AddArray(facetsForceVec); facetsUg->GetCellData()->AddArray(facetsForceLen); facetsUg->GetCellData()->AddArray(facetsTorqueVec); facetsUg->GetCellData()->AddArray(facetsTorqueLen); } if (recActive[REC_MATERIALID]) facetsUg->GetCellData()->AddArray(facetsMaterialId); if (recActive[REC_MASK]) facetsUg->GetCellData()->AddArray(facetsMask); if (recActive[REC_COORDNUMBER]) facetsUg->GetCellData()->AddArray(facetsCoordNumb); #ifdef YADE_VTK_MULTIBLOCK if(!multiblock) #endif { vtkSmartPointer writer = vtkSmartPointer::New(); if(compress) writer->SetCompressor(compressor); if(ascii) writer->SetDataModeToAscii(); string fn=fileName+"facets."+boost::lexical_cast(scene->iter)+".vtu"; writer->SetFileName(fn.c_str()); #ifdef YADE_VTK6 writer->SetInputData(facetsUg); #else writer->SetInput(facetsUg); #endif writer->Write(); } } vtkSmartPointer boxesUg = vtkSmartPointer::New(); if (recActive[REC_BOXES]){ boxesUg->SetPoints(boxesPos); boxesUg->SetCells(VTK_QUAD, boxesCells); if (recActive[REC_COLORS]) boxesUg->GetCellData()->AddArray(boxesColors); if (recActive[REC_STRESS]){ boxesUg->GetCellData()->AddArray(boxesStressVec); boxesUg->GetCellData()->AddArray(boxesStressLen); } if (recActive[REC_FORCE]){ boxesUg->GetCellData()->AddArray(boxesForceVec); boxesUg->GetCellData()->AddArray(boxesForceLen); boxesUg->GetCellData()->AddArray(boxesTorqueVec); boxesUg->GetCellData()->AddArray(boxesTorqueLen); } if (recActive[REC_MATERIALID]) boxesUg->GetCellData()->AddArray(boxesMaterialId); if (recActive[REC_MASK]) boxesUg->GetCellData()->AddArray(boxesMask); #ifdef YADE_VTK_MULTIBLOCK if(!multiblock) #endif { vtkSmartPointer writer = vtkSmartPointer::New(); if(compress) writer->SetCompressor(compressor); if(ascii) writer->SetDataModeToAscii(); string fn=fileName+"boxes."+boost::lexical_cast(scene->iter)+".vtu"; writer->SetFileName(fn.c_str()); #ifdef YADE_VTK6 writer->SetInputData(boxesUg); #else writer->SetInput(boxesUg); #endif writer->Write(); } } vtkSmartPointer intrPd = vtkSmartPointer::New(); if (recActive[REC_INTR]){ intrPd->SetPoints(intrBodyPos); intrPd->SetLines(intrCells); intrPd->GetCellData()->AddArray(intrForceN); intrPd->GetCellData()->AddArray(intrAbsForceT); #ifdef YADE_LIQMIGRATION if (recActive[REC_LIQ]) { intrPd->GetCellData()->AddArray(liqVol); intrPd->GetCellData()->AddArray(liqVolNorm); } #endif if (recActive[REC_JCFPM]) { intrPd->GetCellData()->AddArray(intrIsCohesive); intrPd->GetCellData()->AddArray(intrIsOnJoint); } if (recActive[REC_WPM]){ intrPd->GetCellData()->AddArray(wpmNormalForce); intrPd->GetCellData()->AddArray(wpmLimitFactor); } #ifdef YADE_VTK_MULTIBLOCK if(!multiblock) #endif { vtkSmartPointer writer = vtkSmartPointer::New(); if(compress) writer->SetCompressor(compressor); if(ascii) writer->SetDataModeToAscii(); string fn=fileName+"intrs."+boost::lexical_cast(scene->iter)+".vtp"; writer->SetFileName(fn.c_str()); #ifdef YADE_VTK6 writer->SetInputData(intrPd); #else writer->SetInput(intrPd); #endif writer->Write(); } } vtkSmartPointer pericellUg = vtkSmartPointer::New(); if (recActive[REC_PERICELL]){ pericellUg->SetPoints(pericellPoints); pericellUg->SetCells(12,pericellHexa); #ifdef YADE_VTK_MULTIBLOCK if(!multiblock) #endif { vtkSmartPointer writer = vtkSmartPointer::New(); if(compress) writer->SetCompressor(compressor); if(ascii) writer->SetDataModeToAscii(); string fn=fileName+"pericell."+boost::lexical_cast(scene->iter)+".vtu"; writer->SetFileName(fn.c_str()); #ifdef YADE_VTK6 writer->SetInputData(pericellUg); #else writer->SetInput(pericellUg); #endif writer->Write(); } } if (recActive[REC_CRACKS]) { string fileCracks = "cracks_"+Key+".txt"; std::ifstream file (fileCracks.c_str(),std::ios::in); vtkSmartPointer crackUg = vtkSmartPointer::New(); if(file){ while ( !file.eof() ){ std::string line; Real i,p0,p1,p2,t,s,n0,n1,n2; while ( std::getline(file, line)) {/* writes into string "line", a line of file "file". To go along diff. lines*/ file >> i >> p0 >> p1 >> p2 >> t >> s >> n0 >> n1 >> n2; vtkIdType pid[1]; pid[0] = crackPos->InsertNextPoint(p0, p1, p2); crackCells->InsertNextCell(1,pid); crackType->InsertNextValue(t); crackSize->InsertNextValue(s); iter->InsertNextValue(i); Real n[3] = { n0, n1, n2 }; crackNorm->InsertNextTupleValue(n); } } file.close(); } // crackUg->SetPoints(crackPos); crackUg->SetCells(VTK_VERTEX, crackCells); crackUg->GetPointData()->AddArray(iter); crackUg->GetPointData()->AddArray(crackType); crackUg->GetPointData()->AddArray(crackSize); crackUg->GetPointData()->AddArray(crackNorm); //see https://www.mail-archive.com/paraview@paraview.org/msg08166.html to obtain Paraview 2D glyphs conforming to this normal vtkSmartPointer writer = vtkSmartPointer::New(); if(compress) writer->SetCompressor(compressor); if(ascii) writer->SetDataModeToAscii(); string fn=fileName+"cracks."+boost::lexical_cast(scene->iter)+".vtu"; writer->SetFileName(fn.c_str()); #ifdef YADE_VTK6 writer->SetInputData(crackUg); #else writer->SetInput(crackUg); #endif writer->Write(); } #ifdef YADE_VTK_MULTIBLOCK if(multiblock){ vtkSmartPointer multiblockDataset = vtkSmartPointer::New(); int i=0; if(recActive[REC_SPHERES]) multiblockDataset->SetBlock(i++,spheresUg); if(recActive[REC_FACETS]) multiblockDataset->SetBlock(i++,facetsUg); if(recActive[REC_INTR]) multiblockDataset->SetBlock(i++,intrPd); if(recActive[REC_PERICELL]) multiblockDataset->SetBlock(i++,pericellUg); vtkSmartPointer writer = vtkSmartPointer::New(); if(ascii) writer->SetDataModeToAscii(); string fn=fileName+boost::lexical_cast(scene->iter)+".vtm"; writer->SetFileName(fn.c_str()); #ifdef YADE_VTK6 writer->SetInputData(multiblockDataset); #else writer->SetInput(multiblockDataset); #endif writer->Write(); } #endif }; void VTKRecorder::addWallVTK (vtkSmartPointer& boxes, vtkSmartPointer& boxesPos, Vector3r& W1, Vector3r& W2, Vector3r& W3, Vector3r& W4) { //Function for exporting walls of boxes vtkIdType nbPoints=boxesPos->GetNumberOfPoints(); boxesPos->InsertNextPoint(W1[0], W1[1], W1[2]); boxes->GetPointIds()->SetId(0,nbPoints+0); boxesPos->InsertNextPoint(W2[0], W2[1], W2[2]); boxes->GetPointIds()->SetId(1,nbPoints+1); boxesPos->InsertNextPoint(W3[0], W3[1], W3[2]); boxes->GetPointIds()->SetId(2,nbPoints+2); boxesPos->InsertNextPoint(W4[0], W4[1], W4[2]); boxes->GetPointIds()->SetId(3,nbPoints+3); }; #endif /* YADE_VTK */ #undef GET_MASK trunk-2017.01a/pkg/dem/VTKRecorder.hpp000066400000000000000000000157511304022710500173640ustar00rootroot00000000000000#pragma once #include #include #include // multiblock features don't seem to exist prioor to 5.2 #if (VTK_MAJOR_VERSION==5 && VTK_MINOR_VERSION>=2) || (VTK_MAJOR_VERSION > 5) #define YADE_VTK_MULTIBLOCK #endif class VTKRecorder: public PeriodicEngine { public: enum {REC_SPHERES=0,REC_FACETS,REC_BOXES,REC_COLORS,REC_MASS,REC_CPM,REC_INTR,REC_VELOCITY,REC_ID,REC_CLUMPID,REC_SENTINEL,REC_MATERIALID,REC_STRESS,REC_MASK,REC_RPM,REC_JCFPM,REC_CRACKS,REC_WPM,REC_PERICELL,REC_LIQ,REC_BSTRESS,REC_FORCE,REC_COORDNUMBER}; virtual void action(); void addWallVTK (vtkSmartPointer& boxes, vtkSmartPointer& boxesPos, Vector3r& W1, Vector3r& W2, Vector3r& W3, Vector3r& W4); YADE_CLASS_BASE_DOC_ATTRS_CTOR(VTKRecorder,PeriodicEngine,"Engine recording snapshots of simulation into series of \\*.vtu files, readable by VTK-based postprocessing programs such as Paraview. Both bodies (spheres and facets) and interactions can be recorded, with various vector/scalar quantities that are defined on them.\n\n:yref:`PeriodicEngine.initRun` is initialized to ``True`` automatically.", ((bool,compress,false,,"Compress output XML files [experimental].")) ((bool,ascii,false,,"Store data as readable text in the XML file (sets `vtkXMLWriter `__ data mode to ``vtkXMLWriter::Ascii``, while the default is ``Appended``")) ((bool,skipFacetIntr,true,,"Skip interactions that are not of sphere-sphere type (e.g. sphere-facet, sphere-box...), when saving interactions")) ((bool,skipNondynamic,false,,"Skip non-dynamic spheres (but not facets).")) #ifdef YADE_VTK_MULTIBLOCK ((bool,multiblock,false,,"Use multi-block (``.vtm``) files to store data, rather than separate ``.vtu`` files.")) #endif ((string,fileName,"",,"Base file name; it will be appended with {spheres,intrs,facets}-243100.vtu (unless *multiblock* is ``True``) depending on active recorders and step number (243100 in this case). It can contain slashes, but the directory must exist already.")) ((vector,recorders,vector(1,string("all")),,"List of active recorders (as strings). ``all`` (the default value) enables all base and generic recorders.\n\n.. admonition:: Base recorders\n\n\tBase recorders save the geometry (unstructured grids) on which other data is defined. They are implicitly activated by many of the other recorders. Each of them creates a new file (or a block, if :yref:`multiblock ` is set).\n\n\t``spheres``\n\t\tSaves positions and radii (``radii``) of :yref:`spherical` particles.\n\t``facets``\n\t\tSave :yref:`facets` positions (vertices).\n\t``boxes``\n\t\tSave :yref:`boxes` positions (edges).\n\t``intr``\n\t\tStore interactions as lines between nodes at respective particles positions. Additionally stores magnitude of normal (``forceN``) and shear (``absForceT``) forces on interactions (the :yref:`geom must be of type :yref:`NormShearPhys`). \n\n.. admonition:: Generic recorders\n\n\tGeneric recorders do not depend on specific model being used and save commonly useful data.\n\n\t``id``\n\t\tSaves id's (field ``id``) of spheres; active only if ``spheres`` is active.\n\t``mass``\n\t\tSaves masses (field ``mass``) of spheres; active only if ``spheres`` is active.\n\t``clumpId``\n\t\tSaves id's of clumps to which each sphere belongs (field ``clumpId``); active only if ``spheres`` is active.\n\t``colors``\n\t\tSaves colors of :yref:`spheres` and of :yref:`facets` (field ``color``); only active if ``spheres`` or ``facets`` are activated.\n\t``mask``\n\t\tSaves groupMasks of :yref:`spheres` and of :yref:`facets` (field ``mask``); only active if ``spheres`` or ``facets`` are activated.\n\t``materialId``\n\t\tSaves materialID of :yref:`spheres` and of :yref:`facets`; only active if ``spheres`` or ``facets`` are activated.\n\t``coordNumber``\n\t\tSaves coordination number (number of neighbours) of :yref:`spheres` and of :yref:`facets`; only active if ``spheres`` or ``facets`` are activated.\n\t``velocity``\n\t\tSaves linear and angular velocities of spherical particles as Vector3 and length(fields ``linVelVec``, ``linVelLen`` and ``angVelVec``, ``angVelLen`` respectively``); only effective with ``spheres``.\n\t``stress``\n\t\tSaves stresses of :yref:`spheres` and of :yref:`facets` as Vector3 and length; only active if ``spheres`` or ``facets`` are activated.\n\t``force``\n\t\tSaves force and torque of :yref:`spheres`, :yref:`facets` and :yref:`boxes` as Vector3 and length (norm); only active if ``spheres``, ``facets`` or ``boxes`` are activated.\n\t``pericell``\n\t\tSaves the shape of the cell (simulation has to be periodic).\n\t``bstresses``\n\t\tSaves per-particle principal stresses (sigI >= sigII >= sigIII) and associated principal directions (dirI/II/III). Per-particle stress tensors are given by :yref:`bodyStressTensors` (positive values for tensile states).\n\n.. admonition:: Specific recorders\n\n\tThe following should only be activated in appropriate cases, otherwise crashes can occur due to violation of type presuppositions.\n\n\t``cpm``\n\t\tSaves data pertaining to the :yref:`concrete model`: ``cpmDamage`` (normalized residual strength averaged on particle), ``cpmStress`` (stress on particle); ``intr`` is activated automatically by ``cpm``\n\t``wpm``\n\t\tSaves data pertaining to the :yref:`wire particle model`: ``wpmForceNFactor`` shows the loading factor for the wire, e.g. normal force divided by threshold normal force.\n\t``jcfpm``\n\t\tSaves data pertaining to the :yref:`rock (smooth)-jointed model`: ``damage`` is defined by :yref:`JCFpmState.tensBreak` + :yref:`JCFpmState.shearBreak`; ``intr`` is activated automatically by ``jcfpm``, and :yref:`on joint` or :yref:`cohesive` interactions can be vizualized.\n\t``cracks``\n\t\tSaves other data pertaining to the :yref:`rock model`: ``cracks`` shows locations where cohesive bonds failed during the simulation, with their types (0/1 for tensile/shear breakages), their sizes (0.5*(R1+R2)), and their normal directions. The :yref:`corresponding attribute` has to be activated, and Key attributes have to be consistent.\n\n")) ((string,Key,"",,"Necessary if :yref:`recorders` contains 'cracks'. A string specifying the name of file 'cracks___.txt' that is considered in this case (see :yref:`corresponding attribute`).")) ((int,mask,0,,"If mask defined, only bodies with corresponding groupMask will be exported. If 0, all bodies will be exported.")), /*ctor*/ initRun=true; ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(VTKRecorder); trunk-2017.01a/pkg/dem/ViscoelasticCapillarPM.cpp000066400000000000000000000560161304022710500215610ustar00rootroot00000000000000#include "ViscoelasticCapillarPM.hpp" #include #include #include #include #include YADE_PLUGIN((ViscElCapMat)(ViscElCapPhys)(Ip2_ViscElCapMat_ViscElCapMat_ViscElCapPhys)(Law2_ScGeom_ViscElCapPhys_Basic)); /* ViscElCapMat */ ViscElCapMat::~ViscElCapMat(){} /* ViscElCapPhys */ ViscElCapPhys::~ViscElCapPhys(){} /* Ip2_ViscElCapMat_ViscElCapMat_ViscElCapPhys */ void Ip2_ViscElCapMat_ViscElCapMat_ViscElCapPhys::go(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction) { // no updates of an existing contact if(interaction->phys) return; TIMING_DELTAS_START(); TIMING_DELTAS_CHECKPOINT("setup"); shared_ptr phys (new ViscElCapPhys()); Calculate_ViscElMat_ViscElMat_ViscElPhys(b1, b2, interaction, phys); ViscElCapMat* mat1 = static_cast(b1.get()); ViscElCapMat* mat2 = static_cast(b2.get()); TIMING_DELTAS_CHECKPOINT("collide_materials"); if (mat1->Capillar and mat2->Capillar) { if (mat1->Vb == mat2->Vb) { phys->Vb = mat1->Vb; } else { throw runtime_error("Vb should be equal for both particles!."); } if (mat1->gamma == mat2->gamma) { phys->gamma = mat1->gamma; } else { throw runtime_error("Gamma should be equal for both particles!."); } if (mat1->theta == mat2->theta) { phys->theta = (mat1->theta*M_PI/180.0); } else { throw runtime_error("Theta should be equal for both particles!."); } if (mat1->dcap == mat2->dcap) { phys->dcap = mat1->dcap; } else { throw runtime_error("Theta should be equal for both particles!."); } if (mat1->CapillarType == mat2->CapillarType and mat2->CapillarType != ""){ if (mat1->CapillarType == "Willett_numeric") {phys->CapillarType = Willett_numeric;} else if (mat1->CapillarType == "Willett_analytic") {phys->CapillarType = Willett_analytic;} else if (mat1->CapillarType == "Weigert") {phys->CapillarType = Weigert;} else if (mat1->CapillarType == "Rabinovich") {phys->CapillarType = Rabinovich;} else if (mat1->CapillarType == "Lambert") {phys->CapillarType = Lambert;} else if (mat1->CapillarType == "Soulie") {phys->CapillarType = Soulie;} else {phys->CapillarType = None_Capillar;} } else { throw runtime_error("CapillarType should be equal for both particles!."); } phys->Capillar=true; } #ifdef YADE_LIQMIGRATION phys->LiqMigrEnabled = mat1->LiqMigrEnabled && mat2->LiqMigrEnabled; #endif interaction->phys = phys; } /* Law2_ScGeom_ViscElCapPhys_Basic */ bool Law2_ScGeom_ViscElCapPhys_Basic::go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I) { TIMING_DELTAS_START(); TIMING_DELTAS_CHECKPOINT("setup"); Vector3r force = Vector3r::Zero(); const id_t id1 = I->getId1(); const id_t id2 = I->getId2(); const ScGeom& geom=*static_cast(_geom.get()); Scene* scene=Omega::instance().getScene().get(); ViscElCapPhys& phys=*static_cast(_phys.get()); const BodyContainer& bodies = *scene->bodies; /* * This part for implementation of the capillar model. * All main equations are in calculateCapillarForce function. * There is only the determination of critical distance between spheres, * after that the liquid bridge will be broken. */ TIMING_DELTAS_CHECKPOINT("create_liq_bridge"); if (phys.Capillar and not(phys.liqBridgeCreated) and geom.penetrationDepth>=0) { phys.liqBridgeCreated = true; phys.liqBridgeActive = false; #ifdef YADE_LIQMIGRATION if (phys.LiqMigrEnabled) { scene->addIntrs.push_back(I); } #endif Sphere* s1=dynamic_cast(bodies[id1]->shape.get()); Sphere* s2=dynamic_cast(bodies[id2]->shape.get()); if (s1 and s2) { phys.R = 2 * s1->radius * s2->radius / (s1->radius + s2->radius); } else if (s1 and not(s2)) { phys.R = s1->radius; } else { phys.R = s2->radius; } } TIMING_DELTAS_CHECKPOINT("calculate_scrit"); phys.sCrit = this->critDist(phys.Vb, phys.R, phys.theta); TIMING_DELTAS_CHECKPOINT("force_calculation_liquid"); if (geom.penetrationDepth<0) { if (phys.liqBridgeCreated and -geom.penetrationDepth(bodies[id1]->state.get()); const State& de2 = *static_cast(bodies[id2]->state.get()); Vector3r& shearForce = phys.shearForce; if (I->isFresh(scene)) shearForce=Vector3r(0,0,0); shearForce = geom.rotate(shearForce); const Vector3r shift2 = scene->isPeriodic ? scene->cell->intrShiftPos(I->cellDist): Vector3r::Zero(); const Vector3r shiftVel = scene->isPeriodic ? scene->cell->intrShiftVel(I->cellDist): Vector3r::Zero(); const Vector3r c1x = (geom.contactPoint - de1.pos); const Vector3r c2x = (geom.contactPoint - de2.pos - shift2); const Vector3r relativeVelocity = (de1.vel+de1.angVel.cross(c1x)) - (de2.vel+de2.angVel.cross(c2x)) + shiftVel; const auto normalVelocity = geom.normal.dot(relativeVelocity); dampCapForceScalar = -phys.dcap * normalVelocity; } phys.normalForce = -(normalCapForceScalar + dampCapForceScalar)*geom.normal; if (I->isActive) { addForce (id1,-phys.normalForce,scene); addForce (id2, phys.normalForce,scene); }; return true; } else { if (phys.liqBridgeActive) { VLiqBridg -= phys.Vb; NLiqBridg -= 1; } #ifdef YADE_LIQMIGRATION if (phys.Vb > 0.0 and ((phys.Vf1+phys.Vf2) == 0.0)) { phys.Vf1 = phys.Vb/2.0; phys.Vf2 = phys.Vb/2.0; } const std::pair B1 = {id1, phys.Vf1}; const std::pair B2 = {id2, phys.Vf2}; scene->delIntrs.push_back(B1); scene->delIntrs.push_back(B2); #endif return false; }; }; if (phys.liqBridgeActive) { phys.liqBridgeActive=false; VLiqBridg -= phys.Vb; NLiqBridg -= 1; } if (I->isActive) { Vector3r torque1 = Vector3r::Zero(); Vector3r torque2 = Vector3r::Zero(); TIMING_DELTAS_CHECKPOINT("force_calculation_penetr"); if (computeForceTorqueViscEl(_geom, _phys, I, force, torque1, torque2)) { addForce (id1,-force,scene); addForce (id2, force,scene); addTorque(id1, torque1,scene); addTorque(id2, torque2,scene); return true; } else { return false; } } return true; } Real Law2_ScGeom_ViscElCapPhys_Basic::critDist(const Real& Vb, const Real& R, const Real& Theta) { const Real Vstar = Vb/(R*R*R); const Real Sstar = (1+0.5*Theta)*(pow(Vstar,1/3.0) + 0.1*pow(Vstar,2.0/3.0)); // [Willett2000], equation (15), use the full-length e.g 2*Sc const Real critDist = Sstar*R; return critDist; } //========================================================================================= //======================Capillary bridge models============================================ //========================================================================================= Real Law2_ScGeom_ViscElCapPhys_Basic::Willett_numeric_f(const ScGeom& geom, ViscElCapPhys& phys) { /* * Capillar model from [Willett2000] */ const Real R = phys.R; const Real s = -geom.penetrationDepth; const Real Vb = phys.Vb; const Real VbS = Vb/(R*R*R); const Real Th1 = phys.theta; const Real Th2 = phys.theta*phys.theta; const Real Gamma = phys.gamma; /* * [Willett2000], equations in Attachment */ const Real f1 = (-0.44507 + 0.050832*Th1 - 1.1466*Th2) + (-0.1119 - 0.000411*Th1 - 0.1490*Th2) * log(VbS) + (-0.012101 - 0.0036456*Th1 - 0.01255*Th2) *log(VbS)*log(VbS) + (-0.0005 - 0.0003505*Th1 - 0.00029076*Th2) *log(VbS)*log(VbS)*log(VbS); const Real f2 = (1.9222 - 0.57473*Th1 - 1.2918*Th2) + (-0.0668 - 0.1201*Th1 - 0.22574*Th2) * log(VbS) + (-0.0013375 - 0.0068988*Th1 - 0.01137*Th2) *log(VbS)*log(VbS); const Real f3 = (1.268 - 0.01396*Th1 - 0.23566*Th2) + (0.198 + 0.092*Th1 - 0.06418*Th2) * log(VbS) + (0.02232 + 0.02238*Th1 - 0.009853*Th2) *log(VbS)*log(VbS) + (0.0008585 + 0.001318*Th1 - 0.00053*Th2) *log(VbS)*log(VbS)*log(VbS); const Real f4 = (-0.010703 + 0.073776*Th1 - 0.34742*Th2) + (0.03345 + 0.04543*Th1 - 0.09056*Th2) * log(VbS) + (0.0018574 + 0.004456*Th1 - 0.006257*Th2) *log(VbS)*log(VbS); const Real sPl = (s/2.0)/sqrt(Vb/R); const Real lnFS = f1 - f2*exp(f3*log(sPl) + f4*log(sPl)*log(sPl)); const Real FS = exp(lnFS); const Real fC = FS * 2.0 * M_PI* R * Gamma; return fC; } Real Law2_ScGeom_ViscElCapPhys_Basic::Willett_analytic_f(const ScGeom& geom, ViscElCapPhys& phys) { /* * Capillar model from Willet [Willett2000] (analytical solution), but * used also in the work of Herminghaus [Herminghaus2005] */ const Real R = phys.R; const Real Gamma = phys.gamma; const Real s = -geom.penetrationDepth; const Real Vb = phys.Vb; /* Real sPl = s/sqrt(Vb/R); // [Herminghaus2005], equation (sentence between (7) and (8)) fC = 2.0 * M_PI* R * Gamma * cos(phys.theta)/(1 + 1.05*sPl + 2.5 *sPl * sPl); // [Herminghaus2005], equation (7) */ const Real sPl = (s/2.0)/sqrt(Vb/R); // [Willett2000], equation (sentence after (11)), s - half-separation, so s*2.0 const Real f_star = cos(phys.theta)/(1 + 2.1*sPl + 10.0 * pow(sPl, 2.0)); // [Willett2000], equation (12) const Real fC = f_star * (2*M_PI*R*Gamma); // [Willett2000], equation (13), against F return fC; } Real Law2_ScGeom_ViscElCapPhys_Basic::Weigert_f(const ScGeom& geom, ViscElCapPhys& phys) { /* * Capillar model from [Weigert1999] */ const Real R = phys.R; const Real a = -geom.penetrationDepth; const Real Ca = (1.0 + 6.0*a/(R*2.0)); // [Weigert1999], equation (16) const Real Ct = (1.0 + 1.1*sin(phys.theta)); // [Weigert1999], equation (17) /* Real Eps = 0.36; // Porosity Real fi = phys.Vb/(2.0*M_PI/6.0*pow(R*2.0,3.)); // [Weigert1999], equation (13) Real S = M_PI*(1-Eps)/(pow(Eps, 2.0))*fi; // [Weigert1999], equation (14) Real beta = asin(pow(((S/0.36)*(pow(Eps, 2.0)/(1-Eps))*(1.0/Ca)*(1.0/Ct)), 1.0/4.0)); // [Weigert1999], equation (19) */ const Real beta = asin(pow(phys.Vb/(0.12*Ca*Ct*pow(2.0*R, 3.0)), 1.0/4.0)); // [Weigert1999], equation (15), against Vb const Real r1 = (2.0*R*(1-cos(beta)) + a)/(2.0*cos(beta+phys.theta)); // [Weigert1999], equation (5) const Real r2 = R*sin(beta) + r1*(sin(beta+phys.theta)-1); // [Weigert1999], equation (6) const Real Pk = phys.gamma*(1/r1 - 1/r2); // [Weigert1999], equation (22), // see also a sentence over the equation // "R1 was taken as positive and R2 was taken as negative" //fC = M_PI*2.0*R*phys.gamma/(1+tan(0.5*beta)); // [Weigert1999], equation (23), [Fisher] const Real fC = M_PI/4.0*pow((2.0*R),2.0)*pow(sin(beta),2.0)*Pk + phys.gamma*M_PI*2.0*R*sin(beta)*sin(beta+phys.theta); // [Weigert1999], equation (21) return fC; } Real Law2_ScGeom_ViscElCapPhys_Basic::Rabinovich_f(const ScGeom& geom, ViscElCapPhys& phys) { /* * Capillar model from Rabinovich [Rabinov2005] * * This formulation from Rabinovich has been later verified and corrected * by Lambert [Lambert2008]. So we can calculate both formulations * */ const Real R = phys.R; const Real Gamma = phys.gamma; const Real H = -geom.penetrationDepth; const Real V = phys.Vb; Real fC = 0.0; Real dsp = 0.0; if (H!=0.0) { dsp = H/2.0*(-1.0 + sqrt(1.0 + 2.0*V/(M_PI*R*H*H))); // [Rabinov2005], equation (20) fC = -(2*M_PI*R*Gamma*cos(phys.theta))/(1+(H/(2*dsp))); // [Lambert2008], equation (65), taken from [Rabinov2005] const Real alpha = sqrt(H/R*(-1+ sqrt(1 + 2.0*V/(M_PI*R*H*H)))); // [Rabinov2005], equation (A3) fC -= 2*M_PI*R*Gamma*sin(alpha)*sin(phys.theta + alpha); // [Rabinov2005], equation (19) } else { fC = -(2*M_PI*R*Gamma*cos(phys.theta)); const Real alpha = 0.0; fC -= 2*M_PI*R*Gamma*sin(alpha)*sin(phys.theta + alpha); // [Rabinov2005], equation (19) } fC *=-1; return fC; } Real Law2_ScGeom_ViscElCapPhys_Basic::Lambert_f(const ScGeom& geom, ViscElCapPhys& phys) { /* * Capillar model from Rabinovich [Rabinov2005] * * This formulation from Rabinovich has been later verified and corrected * by Lambert [Lambert2008]. So we can calculate both formulations * */ const Real R = phys.R; const Real Gamma = phys.gamma; const Real H = -geom.penetrationDepth; const Real V = phys.Vb; Real fC = 0.0; Real dsp = 0.0; if (H!=0.0) { dsp = H/2.0*(-1.0 + sqrt(1.0 + 2.0*V/(M_PI*R*H*H))); // [Rabinov2005], equation (20) fC = -(2*M_PI*R*Gamma*cos(phys.theta))/(1+(H/(2*dsp))); // [Lambert2008], equation (65), taken from [Rabinov2005] } else { fC = -(2*M_PI*R*Gamma*cos(phys.theta)); } fC *=-1; return fC; } Real Law2_ScGeom_ViscElCapPhys_Basic::Soulie_f(const ScGeom& geom, ViscElCapPhys& phys) { /* * Capillar model from Soulie [Soulie2006] * * !!! In this implementation the radiis of particles are taken equal * to get the symmetric forces. * * Please, use this model only for testing purposes. * */ const Real R = phys.R; const Real Gamma = phys.gamma; const Real D = -geom.penetrationDepth; const Real V = phys.Vb; const Real Theta = phys.theta; const Real a = -1.1*pow((V/(R*R*R)), -0.53); const Real b = (-0.148*log(V/(R*R*R)) - 0.96)*Theta*Theta -0.0082*log(V/(R*R*R)) + 0.48; const Real c = 0.0018*log(V/(R*R*R)) + 0.078; const Real fC = Mathr::PI*Gamma*sqrt(R*R)*(c+exp(a*D/R+b)); return fC; } Real Law2_ScGeom_ViscElCapPhys_Basic::None_f(const ScGeom& geom, ViscElCapPhys& phys) { return 0; } #ifdef YADE_LIQMIGRATION YADE_PLUGIN((LiqControl)); void LiqControl::action(){ // This function implements liquid migration model, introduced here [Mani2013] mapBodyInt bI; mapBodyInt bodyNeedUpdate; // Calculate, how much new contacts will be at each body for (unsigned int i=0; iaddIntrs.size(); i++) { shared_ptr b1 = Body::byId(scene->addIntrs[i]->getId1(),scene); shared_ptr b2 = Body::byId(scene->addIntrs[i]->getId2(),scene); if(not(mask!=0 && ((b1->groupMask & b2->groupMask & mask)==0))) { addBodyMapInt( bI, scene->addIntrs[i]->getId1() ); addBodyMapInt( bI, scene->addIntrs[i]->getId2() ); } } // Update volume water at each deleted interaction for each body for (unsigned int i=0; idelIntrs.size(); i++) { shared_ptr b = Body::byId(scene->delIntrs[i].first,scene); b->state->Vf += scene->delIntrs[i].second; addBodyMapInt(bodyNeedUpdate, scene->delIntrs[i].first); liqVolRup += scene->delIntrs[i].second; } scene->delIntrs.clear(); // Update volume bridge at each new added interaction mapBodyReal bodyUpdateLiquid; for (unsigned int i=0; iaddIntrs.size(); i++) { shared_ptr b1 = Body::byId(scene->addIntrs[i]->getId1(),scene); shared_ptr b2 = Body::byId(scene->addIntrs[i]->getId2(),scene); const id_t id1 = b1->id; const id_t id2 = b2->id; ViscElCapPhys* Vb=dynamic_cast(scene->addIntrs[i]->phys.get()); if(mask!=0 && ((b1->groupMask & b2->groupMask & mask)==0)) { Vb->Vb = 0.0; Vb->Vf1 = 0.0; Vb->Vf2 = 0.0; Vb->Vmax = 0.0; } else { const Real Vmax = vMax(b1, b2); Vb->Vmax = Vmax; Real Vf1 = 0.0; Real Vf2 = 0.0; if ((b1->state->Vmin)state->Vf) { Vf1 = (b1->state->Vf - b1->state->Vmin)/bI[id1]; } if ((b2->state->Vmin)state->Vf) { Vf2 = (b2->state->Vf - b2->state->Vmin)/bI[id2]; } Real Vrup = Vf1+Vf2; if (Vrup > Vmax) { Vf1 *= Vmax/Vrup; Vf2 *= Vmax/Vrup; Vrup = Vf1 + Vf2; } liqVolShr += Vrup; addBodyMapReal(bodyUpdateLiquid, id1, -Vf1); addBodyMapReal(bodyUpdateLiquid, id2, -Vf2); Vb->Vb = Vrup; if (particleconserve) { Vb->Vf1 = Vf1; Vb->Vf2 = Vf2; } else { Vb->Vf1 = Vrup/2.0; Vb->Vf2 = Vrup/2.0; } } } scene->addIntrs.clear(); // Update water volume in body for (mapBodyReal::const_iterator it = bodyUpdateLiquid.begin(); it != bodyUpdateLiquid.end(); ++it) { Body::byId(it->first)->state->Vf += it->second; } // Update contacts around body for (mapBodyInt::const_iterator it = bodyNeedUpdate.begin(); it != bodyNeedUpdate.end(); ++it) { updateLiquid(Body::byId(it->first)); } } void LiqControl::updateLiquid(shared_ptr b){ if (b->state->Vf<=b->state->Vmin) { return; } else { // How much liquid can body share const Real LiqCanBeShared = b->state->Vf - b->state->Vmin; // Check how much liquid can accept contacts Real LiqContactsAccept = 0.0; unsigned int contactN = 0; for(Body::MapId2IntrT::iterator it=b->intrs.begin(),end=b->intrs.end(); it!=end; ++it) { if(!((*it).second) or !(((*it).second)->isReal())) continue; ViscElCapPhys* physT=dynamic_cast(((*it).second)->phys.get()); if ((physT->Vb < physT->Vmax) and (physT->Vmax > 0)) { LiqContactsAccept+=physT->Vmax-physT->Vb; contactN++; } } if (contactN>0) { //There are some contacts, which can be filled Real FillLevel = 0.0; if (LiqContactsAccept > LiqCanBeShared) { // Share all available liquid from body to contacts const Real LiquidWillBeShared = b->state->Vf - b->state->Vmin; b->state->Vf = b->state->Vmin; FillLevel = LiquidWillBeShared/LiqContactsAccept; } else { // Not all available liquid from body can be shared b->state->Vf -= LiqContactsAccept; FillLevel = 1.0; } for(Body::MapId2IntrT::iterator it=b->intrs.begin(),end=b->intrs.end(); it!=end; ++it) { if(!((*it).second) or !(((*it).second)->isReal())) continue; ViscElCapPhys* physT=dynamic_cast(((*it).second)->phys.get()); if ((physT->Vb < physT->Vmax) and (physT->Vmax > 0)) { const Real addVolLiq = (physT->Vmax - physT->Vb)*FillLevel; liqVolShr += addVolLiq; physT->Vb += addVolLiq; if (particleconserve) { if (((*it).second)->getId1() == (*it).first) { physT->Vf2+=addVolLiq; } else if (((*it).second)->getId2() == (*it).first) { physT->Vf1+=addVolLiq; } } else { physT->Vf1+=addVolLiq/2.0; physT->Vf2+=addVolLiq/2.0; } } } return; } else { return; } } } void LiqControl::addBodyMapInt( mapBodyInt & m, Body::id_t b ){ mapBodyInt::const_iterator got; got = m.find (b); if ( got == m.end() ) { m.insert (mapBodyInt::value_type(b,1)); } else { m[b] += 1; } } void LiqControl::addBodyMapReal( mapBodyReal & m, Body::id_t b, Real addV ) { mapBodyReal::const_iterator got; got = m.find (b); if ( got == m.end() ) { m.insert (mapBodyReal::value_type(b, addV)); } else { m[b] += addV; } } Real LiqControl::vMax(shared_ptr const b1, shared_ptr const b2) { Sphere* s1=dynamic_cast(b1->shape.get()); Sphere* s2=dynamic_cast(b2->shape.get()); Real minR = 0.0; if (s1 and s2) { minR = std::min (s1->radius, s2->radius); } else if (s1 and not(s2)) { minR = s1->radius; } else { minR = s2->radius; } return vMaxCoef*minR*minR*minR; } Real liqVolIterBody (shared_ptr b) { Real LiqVol = 0.0; if (!b) { return LiqVol; } else { for(Body::MapId2IntrT::iterator it=b->intrs.begin(),end=b->intrs.end(); it!=end; ++it) { if(!((*it).second) or !(((*it).second)->isReal())) continue; ViscElCapPhys* physT=dynamic_cast(((*it).second)->phys.get()); if (physT and physT->Vb and physT->Vb>0) { if (((*it).second)->id1 == b->id) { if (physT->Vf1 > 0 or physT->Vf2 > 0) { LiqVol += physT->Vf1; } else { LiqVol += physT->Vb/2.0; } } else { if (physT->Vf1 > 0 or physT->Vf2 > 0) { LiqVol += physT->Vf2; } else { LiqVol += physT->Vb/2.0; } } } } return LiqVol; } } Real LiqControl::liqVolBody (id_t id) const { Scene* scene=Omega::instance().getScene().get(); const BodyContainer& bodies = *scene->bodies; if (bodies[id]) { if (bodies[id]->state->Vf > 0) { return bodies[id]->state->Vf + liqVolIterBody(bodies[id]); } else { return liqVolIterBody(bodies[id]); } } else return -1; } Real LiqControl::totalLiqVol(int mask=0) const{ Scene* scene=Omega::instance().getScene().get(); Real totalLiqVol = 0.0; FOREACH(const shared_ptr& b, *scene->bodies){ if((mask>0 && (b->groupMask & mask)==0) or (!b)) continue; totalLiqVol += liqVolIterBody(b); if (b->state->Vf > 0) {totalLiqVol +=b->state->Vf;} } return totalLiqVol; } bool LiqControl::addLiqInter(id_t id1, id_t id2, Real liq) { if (id1==id2 or liq<=0) return false; Scene* scene=Omega::instance().getScene().get(); shared_ptr& intrs=scene->interactions; const shared_ptr& I=intrs->find(id1,id2); if (I->isReal()) { ViscElCapPhys* physT=dynamic_cast(I->phys.get()); if (physT and physT->Vb <= physT->Vmax and liq <= (physT->Vmax - physT->Vb)) { physT->Vb += liq; physT->Vf1 += liq/2.0; physT->Vf2 += liq/2.0; return true; } } return false; } #endif trunk-2017.01a/pkg/dem/ViscoelasticCapillarPM.hpp000066400000000000000000000152771304022710500215720ustar00rootroot00000000000000#pragma once #include "ViscoelasticPM.hpp" #include #include #include class ViscElCapMat : public ViscElMat { public: virtual ~ViscElCapMat(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(ViscElCapMat,ViscElMat,"Material for extended viscoelastic model of contact with capillary parameters.", ((bool,Capillar,false,,"True, if capillar forces need to be added.")) #ifdef YADE_LIQMIGRATION ((bool,LiqMigrEnabled,true,,"True, if liquid migration mechanism is needed. On by default.")) #endif ((Real,Vb,0.0,,"Liquid bridge volume [m^3]")) ((Real,gamma,0.0,,"Surface tension [N/m]")) ((Real,theta,0.0,,"Contact angle [°]")) ((Real,dcap,0.0,,"Damping coefficient for the capillary phase [-]")) ((std::string,CapillarType,"",,"Different types of capillar interaction: Willett_numeric, Willett_analytic [Willett2000]_ , Weigert [Weigert1999]_ , Rabinovich [Rabinov2005]_ , Lambert (simplified, corrected Rabinovich model) [Lambert2008]_ ")), createIndex(); ); REGISTER_CLASS_INDEX(ViscElCapMat,ViscElMat); }; REGISTER_SERIALIZABLE(ViscElCapMat); /// Interaction physics enum CapType {None_Capillar, Willett_numeric, Willett_analytic, Weigert, Rabinovich, Lambert, Soulie}; class ViscElCapPhys : public ViscElPhys{ typedef Real (* CapillarFunction)(const ScGeom& geom, ViscElCapPhys& phys); public: virtual ~ViscElCapPhys(); Real R; YADE_CLASS_BASE_DOC_ATTRS_CTOR(ViscElCapPhys,ViscElPhys,"IPhys created from :yref:`ViscElCapMat`, for use with :yref:`Law2_ScGeom_ViscElCapPhys_Basic`.", ((bool,Capillar,false,,"True, if capillar forces need to be added.")) ((bool,liqBridgeCreated,false,,"Whether liquid bridge was created, only after a normal contact of spheres")) ((bool,liqBridgeActive,false,, "Whether liquid bridge is active at the moment")) ((Real,sCrit,false,,"Critical bridge length [m]")) ((Real,Vb,0.0,,"Liquid bridge volume [m^3]")) ((Real,gamma,0.0,,"Surface tension [N/m]")) ((Real,theta,0.0,,"Contact angle [rad]")) ((CapType,CapillarType,None_Capillar,,"Different types of capillar interaction: Willett_numeric, Willett_analytic, Weigert, Rabinovich, Lambert, Soulie")) ((Real,dcap,0.0,,"Damping coefficient for the capillary phase [-]")) #ifdef YADE_LIQMIGRATION ((bool,LiqMigrEnabled,,,"True, if liquid migration mechanism is needed.")) ((Real,Vmax,0.0,,"Maximal liquid bridge volume [m^3]")) ((Real,Vf1,0.0,, "Liquid which will be returned to the 1st body after rupture [m^3]")) ((Real,Vf2,0.0,, "Liquid which will be returned to the 2nd body after rupture [m^3]")) #endif , createIndex(); ) REGISTER_CLASS_INDEX(ViscElCapPhys,ViscElPhys); }; REGISTER_SERIALIZABLE(ViscElCapPhys); /// Convert material to interaction physics. class Ip2_ViscElCapMat_ViscElCapMat_ViscElCapPhys: public Ip2_ViscElMat_ViscElMat_ViscElPhys { public : virtual void go(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction); YADE_CLASS_BASE_DOC(Ip2_ViscElCapMat_ViscElCapMat_ViscElCapPhys,Ip2_ViscElMat_ViscElMat_ViscElPhys,"Convert 2 instances of :yref:`ViscElCapMat` to :yref:`ViscElCapPhys` using the rule of consecutive connection."); FUNCTOR2D(ViscElCapMat,ViscElCapMat); }; REGISTER_SERIALIZABLE(Ip2_ViscElCapMat_ViscElCapMat_ViscElCapPhys); /// Constitutive law class Law2_ScGeom_ViscElCapPhys_Basic: public LawFunctor { public : virtual bool go(shared_ptr&, shared_ptr&, Interaction*); static Real Willett_numeric_f (const ScGeom& geom, ViscElCapPhys& phys); static Real Willett_analytic_f (const ScGeom& geom, ViscElCapPhys& phys); static Real Weigert_f (const ScGeom& geom, ViscElCapPhys& phys); static Real Rabinovich_f (const ScGeom& geom, ViscElCapPhys& phys); static Real Lambert_f (const ScGeom& geom, ViscElCapPhys& phys); static Real Soulie_f (const ScGeom& geom, ViscElCapPhys& phys); static Real None_f (const ScGeom& geom, ViscElCapPhys& phys); std::deque > CapFunctionsPool; Real critDist(const Real& Vb, const Real& R, const Real& Theta); FUNCTOR2D(ScGeom,ViscElCapPhys); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(Law2_ScGeom_ViscElCapPhys_Basic,LawFunctor,"Extended version of Linear viscoelastic model with capillary parameters.", ((OpenMPAccumulator,VLiqBridg,,Attr::noSave,"The total volume of liquid bridges")) ((OpenMPAccumulator, NLiqBridg,,Attr::noSave,"The total number of liquid bridges")) ,{ //enum CapType {None_Capillar, Willett_numeric, Willett_analytic, Weigert, Rabinovich, Lambert, Soulie}; CapFunctionsPool.resize(20, nullptr); CapFunctionsPool[None_Capillar] = None_f; CapFunctionsPool[Willett_numeric] = Willett_numeric_f; CapFunctionsPool[Willett_analytic] = Willett_analytic_f; CapFunctionsPool[Weigert] = Weigert_f; CapFunctionsPool[Rabinovich] = Rabinovich_f; CapFunctionsPool[Lambert] = Lambert_f; CapFunctionsPool[Soulie] = Soulie_f; } ,/* py */ ; ) DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_ScGeom_ViscElCapPhys_Basic); #ifdef YADE_LIQMIGRATION typedef boost::unordered_map mapBodyInt; typedef boost::unordered_map mapBodyReal; class LiqControl: public PartialEngine{ public: virtual void action(); void addBodyMapInt( mapBodyInt & m, Body::id_t b ); void addBodyMapReal( mapBodyReal & m, Body::id_t b, Real addV ); Real vMax(shared_ptr b1, shared_ptr b2); Real totalLiqVol(int mask) const; Real liqVolBody(id_t id) const; bool addLiqInter(id_t id1, id_t id2, Real liq); void updateLiquid(shared_ptr b); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(LiqControl,PartialEngine,"This engine implements liquid migration model, introduced here [Mani2013]_ . ", ((int,mask,0,, "Bitmask for liquid creation.")) ((Real,liqVolRup,0.,, "Liquid volume (integral value), which has been freed after rupture occured, [m^3].")) ((Real,liqVolShr,0.,, "Liquid volume (integral value), which has been shared among of contacts, [m^3].")) ((Real,vMaxCoef,0.03,, "Coefficient for vMax, [-].")) ((bool,particleconserve,false,, "If True, the particle will have the same liquid volume during simulation e.g. liquid will not migrate [false].")) ,/* ctor */ ,/* py */ .def("totalLiq",&LiqControl::totalLiqVol,(boost::python::arg("mask")=0),"Return total volume of water in simulation.") .def("liqBody",&LiqControl::liqVolBody,(boost::python::arg("id")=-1),"Return total volume of water in body.") .def("addLiqInter",&LiqControl::addLiqInter,(boost::python::arg("id1")=-1, boost::python::arg("id2")=-1, boost::python::arg("liq")=-1),"Add liquid into the interaction.") ); }; Real liqVolIterBody (shared_ptr b); REGISTER_SERIALIZABLE(LiqControl); #endif trunk-2017.01a/pkg/dem/ViscoelasticPM.cpp000066400000000000000000000305531304022710500201070ustar00rootroot00000000000000// 2009 © Sergei Dorofeenko #include"ViscoelasticPM.hpp" #include #include #include #include #include #ifdef YADE_SPH #include #endif using std::isfinite; YADE_PLUGIN((ViscElMat)(ViscElPhys)(Ip2_ViscElMat_ViscElMat_ViscElPhys)(Law2_ScGeom_ViscElPhys_Basic)); /* ViscElMat */ ViscElMat::~ViscElMat(){} /* ViscElPhys */ ViscElPhys::~ViscElPhys(){} Real Ip2_ViscElMat_ViscElMat_ViscElPhys::epsilon = 1.0e-8; /* Ip2_ViscElMat_ViscElMat_ViscElPhys */ void Ip2_ViscElMat_ViscElMat_ViscElPhys::go(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction) { // no updates of an existing contact if(interaction->phys) return; shared_ptr phys (new ViscElPhys()); Calculate_ViscElMat_ViscElMat_ViscElPhys(b1, b2, interaction, phys); interaction->phys = phys; } /* Law2_ScGeom_ViscElPhys_Basic */ bool Law2_ScGeom_ViscElPhys_Basic::go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I) { Vector3r force = Vector3r::Zero(); Vector3r torque1 = Vector3r::Zero(); Vector3r torque2 = Vector3r::Zero(); if (computeForceTorqueViscEl(_geom, _phys, I, force, torque1, torque2) and (I->isActive)) { const int id1 = I->getId1(); const int id2 = I->getId2(); addForce (id1,-force,scene); addForce (id2, force,scene); addTorque(id1, torque1,scene); addTorque(id2, torque2,scene); return true; } else return false; } bool computeForceTorqueViscEl(shared_ptr& _geom, shared_ptr& _phys, Interaction* I, Vector3r & force, Vector3r & torque1, Vector3r & torque2) { ViscElPhys& phys=*static_cast(_phys.get()); const ScGeom& geom=*static_cast(_geom.get()); Scene* scene=Omega::instance().getScene().get(); #ifdef YADE_SPH //======================================================================================================= if (phys.SPHmode) { if (computeForceSPH(_geom, _phys, I, force)) { return true; } else { return false; } } //======================================================================================================= #endif const int id1 = I->getId1(); const int id2 = I->getId2(); if (geom.penetrationDepth<0) { return false; } else { const BodyContainer& bodies = *scene->bodies; const State& de1 = *static_cast(bodies[id1]->state.get()); const State& de2 = *static_cast(bodies[id2]->state.get()); Vector3r& shearForce = phys.shearForce; if (I->isFresh(scene)) shearForce=Vector3r(0,0,0); const Real& dt = scene->dt; shearForce = geom.rotate(shearForce); // Handle periodicity. const Vector3r shift2 = scene->isPeriodic ? scene->cell->intrShiftPos(I->cellDist): Vector3r::Zero(); const Vector3r shiftVel = scene->isPeriodic ? scene->cell->intrShiftVel(I->cellDist): Vector3r::Zero(); const Vector3r c1x = (geom.contactPoint - de1.pos); const Vector3r c2x = (geom.contactPoint - de2.pos - shift2); const Vector3r relativeVelocity = (de1.vel+de1.angVel.cross(c1x)) - (de2.vel+de2.angVel.cross(c2x)) + shiftVel; const Real normalVelocity = geom.normal.dot(relativeVelocity); const Vector3r shearVelocity = relativeVelocity-normalVelocity*geom.normal; // As Chiara Modenese suggest, we store the elastic part // and then add the viscous part if we pass the Mohr-Coulomb criterion. // See http://www.mail-archive.com/yade-users@lists.launchpad.net/msg01391.html shearForce += phys.ks*dt*shearVelocity; // the elastic shear force have a history, but Vector3r shearForceVisc = Vector3r::Zero(); // the viscous shear damping haven't a history because it is a function of the instant velocity // Prevent appearing of attraction forces due to a viscous component // [Radjai2011], page 3, equation [1.7] // [Schwager2007] phys.Fn = phys.kn * geom.penetrationDepth; phys.Fv = phys.cn * normalVelocity; const Real normForceReal = phys.Fn + phys.Fv; if (normForceReal < 0) { phys.normalForce = Vector3r::Zero(); } else { phys.normalForce = normForceReal * geom.normal; } Vector3r momentResistance = Vector3r::Zero(); if (phys.mR>0.0) { const Vector3r relAngVel = de1.angVel - de2.angVel; relAngVel.normalized(); if (phys.mRtype == 1) { momentResistance = -phys.mR*phys.normalForce.norm()*relAngVel; // [Zhou1999536], equation (3) } else if (phys.mRtype == 2) { momentResistance = -phys.mR*(c1x.cross(de1.angVel) - c2x.cross(de2.angVel)).norm()*phys.normalForce.norm()*relAngVel; // [Zhou1999536], equation (4) } } const Real maxFs = phys.normalForce.squaredNorm() * std::pow(phys.tangensOfFrictionAngle,2); if( shearForce.squaredNorm() > maxFs ) { // Then Mohr-Coulomb is violated (so, we slip), // we have the max value of the shear force, so // we consider only friction damping. const Real ratio = sqrt(maxFs) / shearForce.norm(); shearForce *= ratio; } else { // Then no slip occurs we consider friction damping + viscous damping. shearForceVisc = phys.cs*shearVelocity; } force = phys.normalForce + shearForce + shearForceVisc; torque1 = -c1x.cross(force)+momentResistance; torque2 = c2x.cross(force)-momentResistance; return true; } } void Ip2_ViscElMat_ViscElMat_ViscElPhys::Calculate_ViscElMat_ViscElMat_ViscElPhys(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction, shared_ptr phys) { ViscElMat* mat1 = static_cast(b1.get()); ViscElMat* mat2 = static_cast(b2.get()); Real mass1 = 1.0; Real mass2 = 1.0; if ((isfinite(mat1->kn) and not (isfinite(mat2->kn))) or (isfinite(mat2->kn) and not (isfinite(mat1->kn))) or (isfinite(mat1->ks) and not (isfinite(mat2->ks))) or (isfinite(mat2->ks) and not (isfinite(mat1->ks))) or (isfinite(mat1->cn) and not (isfinite(mat2->cn))) or (isfinite(mat2->cn) and not (isfinite(mat1->cn))) or (isfinite(mat1->cs) and not (isfinite(mat2->cs))) or (isfinite(mat2->cs) and not (isfinite(mat1->cs))) or (isfinite(mat1->tc) and not (isfinite(mat2->tc))) or (isfinite(mat2->tc) and not (isfinite(mat1->tc))) or (isfinite(mat1->en) and not (isfinite(mat2->en))) or (isfinite(mat2->en) and not (isfinite(mat1->en))) or (isfinite(mat1->et) and not (isfinite(mat2->et))) or (isfinite(mat2->et) and not (isfinite(mat1->et)))) { throw runtime_error("Both materials should have the same defined set of variables e.g. tc, ks etc.!"); } mass1 = Body::byId(interaction->getId1())->state->mass; mass2 = Body::byId(interaction->getId2())->state->mass; if (mass1 == 0.0 and mass2 > 0.0) { mass1 = mass2; } else if (mass2 == 0.0 and mass1 > 0.0) { mass2 = mass1; } // See [Pournin2001, just below equation (19)] const Real massR = mass1*mass2/(mass1+mass2); GenericSpheresContact* sphCont=YADE_CAST(interaction->geom.get()); Real R1=sphCont->refR1>0?sphCont->refR1:sphCont->refR2; Real R2=sphCont->refR2>0?sphCont->refR2:sphCont->refR1; Real kn1 = 0.0; Real kn2 = 0.0; Real cn1 = 0.0; Real cn2 = 0.0; Real ks1 = 0.0; Real ks2 = 0.0; Real cs1 = 0.0; Real cs2 = 0.0; if (((isfinite(mat1->tc)) and (isfinite(mat1->en)) and (isfinite(mat1->et))) or ((tc) and (en) and (et))) { //Set parameters according to [Pournin2001] const Real Tc = (tc) ? (*tc)(mat1->id,mat2->id) : (mat1->tc+mat2->tc)/2.0; const Real En = (en) ? (*en)(mat1->id,mat2->id) : (mat1->en+mat2->en)/2.0; const Real Et = (et) ? (*et)(mat1->id,mat2->id) : (mat1->et+mat2->et)/2.0; // Factor 2 at the end of each expression is necessary, because we calculate // individual kn1, kn2, ks1, ks2 etc., because kn1 = 2*kn, ks1 = 2*ks // http://www.mail-archive.com/yade-users@lists.launchpad.net/msg08778.html kn1 = kn2 = 1/Tc/Tc * ( Mathr::PI*Mathr::PI + pow(log(En),2) )*massR*2; cn1 = cn2 = -2.0 /Tc * log(En)*massR*2; ks1 = ks2 = 2.0/7.0 /Tc/Tc * ( Mathr::PI*Mathr::PI + pow(log(Et),2) )*massR*2; cs1 = cs2 = -4.0/7.0 /Tc * log(Et)*massR*2; // ^^^ // It seems to be an error in [Pournin2001] (22) Eq.4, missing factor 2 // Thanks to Dominik Boemer for pointing this out // http://www.mail-archive.com/yade-users@lists.launchpad.net/msg08741.html if (std::abs(cn1) <= Mathr::ZERO_TOLERANCE ) cn1=0; if (std::abs(cn2) <= Mathr::ZERO_TOLERANCE ) cn2=0; if (std::abs(cs1) <= Mathr::ZERO_TOLERANCE ) cs1=0; if (std::abs(cs2) <= Mathr::ZERO_TOLERANCE ) cs2=0; } else if ((isfinite(mat1->kn)) and (isfinite(mat1->ks)) and (isfinite(mat1->cn)) and (isfinite(mat1->cs))) { //Set parameters explicitly kn1 = mat1->kn; kn2 = mat2->kn; ks1 = mat1->ks; ks2 = mat2->ks; cn1 = mat1->cn; cn2 = mat2->cn; cs1 = mat1->cs; cs2 = mat2->cs; } else { //Set parameters on the base of young modulus kn1 = 2*mat1->young*R1; kn2 = 2*mat2->young*R2; ks1 = kn1*mat1->poisson; ks2 = kn2*mat2->poisson; if ((isfinite(mat1->cn)) and (isfinite(mat1->cs))) { cn1 = mat1->cn; cn2 = mat2->cn; cs1 = mat1->cs; cs2 = mat2->cs; } else if( isfinite(mat1->en) and isfinite(mat1->et)) { const Real En = (en) ? (*en)(mat1->id,mat2->id) : (mat1->en+mat2->en)/2.0; cn1 = cn2 = 2.0*find_cn_from_en(En, massR,contactParameterCalculation(kn1,kn2),interaction); cs1 = cs2 = 0; } } const Real mR1 = mat1->mR; const Real mR2 = mat2->mR; const int mRtype1 = mat1->mRtype; const int mRtype2 = mat2->mRtype; phys->kn = contactParameterCalculation(kn1,kn2); phys->ks = contactParameterCalculation(ks1,ks2); phys->cn = contactParameterCalculation(cn1,cn2); phys->cs = contactParameterCalculation(cs1,cs2); if ((mR1>0) or (mR2>0)) { phys->mR = 2.0/( ((mR1>0)?1/mR1:0) + ((mR2>0)?1/mR2:0) ); } else { phys->mR = 0; } if (frictAngle) { phys->tangensOfFrictionAngle = std::tan((*frictAngle)(mat1->id,mat2->id)); } else { phys->tangensOfFrictionAngle = std::tan(std::min(mat1->frictionAngle, mat2->frictionAngle)); } phys->shearForce = Vector3r(0,0,0); if ((mRtype1 != mRtype2) or (mRtype1>2) or (mRtype2>2) or (mRtype1<1) or (mRtype2<1) ) { throw runtime_error("mRtype should be equal for both materials and have the values 1 or 2!"); } else { phys->mRtype = mRtype1; } #ifdef YADE_SPH if (mat1->SPHmode and mat2->SPHmode) { phys->SPHmode=true; phys->mu=(mat1->mu+mat2->mu); phys->h=(mat1->h+mat2->h)/2.0; } phys->kernelFunctionCurrentPressure = returnKernelFunction (mat1->KernFunctionPressure, mat2->KernFunctionPressure, Grad); phys->kernelFunctionCurrentVisco = returnKernelFunction (mat1->KernFunctionVisco, mat2->KernFunctionVisco, Lapl); #endif } /* Contact parameter calculation function */ Real contactParameterCalculation(const Real& l1, const Real& l2){ // If one of paramaters > 0. we DO NOT return 0 Real a = (l1?1/l1:0) + (l2?1/l2:0); if (a) return 1/a; else return 0; } Real find_cn_from_en(const Real& en, const Real& m, const Real& kn, const shared_ptr& interaction){ Real eps = Ip2_ViscElMat_ViscElMat_ViscElPhys::epsilon; Real cn = eps ; //initial small value Real en_temp=get_en_from_cn(cn,m ,kn); int i =0; Real error = 1.0/eps; while (error > 1.0e-2 or error!=error){ if(i>15){ cn = 0.; en_temp = 1.; cerr<<"Warning in ViscoelasticPM.cpp : Newton-Raphson algorithm did not converged within 15 iterations for contact between "<id1<<" and "<id2<<". Continue with values : cn="<& b1, const shared_ptr& b2, const shared_ptr& interaction); YADE_CLASS_BASE_DOC_ATTRS(Ip2_ViscElMat_ViscElMat_ViscElPhys,IPhysFunctor,"Convert 2 instances of :yref:`ViscElMat` to :yref:`ViscElPhys` using the rule of consecutive connection.", ((shared_ptr,tc,,,"Instance of :yref:`MatchMaker` determining contact time")) ((shared_ptr,en,,,"Instance of :yref:`MatchMaker` determining restitution coefficient in normal direction")) ((shared_ptr,et,,,"Instance of :yref:`MatchMaker` determining restitution coefficient in tangential direction")) ((shared_ptr,frictAngle,,,"Instance of :yref:`MatchMaker` determining how to compute interaction's friction angle. If ``None``, minimum value is used.")) ); virtual void Calculate_ViscElMat_ViscElMat_ViscElPhys(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction, shared_ptr phys); FUNCTOR2D(ViscElMat,ViscElMat); }; REGISTER_SERIALIZABLE(Ip2_ViscElMat_ViscElMat_ViscElPhys); /// Constitutive law /// This class provides linear viscoelastic contact model class Law2_ScGeom_ViscElPhys_Basic: public LawFunctor { public : virtual bool go(shared_ptr&, shared_ptr&, Interaction*); public : FUNCTOR2D(ScGeom,ViscElPhys); YADE_CLASS_BASE_DOC(Law2_ScGeom_ViscElPhys_Basic,LawFunctor,"Linear viscoelastic model operating on ScGeom and ViscElPhys. " "The contact law is visco-elastic in the normal direction, and visco-elastic frictional in the tangential direction. " "The normal contact is modelled as a spring of equivalent stiffness $k_n$, placed in parallel with a viscous damper " "of equivalent viscosity $c_n$. As for the tangential contact, it is made of a spring-dashpot system (in parallel " "with equivalent stiffness $k_s$ and viscosity $c_s$) in serie with a slider of friction coefficient " "$\\mu = \\tan \\phi$.\n\nThe friction coefficient $\\mu = \\tan \\phi$ is always evaluated as " "$\\tan(\\min(\\phi_1,\\phi_2))$, where $\\phi_1$ and $\\phi_2$ are respectively the friction angle of particle 1 " "and 2. For the other parameters, depending on the material input, the equivalent parameters of the contact " "($K_n$,$C_n$,$K_s$,$C_s$,$\\phi$) are evaluated differently. In the following, the quantities in parenthesis are " "the material constant which are precised for each particle. They are then associated to particle 1 and 2 (e.g. " "$kn_1$,$kn_2$,$cn_1$...), and should not be confused with the equivalent parameters of the contact " "($K_n$,$C_n$,$K_s$,$C_s$,$\\phi$). \n\n - If contact time (tc), normal and tangential restitution coefficient " "(en,et) are precised, the equivalent parameters are evaluated following the formulation of " "Pournin [Pournin2001]_.\n\n - If normal and tangential stiffnesses (kn, ks) and damping constant (cn,cs) " "of each particle are precised, the equivalent stiffnesses and damping constants of each contact made of " "two particles 1 and 2 is made $A = 2\\frac{a_1 a_2}{a_1 + a_2}$, where A is $K_n$, $K_s$, $C_n$ and $C_s$, " "and 1 and 2 refer to the value associated to particle 1 and 2.\n\n - Alternatively it is possible to precise " "the Young modulus (young) and poisson's ratio (poisson) instead of the normal and spring constant (kn and ks). " "In this case, the equivalent parameters are evaluated the same way as the previous case with $kn_x = E_x d_x$, " "$ks_x = v_x kn_x$, where $E_x$, $v_x$ and $d_x$ are Young modulus, poisson's ratio and diameter of particle x. " "\n\n - If Yound modulus (young), poisson's ratio (poisson), normal and tangential restitution coefficient (en,et) " "are precised, the equivalent stiffnesses are evaluated as previously: $K_n = 2\\frac{kn_1 kn_2}{kn_1 + kn_2}$, " "$kn_x = E_x d_x$, $K_s = 2(ks_1 ks_2)/(ks_1 + ks_2)$, $ks_x = v kn_x$. The damping constant is computed at each " "contact in order to fulfill the normal restitution coefficient $e_n = (en_1 en_2)/(en_1 + en_2)$. This is " "achieved resolving numerically equation 21 of [Schwager2007]_ (There is in fact a mistake in the article from " "equation 18 to 19, so that there is a change in sign). Be careful in this configuration the tangential " "restitution coefficient is set to 1 (no tangential damping). This formulation imposes directly the normal " "restitution coefficient of the collisions instead of the damping constant."); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_ScGeom_ViscElPhys_Basic); Real contactParameterCalculation(const Real& l1,const Real& l2); bool computeForceTorqueViscEl(shared_ptr& _geom, shared_ptr& _phys, Interaction* I, Vector3r & force, Vector3r & torque1, Vector3r & torque2); Real get_en_from_cn(const Real& cn, const Real& m, const Real& kn); Real find_cn_from_en(const Real& en, const Real& m, const Real& kn, const shared_ptr& interaction); trunk-2017.01a/pkg/dem/WirePM.cpp000066400000000000000000000305261304022710500163650ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2010 by Klaus Thoeni * * klaus.thoeni@newcastle.edu.au * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include"WirePM.hpp" #include #include #include #include "../../lib/base/Math.hpp" #include #include #include #include YADE_PLUGIN((WireMat)(WireState)(WirePhys)(Ip2_WireMat_WireMat_WirePhys)(Law2_ScGeom_WirePhys_WirePM)); /********************** WireMat ****************************/ CREATE_LOGGER(WireMat); void WireMat::postLoad(WireMat&){ //BUG: ????? postLoad is called twice, LOG_TRACE( "WireMat::postLoad - update material parameters" ); // compute cross-section area for single wire as = pow(diameter*0.5,2)*Mathr::PI; // check for stress strain curve for single wire if(strainStressValues.empty()) return; // uninitialized object, don't do nothing at all if(strainStressValues.size() < 2) throw std::invalid_argument("WireMat.strainStressValues: at least two points must be given."); if(strainStressValues[0](0) == 0. && strainStressValues[0](1) == 0.) throw std::invalid_argument("WireMat.strainStressValues: Definition must start with values greater than zero (strain>0,stress>0)"); switch(type) { case 0: LOG_DEBUG("WireMat - Bertrand's approach"); if(!strainStressValuesDT.empty()) throw std::invalid_argument("Use of WireMat.strainStressValuesDT has no effect!"); break; case 1: // check stress strain curve four double twist if type=1 LOG_DEBUG("WireMat - New approach with two curves"); if(isDoubleTwist) { if(strainStressValuesDT.empty()) throw runtime_error("WireMat.strainStressValuesDT not defined"); if(strainStressValuesDT.size() < 2) throw std::invalid_argument("WireMat.strainStressValuesDT: at least two points must be given."); if(strainStressValuesDT[0](0) == 0. && strainStressValuesDT[0](1)) throw std::invalid_argument("WireMat.strainStressValuesDT: Definition must start with values greater than zero (strain>0,stress>0)"); } break; case 2: // check stress strain curve four double twist if type=2 LOG_DEBUG("WireMat - New approach with two curves and initial shift"); if(isDoubleTwist) { if(strainStressValuesDT.empty()) throw runtime_error("WireMat.strainStressValuesDT not defined"); if(strainStressValuesDT.size() < 2) throw std::invalid_argument("WireMat.strainStressValuesDT: at least two points must be given."); if(strainStressValuesDT[0](0) == 0. && strainStressValuesDT[0](1)) throw std::invalid_argument("WireMat.strainStressValuesDT: Definition must start with values greater than zero (strain>0,stress>0)"); } break; default: throw std::invalid_argument("WireMat.type: Type must be 0, 1 or 2."); break; } } /********************** Law2_ScGeom_WirePhys_WirePM ****************************/ CREATE_LOGGER(Law2_ScGeom_WirePhys_WirePM); bool Law2_ScGeom_WirePhys_WirePM::go(shared_ptr& ig, shared_ptr& ip, Interaction* contact){ LOG_TRACE( "Law2_ScGeom_WirePhys_WirePM::go - contact law" ); ScGeom* geom = static_cast(ig.get()); WirePhys* phys = static_cast(ip.get()); const int &id1 = contact->getId1(); const int &id2 = contact->getId2(); Body* b1 = Body::byId(id1,scene).get(); Body* b2 = Body::byId(id2,scene).get(); Real displN = geom->penetrationDepth; // NOTE: ScGeom -> penetrationDepth>0 when spheres interpenetrate, and therefore, for wire always negative /* get reference to values since values are updated/changed in order to take unloading into account */ vector &DFValues = phys->displForceValues; vector &kValues = phys->stiffnessValues; Real kn = phys->kn; Real D = displN - phys->initD; // interparticular distance is computed depending on the equilibrium distance /* check whether the particles are linked or not */ if ( !phys->isLinked ) { // destroy the interaction before calculation return false; } if ( (phys->isLinked) && (D < DFValues.back()(0)) ) { // spheres are linked but failure because of reaching maximal admissible displacement phys->isLinked=false; // update body state with the number of broken links WireState* st1=dynamic_cast(b1->state.get()); WireState* st2=dynamic_cast(b2->state.get()); st1->numBrokenLinks+=1; st2->numBrokenLinks+=1; return false; } /* compute normal force Fn */ Real Fn = 0.; if ( D > DFValues[0](0) ) { // unloading LOG_TRACE("WirePM: Unloading"); Fn = kn * (D-phys->plastD); } else { // loading LOG_TRACE("WirePM: Loading"); for (unsigned int i=1; i DFValues[i](0) ) { Fn = DFValues[i-1](1) + (D-DFValues[i-1](0))*kValues[i-1]; phys->plastD = D - Fn/kn; // update values for unloading DFValues[0](0) = D; DFValues[0](1) = Fn; break; } } } /* compression forces cannot be applied to wires */ if (Fn > 0.) Fn = 0.; TRVAR3( displN, D, Fn ); phys->normalForce = Fn*geom->normal; // NOTE: normal is position2-position1 - It is directed from particle1 to particle2 /* compute a limit value to check how far the interaction is from failing */ Real limitFactor = 0.; if (Fn < 0.) limitFactor = std::abs(D/(DFValues.back()(0))); phys->limitFactor = limitFactor; State* st1 = Body::byId(id1,scene)->state.get(); State* st2 = Body::byId(id2,scene)->state.get(); /* apply forces */ Vector3r f = phys->normalForce; // these lines to adapt to periodic boundary conditions if ( !scene->isPeriodic ) applyForceAtContactPoint(f , geom->contactPoint , id2, st2->se3.position, id1, st1->se3.position); else { // in scg we do not wrap particles positions, hence "applyForceAtContactPoint" cannot be used when scene is periodic scene->forces.addForce(id1,-f); scene->forces.addForce(id2,f); } /* set shear force to zero */ phys->shearForce = Vector3r::Zero(); return true; } /********************** Ip2_WireMat_WireMat_WirePhys ****************************/ CREATE_LOGGER(Ip2_WireMat_WireMat_WirePhys); void Ip2_WireMat_WireMat_WirePhys::go(const shared_ptr& b1, const shared_ptr& b2, const shared_ptr& interaction){ /* avoid any updates if interactions which already exist */ if(interaction->phys) return; //TODO: make boolean to make sure physics are never updated, optimisation of contact detection mesh (no contact detection after link is created) LOG_TRACE( "Ip2_WireMat_WireMat_WirePhys::go - create interaction physics" ); ScGeom* geom=dynamic_cast(interaction->geom.get()); assert(geom); /* set equilibrium distance, e.g. initial distance between particle (stress free state) */ shared_ptr contactPhysics(new WirePhys()); Real initD = geom->penetrationDepth; contactPhysics->normalForce = Vector3r::Zero(); /* get values from material */ const shared_ptr& mat1 = YADE_PTR_CAST(b1); const shared_ptr& mat2 = YADE_PTR_CAST(b2); Real crossSection; vector SSValues; /* check properties of interaction */ if ( mat1->id == mat2->id ) { // interaction of two bodies of the same material crossSection = mat1->as; SSValues = mat1->strainStressValues; if ( (mat1->isDoubleTwist) && (std::abs(interaction->getId1()-interaction->getId2())==1) ) {// bodies which id differs by 1 are double twisted contactPhysics->isDoubleTwist = true; if ( mat1->type==1 || mat1->type==2 ) { SSValues = mat1->strainStressValuesDT; crossSection *= 2.; } } else { contactPhysics->isDoubleTwist = false; } } else { // interaction of two bodies of two different materials, take weaker material and no double-twist contactPhysics->isDoubleTwist = false; if ( mat1->diameter <= mat2->diameter){ crossSection = mat1->as; SSValues = mat1->strainStressValues; } else { crossSection = mat2->as; SSValues = mat2->strainStressValues; } } Real R1 = geom->radius1; Real R2 = geom->radius2; Real l0 = R1 + R2 - initD; // initial length of the wire (can be single or double twisted) /* compute displacement-force values */ vector DFValues; vector kValues; Real dl = 0.; bool isShifted = false; /* account for random distortion if type=2 */ if ( mat1->type==2 ) { isShifted = true; if (mat1->seed==-1) dl = l0*mat1->lambdau; else { // initialize random number generator static boost::minstd_rand randGen(mat1->seed!=0?mat1->seed:(int)TimingInfo::getNow(true)); static boost::variate_generator > rnd(randGen, boost::triangle_distribution(0,0.5,1)); Real rndu = rnd(); TRVAR1( rndu ); dl = l0*mat1->lambdau*rndu; isShifted = true; } } else if ( mat2->type==2 ) { isShifted = true; if (mat2->seed==-1) dl = l0*mat2->lambdau; else { // initialize random number generator static boost::minstd_rand randGen(mat2->seed!=0?mat2->seed:(int)TimingInfo::getNow(true)); static boost::variate_generator > rnd(randGen, boost::triangle_distribution(0,0.5,1)); Real rndu = rnd(); TRVAR1( rndu ); dl = l0*mat2->lambdau*rndu; } } contactPhysics->dL=dl; contactPhysics->isShifted=isShifted; // update geometry values l0 += dl; contactPhysics->initD = initD; /* compute threshold displacement-force values (tension negative since ScGem is used!) */ for ( vector::iterator it = SSValues.begin(); it != SSValues.end(); it++ ) { Vector2r values = Vector2r::Zero(); // values(0) = -(*it)(0)*l0; values(0) = -(*it)(0)*l0-dl; values(1) = -(*it)(1)*crossSection; DFValues.push_back(values); } /* compute elastic stiffness for unloading*/ Real k = DFValues[0](1) / (DFValues[0](0)+dl); /* update values if the interaction is a double twist and type=0 */ if ( contactPhysics->isDoubleTwist && mat1->type==0 ) { // type=0 (force displacement values are computed by manipulating the values of the single wire by using the parameters lambdak and lambdaEps) Real alpha = atan( l0 / (3.*Mathr::PI*mat1->diameter) ); Real kh = k * ( l0*mat1->diameter/crossSection ) / ( 48.*cos(alpha) * ( 41./9.*(1.+mat1->poisson) + 17./4.*pow(tan(alpha),2) ) ); k = 2. * ( mat1->lambdak*kh + (1-mat1->lambdak)*k ); Real F = k * DFValues[0](0); Real mappingF = F/DFValues[0](1); DFValues[0](1) = F; for (unsigned int i = 1; ilambdaEps; DFValues[i](1) *= mappingF; } } else { // type=1 and type=2 (force displacement values have already been computed by given stress-strain curve) } /* store elastic/unloading stiffness as kn in physics */ contactPhysics->kn = k; contactPhysics->ks = 0.; TRVAR1( k ); /* consider an additional point for the initial shift if type==2 */ if ( mat1->type==2 ) { Vector2r values = Vector2r::Zero(); values(0) = -dl+mat1->lambdaF*(DFValues[0](0)+dl); values(1) = DFValues[0](1)*mat1->lambdaF; k = values(1) / values(0); if ( mat1->lambdaF<1. ) DFValues.insert( DFValues.begin(), values ); } else if ( mat2->type==2 ) { Vector2r values = Vector2r::Zero(); values(0) = -dl+mat2->lambdaF*(DFValues[0](0)+dl); values(1) = DFValues[0](1)*mat2->lambdaF; k = values(1) / values(0); if ( mat2->lambdaF<1. ) DFValues.insert( DFValues.begin(), values ); } /* compute stiffness-values of wire */ kValues.push_back(k); for( unsigned int i = 1 ; i < DFValues.size(); i++ ) { Real deltau = -DFValues[i](0) + DFValues[i-1](0); Real deltaF = -DFValues[i](1) + DFValues[i-1](1); k = deltaF/deltau; kValues.push_back(k); } /* add zero values for first point */ DFValues.insert( DFValues.begin(), Vector2r::Zero() ); /* store values in physics */ contactPhysics->displForceValues = DFValues; contactPhysics->stiffnessValues = kValues; /* set particles as linked */ if ( (scene->iter < linkThresholdIteration)) contactPhysics->isLinked=true; else contactPhysics->isLinked=false; interaction->phys = contactPhysics; } WirePhys::~WirePhys(){} trunk-2017.01a/pkg/dem/WirePM.hpp000066400000000000000000000211261304022710500163660ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2010 by Klaus Thoeni * * klaus.thoeni@newcastle.edu.au * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ /** === OVERVIEW OF WirePM === A particle model to simulate single wires and rockfall meshes (see Bertrad et al. 2005, Bertrad et al. 2008, Thoeni et al. 2013). Features of the interaction law: 1. The law is designed for particles which do not touch. A link will be created by defining an interaction radius and running the threshold iteration. 2. The contact law is for tension only. Compressive forces never exist between the particles. However, elastic unloading is considered. 3. The force displacement curve which defines the interaction forces is piecewise linear and defined by the stress-strain curve of the wire material. Any piecewise linear curve can be used. 4. Three different types of wire models are available. */ #pragma once #include #include #include #include /** This class holds information associated with each body state*/ class WireState: public State { YADE_CLASS_BASE_DOC_ATTRS_CTOR(WireState,State,"Wire state information of each body.\n\nNone of that is used for computation (at least not now), only for post-processing.", ((int,numBrokenLinks,0,,"Number of broken links (e.g. number of wires connected to the body which are broken). [-]")) , createIndex(); ); REGISTER_CLASS_INDEX(WireState,State); }; REGISTER_SERIALIZABLE(WireState); /** This class holds information associated with each body */ class WireMat: public FrictMat { public: virtual shared_ptr newAssocState() const { return shared_ptr(new WireState); } virtual bool stateTypeOk(State* s) const { return (bool)dynamic_cast(s); } void postLoad(WireMat&); YADE_CLASS_BASE_DOC_ATTRS_CTOR(WireMat,FrictMat,"Material for use with the Wire classes. In conjunction with the corresponding functors it can be used to model steel wire meshes [Thoeni2014]_, geotextiles [Cheng2016]_ and more.", ((Real,diameter,0.0027,,"Diameter of the single wire in [m] (the diameter is used to compute the cross-section area of the wire).")) ((unsigned int,type,0,,"Three different types are considered:\n\n" "== ===============================================================\n" "0 Corresponds to Bertrand's approach (see [Bertrand2008]_): only one stress-strain curve is used\n" "1 New approach: two separate stress-strain curves can be used (see [Thoeni2013]_)\n" "2 New approach with stochastically distorted contact model: two separate stress-strain curves with changed initial stiffness and horizontal shift (shift is random if $\\text{seed}\\geq0$, for more details see [Thoeni2013]_)\n" "== ===============================================================\n\n" "By default the type is 0." )) ((vector,strainStressValues,,Attr::triggerPostLoad,"Piecewise linear definition of the stress-strain curve by set of points (strain[-]>0,stress[Pa]>0) for one single wire. Tension only is considered and the point (0,0) is not needed! NOTE: Vector needs to be initialized!")) ((vector,strainStressValuesDT,,Attr::triggerPostLoad,"Piecewise linear definition of the stress-strain curve by set of points (strain[-]>0,stress[Pa]>0) for the double twist. Tension only is considered and the point (0,0) is not needed! If this value is given the calculation will be based on two different stress-strain curves without considering the parameter introduced by [Bertrand2008]_ (see [Thoeni2013]_).")) ((bool,isDoubleTwist,false,,"Type of the mesh. If true two particles of the same material which body ids differ by one will be considered as double-twisted interaction.")) ((Real,lambdaEps,0.47,,"Parameter between 0 and 1 to reduce strain at failure of a double-twisted wire (as used by [Bertrand2008]_). [-]")) ((Real,lambdak,0.73,,"Parameter between 0 and 1 to compute the elastic stiffness of a double-twisted wire (as used by [Bertrand2008]_): $k^D=2(\\lambda_k k_h + (1-\\lambda_k)k^S)$. [-]")) ((int,seed,12345,,"Integer used to initialize the random number generator for the calculation of the distortion. If the integer is equal to 0 a internal seed number based on the time is computed. [-]")) ((Real,lambdau,0.2,,"Parameter between 0 and 1 introduced by [Thoeni2013]_ which defines the maximum shift of the force-displacement curve in order to take an additional initial elongation (e.g. wire distortion/imperfections, slipping, system flexibility) into account: $\\Delta l^*=\\lambda_u l_0 \\text{rnd(seed)}$. [-]")) ((Real,lambdaF,1.0,,"Parameter between 0 and 1 introduced by [Thoeni2013]_ which defines where the shifted force-displacement curve intersects with the new initial stiffness: $F^*=\\lambda_F F_{\\text{elastic}}$. [-]")) ((Real,as,0.,Attr::readonly,"Cross-section area of a single wire used to transform stress into force. [m²]")) , createIndex(); ); DECLARE_LOGGER; REGISTER_CLASS_INDEX(WireMat,FrictMat); }; REGISTER_SERIALIZABLE(WireMat); /** This class holds information associated with each interaction */ // NOTE: even if WirePhys has no shear force it is derived from FrictPhys since all implemented functions (e.g. unbalancedForce) work properly for FrictPhys only class WirePhys: public FrictPhys { public: virtual ~WirePhys(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(WirePhys,FrictPhys,"Representation of a single interaction of the WirePM type, storage for relevant parameters", ((Real,initD,0.,,"Equilibrium distance for particles. Computed as the initial inter-particular distance when particle are linked.")) ((bool,isLinked,false,,"If true particles are linked and will interact. Interactions are linked automatically by the definition of the corresponding interaction radius. The value is false if the wire breaks (no more interaction).")) ((bool,isDoubleTwist,false,,"If true the properties of the interaction will be defined as a double-twisted wire.")) ((vector,displForceValues,,Attr::readonly,"Defines the values for force-displacement curve.")) ((vector,stiffnessValues,,Attr::readonly,"Defines the values for the various stiffnesses (the elastic stiffness is stored as kn).")) ((Real,plastD,0.,Attr::readonly,"Plastic part of the inter-particular distance of the previous step. \n\n.. note::\n\t Only elastic displacements are reversible (the elastic stiffness is used for unloading) and compressive forces are inadmissible. The compressive stiffness is assumed to be equal to zero.\n\n..")) ((Real,limitFactor,0.,Attr::readonly,"This value indicates on how far from failing the wire is, e.g. actual normal displacement divided by admissible normal displacement.")) ((bool,isShifted,false,Attr::readonly,"If true :yref:`WireMat` type=2 and the force-displacement curve will be shifted.")) ((Real,dL,0.,Attr::readonly,"Additional wire length for considering the distortion for :yref:`WireMat` type=2 (see [Thoeni2013]_).")) , createIndex(); , ); DECLARE_LOGGER; REGISTER_CLASS_INDEX(WirePhys,FrictPhys); }; REGISTER_SERIALIZABLE(WirePhys); /** 2d functor creating IPhys (Ip2) taking WireMat and WireMat of 2 bodies, returning type WirePhys */ class Ip2_WireMat_WireMat_WirePhys: public IPhysFunctor{ public: virtual void go(const shared_ptr& pp1, const shared_ptr& pp2, const shared_ptr& interaction); FUNCTOR2D(WireMat,WireMat); YADE_CLASS_BASE_DOC_ATTRS(Ip2_WireMat_WireMat_WirePhys,IPhysFunctor,"Converts 2 :yref:`WireMat` instances to :yref:`WirePhys` with corresponding parameters.", ((int,linkThresholdIteration,1,,"Iteration to create the link.")) ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Ip2_WireMat_WireMat_WirePhys); /** 2d functor creating the interaction law (Law2) based on SphereContactGeometry (ScGeom) and WirePhys of 2 bodies, returning type WirePM */ class Law2_ScGeom_WirePhys_WirePM: public LawFunctor{ public: virtual bool go(shared_ptr& _geom, shared_ptr& _phys, Interaction* I); FUNCTOR2D(ScGeom,WirePhys); YADE_CLASS_BASE_DOC_ATTRS(Law2_ScGeom_WirePhys_WirePM,LawFunctor,"Constitutive law for the wire model.", ((int,linkThresholdIteration,1,,"Iteration to create the link.")) ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(Law2_ScGeom_WirePhys_WirePM); trunk-2017.01a/pkg/dem/deformablecohesive/000077500000000000000000000000001304022710500203365ustar00rootroot00000000000000trunk-2017.01a/pkg/dem/deformablecohesive/Bo1_DeformableElement_Aabb.cpp000066400000000000000000000046531304022710500260320ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include #include #include void Bo1_DeformableElement_Aabb::go(const shared_ptr& cm, shared_ptr& bv, const Se3r& se3, const Body* b){ DeformableElement* deformableElement = static_cast(cm.get()); if(!bv){ bv=shared_ptr(new Aabb); } Aabb* aabb=static_cast(bv.get()); Vector3r min,max; //Not sure this is the best of all possible algorithms, therefore, I think it can be improved for (DeformableElement::NodeMap::iterator it = deformableElement->localmap.begin(); it != deformableElement->localmap.end(); it++) { if(it->first->state->pos(0)first->state->pos(0); } if(it->first->state->pos(1)first->state->pos(1); } if(it->first->state->pos(0)first->state->pos(2); } if(it->first->state->pos(0)>max(0)) { max(0)=it->first->state->pos(0); } if(it->first->state->pos(1)>max(1)) { max(1)=it->first->state->pos(1); } if(it->first->state->pos(2)>max(2)) { max(2)=it->first->state->pos(2); } } aabb->min=min; aabb->max=max; // if(!scene->isPeriodic){ // aabb->min=se3.position-halfSize; aabb->max=se3.position+halfSize; // return; // } // // adjust box size along axes so that DeformableElement doesn't stick out of the box even if sheared (i.e. parallelepiped) // if(scene->cell->hasShear()) { // Vector3r refHalfSize(halfSize); // const Vector3r& cos=scene->cell->getCos(); // for(int i=0; i<3; i++){ // //cerr<<"cos["<min = scene->cell->unshearPt(se3.position)-halfSize; // aabb->max = scene->cell->unshearPt(se3.position)+halfSize; } YADE_PLUGIN((Bo1_DeformableElement_Aabb)); trunk-2017.01a/pkg/dem/deformablecohesive/Bo1_DeformableElement_Aabb.hpp000066400000000000000000000025721304022710500260350ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include class Bo1_DeformableElement_Aabb : public BoundFunctor { public : void go(const shared_ptr& cm, shared_ptr& bv, const Se3r&, const Body*); FUNCTOR1D(DeformableElement); YADE_CLASS_BASE_DOC_ATTRS(Bo1_DeformableElement_Aabb,BoundFunctor,"Functor creating :yref:`Aabb` from :yref:`DeformableElement`.", ((Real,aabbEnlargeFactor,((void)"deactivated",-1),,"Relative enlargement of the bounding box; deactivated if negative.\n\n.. note::\n\tThis attribute is used to create distant interaction, but is only meaningful with an :yref:`IGeomFunctor` which will not simply discard such interactions: :yref:`Ig2_Sphere_Sphere_ScGeom::interactionDetectionFactor` should have the same value as :yref:`aabbEnlargeFactor`.")) ); }; REGISTER_SERIALIZABLE(Bo1_DeformableElement_Aabb); trunk-2017.01a/pkg/dem/deformablecohesive/Bo1_Node_Aabb.cpp000066400000000000000000000032001304022710500233300ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include #include #include void Bo1_Node_Aabb::go(const shared_ptr& cm, shared_ptr& bv, const Se3r& se3, const Body* b){ Node* node = static_cast(cm.get()); if(!bv){ bv=shared_ptr(new Aabb); } Aabb* aabb=static_cast(bv.get()); Vector3r halfSize = (aabbEnlargeFactor>0?aabbEnlargeFactor:1.)*Vector3r(node->radius,node->radius,node->radius); if(!scene->isPeriodic){ aabb->min=se3.position-halfSize; aabb->max=se3.position+halfSize; return; } // adjust box size along axes so that Node doesn't stick out of the box even if sheared (i.e. parallelepiped) if(scene->cell->hasShear()) { Vector3r refHalfSize(halfSize); const Vector3r& cos=scene->cell->getCos(); for(int i=0; i<3; i++){ //cerr<<"cos["<min = scene->cell->unshearPt(se3.position)-halfSize; aabb->max = scene->cell->unshearPt(se3.position)+halfSize; } YADE_PLUGIN((Bo1_Node_Aabb)); trunk-2017.01a/pkg/dem/deformablecohesive/Bo1_Node_Aabb.hpp000066400000000000000000000024541304022710500233470ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include class Bo1_Node_Aabb : public BoundFunctor { public : void go(const shared_ptr& cm, shared_ptr& bv, const Se3r&, const Body*); FUNCTOR1D(Node); YADE_CLASS_BASE_DOC_ATTRS(Bo1_Node_Aabb,BoundFunctor,"Functor creating :yref:`Aabb` from :yref:`Node`.", ((Real,aabbEnlargeFactor,((void)"deactivated",-1),,"Relative enlargement of the bounding box; deactivated if negative.\n\n.. note::\n\tThis attribute is used to create distant interaction, but is only meaningful with an :yref:`IGeomFunctor` which will not simply discard such interactions: :yref:`Ig2_Sphere_Sphere_ScGeom::interactionDetectionFactor` should have the same value as :yref:`aabbEnlargeFactor`.")) ); }; REGISTER_SERIALIZABLE(Bo1_Node_Aabb); trunk-2017.01a/pkg/dem/deformablecohesive/CohesiveMat.cpp000066400000000000000000000015141304022710500232520ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include YADE_PLUGIN((CohesiveDeformableElementMaterial)(LinCohesiveElasticMaterial)(LinCohesiveStiffPropDampElastMat)); CohesiveDeformableElementMaterial::~CohesiveDeformableElementMaterial(void){} LinCohesiveElasticMaterial::~LinCohesiveElasticMaterial(void){} LinCohesiveStiffPropDampElastMat::~LinCohesiveStiffPropDampElastMat(void){} trunk-2017.01a/pkg/dem/deformablecohesive/CohesiveMat.hpp000066400000000000000000000041751304022710500232650ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include /*! Elastic material */ class CohesiveDeformableElementMaterial: public Material{ public: virtual ~CohesiveDeformableElementMaterial(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(CohesiveDeformableElementMaterial,Material,"Deformable Element Material.", // ((Real,density,1,,"Density of the material.")) , /*ctor*/ createIndex(); ); REGISTER_CLASS_INDEX(CohesiveDeformableElementMaterial,Material); }; REGISTER_SERIALIZABLE(CohesiveDeformableElementMaterial); class LinCohesiveElasticMaterial: public CohesiveDeformableElementMaterial{ public: virtual ~LinCohesiveElasticMaterial(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(LinCohesiveElasticMaterial,CohesiveDeformableElementMaterial,"Linear Isotropic Elastic material", ((Real,youngmodulus,.78e5,,"Young's modulus. Initially aluminium.")) ((Real,poissonratio,.33,,"Poisson ratio. Initially aluminium.")), createIndex(); ); REGISTER_CLASS_INDEX(LinCohesiveElasticMaterial,CohesiveDeformableElementMaterial); }; REGISTER_SERIALIZABLE(LinCohesiveElasticMaterial); /*Stiffness proportional damping material*/ class LinCohesiveStiffPropDampElastMat: public LinCohesiveElasticMaterial{ public: virtual ~LinCohesiveStiffPropDampElastMat(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(LinCohesiveStiffPropDampElastMat,LinCohesiveElasticMaterial,"Elastic material with Rayleigh Damping.", ((Real,alpha,0,,"Mass propotional damping constant of Rayleigh Damping.")) ((Real,beta,0,,"Stiffness propotional damping constant of Rayleigh Damping.")), createIndex(); ); REGISTER_CLASS_INDEX(LinCohesiveStiffPropDampElastMat,LinCohesiveElasticMaterial); }; REGISTER_SERIALIZABLE(LinCohesiveStiffPropDampElastMat); trunk-2017.01a/pkg/dem/deformablecohesive/DeformableCohesiveElement.cpp000066400000000000000000000053421304022710500261060ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include #include #include #include #include #include #include #include DeformableCohesiveElement::~DeformableCohesiveElement(){ } YADE_PLUGIN((DeformableCohesiveElement)); CREATE_LOGGER(DeformableCohesiveElement); void DeformableCohesiveElement::addPair(const shared_ptr& nodeBody1,const shared_ptr& nodeBody2) { const shared_ptr node1=YADE_PTR_CAST(nodeBody1->shape);//Should be checked dynamically otherwise it will always cast: every shape is castable to Node shape const shared_ptr node2=YADE_PTR_CAST(nodeBody2->shape);//Should be checked dynamically otherwise it will always cast: every shape is castable to Node shape Body::id_t subId1=nodeBody1->getId(); Body::id_t subId2=nodeBody2->getId(); if(node1||node2){} else{ throw std::invalid_argument(("One of the nodes that is given is not a Node therefore cannot be added to the cohesive deformable element "));} if(subId1<0||subId2<0){throw std::invalid_argument(("One of the node that is given is not a member of the scene therefore it has no state, not adding exiting"));} if(this->localmap.count(nodeBody1)!=0) throw std::invalid_argument(("Node that has Body id #"+boost::lexical_cast(subId1)+" is already part of this cohesive deformable element")); if(this->localmap.count(nodeBody2)!=0) throw std::invalid_argument(("Node that has Body id #"+boost::lexical_cast(subId2)+" is already part of this cohesive deformable element")); nodepair pair; pair.node1=nodeBody1; pair.node2=nodeBody2; this->nodepairs[pair]=Se3r(); // Add body to localmap this->nodepairs[pair].position=nodeBody1->state->pos-nodeBody2->state->pos;// Initial difference on positions return; } void DeformableCohesiveElement::delPair(const shared_ptr& node1,const shared_ptr& node2) { // erase the subBody; removing body that is not part of the element throws // if(this->localmap.erase(subBody)!=1) throw std::invalid_argument(("Node #"+boost::lexical_cast(subBody->id)+" not a part of the deformable element, not removing...").c_str()); // LOG_DEBUG("Removed node #"<id); } trunk-2017.01a/pkg/dem/deformablecohesive/DeformableCohesiveElement.hpp000066400000000000000000000062571304022710500261210ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include #include //#include //Node shape /* Before starting the implementation of the deformable element, I am really dissappointed that deformableelement's algorithm relies on its shape. Shape means "shape" and I think it should not contain any other physical meaning or anything else. With respect to this view; The deformable element class is derived from the body and knows the information of its members that are node shaped bodies. */ //class NewtonIntegrator; class DeformableCohesiveElement: public DeformableElement { public: struct nodepair:public Serializable{ public: YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(nodepair,Serializable,"Geometry of a body", ((shared_ptr,node1,,,"Node1 of node pair")) ((shared_ptr,node2,,,"Node2 of node pair")), /*ctor*/, /*py*/ ); // Comparison operator for table sorting. bool operator<(const nodepair& param) const { if (node1.get() < param.node1.get()) return true; if (node1.get() > param.node1.get()) return false; if (node2.get() < param.node2.get()) return true; if (node2.get() > param.node2.get()) return false; LOG_ERROR("Incomplete 'if' sequence"); return false; } }; typedef std::map NodePairsMap;//Initial node differences typedef std::map localTriad;//Updated on every step unsigned int max_pair; Matrix calculateStiffness(Real, Real ,Vector3r,Vector3r,Vector3r,Vector3r); Matrix calculateMassMatrix(Real, Real); virtual ~DeformableCohesiveElement(); void initialize(void){max_pair=3;} void addPair(const shared_ptr& node1,const shared_ptr& node2); void delPair(const shared_ptr& node1,const shared_ptr& node2); YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(DeformableCohesiveElement,DeformableElement,"Tetrahedral Deformable Element Composed of Nodes", ((NodePairsMap,nodepairs,,,"Ids and relative position+orientation difference of members of the cohesive deformable element in the inital condition (should not be accessed directly)")) , , createIndex(); /*ctor*/ initialize(); , /*py*/ .def("addPair",&DeformableCohesiveElement::addPair,"Add a node shared_pt<:yref:'Body'>& as into the element") .def("removePair",&DeformableCohesiveElement::delPair,"Add a node shared_pt<:yref:'Body'>& as into the element") ); DECLARE_LOGGER; REGISTER_CLASS_INDEX(DeformableCohesiveElement,DeformableElement); }; // necessary using namespace yade; REGISTER_SERIALIZABLE(DeformableCohesiveElement); trunk-2017.01a/pkg/dem/deformablecohesive/DeformableElement.cpp000066400000000000000000000070741304022710500244240ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include #include #include #include #include #include #include #include #include DeformableElement::~DeformableElement(){ } YADE_PLUGIN((DeformableElement)); boost::python::dict DeformableElement::localmap_get(){ boost::python::dict ret; FOREACH(NodeMap::value_type& b, localmap){ ret[b.first]=boost::python::make_tuple(b.second.position,b.second.orientation); } return ret; } void DeformableElement::addFace(Vector3r& indexes){ faces.push_back(indexes); } //std::vector DeformableElement::getDisplacements(void) //{ // //} shared_ptr DeformableElement::getNode(int id){ NodeMap::iterator i1(this->localmap.begin()); std::advance(i1,id); return i1->first; } void DeformableElement::removeLastFace(void){ faces.pop_back(); } void DeformableElement::addNode(const shared_ptr& nodeBody){ if(this->localmap.size()==maxNodeCount) { std::string errormessage ="This element cannot hold more than"+ boost::lexical_cast(maxNodeCount); throw std::out_of_range(errormessage); return; } const shared_ptr node=YADE_PTR_CAST(nodeBody->shape);//Should be checked dynamically otherwise it will always cast: every shape is castable to Node shape Body::id_t subId=nodeBody->getId(); if(node){} else{ throw std::invalid_argument(("The body that is given #"+boost::lexical_cast(subId)+" is not a Node therefore cannot be added to the deformable element "));} if(subId<0){throw std::invalid_argument(("The Node that is given is not a member of the scene therefore it has no state, not adding exiting"));} if(this->localmap.count(nodeBody)!=0) throw std::invalid_argument(("Node that has Body id #"+boost::lexical_cast(subId)+" is already part of this deformable element")); // Add body to localmap this->localmap[nodeBody]=Se3r();// meaningful values will be put in by DeformableElement::updateProperties // Get first node //Scene* scene(Omega::instance().getScene().get()); // get scene //const shared_ptr& member=localmap.begin()->first; //Substract from the current node, therefore find the local value, localmap[nodeBody].position=nodeBody->state->pos; //cout<<"Local map of "<(subBody->id)+" not a part of the deformable element, not removing...").c_str()); LOG_DEBUG("Removed node #"<id); } trunk-2017.01a/pkg/dem/deformablecohesive/DeformableElement.hpp000066400000000000000000000065111304022710500244240ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include #include //#include //Node shape /* Before starting the implementation of the deformable element, I am really dissappointed that deformableelement's algorithm relies on its shape. Shape means "shape" and I think it should not contain any other physical meaning or anything else. With respect to this view; The deformable element class is derived from the body and knows the information of its members that are node shaped bodies. */ class NewtonIntegrator; class InternalForceFunctor; namespace yade{ typedef Eigen::MatrixXd Matrix; class DeformableElement: public Shape { public: typedef std::map,Se3r> NodeMap;//Node id's with initial positions first node is selected as the reference node typedef std::vector Triangles; // Used for drawing the element unsigned int maxNodeCount;//Maximum number of nodes of this element Se3r referenceCoord;//Reference node position in global coordinates virtual ~DeformableElement(); void addNode(const shared_ptr& subBody); shared_ptr getNode(int id); void delNode(const shared_ptr& subBody); std::vector getDisplacements(void); void addFace(Vector3r&); void removeLastFace(void); //! Recalculate physical properties of DeformableElement. //virtual void getMassMatrix()=0; Se3r frame_get() const { const shared_ptr& member=localmap.begin()->first; return member->state->se3; } void frame_set(Se3r) const { return; } boost::python::dict localmap_get(); virtual Real getVolume(){return -1;} YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(DeformableElement,Shape,"Deformable aggregate of nodes", ((NodeMap,localmap,,,"Ids and relative positions+orientations of members of the deformable element (should not be accessed directly)")) ((Se3r,elementframe,,,"Position and orientation of the element frame")) ((Triangles,faces,,,"Faces of the element for drawing")) , , createIndex(); /*ctor*/ //init(); , /*py*/ .add_property("elementframe",&DeformableElement::frame_get) .def("addNode",&DeformableElement::addNode,"Add a node shared_pt<:yref:'Body'>& as into the element") .def("getNode",&DeformableElement::getNode,"Get a node shared_pt<:yref:'Body'>& as into the element") .def("delNode",&DeformableElement::delNode,"Remove a node shared_pt<:yref:'Body'>& from the element") .def("addFace",&DeformableElement::addFace,"Add a face into the element") .def("removeLastFace",&DeformableElement::removeLastFace,"Remove a face from the element") .def("getVolume",&DeformableElement::getVolume,"Get volume of the element") ); REGISTER_CLASS_INDEX(DeformableElement,Shape); }; } // necessary using namespace yade; REGISTER_SERIALIZABLE(DeformableElement); trunk-2017.01a/pkg/dem/deformablecohesive/FEInternalForceDispatchers.cpp000066400000000000000000000032431304022710500262040ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include #include YADE_PLUGIN((InternalForceFunctor)(InternalForceDispatcher)); InternalForceFunctor::~InternalForceFunctor(){}; /******************************************************************** InternalForceDispatcher *********************************************************************/ CREATE_LOGGER(InternalForceDispatcher); void InternalForceDispatcher::action() { //There is no need to make an action for this dispatcher its main misson is to return functors for the shape that is given. } //void InternalForceDispatcher::explicitAction(const shared_ptr deformableelement,const Body* bdy){ // // updateScenePtr(); // shared_ptr deformableElement=deformableelement; // if(!deformableElement->functorCache.iff){ // deformableElement->functorCache.iff=getFunctor1D(deformableElement); // if(!deformableElement->functorCache.iff) throw invalid_argument("InternalForceDispatcher::explicitAction did not find a suitable dispatch for type"+deformableElement->getClassName()); // deformableElement->functorCache.iff->go(deformableElement,bdy); // } // // //} trunk-2017.01a/pkg/dem/deformablecohesive/FEInternalForceDispatchers.hpp000066400000000000000000000034631304022710500262150ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER burak.er@btu.edu.tr * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include #include #include #include #include #include #include #include #include /*Functor of Internal Force Calculation*/ class InternalForceFunctor: public Functor2D< /*dispatch types*/ Shape, Material, /*return type*/ void , /*argument types*/ TYPELIST_3(const shared_ptr&,const shared_ptr&,const shared_ptr&) >{ public: virtual ~InternalForceFunctor(); YADE_CLASS_BASE_DOC(InternalForceFunctor,Functor,"Functor for creating/updating :yref:`Body::bound`."); }; REGISTER_SERIALIZABLE(InternalForceFunctor); /*Dispatcher of Internal Force Functors*/ class InternalForceDispatcher: public Dispatcher2D< /* functor type*/ InternalForceFunctor >{ public: virtual void action(); // void explicitAction(const shared_ptr& deformableelement,const Body* bdy); //virtual bool isActivated(){ return activated; } DECLARE_LOGGER; YADE_DISPATCHER2D_FUNCTOR_DOC_ATTRS_CTOR_PY(InternalForceDispatcher,InternalForceFunctor,/*doc is optional*/,/*attrs*/,/*ctor*/,/*py*/); }; REGISTER_SERIALIZABLE(InternalForceDispatcher); trunk-2017.01a/pkg/dem/deformablecohesive/FEInternalForceEngine.cpp000066400000000000000000000070531304022710500251430ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include #include #include YADE_PLUGIN((FEInternalForceEngine)); CREATE_LOGGER(FEInternalForceEngine); void FEInternalForceEngine::pyHandleCustomCtorArgs(boost::python::tuple& t, boost::python::dict& d){ cout<<"Entered the initialization function"; if(boost::python::len(t)==0) return; // nothing to do if(boost::python::len(t)!=1) throw invalid_argument("At least 1 functors must be given"); boost::python::list vv=boost::python::extract(t[0])(); // FOREACH(shared_ptr iff, vv) this->internalforcedispatcher->add(iff); for( int i=0;iinternalforcedispatcher->add(boost::python::extract>(vv[i])); t=boost::python::tuple(); // empty the args; not sure if this is OK, as there is some refcounting in raw_constructor code cout<<"Added to the list"; } void FEInternalForceEngine::action(){ // update Scene* of the dispatcher internalforcedispatcher->scene=scene; // ask dispatcher to update Scene* of their functors internalforcedispatcher->updateScenePtr(); // call InternalForceFunctor::preStep //FOREACH(const shared_ptr& iff, internalforcedispatcher->functors) iff->preStep(); /* initialize callbacks; they return pointer (used only in this timestep) to the function to be called returning NULL deactivates the callback in this timestep */ // // pair of callback object and pointer to the function to be called // vector callbackPtrs; // FOREACH(const shared_ptr cb, callbacks){ // cb->scene=scene; // callbackPtrs.push_back(cb->stepInit()); // } // assert(callbackPtrs.size()==callbacks.size()); // size_t callbacksSize=callbacks.size(); // cache transformed cell size // Matrix3r cellHsize; if(scene->isPeriodic) cellHsize=scene->cell->hSize; #ifdef YADE_OPENMP const long size=scene->bodies->size(); #pragma omp parallel for schedule(guided) num_threads(ompThreads>0 ? ompThreads : omp_get_max_threads()) for(long i=0; i& bdy=(*scene->bodies)[i]; #else FOREACH(const shared_ptr& bdy, *scene->bodies){ #endif //Try to get internal functor if(bdy->shape->internalforcefunctor.get()==0) { //If there isn't any internalforcefunctor; try to get one bdy->shape->internalforcefunctor=internalforcedispatcher->getFunctor(bdy->shape,bdy->material); //İf we found any of them that is suitable to this element??? if(bdy->shape->internalforcefunctor!=0){ //If yes try to apply internal force functor shared_ptr deformableElement=YADE_PTR_CAST(bdy->shape); bdy->shape->internalforcefunctor->go(deformableElement,bdy->material,bdy); } } else{ //Take functor from cache and call it's go functor shared_ptr deformableElement=YADE_PTR_CAST(bdy->shape); bdy->shape->internalforcefunctor->go(deformableElement,bdy->material,bdy); } } } trunk-2017.01a/pkg/dem/deformablecohesive/FEInternalForceEngine.hpp000066400000000000000000000041031304022710500251410ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER burak.er@btu.edu.tr * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #ifdef USE_TIMING_DELTAS #define TIMING_DELTAS_CHECKPOINT(cpt) timingDeltas->checkpoint(cpt) #define TIMING_DELTAS_START() timingDeltas->start() #else #define TIMING_DELTAS_CHECKPOINT(cpt) #define TIMING_DELTAS_START() #endif class FEInternalForceEngine: public GlobalEngine { // #ifdef YADE_OPENMP // std::vector > eraseAfterLoopIds; // void eraseAfterLoop(Body::id_t id1,Body::id_t id2){ eraseAfterLoopIds[omp_get_thread_num()].push_back(idPair(id1,id2)); } // #else // list eraseAfterLoopIds; // void eraseAfterLoop(Body::id_t id1,Body::id_t id2){ eraseAfterLoopIds.push_back(idPair(id1,id2)); } // #endif public: virtual void pyHandleCustomCtorArgs(boost::python::tuple& t, boost::python::dict& d); virtual void action(); YADE_CLASS_BASE_DOC_ATTRS_CTOR_PY(FEInternalForceEngine,GlobalEngine,"Unified dispatcher for handling Finite Element internal force loop at every step, for parallel performance reasons.\n\n.. admonition:: Special constructor\n\n\tConstructs from 3 lists of :yref:`Ig2`, :yref:`Ip2`, :yref:`Law` functors respectively; they will be passed to interal dispatchers, which you might retrieve.", ((shared_ptr,internalforcedispatcher,new InternalForceDispatcher,Attr::readonly,":yref:`InternalForceDispatcher` object that is used for dispatching of element types.")) , /*ctor*/ , /*py*/ ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(FEInternalForceEngine); trunk-2017.01a/pkg/dem/deformablecohesive/Gl1_DeformableElement.cpp000066400000000000000000000066611304022710500251300ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef YADE_OPENGL #include #include #include typedef DeformableElement::NodeMap NodeMap; void Gl1_DeformableElement::go(const shared_ptr& cm, const shared_ptr& ,bool wire,const GLViewInfo&) { DeformableElement* element = static_cast(cm.get()); std::vector triangles = element->faces; if(!(cm->wire || wire)){ glDisable(GL_CULL_FACE); //Vector3r normal=(facet->vertices[1]-facet->vertices[0]).cross(facet->vertices[2]-facet->vertices[1]); normal.normalize(); glColor3v(cm->color); glBegin(GL_TRIANGLES); FOREACH(Vector3r vertices,triangles){ NodeMap::iterator i1(element->localmap.begin()); NodeMap::iterator i2(i1); NodeMap::iterator i3(i1); NodeMap::iterator i4(i1); //Find the opposite vertex total indice sum equals to six therefore the last one is going to be 6-sum of indices // I accept it is very uncommon int oppositevertexindex=6-vertices.sum(); std::advance(i1,vertices[0]); std::advance(i2,vertices[1]); std::advance(i3,vertices[2]); std::advance(i4,oppositevertexindex); const shared_ptr& member1=i1->first; const shared_ptr& member2=i2->first; const shared_ptr& member3=i3->first; Vector3r& vertex0=i1->first->state->pos; Vector3r& vertex1=i2->first->state->pos; Vector3r& vertex2=i3->first->state->pos; Vector3r& vertex3=i4->first->state->pos; Vector3r normal=(vertex1-vertex0).cross(vertex2-vertex0); normal.normalize(); if((vertex3-vertex0).dot(normal)>0) normal=-normal; glNormal3v(normal); // this makes every triangle different WRT the light glVertex3v(member1->state->pos); glVertex3v(member2->state->pos); glVertex3v(member3->state->pos); } } glEnd(); glBegin(GL_LINE_LOOP); glColor3v(Vector3r(0,0,0)); FOREACH(Vector3r vertices,triangles){ NodeMap::iterator i1(element->localmap.begin()); NodeMap::iterator i2(i1); NodeMap::iterator i3(i1); std::advance(i1,vertices[0]); std::advance(i2,vertices[1]); std::advance(i3,vertices[2]); const shared_ptr& member1=i1->first; const shared_ptr& member2=i2->first; const shared_ptr& member3=i3->first; glVertex3v(member1->state->pos); glVertex3v(member2->state->pos); glVertex3v(member3->state->pos); } glEnd(); } YADE_PLUGIN((Gl1_DeformableElement)); #endif /* YADE_OPENGL */ trunk-2017.01a/pkg/dem/deformablecohesive/Gl1_DeformableElement.hpp000066400000000000000000000016131304022710500251250ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include class Gl1_DeformableElement : public GlShapeFunctor { public: virtual void go(const shared_ptr&, const shared_ptr&,bool,const GLViewInfo&); YADE_CLASS_BASE_DOC(Gl1_DeformableElement,GlShapeFunctor,"Renders :yref:`Node` object" ); RENDERS(DeformableElement); }; REGISTER_SERIALIZABLE(Gl1_DeformableElement); trunk-2017.01a/pkg/dem/deformablecohesive/Gl1_Node.cpp000066400000000000000000000142071304022710500224360ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER burak.er@btu.edu.tr * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef YADE_OPENGL #include #include #include bool Gl1_Node::wire; bool Gl1_Node::stripes; int Gl1_Node::glutSlices; int Gl1_Node::glutStacks; Real Gl1_Node::quality; bool Gl1_Node::localSpecView; vector Gl1_Node::vertices, Gl1_Node::faces; int Gl1_Node::glStripedSphereList=-1; int Gl1_Node::glGlutSphereList=-1; Real Gl1_Node::prevQuality=0; void Gl1_Node::go(const shared_ptr& cm, const shared_ptr& ,bool wire2, const GLViewInfo&) { glClearDepth(1.0f); glEnable(GL_NORMALIZE); Real r=(static_cast(cm.get()))->radius; glColor3v(cm->color); if (wire || wire2) glutWireSphere(r,quality*glutSlices,quality*glutStacks); else { //Check if quality has been modified or if previous lists are invalidated (e.g. by creating a new qt view), then regenerate lists bool somethingChanged = (abs(quality-prevQuality)>0.001 || glIsList(glStripedSphereList)!=GL_TRUE); if (somethingChanged) {initStripedGlList(); initGlutGlList(); prevQuality=quality;} glScalef(r,r,r); if(stripes) glCallList(glStripedSphereList); else glCallList(glGlutSphereList); } return; } YADE_PLUGIN((Gl1_Node)); void Gl1_Node::subdivideTriangle(Vector3r& v1,Vector3r& v2,Vector3r& v3, int depth){ Vector3r v; //Change color only at the appropriate level, i.e. 8 times in total, since we draw 8 mono-color sectors one after another if (depth==int(quality) || quality<=0){ v = (v1+v2+v3)/3.0; GLfloat matEmit[4]; if (v[1]*v[0]*v[2]>0){ matEmit[0] = 0.3; matEmit[1] = 0.3; matEmit[2] = 0.3; matEmit[3] = 1.f; }else{ matEmit[0] = 0.15; matEmit[1] = 0.15; matEmit[2] = 0.15; matEmit[3] = 0.2; } glMaterialfv(GL_FRONT, GL_EMISSION, matEmit); } if (depth==1){//Then display 4 triangles Vector3r v12 = v1+v2; Vector3r v23 = v2+v3; Vector3r v31 = v3+v1; v12.normalize(); v23.normalize(); v31.normalize(); //Use TRIANGLE_STRIP for faster display of adjacent facets glBegin(GL_TRIANGLE_STRIP); glNormal3v(v1); glVertex3v(v1); glNormal3v(v31); glVertex3v(v31); glNormal3v(v12); glVertex3v(v12); glNormal3v(v23); glVertex3v(v23); glNormal3v(v2); glVertex3v(v2); glEnd(); //terminate with this triangle left behind glBegin(GL_TRIANGLES); glNormal3v(v3); glVertex3v(v3); glNormal3v(v23); glVertex3v(v23); glNormal3v(v31); glVertex3v(v31); glEnd(); return; } Vector3r v12 = v1+v2; Vector3r v23 = v2+v3; Vector3r v31 = v3+v1; v12.normalize(); v23.normalize(); v31.normalize(); subdivideTriangle(v1,v12,v31,depth-1); subdivideTriangle(v2,v23,v12,depth-1); subdivideTriangle(v3,v31,v23,depth-1); subdivideTriangle(v12,v23,v31,depth-1); } void Gl1_Node::initStripedGlList() { if (!vertices.size()){//Fill vectors with vertices and facets //Define 6 points for +/- coordinates vertices.push_back(Vector3r(-1,0,0));//0 vertices.push_back(Vector3r(1,0,0));//1 vertices.push_back(Vector3r(0,-1,0));//2 vertices.push_back(Vector3r(0,1,0));//3 vertices.push_back(Vector3r(0,0,-1));//4 vertices.push_back(Vector3r(0,0,1));//5 //Define 8 sectors of the sphere faces.push_back(Vector3r(3,4,1)); faces.push_back(Vector3r(3,0,4)); faces.push_back(Vector3r(3,5,0)); faces.push_back(Vector3r(3,1,5)); faces.push_back(Vector3r(2,1,4)); faces.push_back(Vector3r(2,4,0)); faces.push_back(Vector3r(2,0,5)); faces.push_back(Vector3r(2,5,1)); } //Generate the list. Only once for each qtView, or more if quality is modified. glDeleteLists(glStripedSphereList,1); glStripedSphereList = glGenLists(1); glNewList(glStripedSphereList,GL_COMPILE); glEnable(GL_LIGHTING); glShadeModel(GL_SMOOTH); // render the sphere now for (int i=0;i<8;i++) subdivideTriangle(vertices[(unsigned int)faces[i][0]],vertices[(unsigned int)faces[i][1]],vertices[(unsigned int)faces[i][2]],1+ (int) quality); glEndList(); } void Gl1_Node::initGlutGlList(){ //Generate the "no-stripes" display list, each time quality is modified glDeleteLists(glGlutSphereList,1); glGlutSphereList = glGenLists(1); glNewList(glGlutSphereList,GL_COMPILE); glEnable(GL_LIGHTING); glShadeModel(GL_SMOOTH); glutSolidSphere(1.0,max(quality*glutSlices,(Real)2.),max(quality*glutStacks,(Real)3.)); glEndList(); } #endif /* YADE_OPENGL */ // ///The old Galizzi's lists // if (!vertices.size()) { // Real X = 0.525731112119133606; // Real Z = 0.850650808352039932; // vertices.push_back(Vector3r(-X,0,Z));//0 // vertices.push_back(Vector3r(X,0,Z));//1 // vertices.push_back(Vector3r(-X,0,-Z));//2 // vertices.push_back(Vector3r(X,0,-Z));//3 // vertices.push_back(Vector3r(0,Z,X));//4 // vertices.push_back(Vector3r(0,Z,-X));//5 // vertices.push_back(Vector3r(0,-Z,X));//6 // vertices.push_back(Vector3r(0,-Z,-X));//7 // vertices.push_back(Vector3r(Z,X,0));//8 // vertices.push_back(Vector3r(-Z,X,0));//9 // vertices.push_back(Vector3r(Z,-X,0));//10 // vertices.push_back(Vector3r(-Z,-X,0));//11 // faces.push_back(Vector3r(0,4,1)); // faces.push_back(Vector3r(0,9,4)); // faces.push_back(Vector3r(9,5,4)); // faces.push_back(Vector3r(4,5,8)); // faces.push_back(Vector3r(4,8,1)); // faces.push_back(Vector3r(8,10,1)); // faces.push_back(Vector3r(8,3,10)); // faces.push_back(Vector3r(5,3,8)); // faces.push_back(Vector3r(5,2,3)); // faces.push_back(Vector3r(2,7,3)); // faces.push_back(Vector3r(7,10,3)); // faces.push_back(Vector3r(7,6,10)); // faces.push_back(Vector3r(7,11,6)); // faces.push_back(Vector3r(11,0,6)); // faces.push_back(Vector3r(0,1,6)); // faces.push_back(Vector3r(6,1,10)); // faces.push_back(Vector3r(9,0,11)); // faces.push_back(Vector3r(9,11,2)); // faces.push_back(Vector3r(9,2,5)); // faces.push_back(Vector3r(7,2,11));} trunk-2017.01a/pkg/dem/deformablecohesive/Gl1_Node.hpp000066400000000000000000000051671304022710500224500ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER burak.er@btu.edu.tr * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include class Gl1_Node : public GlShapeFunctor{ private: // for stripes static vector vertices, faces; static int glStripedSphereList; static int glGlutSphereList; void subdivideTriangle(Vector3r& v1,Vector3r& v2,Vector3r& v3, int depth); // void drawSphere(const Vector3r& color); //Generate GlList for GLUT sphere void initGlutGlList(); //Generate GlList for sliced spheres void initStripedGlList(); //for regenerating glutSphere list if needed static Real prevQuality; public: virtual void go(const shared_ptr&, const shared_ptr&,bool,const GLViewInfo&); YADE_CLASS_BASE_DOC_STATICATTRS(Gl1_Node,GlShapeFunctor,"Renders :yref:`Node` object", ((Real,quality,1.0,,"Change discretization level of spheres. quality>1 for better image quality, at the price of more cpu/gpu usage, 0`_)")) ((int,glutStacks,6,(Attr::noSave | Attr::readonly),"Base number of sphere stacks, multiplied by :yref:`Gl1_Node::quality` before use; not used with ``stripes`` (see `glut{Solid,Wire}Sphere reference `_)")) ); RENDERS(Node); }; REGISTER_SERIALIZABLE(Gl1_Node); trunk-2017.01a/pkg/dem/deformablecohesive/If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat.cpp000066400000000000000000000056541304022710500330240ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER burak.er@btu.edu.tr * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include #include YADE_PLUGIN((If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat)); If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat::~If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat(){}; /******************************************************************** InternalForceDispatcher *********************************************************************/ typedef std::map NodePairsMap;//Initial node differences CREATE_LOGGER(If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat); void If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat::go(const shared_ptr& element,const shared_ptr& material,const shared_ptr& bdy) { shared_ptr interactionelement=YADE_PTR_CAST(element); shared_ptr mat=YADE_PTR_CAST(material); NodePairsMap::iterator i1(interactionelement->nodepairs.begin()); shared_ptr node11=i1->first.node1;shared_ptr node12=i1->first.node2; Vector3r initial1=i1->second.position; std::advance(i1,1); shared_ptr node21= i1->first.node1;shared_ptr node22=i1->first.node2; Vector3r initial2=i1->second.position; std::advance(i1,1); shared_ptr node31= i1->first.node1;shared_ptr node32=i1->first.node2; Vector3r initial3=i1->second.position; Vector3r disp1=(node11->state->pos-node12->state->pos)-initial1; Vector3r disp2=(node21->state->pos-node22->state->pos)-initial2; Vector3r disp3=(node31->state->pos-node32->state->pos)-initial3; Vector3r l1=node11->state->pos-node21->state->pos; Vector3r l2=node31->state->pos-node21->state->pos; Real A=0.5*fabs(l1.cross(l2).norm()); Vector3r f1=(0.083333333)*A*mat->youngmodulus*(2*disp1+disp2+disp3); Vector3r f2=(0.083333333)*A*mat->youngmodulus*(disp1+2*disp2+disp3); Vector3r f3=(0.083333333)*A*mat->youngmodulus*(disp1+disp2+2*disp3); //cout<<"forces are \n"<forces.addForce(node11->getId(),-f1); scene->forces.addForce(node12->getId(),f1); scene->forces.addForce(node21->getId(),-f2); scene->forces.addForce(node22->getId(),f2); scene->forces.addForce(node31->getId(),-f3); scene->forces.addForce(node32->getId(),f3); return; } trunk-2017.01a/pkg/dem/deformablecohesive/If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat.hpp000066400000000000000000000031311304022710500330150ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER burak.er@btu.edu.tr * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include #include #include #include #include #include #include #include #include #include #include class If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat : public InternalForceFunctor { public : virtual void go(const shared_ptr&,const shared_ptr&,const shared_ptr&); virtual ~If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat(); FUNCTOR2D(Lin4NodeTetra_Lin4NodeTetra_InteractionElement,LinCohesiveStiffPropDampElastMat); YADE_CLASS_BASE_DOC(If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat,InternalForceFunctor,"Apply internal forces of the tetrahedral element using lumped mass theory") }; REGISTER_SERIALIZABLE(If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat); trunk-2017.01a/pkg/dem/deformablecohesive/If2_Lin4NodeTetra_LinIsoRayleighDampElast.cpp000066400000000000000000000066021304022710500307170ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER burak.er@btu.edu.tr * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include #include YADE_PLUGIN((If2_Lin4NodeTetra_LinIsoRayleighDampElast)); If2_Lin4NodeTetra_LinIsoRayleighDampElast::~If2_Lin4NodeTetra_LinIsoRayleighDampElast(){}; /******************************************************************** InternalForceDispatcher *********************************************************************/ typedef DeformableElement::NodeMap NodeMap; #define VECTOR12_TEMPLATE(Scalar) Eigen::Matrix typedef VECTOR12_TEMPLATE(Real) Vector12r; CREATE_LOGGER(If2_Lin4NodeTetra_LinIsoRayleighDampElast); void If2_Lin4NodeTetra_LinIsoRayleighDampElast::go(const shared_ptr& element,const shared_ptr& material,const shared_ptr& bdy) { shared_ptr tetel=YADE_PTR_CAST(element); shared_ptr mat=YADE_PTR_CAST(material); DeformableElement::NodeMap::iterator i0(tetel->localmap.begin()); DeformableElement::NodeMap::iterator i1(i0); DeformableElement::NodeMap::iterator i2(i0); DeformableElement::NodeMap::iterator i3(i0); std::advance(i1,1); std::advance(i2,2); std::advance(i3,3); if(tetel->massMatrixInvProductstiffnessMatrix==0) { Vector3r node0relpos=Vector3r(0,0,0); Vector3r node1relpos=i1->second.position-i0->second.position; Vector3r node2relpos=i2->second.position-i0->second.position; Vector3r node3relpos=i3->second.position-i0->second.position; // I dont know wheter this is optimum or not tetel->massMatrixInvProductstiffnessMatrix=shared_ptr ( new Matrix( tetel->calculateMassMatrix(mat->density,mat->poissonratio).inverse()* tetel->calculateStiffness(mat->youngmodulus,mat->poissonratio,node0relpos,node1relpos,node2relpos,node3relpos) ) ); } //apply internal forces to the tetrahedron //Calculate displacements Vector12r displacements; Vector12r displacementvelocity; displacements<first->state->pos - i0->second.position, i1->first->state->pos - i1->second.position, i2->first->state->pos - i2->second.position, i3->first->state->pos - i3->second.position; displacementvelocity<first->state->vel, i1->first->state->vel, i2->first->state->vel, i3->first->state->vel; //Now calculate the forces Vector12r forces=-(*tetel->massMatrixInvProductstiffnessMatrix)*displacements-(mat->alpha*Matrix::Identity(12,12)+(*tetel->massMatrixInvProductstiffnessMatrix)*(mat->beta))*displacementvelocity; scene->forces.addForce(i0->first->getId(),forces.segment(0,3)); scene->forces.addForce(i1->first->getId(),forces.segment(3,3)); scene->forces.addForce(i2->first->getId(),forces.segment(6,3)); scene->forces.addForce(i3->first->getId(),forces.segment(9,3)); return; } trunk-2017.01a/pkg/dem/deformablecohesive/If2_Lin4NodeTetra_LinIsoRayleighDampElast.hpp000066400000000000000000000027451304022710500307300ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER burak.er@btu.edu.tr * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include #include #include #include #include #include #include #include #include #include #include class If2_Lin4NodeTetra_LinIsoRayleighDampElast : public InternalForceFunctor { public : virtual void go(const shared_ptr&,const shared_ptr&,const shared_ptr&); virtual ~If2_Lin4NodeTetra_LinIsoRayleighDampElast(); FUNCTOR2D(Lin4NodeTetra,LinIsoRayleighDampElastMat); YADE_CLASS_BASE_DOC(If2_Lin4NodeTetra_LinIsoRayleighDampElast,InternalForceFunctor,"Apply internal forces of the tetrahedral element using lumped mass theory") }; REGISTER_SERIALIZABLE(If2_Lin4NodeTetra_LinIsoRayleighDampElast); trunk-2017.01a/pkg/dem/deformablecohesive/Lin4NodeTetra.cpp000066400000000000000000000070751304022710500234670ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include #include #include #include #include #include #include #include YADE_PLUGIN((Lin4NodeTetra)); CREATE_LOGGER(Lin4NodeTetra); Lin4NodeTetra::~Lin4NodeTetra(){ } void Lin4NodeTetra::initialize(void){ maxNodeCount=4; } Matrix Lin4NodeTetra::calculateMassMatrix(Real density,Real v) { Matrix mass(12,12); mass<<2,0,0,1,0,0,1,0,0,1,0,0, 0,2,0,0,1,0,0,1,0,0,1,0, 0,0,2,0,0,1,0,0,1,0,0,1, 1,0,0,2,0,0,1,0,0,1,0,0, 0,1,0,0,2,0,0,1,0,0,1,0, 0,0,1,0,0,2,0,0,1,0,0,1, 1,0,0,1,0,0,2,0,0,1,0,0, 0,1,0,0,1,0,0,2,0,0,1,0, 0,0,1,0,0,1,0,0,2,0,0,1, 1,0,0,1,0,0,1,0,0,2,0,0, 0,1,0,0,1,0,0,1,0,0,2,0, 0,0,1,0,0,1,0,0,1,0,0,2; mass=0.05*(density*v)*mass; return mass; } Matrix Lin4NodeTetra::calculateStiffness(Real E, Real v,Vector3r pos0,Vector3r pos1,Vector3r pos2,Vector3r pos3) { /* * The calculation is relative, therefore, we do not need position of the first node. * All other nodes are calculated with respect to first node which is at zero on local coordinates. * The local coordinates are the coordinates that is fixed at node0 and parallel to global axes. * * */ Vector3r pos01=-pos1; Vector3r pos02=-pos2; Vector3r pos03=-pos3; Vector3r pos12= pos1-pos2; Vector3r pos13= pos1-pos3; Vector3r pos23= pos2-pos3; Matrix J(4,4); J.col(0)<<1,pos0; J.col(1)<<1,pos1; J.col(2)<<1,pos2; J.col(3)<<1,pos3; Real x12=pos01(0), x13=pos02(0), x14=pos03(0), x23= pos12(0), x24=pos13(0), x34= pos23(0); Real x21=-x12, x31=-x13, /*x41=-x14,*/ x32=-x23, x42=-x24, x43=-x34; Real y12=pos01(1), y13=pos02(1), y14=pos03(1), y23= pos12(1), y24=pos13(1), y34= pos23(1); Real y21=-y12, y31=-y13, /*y41=-y14,*/ y32=-y23, y42=-y24, y43=-y34; Real z12=pos01(2), z13=pos02(2), z14=pos03(2), z23= pos12(2), z24=pos13(2), z34= pos23(2); Real z21=-z12, z31=-z13, /*z41=-z14,*/ z32=-z23, z42=-z24, z43=-z34; Real V=fabs(((0.166666667)*J.determinant())); Real a1=y42*z32-y32*z42, b1=x32*z42-x42*z32, c1=x42*y32-x32*y42; Real a2=y31*z43-y34*z13, b2=x43*z31-x13*z34, c2=x31*y43-x34*y13; Real a3=y24*z14-y14*z24, b3=x14*z24-x24*z14, c3=x24*y14-x14*y24; Real a4=y13*z21-y12*z31, b4=x21*z13-x31*z12, c4=x13*y21-x12*y31; //std::cout<<"Volume of the element is "< #include #include #include #include class NewtonIntegrator; namespace yade{ #define VECTOR4_TEMPLATE(Scalar) Eigen::Matrix typedef VECTOR4_TEMPLATE(Real) Vector4r; class Lin4NodeTetra: public DeformableElement { public: friend class If2_Lin4NodeTetra_LinIsoRayleighDampElast; shared_ptr massMatrixInvProductstiffnessMatrix; Matrix calculateStiffness(Real, Real ,Vector3r,Vector3r,Vector3r,Vector3r); Matrix calculateMassMatrix(Real, Real); virtual ~Lin4NodeTetra(); void initialize(void); Real getVolume(void){ NodeMap::iterator i0(localmap.begin()); NodeMap::iterator i1(i0); NodeMap::iterator i2(i0); NodeMap::iterator i3(i0); std::advance(i1,1); std::advance(i2,2); std::advance(i3,3); Matrix J(4,4); Vector3r pos0=Vector3r(0,0,0); Vector3r pos1=i1->second.position-i0->second.position; Vector3r pos2=i2->second.position-i0->second.position; Vector3r pos3=i3->second.position-i0->second.position; /* Vector3r pos01=-pos1; Vector3r pos02=-pos2; Vector3r pos03=-pos3; Vector3r pos12= pos1-pos2; Vector3r pos13= pos1-pos3; Vector3r pos23= pos2-pos3; */ J.col(0)<<1,pos0; J.col(1)<<1,pos1; J.col(2)<<1,pos2; J.col(3)<<1,pos3; /* Real x12=pos01(0), x13=pos02(0), x14=pos03(0), x23= pos12(0), x24=pos13(0), x34= pos23(0); Real x21=-x12, x31=-x13, x41=-x14, x32=-x23, x42=-x24, x43=-x34; Real y12=pos01(1), y13=pos02(1), y14=pos03(1), y23= pos12(1), y24=pos13(1), y34= pos23(1); Real y21=-y12, y31=-y13, y41=-y14, y32=-y23, y42=-y24, y43=-y34; Real z12=pos01(2), z13=pos02(2), z14=pos03(2), z23= pos12(2), z24=pos13(2), z34= pos23(2); Real z21=-z12, z31=-z13, z41=-z14, z32=-z23, z42=-z24, z43=-z34; */ Real V=fabs(((0.166666667)*J.determinant())); return V; } YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(Lin4NodeTetra,DeformableElement,"Tetrahedral Deformable Element Composed of Nodes", , , createIndex(); /*ctor*/ initialize(); , /*py*/ ); DECLARE_LOGGER; REGISTER_CLASS_INDEX(Lin4NodeTetra,DeformableElement); }; } // necessary using namespace yade; REGISTER_SERIALIZABLE(Lin4NodeTetra); trunk-2017.01a/pkg/dem/deformablecohesive/Lin4NodeTetra_Lin4NodeTetra_InteractionElement.cpp000066400000000000000000000020601304022710500320210ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include #include #include #include #include #include #include #include YADE_PLUGIN((Lin4NodeTetra_Lin4NodeTetra_InteractionElement)); CREATE_LOGGER(Lin4NodeTetra_Lin4NodeTetra_InteractionElement); Lin4NodeTetra_Lin4NodeTetra_InteractionElement::~Lin4NodeTetra_Lin4NodeTetra_InteractionElement(){ } void Lin4NodeTetra_Lin4NodeTetra_InteractionElement::initialize(void){ } trunk-2017.01a/pkg/dem/deformablecohesive/Lin4NodeTetra_Lin4NodeTetra_InteractionElement.hpp000066400000000000000000000026121304022710500320310ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include #include #include #include #include #include class Lin4NodeTetra_Lin4NodeTetra_InteractionElement: public DeformableCohesiveElement { public: friend class If2_2xLin4NodeTetra_LinCohesiveStiffPropDampElastMat; virtual ~Lin4NodeTetra_Lin4NodeTetra_InteractionElement(); void initialize(void); YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(Lin4NodeTetra_Lin4NodeTetra_InteractionElement,DeformableCohesiveElement,"Tetrahedral Deformable Element Composed of Nodes", , , createIndex(); /*ctor*/ initialize(); , /*py*/ ); DECLARE_LOGGER; REGISTER_CLASS_INDEX(Lin4NodeTetra_Lin4NodeTetra_InteractionElement,DeformableCohesiveElement); }; // necessary using namespace yade; REGISTER_SERIALIZABLE(Lin4NodeTetra_Lin4NodeTetra_InteractionElement); trunk-2017.01a/pkg/dem/deformablecohesive/LinElastMat.cpp000066400000000000000000000013761304022710500232260ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #include YADE_PLUGIN((DeformableElementMaterial)(LinIsoElastMat)(LinIsoRayleighDampElastMat)); DeformableElementMaterial::~DeformableElementMaterial(void){} LinIsoElastMat::~LinIsoElastMat(void){} LinIsoRayleighDampElastMat::~LinIsoRayleighDampElastMat(void){} trunk-2017.01a/pkg/dem/deformablecohesive/LinElastMat.hpp000066400000000000000000000036711304022710500232330ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #pragma once #include #include /*! Elastic material */ class DeformableElementMaterial: public Material{ public: virtual ~DeformableElementMaterial(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(DeformableElementMaterial,Material,"Deformable Element Material.", ((Real,density,1,,"Density of the material.")), /*ctor*/ createIndex(); ); REGISTER_CLASS_INDEX(DeformableElementMaterial,Material); }; REGISTER_SERIALIZABLE(DeformableElementMaterial); class LinIsoElastMat: public DeformableElementMaterial{ public: virtual ~LinIsoElastMat(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(LinIsoElastMat,DeformableElementMaterial,"Linear Isotropic Elastic material", ((Real,youngmodulus,.78e5,,"Young's modulus. Initially aluminium.")) ((Real,poissonratio,.33,,"Poisson ratio. Initially aluminium.")), createIndex(); ); REGISTER_CLASS_INDEX(LinIsoElastMat,DeformableElementMaterial); }; REGISTER_SERIALIZABLE(LinIsoElastMat); /*Standard damped linear elastic material*/ class LinIsoRayleighDampElastMat: public LinIsoElastMat{ public: virtual ~LinIsoRayleighDampElastMat(); YADE_CLASS_BASE_DOC_ATTRS_CTOR(LinIsoRayleighDampElastMat,LinIsoElastMat,"Elastic material with Rayleigh Damping.", ((Real,alpha,0,,"Mass propotional damping constant of Rayleigh Damping.")) ((Real,beta,0,,"Stiffness propotional damping constant of Rayleigh Damping.")), createIndex(); ); REGISTER_CLASS_INDEX(LinIsoRayleighDampElastMat,LinIsoElastMat); }; REGISTER_SERIALIZABLE(LinIsoRayleighDampElastMat); trunk-2017.01a/pkg/dem/deformablecohesive/Node.cpp000066400000000000000000000001241304022710500217240ustar00rootroot00000000000000#include Node::~Node(){} YADE_PLUGIN((Node)); trunk-2017.01a/pkg/dem/deformablecohesive/Node.hpp000066400000000000000000000021051304022710500217320ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by Burak ER * * * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifndef NODE_HPP_ #define NODE_HPP_ #include //TODO: Look at Sphere hack to work around problem // HACK to work around https://bugs.launchpad.net/yade/+bug/528509 // see comments there for explanation namespace yade{ class Node: public Shape{ public: Node(Real _radius): radius(_radius){ createIndex();} virtual ~Node (); YADE_CLASS_BASE_DOC_ATTRS_CTOR(Node,Shape,"Geometry of node particle.", ((Real,radius,0.1,,"Radius [m]")), createIndex(); /*ctor*/ ); REGISTER_CLASS_INDEX(Node,Shape); }; } // necessary using namespace yade; // must be outside yade namespace REGISTER_SERIALIZABLE(Node); #endif trunk-2017.01a/pkg/lbm/000077500000000000000000000000001304022710500145155ustar00rootroot00000000000000trunk-2017.01a/pkg/lbm/HydrodynamicsLawLBM.cpp000066400000000000000000002062271304022710500210460ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2009-2012 by Franck Lominé * * franck.lomine@insa-rennes.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * * * * Luc Scholtès luc.scholtes@univ-lorraine.fr * * and Luc Sibille luc.sibille@3sr-grenoble.fr also contributed to this * * code. * * * * Lominé F., Scholtès L., Sibille L., Poullain P. (2013) * * Modelling of fluid-solid interaction in granular media with coupled * * LB/DE methods: application to piping erosion. International Journal * * for Numerical and Analytical Methods in Geomechanics, 37(6):577-596 * * doi: 10.1002/nag.1109 * * * * Sibille L., Lominé F., Marot D. (2012) Investigation In Modelling * * Piping Erosion With a Coupled «Lattice Boltzmann – Discrete Element» * * Numerical Method. in Proc. 6th Int. Conference on Scour and Erosion * * (ICSE-6), pp. 93-100. * * * *************************************************************************/ #ifdef LBM_ENGINE #include"HydrodynamicsLawLBM.hpp" #include #include #include #include #include #include namespace bfs=boost::filesystem; inline Vector3i vect3rToVect3i(Vector3r vect){Vector3i newvect((int)vect[0],(int)vect[1],(int)vect[2]);return(newvect);} HydrodynamicsLawLBM::~HydrodynamicsLawLBM() {}; bool HydrodynamicsLawLBM::isActivated(){ DEM_ITER=scene->iter;//+1; if(EngineIsActivated){ if((DEM_ITER % DemIterLbmIterRatio==0)&&(DEM_ITER!=DemIterLbmIterRatio)) { if(DEM_ITER==0){DEMdt0 = scene->dt;scene->dt=1.e-50;} return(true);} else{ if(applyForcesAndTorques) CalculateAndApplyForcesAndTorquesOnBodies(false,true); return(false); } }else return(false); } void HydrodynamicsLawLBM::action() { timingDeltas->start(); NB_BODIES= scene->bodies->size(); int I, J, step=0; NbFluidNodes=0; NbSolidNodes=0; Real CurMinVelOfPtc=1000000.; Real CurMaxVelOfPtc=-1000000.; int ErrorCriterion=2; /*------------------------------------------------------------------*/ /* AT FIRST ITERATION */ /*------------------------------------------------------------------*/ if(firstRun){ // createNewFiles(); //this line is move further to create files only when the recording configuration chosen by the operator is known bool initVbCutOff=false; if(VbCutOff==-1) initVbCutOff=true; halfWallthickness=1000000.; NB_WALLS=0; //NB_DYNWALLS=0; NB_DYNGRAINS=0; LBMbody tmpbody; FOREACH(const shared_ptr& b, *scene->bodies){ if(!b) continue; // deleted bodies if (b->shape->getClassName()=="Box"){ Vector3r ext(YADE_PTR_CAST ( b->shape )->extents); if (ext[0]isDynamic()) NB_DYNWALLS++; } if (b->shape->getClassName()=="Sphere"){ const shared_ptr& sph = YADE_PTR_CAST ( b->shape ); if(IdFirstSphere==-1) IdFirstSphere=b->getId(); tmpbody.setAsPtc(); Real r=sph->radius; if(b->isDynamic()){ NB_DYNGRAINS++; /*--- computation of the initial volume ---*/ if(!strcmp(model.c_str(), "d2q9" )) Vo += Mathr::PI*(r*r); else Vo += 4./3.*Mathr::PI*(r*r*r); if(initVbCutOff) VbCutOff=max(VbCutOff,b->state->vel.norm()+r*b->state->angVel.norm()); tmpbody.saveProperties=true; }else{ if(b->state->pos[1]>0.) tmpbody.saveProperties=true; else tmpbody.saveProperties=false; } /*--- computation of Rmean Rmax Rmin --*/ MaxBodyRadius=max(r,MaxBodyRadius); MinBodyRadius=min(r,MinBodyRadius); MeanBodyRadius+=r; } LBbodies.push_back(tmpbody); } Wallthickness=2.0*halfWallthickness; NB_GRAINS=NB_BODIES-NB_WALLS; //Luc: is it right to count the walls as dynamic bodies? //Franck why not ? Enhancement (see next line is coming ;-)) NB_DYNBODIES=NB_WALLS+NB_DYNGRAINS; //NB_DYNBODIES=NB_DYNWALLS+NB_DYNGRAINS; MeanBodyRadius=MeanBodyRadius/NB_GRAINS; InitialNumberOfDynamicParticles=NB_DYNGRAINS; /*-------------------------------------------------------------------------*/ /* D2Q9 model configuration */ /*-------------------------------------------------------------------------*/ if(!strcmp(model.c_str(), "d2q9" )){ dim=2; /*--------------------------------------*/ /* D2Q9 model: 6 2 5 */ /* 3 _\|/__1 */ /* /|\ */ /* 7 4 8 */ /*--------------------------------------*/ /*----------- D2Q9 constants ---------*/ w.push_back(4.0/9.0); for(int aa=1;aa<=4;aa++) w.push_back(1.0/9.0); for(int aa=5;aa<=8;aa++) w.push_back(1.0/36.0); /*--------- node position vectors ----*/ eib.push_back(Vector3r( 0., 0., 0.)); //0 eib.push_back(Vector3r( 1., 0., 0.)); //1 eib.push_back(Vector3r( 0., 1., 0.)); //2 eib.push_back(Vector3r(-1., 0., 0.)); //3 eib.push_back(Vector3r( 0.,-1., 0.)); //4 eib.push_back(Vector3r( 1., 1., 0.)); //5 eib.push_back(Vector3r(-1., 1., 0.)); //6 eib.push_back(Vector3r(-1.,-1., 0.)); //7 eib.push_back(Vector3r( 1.,-1., 0.)); //8 NbDir=(int) eib.size(); /*-------------- opposite nodes --------*/ opp.push_back(0); opp.push_back(3); opp.push_back(4); opp.push_back(1); opp.push_back(2); opp.push_back(7); opp.push_back(8); opp.push_back(5); opp.push_back(6); }else {cerr<<"This model is not implemented yet: "<=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res=0&&res0)&&(SAVE_OBSERVEDPTC)) ObservedPtc=IdFirstSphere; //Condition If(SAVE_OBSERVEDPTC) is added to save observedPtc only if it is required by the operator if ((SAVE_OBSERVEDPTC)&&((unsigned)ObservedPtc>=LBbodies.size())){cerr<<"Error: ObservedPtc>bodies.size()"<=0&&res=0&&res=0&&resstate.get(); State* sWallYp=Body::byId(WallYp_id,scene)->state.get(); State* sWallXm=Body::byId(WallXm_id,scene)->state.get(); State* sWallXp=Body::byId(WallXp_id,scene)->state.get(); State* sWallZp=Body::byId(WallZp_id,scene)->state.get(); State* sWallZm=Body::byId(WallZm_id,scene)->state.get(); height = sWallYp->se3.position.y() - sWallYm->se3.position.y(); width = sWallXp->se3.position.x() - sWallXm->se3.position.x(); depth = sWallZp->se3.position.z() - sWallZm->se3.position.z(); Lx0 = width-Wallthickness; Ly0 = height-Wallthickness; Lz0 = depth-Wallthickness; Real Lx1 = width+Wallthickness; Real Ly1 = height+Wallthickness; Real Lz1 = depth+Wallthickness; /*--------------------------------------------------------------*/ /* Computation of number of lattice nodes in each direction */ /*--------------------------------------------------------------*/ dx = Lx0 / (Real) (Nx-1); invdx=1./dx; //Number of nodes (after-correction) Ny = ceil(invdx*Ly1)+1; dx = Ly1 / (Real) (Ny-1); invdx=1./dx; dx2=dx*dx; Nx = ceil(invdx*Lx1)+1; Ny = ceil(invdx*Ly1)+1; Nz=1; cerr <<"LXYZ0= "<se3.position.x()- halfWallthickness<0.){cerr <<"Wall position error: please avoid negatives region (X)"<se3.position.z()- halfWallthickness<0.)){cerr <<"Wall position error: please avoid negatives region (Z)"<=Nx*Ny)){ cerr <<"Warning ObservedNode is >= Nx*Ny ... exit"<state.get(); State* sWallYp=Body::byId(WallYp_id,scene)->state.get(); State* sWallXm=Body::byId(WallXm_id,scene)->state.get(); State* sWallXp=Body::byId(WallXp_id,scene)->state.get(); State* sWallZp=Body::byId(WallZp_id,scene)->state.get(); State* sWallZm=Body::byId(WallZm_id,scene)->state.get(); timingDeltas->checkpoint("Reinit:Nodes0"); #pragma omp parallel for for (int nidx=0; nidx=invdx*(sWallXp->se3.position.x() - halfWallthickness))){ nodes[nidx].setAsObstacle(); nodes[nidx].isObstacleBoundary=true; nodes[nidx].body_id=WallXp_id; NbSolidNodes++;} /*--- according to X- ---*/ else if (useWallXm&&(nodes[nidx].i<=invdx*(sWallXm->se3.position.x() + halfWallthickness))){ nodes[nidx].setAsObstacle(); nodes[nidx].isObstacleBoundary=true; nodes[nidx].body_id=WallXm_id; NbSolidNodes++;} /*--- according to Y+ ---*/ else if (useWallYp&&(nodes[nidx].j>=invdx*(sWallYp->se3.position.y() - halfWallthickness))){ nodes[nidx].setAsObstacle(); nodes[nidx].isObstacleBoundary=true; nodes[nidx].body_id=WallYp_id; NbSolidNodes++;} /*--- according to Y- ---*/ else if (useWallYm&&(nodes[nidx].j<=invdx*(sWallYm->se3.position.y() + halfWallthickness))){ nodes[nidx].setAsObstacle(); nodes[nidx].isObstacleBoundary=true; nodes[nidx].body_id=WallYm_id; NbSolidNodes++;} /*--- according to Z+ ---*/ else if (useWallZp&&(nodes[nidx].k>=invdx*(sWallZp->se3.position.z() - halfWallthickness))){ nodes[nidx].setAsObstacle(); nodes[nidx].isObstacleBoundary=true; nodes[nidx].body_id=WallZp_id; NbSolidNodes++;} /*--- according to Z- ---*/ else if (useWallZm&&(nodes[nidx].k<=invdx*(sWallZm->se3.position.z() + halfWallthickness))){ nodes[nidx].setAsObstacle(); nodes[nidx].isObstacleBoundary=true; nodes[nidx].body_id=WallZm_id; NbSolidNodes++;} if(firstRun){nodes[nidx].wasObstacle=nodes[nidx].isObstacle;} } /*---------------------------------------------------------------*/ /*- Solid particle detection and recording of their properties --*/ /*---------------------------------------------------------------*/ NumberOfDynamicParticles=0; if(removingCriterion!=0) IdOfNextErodedPtc.clear(); FOREACH(const shared_ptr& b, *scene->bodies){ if(!b) continue; // deleted bodies State* state=b->state.get(); const int id=b->getId(); //if ((b->shape->getClassName()=="Sphere")&&(b->isDynamic())){ //ModLuc: removing of b->isDynamic() in order that non dynamic particle can be seen by the LBM if (b->shape->getClassName()=="Sphere"){ const shared_ptr& sphere = YADE_PTR_CAST ( b->shape ); LBbodies[id].pos=invdx*state->pos; LBbodies[id].vel=(state->vel)/c; LBbodies[id].AVel= (state->angVel)*dt; LBbodies[id].radius=invdx*RadFactor*(sphere->radius); CurMinVelOfPtc=min(CurMinVelOfPtc,state->vel.norm()); CurMaxVelOfPtc=max(CurMaxVelOfPtc,state->vel.norm()); Vector3r posMax=LBbodies[id].pos+ Vector3r(LBbodies[id].radius,LBbodies[id].radius,LBbodies[id].radius); Vector3r posMin=LBbodies[id].pos- Vector3r(LBbodies[id].radius,LBbodies[id].radius,LBbodies[id].radius); Vector3r dist=Vector3r::Zero(); for(int ii=posMin[0]-1;ii<=posMax[0]+1;ii++) for(int jj=posMin[1]-1;jj<=posMax[1]+1;jj++){ if((ii==-1)||(ii==Nx)||(jj==-1)||(jj==Ny)) continue; if((ii<-1)||(ii>Nx)||(jj<-1)||(jj>Ny)) continue; if (LBbodies[id].radius < Rmin) Rmin = LBbodies[id].radius; int nidx=ii+jj*Nx; dist=nodes[nidx].posb-LBbodies[id].pos; if(dist.norm()isDynamic() to remove only dynamic particles and not already removed particles changed into non dynamic if((removingCriterion!=0)&&(b->isDynamic())){ switch(removingCriterion){ case 1: /* criterion with respect to the particle postion in x direction */ if(LBbodies[id].pos.x()>(invdx*(sWallXp->se3.position.x())-1.05*MaxBodyRadius/RadFactor)){ IdOfNextErodedPtc.push_back(id); } break; case 2: /* criterion on particle velocity */ if((LBbodies[id].vel.norm()>VelocityThreshold)||(LBbodies[id].pos.x()>(invdx*(sWallXp->se3.position.x())-2.*LBbodies[id].radius))) {IdOfNextErodedPtc.push_back(id);} break; default: exit(-1); break; } } //NumberOfDynamicParticles++; //ModLuc: to still count only dynamic particles and not all particles if(b->isDynamic()) NumberOfDynamicParticles++; } LBbodies[id].force=Vector3r::Zero(); LBbodies[id].momentum=Vector3r::Zero(); } /*------------------------------------------------------------------*/ /*------------------ detection of boundary nodes -------------------*/ /*------------------------------------------------------------------*/ #pragma omp parallel for for (int nidx=0; nidx1) ) MODE = 1; if((IterSubCyclingStart<=0) && (IterMax==1) ) MODE = 2; if(IterSubCyclingStart>0) MODE = 3; /*------------------------------------------------------------------*/ /*---------------------------- SUBCYCLING --------------------------*/ /*------------------------------------------------------------------*/ if(MODE==3&&IterMaxdt=newDEMdt; if(SaveMode==2){ IterSave=TimeSave/(dt); if(TimeSavedt; DEM_TIME=DEM_ITER*DEMdt; for (iter=0; iter& b, *scene->bodies){ if(!b) continue; const int id=b->getId(); LBbodies[id].force=Vector3r::Zero(); LBbodies[id].momentum=Vector3r::Zero();} } /*------------------------------------------------------------------*/ /* GENERAL REINITIALIZATION */ /*------------------------------------------------------------------*/ // Vector3r WallBottomVel=Vector3r::Zero();//m s-1 FmoyCur=0.; VmeanFluidC=0.; VmaxC=-1000000.; VminC=1000000.; RhomaxC=-1000000.; RhominC=1000000.;RhoTot=0.; /*------------------------------------------------------------------*/ /* Loop on nodes */ /*------------------------------------------------------------------*/ #pragma omp parallel for for (int nidx=0; nidxc*nodes[nidx].velb.norm()) VminC=c*nodes[nidx].velb.norm(); if(RhomaxCRho*nodes[nidx].rhob) RhominC=Rho*nodes[nidx].rhob; if(!nodes[nidx].isObstacle) VmeanFluidC+=c*nodes[nidx].velb.norm(); } #pragma omp parallel for for(unsigned int lid=0;lid=5) {links[lid].VbMid=Vector3r::Zero();links[lid].ct=0.;} nodes[fid].f[opp[idx_sigma_i]] = nodes[fid].fpostcol[idx_sigma_i] - 2.0*links[lid].ct; nodes[sid].f[idx_sigma_i] = nodes[sid].fpostcol[opp[idx_sigma_i]]+ 2.0*links[lid].ct; if( (MODE==2)||((MODE==3)&&(IterMax==1)) ) {links[lid].ReinitDynamicalProperties();} } VmeanFluidC=VmeanFluidC/NbFluidNodes; /*---------------------------------------------*/ /* Stop criteria */ /*---------------------------------------------*/ // if(use_ConvergenceCriterion){ // switch(ErrorCriterion){ // case 1: // /*--------------------------------------------------------*/ // /* Criterion based on the mean force */ // /*--------------------------------------------------------*/ // if((LBM_ITER > 1000) & (LBM_ITER % 10 == 0)){ // for (int s=NB_WALLS ; s 100) & (LBM_ITER % 10 == 0)){ // if (VmeanFluidC!=0.){ // Real ErrorA = std::abs(VmeanFluidC-PrevVmeanFluidC)/std::abs(VmeanFluidC); // //Real ErrorB = std::abs(VmeanFluidC-PrevPrevVmeanFluidC)/std::abs(VmeanFluidC); // //Error=max(ErrorA,ErrorB); // Error= ErrorA; // PrevPrevVmeanFluidC=PrevVmeanFluidC; // PrevVmeanFluidC=VmeanFluidC; // } // } // break; // default: // cerr <<"Unknow ErrorCriterion value ! "< (m/s)= "<0)){ cerr <<"| VminPtcC (m/s)\t: "<0)&&(iter+1>=IterSubCyclingStart)) {modeTransition();} if ((Error < ConvergenceThreshold)&&(use_ConvergenceCriterion)) { if(MODE==1) break; if(MODE==3) modeTransition(); } if((EndTime>0)&&(LBM_TIME>EndTime)) LbmEnd(); //if((InitialNumberOfDynamicParticles!=0)&&(NumberPtcEroded==InitialNumberOfDynamicParticles)) LbmEnd(); } /*------------------- End of the LBM loop (iterations) --------------------*/ if(MODE==1) { cerr << "LBM ended after " << step << " iterations"; cerr <<" | LBM_ITER = "<< LBM_ITER<<" | Error = " << Error << endl; } /*--------------------------------------------------------------------------------*/ /*-------------- APPLICATION OF HYDRODYNAMIC FORCES ON SPHERES -------------------*/ /*--------------------------------------------------------------------------------*/ if(applyForcesAndTorques) CalculateAndApplyForcesAndTorquesOnBodies(true,true); /*----------------------------------------------------------------------------*/ /*----------------- SPHERES ARE MOVED OUTSIDE THE SIMULATION DOMAIN --------- */ /*----------------------------------------------------------------------------*/ //if(removingCriterion!=0){ // for(unsigned int aa=0; aa b=Body::byId(IdRemoved); // const shared_ptr& sphere = YADE_PTR_CAST ( b->shape ); // Real r=sphere->radius; // outside_limit=outside_limit+1.1*r; // b->state->pos=Vector3r(outside_limit,0.,0.); // b->setDynamic(false); // NB_DYNGRAINS--; // NB_DYNBODIES--; // outside_limit=outside_limit+1.1*r; // cerr <<"Eroded Ptc: "<=0){ FxLBMfile<< 2.*Rho*c2*dx*(LBbodies[nodes[nidx].body_id].force.x()) << " "; FyLBMfile<< 2.*Rho*c2*dx*(LBbodies[nodes[nidx].body_id].force.y()) << " "; MzLBMfile<< 2.*Rho*c2*dx2*LBbodies[nodes[nidx].body_id].momentum.z() << " "; } else{FxLBMfile<< 0. << " ";FyLBMfile<< 0. << " ";MzLBMfile<< 0. << " ";}} if(SAVE_RHO) Rhofile << Rho*nodes[nidx].rhob << " "; if(SAVE_NODEBD) { int tmp=0; if(nodes[nidx].isObstacleBoundary) tmp=nodes[nidx].isObstacleBoundary; if(nodes[nidx].isFluidBoundary) tmp= -1; NodeBoundaryfile << tmp << " ";} if(SAVE_NODEISNEW) { int tmp=0; if(nodes[nidx].isNewObstacle) tmp=nodes[nidx].isNewObstacle; if(nodes[nidx].isNewFluid) tmp=-1; NewNodefile << tmp << " ";} if(nodes[nidx].i==Nx-1){ if(SAVE_BODIES) Bodiesfile<< endl; if(SAVE_VELOCITY) Vfile<< endl; if(SAVE_VELOCITYCOMP){Vxfile<< endl;Vyfile<< endl;} if(SAVE_FORCES){FxLBMfile << endl;FyLBMfile << endl;MzLBMfile << endl;} if(SAVE_RHO) Rhofile << endl; if(SAVE_NODEBD) NodeBoundaryfile << endl; if(SAVE_NODEISNEW) NewNodefile << endl; } } } std::stringstream cmd; cmd<<"bzip2"; if(SAVE_BODIES) {Bodiesfile.close();cmd<<" "< 0 is done earlier when recording configuration is done spherefile_name.str(""); spherefile_name<0) {ofstream file3(spherefile_name.str().c_str());file3.close();} //For what this line is used for? It seems to work without if(SAVE_OBSERVEDPTC){ //Condition to create observedPtc file only if the recording is required by the operator ofstream file4(ObservedPtcFile.c_str()); file4 <<"#iter t x y z r Vx Vy Vz Wx Wy Wz Fx Fy Fz Mx My Mz"<0) bfs::create_directory(bfs::path(dem_dir)); //ModLuc: to create only necessary directory if(dirDem) bfs::create_directory(bfs::path(dem_dir)); //if(SAVE_CONTACTINFO) bfs::create_directory(bfs::path(cntct_dir)); //ModLuc: to create only necessary directory if(dirCntct) bfs::create_directory(bfs::path(cntct_dir)); return; } void HydrodynamicsLawLBM::writelogfile() { ofstream file(LBMlogFile.c_str()); file <<"File format: 1"<0) file <<"\t NbNodePerPtc= "<& b, *scene->bodies){ if(!b) continue; const int id=b->getId(); //if ( ((b->isDynamic())&&(b->shape->getClassName()=="Sphere")) || (b->shape->getClassName()=="Box") ){ //ModLuc: remove the condition (b->isDynamic()) to be able to apply force and torque on non dynamic bodies, by this way hydrodynamic force and torque on bodies can be read through python even if bodies are non dynamic. if ( (b->shape->getClassName()=="Sphere") || (b->shape->getClassName()=="Box") ){ if(mean){ LBbodies[id].fp=LBbodies[id].force; LBbodies[id].force=0.5*(LBbodies[id].fp+LBbodies[id].fm); LBbodies[id].fm=LBbodies[id].fp; LBbodies[id].mp=LBbodies[id].momentum; LBbodies[id].momentum=0.5*(LBbodies[id].mp+LBbodies[id].mm); LBbodies[id].mm=LBbodies[id].mp; LBbodies[id].Fh=2.*Rho*c2*dx*LBbodies[id].force; LBbodies[id].Mh=2.*Rho*c2*dx2*LBbodies[id].momentum; FhTotale=FhTotale+LBbodies[id].Fh; } if(apply){ scene->forces.addForce(id, LBbodies[id].Fh); scene->forces.addTorque(id, LBbodies[id].Mh); } } } return; } YADE_PLUGIN((HydrodynamicsLawLBM)); #endif //LBM_ENGINE trunk-2017.01a/pkg/lbm/HydrodynamicsLawLBM.hpp000066400000000000000000000472171304022710500210550ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2009-2012 by Franck Lominé * * franck.lomine@insa-rennes.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * * * * Luc Scholtès luc.scholtes@univ-lorraine.fr * * and Luc Sibille luc.sibille@3sr-grenoble.fr also contributed to this * * code. * * * * Lominé F., Scholtès L., Sibille L., Poullain P. (2013) * * Modelling of fluid-solid interaction in granular media with coupled * * LB/DE methods: application to piping erosion. International Journal * * for Numerical and Analytical Methods in Geomechanics, 37(6):577-596 * * doi: 10.1002/nag.1109 * * * * Sibille L., Lominé F., Marot D. (2012) Investigation In Modelling * * Piping Erosion With a Coupled «Lattice Boltzmann – Discrete Element» * * Numerical Method. in Proc. 6th Int. Conference on Scour and Erosion * * (ICSE-6), pp. 93-100. * * * *************************************************************************/ #ifdef LBM_ENGINE #pragma once #include #include #include #include class HydrodynamicsLawLBM : public GlobalEngine { private : std::ofstream ofile; public : bool firstRun, /*! = 1 if it is the first iteration during 1 YADE simulation*/ use_ConvergenceCriterion, /*! use stop condition based on the convergence criterion*/ SAVE_VELOCITY, /*! Switch to save node velocities*/ SAVE_VELOCITYCOMP, /*! Switch to save node velocities in each directions*/ SAVE_RHO, /*! Switch to save node densities*/ SAVE_FORCES, /*! Switch to save node force and momentum on grid*/ SAVE_BODIES, /*! Switch to save particle nodes*/ SAVE_NODEBD, /*! Switch to save fluid or solid boundary nodes*/ SAVE_NODEISNEW, /*! Switch to save new fluid/solid nodes*/ SAVE_DEBUGFILES, /*! Switch to save some debug data*/ SAVE_OBSERVEDPTC, /*! Switch to save properties of the observed particle*/ SAVE_OBSERVEDNODE, /*! Switch to save properties of the observed node*/ SAVE_CONTACTINFO, /*! Switch to save contact properties*/ SAVE_SPHERES, /*! Switch to save spheres properties*/ COMPRESS_DATA, /*! Switch to enable file compression*/ Xperiodicity, /*! Switch to activate lattice periodicity in x direction*/ Yperiodicity, /*! Switch to activate lattice periodicity in y direction*/ Zperiodicity; /*! Switch to activate lattice periodicity in z direction*/ int NB_BODIES, /*! Number of bodies*/ NB_GRAINS, /*! number of grains*/ NB_DYNGRAINS, /*! number of dynamic grains*/ NB_DYNBODIES, /*! number of dynamic bodies*/ NB_WALLS, /*! Number of walls*/ DEM_ITER, /*! Number of iteration of the DEM loop*/ LBM_ITER, /*! Number of iteration of the LBM loop*/ MODE, /*! 1->only a LBM loop, 2->lbm subcycling, 3->lbm subcycling after lbm loop*/ dim, /*! dimension*/ NbDir, /*! number of directions of the lattice model*/ NbNodes, /*! Total number of nodes*/ NbFluidNodes, /*! Number of fluid nodes*/ NbSolidNodes, /*! Number of solid nodes*/ NbParticleNodes, /*! Number of particle nodes*/ NbContacts, /*! Number of Contact*/ InitialNumberOfDynamicParticles,/*! Initial number of dynamic particles*/ NumberOfDynamicParticles, /*! Number of dynamic particles*/ Ny, /*! Number of grid divisions in y direction */ Nz, /*! Number of grid divisions in z direction */ NumberPtcEroded, /*! The bumber of eroded/removed particles*/ iter, /*! LBM Iteration number in current DEM loop (=1 in mode=2)*/ IdFirstSphere; /*! Id of the first sphere*/ Real height, /*! System height */ width, /*! System width */ depth, /*! System depth */ halfWallthickness, /*! Half Wall thickness */ Wallthickness, /*! Wall thickness */ cub, /*! A temporary variable to calculate equilibrium distribution function */ c, /*! Lattice speed */ c2, /*! The squared lattice speed*/ dx, /*! The lattice size*/ invdx, /*! 1 / lattice size*/ dx2, /*! The squared lattice size*/ uMax, /// TODO: PLEASE EXPLAIN uMax cs, /*! c/sqrt(3) */ dt, /*! LBM timestep */ invdt, /*! one over LBM timestep */ nu, /*! LBM kinematic viscosity */ feqb, /*! Equilibrium distribution function*/ omega, /*! 1/tau */ Lx0, /*! LBM grid size in x direction*/ Ly0, /*! LBM grid size in y direction*/ Lz0, /*! LBM grid size in z direction*/ outside_limit, /*! the x coordinate of a point outside the system*/ DEMdt, /*! timestep for the DEM iteration*/ DEMdt0, /*! original timestep for the DEM iteration*/ newDEMdt, /*! the new timestep for the DEM iteration*/ Vr, /*! Volume of the removed particles*/ Vo, /*! Initial volume of dynamic particles */ VmeanFluidC, /*! Current mean fluid velocity */ PrevVmeanFluidC, /*! Previous mean fluid velocity */ PrevPrevVmeanFluidC, /*! Previous previous mean fluid velocity */ VmaxC, /*! Maximum velocity during the current time step*/ VminC, /*! Minimum velocity during the current time step*/ RhomaxC, /*! Maximum density during the current time step*/ RhominC, /*! Minimum density during the current time step*/ LBM_TIME, /*! The time ellapsed in the LB method*/ DEM_TIME, /*! The time ellapsed in the DE method*/ RhoTot, /*! Cumulative density*/ FmoyCur, /*! Mean force at the current LB iteration*/ FmoyPrev, /*! Mean force at the previous LB iteration*/ FmoyPrevPrev, /*! Mean force at 2 previous LB iteration*/ UMaxtheo, /// TODO: PLEASE EXPLAIN UMaxtheo MaxBodyRadius, /*! Max radius of spheres*/ MinBodyRadius, /*! Min radius of spheres*/ MeanBodyRadius; /*! Mean radius of spheres*/ std::string LBMlogFile, /*! Name of the logfile */ LBMmachFile, /*! Name of the stat file */ LBMcontactsFile, /*! Name of the contact file */ RemovedPtcFile, /*! Name of the file to store removed particle informations*/ ObservedPtcFile, /*! Name of the file to store observed particle informations*/ ObservedNodeFile, /*! Name of the file to store observed particle informations*/ lbm_dir, /*! Directory name to save LBM files */ dem_dir, /*! Directory name to save DEM files */ cntct_dir; /*! Directory name to save contact properties */ std::stringstream spherefile_name; /*! Name of the file where sphere data are saved*/ vector IdOfNextErodedPtc, /*! List of particles which will be eroded*/ opp; /*! opposite nodes */ vector w; /*! Weighting factor */ vector nodes; /*! the LBM nodes*/ vector links; /*! the LBM links*/ vector LBbodies; /*! the LBM bodies*/ vector eib; /*! node velocity directions*/ Vector3r FhTotale; ///Total hydrodynamic force virtual ~HydrodynamicsLawLBM (); virtual bool isActivated(); virtual void action(); void save(int iter_number, Real timestep); void saveStats(int iter_number, Real timestep); void saveEroded(int iter_number, Real timestep); void saveContacts(int iter_number, Real timestep); void saveObservedNode(int iter_number, Real timestep); void saveObservedPtc(int iter_number, Real timestep); void createNewFiles(); //void createDirectories(); // ModLuc: to create directories only if necessary void createDirectories(bool dirLBM, bool dirDem, bool dirCntct); void writelogfile(); void modeTransition(); void LbmEnd(); void CalculateAndApplyForcesAndTorquesOnBodies(bool mean,bool apply); YADE_CLASS_BASE_DOC_ATTRS_CTOR(HydrodynamicsLawLBM,GlobalEngine,"Engine to simulate fluid flow (with the lattice Boltzmann method) with a coupling with the discrete element method.\n If you use this Engine, please cite and refer to F. Lominé et al. International Journal For Numerical and Analytical Method in Geomechanics, 2012, doi: 10.1002/nag.1109", ((int,WallYm_id,0,,"Identifier of the Y- wall")) ((bool,useWallYm,true,,"Set true if you want that the LBM see the wall in Ym")) ((int,YmBCType,2,,"Boundary condition for the wall in Ym (-1: unused, 1: pressure condition, 2: velocity condition).")) ((Vector3r,YmBcVel,Vector3r::Zero(),,"(!!! not fully implemented !!) The velocity imposed at the boundary")) ((Real,YmBcRho,-1,,"(!!! not fully implemented !!) The density imposed at the boundary")) ((int,WallYp_id,1,,"Identifier of the Y+ wall")) ((bool,useWallYp,true,,"Set true if you want that the LBM see the wall in Yp")) ((int,YpBCType,2,,"Boundary condition for the wall in Yp (-1: unused, 1: pressure condition, 2: velocity condition).")) ((Vector3r,YpBcVel,Vector3r::Zero(),,"(!!! not fully implemented !!) The velocity imposed at the boundary")) ((Real,YpBcRho,-1,,"(!!! not fully implemented !!) The density imposed at the boundary")) ((int,WallXm_id,2,,"Identifier of the X- wall")) ((bool,useWallXm,false,,"Set true if you want that the LBM see the wall in Xm")) ((int,XmBCType,1,,"Boundary condition for the wall in Xm (-1: unused, 1: pressure condition, 2: velocity condition).")) ((Vector3r,XmBcVel,Vector3r::Zero(),,"(!!! not fully implemented !!) The velocity imposed at the boundary")) ((Real,XmBcRho,-1,,"(!!! not fully implemented !!) The density imposed at the boundary")) ((int,WallXp_id,3,,"Identifier of the X+ wall")) ((bool,useWallXp,false,,"Set true if you want that the LBM see the wall in Xp")) ((int,XpBCType,1,,"Boundary condition for the wall in Xp (-1: unused, 1: pressure condition, 2: velocity condition).")) ((Vector3r,XpBcVel,Vector3r::Zero(),,"(!!! not fully implemented !!) The velocity imposed at the boundary")) ((Real,XpBcRho,-1,,"(!!! not fully implemented !!) The density imposed at the boundary")) ((int,WallZp_id,5,,"Identifier of the Z+ wall")) ((bool,useWallZp,false,,"Set true if you want that the LBM see the wall in Zp")) ((int,ZpBCType,-1,,"Boundary condition for the wall in Zp (-1: unused, 1: pressure condition, 2: velocity condition).")) ((Vector3r,ZpBcVel,Vector3r::Zero(),,"(!!! not fully implemented !!) The velocity imposed at the boundary")) ((Real,zpBcRho,-1,,"(!!! not fully implemented !!) The density imposed at the boundary")) ((int,WallZm_id,4,,"Identifier of the Z- wall")) ((bool,useWallZm,false,,"Set true if you want that the LBM see the wall in Zm")) ((int,ZmBCType,-1,,"Boundary condition for the wall in Zm (-1: unused, 1: pressure condition, 2: velocity condition).")) ((Vector3r,ZmBcVel,Vector3r::Zero(),,"(!!! not fully implemented !!) The velocity imposed at the boundary")) ((Real,ZmBcRho,-1,,"(!!! not fully implemented !!) The density imposed at the boundary")) ((int,XmYmZpBCType,2,,"Boundary condition for the corner node XmYmZp (-1: unused, 1: pressure condition, 2: velocity condition).")) ((int,XmYpZpBCType,2,,"Boundary condition for the corner node XmYpZp (-1: unused, 1: pressure condition, 2: velocity condition).")) ((int,XpYmZpBCType,2,,"Boundary condition for the corner node XpYmZp (-1: unused, 1: pressure condition, 2: velocity condition).")) ((int,XpYpZpBCType,2,,"Boundary condition for the corner node XpYpZp (-1: unused, 1: pressure condition, 2: velocity condition).")) ((int,XmYmZmBCType,-1,,"Boundary condition for the corner node XmYmZm (not used with d2q9, -1: unused, 1: pressure condition, 2: velocity condition).")) ((int,XmYpZmBCType,-1,,"Boundary condition for the corner node XmYpZm (not used with d2q9, -1: unused, 1: pressure condition, 2: velocity condition).")) ((int,XpYmZmBCType,-1,,"Boundary condition for the corner node XpYmZm (not used with d2q9, -1: unused, 1: pressure condition, 2: velocity condition).")) ((int,XpYpZmBCType,-1,,"Boundary condition for the corner node XpYpZm (not used with d2q9, -1: unused, 1: pressure condition, 2: velocity condition).")) ((int,defaultLbmInitMode,0,,"Switch between the two initialisation methods")) ((Vector3r,dP,Vector3r(0.,0.,0.),,"Pressure difference between input and output")) ((Real,Rho,1000.,,"Fluid density")) ((Real,Nu,0.000001,,"Fluid kinematic viscosity")) ((Real,tau,0.6,,"Relaxation time")) ((int,Nx,1000,,"The number of grid division in x direction")) ((int,IterMax,1,,"This variable can be used to do several LBM iterations during one DEM iteration. ")) ((int,IterPrint,1,,"Print info on screen every IterPrint iterations")) ((int,SaveMode,1,,"Save Mode (1-> default, 2-> in time (not yet implemented)")) ((int,IterSave,100,,"Data are saved every IterSave LBM iteration (or see TimeSave)")) ((Real,TimeSave,-1,,"Data are saved at constant time interval (or see IterSave)")) ((int,SaveGridRatio,1,,"Grid data are saved every SaveGridRatio * IterSave LBM iteration (with SaveMode=1)")) ((int,IterSubCyclingStart,-1,,"Iteration number when the subcycling process starts")) ((int,DemIterLbmIterRatio,-1,,"Ratio between DEM and LBM iterations for subcycling")) ((bool,EngineIsActivated,true,,"To activate (or not) the engine")) ((bool,applyForcesAndTorques,true,,"Switch to apply forces and torques")) ((int,ObservedNode,-1,,"The identifier of the node that will be observed (-1 means none)")) ((int,ObservedPtc,-1,,"The identifier of the particle that will be observed (-1 means the first one)")) ((Real,RadFactor,1.0,,"The radius of DEM particules seen by the LBM is the real radius of particules*RadFactor")) ((Real,ConvergenceThreshold,0.000001,,"")) ((std::string,LBMSavedData," ",,"a list of data that will be saved. Can use velocity,velXY,forces,rho,bodies,nodeBD,newNode,observedptc,observednode,contacts,spheres,bz2")) ((std::string,periodicity," ",,"periodicity")) ((std::string,bc," ",,"Boundary condition")) ((std::string,model,"d2q9",,"The LB model. Until now only d2q9 is implemented")) ((int,removingCriterion ,0,,"Criterion to remove a sphere (1->based on particle position, 2->based on particle velocity")) ((Real,VelocityThreshold,-1.,,"Velocity threshold when removingCriterion=2")) ((Real,EndTime,-1,,"the time to stop the simulation")) ((Vector3r,CstBodyForce,Vector3r::Zero(),,"A constant body force (=that does not vary in time or space, otherwise the implementation introduces errors)")) ((Real,VbCutOff,-1,,"the minimum boundary velocity that is taken into account")) , firstRun = true; omega = 1.0/tau; DEM_TIME = 0.; LBM_TIME = 0.; iter = 0; use_ConvergenceCriterion = true; MODE=0; dim=0; NbDir=0; NbNodes=0; NbFluidNodes=0; NbSolidNodes=0; NbParticleNodes=0; NbContacts=0; InitialNumberOfDynamicParticles=0; NumberOfDynamicParticles=0; NumberPtcEroded=0; Vr=0.; Vo=0.; MaxBodyRadius=-1000000.; MinBodyRadius=1000000.; MeanBodyRadius=0.; lbm_dir="lbm-nodes"; dem_dir="dem-bodies"; cntct_dir="contacts"; LBMlogFile ="LBM.log"; LBMmachFile ="LBM.mach"; LBMcontactsFile ="LBM.cntct"; RemovedPtcFile="eroded.dat"; ObservedPtcFile="observedPtc.dat"; ObservedNodeFile="observedNode.dat"; COMPRESS_DATA = false; SAVE_VELOCITY = false; SAVE_VELOCITYCOMP = false; SAVE_RHO = false; SAVE_FORCES = false; SAVE_BODIES = false; SAVE_NODEBD = false; SAVE_NODEISNEW = false; SAVE_DEBUGFILES = false; SAVE_OBSERVEDPTC= false; SAVE_OBSERVEDNODE=false; SAVE_CONTACTINFO =false; SAVE_SPHERES = false; //to save spheres_* files only if it is required by the operator Xperiodicity = false; Yperiodicity = false; Zperiodicity = false; Ny = 0;Nz = 0; FmoyCur=0.;FmoyPrev=0.; FmoyPrevPrev=0.;VmeanFluidC=0.;PrevVmeanFluidC=0.;PrevPrevVmeanFluidC=0.; LBM_ITER=0; DEM_ITER=0; IdFirstSphere=-1; timingDeltas=shared_ptr(new TimingDeltas); ); DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(HydrodynamicsLawLBM); #endif //LBM_ENGINE trunk-2017.01a/pkg/lbm/LBMbody.hpp000066400000000000000000000044541304022710500165250ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2009-2012 by Franck Lominé * * franck.lomine@insa-rennes.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * * * *************************************************************************/ #ifdef LBM_ENGINE #pragma once #include #include class LBMbody: public Serializable{ public: virtual ~LBMbody() {}; //Real radius(){return ext[0];} bool isBox(){if(type==1)return true; else return false;} bool isPtc(){if(type==2)return true; else return false;} void setAsPtc(){type=2;} void setAsBox(){type=1;} YADE_CLASS_BASE_DOC_ATTRS_CTOR(LBMbody,Serializable, "Body class for Lattice Boltzmann Method ", ((Vector3r,force,Vector3r::Zero(),,"Hydrodynamic force, need to be reinitialized (LB unit)")) ((Vector3r,fm,Vector3r::Zero(),,"Hydrodynamic force (LB unit) at t-0.5dt")) ((Vector3r,fp,Vector3r::Zero(),,"Hydrodynamic force (LB unit) at t+0.5dt")) ((Vector3r,momentum,Vector3r::Zero(),,"Hydrodynamic momentum,need to be reinitialized (LB unit)")) ((Vector3r,mm,Vector3r::Zero(),,"Hydrodynamic momentum (LB unit) at t-0.5dt")) ((Vector3r,mp,Vector3r::Zero(),,"Hydrodynamic momentum (LB unit) at t+0.5dt")) ((Vector3r,pos,Vector3r::Zero(),,"Position of body")) ((Vector3r,vel,Vector3r::Zero(),,"Velocity of body")) ((Vector3r,AVel,Vector3r::Zero(),,"Angular velocity of body")) ((Vector3r,Fh,Vector3r::Zero(),,"Hydrodynamical force on body")) ((Vector3r,Mh,Vector3r::Zero(),,"Hydrodynamical momentum on body")) ((Real,radius,-1000.,,"Radius of body (for sphere)")) ((bool,isEroded,false,,"Hydrodynamical force on body")) ((bool,saveProperties,false,,"To save properties of the body")) ((short int,type,-1,," ")) , ); }; REGISTER_SERIALIZABLE(LBMbody); #endif //LBM_ENGINE trunk-2017.01a/pkg/lbm/LBMlink.hpp000066400000000000000000000037761304022710500165330ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2009-2012 by Franck Lominé * * franck.lomine@insa-rennes.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * * * *************************************************************************/ #ifdef LBM_ENGINE #pragma once #include #include class LBMlink: public Serializable{ public: void ReinitDynamicalProperties() { sid=-1; fid=-1; idx_sigma_i=-1; isBd=false; VbMid=Vector3r::Zero(); DistMid=Vector3r::Zero(); ct=0.; return; }; virtual ~LBMlink() {}; YADE_CLASS_BASE_DOC_ATTRS_CTOR(LBMlink,Serializable, "Link class for Lattice Boltzmann Method ", ((int,sid,-1,,"Solid node identifier ")) ((int,fid,-1,,"Fluid node identifier ")) ((short int,i,-1,,"direction index of the link")) ((int,nid1,-1,,"fixed node identifier")) ((int,nid2,-1,,"fixed node identifier or -1 if node points outside")) ((short int,idx_sigma_i,-1,,"sigma_i direction index (Fluid->Solid)")) ((bool,isBd,false,,"True if it is a boundary link")) ((bool,PointingOutside,false,,"True if it is a link pointing outside to the system (from a fluid or solid node)")) ((Vector3r,VbMid,Vector3r::Zero(),,"Velocity of boundary at midpoint")) ((Vector3r,DistMid,Vector3r::Zero(),,"Distance between middle of the link and mass center of body")) ((Real,ct,0.,,"Coupling term in modified bounce back rule")), ); }; REGISTER_SERIALIZABLE(LBMlink); #endif //LBM_ENGINE trunk-2017.01a/pkg/lbm/LBMnode.cpp000066400000000000000000000116351304022710500165070ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2009-2012 by Franck Lominé * * franck.lomine@insa-rennes.fr * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * * * *************************************************************************/ #ifdef LBM_ENGINE #include "LBMnode.hpp" #include "LBMlink.hpp" #include "LBMbody.hpp" YADE_PLUGIN((LBMnode)(LBMlink)(LBMbody)); LBMnode::~LBMnode(){}; void LBMnode::MixteBC(string lbmodel,Real density, Vector3r U, string where){ Real rhoVx=density*U.x(); Real rhoVy=density*U.y(); if(!strcmp(lbmodel.c_str(), "d2q9" )){ if(!strcmp(where.c_str(), "Xm" )){ f[1]=f[3]+(2./3.)*rhoVx; f[5]=f[7]-0.5*(f[2]-f[4])+(1./6.)*rhoVx+ 0.5*rhoVy; f[8]=f[6]+0.5*(f[2]-f[4])+(1./6.)*rhoVx- 0.5*rhoVy; } else if(!strcmp(where.c_str(), "Xp" )){ f[3]=f[1]-(2./3.)*rhoVx; f[7]=f[5]+0.5*(f[2]-f[4])-(1./6.)*rhoVx - 0.5*rhoVy; f[6]=f[8]-0.5*(f[2]-f[4])-(1./6.)*rhoVx + 0.5*rhoVy; } else if(!strcmp(where.c_str(), "Ym" )){ f[2]=f[4]+(2./3.)*rhoVy; f[5]=f[7]-0.5*(f[1]-f[3])+0.5*rhoVx + (1./6.)*rhoVy; f[6]=f[8]+0.5*(f[1]-f[3])-0.5*rhoVx + (1./6.)*rhoVy; } else if(!strcmp(where.c_str(), "Yp" )){ f[4]=f[2]-(2./3.)*rhoVy; f[7]=f[5]+0.5*(f[1]-f[3])-0.5*rhoVx- (1./6.)*rhoVy; f[8]=f[6]-0.5*(f[1]-f[3])+0.5*rhoVx -(1./6.)*rhoVy; } else if(!strcmp(where.c_str(), "XmYmZp" )){ f[1]=f[3]+(2./3.)*rhoVx; f[2]=f[4]+(2./3.)*rhoVy; f[5]=f[7] + (1./6.)*density*(U.x()+U.y()); f[6]=0.5*(density*(1.-U.x() -(2./3.)*U.y())-f[0]-2.*(f[3]+f[4]+f[7])); f[8]=0.5*(density*(1.-(2./3.)*U.x() -U.y())-f[0]-2.*(f[3]+f[4]+f[7])); } else if(!strcmp(where.c_str(), "XmYpZp" )){ f[1]=f[3]+(2./3.)*rhoVx; f[4]=f[2]-(2./3.)*rhoVy; f[5]=0.5*(density*(1.-(2./3.)*U.x()+U.y())-f[0]-2.*(f[2]+f[3]+f[6])); f[7]=0.5*(density*(1.-U.x()+(2./3.)*U.y())-f[0]-2.*(f[2]+f[3]+f[6])); f[8]=f[6]+(1./6.)*density*(U.x()-U.y()); } else if(!strcmp(where.c_str(), "XpYmZp" )){ f[2]=f[4]+(2./3.)*rhoVy; f[3]=f[1]-(2./3.)*rhoVx; f[5]=0.5*(density*(1.+U.x()-(2./3.)*U.y())-f[0]-2.*(f[1]+f[4]+f[8])); f[6]=f[8]-(1./6.)*density*(U.x()-U.y()); f[7]=0.5*(density*(1.+(2./3.)*U.x()-U.y())-f[0]-2.*(f[1]+f[4]+f[8])); } else if(!strcmp(where.c_str(), "XpYpZp" )){ f[3]=f[1]-(2./3.)*rhoVx; f[4]=f[2]-(2./3.)*rhoVy; f[6]=0.5*(density*(1.+(2./3.)*U.x()+U.y())-f[0]-2.*(f[1]+f[2]+f[5])); f[7]=f[5]-(1./6.)*density*(U.x()+U.y()); f[8]=0.5*(density*(1.+U.x()+(2./3.)*U.y())-f[0]-2.*(f[1]+f[2]+f[5])); } else {exit(-1);} }else {exit(-1);} return; } bool LBMnode::checkIsNewObstacle(){ if(isObstacle){ if(!wasObstacle) {isNewObstacle=true;wasObstacle=true;} else {isNewObstacle=false;wasObstacle=true;} return(isNewObstacle); } else return(false); } bool LBMnode::checkIsNewFluid(){ if(!isObstacle){ if(wasObstacle) {isNewFluid=true;wasObstacle=false;} else {isNewFluid=false;wasObstacle=false;} return(isNewFluid); } else return(false); } void LBMnode::DispatchBoundaryConditions(int SizeNx,int SizeNy,int SizeNz){ applyBC =false; applyXmBC =false; applyYmXmBC =false; applyYpXmBC =false; applyXpBC =false; applyYmXpBC =false; applyYpXpBC =false; applyYpBC =false; applyYmBC =false; if((i==0)&&(j>0)&&(j0)&&(j0)&&(i0)&&(i #include class LBMnode: public Serializable{ public: int i, /*! node index in x direction */ j, /*! node index in y direction */ k, /*! node index in z direction */ body_id; /*! the node belongs to the body indexed with body_id*/ short int IsolNb; /*! number of boundary links of a fluid boundary nodes*/ bool isObstacle, /*! the node belongs to an obstacle */ isObstacleBoundary, /*! the node is an obstacle boundary */ isFluidBoundary, /*! the node is a fluid boundary */ wasObstacle, /*! the node was an obstacle */ isNewObstacle, /*! the node is an new obstacle node */ isNewFluid, /*! the node is an new fluid node */ applyBC, /*! the node is subject to the one boundary condition */ applyXmBC, /*! the node is subject to the left boundary condition */ applyXpBC, /*! the node is subject to the right boundary condition */ applyYpBC, /*! the node is subject to the top boundary condition */ applyYmBC, /*! the node is subject to the bottom boundary condition */ applyZpBC, /*! the node is subject to the front boundary condition NOT USED NOW*/ applyZmBC, /*! the node is subject to the back boundary condition NOT USED NOW*/ applyYmXmBC, /*! the node is subject to the bottom-left boundary condition */ applyYpXmBC, /*! the node is subject to the top-left boundary condition */ applyYmXpBC, /*! the node is subject to the bottom-right boundary condition */ applyYpXpBC; /*! the node is subject to the top-right boundary condition */ Vector3r posb, /*! the node position */ velb; /*! the node velocity */ Real rhob; /*! the node density */ /*! the node density */ vector neighbour_id; /*! list of adjacent nodes */ vector links_id; /*! list of links */ vector f; vector fprecol; vector fpostcol; void DispatchBoundaryConditions(int SizeNx,int SizeNy,int SizeNz); bool checkIsNewFluid(); bool checkIsNewObstacle(); void MixteBC(string lbmodel,Real density, Vector3r U, string where); void SetCellIndexesAndPosition(int indI, int indJ, int indK); void setAsObstacle(){isObstacle=true;} void setAsFluid(){isObstacle=false;} virtual ~LBMnode(); YADE_CLASS_BASE_DOC(LBMnode,Serializable,"Node class for Lattice Boltzmann Method "); }; REGISTER_SERIALIZABLE(LBMnode); #endif //LBM_ENGINE trunk-2017.01a/pkg/pfv/000077500000000000000000000000001304022710500145365ustar00rootroot00000000000000trunk-2017.01a/pkg/pfv/DFNFlow.cpp000066400000000000000000000310601304022710500165010ustar00rootroot00000000000000 /************************************************************************* * Copyright (C) 2014 by Bruno Chareyre * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef FLOW_ENGINE #include // #include //keep this #ifdef for commited versions unless you really have stable version that should be compiled by default //it will save compilation time for everyone else //when you want it compiled, you can pass -DDFNFLOW to cmake, or just uncomment the following line // #define DFNFLOW #ifdef DFNFLOW #include "FlowEngine_DFNFlowEngineT.hpp" class DFNCellInfo : public FlowCellInfo_DFNFlowEngineT { public: Real anotherVariable; bool crack; // bool preExistingJoint; // void anotherFunction() {}; // DFNCellInfo() : FlowCellInfo(),crack(false) {} DFNCellInfo() : crack(false) {} }; class DFNVertexInfo : public FlowVertexInfo_DFNFlowEngineT { public: //same here if needed }; typedef CGT::_Tesselation > DFNTesselation; #ifdef LINSOLV class DFNBoundingSphere : public CGT::FlowBoundingSphereLinSolv #else class DFNBoundingSphere : public CGT::FlowBoundingSphere #endif { public: void saveVtk(const char* folder) { RTriangulation& Tri = T[noCache?(!currentTes):currentTes].Triangulation(); static unsigned int number = 0; char filename[80]; mkdir(folder, S_IRWXU | S_IRWXG | S_IROTH | S_IXOTH); sprintf(filename,"%s/out_%d.vtk",folder,number++); int firstReal=-1; //count fictious vertices and cells vtkInfiniteVertices=vtkInfiniteCells=0; FiniteCellsIterator cellEnd = Tri.finite_cells_end(); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++) { bool isDrawable = cell->info().isReal() && cell->vertex(0)->info().isReal() && cell->vertex(1)->info().isReal() && cell->vertex(2)->info().isReal() && cell->vertex(3)->info().isReal(); if (!isDrawable) vtkInfiniteCells+=1; } for (FiniteVerticesIterator v = Tri.finite_vertices_begin(); v != Tri.finite_vertices_end(); ++v) { if (!v->info().isReal()) vtkInfiniteVertices+=1; else if (firstReal==-1) firstReal=vtkInfiniteVertices; } basicVTKwritter vtkfile((unsigned int) Tri.number_of_vertices()-vtkInfiniteVertices, (unsigned int) Tri.number_of_finite_cells()-vtkInfiniteCells); vtkfile.open(filename,"test"); vtkfile.begin_vertices(); double x,y,z; for (FiniteVerticesIterator v = Tri.finite_vertices_begin(); v != Tri.finite_vertices_end(); ++v) { if (v->info().isReal()){ x = (double)(v->point().point()[0]); y = (double)(v->point().point()[1]); z = (double)(v->point().point()[2]); vtkfile.write_point(x,y,z);} } vtkfile.end_vertices(); vtkfile.begin_cells(); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != Tri.finite_cells_end(); ++cell) { bool isDrawable = cell->info().isReal() && cell->vertex(0)->info().isReal() && cell->vertex(1)->info().isReal() && cell->vertex(2)->info().isReal() && cell->vertex(3)->info().isReal(); if (isDrawable){vtkfile.write_cell(cell->vertex(0)->info().id()-firstReal, cell->vertex(1)->info().id()-firstReal, cell->vertex(2)->info().id()-firstReal, cell->vertex(3)->info().id()-firstReal);} } vtkfile.end_cells(); if (permeabilityMap){ vtkfile.begin_data("Permeability",CELL_DATA,SCALARS,FLOAT); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != Tri.finite_cells_end(); ++cell) { bool isDrawable = cell->info().isReal() && cell->vertex(0)->info().isReal() && cell->vertex(1)->info().isReal() && cell->vertex(2)->info().isReal() && cell->vertex(3)->info().isReal(); if (isDrawable){vtkfile.write_data(cell->info().s);} } vtkfile.end_data();} else{ vtkfile.begin_data("Pressure",CELL_DATA,SCALARS,FLOAT); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != Tri.finite_cells_end(); ++cell) { bool isDrawable = cell->info().isReal() && cell->vertex(0)->info().isReal() && cell->vertex(1)->info().isReal() && cell->vertex(2)->info().isReal() && cell->vertex(3)->info().isReal(); if (isDrawable){vtkfile.write_data(cell->info().p());} } vtkfile.end_data();} if (1){ averageRelativeCellVelocity(); vtkfile.begin_data("Velocity",CELL_DATA,VECTORS,FLOAT); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != Tri.finite_cells_end(); ++cell) { bool isDrawable = cell->info().isReal() && cell->vertex(0)->info().isReal() && cell->vertex(1)->info().isReal() && cell->vertex(2)->info().isReal() && cell->vertex(3)->info().isReal(); if (isDrawable){vtkfile.write_data(cell->info().averageVelocity()[0],cell->info().averageVelocity()[1],cell->info().averageVelocity()[2]);} } vtkfile.end_data();} if(1){ vtkfile.begin_data("fracturedCells",CELL_DATA,SCALARS,FLOAT); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != Tri.finite_cells_end(); ++cell) { bool isDrawable = cell->info().isReal() && cell->vertex(0)->info().isReal() && cell->vertex(1)->info().isReal() && cell->vertex(2)->info().isReal() && cell->vertex(3)->info().isReal(); if (isDrawable){vtkfile.write_data(cell->info().crack);} } vtkfile.end_data();} } }; typedef TemplateFlowEngine_DFNFlowEngineT DFNFlowEngineT; REGISTER_SERIALIZABLE(DFNFlowEngineT); YADE_PLUGIN((DFNFlowEngineT)); class DFNFlowEngine : public DFNFlowEngineT { public : void trickPermeability(); void trickPermeability (RTriangulation::Facet_circulator& facet,Real aperture, Real residualAperture); void trickPermeability (RTriangulation::Finite_edges_iterator& edge,Real aperture, Real residualAperture); void setPositionsBuffer(bool current); // void computeTotalFractureArea(Real totalFracureArea,bool printFractureTotalArea);/// Trying to get fracture's surface Real totalFracureArea; /// Trying to get fracture's surface YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(DFNFlowEngine,DFNFlowEngineT,"This is an enhancement of the FlowEngine for intact and fractured rocks that takes into acount pre-existing discontinuities and bond breakage between particles. The local conductivity around the broken link is calculated according to parallel plates model", ((Real, jointResidual, 0,,"calibration parameter for residual aperture of joints")) ((bool, updatePositions, false,,"update particles positions when rebuilding the mesh (experimental)")) ((bool, printFractureTotalArea, 0,,"The final fracture area computed through the network")) /// Trying to get fracture's surface , , , // .def("computeTotalFractureArea",&DFNFlowEngineT::computeTotalFractureArea," Compute and print the total fracture area of the network") /// Trying to get fracture's surface // .def("trickPermeability",&DFNFlowEngineT::trickPermeability,"measure the mean trickPermeability in the period") ) DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(DFNFlowEngine); YADE_PLUGIN((DFNFlowEngine)); //In this version, we never update positions when !updatePositions, i.e. keep triangulating the same positions void DFNFlowEngine::setPositionsBuffer(bool current) { vector& buffer = current? positionBufferCurrent : positionBufferParallel; if (!updatePositions && buffer.size()>0) return; buffer.clear(); buffer.resize(scene->bodies->size()); shared_ptr sph ( new Sphere ); const int Sph_Index = sph->getClassIndexStatic(); FOREACH ( const shared_ptr& b, *scene->bodies ) { if (!b || ignoredBody==b->getId()) continue; posData& dat = buffer[b->getId()]; dat.id=b->getId(); dat.pos=b->state->pos; dat.isSphere= (b->shape->getClassIndex() == Sph_Index); if (dat.isSphere) dat.radius = YADE_CAST(b->shape.get())->radius; dat.exists=true; } } void DFNFlowEngine::trickPermeability(RTriangulation::Facet_circulator& facet, Real aperture, Real residualAperture) { const RTriangulation& Tri = solver->T[solver->currentTes].Triangulation(); const CellHandle& cell1 = facet->first; const CellHandle& cell2 = facet->first->neighbor(facet->second); if ( Tri.is_infinite(cell1) || Tri.is_infinite(cell2)) cerr<<"Infinite cell found in trickPermeability, should be handled somehow, maybe"<info().kNorm()[facet->second]=cell2->info().kNorm()[Tri.mirror_index(cell1, facet->second)] = pow((aperture+residualAperture),3)/(12*viscosity); //For vtk recorder: cell1->info().crack= 1; cell2->info().crack= 1; cell2->info().blocked = cell1->info().blocked = cell2->info().Pcondition = cell1->info().Pcondition = false;//those ones will be included in the flow problem Point& CellCentre1 = cell1->info(); /// Trying to get fracture's surface Point& CellCentre2 = cell2->info(); /// Trying to get fracture's surface CVector networkFractureLength = CellCentre1 - CellCentre2; /// Trying to get fracture's surface double networkFractureDistance = sqrt(networkFractureLength.squared_length()); /// Trying to get fracture's surface Real networkFractureArea = pow(networkFractureDistance,2); /// Trying to get fracture's surface totalFracureArea += networkFractureArea; /// Trying to get fracture's surface // cout <<" ------------------ The total surface area up to here is --------------------" << totalFracureArea << endl; // printFractureTotalArea = totalFracureArea; /// Trying to get fracture's surface } void DFNFlowEngine::trickPermeability(RTriangulation::Finite_edges_iterator& edge, Real aperture, Real residualAperture) { const RTriangulation& Tri = solver->T[solver->currentTes].Triangulation(); RTriangulation::Facet_circulator facet1 = Tri.incident_facets(*edge); RTriangulation::Facet_circulator facet0=facet1++; trickPermeability(facet0, aperture,residualAperture); while ( facet1!=facet0 ) {trickPermeability(facet1, aperture, residualAperture); facet1++;} /// Needs the fracture surface for this edge? // double edgeArea = solver->T[solver->currentTes].computeVFacetArea(edge); cout<<"edge area="<T[solver->currentTes].Triangulation(); const JCFpmPhys* jcfpmphys; const shared_ptr interactions = scene->interactions; int numberOfCrackedOrJoinedInteractions = 0; /// DEBUG Real SumOfApertures = 0.; /// DEBUG Real AverageAperture =0; /// DEBUG Real totalFracureArea=0; /// Trying to get fracture's surface // const shared_ptr& ig; // const ScGeom* geom; // = static_cast(ig.get()); FiniteEdgesIterator edge = Tri.finite_edges_begin(); for( ; edge!= Tri.finite_edges_end(); ++edge) { const VertexInfo& vi1=(edge->first)->vertex(edge->second)->info(); const VertexInfo& vi2=(edge->first)->vertex(edge->third)->info(); const shared_ptr& interaction=interactions->find( vi1.id(),vi2.id() ); if (interaction && interaction->isReal()) { jcfpmphys = YADE_CAST(interaction->phys.get()); if ( jcfpmphys->isOnJoint || jcfpmphys->isBroken ) { numberOfCrackedOrJoinedInteractions +=1; // here are some workarounds // Real residualAperture = jcfpmphys->isOnJoint? jointResidual : 0.1*jointResidual; Real residualAperture = jcfpmphys->isOnJoint? jointResidual : 0.; // do we define a residual aperture for induced cracks? // Real residualAperture = jointResidual; // cout<<"residual aperture = " << residualAperture <isOnJoint && jcfpmphys->crackJointAperture<=0) continue; // avoid trick permeability for closed induced crack (permeability=matrix permeability) Real aperture = jcfpmphys->crackJointAperture; // cout<<"aperture = " << aperture <crackJointAperture, residualAperture); // we should be able to use this line }; } } AverageAperture = SumOfApertures/numberOfCrackedOrJoinedInteractions; /// DEBUG // cout << " Average aperture in joint ( -D ) = " << AverageAperture << endl; /// DEBUG } // Real DFNFlowEngine::computeTotalFractureArea(totalFracureArea,printFractureTotalArea) /// Trying to get fracture's surface // { // if (printFractureTotalArea >0) { // cout<< " The total fracture area computed from the Network is: " << totalFracureArea < * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ // This is an example of how to derive a new FlowEngine with additional data and possibly completely new behaviour. // Every functions of the base engine can be overloaded, and new functions can be added //keep this #ifdef as long as you don't really want to realize a final version publicly, it will save compilation time for everyone else //when you want it compiled, you can pass -DDUMMYFLOW to cmake, or just uncomment the following line // #define DUMMYFLOW #ifdef DUMMYFLOW #include "FlowEngine_DummyFlowEngineT.hpp" /// We can add data to the Info types by inheritance class DummyCellInfo : public FlowCellInfo_DummyFlowEngineT { public: Real anotherVariable; void anotherFunction() {}; }; class DummyVertexInfo : public FlowVertexInfo_DummyFlowEngineT { public: //same here if needed }; typedef TemplateFlowEngine_DummyFlowEngineT DummyFlowEngineT; REGISTER_SERIALIZABLE(DummyFlowEngineT); YADE_PLUGIN((DummyFlowEngineT)); class DummyFlowEngine : public DummyFlowEngineT { public : //We can overload every functions of the base engine to make it behave differently //if we overload action() like this, this engine is doing nothing in a standard timestep, it can still have useful functions virtual void action() {}; //If a new function is specific to the derived engine, put it here, else go to the base TemplateFlowEngine //if it is useful for everyone void fancyFunction(Real what); YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(DummyFlowEngine,DummyFlowEngineT,"documentation here", ((Real, myNewAttribute, 0,,"useless example")) ,/*DummyFlowEngineT()*/, , .def("fancyFunction",&DummyFlowEngine::fancyFunction,(boost::python::arg("what")=0),"test function") ) DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(DummyFlowEngine); YADE_PLUGIN((DummyFlowEngine)); void DummyFlowEngine::fancyFunction(Real what) {std::cerr<<"yes, I'm a new function"< * * Copyright (C) 2009 by Bruno Chareyre * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef YADE_CGAL #ifdef FLOW_ENGINE #include "FlowEngine_FlowEngineT.hpp" // To register properly, we need to first instantiate an intermediate class, then inherit from it with correct class names in YADE_CLASS macro // The intermediate one would be seen with the name "TemplateFlowEngine" by python, thus it would not work when more than one class are derived, they would all // be named "TemplateFlowEngine" ... typedef TemplateFlowEngine_FlowEngineT FlowEngineT; REGISTER_SERIALIZABLE(FlowEngineT); class FlowEngine : public FlowEngineT { public : YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(FlowEngine,FlowEngineT,"An engine to solve flow problem in saturated granular media. Model description can be found in [Chareyre2012a]_ and [Catalano2014a]_. See the example script FluidCouplingPFV/oedometer.py. More documentation to come.\n\n.. note::Multi-threading seems to work fine for Cholesky decomposition, but it fails for the solve phase in which -j1 is the fastest, here we specify thread numbers independently using :yref:`FlowEngine::numFactorizeThreads` and :yref:`FlowEngine::numSolveThreads`. These multhreading settings are only impacting the behaviour of openblas library and are relatively independant of :yref:`FlowEngine::multithread`. However, the settings have to be globally consistent. For instance, :yref:`multithread` =True with yref:`numFactorizeThreads` = yref:`numSolveThreads` = 4 implies that openblas will mobilize 8 processors at some point. If the system does not have so many procs. it will hurt performance.", ,, , //nothing special to define here, we simply re-use FlowEngine methods //.def("meanVelocity",&PeriodicFlowEngine::meanVelocity,"measure the mean velocity in the period") ) DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(FlowEngine); YADE_PLUGIN((FlowEngineT)); CREATE_LOGGER(FlowEngine ); YADE_PLUGIN((FlowEngine)); #endif //FLOW_ENGINE #endif /* YADE_CGAL */ trunk-2017.01a/pkg/pfv/FlowEngine.hpp000066400000000000000000000037351304022710500173140ustar00rootroot00000000000000#pragma once /// Frequently used: typedef CGT::CVector CVector; typedef CGT::Point Point; /// Converters for Eigen and CGAL vectors inline CVector makeCgVect ( const Vector3r& yv ) {return CVector ( yv[0],yv[1],yv[2] );} inline Point makeCgPoint ( const Vector3r& yv ) {return Point ( yv[0],yv[1],yv[2] );} inline Vector3r makeVector3r ( const Point& yv ) {return Vector3r ( yv[0],yv[1],yv[2] );} inline Vector3r makeVector3r ( const CVector& yv ) {return Vector3r ( yv[0],yv[1],yv[2] );} /// The following macros can be used to expose CellInfo members. /// The syntax is CELL_SCALAR_GETTER(double,.p(),pressure), note the "." before member name, data members would be without the "()" #define CELL_SCALAR_GETTER(type, param, getterName) \ type getterName(unsigned int id){\ if (id>=solver->T[solver->currentTes].cellHandles.size()) {LOG_ERROR("id out of range, max value is "<T[solver->currentTes].cellHandles.size()); return 0;}\ return solver->T[solver->currentTes].cellHandles[id]->info()param;} #define CELL_SCALAR_SETTER_EXTRA(type, param, setterName, extra) \ void setterName(unsigned int id, type value){\ if (id>=solver->T[solver->currentTes].cellHandles.size()) {LOG_ERROR("id out of range, max value is "<T[solver->currentTes].cellHandles.size()); return;}\ solver->T[solver->currentTes].cellHandles[id]->info()param=value;\ extra;} #define CELL_SCALAR_SETTER(type, param, setterName) CELL_SCALAR_SETTER_EXTRA(type, param, setterName,return) #define CELL_VECTOR_GETTER(param, getterName) \ Vector3r getterName(unsigned int id){\ if (id>=solver->T[solver->currentTes].cellHandles.size()) {LOG_ERROR("id out of range, max value is "<T[solver->currentTes].cellHandles.size()); return Vector3r(0,0,0);}\ return makeVector3r(solver->T[solver->currentTes].cellHandles[id]->info()param);} #ifdef LINSOLV #define DEFAULTSOLVER CGT::FlowBoundingSphereLinSolv<_Tesselation> #else #define DEFAULTSOLVER CGT::FlowBoundingSphere<_Tesselation> #endif trunk-2017.01a/pkg/pfv/FlowEngine.hpp.in000066400000000000000000001077601304022710500177240ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2009 by Emanuele Catalano * * Copyright (C) 2009 by Bruno Chareyre * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ /*! FlowEngine is an interface between Yade and the fluid solvers defined in lib/triangulation and using the PFV scheme. There are also a few non-trivial functions defined here, such has building triangulation and computating elements volumes. The code strongly relies on CGAL library for building triangulations on the top of sphere packings. CGAL's trangulations introduce the data associated to each element of the triangulation through template parameters (Cell_info and Vertex_info). FlowEngine is thus defined via the template class TemplateFlowEngine(Cellinfo,VertexInfo), for easier addition of variables in various couplings. PeriodicFlowEngine is a variant for periodic boundary conditions. Which solver will be actually used internally to obtain pore pressure will depend partly on compile time flags (libcholmod available and #define LINSOLV), and on runtime settings (useSolver=0: Gauss-Seidel (iterative), useSolver=1: CHOLMOD if available (direct sparse cholesky)). The files defining lower level classes are in yade/lib. The code uses CGAL::Triangulation3 for managing the mesh and storing data. Eigen3::Sparse, suitesparse::cholmod, and metis are used for solving the linear systems with a direct method (Cholesky). An iterative method (Gauss-Seidel) is implemented directly in Yade and can be used as a fallback (see FlowEngine::useSolver). Most classes in lib/triangulation are templates, and are therefore completely defined in header files. A pseudo hpp/cpp split is reproduced for clarity, with hpp/ipp extensions (but again, in the end they are all include files). The files are - RegularTriangulation.h : declaration of info types embeded in the mesh (template parameters of CGAL::Triangulation3), and instanciation of RTriangulation classes - Tesselation.h/ipp : encapsulate RegularTriangulation and adds functions to manipulate the dual (Voronoi) graph of the triangulation - Network.hpp/ipp : specialized for PFV model (the two former are used independently by TesselationWrapper), a set of functions to determine volumes and surfaces of intersections between spheres and various subdomains. Contains two triangulations for smooth transitions while remeshing - e.g. interpolating values in the new mesh using the previous one. - FlowBoundingSphere.hpp/ipp and PeriodicFlow.hpp/ipp + LinSolv variants: implement the solver in itself (mesh, boundary conditions, solving, defining fluid-particles interactions) - FlowEngine.hpp/hpp.in/ipp.in (this file) define a generic flow engine, instantiations of which are FlowEngine and variants (FlowEngine.cpp, PeriodicFlowEngine.cpp,...) */ #pragma once #include #include #include #include #include #include #include template >, class solverT=DEFAULTSOLVER > class TemplateFlowEngine_@TEMPLATE_FLOW_NAME@ : public PartialEngine { public : typedef solverT FlowSolver; typedef FlowSolver Solver;//FIXME: useless alias, search/replace then remove typedef typename FlowSolver::Tesselation Tesselation; typedef typename FlowSolver::RTriangulation RTriangulation; typedef typename FlowSolver::FiniteVerticesIterator FiniteVerticesIterator; typedef typename FlowSolver::FiniteCellsIterator FiniteCellsIterator; typedef typename FlowSolver::CellHandle CellHandle; typedef typename FlowSolver::FiniteEdgesIterator FiniteEdgesIterator; typedef typename FlowSolver::VertexHandle VertexHandle; typedef typename RTriangulation::Triangulation_data_structure::Cell::Info CellInfo; typedef typename RTriangulation::Triangulation_data_structure::Vertex::Info VertexInfo; // protected: shared_ptr solver; shared_ptr backgroundSolver; volatile bool backgroundCompleted; Cell cachedCell; struct posData {Body::id_t id; Vector3r pos; Real radius; bool isSphere; bool isClump; bool exists; posData(){exists=0; isClump=0;}}; vector positionBufferCurrent;//reflect last known positions before we start computations vector positionBufferParallel;//keep the positions from a given step for multithread factorization //copy positions in a buffer for faster and/or parallel access virtual void setPositionsBuffer(bool current); virtual void trickPermeability() {}; public : int retriangulationLastIter; enum {wall_xmin, wall_xmax, wall_ymin, wall_ymax, wall_zmin, wall_zmax}; Vector3r normal [6]; bool currentTes; bool metisForced; double epsVolCumulative; int ReTrg; int ellapsedIter; void initSolver (FlowSolver& flow); #ifdef LINSOLV void setForceMetis (bool force); bool getForceMetis (); #endif void triangulate (Solver& flow); void addBoundary (Solver& flow); void buildTriangulation (double pZero, Solver& flow); void buildTriangulation (Solver& flow); void updateVolumes (Solver& flow); void initializeVolumes (Solver& flow); void boundaryConditions(Solver& flow); void updateBCs () { if (solver->tesselation().maxId>0) boundaryConditions(*solver);//avoids crash at iteration 0, when the packing is not bounded yet else LOG_ERROR("updateBCs not applied"); solver->pressureChanged=true;} void imposeFlux(Vector3r pos, Real flux); unsigned int imposePressure(Vector3r pos, Real p); unsigned int imposePressureFromId(unsigned long id, Real p); void setImposedPressure(unsigned int cond, Real p); void clearImposedPressure(); void clearImposedFlux(); void computeViscousForces(Solver& flow); Real getCellFlux(unsigned int cond); Real getBoundaryFlux(unsigned int boundary) {return solver->boundaryFlux(boundary);} Vector3r fluidForce(unsigned int idSph) { const CGT::CVector& f=solver->T[solver->currentTes].vertex(idSph)->info().forces; return Vector3r(f[0],f[1],f[2]);} Vector3r averageVelocity(); Vector3r shearLubForce(unsigned int id_sph) { return (solver->shearLubricationForces.size()>id_sph)?solver->shearLubricationForces[id_sph]:Vector3r::Zero();} Vector3r shearLubTorque(unsigned int id_sph) { return (solver->shearLubricationTorques.size()>id_sph)?solver->shearLubricationTorques[id_sph]:Vector3r::Zero();} Vector3r pumpLubTorque(unsigned int id_sph) { return (solver->pumpLubricationTorques.size()>id_sph)?solver->pumpLubricationTorques[id_sph]:Vector3r::Zero();} Vector3r twistLubTorque(unsigned int id_sph) { return (solver->twistLubricationTorques.size()>id_sph)?solver->twistLubricationTorques[id_sph]:Vector3r::Zero();} Vector3r normalLubForce(unsigned int id_sph) { return (solver->normalLubricationForce.size()>id_sph)?solver->normalLubricationForce[id_sph]:Vector3r::Zero();} Matrix3r bodyShearLubStress(unsigned int id_sph) { return (solver->shearLubricationBodyStress.size()>id_sph)?solver->shearLubricationBodyStress[id_sph]:Matrix3r::Zero();} Matrix3r bodyNormalLubStress(unsigned int id_sph) { return (solver->normalLubricationBodyStress.size()>id_sph)?solver->normalLubricationBodyStress[id_sph]:Matrix3r::Zero();} Vector3r shearVelocity(unsigned int interaction) { return (solver->deltaShearVel[interaction]);} Vector3r normalVelocity(unsigned int interaction) { return (solver->deltaNormVel[interaction]);} Matrix3r normalStressInteraction(unsigned int interaction) { return (solver->normalStressInteraction[interaction]);} Matrix3r shearStressInteraction(unsigned int interaction) { return (solver->shearStressInteraction[interaction]);} Vector3r normalVect(unsigned int interaction) { return (solver->normalV[interaction]);} Real surfaceDistanceParticle(unsigned int interaction) { return (solver->surfaceDistance[interaction]);} Real edgeSize() { return (solver->edgeIds.size());} Real OSI() { return (solver->onlySpheresInteractions.size());} int onlySpheresInteractions(unsigned int interaction) { return (solver->onlySpheresInteractions[interaction]);} boost::python::list getConstrictions(bool all) { vector csd=solver->getConstrictions(); boost::python::list pycsd; for (unsigned int k=0;k0) pycsd.append(csd[k]); return pycsd;} boost::python::list getConstrictionsFull(bool all) { vector csd=solver->getConstrictionsFull(); boost::python::list pycsd; for (unsigned int k=0;k0) { boost::python::list cons; cons.append(csd[k].first.first); cons.append(csd[k].first.second); cons.append(csd[k].second[0]); cons.append(csd[k].second[1]); cons.append(csd[k].second[2]); cons.append(csd[k].second[3]); pycsd.append(cons);} return pycsd;} template Real volumeCellSingleFictious (Cellhandle cell); template Real volumeCellDoubleFictious (Cellhandle cell); template Real volumeCellTripleFictious (Cellhandle cell); template Real volumeCell (Cellhandle cell); Real surfaceSolidThroatInPore(int cellId, int throatIndex) {return solver->surfaceSolidThroatInPore(solver->T[solver->currentTes].cellHandles[cellId], throatIndex, false, false);} template Vector3r cellBarycenterFromHandle (Cellhandle cell) {return makeVector3r(solver->cellBarycenter(cell));} Vector3r cellBarycenterFromId (unsigned long id) { if (id>=solver->T[solver->currentTes].cellHandles.size()) {LOG_ERROR("id out of range, max value is "<T[solver->currentTes].cellHandles.size()); return Vector3r(0,0,0);} else return cellBarycenterFromHandle(solver->T[solver->currentTes].cellHandles[id]);} void Oedometer_Boundary_Conditions(); void averageRealCellVelocity(); void saveVtk(const char* folder) {solver->saveVtk(folder);} vector avFlVelOnSph(unsigned int idSph) {return solver->averageFluidVelocityOnSphere(idSph);} // void setBoundaryVel(Vector3r vel) {topBoundaryVelocity=vel; updateTriangulation=true;} void pressureProfile(double wallUpY, double wallDownY) {return solver->measurePressureProfile(wallUpY,wallDownY);} double getPorePressure(Vector3r pos){return solver->getPorePressure(pos[0], pos[1], pos[2]);} int getCell(double posX, double posY, double posZ){return solver->getCell(posX, posY, posZ);} unsigned int nCells(){return solver->T[solver->currentTes].cellHandles.size();} CELL_VECTOR_GETTER(,cellCenter) CELL_VECTOR_GETTER(.averageCellVelocity,cellVelocity) CELL_SCALAR_GETTER(double,.p(),cellPressure) CELL_SCALAR_SETTER_EXTRA(double,.p(),setCellPressure,solver->resetRHS()) CELL_SCALAR_GETTER(bool,.Pcondition,cellPImposed) CELL_SCALAR_SETTER_EXTRA(bool,.Pcondition,setCellPImposed,solver->resetLinearSystem()) boost::python::list getVertices(unsigned int id){ boost::python::list ids; if (id>=solver->T[solver->currentTes].cellHandles.size()) {LOG_ERROR("id out of range, max value is "<T[solver->currentTes].cellHandles.size()); return ids;} for (unsigned int i=0;i<4;i++) ids.append(solver->T[solver->currentTes].cellHandles[id]->vertex(i)->info().id()); return ids; } void blockCell(unsigned int id, bool blockPressure){ if (id>=solver->T[solver->currentTes].cellHandles.size()) {LOG_ERROR("id out of range, max value is "<T[solver->currentTes].cellHandles.size()); return;} solver->T[solver->currentTes].cellHandles[id]->info().blocked=true; solver->T[solver->currentTes].cellHandles[id]->info().Pcondition=blockPressure; } Vector3r getBoundaryNormal(int index) { if (index<0 || index>5) LOG_ERROR("index out of range (0-5)"); return normal[max(0,min(5,index))];} void setBoundaryNormal(int index, Vector3r v) { if (index<0 || index>5) LOG_ERROR("index out of range (0-5)"); normal[max(0,min(5,index))]=v;} double averageSlicePressure(double posY){return solver->averageSlicePressure(posY);} double averagePressure(){return solver->averagePressure();} void emulateAction(){ scene = Omega::instance().getScene().get(); action();} #ifdef LINSOLV void exportMatrix(string filename) {if (useSolver==3) solver->exportMatrix(filename.c_str()); else cerr<<"available for Cholmod solver (useSolver==3)"<exportTriplets(filename.c_str()); else cerr<<"available for Cholmod solver (useSolver==3)"<eSolver.cholmod()))<eSolver.cholmod().selected<eSolver.cholmod().called_nd<eSolver.cholmod().called_nd);} #endif virtual ~TemplateFlowEngine_@TEMPLATE_FLOW_NAME@(); virtual void action(); virtual void backgroundAction(); //commodities void compTessVolumes() { solver->T[solver->currentTes].compute(); solver->T[solver->currentTes].computeVolumes(); } Real getVolume (Body::id_t id) { if (solver->T[solver->currentTes].Max_id() <= 0) {emulateAction(); /*LOG_WARN("Not triangulated yet, emulating action");*/} if (solver->T[solver->currentTes].Volume(id) == -1) {compTessVolumes();/* LOG_WARN("Computing all volumes now, as you did not request it explicitely.");*/} return (solver->T[solver->currentTes].Max_id() >= id) ? solver->T[solver->currentTes].Volume(id) : -1;} YADE_CLASS_PYCLASS_BASE_DOC_ATTRS_DEPREC_INIT_CTOR_PY(TemplateFlowEngine_@TEMPLATE_FLOW_NAME@,@TEMPLATE_FLOW_NAME@,PartialEngine,"A generic engine from wich more specialized engines can inherit. It is defined for the sole purpose of inserting the right data classes CellInfo and VertexInfo in the triangulation, and it should not be used directly. Instead, look for specialized engines, e.g. :yref:`FlowEngine`, :yref:`PeriodicFlowEngine`, or :yref:`DFNFlowEngine`.", ((bool,isActivated,true,,"Activates Flow Engine")) ((bool,first,true,,"Controls the initialization/update phases")) ((int,idOffset,0,,"If the bounding walls of the fluid mesh are not walls of the scene (i.e. are not elements of O.bodies), the offset should be set equal to the size of O.bodies. If the bounding walls are bodies of the scene but are not numbered as 0-5 then offset should be the number of bodies comming before the walls. Set offset<0 to get it set equal to O.bodies.size(), it will also update :yref:`FlowEngine::wallIds`.")) ((bool,convertClumps,true,,"If true the clumps will be temptatively converted into equivalent spheres in the triangulation, and clump members are skipped. Else clumps are ignored and spherical clump members are triangulated as independent bodies.")) ((bool,doInterpolate,false,,"Force the interpolation of cell's info while remeshing. By default, interpolation would be done only for compressible fluids. It can be forced with this flag.")) ((double, fluidBulkModulus, 0.,,"Bulk modulus of fluid (inverse of compressibility) K=-dP*V/dV [Pa]. Flow is compressible if fluidBulkModulus > 0, else incompressible.")) ((Real, dt, 0,,"timestep [s]")) ((bool,permeabilityMap,false,,"Enable/disable stocking of average permeability scalar in cell infos.")) ((bool, slipBoundary, true,, "Controls friction condition on lateral walls")) ((bool,waveAction, false,, "Allow sinusoidal pressure condition to simulate ocean waves")) ((double, sineMagnitude, 0,, "Pressure value (amplitude) when sinusoidal pressure is applied (p )")) ((double, sineAverage, 0,,"Pressure value (average) when sinusoidal pressure is applied")) ((bool, debug, false,,"Activate debug messages")) ((double, wallThickness,0,,"Walls thickness")) ((double,pZero,0,,"The value used for initializing pore pressure. It is useless for incompressible fluid, but important for compressible model.")) ((double,tolerance,1e-06,,"Gauss-Seidel tolerance")) ((double,relax,1.9,,"Gauss-Seidel relaxation")) ((bool, updateTriangulation, 0,,"If true the medium is retriangulated. Can be switched on to force retriangulation after some events (else it will be true periodicaly based on :yref:`FlowEngine::defTolerance` and :yref:`FlowEngine::meshUpdateInterval`. Of course, it costs CPU time.")) ((int,meshUpdateInterval,1000,,"Maximum number of timesteps between re-triangulation events. See also :yref:`FlowEngine::defTolerance`.")) ((double, epsVolMax, 0,(Attr::readonly),"Maximal absolute volumetric strain computed at each iteration. |yupdate|")) ((double, defTolerance,0.05,,"Cumulated deformation threshold for which retriangulation of pore space is performed. If negative, the triangulation update will occure with a fixed frequency on the basis of :yref:`FlowEngine::meshUpdateInterval`")) ((double, porosity, 0,(Attr::readonly),"Porosity computed at each retriangulation |yupdate|")) ((bool,meanKStat,false,,"report the local permeabilities' correction")) ((bool,clampKValues,true,,"If true, clamp local permeabilities in [minKdivKmean,maxKdivKmean]*globalK. This clamping can avoid singular values in the permeability matrix and may reduce numerical errors in the solve phase. It will also hide junk values if they exist, or bias all values in very heterogeneous problems. So, use this with care.")) ((Real,minKdivKmean,0.0001,,"define the min K value (see :yref:`FlowEngine::clampKValues`)")) ((Real,maxKdivKmean,100,,"define the max K value (see :yref:`FlowEngine::clampKValues`)")) ((double,permeabilityFactor,1.0,,"Permability multiplier ($m$): $m=1$ (default) attempts to predicty the actual hydraulic conductivity using a Poiseuille equation; $m>0$ multiplies the default values by $m$; $m<0$ defines the conductivity independently of particle size and viscosity as if the material was a homogeneous continuum of conductivity $-m$")) ((double,viscosity,1.0,,"viscosity of the fluid")) ((double,stiffness, 10000,,"equivalent contact stiffness used in the lubrication model")) ((int, useSolver, 0,, "Solver to use. 0:Gauss-Seidel, >0: Cholesky factorization (sparse CHOLMOD)")) ((int, xmin,0,(Attr::readonly),"Index of the boundary $x_{min}$. This index is not equal the the id of the corresponding body in general, it may be used to access the corresponding attributes (e.g. flow.bndCondValue[flow.xmin], flow.wallId[flow.xmin],...).")) ((int, xmax,1,(Attr::readonly),"See :yref:`FlowEngine::xmin`.")) ((int, ymin,2,(Attr::readonly),"See :yref:`FlowEngine::xmin`.")) ((int, ymax,3,(Attr::readonly),"See :yref:`FlowEngine::xmin`.")) ((int, zmin,4,(Attr::readonly),"See :yref:`FlowEngine::xmin`.")) ((int, zmax,5,(Attr::readonly),"See :yref:`FlowEngine::xmin`.")) ((vector, bndCondIsPressure, vector(6,false),,"defines the type of boundary condition for each side. True if pressure is imposed, False for no-flux. Indexes can be retrieved with :yref:`FlowEngine::xmin` and friends.")) ((vector, bndCondValue, vector(6,0),,"Imposed value of a boundary condition. Only applies if the boundary condition is imposed pressure, else the imposed flux is always zero presently (may be generalized to non-zero imposed fluxes in the future).")) ((vector, boundaryVelocity, vector(6,Vector3r::Zero()),, "velocity on top boundary, only change it using :yref:`FlowEngine::setBoundaryVel`")) ((int, ignoredBody,-1,,"DEPRECATED, USE MASK - Id of a sphere to exclude from the triangulation.)")) ((int,mask,0,,"If mask defined, only bodies with corresponding groupMask will be affected by this engine. If 0, all bodies will be affected.")) ((vector, wallIds,vector(6),,"body ids of the boundaries (default values are ok only if aabbWalls are appended before spheres, i.e. numbered 0,...,5)")) ((vector, boundaryUseMaxMin, vector(6,true),,"If true (default value) bounding sphere is added as function of max/min sphere coord, if false as function of yade wall position")) ((bool, viscousShear, false,,"compute viscous shear terms as developped by Donia Marzougui (FIXME: ref.)")) ((bool, shearLubrication, false,,"compute shear lubrication force as developped by Brule (FIXME: ref.) ")) ((bool, pumpTorque, false,,"Compute pump torque applied on particles ")) ((bool, twistTorque, false,,"Compute twist torque applied on particles ")) ((double, eps, 0.00001,,"roughness defined as a fraction of particles size, giving the minimum distance between particles in the lubrication model.")) ((bool, pressureForce, true,,"compute the pressure field and associated fluid forces. WARNING: turning off means fluid flow is not computed at all.")) ((bool, normalLubrication, false,,"compute normal lubrication force as developped by Brule")) ((bool, viscousNormalBodyStress, false,,"compute normal viscous stress applied on each body")) ((bool, viscousShearBodyStress, false,,"compute shear viscous stress applied on each body")) ((bool, multithread, false,,"Build triangulation and factorize in the background (multi-thread mode)")) #ifdef EIGENSPARSE_LIB ((int, numSolveThreads, 1,,"number of openblas threads in the solve phase.")) ((int, numFactorizeThreads, 1,,"number of openblas threads in the factorization phase")) #endif ((vector, boundaryPressure,vector(),,"values defining pressure along x-axis for the top surface. See also :yref:`@TEMPLATE_FLOW_NAME@::boundaryXPos`")) ((vector, boundaryXPos,vector(),,"values of the x-coordinate for which pressure is defined. See also :yref:`@TEMPLATE_FLOW_NAME@::boundaryPressure`")) ((string,blockHook,"",,"Python command to be run when remeshing. Anticipated usage: define blocked cells (see also :yref:`TemplateFlowEngine_@TEMPLATE_FLOW_NAME@.blockCell`), or apply exotic types of boundary conditions which need to visit the newly built mesh")) , /*deprec*/ ((meanK_opt,clampKValues,"the name changed")) ,, timingDeltas=shared_ptr(new TimingDeltas); for (int i=0; i<6; ++i){normal[i]=Vector3r::Zero(); wallIds[i]=i;} normal[wall_ymin].y()=normal[wall_xmin].x()=normal[wall_zmin].z()=1; normal[wall_ymax].y()=normal[wall_xmax].x()=normal[wall_zmax].z()=-1; solver = shared_ptr (new FlowSolver); first=true; epsVolMax=epsVolCumulative=retriangulationLastIter=0; ReTrg=1; backgroundCompleted=true; ellapsedIter=0; metisForced=false; , .def("imposeFlux",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::imposeFlux,(boost::python::arg("pos"),boost::python::arg("p")),"Impose a flux in cell located at 'pos' (i.e. add a source term in the flow problem). Outflux positive, influx negative.") .def("imposePressureFromId",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::imposePressureFromId,(boost::python::arg("id"),boost::python::arg("p")),"Impose pressure in cell of index 'id' (after remeshing the same condition will apply for the same location, regardless of what the new cell index is at this location). The index of the condition itself is returned (for multiple imposed pressures at different points).") .def("imposePressure",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::imposePressure,(boost::python::arg("pos"),boost::python::arg("p")),"Impose pressure in cell of location 'pos'. The index of the condition is returned (for multiple imposed pressures at different points).") .def("setImposedPressure",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::setImposedPressure,(boost::python::arg("cond"),boost::python::arg("p")),"Set pressure value at the point indexed 'cond'.") .def("clearImposedPressure",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::clearImposedPressure,"Clear the list of points with pressure imposed.") .def("clearImposedFlux",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::clearImposedFlux,"Clear the list of points with flux imposed.") .def("getCellFlux",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::getCellFlux,(boost::python::arg("cond")),"Get influx in cell associated to an imposed P (indexed using 'cond').") .def("getBoundaryFlux",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::getBoundaryFlux,(boost::python::arg("boundary")),"Get total flux through boundary defined by its body id.\n\n.. note:: The flux may be not zero even for no-flow condition. This artifact comes from cells which are incident to two or more boundaries (along the edges of the sample, typically). Such flux evaluation on impermeable boundary is just irrelevant, it does not imply that the boundary condition is not applied properly.") .def("getConstrictions",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::getConstrictions,(boost::python::arg("all")=true),"Get the list of constriction radii (inscribed circle) for all finite facets (if all==True) or all facets not incident to a virtual bounding sphere (if all==False). When all facets are returned, negative radii denote facet incident to one or more fictious spheres.") .def("getConstrictionsFull",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::getConstrictionsFull,(boost::python::arg("all")=true),"Get the list of constrictions (inscribed circle) for all finite facets (if all==True), or all facets not incident to a fictious bounding sphere (if all==False). When all facets are returned, negative radii denote facet incident to one or more fictious spheres. The constrictions are returned in the format {{cell1,cell2}{rad,nx,ny,nz}}") .def("edgeSize",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::edgeSize,"Return the number of interactions.") .def("surfaceSolidThroatInPore",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::surfaceSolidThroatInPore,(boost::python::arg("cellId"),boost::python::arg("throatIndex")),"returns solid area in the throat (index 0-3), keeping only that part of the throat in cell.") .def("OSI",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::OSI,"Return the number of interactions only between spheres.") .def("saveVtk",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::saveVtk,(boost::python::arg("folder")="./VTK"),"Save pressure field in vtk format. Specify a folder name for output.") .def("avFlVelOnSph",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::avFlVelOnSph,(boost::python::arg("idSph")),"compute a sphere-centered average fluid velocity") .def("fluidForce",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::fluidForce,(boost::python::arg("idSph")),"Return the fluid force on sphere idSph.") .def("shearLubForce",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::shearLubForce,(boost::python::arg("idSph")),"Return the shear lubrication force on sphere idSph.") .def("shearLubTorque",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::shearLubTorque,(boost::python::arg("idSph")),"Return the shear lubrication torque on sphere idSph.") .def("normalLubForce",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::normalLubForce,(boost::python::arg("idSph")),"Return the normal lubrication force on sphere idSph.") .def("bodyShearLubStress",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::bodyShearLubStress,(boost::python::arg("idSph")),"Return the shear lubrication stress on sphere idSph.") .def("bodyNormalLubStress",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::bodyNormalLubStress,(boost::python::arg("idSph")),"Return the normal lubrication stress on sphere idSph.") .def("shearVelocity",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::shearVelocity,(boost::python::arg("idSph")),"Return the shear velocity of the interaction.") .def("normalVelocity",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::normalVelocity,(boost::python::arg("idSph")),"Return the normal velocity of the interaction.") .def("normalVect",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::normalVect,(boost::python::arg("idSph")),"Return the normal vector between particles.") .def("surfaceDistanceParticle",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::surfaceDistanceParticle,(boost::python::arg("interaction")),"Return the distance between particles.") .def("onlySpheresInteractions",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::onlySpheresInteractions,(boost::python::arg("interaction")),"Return the id of the interaction only between spheres.") .def("pressureProfile",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::pressureProfile,(boost::python::arg("wallUpY"),boost::python::arg("wallDownY")),"Measure pore pressure in 6 equally-spaced points along the height of the sample") .def("getPorePressure",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::getPorePressure,(boost::python::arg("pos")),"Measure pore pressure in position pos[0],pos[1],pos[2]") .def("averageSlicePressure",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::averageSlicePressure,(boost::python::arg("posY")),"Measure slice-averaged pore pressure at height posY") .def("averagePressure",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::averagePressure,"Measure averaged pore pressure in the entire volume, the cells adjacent to the boundaries are ignored if includeBoundaries=False") .def("updateBCs",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::updateBCs,"tells the engine to update it's boundary conditions before running (especially useful when changing boundary pressure - should not be needed for point-wise imposed pressure)") .def("emulateAction",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::emulateAction,"get scene and run action (may be used to manipulate an engine outside the timestepping loop).") .def("getCell",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::getCell,(boost::python::arg("pos")),"get id of the cell containing (X,Y,Z).") .def("getCellBarycenter",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::cellBarycenterFromId,(boost::python::arg("id")),"get barycenter of cell 'id'.") .def("getCellCenter",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::cellCenter,(boost::python::arg("id")),"get voronoi center of cell 'id'.") .def("getCellPressure",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::cellPressure,(boost::python::arg("id")),"get pressure in cell 'id'.") .def("setCellPressure",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::setCellPressure,(boost::python::arg("id"),boost::python::arg("pressure")),"set pressure in cell 'id'.") .def("getCellPImposed",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::cellPImposed,(boost::python::arg("id")),"get the status of cell 'id' wrt imposed pressure.") .def("setCellPImposed",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::setCellPImposed,(boost::python::arg("id"),boost::python::arg("pImposed")),"make cell 'id' assignable with imposed pressure.") .def("nCells",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::nCells,"get the total number of finite cells in the triangulation.") .def("blockCell",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::blockCell,(boost::python::arg("id"),boost::python::arg("blockPressure")),"block cell 'id'. The cell will be excluded from the fluid flow problem and the conductivity of all incident facets will be null. If blockPressure=False, deformation is reflected in the pressure, else it is constantly 0.") .def("getVertices",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::getVertices,(boost::python::arg("id")),"get the vertices of a cell") #ifdef LINSOLV .def("exportMatrix",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::exportMatrix,(boost::python::arg("filename")="matrix"),"Export system matrix to a file with all entries (even zeros will displayed).") .def("exportTriplets",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::exportTriplets,(boost::python::arg("filename")="triplets"),"Export system matrix to a file with only non-zero entries.") .def("cholmodStats",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::cholmodStats,"get statistics of cholmod solver activity") .def("metisUsed",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::metisUsed,"check wether metis lib is effectively used") .add_property("forceMetis",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::getForceMetis,&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::setForceMetis,"If true, METIS is used for matrix preconditioning, else Cholmod is free to choose the best method (which may be METIS to, depending on the matrix). See ``nmethods`` in Cholmod documentation") #endif .def("compTessVolumes",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::compTessVolumes,"Like TesselationWrapper::computeVolumes()") .def("volume",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::getVolume,(boost::python::arg("id")=0),"Returns the volume of Voronoi's cell of a sphere.") .def("averageVelocity",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::averageVelocity,"measure the mean velocity in the period") .def("setBoundaryNormal",&TemplateFlowEngine_@TEMPLATE_FLOW_NAME@::setBoundaryNormal,"define the unit outward-pointing normal of a boundary (0<=index<=5).") ) }; class FlowCellInfo_@TEMPLATE_FLOW_NAME@ : public CGT::SimpleCellInfo { public: //For vector storage of all cells unsigned int index; int volumeSign; bool Pcondition; bool blocked;//exclude cell from the fluid domain Real invVoidV; Real t; int fict; Real volumeVariation; double pression; //average relative (fluid - facet translation) velocity defined for a single cell as 1/Volume * SUM_ON_FACETS(x_average_facet*average_facet_flow_rate) CVector averageCellVelocity; // Surface vectors of facets, pointing from outside toward inside the cell std::vector facetSurfaces; //Ratio between fluid surface and facet surface std::vector facetFluidSurfacesRatio; // Reflects the geometrical property of the cell, so that the force by cell fluid on grain "i" is pressure*unitForceVectors[i] std::vector unitForceVectors; // Store the area of triangle-sphere intersections for each facet (used in forces definition) std::vector facetSphereCrossSections; std::vector cellForce; std::vector rayHydr; std::vector modulePermeability; // Partial surfaces of spheres in the double-tetrahedron linking two voronoi centers. [i][j] is for sphere facet "i" and sphere facetVertices[i][j]. Last component for 1/sum_surfaces in the facet.doInterpolate double solidSurfaces [4][4]; FlowCellInfo_@TEMPLATE_FLOW_NAME@ (void) { modulePermeability.resize(4, 0); cellForce.resize(4,CGAL::NULL_VECTOR); facetSurfaces.resize(4,CGAL::NULL_VECTOR); facetFluidSurfacesRatio.resize(4,0); facetSphereCrossSections.resize(4,CGAL::NULL_VECTOR); unitForceVectors.resize(4,CGAL::NULL_VECTOR); for (int k=0; k<4;k++) for (int l=0; l<3;l++) solidSurfaces[k][l]=0; rayHydr.resize(4, 0); invSumK=index=volumeSign=s=volumeVariation=pression=invVoidV=fict=0; isFictious=false; Pcondition = false; isGhost = false; isvisited = false; isGhost=false; blocked=false; } bool isGhost; double invSumK; bool isvisited; inline Real& volume (void) {return t;} inline const Real& invVoidVolume (void) const {return invVoidV;} inline Real& invVoidVolume (void) {return invVoidV;} inline Real& dv (void) {return volumeVariation;} inline int& fictious (void) {return fict;} inline double& p (void) {return pression;} inline const double shiftedP (void) const {return pression;} //For compatibility with the periodic case inline const std::vector& kNorm (void) const {return modulePermeability;} inline std::vector& kNorm (void) {return modulePermeability;} inline std::vector< CVector >& facetSurf (void) {return facetSurfaces;} inline std::vector& force (void) {return cellForce;} inline std::vector& Rh (void) {return rayHydr;} inline CVector& averageVelocity (void) {return averageCellVelocity;} //used for transfering values between two triangulations, overload with more variables in derived classes (see e.g. SoluteFlow) inline void getInfo(const FlowCellInfo_@TEMPLATE_FLOW_NAME@& otherCellInfo) {p()=otherCellInfo.shiftedP();} }; class FlowVertexInfo_@TEMPLATE_FLOW_NAME@ : public CGT::SimpleVertexInfo { CVector grainVelocity; Real volumeIncidentCells; public: CVector forces; bool isGhost; FlowVertexInfo_@TEMPLATE_FLOW_NAME@ (void) {isGhost=false;} inline CVector& force (void) {return forces;} inline CVector& vel (void) {return grainVelocity;} inline Real& volCells (void) {return volumeIncidentCells;} inline const CVector ghostShift (void) const {return CGAL::NULL_VECTOR;} }; // Implementation of functions in this separate file for clarity #include "FlowEngine_@TEMPLATE_FLOW_NAME@.ipp" trunk-2017.01a/pkg/pfv/FlowEngine.ipp.in000066400000000000000000001163711304022710500177230ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2009 by Emanuele Catalano * * Copyright (C) 2009 by Bruno Chareyre * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef YADE_CGAL #ifdef FLOW_ENGINE #ifdef LINSOLV #include #endif //For pyRunString #include template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::~TemplateFlowEngine_@TEMPLATE_FLOW_NAME@() {} // YADE_PLUGIN((TFlowEng)); template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > unsigned int TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::imposePressure(Vector3r pos, Real p) { // if (!flow) LOG_ERROR("no flow defined yet, run at least one iter"); solver->imposedP.push_back( pair(CGT::Point(pos[0],pos[1],pos[2]),p) ); //force immediate update of boundary conditions updateTriangulation=true; return solver->imposedP.size()-1; } template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > unsigned int TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::imposePressureFromId(unsigned long id, Real p) { return imposePressure(cellBarycenterFromId(id),p); } template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > void TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::action() { if ( !isActivated ) return; timingDeltas->start(); setPositionsBuffer(true); timingDeltas->checkpoint ( "Position buffer" ); if (first) { if (multithread) setPositionsBuffer(false); buildTriangulation(pZero,*solver); initializeVolumes(*solver); backgroundSolver=solver; backgroundCompleted=true; } #ifdef YADE_OPENMP solver->ompThreads = ompThreads>0? ompThreads : omp_get_max_threads(); #endif timingDeltas->checkpoint ( "Triangulating" ); updateVolumes ( *solver ); timingDeltas->checkpoint ( "Update_Volumes" ); epsVolCumulative += epsVolMax; retriangulationLastIter++; if (!updateTriangulation) updateTriangulation = // If not already set true by another function of by the user, check conditions (defTolerance>0 && epsVolCumulative > defTolerance) || retriangulationLastIter>meshUpdateInterval; ///compute flow and and forces here if (pressureForce){ solver->gaussSeidel(scene->dt); timingDeltas->checkpoint ( "Gauss-Seidel (includes matrix construct and factorization in single-thread mode)" ); solver->computeFacetForcesWithCache();} timingDeltas->checkpoint ( "compute_Forces" ); ///Application of vicscous forces scene->forces.sync(); timingDeltas->checkpoint ( "forces.sync()" ); computeViscousForces ( *solver ); timingDeltas->checkpoint ( "viscous forces" ); Vector3r force; Vector3r torque; FiniteVerticesIterator verticesEnd = solver->T[solver->currentTes].Triangulation().finite_vertices_end(); int bodiesLength = scene->bodies->size(); for ( FiniteVerticesIterator vIt = solver->T[solver->currentTes].Triangulation().finite_vertices_begin(); vIt != verticesEnd; vIt++ ) { int vId = vIt->info().id(); force = pressureForce ? Vector3r ( vIt->info().forces[0],vIt->info().forces[1],vIt->info().forces[2] ): Vector3r(0,0,0); torque = Vector3r(0,0,0); if (shearLubrication || viscousShear){ force = force + solver->shearLubricationForces[vId]; torque = torque + solver->shearLubricationTorques[vId]; if (pumpTorque) torque = torque + solver->pumpLubricationTorques[vId]; } if (twistTorque) torque = torque + solver->twistLubricationTorques[vId]; if (normalLubrication) force = force + solver-> normalLubricationForce[vId]; if (vIt->info().id() < bodiesLength) { scene->forces.addForce ( vId, force); scene->forces.addTorque ( vId, torque);} } ///End compute flow and forces timingDeltas->checkpoint ( "Applying Forces" ); #ifdef LINSOLV int sleeping = 0; if (multithread && !first) { while (updateTriangulation && !backgroundCompleted) { /*cout<<"sleeping..."<(0.5*meshUpdateInterval) && backgroundCompleted)) { if (debug) cerr<<"switch flow solver"<0 || doInterpolate) solver->interpolate (solver->T[solver->currentTes], backgroundSolver->T[backgroundSolver->currentTes]); solver=backgroundSolver; backgroundSolver = shared_ptr (new FlowSolver); if (metisForced) {backgroundSolver->eSolver.cholmod().nmethods=1; backgroundSolver->eSolver.cholmod().method[0].ordering=CHOLMOD_METIS;} //Copy imposed pressures/flow from the old solver backgroundSolver->imposedP = vector >(solver->imposedP); backgroundSolver->imposedF = vector >(solver->imposedF); if (debug) cerr<<"switched"< void TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::backgroundAction() { if (useSolver<1) {LOG_ERROR("background calculations not available for Gauss-Seidel"); return;} buildTriangulation ( pZero,*backgroundSolver ); //FIXME: GS is computing too much, we need only matrix factorization in fact backgroundSolver->gaussSeidel(scene->dt); //FIXME(2): and here we need only cached variables, not forces backgroundSolver->computeFacetForcesWithCache(/*onlyCache?*/ true); // boost::this_thread::sleep(boost::posix_time::seconds(5)); backgroundCompleted = true; } template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > void TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::boundaryConditions ( Solver& flow ) { for (int k=0;k<6;k++) { flow.boundary (wallIds[k]).flowCondition=!bndCondIsPressure[k]; flow.boundary (wallIds[k]).value=bndCondValue[k]; flow.boundary (wallIds[k]).velocity = boundaryVelocity[k];//FIXME: needs correct implementation, maybe update the cached pos/vel? } } template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > void TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::setImposedPressure ( unsigned int cond, Real p) { if ( cond>=solver->imposedP.size() ) LOG_ERROR ( "Setting p with cond higher than imposedP size." ); solver->imposedP[cond].second=p; //force immediate update of boundary conditions solver->pressureChanged=true; } template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > void TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::imposeFlux ( Vector3r pos, Real flux){ solver->imposedF.push_back ( pair ( CGT::Point ( pos[0],pos[1],pos[2] ), flux ) ); CellHandle cell=solver->T[solver->currentTes].Triangulation().locate(CGT::Point(pos[0],pos[1],pos[2])); if (cell->info().isGhost) cerr<<"Imposing pressure in a ghost cell."<IPCells.size();kk++){ if (cell==solver->IPCells[kk]) cerr<<"Both flux and pressure are imposed in the same cell."<info().Pcondition) cerr<<"Imposed flux fall in a pressure boundary condition."<IFCells.push_back(cell); } template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > void TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::clearImposedPressure () { solver->imposedP.clear(); solver->IPCells.clear();} template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > void TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::clearImposedFlux () { solver->imposedF.clear(); solver->IFCells.clear();} template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > Real TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::getCellFlux ( unsigned int cond) { if ( cond>=solver->imposedP.size() ) {LOG_ERROR ( "Getting flux with cond higher than imposedP size." ); return 0;} double flux=0; typename Solver::CellHandle& cell= solver->IPCells[cond]; for ( int ngb=0;ngb<4;ngb++ ) { /*if (!cell->neighbor(ngb)->info().Pcondition)*/ flux+= cell->info().kNorm() [ngb]* ( cell->info().p()-cell->neighbor ( ngb )->info().p() ); } return flux+cell->info().dv(); } template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > void TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::initSolver ( FlowSolver& flow ) { flow.Vtotalissimo=0; flow.VSolidTot=0; flow.vPoral=0; flow.sSolidTot=0; flow.slipBoundary=slipBoundary; flow.kFactor = permeabilityFactor; flow.debugOut = debug; flow.useSolver = useSolver; #ifdef EIGENSPARSE_LIB flow.numSolveThreads = numSolveThreads; flow.numFactorizeThreads = numFactorizeThreads; #endif flow.meanKStat = meanKStat; flow.viscosity = viscosity; flow.tolerance=tolerance; flow.relax=relax; flow.clampKValues = clampKValues; flow.maxKdivKmean = maxKdivKmean; flow.minKdivKmean = minKdivKmean; flow.meanKStat = meanKStat; flow.permeabilityMap = permeabilityMap; flow.fluidBulkModulus = fluidBulkModulus; // flow.tesselation().Clear(); flow.tesselation().maxId=-1; flow.blockedCells.clear(); flow.xMin = 1000.0, flow.xMax = -10000.0, flow.yMin = 1000.0, flow.yMax = -10000.0, flow.zMin = 1000.0, flow.zMax = -10000.0; } #ifdef LINSOLV template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > void TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::setForceMetis ( bool force ) { if (force) { metisForced=true; solver->eSolver.cholmod().nmethods=1; solver->eSolver.cholmod().method[0].ordering=CHOLMOD_METIS; } else {cholmod_defaults(&(solver->eSolver.cholmod())); metisForced=false;} } template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > bool TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::getForceMetis () {return (solver->eSolver.cholmod().nmethods==1);} #endif template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > void TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::buildTriangulation ( Solver& flow ) { buildTriangulation ( 0.f,flow ); } template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > void TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::buildTriangulation ( double pZero, Solver& flow ) { if (first) flow.currentTes=0; else { flow.currentTes=!flow.currentTes; if (debug) cout << "--------RETRIANGULATION-----------" << endl;} flow.resetNetwork(); initSolver(flow); addBoundary ( flow ); triangulate ( flow ); if ( debug ) cout << endl << "Tesselating------" << endl << endl; flow.tesselation().compute(); flow.defineFictiousCells(); // For faster loops on cells define this vector flow.tesselation().cellHandles.clear(); flow.tesselation().cellHandles.reserve(flow.tesselation().Triangulation().number_of_finite_cells()); FiniteCellsIterator cell_end = flow.tesselation().Triangulation().finite_cells_end(); int k=0; for ( FiniteCellsIterator cell = flow.tesselation().Triangulation().finite_cells_begin(); cell != cell_end; cell++ ){ flow.tesselation().cellHandles.push_back(cell); cell->info().id=k++;}//define unique numbering now, corresponds to position in cellHandles flow.displayStatistics (); if(!blockHook.empty()){ LOG_INFO("Running blockHook: "<0 || doInterpolate)) flow.interpolate ( flow.T[!flow.currentTes], flow.tesselation() ); if ( waveAction ) flow.applySinusoidalPressure ( flow.tesselation().Triangulation(), sineMagnitude, sineAverage, 30 ); else if (boundaryPressure.size()!=0) flow.applyUserDefinedPressure ( flow.tesselation().Triangulation(), boundaryXPos , boundaryPressure); if (normalLubrication || shearLubrication || viscousShear) flow.computeEdgesSurfaces(); } template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > void TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::setPositionsBuffer(bool current) { vector& buffer = current? positionBufferCurrent : positionBufferParallel; buffer.clear(); buffer.resize(scene->bodies->size()); shared_ptr sph ( new Sphere ); const int Sph_Index = sph->getClassIndexStatic(); FOREACH ( const shared_ptr& b, *scene->bodies ) { if (!b || (mask>0 and !b->maskCompatible(mask)) || (convertClumps && b->isClumpMember()) || (b->isClump() && !convertClumps)) continue; posData& dat = buffer[b->getId()]; dat.id=b->getId(); dat.pos=b->state->pos; dat.isSphere= (b->shape->getClassIndex() == Sph_Index); dat.isClump = b->isClump(); if (dat.isSphere) dat.radius = YADE_CAST(b->shape.get())->radius; if (dat.isClump) { const shared_ptr& clump = YADE_PTR_CAST(b->shape); const shared_ptr& member = Body::byId(clump->members.begin()->first,scene); dat.radius = pow( (3*b->state->mass)/(4*Mathr::PI*member->material->density) , 1.0/3.0); //use equivalent radius of clump (just valid for nearly spherical clumps) } dat.exists=true; } } template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > void TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::addBoundary ( Solver& flow ) { vector& buffer = multithread ? positionBufferParallel : positionBufferCurrent; solver->xMin = Mathr::MAX_REAL, solver->xMax = -Mathr::MAX_REAL, solver->yMin = Mathr::MAX_REAL, solver->yMax = -Mathr::MAX_REAL, solver->zMin = Mathr::MAX_REAL, solver->zMax = -Mathr::MAX_REAL; FOREACH ( const posData& b, buffer ) { if ( !b.exists ) continue; if ( b.isSphere || b.isClump ) { const Real& rad = b.radius; const Real& x = b.pos[0]; const Real& y = b.pos[1]; const Real& z = b.pos[2]; flow.xMin = min ( flow.xMin, x-rad ); flow.xMax = max ( flow.xMax, x+rad ); flow.yMin = min ( flow.yMin, y-rad ); flow.yMax = max ( flow.yMax, y+rad ); flow.zMin = min ( flow.zMin, z-rad ); flow.zMax = max ( flow.zMax, z+rad ); } } //set idOffset if<0, in that case overwrite wallIds and assign values out of range scene->bodies if (idOffset<0) { idOffset = scene->bodies->size(); for (int i=0; i<6; ++i){wallIds[i]=i+idOffset;} } flow.idOffset = idOffset; flow.sectionArea = ( flow.xMax - flow.xMin ) * ( flow.zMax-flow.zMin ); flow.vTotal = ( flow.xMax-flow.xMin ) * ( flow.yMax-flow.yMin ) * ( flow.zMax-flow.zMin ); flow.yMinId=wallIds[ymin]; flow.yMaxId=wallIds[ymax]; flow.xMaxId=wallIds[xmax]; flow.xMinId=wallIds[xmin]; flow.zMinId=wallIds[zmin]; flow.zMaxId=wallIds[zmax]; //FIXME: Id's order in boundsIds is done according to the enumeration of boundaries from TXStressController.hpp, line 31. DON'T CHANGE IT! flow.boundsIds[0]= &flow.xMinId; flow.boundsIds[1]= &flow.xMaxId; flow.boundsIds[2]= &flow.yMinId; flow.boundsIds[3]= &flow.yMaxId; flow.boundsIds[4]= &flow.zMinId; flow.boundsIds[5]= &flow.zMaxId; for (int k=0;k<6;k++) flow.boundary ( *flow.boundsIds[k] ).useMaxMin = boundaryUseMaxMin[k]; flow.cornerMin = CGT::Point ( flow.xMin, flow.yMin, flow.zMin ); flow.cornerMax = CGT::Point ( flow.xMax, flow.yMax, flow.zMax ); //assign BCs types and values boundaryConditions ( flow ); double center[3]; for ( int i=0; i<6; i++ ) { if ( *flow.boundsIds[i]<0 ) continue; CGT::CVector Normal ( normal[i].x(), normal[i].y(), normal[i].z() ); if ( flow.boundary ( *flow.boundsIds[i] ).useMaxMin ) flow.addBoundingPlane(Normal, *flow.boundsIds[i] ); else { for ( int h=0;h<3;h++ ) center[h] = buffer[*flow.boundsIds[i]].pos[h]; // cerr << "id="<<*flow.boundsIds[i] <<" center="< void TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::triangulate ( Solver& flow ) { ///Using Tesselation wrapper (faster) // TesselationWrapper TW; // if (TW.Tes) delete TW.Tes; // TW.Tes = &(flow.tesselation());//point to the current Tes we have in Flowengine // TW.insertSceneSpheres();//TW is now really inserting in TemplateFlowEngine_@TEMPLATE_FLOW_NAME@, using the faster insert(begin,end) // TW.Tes = NULL;//otherwise, Tes would be deleted by ~TesselationWrapper() at the end of the function. ///Using one-by-one insertion vector& buffer = multithread ? positionBufferParallel : positionBufferCurrent; FOREACH ( const posData& b, buffer ) { if ( !b.exists || b.id==ignoredBody ) continue; if ( b.isSphere || b.isClump ) flow.tesselation().insert ( b.pos[0], b.pos[1], b.pos[2], b.radius, b.id ); } flow.tesselation().redirected=true;//By inserting one-by-one, we already redirected flow.shearLubricationForces.resize ( flow.tesselation().maxId+1 ); flow.shearLubricationTorques.resize ( flow.tesselation().maxId+1 ); flow.pumpLubricationTorques.resize ( flow.tesselation().maxId+1 ); flow.twistLubricationTorques.resize ( flow.tesselation().maxId+1 ); flow.shearLubricationBodyStress.resize ( flow.tesselation().maxId+1 ); flow.normalLubricationForce.resize ( flow.tesselation().maxId+1 ); flow.normalLubricationBodyStress.resize ( flow.tesselation().maxId+1 ); } template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > void TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::initializeVolumes ( Solver& flow ) { typedef typename Solver::FiniteVerticesIterator FiniteVerticesIterator; FiniteVerticesIterator vertices_end = flow.tesselation().Triangulation().finite_vertices_end(); CGT::CVector Zero(0,0,0); for (FiniteVerticesIterator V_it = flow.tesselation().Triangulation().finite_vertices_begin(); V_it!= vertices_end; V_it++) V_it->info().forces=Zero; FOREACH(CellHandle& cell, flow.tesselation().cellHandles) { switch ( cell->info().fictious() ) { case ( 0 ) : cell->info().volume() = volumeCell ( cell ); break; case ( 1 ) : cell->info().volume() = volumeCellSingleFictious ( cell ); break; case ( 2 ) : cell->info().volume() = volumeCellDoubleFictious ( cell ); break; case ( 3 ) : cell->info().volume() = volumeCellTripleFictious ( cell ); break; default: break; } if (flow.fluidBulkModulus>0) { cell->info().invVoidVolume() = 1 / ( std::abs(cell->info().volume()) - flow.volumeSolidPore(cell) ); } } if (debug) cout << "Volumes initialised." << endl; } template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > void TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::averageRealCellVelocity() { solver->averageRelativeCellVelocity(); Vector3r Vel ( 0,0,0 ); //AVERAGE CELL VELOCITY FiniteCellsIterator cell_end = solver->T[solver->currentTes].Triangulation().finite_cells_end(); for ( FiniteCellsIterator cell = solver->T[solver->currentTes].Triangulation().finite_cells_begin(); cell != cell_end; cell++ ) { for ( int g=0;g<4;g++ ) { if ( !cell->vertex ( g )->info().isFictious ) { const shared_ptr& sph = Body::byId ( cell->vertex ( g )->info().id(), scene ); for ( int i=0;i<3;i++ ) Vel[i] = Vel[i] + sph->state->vel[i]/4; } } RTriangulation& Tri = solver->T[solver->currentTes].Triangulation(); CGT::Point pos_av_facet; double volume_facet_translation = 0; CGT::CVector Vel_av ( Vel[0], Vel[1], Vel[2] ); for ( int i=0; i<4; i++ ) { volume_facet_translation = 0; if ( !Tri.is_infinite ( cell->neighbor ( i ) ) ) { CGT::CVector Surfk = cell->info()-cell->neighbor ( i )->info(); Real area = sqrt ( Surfk.squared_length() ); Surfk = Surfk/area; CGT::CVector branch = cell->vertex ( facetVertices[i][0] )->point() - cell->info(); pos_av_facet = ( CGT::Point ) cell->info() + ( branch*Surfk ) *Surfk; volume_facet_translation += Vel_av*cell->info().facetSurfaces[i]; cell->info().averageVelocity() = cell->info().averageVelocity() - volume_facet_translation/std::abs(cell->info().volume()) * ( pos_av_facet-CGAL::ORIGIN ); } } } } template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > void TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::updateVolumes ( Solver& flow ) { if ( debug ) cout << "Updating volumes.............." << endl; Real invDeltaT = 1/scene->dt; epsVolMax=0; Real totVol=0; Real totDVol=0; #ifdef YADE_OPENMP const long size=flow.tesselation().cellHandles.size(); #pragma omp parallel for num_threads(ompThreads>0 ? ompThreads : 1) for(long i=0; iinfo().fictious() ) { case ( 3 ) : newVol = volumeCellTripleFictious ( cell ); break; case ( 2 ) : newVol = volumeCellDoubleFictious ( cell ); break; case ( 1 ) : newVol = volumeCellSingleFictious ( cell ); break; case ( 0 ) : newVol = volumeCell (cell ); break; default: newVol = 0; break;} dVol=cell->info().volumeSign* ( newVol - cell->info().volume() ); cell->info().dv() = dVol*invDeltaT; cell->info().volume() = newVol; if (defTolerance>0) { //if the criterion is not used, then we skip these updates a save a LOT of time when Nthreads > 1 #pragma omp atomic totVol+=cell->info().volumeSign*newVol; #pragma omp atomic totDVol+=dVol;} } if (defTolerance>0) epsVolMax = totDVol/totVol; //FIXME: move this loop to FlowBoundingSphere for (unsigned int n=0; ninfo().dv()+=flow.imposedF[n].second; flow.IFCells[n]->info().Pcondition=false;} if ( debug ) cout << "Updated volumes, total =" <info().volumeSign ) ) cell->info().volumeSign= ( volume>0 ) ?1:-1; return volume; } template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > void TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::computeViscousForces ( Solver& flow ) { if (normalLubrication || shearLubrication || viscousShear){ if ( debug ) cout << "Application of viscous forces" << endl; if ( debug ) cout << "Number of edges = " << flow.edgeIds.size() << endl; for ( unsigned int k=0; kinfo().isFictious + Tes.vertex ( id2 )->info().isFictious; if (hasFictious>0 or id1==id2) continue; const shared_ptr& sph1 = Body::byId ( id1, scene ); const shared_ptr& sph2 = Body::byId ( id2, scene ); Sphere* s1=YADE_CAST ( sph1->shape.get() ); Sphere* s2=YADE_CAST ( sph2->shape.get() ); const Real& r1 = s1->radius; const Real& r2 = s2->radius; Vector3r deltaV; Real deltaNormV; Vector3r deltaShearV; Vector3r O1O2Vector; Real O1O2; Vector3r normal; Real surfaceDist; Vector3r O1CVector; Vector3r O2CVector;Real meanRad ;Real Rh; Vector3r deltaAngVel; Vector3r deltaShearAngVel; Vector3r shearLubF; Vector3r normaLubF; Vector3r pumpT; Vector3r deltaAngNormVel; Vector3r twistT; Vector3r angVel1; Vector3r angVel2; //FIXME: if periodic and velGrad!=0, then deltaV should account for velGrad, not the case currently if ( !hasFictious ){ O1O2Vector = sph2->state->pos + makeVector3r(vi2.ghostShift()) - sph1->state->pos - makeVector3r(vi1.ghostShift()); O1O2 = O1O2Vector.norm(); normal= (O1O2Vector/O1O2); surfaceDist = O1O2 - r2 - r1; //FIXME: what is that? O1CVector = (O1O2/2. + (pow(r1,2) - pow(r2,2)) / (2.*O1O2))*normal; O2CVector = -(O1O2Vector - O1CVector); meanRad = (r2 + r1)/2.; Rh = (r1 < r2)? surfaceDist + 0.45 * r1 : surfaceDist + 0.45 * r2; deltaV = (sph2->state->vel + sph2->state->angVel.cross(-r2 * normal)) - (sph1->state->vel+ sph1->state->angVel.cross(r1 * normal)); angVel1 = sph1->state->angVel; angVel2 = sph2->state->angVel; deltaAngVel = sph2->state->angVel - sph1->state->angVel; } else { if ( hasFictious==1 ) {//for the fictious sphere, use velocity of the boundary, not of the body bool v1fictious = Tes.vertex ( id1 )->info().isFictious; int bnd = v1fictious? id1 : id2; int coord = flow.boundary(bnd).coordinate; O1O2 = v1fictious ? std::abs((sph2->state->pos + makeVector3r(Tes.vertex(id2)->info().ghostShift()))[coord] - flow.boundary(bnd).p[coord]) : std::abs((sph1->state->pos + makeVector3r(Tes.vertex(id1)->info().ghostShift()))[coord] - flow.boundary(bnd).p[coord]); if(v1fictious) normal = makeVector3r(flow.boundary(id1).normal); else normal = -makeVector3r(flow.boundary(id2).normal); O1O2Vector = O1O2 * normal; meanRad = v1fictious ? r2:r1; surfaceDist = O1O2 - meanRad; if (v1fictious){ O1CVector = Vector3r::Zero(); O2CVector = - O1O2Vector;} else{ O1CVector = O1O2Vector; O2CVector = Vector3r::Zero();} Rh = surfaceDist + 0.45 * meanRad; Vector3r v1 = ( Tes.vertex ( id1 )->info().isFictious ) ? flow.boundary ( id1 ).velocity:sph1->state->vel + sph1->state->angVel.cross(r1 * normal); Vector3r v2 = ( Tes.vertex ( id2 )->info().isFictious ) ? flow.boundary ( id2 ).velocity:sph2->state->vel + sph2->state->angVel.cross(-r2 * (normal)); deltaV = v2-v1; angVel1 = ( Tes.vertex ( id1 )->info().isFictious ) ? Vector3r::Zero() : sph1->state->angVel; angVel2 = ( Tes.vertex ( id2 )->info().isFictious ) ? Vector3r::Zero() : sph2->state->angVel; deltaAngVel = angVel2 - angVel1; } } deltaShearV = deltaV - ( normal.dot ( deltaV ) ) *normal; deltaShearAngVel = deltaAngVel - ( normal.dot ( deltaAngVel ) ) *normal; flow.deltaShearVel.push_back(deltaShearV); flow.normalV.push_back(normal); flow.surfaceDistance.push_back(max(surfaceDist, 0.) + eps*meanRad); /// Compute the shear Lubrication force and torque on each particle if (shearLubrication) shearLubF = flow.computeShearLubricationForce(deltaShearV,surfaceDist,i,eps,O1O2,meanRad); else if (viscousShear) shearLubF = flow.computeViscousShearForce ( deltaShearV, i , Rh); if (viscousShear || shearLubrication){ flow.shearLubricationForces[id1]+=shearLubF; flow.shearLubricationForces[id2]+=(-shearLubF); flow.shearLubricationTorques[id1]+=O1CVector.cross(shearLubF); flow.shearLubricationTorques[id2]+=O2CVector.cross(-shearLubF); /// Compute the pump Lubrication torque on each particle if (pumpTorque){ pumpT = flow.computePumpTorque(deltaShearAngVel, surfaceDist, i, eps, meanRad ); flow.pumpLubricationTorques[id1]+=(-pumpT); flow.pumpLubricationTorques[id2]+=pumpT;} /// Compute the twist Lubrication torque on each particle if (twistTorque){ deltaAngNormVel = (normal.dot(deltaAngVel))*normal ; twistT = flow.computeTwistTorque(deltaAngNormVel, surfaceDist, i, eps, meanRad ); flow.twistLubricationTorques[id1]+=(-twistT); flow.twistLubricationTorques[id2]+=twistT; } } /// Compute the viscous shear stress on each particle if (viscousShearBodyStress){ flow.shearLubricationBodyStress[id1] += shearLubF * O1CVector.transpose()/ (4.0/3.0 *3.14* pow(r1,3)); flow.shearLubricationBodyStress[id2] += (-shearLubF) * O2CVector.transpose()/ (4.0/3.0 *3.14* pow(r2,3)); flow.shearStressInteraction.push_back(shearLubF * O1O2Vector.transpose()/(4.0/3.0 *3.14* pow(r1,3))); } /// Compute the normal lubrication force applied on each particle if (normalLubrication){ deltaNormV = normal.dot(deltaV); flow.deltaNormVel.push_back(deltaNormV * normal); normaLubF = flow.computeNormalLubricationForce (deltaNormV, surfaceDist, i,eps,stiffness,scene->dt,meanRad)*normal; flow.normalLubricationForce[id1]+=normaLubF; flow.normalLubricationForce[id2]+=(-normaLubF); /// Compute the normal lubrication stress on each particle if (viscousNormalBodyStress){ flow.normalLubricationBodyStress[id1] += normaLubF * O1CVector.transpose()/ (4.0/3.0 *3.14* pow(r1,3)); flow.normalLubricationBodyStress[id2] += (-normaLubF) *O2CVector.transpose() / (4.0/3.0 *3.14* pow(r2,3)); flow.normalStressInteraction.push_back(normaLubF * O1O2Vector.transpose()/(4.0/3.0 *3.14* pow(r1,3))); } } if (!hasFictious) flow.onlySpheresInteractions.push_back(i); } } } template< class _CellInfo, class _VertexInfo, class _Tesselation, class solverT > Vector3r TemplateFlowEngine_@TEMPLATE_FLOW_NAME@<_CellInfo,_VertexInfo,_Tesselation,solverT>::averageVelocity() { solver->averageRelativeCellVelocity(); Vector3r meanVel ( 0,0,0 ); Real volume=0; FiniteCellsIterator cell_end = solver->T[solver->currentTes].Triangulation().finite_cells_end(); for ( FiniteCellsIterator cell = solver->T[solver->currentTes].Triangulation().finite_cells_begin(); cell != cell_end; cell++ ) { //We could also define velocity using cell's center // if ( !cell->info().isReal() ) continue; if ( cell->info().isGhost ) continue; for ( int i=0;i<3;i++ ) meanVel[i]=meanVel[i]+ ( ( cell->info().averageVelocity() ) [i] * std::abs ( cell->info().volume() ) ); volume+=std::abs ( cell->info().volume() ); } return ( meanVel/volume ); } #endif //FLOW_ENGINE #endif /* YADE_CGAL */ trunk-2017.01a/pkg/pfv/PeriodicFlowEngine.cpp000066400000000000000000000603211304022710500207600ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2009 by Bruno Chareyre * * Copyright (C) 2012 by Donia Marzougui * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef YADE_CGAL #ifdef FLOW_ENGINE /// The periodic variant of FlowEngine is defined here. It should become a template class for more flexibility. /// It is a bit more complicated as for FlowEngine, though, because we need template inheriting from template, which breaks YADE_CLASS_XXX logic_error /// See below the commented exemple, for a possible solution #include "FlowEngine_FlowEngine_PeriodicInfo.hpp" class PeriodicCellInfo : public FlowCellInfo_FlowEngine_PeriodicInfo { public: static CVector gradP; //for real cell, baseIndex is the rank of the cell in cellHandles. For ghost cells, it is the baseIndex of the corresponding real cell. //Unlike ordinary index, baseIndex is also indexing cells with imposed pressures int baseIndex; int period[3]; static CVector hSize[3]; static CVector deltaP; int ghost; Real* _pression; PeriodicCellInfo (void){ _pression=&pression; period[0]=period[1]=period[2]=0; baseIndex=-1; volumeSign=0;} ~PeriodicCellInfo (void) {} inline const double shiftedP (void) const {return isGhost? (*_pression)+pShift() :(*_pression) ;} inline const double pShift (void) const {return deltaP[0]*period[0] + deltaP[1]*period[1] +deltaP[2]*period[2];} // inline const double p (void) {return shiftedP();} inline void setP (const Real& p) {pression=p;} bool isReal (void) {return !(isFictious || isGhost);} }; class PeriodicVertexInfo : public FlowVertexInfo_FlowEngine_PeriodicInfo { public: PeriodicVertexInfo& operator= (const CVector &u) { CVector::operator= (u); return *this; } PeriodicVertexInfo& operator= (const float &scalar) { s=scalar; return *this; } PeriodicVertexInfo& operator= (const unsigned int &id) { i= id; return *this; } int period[3]; //FIXME: the name is misleading, even non-ghost can be out of the period and therefore they need to be shifted as well inline const CVector ghostShift (void) const { return period[0]*PeriodicCellInfo::hSize[0]+period[1]*PeriodicCellInfo::hSize[1]+period[2]*PeriodicCellInfo::hSize[2];} PeriodicVertexInfo (void) {isFictious=false; s=0; i=0; period[0]=period[1]=period[2]=0; isGhost=false;} bool isReal (void) {return !(isFictious || isGhost);} }; typedef CGT::TriangulationTypes PeriFlowTriangulationTypes; typedef CGT::PeriodicTesselation > PeriFlowTesselation; #ifdef LINSOLV #define _PeriFlowSolver CGT::PeriodicFlowLinSolv #else #define _PeriFlowSolver CGT::PeriodicFlow #endif typedef TemplateFlowEngine_FlowEngine_PeriodicInfo< PeriodicCellInfo, PeriodicVertexInfo, CGT::PeriodicTesselation > >, _PeriFlowSolver> FlowEngine_PeriodicInfo; REGISTER_SERIALIZABLE(FlowEngine_PeriodicInfo); YADE_PLUGIN((FlowEngine_PeriodicInfo)); class PeriodicFlowEngine : public FlowEngine_PeriodicInfo { public : void triangulate (FlowSolver& flow); void buildTriangulation (Real pzero, FlowSolver& flow); void initializeVolumes (FlowSolver& flow); void updateVolumes (FlowSolver& flow); Real volumeCell (CellHandle cell); Real volumeCellSingleFictious (CellHandle cell); inline void locateCell(CellHandle baseCell, unsigned int& index, int& baseIndex, FlowSolver& flow, unsigned int count=0); virtual ~PeriodicFlowEngine(); virtual void action(); //Cache precomputed values for pressure shifts, based on current hSize and pGrad void preparePShifts(); YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(PeriodicFlowEngine,FlowEngine_PeriodicInfo,"A variant of :yref:`FlowEngine` implementing periodic boundary conditions. The API is very similar.", ((Real,duplicateThreshold, 0.06,,"distance from cell borders that will triger periodic duplication in the triangulation |yupdate|")) ((Vector3r, gradP, Vector3r::Zero(),,"Macroscopic pressure gradient")) ,, wallIds=vector(6,-1); solver = shared_ptr (new FlowSolver); epsVolMax=epsVolCumulative=retriangulationLastIter=0; ReTrg=1; first=true; , //nothing special to define, we re-use FlowEngine methods //.def("meanVelocity",&PeriodicFlowEngine::meanVelocity,"measure the mean velocity in the period") ) DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(PeriodicFlowEngine); CVector PeriodicCellInfo::hSize[]={CVector(),CVector(),CVector()}; CVector PeriodicCellInfo::deltaP=CVector(); CVector PeriodicCellInfo::gradP=CVector(); CREATE_LOGGER ( PeriodicFlowEngine ); PeriodicFlowEngine::~PeriodicFlowEngine(){} void PeriodicFlowEngine:: action() { if ( !isActivated ) return; timingDeltas->start(); preparePShifts(); setPositionsBuffer(true); if (first) { if (multithread) setPositionsBuffer(false); cachedCell= Cell(*(scene->cell)); buildTriangulation(pZero,*solver); if (solver->errorCode>0) {LOG_INFO("triangulation error, pausing"); Omega::instance().pause(); return;} initializeVolumes(*solver); backgroundSolver=solver; backgroundCompleted=true;} // if ( first ) {buildTriangulation ( pZero ); updateTriangulation = false; initializeVolumes();} timingDeltas->checkpoint("Triangulating"); updateVolumes (*solver); epsVolCumulative += epsVolMax; retriangulationLastIter++; if (!updateTriangulation) updateTriangulation = // If not already set true by another function of by the user, check conditions (defTolerance>0 && epsVolCumulative > defTolerance) || retriangulationLastIter>meshUpdateInterval; timingDeltas->checkpoint("Update_Volumes"); ///compute flow and and forces here if (pressureForce){ solver->gaussSeidel(scene->dt); timingDeltas->checkpoint("Gauss-Seidel"); solver->computeFacetForcesWithCache();} timingDeltas->checkpoint("compute_Pressure_Forces"); ///compute vicscous forces scene->forces.sync(); computeViscousForces(*solver); timingDeltas->checkpoint("compute_Viscous_Forces"); Vector3r force; Vector3r torque; const Tesselation& Tes = solver->T[solver->currentTes]; for (int id=0; id<=Tes.maxId; id++){ assert (Tes.vertexHandles[id] != NULL); const Tesselation::VertexInfo& v_info = Tes.vertexHandles[id]->info(); force =(pressureForce) ? Vector3r ( ( v_info.forces ) [0],v_info.forces[1],v_info.forces[2] ) : Vector3r(0,0,0); torque = Vector3r(0,0,0); if (shearLubrication || viscousShear){ force = force +solver->shearLubricationForces[v_info.id()]; torque = torque +solver->shearLubricationTorques[v_info.id()]; if (pumpTorque) torque = torque +solver->pumpLubricationTorques[v_info.id()]; if (twistTorque) torque = torque +solver->twistLubricationTorques[v_info.id()]; } if (normalLubrication) force = force + solver->normalLubricationForce[v_info.id()]; scene->forces.addForce ( v_info.id(), force); scene->forces.addTorque ( v_info.id(), torque); } ///End Compute flow and forces timingDeltas->checkpoint("Applying Forces"); if (multithread && !first) { while (updateTriangulation && !backgroundCompleted) { /*cout<<"sleeping..."<(0.5*meshUpdateInterval)) { if (useSolver==0) LOG_ERROR("background calculations not available for Gauss-Seidel"); if (fluidBulkModulus>0 || doInterpolate) solver->interpolate (solver->T[solver->currentTes], backgroundSolver->T[backgroundSolver->currentTes]); solver=backgroundSolver; backgroundSolver = shared_ptr (new FlowSolver); //Copy imposed pressures/flow from the old solver backgroundSolver->imposedP = vector >(solver->imposedP); backgroundSolver->imposedF = vector >(solver->imposedF); setPositionsBuffer(false); cachedCell= Cell(*(scene->cell)); backgroundCompleted=false; retriangulationLastIter=ellapsedIter; ellapsedIter=0; epsVolCumulative=0; boost::thread workerThread(&PeriodicFlowEngine::backgroundAction,this); workerThread.detach(); initializeVolumes(*solver); computeViscousForces(*solver); } else if (debug && !first) { if (debug && !backgroundCompleted) cerr<<"still computing solver in the background"<cell)); buildTriangulation (pZero, *solver); initializeVolumes(*solver); computeViscousForces(*solver); updateTriangulation = false; epsVolCumulative=0; retriangulationLastIter=0; ReTrg++;} } first=false; timingDeltas->checkpoint("Ending"); } // void PeriodicFlowEngine::backgroundAction() // { // if (useSolver<1) {LOG_ERROR("background calculations not available for Gauss-Seidel"); return;} // buildTriangulation (pZero,*backgroundSolver); // //FIXME: GS is computing too much, we need only matrix factorization in fact // backgroundSolver->gaussSeidel(scene->dt); // backgroundSolver->computeFacetForcesWithCache(/*onlyCache?*/ true); // // boost::this_thread::sleep(boost::posix_time::seconds(10)); // backgroundCompleted = true; // } void PeriodicFlowEngine::triangulate( FlowSolver& flow ) { Tesselation& Tes = flow.tesselation(); vector& buffer = multithread ? positionBufferParallel : positionBufferCurrent; FOREACH ( const posData& b, buffer ) { if ( !b.exists || !b.isSphere || b.id==ignoredBody) continue; Vector3i period; Vector3r wpos; // FIXME: use "sheared" variant if the cell is sheared wpos=cachedCell.wrapPt ( b.pos,period ); const Body::id_t& id = b.id; const Real& rad = b.radius; const Real& x = wpos[0]; const Real& y = wpos[1]; const Real& z = wpos[2]; VertexHandle vh0=Tes.insert ( x, y, z, rad, id ); // VertexHandle vh0=Tes.insert ( b.pos[0], b.pos[1], b.pos[2], b.radius, b.id ); if (vh0==NULL) { flow.errorCode = 2; LOG_ERROR("Vh NULL in PeriodicFlowEngine::triangulate(), check input data"); continue;} for ( int k=0;k<3;k++ ) vh0->info().period[k]=-period[k]; const Vector3r cellSize ( cachedCell.getSize() ); //FIXME: if hasShear, comment in // wpos=scene->cell->unshearPt ( wpos ); // traverse all periodic cells around the body, to see if any of them touches Vector3r halfSize= ( rad+duplicateThreshold ) *Vector3r ( 1,1,1 ); Vector3r pmin,pmax; Vector3i i; for ( i[0]=-1; i[0]<=1; i[0]++ ) for ( i[1]=-1;i[1]<=1; i[1]++ ) for ( i[2]=-1; i[2]<=1; i[2]++ ) { if ( i[0]!=0 || i[1]!=0 || i[2]!=0 ) { // middle; already rendered above Vector3r pos2=wpos+Vector3r ( cellSize[0]*i[0],cellSize[1]*i[1],cellSize[2]*i[2] ); // shift, but without shear! pmin=pos2-halfSize; pmax=pos2+halfSize; if ( (pmin[0]<=cellSize[0]) && (pmax[0]>=0) && (pmin[1]<=cellSize[1]) && (pmax[1]>=0) && (pmin[2]<=cellSize[2]) && (pmax[2]>=0) ) { //with shear: //Vector3r pt=scene->cell->shearPt ( pos2 ); //without shear: const Vector3r& pt= pos2; VertexHandle vh=Tes.insert ( pt[0],pt[1],pt[2],rad,id,false,id ); for ( int k=0;k<3;k++ ) vh->info().period[k]=i[k]-period[k];}} } //re-assign the original vertex pointer since duplicates may have overwrite it Tes.vertexHandles[id]=vh0; } Tes.redirected=true;//By inserting one-by-one, we already redirected flow.shearLubricationForces.resize ( Tes.maxId+1 ); flow.shearLubricationTorques.resize ( Tes.maxId+1 ); flow.pumpLubricationTorques.resize ( Tes.maxId+1 ); flow.twistLubricationTorques.resize ( Tes.maxId+1 ); flow.shearLubricationBodyStress.resize ( Tes.maxId+1 ); flow.normalLubricationForce.resize ( Tes.maxId+1 ); flow.normalLubricationBodyStress.resize ( Tes.maxId+1 ); } Real PeriodicFlowEngine::volumeCell ( CellHandle cell ) { static const Real inv6 = 1/6.; const Vector3r p0 = positionBufferCurrent[cell->vertex(0)->info().id()].pos + makeVector3r(cell->vertex(0)->info().ghostShift()); const Vector3r p1 = positionBufferCurrent[cell->vertex(1)->info().id()].pos + makeVector3r(cell->vertex(1)->info().ghostShift()); const Vector3r p2 = positionBufferCurrent[cell->vertex(2)->info().id()].pos + makeVector3r(cell->vertex(2)->info().ghostShift()); const Vector3r p3 = positionBufferCurrent[cell->vertex(3)->info().id()].pos + makeVector3r(cell->vertex(3)->info().ghostShift()); Real volume = inv6*((p0-p1).cross(p0-p2)).dot(p0-p3); if ( ! ( cell->info().volumeSign ) ) cell->info().volumeSign= ( volume>0 ) ?1:-1; return volume; } Real PeriodicFlowEngine::volumeCellSingleFictious ( CellHandle cell ) { Vector3r V[3]; int b=0; int w=0; cell->info().volumeSign=1; Real Wall_coordinate=0; for ( int y=0;y<4;y++ ) { if ( ! ( cell->vertex ( y )->info().isFictious ) ) { const shared_ptr& sph = Body::byId ( cell->vertex ( y )->info().id(), scene ); V[w]=sph->state->pos+ makeVector3r ( cell->vertex ( y )->info().ghostShift() ); w++; } else { b = cell->vertex ( y )->info().id(); const shared_ptr& wll = Body::byId ( b,scene ); if ( !solver->boundary ( b ).useMaxMin ) Wall_coordinate = wll->state->pos[solver->boundary ( b ).coordinate]+ ( solver->boundary ( b ).normal[solver->boundary ( b ).coordinate] ) *wallThickness/2.; else Wall_coordinate = solver->boundary ( b ).p[solver->boundary ( b ).coordinate]; } } Real Volume = 0.5* ( ( V[0]-V[1] ).cross ( V[0]-V[2] ) ) [solver->boundary ( b ).coordinate] * ( 0.33333333333* ( V[0][solver->boundary ( b ).coordinate]+ V[1][solver->boundary ( b ).coordinate]+ V[2][solver->boundary ( b ).coordinate] ) - Wall_coordinate ); return std::abs ( Volume ); } void PeriodicFlowEngine::locateCell ( CellHandle baseCell, unsigned int& index, int& baseIndex, FlowSolver& flow, unsigned int count) { if (count>10) { LOG_ERROR("More than 10 attempts to locate a cell, duplicateThreshold may be too small, resulting in periodicity inconsistencies."); flow.errorCode=1; return; } PeriFlowTesselation::CellInfo& baseInfo = baseCell->info(); //already located, return FIXME: is inline working correctly? else move this test outside the function, just before the calls if ( baseInfo.index>0 || baseInfo.isGhost ) return; RTriangulation& Tri = flow.tesselation().Triangulation(); Vector3r center ( 0,0,0 ); Vector3i period; if (baseCell->info().fictious()==0) for ( int k=0;k<4;k++ ) center+= 0.25*makeVector3r (baseCell->vertex(k)->point()); else { Real boundPos=0; int coord=0; for ( int k=0;k<4;k++ ) { if ( !baseCell->vertex ( k )->info().isFictious ) center+= 0.3333333333*makeVector3r ( baseCell->vertex ( k )->point() ); else { coord=flow.boundary ( baseCell->vertex ( k )->info().id() ).coordinate; boundPos=flow.boundary ( baseCell->vertex ( k )->info().id() ).p[coord];} } center[coord]=boundPos; } Vector3r wdCenter= cachedCell.wrapPt ( center,period ); if ( period[0]!=0 || period[1]!=0 || period[2]!=0 ) { if ( baseCell->info().index>0 ) { cout<<"indexed cell is found ghost!"<vertex(kk)->info().isGhost) && ((!baseCell->vertex(kk)->info().isFictious))) checkC = true; if (checkC) { bool checkV=true; for (int kk=0; kk<4;kk++) { checkV=false; for (int jj=0; jj<4;jj++) if (baseCell->vertex(kk)->info().id() == ch->vertex(jj)->info().id()) checkV = true; if (!checkV) {cerr <<"periodicity is broken"<vertex(jj)->info().id()<<" "; cerr<<" vs. "; for (int jj=0; jj<4;jj++) cerr<vertex(jj)->info().id()<<" "; cerr<vertex(kk)->info().id() == ch->vertex(jj)->info().id()) checkV = true; // if (!checkV) {cerr <<"periodicity is broken (that's ok probably)"<vertex(jj)->info().id()<<" "; // cerr<<" vs. "; // for (int jj=0; jj<4;jj++) cerr<vertex(jj)->info().id()<<" "; // cerr<info().p() ); baseInfo.index=ch->info().index; baseInfo.baseIndex=ch->info().baseIndex; baseInfo.Pcondition=ch->info().Pcondition; } else { baseInfo.isGhost=false; //index is 1-based, if it is zero it is not initialized, we define it here if ( baseInfo.baseIndex<0 ){ baseInfo.baseIndex=++baseIndex; if (!baseInfo.Pcondition) baseInfo.index=++index;} } } void PeriodicFlowEngine::updateVolumes (FlowSolver& flow) { //FIXME: replace by the non-periodic version if ( debug ) cout << "Updating volumes.............." << endl; Real invDeltaT = 1/scene->dt; double newVol, dVol; epsVolMax=0; Real totVol=0; Real totDVol=0; Real totVol0=0; Real totVol1=0; FOREACH(CellHandle& cell, flow.tesselation().cellHandles){ switch ( cell->info().fictious() ) { case ( 1 ) : newVol = volumeCellSingleFictious ( cell ); totVol1+=newVol; break; case ( 0 ) : newVol = volumeCell ( cell ); totVol0+=newVol; break; default: newVol = 0; break; } totVol+=newVol; dVol=cell->info().volumeSign * ( newVol - cell->info().volume() ); totDVol+=dVol; if (newVol != 0) { epsVolMax = max ( epsVolMax, std::abs ( dVol/newVol ) ); } cell->info().dv() = dVol * invDeltaT; cell->info().volume() = newVol; } for (unsigned int n=0; ninfo().dv()+=flow.imposedF[n].second; flow.IFCells[n]->info().Pcondition=false;} if ( debug ) cout << "Updated volumes, total =" <info().forces=Zero; FOREACH(CellHandle& cell, flow.tesselation().cellHandles){ switch ( cell->info().fictious() ) { case ( 0 ) : cell->info().volume() = volumeCell ( cell ); break; case ( 1 ) : cell->info().volume() = volumeCellSingleFictious ( cell ); break; default: cell->info().volume() = 0; break; } //FIXME: the void volume is negative sometimes, hence crashing... if (flow.fluidBulkModulus>0) { cell->info().invVoidVolume() = 1. / (max(0.1*cell->info().volume(),std::abs(cell->info().volume()) - flow.volumeSolidPore(cell)) ); } } if ( debug ) cout << "Volumes initialised." << endl; } void PeriodicFlowEngine::buildTriangulation ( double pZero, FlowSolver& flow) { if (first) flow.currentTes=0; else { flow.currentTes=!flow.currentTes; if ( debug ) cout << "--------RETRIANGULATION-----------" << endl;} flow.resetNetwork(); initSolver(flow); addBoundary ( flow ); if ( debug ) cout << endl << "Added boundaries------" << endl << endl; triangulate (flow); if ( debug ) cout << endl << "Tesselating------" << endl << endl; flow.tesselation().compute(); flow.defineFictiousCells(); //FIXME: this is already done in addBoundary(?) boundaryConditions ( flow ); if ( debug ) cout << endl << "boundaryConditions------" << endl << endl; flow.initializePressure ( pZero ); if ( debug ) cout << endl << "initializePressure------" << endl << endl; // Define the ghost cells and add indexes to the cells inside the period (the ones that will contain the pressure unknowns) //This must be done after boundary conditions and initialize pressure, else the indexes are not good (not accounting imposedP): FIXME unsigned int index=0; int baseIndex=-1; FlowSolver::Tesselation& Tes = flow.tesselation(); Tes.cellHandles.resize(Tes.Triangulation().number_of_finite_cells()); const FiniteCellsIterator cellend=Tes.Triangulation().finite_cells_end(); for ( FiniteCellsIterator cell=Tes.Triangulation().finite_cells_begin(); cell!=cellend; cell++ ){ locateCell ( cell,index,baseIndex,flow ); if (flow.errorCode>0) {LOG_ERROR("problem here, flow.errorCode>0"); return;} //Fill this vector than can be later used to speedup loops if (!cell->info().isGhost) Tes.cellHandles[cell->info().baseIndex]=cell; cell->info().id=cell->info().baseIndex; } Tes.cellHandles.resize(baseIndex+1); /// Call blockHook here if defined, valid indices and ghost status are available if(!blockHook.empty()){ LOG_INFO("Running blockHook: "<0 || doInterpolate)) flow.interpolate ( flow.T[!flow.currentTes], Tes ); // if ( !first && (useSolver==0 || fluidBulkModulus>0)) flow.interpolate ( flow.T[!flow.currentTes], flow.tesselation() ); if ( waveAction ) flow.applySinusoidalPressure ( Tes.Triangulation(), sineMagnitude, sineAverage, 30 ); if (normalLubrication || shearLubrication || viscousShear) flow.computeEdgesSurfaces(); if ( debug ) cout << endl << "end buildTri------" << endl << endl; } void PeriodicFlowEngine::preparePShifts() { CellInfo::gradP = makeCgVect ( gradP ); CellInfo::hSize[0] = makeCgVect ( scene->cell->hSize.col ( 0 ) ); CellInfo::hSize[1] = makeCgVect ( scene->cell->hSize.col ( 1 ) ); CellInfo::hSize[2] = makeCgVect ( scene->cell->hSize.col ( 2 ) ); CellInfo::deltaP=CGT::CVector ( CellInfo::hSize[0]*CellInfo::gradP, CellInfo::hSize[1]*CellInfo::gradP, CellInfo::hSize[2]*CellInfo::gradP ); } YADE_PLUGIN((PeriodicFlowEngine)); #endif //FLOW_ENGINE #endif /* YADE_CGAL */ trunk-2017.01a/pkg/pfv/SoluteFlowEngine.cpp000066400000000000000000000215141304022710500204760ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2013 by T. Sweijen (T.sweijen@uu.nl) * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef YADE_CGAL #ifdef FLOW_ENGINE // #define SOLUTE_FLOW #ifdef SOLUTE_FLOW #include "FlowEngine_SoluteFlowEngineT.hpp" #include class SoluteCellInfo : public FlowCellInfo_SoluteFlowEngineT { public: Real solute_concentration; SoluteCellInfo (void) : FlowCellInfo_SoluteFlowEngineT() {solute_concentration=0;} inline Real& solute (void) {return solute_concentration;} inline const Real& solute (void) const {return solute_concentration;} inline void getInfo (const SoluteCellInfo& otherCellInfo) {FlowCellInfo_SoluteFlowEngineT::getInfo(otherCellInfo); solute()=otherCellInfo.solute();} }; typedef TemplateFlowEngine_SoluteFlowEngineT SoluteFlowEngineT; REGISTER_SERIALIZABLE(SoluteFlowEngineT); YADE_PLUGIN((SoluteFlowEngineT)); class SoluteFlowEngine : public SoluteFlowEngineT { public : void initializeSoluteTransport(); void soluteTransport (double deltatime, double D); double getConcentration(unsigned int id){return solver->T[solver->currentTes].cellHandles[id]->info().solute(); } double insertConcentration(unsigned int id,double conc){ solver->T[solver->currentTes].cellHandles[id]->info().solute() = conc; return conc;} void soluteBC(unsigned int bc_id1, unsigned int bc_id2, double bc_concentration1, double bc_concentration2,unsigned int s); double getConcentrationPlane (double Yobs,double Yr, int xyz); ///Elaborate the description as you wish YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(SoluteFlowEngine,SoluteFlowEngineT,"A variant of :yref:`FlowEngine` with solute transport).", ///No additional variable yet, else input here // ((Vector3r, gradP, Vector3r::Zero(),,"Macroscopic pressure gradient")) ,,, .def("soluteTransport",&SoluteFlowEngine::soluteTransport,(boost::python::arg("deltatime"),boost::python::arg("D")),"Solute transport (advection and diffusion) engine for diffusion use a diffusion coefficient (D) other than 0.") .def("getConcentration",&SoluteFlowEngine::getConcentration,(boost::python::arg("id")),"get concentration of pore with ID") .def("insertConcentration",&SoluteFlowEngine::insertConcentration,(boost::python::arg("id"),boost::python::arg("conc")),"Insert Concentration (ID, Concentration)") .def("solute_BC",&SoluteFlowEngine::soluteBC,(boost::python::arg("bc_id1"),boost::python::arg("bc_id2"),boost::python::arg("bc_concentration1"),boost::python::arg("bc_concentration2"),boost::python::arg("s")),"Enter X,Y,Z for concentration observation'.") //I guess there is getConcentrationPlane missing here, but it is not on github ) }; REGISTER_SERIALIZABLE(SoluteFlowEngine); // PeriodicFlowEngine::~PeriodicFlowEngine(){} void SoluteFlowEngine::initializeSoluteTransport () { //Prepare a list with concentrations in range of 0,nCells. Or resets the list of concentrations to 0 // typedef typename Solver::element_type Flow; // typedef typename Flow::Finite_vertices_iterator Finite_vertices_iterator; // typedef typename Solver::element_type Flow; FOREACH(CellHandle& cell, solver->T[solver->currentTes].cellHandles) { cell->info().solute() = 0.0; } } void SoluteFlowEngine::soluteTransport (double deltatime, double D) { //soluteTransport is a function to solve transport of solutes for advection (+diffusion). //Call this function with a pyRunner in the python script, implement a diffusion coefficient and a dt. // Optimalization has to be done such that the coefficient matrix is not solved for each time step,only after triangulation. // Extensive testing has to be done to check its ability to simulate a deforming porous media. double coeff = 0.00; double coeff1 = 0.00; //Coefficient for off-diagonal element double coeff2 = 0.00; //Coefficient for diagonal element double qin = 0.00; //Flux into the pore per pore throat double Qout=0.0; //Total Flux out of the pore int ncells = 0; //Number of cells int ID = 0; //double D = 0.0; double invdistance = 0.0; //Fluid facet area divided by pore throat length for each pore throat double invdistancelocal = 0.0; //Sum of invdistance ncells=solver->T[solver->currentTes].cellHandles.size(); Eigen::SparseMatrix Aconc(ncells,ncells); typedef Eigen::Triplet ETriplet2; std::vector tripletList2; Eigen::SparseLU,Eigen::COLAMDOrdering > eSolver2; // Prepare (copy) concentration vector Eigen::VectorXd eb2(ncells); Eigen::VectorXd ex2(ncells); FOREACH(CellHandle& cell, solver->T[solver->currentTes].cellHandles){ eb2[cell->info().id]=cell->info().solute(); } // Fill coefficient matrix FOREACH(CellHandle& cell, solver->T[solver->currentTes].cellHandles){ cell->info().invVoidVolume() = 1 / ( std::abs(cell->info().volume()) - std::abs(solver->volumeSolidPore(cell) ) ); invdistance=0.0; unsigned int i=cell->info().id; for (unsigned int ngb=0;ngb<4;ngb++){ CGT::Point& p2 = cell ->neighbor(ngb)->info(); CGT::Point& p1 = cell->info(); CGT::CVector l = p1-p2; CGT::Real fluidSurf = sqrt(cell->info().facetSurfaces[ngb].squared_length())*cell->info().facetFluidSurfacesRatio[ngb]; invdistancelocal = (fluidSurf/sqrt(l.squared_length())); invdistance+=(fluidSurf/sqrt(l.squared_length())); coeff = deltatime*cell->info().invVoidVolume(); ID = cell->neighbor(ngb)->info().id; qin=std::abs(cell->info().kNorm() [ngb])* ( cell->neighbor ( ngb )->info().p()-cell->info().p()); Qout=Qout+max(qin,0.0); coeff1=-1*coeff*(std::abs(max(qin,0.0))-(D*invdistancelocal)); if (coeff1 != 0.0){ tripletList2.push_back(ETriplet2(i,ID,coeff1)); } } coeff2=1.0+(coeff*std::abs(Qout))+(coeff*D*invdistance); tripletList2.push_back(ETriplet2(i,i,coeff2)); Qout=0.0; } //Solve Matrix Aconc.setFromTriplets(tripletList2.begin(), tripletList2.end()); //if (eSolver2.signDeterminant() < 1){cerr << "determinant is negative!!!!!!! " << eSolver2.signDeterminant()<T[solver->currentTes].cellHandles){ averageConc+=cell->info().solute();} //Copy data to concentration array FOREACH(CellHandle& cell, solver->T[solver->currentTes].cellHandles){ cell->info().solute()= ex2[cell->info().id]; } tripletList2.clear(); } void SoluteFlowEngine::soluteBC(unsigned int bcid1, unsigned int bcid2, double bcconcentration1, double bcconcentration2, unsigned int s) { //Boundary conditions according to soluteTransport. //It simply assigns boundary concentrations to cells with a common vertices (e.g. infinite large sphere which makes up the boundary condition in flowEngine) //s is a switch, if 0 only bc_id1 is used (advection only). If >0 than both bc_id1 and bc_id2 are used. //NOTE (bruno): cell cirulators can be use to get all cells having bcid2 has a vertex more efficiently (see e.g. FlowBoundingSphere.ipp:721) FOREACH(CellHandle& cell, solver->T[solver->currentTes].cellHandles) { for (unsigned int ngb=0;ngb<4;ngb++){ if (cell->vertex(ngb)->info().id() == bcid1){cell->info().solute() = bcconcentration1;} if (s > 0){if (cell->vertex(ngb)->info().id() == bcid2){cell->info().solute() = bcconcentration2;}} } } } double SoluteFlowEngine::getConcentrationPlane (double Yobs,double Yr, int xyz) { //Get the concentration within a certain plane (Y_obs), whilst the cells are located in a small volume around this plane //The concentration in cells are weighed for their distance to the observation point //for a point on the x-axis (xyz=0), point on the y-axis (xyz=1), point on the z-axis (xyz=2) double sumConcentration = 0.0; double sumFraction=0.0; double concentration=0.0; //Find cells within designated volume FOREACH(CellHandle& cell, solver->T[solver->currentTes].cellHandles) { CGT::Point& p1 = cell->info(); if (std::abs(p1[xyz]) < std::abs(std::abs(Yobs) + std::abs(Yr))){ if(std::abs(p1[xyz]) > std::abs(std::abs(Yobs) - std::abs(Yr))){ sumConcentration += cell->info().solute()*(1-(std::abs(p1[xyz])-std::abs(Yobs))/std::abs(Yr)); sumFraction += (1-(std::abs(p1[xyz])-std::abs(Yobs))/std::abs(Yr)); } } } concentration = sumConcentration / sumFraction; return concentration; } YADE_PLUGIN ( ( SoluteFlowEngine ) ); #endif //SOLUTE_FLOW #endif //FLOW_ENGINE #endif /* YADE_CGAL */ trunk-2017.01a/pkg/pfv/TwoPhaseFlowEngine.cpp000066400000000000000000001443351304022710500207640ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2014 by Bruno Chareyre * * Copyright (C) 2013 by T. Sweijen (T.sweijen@uu.nl) * * Copyright (C) 2012 by Chao Yuan * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ // This is an example of how to derive a new FlowEngine with additional data and possibly completely new behaviour. // Every functions of the base engine can be overloaded, and new functions can be added //keep this #ifdef as long as you don't really want to realize a final version publicly, it will save compilation time for everyone else //when you want it compiled, you can pass -DTWOPHASEFLOW to cmake, or just uncomment the following line #include "TwoPhaseFlowEngine.hpp" #ifdef TWOPHASEFLOW YADE_PLUGIN((TwoPhaseFlowEngineT)); YADE_PLUGIN((TwoPhaseFlowEngine)); YADE_PLUGIN((PhaseCluster)); PhaseCluster::~PhaseCluster(){} void TwoPhaseFlowEngine::initialization() { scene = Omega::instance().getScene().get();//here define the pointer to Yade's scene setPositionsBuffer(true);//copy sphere positions in a buffer... buildTriangulation(0.0,*solver);//create a triangulation and initialize pressure in the elements (connecting with W-reservoir), everything will be contained in "solver" // initializeCellIndex();//initialize cell index // if(isInvadeBoundary) {computePoreThroatRadius();} // else {computePoreThroatRadiusTrickyMethod1();}//save pore throat radius before drainage. Thomas, here you can also revert this to computePoreThroatCircleRadius(). // Determine the entry-pressure if(entryPressureMethod == 1 && isInvadeBoundary){computePoreThroatRadiusMethod1();} //MS-P method else if(entryPressureMethod == 1 && isInvadeBoundary == false){computePoreThroatRadiusTrickyMethod1();} //MS-P method else if(entryPressureMethod == 2){computePoreThroatRadiusMethod2();} //Inscribed circle} else if(entryPressureMethod == 3){computePoreThroatRadiusMethod3();} //Area equivalent circle} else if(entryPressureMethod > 3){cout << endl << "ERROR - Method for determining the entry pressure does not exist";} computePoreBodyRadius();//save pore body radius before imbibition computePoreBodyVolume();//save capillary volume of all cells, for fast calculating saturation computeSolidLine();//save cell->info().solidLine[j][y] initializeReservoirs();//initial pressure, reservoir flags and local pore saturation // if(isCellLabelActivated) updateReservoirLabel(); solver->noCache = true; } void TwoPhaseFlowEngine::computePoreBodyVolume() { initializeVolumes(*solver); RTriangulation& tri = solver->T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); for (FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++) { cell->info().poreBodyVolume = std::abs( cell->info().volume() ) - std::abs(solver->volumeSolidPore(cell)); } } void TwoPhaseFlowEngine::computePoreThroatRadiusMethod2() { //Calculate the porethroat radii of the inscribed sphere in each pore-body. RTriangulation& tri = solver->T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); for (FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++) { for(unsigned int i = 0; i<4;i++){ cell->info().poreThroatRadius[i] = solver->computeEffectiveRadius(cell,i); } } } void TwoPhaseFlowEngine::computePoreThroatRadiusMethod3() { //Calculate the porethroat radii of the surface equal circle of a throat RTriangulation& tri = solver->T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); for (FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++) { for(unsigned int i = 0; i<4;i++){ cell->info().poreThroatRadius[i] = solver->computeEquivalentRadius(cell,i); } } } void TwoPhaseFlowEngine::computePoreBodyRadius() { // This routine finds the radius of the inscribed sphere within each pore-body // Following Mackay et al., 1972. double d01 = 0.0, d02 = 0.0, d03 = 0.0, d12 = 0.0, d13 = 0.0, d23 = 0.0, Rin = 0.0, r0 = 0.0, r1 = 0.0, r2 =0.0, r3 = 0.0; bool check = false; unsigned int i = 0; double dR=0.0, tempR = 0.0; bool initialSign = false; //False = negative, true is positive bool first = true; Eigen::MatrixXd M(6,6); FOREACH(CellHandle& cell, solver->T[solver->currentTes].cellHandles){ //Distance between multiple particles, can be done more efficient d01 = d02 = d03 = d12 = d13 = d23 = r0 = r1 = r2= r3 = 0.0; d01 = pow((cell->vertex(0)->point().x()-cell->vertex(1)->point().x()),2)+ pow((cell->vertex(0)->point().y()-cell->vertex(1)->point().y()),2)+ pow((cell->vertex(0)->point().z()-cell->vertex(1)->point().z()),2); d02 = pow((cell->vertex(0)->point().x()-cell->vertex(2)->point().x()),2)+ pow((cell->vertex(0)->point().y()-cell->vertex(2)->point().y()),2)+ pow((cell->vertex(0)->point().z()-cell->vertex(2)->point().z()),2); d03 = pow((cell->vertex(0)->point().x()-cell->vertex(3)->point().x()),2)+ pow((cell->vertex(0)->point().y()-cell->vertex(3)->point().y()),2)+ pow((cell->vertex(0)->point().z()-cell->vertex(3)->point().z()),2); d12 =pow((cell->vertex(1)->point().x()-cell->vertex(2)->point().x()),2)+ pow((cell->vertex(1)->point().y()-cell->vertex(2)->point().y()),2)+ pow((cell->vertex(1)->point().z()-cell->vertex(2)->point().z()),2); d13 = pow((cell->vertex(1)->point().x()-cell->vertex(3)->point().x()),2)+ pow((cell->vertex(1)->point().y()-cell->vertex(3)->point().y()),2)+ pow((cell->vertex(1)->point().z()-cell->vertex(3)->point().z()),2); d23 = pow((cell->vertex(2)->point().x()-cell->vertex(3)->point().x()),2)+ pow((cell->vertex(2)->point().y()-cell->vertex(3)->point().y()),2)+ pow((cell->vertex(2)->point().z()-cell->vertex(3)->point().z()),2); //Radii of the particles r0 = sqrt(cell -> vertex(0) -> point().weight()); r1 = sqrt(cell -> vertex(1) -> point().weight()); r2 = sqrt(cell -> vertex(2) -> point().weight()); r3 = sqrt(cell -> vertex(3) -> point().weight()); //Fill coefficient matrix M(0,0) = 0.0; M(1,0) = d01; M(2,0) = d02; M(3,0) = d03; M(4,0) = pow((r0+Rin),2); M(5,0) = 1.0; M(0,1) = d01; M(1,1) = 0.0; M(2,1) = d12; M(3,1) = d13; M(4,1) = pow((r1+Rin),2); M(5,1) = 1.0; M(0,2) = d02; M(1,2) = d12; M(2,2) = 0.0; M(3,2) = d23; M(4,2) = pow((r2+Rin),2); M(5,2) = 1.0; M(0,3) = d03; M(1,3) = d13; M(2,3) = d23; M(3,3) = 0.0; M(4,3) = pow((r3+Rin),2); M(5,3) = 1.0; M(0,4) = pow((r0+Rin),2); M(1,4) = pow((r1+Rin),2); M(2,4) = pow((r2+Rin),2); M(3,4) = pow((r3+Rin),2); M(4,4) = 0.0; M(5,4) = 1.0; M(0,5) = 1.0; M(1,5) = 1.0; M(2,5) = 1.0; M(3,5) = 1.0; M(4,5) = 1.0; M(5,5) = 0.0; i = 0; check = false; dR = Rin = 0.0 + (min(r0,min(r1,min(r2,r3))) / 50.0); //Estimate an initial dR first = true; //Iterate untill check = true, such that an accurate answer as been found while (check == false){ i = i + 1; tempR = Rin; Rin = Rin + dR; M(4,0) = pow((r0+Rin),2); M(4,1) = pow((r1+Rin),2); M(4,2) = pow((r2+Rin),2); M(4,3) = pow((r3+Rin),2); M(0,4) = pow((r0+Rin),2); M(1,4) = pow((r1+Rin),2); M(2,4) = pow((r2+Rin),2); M(3,4) = pow((r3+Rin),2); if (first){ first = false; if(M.determinant() < 0.0){initialSign = false;} //Initial D is negative if(M.determinant() > 0.0){initialSign = true;} // Initial D is positive } if(std::abs(M.determinant()) < 1E-30){check = true;} if((initialSign==true) && (check ==false)){ if(M.determinant() < 0.0){ Rin = Rin -dR; dR = dR / 2.0; } } if((initialSign==false) && (check ==false)){ if(M.determinant() > 0.0){ Rin = Rin -dR; dR = dR / 2.0; } } if(solver->debugOut) {cout << endl << i << " "< 4000){ cout << endl << "error, finding solution takes too long cell:" << cell->info().id; check = true; } if ( std::abs(tempR - Rin)/Rin < 0.001){check = true;} } cell -> info().poreBodyRadius = Rin; } } void TwoPhaseFlowEngine::computePoreThroatRadiusMethod1() { RTriangulation& tri = solver->T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); CellHandle neighbourCell; for (FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++) { for (int j=0; j<4; j++) { neighbourCell = cell->neighbor(j); if (!tri.is_infinite(neighbourCell)) { cell->info().poreThroatRadius[j]=computeEffPoreThroatRadius(cell, j); neighbourCell->info().poreThroatRadius[tri.mirror_index(cell, j)]= cell->info().poreThroatRadius[j];}}} } double TwoPhaseFlowEngine::computeEffPoreThroatRadius(CellHandle cell, int j) { double rInscribe = std::abs(solver->computeEffectiveRadius(cell, j)); CellHandle cellh = CellHandle(cell); int facetNFictious = solver->detectFacetFictiousVertices (cellh,j); double r; if(facetNFictious==0) {r=computeEffPoreThroatRadiusFine(cell,j);} else r=rInscribe; return r; } double TwoPhaseFlowEngine::computeEffPoreThroatRadiusFine(CellHandle cell, int j) { RTriangulation& tri = solver->T[solver->currentTes].Triangulation(); if (tri.is_infinite(cell->neighbor(j))) return 0; Vector3r pos[3]; //solid pos double r[3]; //solid radius double e[3]; //edges of triangulation double g[3]; //gap radius between solid for (int i=0; i<3; i++) { pos[i] = makeVector3r(cell->vertex(facetVertices[j][i])->point().point()); r[i] = sqrt(cell->vertex(facetVertices[j][i])->point().weight()); } e[0] = (pos[1]-pos[2]).norm(); e[1] = (pos[2]-pos[0]).norm(); e[2] = (pos[1]-pos[0]).norm(); g[0] = ((e[0]-r[1]-r[2])>0) ? 0.5*(e[0]-r[1]-r[2]):0 ; g[1] = ((e[1]-r[2]-r[0])>0) ? 0.5*(e[1]-r[2]-r[0]):0 ; g[2] = ((e[2]-r[0]-r[1])>0) ? 0.5*(e[2]-r[0]-r[1]):0 ; double rmin= (std::max(g[0],std::max(g[1],g[2]))==0) ? 1.0e-10:std::max(g[0],std::max(g[1],g[2])) ; double rmax = std::abs(solver->computeEffectiveRadius(cell, j)); // if(rmin>rmax) { cerr<<"WARNING! rmin>rmax. rmin="<vtkInfiniteVertices=solver->vtkInfiniteCells=0; FiniteCellsIterator cellEnd = Tri.finite_cells_end(); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++) { bool isDrawable = cell->info().isReal() && cell->vertex(0)->info().isReal() && cell->vertex(1)->info().isReal() && cell->vertex(2)->info().isReal() && cell->vertex(3)->info().isReal(); if (!isDrawable) solver->vtkInfiniteCells+=1; } for (FiniteVerticesIterator v = Tri.finite_vertices_begin(); v != Tri.finite_vertices_end(); ++v) { if (!v->info().isReal()) solver->vtkInfiniteVertices+=1; else if (firstReal==-1) firstReal=solver->vtkInfiniteVertices;} basicVTKwritter vtkfile((unsigned int) Tri.number_of_vertices()-solver->vtkInfiniteVertices, (unsigned int) Tri.number_of_finite_cells()-solver->vtkInfiniteCells); vtkfile.open(filename,"test"); vtkfile.begin_vertices(); double x,y,z; for (FiniteVerticesIterator v = Tri.finite_vertices_begin(); v != Tri.finite_vertices_end(); ++v) { if (v->info().isReal()){ x = (double)(v->point().point()[0]); y = (double)(v->point().point()[1]); z = (double)(v->point().point()[2]); vtkfile.write_point(x,y,z);} } vtkfile.end_vertices(); vtkfile.begin_cells(); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != Tri.finite_cells_end(); ++cell) { bool isDrawable = cell->info().isReal() && cell->vertex(0)->info().isReal() && cell->vertex(1)->info().isReal() && cell->vertex(2)->info().isReal() && cell->vertex(3)->info().isReal(); if (isDrawable){vtkfile.write_cell(cell->vertex(0)->info().id()-firstReal, cell->vertex(1)->info().id()-firstReal, cell->vertex(2)->info().id()-firstReal, cell->vertex(3)->info().id()-firstReal);} } vtkfile.end_cells(); vtkfile.begin_data("Saturation",CELL_DATA,SCALARS,FLOAT); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != Tri.finite_cells_end(); ++cell) { bool isDrawable = cell->info().isReal() && cell->vertex(0)->info().isReal() && cell->vertex(1)->info().isReal() && cell->vertex(2)->info().isReal() && cell->vertex(3)->info().isReal(); if (isDrawable){vtkfile.write_data(cell->info().saturation);} } vtkfile.end_data(); vtkfile.begin_data("Label",CELL_DATA,SCALARS,FLOAT); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != Tri.finite_cells_end(); ++cell) { bool isDrawable = cell->info().isReal() && cell->vertex(0)->info().isReal() && cell->vertex(1)->info().isReal() && cell->vertex(2)->info().isReal() && cell->vertex(3)->info().isReal(); if (isDrawable){vtkfile.write_data(cell->info().label);} } vtkfile.end_data(); } void TwoPhaseFlowEngine::computePoreThroatRadiusTrickyMethod1() { computePoreThroatRadiusMethod1(); RTriangulation& tri = solver->T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); CellHandle neighbourCell; for (FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++) { for (int j=0; j<4; j++) { neighbourCell = cell->neighbor(j); if(cell->info().isFictious && neighbourCell->info().isFictious) {cell->info().poreThroatRadius[j]=-1.0; neighbourCell->info().poreThroatRadius[tri.mirror_index(cell, j)]= cell->info().poreThroatRadius[j];} } } } void TwoPhaseFlowEngine::computeSolidLine() { RTriangulation& Tri = solver->T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = Tri.finite_cells_end(); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++) { for(int j=0; j<4; j++) { solver->lineSolidPore(cell, j); } } if(solver->debugOut) {cout<<"----computeSolidLine-----."<pressureChanged=true; solver->reApplyBoundaryConditions(); ///keep boundingCells[2] as W-reservoir. for (FlowSolver::VCellIterator it = solver->boundingCells[2].begin(); it != solver->boundingCells[2].end(); it++) { (*it)->info().isWRes = true; (*it)->info().isNWRes = false; (*it)->info().saturation=1.0; } ///keep boundingCells[3] as NW-reservoir. for (FlowSolver::VCellIterator it = solver->boundingCells[3].begin(); it != solver->boundingCells[3].end(); it++) { (*it)->info().isNWRes = true; (*it)->info().isWRes = false; (*it)->info().saturation=0.0; } RTriangulation& tri = solver->T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); ///if we start from drainage if(drainageFirst) { for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if (cell->info().Pcondition) continue; cell->info().p()=bndCondValue[2]; cell->info().isWRes = true; cell->info().isNWRes= false; cell->info().saturation=1.0; } } ///if we start from imbibition if(!drainageFirst) { for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if (cell->info().Pcondition) continue; cell->info().p()=bndCondValue[3]; cell->info().isWRes = false; cell->info().isNWRes= true; cell->info().saturation=0.0; } } if(solver->debugOut) {cout<<"----initializeReservoirs----"<T[solver->currentTes].cellHandles.size(); RTriangulation& tri = solver->T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); for (FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++) { if(cell->info().isGhost == false && cell->info().id < solver->T[solver->currentTes].cellHandles.size()){ filePoreBodyRadius << cell->info().poreBodyRadius << '\n'; filePoreBodyVolume << cell->info().poreBodyRadius << '\n'; CVector center ( 0,0,0 ); for ( int k=0;k<4;k++ ){ center= center + 0.25* (cell->vertex(k)->point()-CGAL::ORIGIN);} fileLocation << center<< '\n'; for (unsigned int i=0;i<4;i++){ if(cell->neighbor(i)->info().isGhost == false && cell->neighbor(i)->info().id < solver->T[solver->currentTes].cellHandles.size() && (cell->info().id < cell->neighbor(i)->info().id)){ fileNeighbor << cell->neighbor(i)->info().id << '\n'; fileThroatRadius << cell->info().poreThroatRadius[i] << '\n'; fileThroats << cell->info().id << " " << cell->neighbor(i)->info().id << '\n'; } } } if(cell->info().isFictious == 1 && cell->info().isGhost == false && cell->info().id < solver->T[solver->currentTes].cellHandles.size()){ //add boundary condition if(cell->info().isFictious == 1 &&(cell->vertex(0)->info().id() == 3 || cell->vertex(1)->info().id() == 3 || cell->vertex(2)->info().id() == 3 || cell->vertex(3)->info().id() == 3)){ filePoreBoundary << "3" << '\n'; } else if(cell->info().isFictious == 1 &&(cell->vertex(0)->info().id() == 2 || cell->vertex(1)->info().id() == 2 || cell->vertex(2)->info().id() == 2 || cell->vertex(3)->info().id() == 2)){ filePoreBoundary << "2" << '\n'; } else{filePoreBoundary << "2" << '\n';} } if(cell->info().isFictious == 0 && cell->info().isGhost == false && cell->info().id < solver->T[solver->currentTes].cellHandles.size()){ filePoreBoundary << "0" << '\n'; } } filePoreBodyRadius.close(); filePoreBoundary.close(); filePoreBodyVolume.close(); fileLocation.close(); fileNeighbor.close(); fileThroatRadius.close(); } double TwoPhaseFlowEngine:: computePoreSatAtInterface(int ID) { // //This function calculates the new saturation of pore at the interface between wetting/nonwetting // //filled pores. It substracts the outgoing flux from the water volume // RTriangulation& tri = solver->T[solver->currentTes].Triangulation(); // FiniteCellsIterator cellEnd = tri.finite_cells_end(); // for (FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++) { // if(cell->info().id == ID){ // // double qout = 0.0, Vw = 0.0, dt = 0.0; // // for(unsigned int ngb = 0; ngb < 4; ngb++) // { // //find out/influx of water // if((cell->neighbor(ngb)->info().isWRes) && (cell->neighbor(ngb)->info().isFictious == 0)){ // qout= qout + std::abs(cell->info().kNorm() [ngb])*(cell->info().p()-cell->neighbor ( ngb )->info().p()); // } // } // // Vw = (cell->info().saturation * cell->info().poreBodyVolume) - (qout * scene->dt); // // //Functionality to calculate the smallest time step // if((1e-16 < Vw) && (Vw < 1e16)){ // if((1e-16 < qout) && (qout < 1e16)){ // dt = (Vw / qout); // if(dt!=0.0){dtDynTPF = std::min(dt,dtDynTPF);} // } // } // cell->info().saturation = Vw / cell->info().poreBodyVolume; // // // The following constrains check the value of saturation // if(std::abs(cell->info().saturation) < 1e-6){cell->info().saturation = 0.0;} // To prevent dt going to 0 // if(cell->info().saturation < 0.0){ // cout << endl << "dt was too large!, negative saturation in cell "<< cell->info().id; // cell->info().saturation = 0.0; // } // if(cell->info().saturation > 1.0){ // cout << endl <<"dt was too large!,saturation larger than 1 in cell " << cell->info().id; // cell->info().saturation = 1.0;} // return cell->info().saturation; // } // } return 0; } void TwoPhaseFlowEngine:: computePoreCapillaryPressure(CellHandle cell) { //This formula relates the pore-saturation to the capillary-pressure, and the water-pressure //based on Joekar-Niasar, for cubic pores. NOTE: Needs to be changed into a proper set of equations /* double Re = 0.0, Pc = 0.0, Pg = 0.0; for(unsigned int i = 0; i<4;i++) { Re = max(Re,cell->info().poreThroatRadius[i]); } Pc = surfaceTension / (Re * (1.0-exp(-6.83 * cell->info().saturation))); Pg = std::max(bndCondValue[2],bndCondValue[3]); cell->info().p() = Pg - Pc; */ } void TwoPhaseFlowEngine:: updateReservoirLabel() { clusters[0]->reset(); clusters[0]->label=0; clusters[1]->reset(); clusters[1]->label=1; RTriangulation& tri = solver->T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if (cell->info().isNWRes) clusterGetPore(clusters[0].get(),cell); else if (cell->info().isWRes) { clusterGetPore(clusters[1].get(),cell); for (int facet = 0; facet < 4; facet ++) if (!cell->neighbor(facet)->info().isWRes) clusterGetFacet(clusters[1].get(),cell,facet);} else if (cell->info().label>1) continue; else cell->info().label=-1; } } void TwoPhaseFlowEngine::clusterGetFacet(PhaseCluster* cluster, CellHandle cell, int facet) { cell->info().hasInterface = true; double interfArea = sqrt((cell->info().facetSurfaces[facet]*cell->info().facetFluidSurfacesRatio[facet]).squared_length()); cluster->interfaces.push_back(std::pair,double>( std::pair(cell->info().id,cell->neighbor(facet)->info().id),interfArea)); cluster->interfacialArea += interfArea; if (cluster->entryRadius < cell->info().poreThroatRadius[facet]){ cluster->entryRadius = cell->info().poreThroatRadius[facet]; cluster->entryPore = cell->info().id;} } void TwoPhaseFlowEngine::clusterGetPore(PhaseCluster* cluster, CellHandle cell) { cell->info().label=cluster->label; cluster->volume+=cell->info().poreBodyVolume; cluster->pores.push_back(cell); } // int TwoPhaseFlowEngine:: getMaxCellLabel() // { // int maxLabel=-1; // RTriangulation& tri = solver->T[solver->currentTes].Triangulation(); // FiniteCellsIterator cellEnd = tri.finite_cells_end(); // for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { // if (cell->info().label>maxLabel) maxLabel=cell->info().label; // } // return maxLabel; // } void TwoPhaseFlowEngine::updateCellLabel() { // int currentLabel = getMaxCellLabel();//FIXME: A loop on cells for each new label?? is it serious?? updateReservoirLabel(); int currentLabel = clusters.size(); RTriangulation& tri = solver->T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if (cell->info().label==-1) { shared_ptr clst (new PhaseCluster()); clst->label=currentLabel; clusters.push_back(clst); updateSingleCellLabelRecursion(cell,clusters.back().get()); currentLabel++; } } } void TwoPhaseFlowEngine::updateSingleCellLabelRecursion(CellHandle cell, PhaseCluster* cluster) { clusterGetPore(cluster,cell); // cell->info().label=label; // cluster->volume+=cell->info(). // cluster->pores.push_back(cell); for (int facet = 0; facet < 4; facet ++) { CellHandle nCell = cell->neighbor(facet); if (solver->T[solver->currentTes].Triangulation().is_infinite(nCell)) continue; // if (nCell->info().Pcondition) continue; // if ( (nCell->info().isFictious) && (!isInvadeBoundary) ) continue; //TODO:the following condition may relax to relate to nCell->info().hasInterface if ( (nCell->info().saturation==cell->info().saturation) && (nCell->info().label!=cell->info().label) ) updateSingleCellLabelRecursion(nCell,cluster); else if (nCell->info().isNWRes) clusterGetFacet(cluster,cell,facet); } } boost::python::list TwoPhaseFlowEngine::pyClusters() { boost::python::list ret; for(vector >::iterator it=clusters.begin(); it!=clusters.end(); ++it) ret.append(*it); return ret;} void TwoPhaseFlowEngine::updatePressure() { boundaryConditions(*solver); solver->pressureChanged=true; solver->reApplyBoundaryConditions(); RTriangulation& tri = solver->T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if (cell->info().isWRes==true) {cell->info().p()=bndCondValue[2];} if (cell->info().isNWRes==true) {cell->info().p()=bndCondValue[3];} if (isPhaseTrapped) { if ( cell->info().isTrapW ) {cell->info().p()=bndCondValue[3]-cell->info().trapCapP;} if ( cell->info().isTrapNW) {cell->info().p()=bndCondValue[2]+cell->info().trapCapP;} //check cell reservoir info. if ( !cell->info().isWRes && !cell->info().isNWRes && !cell->info().isTrapW && !cell->info().isTrapNW ) {cerr<<"ERROR! NOT FIND Cell Info!";} // {cell->info().p()=bndCondValue[2]; if (isInvadeBoundary) cerr<<"Something wrong in updatePressure.(isInvadeBoundary)";} } } } void TwoPhaseFlowEngine::invasion() { if (isPhaseTrapped) invasion1(); else invasion2(); } ///mode1 and mode2 can share the same invasionSingleCell(), invasionSingleCell() ONLY change neighbor pressure and neighbor saturation, independent of reservoirInfo. void TwoPhaseFlowEngine::invasionSingleCell(CellHandle cell) { double localPressure=cell->info().p(); double localSaturation=cell->info().saturation; for (int facet = 0; facet < 4; facet ++) { CellHandle nCell = cell->neighbor(facet); if (solver->T[solver->currentTes].Triangulation().is_infinite(nCell)) continue; if (nCell->info().Pcondition) continue;//FIXME:defensive // if ( (nCell->info().isFictious) && (!isInvadeBoundary) ) continue; if (cell->info().poreThroatRadius[facet]<0) continue; if ( (nCell->info().saturation==localSaturation) && (nCell->info().p() != localPressure) && ((nCell->info().isTrapNW)||(nCell->info().isTrapW)) ) { nCell->info().p() = localPressure; if(solver->debugOut) {cerr<<"merge trapped phase"<info().saturation>localSaturation) ) { double nPcThroat=surfaceTension/cell->info().poreThroatRadius[facet]; double nPcBody=surfaceTension/nCell->info().poreBodyRadius; if( (localPressure-nCell->info().p()>nPcThroat) && (localPressure-nCell->info().p()>nPcBody) ) { nCell->info().p() = localPressure; nCell->info().saturation=localSaturation; nCell->info().hasInterface=false; if(solver->debugOut) {cerr<<"drainage"<info().p()>nPcThroat) && (localPressure-nCell->info().p()info().hasInterface==false) && (nCell->info().hasInterface==false) ) { // if(solver->debugOut) {cerr<<"invasion paused into pore interface "<info().hasInterface=true; // } // else continue; } else if ( (nCell->info().saturationinfo().poreThroatRadius[facet]; double nPcBody=surfaceTension/nCell->info().poreBodyRadius; if( (nCell->info().p()-localPressureinfo().p()-localPressureinfo().p() = localPressure; nCell->info().saturation=localSaturation; if(solver->debugOut) {cerr<<"imbibition"<info().p()-localPressureinfo().p()-localPressure>nPcThroat) /*&& (cell->info().hasInterface==false) && (nCell->info().hasInterface==false)*/ ) { // nCell->info().p() = localPressure; // nCell->info().saturation=localSaturation; // if(solver->debugOut) {cerr<<"imbibition paused pore interface"<info().hasInterface=true; // } // else continue; } else continue; } } ///invasion mode 1: withTrap void TwoPhaseFlowEngine::invasion1() { if(solver->debugOut) {cout<<"----start invasion1----"<debugOut) {cout<<"----invasion1.updatePressure----"<T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); if(isDrainageActivated) { for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if(cell->info().isNWRes) invasionSingleCell(cell); } } if(isImbibitionActivated) { for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if(cell->info().isWRes) invasionSingleCell(cell); } } if(solver->debugOut) {cout<<"----invasion1.invasionSingleCell----"<info().saturation updateReservoirs1(); if(solver->debugOut) {cout<<"----invasion1.update W, NW reservoirInfo----"<debugOut) {cout<<"----invasion1.checkWTrap----"<info().isTrapW ) {cell->info().p()=bndCondValue[3]-cell->info().trapCapP;} if ( cell->info().isTrapNW) {cell->info().p()=bndCondValue[2]+cell->info().trapCapP;} } if(solver->debugOut) {cout<<"----invasion1.update trapped W-phase/NW-phase Pressure----"<debugOut) {cout<<"----update cell labels----"<T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { // if( (cell->info().isFictious) && (!cell->info().Pcondition) && (!isInvadeBoundary) ) continue; if( (cell->info().isWRes) || (cell->info().isNWRes) || (cell->info().isTrapW) || (cell->info().isTrapNW) ) continue; cell->info().trapCapP=pressure; if(cell->info().saturation==1.0) cell->info().isTrapW=true; if(cell->info().saturation==0.0) cell->info().isTrapNW=true; } } void TwoPhaseFlowEngine::updateReservoirs1() { RTriangulation& tri = solver->T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if(cell->info().Pcondition) continue; cell->info().isWRes = false; cell->info().isNWRes = false; } for (FlowSolver::VCellIterator it = solver->boundingCells[2].begin(); it != solver->boundingCells[2].end(); it++) { if ((*it)==NULL) continue; WResRecursion(*it); } for (FlowSolver::VCellIterator it = solver->boundingCells[3].begin(); it != solver->boundingCells[3].end(); it++) { if ((*it)==NULL) continue; NWResRecursion(*it); } } void TwoPhaseFlowEngine::WResRecursion(CellHandle cell) { for (int facet = 0; facet < 4; facet ++) { CellHandle nCell = cell->neighbor(facet); if (solver->T[solver->currentTes].Triangulation().is_infinite(nCell)) continue; if (nCell->info().Pcondition) continue; // if ( (nCell->info().isFictious) && (!isInvadeBoundary) ) continue; if (nCell->info().saturation != 1.0) continue; if (nCell->info().isWRes==true) continue; nCell->info().isWRes = true; nCell->info().isNWRes = false; nCell->info().isTrapW = false; nCell->info().trapCapP=0.0; WResRecursion(nCell); } } void TwoPhaseFlowEngine::NWResRecursion(CellHandle cell) { for (int facet = 0; facet < 4; facet ++) { CellHandle nCell = cell->neighbor(facet); if (solver->T[solver->currentTes].Triangulation().is_infinite(nCell)) continue; if (nCell->info().Pcondition) continue; // if ( (nCell->info().isFictious) && (!isInvadeBoundary) ) continue; if (nCell->info().saturation != 0.0) continue; if (nCell->info().isNWRes==true) continue; nCell->info().isNWRes = true; nCell->info().isWRes = false; nCell->info().isTrapNW = false; nCell->info().trapCapP=0.0; NWResRecursion(nCell); } } ///invasion mode 2: withoutTrap void TwoPhaseFlowEngine::invasion2() { if(solver->debugOut) {cout<<"----start invasion2----"<debugOut) {cout<<"----invasion2.updatePressure----"<T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); if(isDrainageActivated) { for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if(cell->info().isNWRes) invasionSingleCell(cell); } } ///drainageSingleCell by Pressure difference, change Pressure and Saturation. if(isImbibitionActivated) { for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if(cell->info().isWRes) invasionSingleCell(cell); } } if(solver->debugOut) {cout<<"----invasion2.invasionSingleCell----"<debugOut) {cout<<"----drainage2.update W, NW reservoirInfo----"<T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if (cell->info().p()==bndCondValue[2]) {cell->info().isWRes=true; cell->info().isNWRes=false;} else if (cell->info().p()==bndCondValue[3]) {cell->info().isNWRes=true; cell->info().isWRes=false;} else {cerr<<"drainage mode2: updateReservoir Error!"<T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if (cell->info().isNWRes == true) { for (int facet=0; facet<4; facet ++) { CellHandle nCell = cell->neighbor(facet); if (tri.is_infinite(nCell)) continue; if (nCell->info().Pcondition) continue; // if ( (nCell->info().isFictious) && (!isInvadeBoundary) ) continue; if ( nCell->info().isWRes == true && cell->info().poreThroatRadius[facet]>0) { double nCellP = std::max( (surfaceTension/cell->info().poreThroatRadius[facet]),(surfaceTension/nCell->info().poreBodyRadius) ); // double nCellP = surfaceTension/cell->info().poreThroatRadius[facet]; nextEntry = std::min(nextEntry,nCellP);}}}} if (nextEntry==1e50) { cout << "End drainage !" << endl; return nextEntry=0; } else return nextEntry; } double TwoPhaseFlowEngine::getMaxImbibitionPc() { double nextEntry = -1e50; RTriangulation& tri = solver->T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if (cell->info().isWRes == true) { for (int facet=0; facet<4; facet ++) { CellHandle nCell = cell->neighbor(facet); if (tri.is_infinite(nCell)) continue; if (nCell->info().Pcondition) continue; // if ( (nCell->info().isFictious) && (!isInvadeBoundary) ) continue; if ( nCell->info().isNWRes == true && cell->info().poreThroatRadius[facet]>0) { double nCellP = std::min( (surfaceTension/nCell->info().poreBodyRadius), (surfaceTension/cell->info().poreThroatRadius[facet])); nextEntry = std::max(nextEntry,nCellP);}}}} if (nextEntry==-1e50) { cout << "End imbibition !" << endl; return nextEntry=0; } else return nextEntry; } double TwoPhaseFlowEngine::getSaturation(bool isSideBoundaryIncluded) { if( (!isInvadeBoundary) && (isSideBoundaryIncluded)) cerr<<"In isInvadeBoundary=false drainage, isSideBoundaryIncluded can't set true."<T[solver->currentTes].Triangulation(); double poresVolume = 0.0; //total pores volume double wVolume = 0.0; //NW-phase volume FiniteCellsIterator cellEnd = tri.finite_cells_end(); for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if (cell->info().Pcondition) continue; if ( (cell->info().isFictious) && (!isSideBoundaryIncluded) ) continue; poresVolume = poresVolume + cell->info().poreBodyVolume; if (cell->info().saturation>0.0) { wVolume = wVolume + cell->info().poreBodyVolume * cell->info().saturation; } } return wVolume/poresVolume; } ///compute forces void TwoPhaseFlowEngine::computeFacetPoreForcesWithCache(bool onlyCache) { RTriangulation& Tri = solver->T[solver->currentTes].Triangulation(); CVector nullVect(0,0,0); //reset forces if (!onlyCache) for (FiniteVerticesIterator v = Tri.finite_vertices_begin(); v != Tri.finite_vertices_end(); ++v) v->info().forces=nullVect; // #ifdef parallel_forces // if (solver->noCache) { // solver->perVertexUnitForce.clear(); solver->perVertexPressure.clear(); // solver->perVertexUnitForce.resize(solver->T[solver->currentTes].maxId+1); // solver->perVertexPressure.resize(solver->T[solver->currentTes].maxId+1);} // #endif // CellHandle neighbourCell; // VertexHandle mirrorVertex; CVector tempVect; //FIXME : Ema, be carefull with this (noCache), it needs to be turned true after retriangulation if (solver->noCache) {//WARNING:all currentTes must be solver->T[solver->currentTes], should NOT be solver->T[currentTes] for (FlowSolver::VCellIterator cellIt=solver->T[solver->currentTes].cellHandles.begin(); cellIt!=solver->T[solver->currentTes].cellHandles.end(); cellIt++) { CellHandle& cell = *cellIt; //reset cache for (int k=0; k<4; k++) cell->info().unitForceVectors[k]=nullVect; for (int j=0; j<4; j++) if (!Tri.is_infinite(cell->neighbor(j))) { const CVector& Surfk = cell->info().facetSurfaces[j]; //FIXME : later compute that fluidSurf only once in hydraulicRadius, for now keep full surface not modified in cell->info for comparison with other forces schemes //The ratio void surface / facet surface Real area = sqrt(Surfk.squared_length()); if (area<=0) cerr <<"AREA <= 0!! AREA="<& crossSections = cell->info().facetSphereCrossSections; CVector fluidSurfk = cell->info().facetSurfaces[j]*cell->info().facetFluidSurfacesRatio[j]; /// handle fictious vertex since we can get the projected surface easily here if (cell->vertex(j)->info().isFictious) { Real projSurf=std::abs(Surfk[solver->boundary(cell->vertex(j)->info().id()).coordinate]); tempVect=-projSurf*solver->boundary(cell->vertex(j)->info().id()).normal; cell->vertex(j)->info().forces = cell->vertex(j)->info().forces+tempVect*cell->info().p(); //define the cached value for later use with cache*p cell->info().unitForceVectors[j]=cell->info().unitForceVectors[j]+ tempVect; } /// Apply weighted forces f_k=sqRad_k/sumSqRad*f CVector facetUnitForce = -fluidSurfk*cell->info().solidLine[j][3]; CVector facetForce = cell->info().p()*facetUnitForce; for (int y=0; y<3; y++) { cell->vertex(facetVertices[j][y])->info().forces = cell->vertex(facetVertices[j][y])->info().forces + facetForce*cell->info().solidLine[j][y]; //add to cached value cell->info().unitForceVectors[facetVertices[j][y]]=cell->info().unitForceVectors[facetVertices[j][y]]+facetUnitForce*cell->info().solidLine[j][y]; //uncomment to get total force / comment to get only pore tension forces if (!cell->vertex(facetVertices[j][y])->info().isFictious) { cell->vertex(facetVertices[j][y])->info().forces = cell->vertex(facetVertices[j][y])->info().forces -facetNormal*cell->info().p()*crossSections[j][y]; //add to cached value cell->info().unitForceVectors[facetVertices[j][y]]=cell->info().unitForceVectors[facetVertices[j][y]]-facetNormal*crossSections[j][y]; } } // #ifdef parallel_forces // solver->perVertexUnitForce[cell->vertex(j)->info().id()].push_back(&(cell->info().unitForceVectors[j])); // solver->perVertexPressure[cell->vertex(j)->info().id()].push_back(&(cell->info().p())); // #endif } } solver->noCache=false;//cache should always be defined after execution of this function } if (onlyCache) return; // else {//use cached values when triangulation doesn't change // #ifndef parallel_forces for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != Tri.finite_cells_end(); cell++) { for (int yy=0; yy<4; yy++) cell->vertex(yy)->info().forces = cell->vertex(yy)->info().forces + cell->info().unitForceVectors[yy]*cell->info().p(); } // #else // #pragma omp parallel for num_threads(ompThreads) // for (int vn=0; vn<= solver->T[solver->currentTes].maxId; vn++) { // VertexHandle& v = solver->T[solver->currentTes].vertexHandles[vn]; // const int& id = v->info().id(); // CVector tf (0,0,0); // int k=0; // for (vector::iterator c = solver->perVertexPressure[id].begin(); c != solver->perVertexPressure[id].end(); c++) // tf = tf + (*(solver->perVertexUnitForce[id][k++]))*(**c); // v->info().forces = tf; // } // #endif // } if (solver->debugOut) { CVector totalForce = nullVect; for (FiniteVerticesIterator v = Tri.finite_vertices_begin(); v != Tri.finite_vertices_end(); ++v) { if (!v->info().isFictious) totalForce = totalForce + v->info().forces; else if (solver->boundary(v->info().id()).flowCondition==1) totalForce = totalForce + v->info().forces; } cout << "totalForce = "<< totalForce << endl; } } bool TwoPhaseFlowEngine::detectBridge(RTriangulation::Finite_edges_iterator& edge) { bool dryBridgeExist=true; const RTriangulation& Tri = solver->T[solver->currentTes].Triangulation(); RTriangulation::Cell_circulator cell1 = Tri.incident_cells(*edge); RTriangulation::Cell_circulator cell0 = cell1++; if(cell0->info().saturation==1) {dryBridgeExist=false; return dryBridgeExist;} else { while (cell1!=cell0) { if(cell1->info().saturation==1) {dryBridgeExist=false;break;} else cell1++;} return dryBridgeExist; } } #endif //TwoPhaseFLOW trunk-2017.01a/pkg/pfv/TwoPhaseFlowEngine.hpp000066400000000000000000000407151304022710500207660ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2014 by Bruno Chareyre * * Copyright (C) 2013 by Thomas. Sweijen * * Copyright (C) 2012 by Chao Yuan * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ // This is an example of how to derive a new FlowEngine with additional data and possibly completely new behaviour. // Every functions of the base engine can be overloaded, and new functions can be added //keep this #ifdef as long as you don't really want to realize a final version publicly, it will save compilation time for everyone else //when you want it compiled, you can pass -DTWOPHASEFLOW to cmake, or just uncomment the following line //#define TWOPHASEFLOW #ifdef TWOPHASEFLOW #include "FlowEngine_TwoPhaseFlowEngineT.hpp" /// We can add data to the Info types by inheritance class TwoPhaseCellInfo : public FlowCellInfo_TwoPhaseFlowEngineT { public: bool isWRes;//Flags for marking cell(pore unit) state: isWettingReservoirCell, isNonWettingReservoirCell, isTrappedWettingCell, isTrappedNonWettingCell bool isNWRes; bool isTrapW; bool isTrapNW; double saturation;//the saturation of single pore (will be used in quasi-static imbibition and dynamic flow) double trapCapP;//for calculating the pressure of trapped pore, cell->info().p() = pressureNW- trapCapP. OR cell->info().p() = pressureW + trapCapP bool hasInterface; //Indicated whether a NW-W interface is present within the pore body std::vector poreThroatRadius; double poreBodyRadius; double poreBodyVolume; int windowsID;//a temp cell info for experiment comparison(used by chao) double solidLine [4][4];//the length of intersecting line between sphere and facet. [i][j] is for facet "i" and sphere (facetVertices)"[i][j]". Last component [i][3] for 1/sumLines in the facet "i" (used by chao). int label;//for marking disconnected clusters. NW-res: 0; W-res: 1; W-clusters by 2,3,4... TwoPhaseCellInfo (void) { isWRes = true; isNWRes = false; isTrapW = false; isTrapNW = false; saturation = 1.0; hasInterface = false; trapCapP = 0; poreThroatRadius.resize(4, 0); poreBodyRadius = 0; poreBodyVolume = 0; windowsID = 0; for (int k=0; k<4;k++) for (int l=0; l<4;l++) solidLine[k][l]=0; label=-1; } }; class TwoPhaseVertexInfo : public FlowVertexInfo_TwoPhaseFlowEngineT { public: //same here if needed }; typedef TemplateFlowEngine_TwoPhaseFlowEngineT TwoPhaseFlowEngineT; REGISTER_SERIALIZABLE(TwoPhaseFlowEngineT); // A class to represent isolated single-phase cluster (main application in convective drying at the moment) class PhaseCluster : public Serializable { double totalCellVolume; // CellHandle entryPoreHandle; public : virtual ~PhaseCluster(); vector pores; vector,double> > interfaces; TwoPhaseFlowEngineT::RTriangulation* tri; void reset() {label=entryPore=-1;volume=entryRadius=interfacialArea=0; pores.clear(); interfaces.clear();} vector getPores() { vector res; for (vector::iterator it = pores.begin(); it!=pores.end(); it++) res.push_back((*it)->info().id); return res;} boost::python::list getInterfaces(){ boost::python::list ints; for (vector,double> >::iterator it = interfaces.begin(); it!=interfaces.end(); it++) ints.append(boost::python::make_tuple(it->first.first,it->first.second,it->second)); return ints; } YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(PhaseCluster,Serializable,"Preliminary.", ((int,label,-1,,"Unique label of this cluster, should be reflected in pores of this cluster.")) ((double,volume,0,,"cumulated volume of all pores.")) ((double,entryRadius,0,,"smallest entry capillary pressure.")) ((int,entryPore,-1,,"the pore of the cluster incident to the throat with smallest entry Pc.")) ((double,interfacialArea,0,,"interfacial area of the cluster")) ,,, .def("getPores",&PhaseCluster::getPores,"get the list of pores by index") .def("getInterfaces",&PhaseCluster::getInterfaces,"get the list of interfacial pore-throats associated to a cluster, listed as [id1,id2,area] where id2 is the neighbor pore outside the cluster.") ) }; REGISTER_SERIALIZABLE(PhaseCluster); class TwoPhaseFlowEngine : public TwoPhaseFlowEngineT { public : double totalCellVolume; vector > clusters; // the list of clusters //We can overload every functions of the base engine to make it behave differently //if we overload action() like this, this engine is doing nothing in a standard timestep, it can still have useful functions virtual void action() {}; //If a new function is specific to the derived engine, put it here, else go to the base TemplateFlowEngine if it is useful for everyone //compute pore body radius void computePoreBodyVolume(); void computePoreBodyRadius(); void computeSolidLine(); //compute entry pore throat radius (drainage) void computePoreThroatRadiusMethod1();//MS-P method void computePoreThroatRadiusTrickyMethod1();//set the radius of pore throat between side pores negative. double computeEffPoreThroatRadius(CellHandle cell, int j); double computeEffPoreThroatRadiusFine(CellHandle cell, int j); double bisection(CellHandle cell, int j, double a, double b); double computeTriRadian(double a, double b, double c); double computeDeltaForce(CellHandle cell,int j, double rC); void computePoreThroatRadiusMethod2();//radius of the inscribed circle void computePoreThroatRadiusMethod3();//radius of area-equivalent circle ///begin of invasion (mainly drainage) model void initialization(); void initializeReservoirs(); void invasion();//functions can be shared by two modes void invasionSingleCell(CellHandle cell); void updatePressure(); double getMinDrainagePc(); double getMaxImbibitionPc(); double getSaturation(bool isSideBoundaryIncluded=false); void invasion1();//with-trap void updateReservoirs1(); void WResRecursion(CellHandle cell); void NWResRecursion(CellHandle cell); void checkTrap(double pressure); void updateReservoirLabel(); void updateCellLabel(); void updateSingleCellLabelRecursion(CellHandle cell, PhaseCluster* cluster); void clusterGetFacet(PhaseCluster* cluster, CellHandle cell, int facet);//update cluster inetrfacial area and max entry radius wrt to a facet void clusterGetPore(PhaseCluster* cluster, CellHandle cell);//add pore to cluster, updating flags and cluster volume boost::python::list pyClusters(); // int getMaxCellLabel(); void invasion2();//without-trap void updateReservoirs2(); ///end of invasion model //compute forces void computeFacetPoreForcesWithCache(bool onlyCache=false); void computeCapillaryForce() {computeFacetPoreForcesWithCache(false);} //combine with pendular model boost::python::list getPotentialPendularSpheresPair() { RTriangulation& Tri = solver->T[solver->currentTes].Triangulation(); boost::python::list bridgeIds; FiniteEdgesIterator ed_it = Tri.finite_edges_begin(); for ( ; ed_it!=Tri.finite_edges_end(); ed_it++ ) { if (detectBridge(ed_it)==true) { const VertexInfo& vi1=(ed_it->first)->vertex(ed_it->second)->info(); const VertexInfo& vi2=(ed_it->first)->vertex(ed_it->third)->info(); const int& id1 = vi1.id(); const int& id2 = vi2.id(); bridgeIds.append(boost::python::make_tuple(id1,id2));}} return bridgeIds; } bool detectBridge(RTriangulation::Finite_edges_iterator& edge); //post-processing void savePoreNetwork(); void saveVtk(const char* folder) {bool initT=solver->noCache; solver->noCache=false; solver->saveVtk(folder); solver->noCache=initT;} void savePhaseVtk(const char* folder); boost::python::list cellporeThroatRadius(unsigned int id){ // Temporary function to allow for simulations in Python, can be easily accessed in c++ boost::python::list ids; if (id>=solver->T[solver->currentTes].cellHandles.size()) {LOG_ERROR("id out of range, max value is "<T[solver->currentTes].cellHandles.size()); return ids;} for (unsigned int i=0;i<4;i++) ids.append(solver->T[solver->currentTes].cellHandles[id]->info().poreThroatRadius[i]); return ids; } boost::python::list getNeighbors(unsigned int id){ // Temporary function to allow for simulations in Python, can be easily accessed in c++ boost::python::list ids; if (id>=solver->T[solver->currentTes].cellHandles.size()) {LOG_ERROR("id out of range, max value is "<T[solver->currentTes].cellHandles.size()); return ids;} for (unsigned int i=0;i<4;i++) ids.append(solver->T[solver->currentTes].cellHandles[id]->neighbor(i)->info().id); return ids; } //TODO double computePoreSatAtInterface(int ID); void computePoreCapillaryPressure(CellHandle cell); //FIXME, needs to trigger initSolver() Somewhere, else changing flow.debug or other similar things after first calculation has no effect //FIXME, I removed indexing cells from inside UnsatEngine (SoluteEngine shouldl be ok (?)) in order to get pressure computed, problem is they are not indexed at all if flow is not calculated void computeOnePhaseFlow() {scene = Omega::instance().getScene().get(); if (!solver) cerr<<"no solver!"<gaussSeidel(scene->dt);initSolver(*solver);} CELL_SCALAR_GETTER(bool,.isWRes,cellIsWRes) CELL_SCALAR_GETTER(bool,.isNWRes,cellIsNWRes) CELL_SCALAR_GETTER(bool,.isTrapW,cellIsTrapW) CELL_SCALAR_GETTER(bool,.isTrapNW,cellIsTrapNW) CELL_SCALAR_SETTER(bool,.isNWRes,setCellIsNWRes) CELL_SCALAR_GETTER(Real,.saturation,cellSaturation) CELL_SCALAR_SETTER(Real,.saturation,setCellSaturation) CELL_SCALAR_GETTER(bool,.isFictious,cellIsFictious) //Temporary function to allow for simulations in Python CELL_SCALAR_GETTER(bool,.hasInterface,cellHasInterface) //Temporary function to allow for simulations in Python CELL_SCALAR_GETTER(Real,.poreBodyRadius,cellInSphereRadius) //Temporary function to allow for simulations in Python CELL_SCALAR_GETTER(Real,.poreBodyVolume,cellVoidVolume) //Temporary function to allow for simulations in Python CELL_SCALAR_SETTER(bool,.hasInterface,setCellHasInterface) //Temporary function to allow for simulations in Python CELL_SCALAR_GETTER(int,.label,cellLabel) YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(TwoPhaseFlowEngine,TwoPhaseFlowEngineT,"documentation here", ((double,surfaceTension,0.0728,,"Water Surface Tension in contact with air at 20 Degrees Celsius is: 0.0728(N/m)")) ((bool,recursiveInvasion,true,,"If true the invasion stops only when no entry pc is less than current capillary pressure, implying simultaneous invasion of many pores. Else only one pore invasion per invasion step.")) ((bool,initialWetting,true,,"Initial wetting saturated (=true) or non-wetting saturated (=false)")) ((bool, isPhaseTrapped,true,,"If True, both phases can be entrapped by the other, which would correspond to snap-off. If false, both phases are always connected to their reservoirs, thus no snap-off.")) ((bool, isInvadeBoundary, true,,"Invasion side boundary condition. If True, pores of side boundary can be invaded; if False, the pore throats connecting side boundary are closed, those pores are excluded in saturation calculation.")) ((bool, drainageFirst, true,,"If true, activate drainage first (initial saturated), then imbibition; if false, activate imbibition first (initial unsaturated), then drainage.")) ((double,dtDynTPF,0.0,,"Parameter which stores the smallest time step, based on the residence time")) ((int,entryPressureMethod,1,,"integer to define the method used to determine the pore throat radii and the according entry pressures. 1)radius of entry pore throat based on MS-P method; 2) radius of the inscribed circle; 3) radius of the circle with equivalent surface area of the pore throat.")) ((double,partiallySaturatedPores,false,,"Include partially saturated pores or not?")) ((bool, isCellLabelActivated, false,, "Activate cell labels for marking disconnected wetting clusters. NW-reservoir label 0; W-reservoir label 1; disconnected W-clusters label from 2. ")) ((bool, computeForceActivated, true,,"Activate capillary force computation. WARNING: turning off means capillary force is not computed at all, but the drainage can still work.")) ((bool, isDrainageActivated, true,, "Activates drainage.")) ((bool, isImbibitionActivated, false,, "Activates imbibition.")) ,/*TwoPhaseFlowEngineT()*/, clusters.resize(2); clusters[0]=shared_ptr(new PhaseCluster); clusters[1]=shared_ptr(new PhaseCluster); , .def("getCellIsFictious",&TwoPhaseFlowEngine::cellIsFictious,"Check the connection between pore and boundary. If true, pore throat connects the boundary.") .def("setCellIsNWRes",&TwoPhaseFlowEngine::setCellIsNWRes,"set status whether 'wetting reservoir' state") .def("savePhaseVtk",&TwoPhaseFlowEngine::savePhaseVtk,(boost::python::arg("folder")="./phaseVtk"),"Save the saturation of local pores in vtk format. Sw(NW-pore)=0, Sw(W-pore)=1. Specify a folder name for output.") .def("getCellIsWRes",&TwoPhaseFlowEngine::cellIsWRes,"get status wrt 'wetting reservoir' state") .def("getCellIsNWRes",&TwoPhaseFlowEngine::cellIsNWRes,"get status wrt 'non-wetting reservoir' state") .def("getCellIsTrapW",&TwoPhaseFlowEngine::cellIsTrapW,"get status wrt 'trapped wetting phase' state") .def("getCellIsTrapNW",&TwoPhaseFlowEngine::cellIsTrapNW,"get status wrt 'trapped non-wetting phase' state") .def("getCellSaturation",&TwoPhaseFlowEngine::cellSaturation,"get saturation of one pore") .def("setCellSaturation",&TwoPhaseFlowEngine::setCellSaturation,"change saturation of one pore") .def("computeOnePhaseFlow",&TwoPhaseFlowEngine::computeOnePhaseFlow,"compute pressure and fluxes in the W-phase") .def("initialization",&TwoPhaseFlowEngine::initialization,"Initialize invasion setup. Build network, compute pore geometry info and initialize reservoir boundary conditions. ") .def("computePoreSatAtInterface",&TwoPhaseFlowEngine::computePoreSatAtInterface,(boost::python::arg("ID")),"compute pressure and fluxes in the W-phase") .def("getPoreThroatRadius",&TwoPhaseFlowEngine::cellporeThroatRadius,"get 4 pore throat radii") .def("getNeighbors",&TwoPhaseFlowEngine::getNeighbors,"get 4 neigboring cells") .def("getCellHasInterface",&TwoPhaseFlowEngine::cellHasInterface,"indicates whether a NW-W interface is present within the cell") .def("getCellInSphereRadius",&TwoPhaseFlowEngine::cellInSphereRadius,"get the radius of the inscribed sphere in a pore unit") .def("getCellVoidVolume",&TwoPhaseFlowEngine::cellVoidVolume,"get the volume of pore space in each pore unit") .def("setCellHasInterface",&TwoPhaseFlowEngine::setCellHasInterface,"change wheter a cell has a NW-W interface") .def("savePoreNetwork",&TwoPhaseFlowEngine::savePoreNetwork,"Extract the pore network of the granular material") .def("getCellLabel",&TwoPhaseFlowEngine::cellLabel,"get cell label. 0 for NW-reservoir; 1 for W-reservoir; others for disconnected W-clusters.") .def("getMinDrainagePc",&TwoPhaseFlowEngine::getMinDrainagePc,"Get the minimum entry capillary pressure for the next drainage step.") .def("getMaxImbibitionPc",&TwoPhaseFlowEngine::getMaxImbibitionPc,"Get the maximum entry capillary pressure for the next imbibition step.") .def("getSaturation",&TwoPhaseFlowEngine::getSaturation,(boost::python::arg("isSideBoundaryIncluded")),"Get saturation of entire packing. If isSideBoundaryIncluded=false (default), the pores of side boundary are excluded in saturation calculating; if isSideBoundaryIncluded=true (only in isInvadeBoundary=true drainage mode), the pores of side boundary are included in saturation calculating.") .def("invasion",&TwoPhaseFlowEngine::invasion,"Run the drainage invasion.") .def("computeCapillaryForce",&TwoPhaseFlowEngine::computeCapillaryForce,"Compute capillary force. ") .def("saveVtk",&TwoPhaseFlowEngine::saveVtk,(boost::python::arg("folder")="./VTK"),"Save pressure field in vtk format. Specify a folder name for output.") .def("getPotentialPendularSpheresPair",&TwoPhaseFlowEngine::getPotentialPendularSpheresPair,"Get the list of sphere ID pairs of potential pendular liquid bridge.") .def("getClusters",&TwoPhaseFlowEngine::pyClusters/*,(boost::python::arg("folder")="./VTK")*/,"Get the list of clusters.") ) DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(TwoPhaseFlowEngine); #endif //TwoPhaseFLOW trunk-2017.01a/pkg/pfv/UnsaturatedEngine.cpp000066400000000000000000000447231304022710500207010ustar00rootroot00000000000000/************************************************************************* * Copyright (C) 2012 by Chao Yuan * * Copyright (C) 2012 by Bruno Chareyre * * * * This program is free software; it is licensed under the terms of the * * GNU General Public License v2 or later. See file LICENSE for details. * *************************************************************************/ #ifdef FLOW_ENGINE #include "TwoPhaseFlowEngine.hpp" //keep this #ifdef for commited versions unless you really have stable version that should be compiled by default //it will save compilation time for everyone else //when you want it compiled, you can pass -DTWOPHASEFLOW to cmake, or just uncomment the following line #ifdef TWOPHASEFLOW class UnsaturatedEngine : public TwoPhaseFlowEngine { public : double totalCellVolume; double computeCellInterfacialArea(CellHandle cell, int j, double rC); // void computeSolidLine(); //record and test functions void checkLatticeNodeY(double y); //temporary functions void initializeCellWindowsID(); double getWindowsSaturation(int i, bool isSideBoundaryIncluded=false); bool checknoCache() {return solver->noCache;} double getInvadeDepth(); double getSphericalSubdomainSaturation(Vector3r pos, double radius); double getCuboidSubdomainSaturation(Vector3r pos1, Vector3r pos2, bool isSideBoundaryIncluded); double getCuboidSubdomainPorosity(Vector3r pos1, Vector3r pos2, bool isSideBoundaryIncluded); double getSpecificInterfacialArea(); void printSomething(); virtual ~UnsaturatedEngine(); virtual void action(); YADE_CLASS_BASE_DOC_ATTRS_INIT_CTOR_PY(UnsaturatedEngine,TwoPhaseFlowEngine,"Preliminary version engine of a drainage model for unsaturated soils. Note:Air reservoir is on the top; water reservoir is on the bottom.(deprecated engine, use TwoPhaseFlowEngine instead)", ((int, windowsNo, 10,, "Number of genrated windows(or zoomed samples).")) ,,, .def("getSpecificInterfacialArea",&UnsaturatedEngine::getSpecificInterfacialArea,"get specific interfacial area (defined as the amount of fluid-fluid interfacial area per unit volume pf the porous medium).") .def("checkLatticeNodeY",&UnsaturatedEngine::checkLatticeNodeY,(boost::python::arg("y")),"Check the slice of lattice nodes for yNormal(y). 0: out of sphere; 1: inside of sphere.") .def("getInvadeDepth",&UnsaturatedEngine::getInvadeDepth,"Get NW-phase invasion depth. (the distance from NW-reservoir to front of NW-W interface.)") .def("getSphericalSubdomainSaturation",&UnsaturatedEngine::getSphericalSubdomainSaturation,(boost::python::arg("pos"),boost::python::arg("radius")),"Get saturation of spherical subdomain defined by (pos, radius). The subdomain exclude boundary pores.") .def("getCuboidSubdomainSaturation",&UnsaturatedEngine::getCuboidSubdomainSaturation,(boost::python::arg("pos1"),boost::python::arg("pos2"),boost::python::arg("isSideBoundaryIncluded")),"Get saturation of cuboid subdomain defined by (pos1,pos2). If isSideBoundaryIncluded=false, the pores of side boundary are excluded in saturation calculating; if isSideBoundaryIncluded=true (only in isInvadeBoundary=true drainage mode), the pores of side boundary are included in saturation calculating.") .def("getCuboidSubdomainPorosity",&UnsaturatedEngine::getCuboidSubdomainPorosity,(boost::python::arg("pos1"),boost::python::arg("pos2"),boost::python::arg("isSideBoundaryIncluded")),"Get the porosity of cuboid subdomain defined by (pos1,pos2). If isSideBoundaryIncluded=false, the pores of side boundary are excluded in porosity calculating; if isSideBoundaryIncluded=true (only in isInvadeBoundary=true drainage mode), the pores of side boundary are included in porosity calculating.") .def("checknoCache",&UnsaturatedEngine::checknoCache,"check noCache. (temporary function.)") .def("getWindowsSaturation",&UnsaturatedEngine::getWindowsSaturation,(boost::python::arg("windowsID"),boost::python::arg("isSideBoundaryIncluded")), "get saturation of subdomain with windowsID. If isSideBoundaryIncluded=false (default), the pores of side boundary are excluded in saturation calculating; if isSideBoundaryIncluded=true (only in isInvadeBoundary=true drainage mode), the pores of side boundary are included in saturation calculating.") .def("initializeCellWindowsID",&UnsaturatedEngine::initializeCellWindowsID,"Initialize cell windows index. A temporary function for comparison with experiments, will delete soon") .def("printSomething",&UnsaturatedEngine::printSomething,"print debug.") ) DECLARE_LOGGER; }; REGISTER_SERIALIZABLE(UnsaturatedEngine); YADE_PLUGIN((UnsaturatedEngine)); UnsaturatedEngine::~UnsaturatedEngine(){} /*void UnsaturatedEngine::initialDrainage() { cout<<"This is UnsaturatedEngine test program"<T[solver->currentTes].Triangulation(); if (tri.number_of_vertices()==0) { cout<< "triangulation is empty: building a new one" << endl; scene = Omega::instance().getScene().get();//here define the pointer to Yade's scene setPositionsBuffer(true);//copy sphere positions in a buffer... buildTriangulation(bndCondValue[2],*solver);//create a triangulation and initialize pressure in the elements, everything will be contained in "solver" initialReservoirs(); initializeCellIndex();//initialize cell index computePoreThroatRadius();//save all pore radii before drainage computeTotalPoresVolume();//save total volume of porous medium, considering different invading boundaries condition (isInvadeBoundary==True or False), aiming to calculate specific interfacial area. computePoreBodyVolume();//save capillary volume of all cells, for fast calculating saturation computeSolidLine();//save cell->info().solidLine[j][y] } solver->noCache = true; }*/ void UnsaturatedEngine::action() { /* //the drainage is in quasi-static regime, so it can work outside Omega. if ( !isActivated ) return; RTriangulation& tri = solver->T[solver->currentTes].Triangulation(); if ( (tri.number_of_vertices()==0) || (updateTriangulation) ) { cout<< "triangulation is empty: building a new one" << endl; scene = Omega::instance().getScene().get();//here define the pointer to Yade's scene setPositionsBuffer(true);//copy sphere positions in a buffer... buildTriangulation(bndCondValue[2],*solver);//create a triangulation and initialize pressure in the elements, everything will be contained in "solver" initialReservoirs(); initializeCellIndex();//initialize cell index computePoreThroatRadius();//save all pore radii before drainage computeTotalPoresVolume();//save total volume of porous medium, considering different invading boundaries condition (isInvadeBoundary==True or False), aiming to calculate specific interfacial area. computePoreBodyVolume();//save capillary volume of all cells, for calculating saturation computeSolidLine();//save cell->info().solidLine[j][y] solver->noCache = true; } ///compute drainage if (pressureForce) { drainage();} ///compute force if(computeForceActivated){ computeCapillaryForce(); Vector3r force; FiniteVerticesIterator vertices_end = solver->T[solver->currentTes].Triangulation().finite_vertices_end(); for ( FiniteVerticesIterator V_it = solver->T[solver->currentTes].Triangulation().finite_vertices_begin(); V_it != vertices_end; V_it++ ) { force = pressureForce ? Vector3r ( V_it->info().forces[0],V_it->info().forces[1],V_it->info().forces[2] ): Vector3r(0,0,0); scene->forces.addForce ( V_it->info().id(), force); }} */} double UnsaturatedEngine::getSpecificInterfacialArea() { RTriangulation& tri = solver->T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); double interfacialArea=0; for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { // if (cell->info().Pcondition==true) continue;//NOTE:reservoirs cells interfacialArea should not be included. if(cell->info().isFictious) continue; if (cell->info().isNWRes==true) { for (int facet = 0; facet < 4; facet ++) { if (tri.is_infinite(cell->neighbor(facet))) continue; if (cell->neighbor(facet)->info().Pcondition==true) continue; if ( (cell->neighbor(facet)->info().isFictious) && (!isInvadeBoundary) ) continue; if (cell->neighbor(facet)->info().isNWRes==false) interfacialArea = interfacialArea + computeCellInterfacialArea(cell, facet, cell->info().poreThroatRadius[facet]);}}} // cerr<<"InterArea:"<computeEffectiveRadius(cell, j)); CellHandle cellh = CellHandle(cell); int facetNFictious = solver->detectFacetFictiousVertices (cellh,j); if(facetNFictious==0) { RTriangulation& tri = solver->T[solver->currentTes].Triangulation(); if (tri.is_infinite(cell->neighbor(j))) return 0; Vector3r pos[3]; //solid pos double r[3]; //solid radius double rRc[3]; //r[i] + rC (rC: capillary radius) double e[3]; //edges of triangulation double rad[4][3]; //angle in radian for (int i=0; i<3; i++) { pos[i] = makeVector3r(cell->vertex(facetVertices[j][i])->point().point()); r[i] = sqrt(cell->vertex(facetVertices[j][i])->point().weight()); rRc[i] = r[i]+rC; } e[0] = (pos[1]-pos[2]).norm(); e[1] = (pos[2]-pos[0]).norm(); e[2] = (pos[1]-pos[0]).norm(); rad[3][0]=acos(((pos[1]-pos[0]).dot(pos[2]-pos[0]))/(e[2]*e[1])); rad[3][1]=acos(((pos[2]-pos[1]).dot(pos[0]-pos[1]))/(e[0]*e[2])); rad[3][2]=acos(((pos[0]-pos[2]).dot(pos[1]-pos[2]))/(e[1]*e[0])); rad[0][0]=computeTriRadian(e[0],rRc[1],rRc[2]); rad[0][1]=computeTriRadian(rRc[2],e[0],rRc[1]); rad[0][2]=computeTriRadian(rRc[1],rRc[2],e[0]); rad[1][0]=computeTriRadian(rRc[2],e[1],rRc[0]); rad[1][1]=computeTriRadian(e[1],rRc[0],rRc[2]); rad[1][2]=computeTriRadian(rRc[0],rRc[2],e[1]); rad[2][0]=computeTriRadian(rRc[1],e[2],rRc[0]); rad[2][1]=computeTriRadian(rRc[0],rRc[1],e[2]); rad[2][2]=computeTriRadian(e[2],rRc[0],rRc[1]); double sW0=0.5*rRc[1]*rRc[2]*sin(rad[0][0])-0.5*rad[0][0]*pow(rC,2)-0.5*rad[0][1]*pow(r[1],2)-0.5*rad[0][2]*pow(r[2],2) ; double sW1=0.5*rRc[2]*rRc[0]*sin(rad[1][1])-0.5*rad[1][1]*pow(rC,2)-0.5*rad[1][2]*pow(r[2],2)-0.5*rad[1][0]*pow(r[0],2) ; double sW2=0.5*rRc[0]*rRc[1]*sin(rad[2][2])-0.5*rad[2][2]*pow(rC,2)-0.5*rad[2][0]*pow(r[0],2)-0.5*rad[2][1]*pow(r[1],2) ; double sW=sW0+sW1+sW2; double sVoid=sqrt(cell->info().facetSurfaces[j].squared_length()) * cell->info().facetFluidSurfacesRatio[j]; double sInterface=sVoid-sW; return sInterface; } else { return Mathr::PI*pow(rInscribe,2); } } // ------------------for checking---------- void UnsaturatedEngine::checkLatticeNodeY(double y) { RTriangulation& tri = solver->T[solver->currentTes].Triangulation(); if((yyMin)||(y>solver->yMax)) { cerr<<"y is out of range! "<<"pleas set y between "<yMin<<" and "<yMax<xMax-solver->xMin)/N; double deltaZ = (solver->zMax-solver->zMin)/N; for (int j=0; jxMin+j*deltaX; double z=solver->zMin+k*deltaZ; int M=0; Vector3r LatticeNode = Vector3r(x,y,z); for (FiniteVerticesIterator V_it = tri.finite_vertices_begin(); V_it != tri.finite_vertices_end(); V_it++) { if(V_it->info().isFictious) continue; Vector3r SphereCenter = makeVector3r(V_it->point().point()); if ((LatticeNode-SphereCenter).squaredNorm() < V_it->point().weight()) { M=1; break;}} file << M;} file << "\n";} file.close();} } void UnsaturatedEngine::printSomething() { RTriangulation& Tri = solver->T[solver->currentTes].Triangulation(); FiniteEdgesIterator ed_it; for ( FiniteEdgesIterator ed_it = Tri.finite_edges_begin(); ed_it!=Tri.finite_edges_end();ed_it++ ) { const VertexInfo& vi1=(ed_it->first)->vertex(ed_it->second)->info(); const VertexInfo& vi2=(ed_it->first)->vertex(ed_it->third)->info(); const int& id1 = vi1.id(); const int& id2 = vi2.id(); cerr<T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { for (int i=1; i<(windowsNo+1); i++) { if ( (cell->info()[1]>(solver->yMin+(i-1)*(solver->yMax-solver->yMin)/windowsNo) ) && (cell->info()[1] < (solver->yMin+i*(solver->yMax-solver->yMin)/windowsNo)) ) {cell->info().windowsID=i; break;} } } } double UnsaturatedEngine::getWindowsSaturation(int i, bool isSideBoundaryIncluded) { if( (!isInvadeBoundary) && (isSideBoundaryIncluded)) cerr<<"In isInvadeBoundary=false drainage, isSideBoundaryIncluded can't set true."<T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if (cell->info().Pcondition) continue; if ( (cell->info().isFictious) && (!isSideBoundaryIncluded) ) continue; if (cell->info().windowsID != i) continue; poresVolume = poresVolume + cell->info().poreBodyVolume; if (cell->info().saturation>0.0) { wVolume = wVolume + cell->info().poreBodyVolume * cell->info().saturation; } } return wVolume/poresVolume; } double UnsaturatedEngine::getCuboidSubdomainSaturation(Vector3r pos1, Vector3r pos2, bool isSideBoundaryIncluded) { if( (!isInvadeBoundary) && (isSideBoundaryIncluded)) cerr<<"In isInvadeBoundary=false drainage, isSideBoundaryIncluded can't set true."<T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if (cell->info().Pcondition) continue; if ( (cell->info().isFictious) && (!isSideBoundaryIncluded) ) continue; if ( ((pos1[0]-cell->info()[0])*(pos2[0]-cell->info()[0])<0) && ((pos1[1]-cell->info()[1])*(pos2[1]-cell->info()[1])<0) && ((pos1[2]-cell->info()[2])*(pos2[2]-cell->info()[2])<0) ) { poresVolume = poresVolume + cell->info().poreBodyVolume; if (cell->info().saturation>0.0) { wVolume = wVolume + cell->info().poreBodyVolume * cell->info().saturation; } } } return wVolume/poresVolume; } double UnsaturatedEngine::getCuboidSubdomainPorosity(Vector3r pos1, Vector3r pos2, bool isSideBoundaryIncluded) { if( (!isInvadeBoundary) && (isSideBoundaryIncluded)) cerr<<"In isInvadeBoundary=false drainage, isSideBoundaryIncluded can't set true."<T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if (cell->info().Pcondition) continue; if ( (cell->info().isFictious) && (!isSideBoundaryIncluded) ) continue; if ( ((pos1[0]-cell->info()[0])*(pos2[0]-cell->info()[0])<0) && ((pos1[1]-cell->info()[1])*(pos2[1]-cell->info()[1])<0) && ((pos1[2]-cell->info()[2])*(pos2[2]-cell->info()[2])<0) ) { totalCellVolume = totalCellVolume + std::abs( cell->info().volume() ); totalVoidVolume = totalVoidVolume + cell->info().poreBodyVolume; } } if(totalVoidVolume==0 || totalCellVolume==0) cerr<<"subdomain too small!"<T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = tri.finite_cells_end(); for ( FiniteCellsIterator cell = tri.finite_cells_begin(); cell != cellEnd; cell++ ) { if (cell->info().isNWRes) { yPosMax=std::max(yPosMax,cell->info()[1]); yPosMin=std::min(yPosMin,cell->info()[1]); } } return std::abs(yPosMax-yPosMin); } double UnsaturatedEngine::getSphericalSubdomainSaturation(Vector3r pos, double radius) { double poresVolume=0.0; double wVolume=0.0; RTriangulation& Tri = solver->T[solver->currentTes].Triangulation(); FiniteCellsIterator cellEnd = Tri.finite_cells_end(); for (FiniteCellsIterator cell = Tri.finite_cells_begin(); cell != cellEnd; cell++) { Vector3r cellPos = makeVector3r(cell->info()); double dist=(pos-cellPos).norm(); if(dist>radius) continue; if(cell->info().isFictious) { cerr<<"The radius of subdomain is too large, or the center of subdomain is out of packing. Please reset subdomain again."<info().poreBodyVolume; if(cell->info().saturation>0.0) { wVolume=wVolume+cell->info().poreBodyVolume * cell->info().saturation; } } return wVolume/poresVolume; } //--------------end of comparison with experiment---------------------------- #endif //TWOPHASEFLOW #endif //FLOW_ENGINE trunk-2017.01a/py/000077500000000000000000000000001304022710500136125ustar00rootroot00000000000000trunk-2017.01a/py/3rd-party/000077500000000000000000000000001304022710500154375ustar00rootroot00000000000000trunk-2017.01a/py/3rd-party/README000066400000000000000000000025261304022710500163240ustar00rootroot00000000000000pygts-0.3.1: homepage: http://pygts.sourceforge.net/ documentation: http://pygts.svn.sourceforge.net/viewvc/pygts/doc/gts.html license: GNU GPL v2 note: the local version is only the 'gts' directory of the source archive (doc, examples, test ommited). Distutils are not used for building either. patch: pygts.py has the following lines added at the beginning: # added by eudoxos 29.1.2011, fixes https://bugs.launchpad.net/yade/+bug/668329 ## force decimal separator to be always . (decimal point), not , (decimal comma) -- unless LC_ALL is set, then we are stuck ## this was reason for bogus gts imports ## adding to yade main does not solve the problem for some reason import locale locale.setlocale(locale.LC_NUMERIC,'C') boost-python-indexing-suite-v2-noSymlinkHeaders: homepage: http://www.language-binding.net/pyplusplus/pyplusplus.html (part of Py++-1.0.0) documentation: http://www.language-binding.net/pyplusplus/documentation/indexing_suite_v2.html.html source: https://pygccxml.svn.sourceforge.net/svnroot/pygccxml/pyplusplus_dev/indexing_suite_v2 revision 1755 license: Boost software license 1.0 note: only headers are copied here mtTkinter-0.4: homepage: http://tkinter.unpythonic.net/wiki/mtTkinter source: http://tkinter.unpythonic.net/wiki/mtTkinter?action=AttachFile&do=get&target=mtTkinter-0.4.tar.gz license: gpl lgpl trunk-2017.01a/py/3rd-party/mtTkinter-0.4/000077500000000000000000000000001304022710500177175ustar00rootroot00000000000000trunk-2017.01a/py/3rd-party/mtTkinter-0.4/gpl.txt000066400000000000000000001045131304022710500212460ustar00rootroot00000000000000 GNU GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. 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But first, please read . trunk-2017.01a/py/3rd-party/mtTkinter-0.4/lgpl.txt000066400000000000000000000167431304022710500214310ustar00rootroot00000000000000 GNU LESSER GENERAL PUBLIC LICENSE Version 3, 29 June 2007 Copyright (C) 2007 Free Software Foundation, Inc. Everyone is permitted to copy and distribute verbatim copies of this license document, but changing it is not allowed. This version of the GNU Lesser General Public License incorporates the terms and conditions of version 3 of the GNU General Public License, supplemented by the additional permissions listed below. 0. Additional Definitions. As used herein, "this License" refers to version 3 of the GNU Lesser General Public License, and the "GNU GPL" refers to version 3 of the GNU General Public License. "The Library" refers to a covered work governed by this License, other than an Application or a Combined Work as defined below. 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Each version is given a distinguishing version number. If the Library as you received it specifies that a certain numbered version of the GNU Lesser General Public License "or any later version" applies to it, you have the option of following the terms and conditions either of that published version or of any later version published by the Free Software Foundation. If the Library as you received it does not specify a version number of the GNU Lesser General Public License, you may choose any version of the GNU Lesser General Public License ever published by the Free Software Foundation. If the Library as you received it specifies that a proxy can decide whether future versions of the GNU Lesser General Public License shall apply, that proxy's public statement of acceptance of any version is permanent authorization for you to choose that version for the Library. trunk-2017.01a/py/3rd-party/mtTkinter-0.4/mtTkinter.py000066400000000000000000000207531304022710500222610ustar00rootroot00000000000000'''Thread-safe version of Tkinter. Copyright (c) 2009, Allen B. Taylor This module is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU Lesser Public License for more details. You should have received a copy of the GNU Lesser Public License along with this program. If not, see . Usage: import mtTkinter as Tkinter # Use "Tkinter." as usual. or from mtTkinter import * # Use Tkinter module definitions as usual. This module modifies the original Tkinter module in memory, making all functionality thread-safe. It does this by wrapping the Tk class' tk instance with an object that diverts calls through an event queue when the call is issued from a thread other than the thread in which the Tk instance was created. The events are processed in the creation thread via an 'after' event. The modified Tk class accepts two additional keyword parameters on its __init__ method: mtDebug: 0 = No debug output (default) 1 = Minimal debug output ... 9 = Full debug output mtCheckPeriod: Amount of time in milliseconds (default 100) between checks for out-of-thread events when things are otherwise idle. Decreasing this value can improve GUI responsiveness, but at the expense of consuming more CPU cycles. Note that, because it modifies the original Tkinter module (in memory), other modules that use Tkinter (e.g., Pmw) reap the benefits automagically as long as mtTkinter is imported at some point before extra threads are created. Author: Allen B. Taylor, a.b.taylor@gmail.com ''' from Tkinter import * import threading import Queue class _Tk(object): """ Wrapper for underlying attribute tk of class Tk. """ def __init__(self, tk, mtDebug = 0, mtCheckPeriod = 10): self._tk = tk # Create the incoming event queue. self._eventQueue = Queue.Queue(1) # Identify the thread from which this object is being created so we can # tell later whether an event is coming from another thread. self._creationThread = threading.currentThread() # Store remaining values. self._debug = mtDebug self._checkPeriod = mtCheckPeriod def __getattr__(self, name): # Divert attribute accesses to a wrapper around the underlying tk # object. return _TkAttr(self, getattr(self._tk, name)) class _TkAttr(object): """ Thread-safe callable attribute wrapper. """ def __init__(self, tk, attr): self._tk = tk self._attr = attr def __call__(self, *args, **kwargs): """ Thread-safe method invocation. Diverts out-of-thread calls through the event queue. Forwards all other method calls to the underlying tk object directly. """ # Check if we're in the creation thread. if threading.currentThread() == self._tk._creationThread: # We're in the creation thread; just call the event directly. if self._tk._debug >= 8 or \ self._tk._debug >= 3 and self._attr.__name__ == 'call' and \ len(args) >= 1 and args[0] == 'after': print 'Calling event directly:', \ self._attr.__name__, args, kwargs return self._attr(*args, **kwargs) else: # We're in a different thread than the creation thread; enqueue # the event, and then wait for the response. responseQueue = Queue.Queue(1) if self._tk._debug >= 1: print 'Marshalling event:', self._attr.__name__, args, kwargs self._tk._eventQueue.put((self._attr, args, kwargs, responseQueue)) isException, response = responseQueue.get() # Handle the response, whether it's a normal return value or # an exception. if isException: exType, exValue, exTb = response raise exType, exValue, exTb else: return response # Define a hook for class Tk's __init__ method. def _Tk__init__(self, *args, **kwargs): # We support some new keyword arguments that the original __init__ method # doesn't expect, so separate those out before doing anything else. new_kwnames = ('mtCheckPeriod', 'mtDebug') new_kwargs = {} for name, value in kwargs.items(): if name in new_kwnames: new_kwargs[name] = value del kwargs[name] # Call the original __init__ method, creating the internal tk member. self.__original__init__mtTkinter(*args, **kwargs) # Replace the internal tk member with a wrapper that handles calls from # other threads. self.tk = _Tk(self.tk, **new_kwargs) # Set up the first event to check for out-of-thread events. self.after_idle(_CheckEvents, self) # Replace Tk's original __init__ with the hook. Tk.__original__init__mtTkinter = Tk.__init__ Tk.__init__ = _Tk__init__ def _CheckEvents(tk): "Event checker event." used = False try: # Process all enqueued events, then exit. while True: try: # Get an event request from the queue. method, args, kwargs, responseQueue = \ tk.tk._eventQueue.get_nowait() except: # No more events to process. break else: # Call the event with the given arguments, and then return # the result back to the caller via the response queue. used = True if tk.tk._debug >= 2: print 'Calling event from main thread:', \ method.__name__, args, kwargs try: responseQueue.put((False, method(*args, **kwargs))) except SystemExit, ex: raise SystemExit, ex except Exception, ex: # Calling the event caused an exception; return the # exception back to the caller so that it can be raised # in the caller's thread. from sys import exc_info exType, exValue, exTb = exc_info() responseQueue.put((True, (exType, exValue, exTb))) finally: # Schedule to check again. If we just processed an event, check # immediately; if we didn't, check later. if used: tk.after_idle(_CheckEvents, tk) else: tk.after(tk.tk._checkPeriod, _CheckEvents, tk) # Test thread entry point. def _testThread(root): text = "This is Tcl/Tk version %s" % TclVersion if TclVersion >= 8.1: try: text = text + unicode("\nThis should be a cedilla: \347", "iso-8859-1") except NameError: pass # no unicode support try: if root.globalgetvar('tcl_platform(threaded)'): text = text + "\nTcl is built with thread support" else: raise RuntimeError except: text = text + "\nTcl is NOT built with thread support" text = text + "\nmtTkinter works with or without Tcl thread support" label = Label(root, text=text) label.pack() button = Button(root, text="Click me!", command=lambda root=root: root.button.configure( text="[%s]" % root.button['text'])) button.pack() root.button = button quit = Button(root, text="QUIT", command=root.destroy) quit.pack() # The following three commands are needed so the window pops # up on top on Windows... root.iconify() root.update() root.deiconify() # Simulate button presses... button.invoke() root.after(1000, _pressOk, root, button) # Test button continuous press event. def _pressOk(root, button): button.invoke() try: root.after(1000, _pressOk, root, button) except: pass # Likely we're exiting # Test. Mostly borrowed from the Tkinter module, but the important bits moved # into a separate thread. if __name__ == '__main__': import threading root = Tk(mtDebug = 1) thread = threading.Thread(target = _testThread, args=(root,)) thread.start() root.mainloop() thread.join() trunk-2017.01a/py/3rd-party/pygts-0.3.1/000077500000000000000000000000001304022710500172425ustar00rootroot00000000000000trunk-2017.01a/py/3rd-party/pygts-0.3.1/__init__.py000066400000000000000000000067271304022710500213670ustar00rootroot00000000000000# pygts - python package for the manipulation of triangulated surfaces # # Copyright (C) 2009 Thomas J. Duck # All rights reserved. # # Thomas J. Duck # Department of Physics and Atmospheric Science, # Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 # # NOTICE # # This library is free software; you can redistribute it and/or # modify it under the terms of the GNU Library General Public # License as published by the Free Software Foundation; either # version 2 of the License, or (at your option) any later version. # # This library is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # Library General Public License for more details. # # You should have received a copy of the GNU Library General Public # License along with this library; if not, write to the # Free Software Foundation, Inc., 59 Temple Place - Suite 330, # Boston, MA 02111-1307, USA. """A package for constructing and manipulating triangulated surfaces. PyGTS is a python binding for the GNU Triangulated Surface (GTS) Library, which may be used to build, manipulate, and perform computations on triangulated surfaces. The following geometric primitives are provided: * Point - a point in 3D space * Vertex - a Point in 3D space that may be used to define a Segment * Segment - a line defined by two Vertex end-points * Edge - a Segment that may be used to define the edge of a Triangle * Triangle - a triangle defined by three Edges * Face - a Triangle that may be used to define a face on a Surface * Surface - a surface composed of Faces A tetrahedron is assembled from these primitives as follows. First, create Vertices for each of the tetrahedron's points: .. code-block:: python import gts v1 = gts.Vertex(1,1,1) v2 = gts.Vertex(-1,-1,1) v3 = gts.Vertex(-1,1,-1) v4 = gts.Vertex(1,-1,-1) Next, connect the four vertices to create six unique Edges: .. code-block:: python e1 = gts.Edge(v1,v2) e2 = gts.Edge(v2,v3) e3 = gts.Edge(v3,v1) e4 = gts.Edge(v1,v4) e5 = gts.Edge(v4,v2) e6 = gts.Edge(v4,v3) The four triangular faces are composed using three edges each: .. code-block:: python f1 = gts.Face(e1,e2,e3) f2 = gts.Face(e1,e4,e5) f3 = gts.Face(e2,e5,e6) f4 = gts.Face(e3,e4,e6) Finally, the surface is assembled from the faces: .. code-block:: python s = gts.Surface() for face in [f1,f2,f3,f4]: s.add(face) Some care must be taken in the orientation of the faces. In the above example, the surface normals are pointing inward, and so the surface technically defines a void, rather than a solid. To create a tetrahedron with surface normals pointing outward, use the following instead: .. code-block:: python f1.revert() s = Surface() for face in [f1,f2,f3,f4]: if not face.is_compatible(s): face.revert() s.add(face) Once the Surface is constructed, there are many different operations that can be performed. For example, the volume can be calculated using: .. code-block:: python s.volume() The difference between two Surfaces s1 and s2 is given by: .. code-block:: python s3 = s2.difference(s1) Etc. It is also possible to read in GTS data files and plot surfaces to the screen. See the example programs packaged with PyGTS for more information. """ from pygts import * trunk-2017.01a/py/3rd-party/pygts-0.3.1/cleanup.c000066400000000000000000000346611304022710500210470ustar00rootroot00000000000000/* pygts - python package for the manipulation of triangulated surfaces * * Copyright (C) 1999 Stphane Popinet * Copyright (C) 2009 Thomas J. Duck * All rights reserved. * * Thomas J. Duck * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ /* * Below are functions for cleaning up duplicated edges and faces on * a surface. This file contains modified functions from the GTS * distribution. */ #include "pygts.h" /** * Original documentation from GTS's vertex.c: * * gts_vertices_merge: * @vertices: a list of #GtsVertex. * @epsilon: half the size of the bounding box to consider for each vertex. * @check: function called for each pair of vertices about to be merged * or %NULL. * * For each vertex v in @vertices look if there are any vertex of * @vertices contained in a box centered on v of size 2*@epsilon. If * there are and if @check is not %NULL and returns %TRUE, replace * them with v (using gts_vertex_replace()), destroy them and remove * them from list. This is done efficiently using Kd-Trees. * * Returns: the updated list of vertices. */ /* This function is modified from the original in GTS in order to avoid * deallocating any objects referenced by the live-objects table. The * approach is similar to what is used for replace() in vertex.c. */ GList* pygts_vertices_merge(GList* vertices, gdouble epsilon, gboolean (* check) (GtsVertex *, GtsVertex *)) { GPtrArray *array; GList *i, *next; GNode *kdtree; GtsVertex *v; GtsBBox *bbox; GSList *selected, *j; GtsVertex *sv; PygtsObject *obj; PygtsVertex *vertex=NULL; GSList *parents=NULL, *ii,*cur; g_return_val_if_fail(vertices != NULL, 0); array = g_ptr_array_new(); i = vertices; while (i) { g_ptr_array_add(array, i->data); i = g_list_next(i); } kdtree = gts_kdtree_new(array, NULL); g_ptr_array_free(array, TRUE); i = vertices; while(i) { v = i->data; if (!GTS_OBJECT(v)->reserved) { /* Do something only if v is active */ /* build bounding box */ bbox = gts_bbox_new(gts_bbox_class(), v, GTS_POINT(v)->x - epsilon, GTS_POINT(v)->y - epsilon, GTS_POINT(v)->z - epsilon, GTS_POINT(v)->x + epsilon, GTS_POINT(v)->y + epsilon, GTS_POINT(v)->z + epsilon); /* select vertices which are inside bbox using kdtree */ j = selected = gts_kdtree_range(kdtree, bbox, NULL); while(j) { sv = j->data; if( sv!=v && !GTS_OBJECT(sv)->reserved && (!check||(*check)(sv, v)) ) { /* sv is not v and is active */ if( (obj = g_hash_table_lookup(obj_table,GTS_OBJECT(sv))) !=NULL ) { vertex = PYGTS_VERTEX(obj); /* Detach and save any parent segments */ ii = sv->segments; while(ii!=NULL) { cur = ii; ii = g_slist_next(ii); if(PYGTS_IS_PARENT_SEGMENT(cur->data)) { sv->segments = g_slist_remove_link(sv->segments, cur); parents = g_slist_prepend(parents,cur->data); g_slist_free_1(cur); } } } gts_vertex_replace(sv, v); GTS_OBJECT(sv)->reserved = sv; /* mark sv as inactive */ /* Reattach the parent segments */ if( vertex != NULL ) { ii = parents; while(ii!=NULL) { sv->segments = g_slist_prepend(sv->segments, ii->data); ii = g_slist_next(ii); } g_slist_free(parents); parents = NULL; } vertex = NULL; } j = g_slist_next(j); } g_slist_free(selected); gts_object_destroy(GTS_OBJECT(bbox)); } i = g_list_next(i); } gts_kdtree_destroy(kdtree); /* destroy inactive vertices and removes them from list */ /* we want to control vertex destruction */ gts_allow_floating_vertices = TRUE; i = vertices; while (i) { v = i->data; next = g_list_next(i); if(GTS_OBJECT(v)->reserved) { /* v is inactive */ if( g_hash_table_lookup(obj_table,GTS_OBJECT(v))==NULL ) { gts_object_destroy(GTS_OBJECT(v)); } else { GTS_OBJECT(v)->reserved = 0; } vertices = g_list_remove_link(vertices, i); g_list_free_1(i); } i = next; } gts_allow_floating_vertices = FALSE; return vertices; } static void build_list(gpointer data, GSList ** list) { *list = g_slist_prepend(*list, data); } static void build_list1(gpointer data, GList ** list) { *list = g_list_prepend(*list, data); } void pygts_vertex_cleanup(GtsSurface *s, gdouble threshold) { GList * vertices = NULL; /* merge vertices which are close enough */ /* build list of vertices */ gts_surface_foreach_vertex(s, (GtsFunc) build_list1, &vertices); /* merge vertices: we MUST update the variable vertices because this function modifies the list (i.e. removes the merged vertices). */ vertices = pygts_vertices_merge(vertices, threshold, NULL); /* free the list */ g_list_free(vertices); } void pygts_edge_cleanup(GtsSurface *s) { GSList *edges = NULL; GSList *i, *ii, *cur, *parents=NULL; PygtsEdge *edge; GtsEdge *e, *duplicate; g_return_if_fail(s != NULL); /* build list of edges */ gts_surface_foreach_edge(s, (GtsFunc)build_list, &edges); /* remove degenerate and duplicate edges. Note: we could use gts_edges_merge() to remove the duplicates and then remove the degenerate edges but it is more efficient to do everything at once (and it's more pedagogical too ...) */ /* We want to control manually the destruction of edges */ gts_allow_floating_edges = TRUE; i = edges; while(i) { e = i->data; if(GTS_SEGMENT(e)->v1 == GTS_SEGMENT(e)->v2) { /* edge is degenerate */ if( !g_hash_table_lookup(obj_table,GTS_OBJECT(e)) ) { /* destroy e */ gts_object_destroy(GTS_OBJECT(e)); } } else { if((duplicate = gts_edge_is_duplicate(e))) { /* Detach and save any parent triangles */ if( (edge = PYGTS_EDGE(g_hash_table_lookup(obj_table,GTS_OBJECT(e)))) !=NULL ) { ii = e->triangles; while(ii!=NULL) { cur = ii; ii = g_slist_next(ii); if(PYGTS_IS_PARENT_TRIANGLE(cur->data)) { e->triangles = g_slist_remove_link(e->triangles, cur); parents = g_slist_prepend(parents,cur->data); g_slist_free_1(cur); } } } /* replace e with its duplicate */ gts_edge_replace(e, duplicate); /* Reattach the parent segments */ if( edge != NULL ) { ii = parents; while(ii!=NULL) { e->triangles = g_slist_prepend(e->triangles, ii->data); ii = g_slist_next(ii); } g_slist_free(parents); parents = NULL; } if( !g_hash_table_lookup(obj_table,GTS_OBJECT(e)) ) { /* destroy e */ gts_object_destroy(GTS_OBJECT (e)); } } } i = g_slist_next(i); } /* don't forget to reset to default */ gts_allow_floating_edges = FALSE; /* free list of edges */ g_slist_free (edges); } void pygts_face_cleanup(GtsSurface * s) { GSList *triangles = NULL; GSList * i; g_return_if_fail(s != NULL); /* build list of triangles */ gts_surface_foreach_face(s, (GtsFunc) build_list, &triangles); /* remove duplicate and degenerate triangles */ i = triangles; while(i) { GtsTriangle * t = i->data; if (!gts_triangle_is_ok(t)) { /* destroy t, its edges (if not used by any other triangle) and its corners (if not used by any other edge) */ if( g_hash_table_lookup(obj_table,GTS_OBJECT(t))==NULL ) { gts_object_destroy(GTS_OBJECT(t)); } else { gts_surface_remove_face(PYGTS_SURFACE_AS_GTS_SURFACE(s),GTS_FACE(t)); } } i = g_slist_next(i); } /* free list of triangles */ g_slist_free(triangles); } /* old main program (below) - retained as an example of how to use the * functions above. */ /* cleanup - using a given threshold merge vertices which are too close. Eliminate degenerate and duplicate edges. Eliminate duplicate triangles . */ /* static int */ /* main (int argc, char * argv[]) */ /* { */ /* GtsSurface * s, * m; */ /* GList * vertices = NULL; */ /* gboolean verbose = FALSE, sever = FALSE, boundary = FALSE; */ /* gdouble threshold; */ /* int c = 0; */ /* GtsFile * fp; */ /* gboolean (* check) (GtsVertex *, GtsVertex *) = NULL; */ /* if (!setlocale (LC_ALL, "POSIX")) */ /* g_warning ("cannot set locale to POSIX"); */ /* s = gts_surface_new (gts_surface_class (), */ /* gts_face_class (), */ /* gts_edge_class (), */ /* gts_vertex_class ()); */ /* /\* parse options using getopt *\/ */ /* while (c != EOF) { */ /* #ifdef HAVE_GETOPT_LONG */ /* static struct option long_options[] = { */ /* {"2D", no_argument, NULL, 'c'}, */ /* {"boundary", no_argument, NULL, 'b'}, */ /* {"merge", required_argument, NULL, 'm'}, */ /* {"sever", no_argument, NULL, 's'}, */ /* {"help", no_argument, NULL, 'h'}, */ /* {"verbose", no_argument, NULL, 'v'}, */ /* { NULL } */ /* }; */ /* int option_index = 0; */ /* switch ((c = getopt_long (argc, argv, "hvsm:bc", */ /* long_options, &option_index))) { */ /* #else /\* not HAVE_GETOPT_LONG *\/ */ /* switch ((c = getopt (argc, argv, "hvsm:bc"))) { */ /* #endif /\* not HAVE_GETOPT_LONG *\/ */ /* case 'c': /\* 2D *\/ */ /* check = check_boundaries; */ /* break; */ /* case 'b': /\* boundary *\/ */ /* boundary = TRUE; */ /* break; */ /* case 's': /\* sever *\/ */ /* sever = TRUE; */ /* break; */ /* case 'm': { /\* merge *\/ */ /* FILE * fptr = fopen (optarg, "rt"); */ /* GtsFile * fp; */ /* if (fptr == NULL) { */ /* fprintf (stderr, "cleanup: cannot open file `%s' for merging\n", */ /* optarg); */ /* return 1; /\* failure *\/ */ /* } */ /* m = gts_surface_new (gts_surface_class (), */ /* gts_face_class (), */ /* gts_edge_class (), */ /* s->vertex_class); */ /* fp = gts_file_new (fptr); */ /* if (gts_surface_read (m, fp)) { */ /* fprintf (stderr, "cleanup: file `%s' is not a valid GTS file\n", */ /* optarg); */ /* fprintf (stderr, "%s:%d:%d: %s\n", */ /* optarg, fp->line, fp->pos, fp->error); */ /* return 1; /\* failure *\/ */ /* } */ /* gts_file_destroy (fp); */ /* fclose (fptr); */ /* gts_surface_merge (s, m); */ /* gts_object_destroy (GTS_OBJECT (m)); */ /* break; */ /* } */ /* case 'v': /\* verbose *\/ */ /* verbose = TRUE; */ /* break; */ /* case 'h': /\* help *\/ */ /* fprintf (stderr, */ /* "Usage: cleanup [OPTION] THRESHOLD < FILE\n" */ /* "Merge vertices of the GTS surface FILE if they are closer than THRESHOLD,\n" */ /* "eliminate degenerate, duplicate edges and duplicate triangles.\n" */ /* "\n" */ /* " -c --2D 2D boundary merging\n" */ /* " -b --boundary only consider boundary vertices for merging\n" */ /* " -s --sever sever \"contact\" vertices\n" */ /* " -m FILE --merge merge surface FILE\n" */ /* " -v --verbose print statistics about the surface\n" */ /* " -h --help display this help and exit\n" */ /* "\n" */ /* "Report bugs to %s\n", */ /* GTS_MAINTAINER); */ /* return 0; /\* success *\/ */ /* break; */ /* case '?': /\* wrong options *\/ */ /* fprintf (stderr, "Try `cleanup --help' for more information.\n"); */ /* return 1; /\* failure *\/ */ /* } */ /* } */ /* if (optind >= argc) { /\* missing threshold *\/ */ /* fprintf (stderr, */ /* "cleanup: missing THRESHOLD\n" */ /* "Try `cleanup --help' for more information.\n"); */ /* return 1; /\* failure *\/ */ /* } */ /* threshold = atof (argv[optind]); */ /* if (threshold < 0.0) { /\* threshold must be positive *\/ */ /* fprintf (stderr, */ /* "cleanup: THRESHOLD must be >= 0.0\n" */ /* "Try `cleanup --help' for more information.\n"); */ /* return 1; /\* failure *\/ */ /* } */ /* /\* read surface in *\/ */ /* m = gts_surface_new (gts_surface_class (), */ /* gts_face_class (), */ /* gts_edge_class (), */ /* s->vertex_class); */ /* fp = gts_file_new (stdin); */ /* if (gts_surface_read (m, fp)) { */ /* fputs ("cleanup: file on standard input is not a valid GTS file\n", */ /* stderr); */ /* fprintf (stderr, "stdin:%d:%d: %s\n", fp->line, fp->pos, fp->error); */ /* return 1; /\* failure *\/ */ /* } */ /* gts_surface_merge (s, m); */ /* gts_object_destroy (GTS_OBJECT (m)); */ /* /\* if verbose on print stats *\/ */ /* if (verbose) */ /* gts_surface_print_stats (s, stderr); */ /* /\* merge vertices which are close enough *\/ */ /* /\* build list of vertices *\/ */ /* gts_surface_foreach_vertex (s, boundary ? (GtsFunc) build_list2 : (GtsFunc) build_list1, */ /* &vertices); */ /* /\* merge vertices: we MUST update the variable vertices because this function */ /* modifies the list (i.e. removes the merged vertices). *\/ */ /* vertices = gts_vertices_merge (vertices, threshold, check); */ /* /\* free the list *\/ */ /* g_list_free (vertices); */ /* /\* eliminate degenerate and duplicate edges *\/ */ /* edge_cleanup (s); */ /* /\* eliminate duplicate triangles *\/ */ /* triangle_cleanup (s); */ /* if (sever) */ /* gts_surface_foreach_vertex (s, (GtsFunc) vertex_cleanup, NULL); */ /* /\* if verbose on print stats *\/ */ /* if (verbose) { */ /* GtsBBox * bb = gts_bbox_surface (gts_bbox_class (), s); */ /* gts_surface_print_stats (s, stderr); */ /* fprintf (stderr, "# Bounding box: [%g,%g,%g] [%g,%g,%g]\n", */ /* bb->x1, bb->y1, bb->z1, */ /* bb->x2, bb->y2, bb->z2); */ /* } */ /* /\* write surface *\/ */ /* gts_surface_write (s, stdout); */ /* return 0; /\* success *\/ */ /* } */ trunk-2017.01a/py/3rd-party/pygts-0.3.1/cleanup.h000066400000000000000000000031231304022710500210410ustar00rootroot00000000000000/* pygts - python package for the manipulation of triangulated surfaces * * Copyright (C) 2009 Thomas J. Duck * All rights reserved. * * Thomas J. Duck * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ /* * Below are functions for cleaning up duplicated edges and faces on * a surface. This file was adapted from the example file of the same * name in the GTS distribution. */ #ifndef __PYGTS_CLEANUP_H__ #define __PYGTS_CLEANUP_H__ GList* pygts_vertices_merge(GList* vertices, gdouble epsilon, gboolean (* check) (GtsVertex *, GtsVertex *)); void pygts_vertex_cleanup(GtsSurface *s, gdouble threhold); void pygts_edge_cleanup(GtsSurface * s); void pygts_face_cleanup(GtsSurface * s); #endif /* __PYGTS_CLEANUP_H__ */ trunk-2017.01a/py/3rd-party/pygts-0.3.1/edge.c000066400000000000000000000377111304022710500203230ustar00rootroot00000000000000/* pygts - python package for the manipulation of triangulated surfaces * * Copyright (C) 2009 Thomas J. Duck * All rights reserved. * * Thomas J. Duck * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ #include "pygts.h" #if PYGTS_DEBUG #define SELF_CHECK if(!pygts_edge_check((PyObject*)self)) { \ PyErr_SetString(PyExc_RuntimeError, \ "problem with self object (internal error)"); \ return NULL; \ } #else #define SELF_CHECK #endif /*-------------------------------------------------------------------------*/ /* Methods exported to python */ static PyObject* is_ok(PygtsEdge *self, PyObject *args) { if(pygts_edge_is_ok(self)) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* is_unattached(PygtsEdge *self, PyObject *args) { guint n; SELF_CHECK /* Check for attachments other than to the gtsobj_parent */ n = g_slist_length(PYGTS_EDGE_AS_GTS_EDGE(self)->triangles); if( n > 1 ) { Py_INCREF(Py_False); return Py_False; } else if( n == 1 ){ Py_INCREF(Py_True); return Py_True; } else { PyErr_SetString(PyExc_RuntimeError,"Edge lost parent (internal error)"); return NULL; } } /* replace() works, but can break Triangles and so is disabled */ /* static PyObject* */ /* replace(PygtsEdge *self, PyObject *args) */ /* { */ /* PyObject *e2_; */ /* PygtsEdge *e2; */ /* GSList *parents=NULL, *i, *cur; */ /* #if PYGTS_DEBUG */ /* if(!pygts_edge_check((PyObject*)self)) { */ /* PyErr_SetString(PyExc_TypeError, */ /* "problem with self object (internal error)"); */ /* return NULL; */ /* } */ /* #endif */ /* /\* Parse the args *\/ */ /* if(! PyArg_ParseTuple(args, "O", &e2_) ) { */ /* return NULL; */ /* } */ /* /\* Convert to PygtsObjects *\/ */ /* if(!pygts_edge_check(e2_)) { */ /* PyErr_SetString(PyExc_TypeError,"expected an Edge"); */ /* return NULL; */ /* } */ /* e2 = PYGTS_EDGE(e2_); */ /* if(PYGTS_OBJECT(self)->gtsobj!=PYGTS_OBJECT(e2)->gtsobj) { */ /* /\* (Ignore self-replacement) *\/ */ /* /\* Detach and save any parent triangles *\/ */ /* i = GTS_EDGE(PYGTS_OBJECT(self)->gtsobj)->triangles; */ /* while(i!=NULL) { */ /* cur = i; */ /* i = i->next; */ /* if(PYGTS_IS_PARENT_TRIANGLE(cur->data)) { */ /* GTS_EDGE(PYGTS_OBJECT(self)->gtsobj)->triangles = */ /* g_slist_remove_link(GTS_EDGE(PYGTS_OBJECT(self)->gtsobj)->triangles, */ /* cur); */ /* parents = g_slist_prepend(parents,cur->data); */ /* g_slist_free_1(cur); */ /* } */ /* } */ /* /\* Perform the replace operation *\/ */ /* gts_edge_replace(GTS_EDGE(PYGTS_OBJECT(self)->gtsobj), */ /* GTS_EDGE(PYGTS_OBJECT(e2)->gtsobj)); */ /* /\* Reattach the parent segments *\/ */ /* i = parents; */ /* while(i!=NULL) { */ /* GTS_EDGE(PYGTS_OBJECT(self)->gtsobj)->triangles = */ /* g_slist_prepend(GTS_EDGE(PYGTS_OBJECT(self)->gtsobj)->triangles, */ /* i->data); */ /* i = i->next; */ /* } */ /* g_slist_free(parents); */ /* } */ /* #if PYGTS_DEBUG */ /* if(!pygts_edge_check((PyObject*)self)) { */ /* PyErr_SetString(PyExc_TypeError, */ /* "problem with self object (internal error)"); */ /* return NULL; */ /* } */ /* #endif */ /* Py_INCREF(Py_None); */ /* return Py_None; */ /* } */ static PyObject* face_number(PygtsEdge *self, PyObject *args) { PyObject *s_; GtsSurface *s; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &s_) ) { return NULL; } /* Convert to PygtsObjects */ if(!pygts_surface_check(s_)) { PyErr_SetString(PyExc_TypeError,"expected a Surface"); return NULL; } s = PYGTS_SURFACE_AS_GTS_SURFACE(s_); return Py_BuildValue("i", gts_edge_face_number(PYGTS_EDGE_AS_GTS_EDGE(self),s)); } static PyObject* belongs_to_tetrahedron(PygtsEdge *self, PyObject *args) { SELF_CHECK if(gts_edge_belongs_to_tetrahedron(PYGTS_EDGE_AS_GTS_EDGE(self))) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* is_boundary(PygtsEdge *self, PyObject *args) { PyObject *s_; GtsSurface *s; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &s_) ) { return NULL; } /* Convert to PygtsObjects */ if(!pygts_surface_check(s_)) { PyErr_SetString(PyExc_TypeError,"expected a Surface"); return NULL; } s = PYGTS_SURFACE_AS_GTS_SURFACE(s_); /* Make the call and return */ if(gts_edge_is_boundary(PYGTS_EDGE_AS_GTS_EDGE(self),s)!=NULL) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* contacts(PygtsEdge *self, PyObject *args) { SELF_CHECK return Py_BuildValue("i", gts_edge_is_contact(PYGTS_EDGE_AS_GTS_EDGE(self))); } /* Methods table */ static PyMethodDef methods[] = { {"is_ok", (PyCFunction)is_ok, METH_NOARGS, "True if this Edge e is not degenerate or duplicate.\n" "False otherwise. Degeneracy implies e.v1.id == e.v2.id.\n" "\n" "Signature: e.is_ok()\n" }, {"is_unattached", (PyCFunction)is_unattached, METH_NOARGS, "True if this Edge e is not part of any Triangle.\n" "\n" "Signature: e.is_unattached()\n" }, /* Edge replace() method works but results in Triangles that are "not ok"; * i.e., they have edges that don't connect. We don't want that problem * and so the method has been disabled. */ /* {"replace", (PyCFunction)replace, METH_VARARGS, "Replaces this Edge e1 with Edge e2 in all Triangles that have e1.\n" "Edge e1 itself is left unchanged.\n" "\n" "Signature: e1.replace(e2).\n" }, */ {"face_number", (PyCFunction)face_number, METH_VARARGS, "Returns number of faces using this Edge e on Surface s.\n" "\n" "Signature: e.face_number(s)\n" }, {"is_boundary", (PyCFunction)is_boundary, METH_VARARGS, "Returns True if this Edge e is a boundary on Surface s.\n" "Otherwise False.\n" "\n" "Signature: e.is_boundary(s)\n" }, {"belongs_to_tetrahedron", (PyCFunction)belongs_to_tetrahedron, METH_NOARGS, "Returns True if this Edge e belongs to a tetrahedron.\n" "Otherwise False.\n" "\n" "Signature: e.belongs_to_tetrahedron()\n" }, {"contacts", (PyCFunction)contacts, METH_NOARGS, "Returns number of sets of connected triangles share this Edge e\n" "as a contact Edge.\n" "\n" "Signature: e.contacts()\n" }, {NULL} /* Sentinel */ }; /*-------------------------------------------------------------------------*/ /* Python type methods */ static GtsObject* parent(GtsEdge *e1); static PyObject * new(PyTypeObject *type, PyObject *args, PyObject *kwds) { PyObject *o; PygtsObject *obj; GtsEdge *tmp; GtsObject *edge=NULL; PyObject *v1_,*v2_; PygtsVertex *v1,*v2; guint alloc_gtsobj = TRUE; guint N; /* Parse the args */ if(kwds) { o = PyDict_GetItemString(kwds,"alloc_gtsobj"); if(o==Py_False) { alloc_gtsobj = FALSE; } if(o!=NULL) { PyDict_DelItemString(kwds, "alloc_gtsobj"); } } if(kwds) { Py_INCREF(Py_False); PyDict_SetItemString(kwds,"alloc_gtsobj", Py_False); } /* Allocate the gtsobj (if needed) */ if( alloc_gtsobj ) { /* Parse the args */ if( (N = PyTuple_Size(args)) < 2 ) { PyErr_SetString(PyExc_TypeError,"expected two Vertices"); return NULL; } v1_ = PyTuple_GET_ITEM(args,0); v2_ = PyTuple_GET_ITEM(args,1); /* Convert to PygtsObjects */ if(!pygts_vertex_check(v1_)) { PyErr_SetString(PyExc_TypeError,"expected two Vertices"); return NULL; } if(!pygts_vertex_check(v2_)) { PyErr_SetString(PyExc_TypeError,"expected two Vertices"); return NULL; } v1 = PYGTS_VERTEX(v1_); v2 = PYGTS_VERTEX(v2_); /* Error check */ if(PYGTS_OBJECT(v1)->gtsobj == PYGTS_OBJECT(v2)->gtsobj) { PyErr_SetString(PyExc_ValueError,"Vertices given are the same"); return NULL; } /* Create the GtsEdge */ edge = GTS_OBJECT(gts_edge_new(gts_edge_class(), GTS_VERTEX(v1->gtsobj), GTS_VERTEX(v2->gtsobj))); if( edge == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Edge"); return NULL; } /* Check for duplicate */ tmp = gts_edge_is_duplicate(GTS_EDGE(edge)); if( tmp != NULL ) { gts_object_destroy(edge); edge = GTS_OBJECT(tmp); } /* If corresponding PyObject found in object table, we are done */ if( (obj=g_hash_table_lookup(obj_table,edge)) != NULL ) { Py_INCREF(obj); return (PyObject*)obj; } } /* Chain up */ obj = PYGTS_OBJECT(PygtsSegmentType.tp_new(type,args,kwds)); if( alloc_gtsobj ) { obj->gtsobj = edge; /* Create a parent GtsTriangle */ if( (obj->gtsobj_parent = parent(GTS_EDGE(obj->gtsobj))) == NULL ) { gts_object_destroy(obj->gtsobj); obj->gtsobj = NULL; return NULL; } pygts_object_register(PYGTS_OBJECT(obj)); } return (PyObject*)obj; } static int init(PygtsEdge *self, PyObject *args, PyObject *kwds) { gint ret; /* Chain up */ if( (ret=PygtsSegmentType.tp_init((PyObject*)self,args,kwds)) != 0 ){ return ret; } return 0; } /* Methods table */ PyTypeObject PygtsEdgeType = { PyObject_HEAD_INIT(NULL) 0, /* ob_size */ "gts.Edge", /* tp_name */ sizeof(PygtsEdge), /* tp_basicsize */ 0, /* tp_itemsize */ 0, /* tp_dealloc */ 0, /* tp_print */ 0, /* tp_getattr */ 0, /* tp_setattr */ 0, /* tp_compare */ 0, /* tp_repr */ 0, /* tp_as_number */ 0, /* tp_as_sequence */ 0, /* tp_as_mapping */ 0, /* tp_hash */ 0, /* tp_call */ 0, /* tp_str */ 0, /* tp_getattro */ 0, /* tp_setattro */ 0, /* tp_as_buffer */ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ "Edge object", /* tp_doc */ 0, /* tp_traverse */ 0, /* tp_clear */ 0, /* tp_richcompare */ 0, /* tp_weaklistoffset */ 0, /* tp_iter */ 0, /* tp_iternext */ methods, /* tp_methods */ 0, /* tp_members */ 0, /* tp_getset */ 0, /* tp_base */ 0, /* tp_dict */ 0, /* tp_descr_get */ 0, /* tp_descr_set */ 0, /* tp_dictoffset */ (initproc)init, /* tp_init */ 0, /* tp_alloc */ (newfunc)new /* tp_new */ }; /*-------------------------------------------------------------------------*/ /* Pygts functions */ gboolean pygts_edge_check(PyObject* o) { if(! PyObject_TypeCheck(o, &PygtsEdgeType)) { return FALSE; } else { #if PYGTS_DEBUG return pygts_edge_is_ok(PYGTS_EDGE(o)); #else return TRUE; #endif } } gboolean pygts_edge_is_ok(PygtsEdge *e) { GSList *parent; PygtsObject *obj; obj = PYGTS_OBJECT(e); if(!pygts_segment_is_ok(PYGTS_SEGMENT(e))) return FALSE; /* Check for a valid parent */ g_return_val_if_fail(obj->gtsobj_parent!=NULL,FALSE); g_return_val_if_fail(PYGTS_IS_PARENT_TRIANGLE(obj->gtsobj_parent),FALSE); parent = g_slist_find(GTS_EDGE(obj->gtsobj)->triangles, obj->gtsobj_parent); g_return_val_if_fail(parent!=NULL,FALSE); return TRUE; } static GtsObject* parent(GtsEdge *e1) { GtsVertex *v1,*v2,*v3; GtsPoint *p1,*p2; GtsEdge *e2, *e3; GtsTriangle *p; /* Create a third vertex for the triangle */ v1 = GTS_SEGMENT(e1)->v1; v2 = GTS_SEGMENT(e1)->v2; p1 = GTS_POINT(v1); p2 = GTS_POINT(v2); v3 = gts_vertex_new(pygts_parent_vertex_class(), p1->x+p2->x,p1->y+p2->y,p1->z+p2->z); if( v3 == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Vertex"); return NULL; } /* Create another two edges */ if( (e2 = gts_edge_new(pygts_parent_edge_class(),v2,v3)) == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Edge"); return NULL; } if( (e3 = gts_edge_new(pygts_parent_edge_class(),v3,v1)) == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Edge"); gts_object_destroy(GTS_OBJECT(e2)); return NULL; } /* Create and return the parent */ if( (p = gts_triangle_new(pygts_parent_triangle_class(),e1,e2,e3)) == NULL ) { gts_object_destroy(GTS_OBJECT(e2)); gts_object_destroy(GTS_OBJECT(e3)); PyErr_SetString(PyExc_MemoryError, "could not create Triangle"); return NULL; } return GTS_OBJECT(p); } PygtsEdge * pygts_edge_new(GtsEdge *e) { PyObject *args, *kwds; PygtsObject *edge; /* Check for Edge in the object table */ if( (edge = PYGTS_OBJECT(g_hash_table_lookup(obj_table,GTS_OBJECT(e)))) !=NULL ) { Py_INCREF(edge); return PYGTS_EDGE(edge); } /* Build a new Edge */ args = Py_BuildValue("OO",Py_None,Py_None); kwds = Py_BuildValue("{s:O}","alloc_gtsobj",Py_False); edge = PYGTS_EDGE(PygtsEdgeType.tp_new(&PygtsEdgeType, args, kwds)); Py_DECREF(args); Py_DECREF(kwds); if( edge == NULL ) { PyErr_SetString(PyExc_MemoryError,"could not create Edge"); return NULL; } edge->gtsobj = GTS_OBJECT(e); /* Attach the parent */ if( (edge->gtsobj_parent = parent(e)) == NULL ) { Py_DECREF(edge); return NULL; } /* Register and return */ pygts_object_register(edge); return PYGTS_EDGE(edge); } GtsTriangleClass* pygts_parent_triangle_class(void) { static GtsTriangleClass *klass = NULL; GtsObjectClass *super = NULL; if (klass == NULL) { super = GTS_OBJECT_CLASS(gts_triangle_class()); GtsObjectClassInfo pygts_parent_triangle_info = { "PygtsParentTriangle", sizeof(PygtsParentTriangle), sizeof(GtsTriangleClass), (GtsObjectClassInitFunc)(super->info.class_init_func), (GtsObjectInitFunc)(super->info.object_init_func), (GtsArgSetFunc) NULL, (GtsArgGetFunc) NULL }; klass = gts_object_class_new(gts_object_class(), &pygts_parent_triangle_info); } return klass; } GtsEdgeClass* pygts_parent_edge_class(void) { static GtsEdgeClass *klass = NULL; GtsObjectClass *super = NULL; if (klass == NULL) { super = GTS_OBJECT_CLASS(pygts_parent_segment_class()); GtsObjectClassInfo pygts_parent_edge_info = { "PygtsParentEdge", sizeof(PygtsParentEdge), sizeof(GtsEdgeClass), (GtsObjectClassInitFunc)(super->info.class_init_func), (GtsObjectInitFunc)(super->info.object_init_func), (GtsArgSetFunc) NULL, (GtsArgGetFunc) NULL }; klass = gts_object_class_new(gts_object_class(), &pygts_parent_edge_info); } return klass; } trunk-2017.01a/py/3rd-party/pygts-0.3.1/edge.h000066400000000000000000000051331304022710500203210ustar00rootroot00000000000000/* pygts - python package for the manipulation of triangulated surfaces * * Copyright (C) 2009 Thomas J. Duck * All rights reserved. * * Thomas J. Duck * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ #ifndef __PYGTS_EDGE_H__ #define __PYGTS_EDGE_H__ typedef struct _PygtsObject PygtsEdge; #define PYGTS_EDGE(obj) ((PygtsEdge*)obj) #define PYGTS_EDGE_AS_GTS_EDGE(o) (GTS_EDGE(PYGTS_OBJECT(o)->gtsobj)) extern PyTypeObject PygtsEdgeType; gboolean pygts_edge_check(PyObject* o); gboolean pygts_edge_is_ok(PygtsEdge *e); PygtsEdge* pygts_edge_new(GtsEdge *e); /*-------------------------------------------------------------------------*/ /* Parent GTS triangle for GTS edges */ /* Define a GtsTriangle subclass that can be readily identified as the parent * of an encapsulated GtsEdge. The pygts_parent_triangle_class() function * is defined at the bottom, and is what ultimately allows the distinction * to be made. This capability is used for edge replacement operations. */ typedef struct _GtsTriangle PygtsParentTriangle; #define PYGTS_PARENT_TRIANGLE(obj) GTS_OBJECT_CAST(obj,\ GtsTriangle,\ pygts_parent_triangle_class()) #define PYGTS_IS_PARENT_TRIANGLE(obj)(gts_object_is_from_class(obj,\ pygts_parent_triangle_class())) GtsTriangleClass* pygts_parent_triangle_class(void); /* GTS edges in parent triangles */ typedef struct _GtsEdge PygtsParentEdge; #define PYGTS_PARENT_EDGE(obj) GTS_OBJECT_CAST(obj,\ GtsEdge,\ pygts_parent_edge_class()) #define PYGTS_IS_PARENT_EDGE(obj)(gts_object_is_from_class(obj,\ pygts_parent_edge_class())) GtsEdgeClass* pygts_parent_edge_class(void); #endif /* __PYGTS_EDGE_H__ */ trunk-2017.01a/py/3rd-party/pygts-0.3.1/face.c000066400000000000000000000400471304022710500203110ustar00rootroot00000000000000/* pygts - python package for the manipulation of triangulated surfaces * * Copyright (C) 2009 Thomas J. Duck * All rights reserved. * * Thomas J. Duck * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ #include "pygts.h" #if PYGTS_DEBUG #define SELF_CHECK if(!pygts_face_check((PyObject*)self)) { \ PyErr_SetString(PyExc_RuntimeError, \ "problem with self object (internal error)"); \ return NULL; \ } #else #define SELF_CHECK #endif /*-------------------------------------------------------------------------*/ /* Methods exported to python */ static PyObject* is_ok(PygtsFace *self, PyObject *args) { if(pygts_face_is_ok(self)) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* is_unattached(PygtsFace *self, PyObject *args) { guint n; /* Check for attachments other than to the gtsobj_parent */ n = g_slist_length(PYGTS_FACE_AS_GTS_FACE(self)->surfaces); if( n > 1 ) { Py_INCREF(Py_False); return Py_False; } else if( n == 1 ){ Py_INCREF(Py_True); return Py_True; } else { PyErr_SetString(PyExc_RuntimeError, "Face lost parent (internal error)"); return NULL; } } static PyObject* neighbor_number(PygtsFace *self, PyObject *args) { PyObject *s_=NULL; PygtsSurface *s=NULL; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &s_) ) return NULL; /* Convert to PygtsObjects */ if( pygts_surface_check(s_) ) { s = PYGTS_SURFACE(s_); } else { PyErr_SetString(PyExc_TypeError, "expected a Surface"); return NULL; } return Py_BuildValue("i", gts_face_neighbor_number(PYGTS_FACE_AS_GTS_FACE(self), PYGTS_SURFACE_AS_GTS_SURFACE(s))); } static PyObject* neighbors(PygtsFace *self, PyObject *args) { PyObject *s_=NULL; PygtsSurface *s=NULL; guint i,N; PyObject *tuple; GSList *faces,*f; PygtsFace *face; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &s_) ) return NULL; /* Convert to PygtsObjects */ if( pygts_surface_check(s_) ) { s = PYGTS_SURFACE(s_); } else { PyErr_SetString(PyExc_TypeError, "expected a Surface"); return NULL; } N = gts_face_neighbor_number(PYGTS_FACE_AS_GTS_FACE(self), PYGTS_SURFACE_AS_GTS_SURFACE(s)); if( (tuple=PyTuple_New(N)) == NULL) { PyErr_SetString(PyExc_MemoryError, "Could not create tuple"); return NULL; } /* Get the neighbors */ faces = gts_face_neighbors(PYGTS_FACE_AS_GTS_FACE(self), PYGTS_SURFACE_AS_GTS_SURFACE(s)); f = faces; for(i=0;idata))) == NULL ) { Py_DECREF(tuple); return NULL; } PyTuple_SET_ITEM(tuple, i, (PyObject*)face); f = g_slist_next(f); } return (PyObject*)tuple; } static PyObject* is_compatible(PygtsFace *self, PyObject *args) { PyObject *o1_=NULL; GtsEdge *e=NULL; PygtsTriangle *t=NULL; PygtsSurface *s=NULL; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &o1_) ) return NULL; /* Convert to PygtsObjects */ if( pygts_triangle_check(o1_) ) { t = PYGTS_TRIANGLE(o1_); } else { if( pygts_surface_check(o1_) ) { s = PYGTS_SURFACE(o1_); } else { PyErr_SetString(PyExc_TypeError, "expected a Triangle or Surface"); return NULL; } } if(t!=NULL) { if( (e = gts_triangles_common_edge(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self), PYGTS_TRIANGLE_AS_GTS_TRIANGLE(t))) == NULL ) { PyErr_SetString(PyExc_RuntimeError, "Faces do not share common edge"); return NULL; } if(gts_triangles_are_compatible(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self), PYGTS_TRIANGLE_AS_GTS_TRIANGLE(t), e)==TRUE) { Py_INCREF(Py_True); return Py_True; } } else { if(gts_face_is_compatible(PYGTS_FACE_AS_GTS_FACE(self), PYGTS_SURFACE_AS_GTS_SURFACE(s))==TRUE) { Py_INCREF(Py_True); return Py_True; } } Py_INCREF(Py_False); return Py_False; } static PyObject* is_on(PygtsFace *self, PyObject *args) { PyObject *s_=NULL; PygtsSurface *s=NULL; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &s_) ) return NULL; /* Convert to PygtsObjects */ if( pygts_surface_check(s_) ) { s = PYGTS_SURFACE(s_); } else { PyErr_SetString(PyExc_TypeError, "expected a Surface"); return NULL; } if( gts_face_has_parent_surface(PYGTS_FACE_AS_GTS_FACE(self), PYGTS_SURFACE_AS_GTS_SURFACE(s)) ) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } /* Methods table */ static PyMethodDef methods[] = { {"is_ok", (PyCFunction)is_ok, METH_NOARGS, "True if this Face f is non-degenerate and non-duplicate.\n" "False otherwise.\n" "\n" "Signature: f.is_ok()\n" }, {"is_unattached", (PyCFunction)is_unattached, METH_NOARGS, "True if this Face f is not part of any Surface.\n" "\n" "Signature: f.is_unattached().\n" }, {"neighbor_number", (PyCFunction)neighbor_number, METH_VARARGS, "Returns the number of neighbors of Face f belonging to Surface s.\n" "\n" "Signature: f.neighbor_number(s).\n" }, {"neighbors", (PyCFunction)neighbors, METH_VARARGS, "Returns a tuple of neighbors of this Face f belonging to Surface s.\n" "\n" "Signature: f.neighbors(s).\n" }, {"is_compatible", (PyCFunction)is_compatible, METH_VARARGS, "True if Face f is compatible with all neighbors in Surface s.\n" "False otherwise.\n" "\n" "Signature: f.is_compatible(s).\n" }, {"is_on", (PyCFunction)is_on, METH_VARARGS, "True if this Face f is on Surface s. False otherwise.\n" "\n" "Signature: f.is_on(s).\n" }, {NULL} /* Sentinel */ }; /*-------------------------------------------------------------------------*/ /* Python type methods */ static GtsObject * parent(GtsFace *face); static PyObject * new(PyTypeObject *type, PyObject *args, PyObject *kwds) { PyObject *o; PygtsObject *obj; guint alloc_gtsobj = TRUE; PyObject *o1_,*o2_,*o3_; GtsVertex *v1=NULL, *v2=NULL, *v3=NULL; GtsEdge *e1=NULL,*e2=NULL,*e3=NULL,*e; GtsSegment *s1,*s2,*s3; gboolean flag=FALSE; /* Flag when the args are gts.Point objects */ GtsFace *f; GtsTriangle *t; guint N; /* Parse the args */ if(kwds) { o = PyDict_GetItemString(kwds,"alloc_gtsobj"); if(o==Py_False) { alloc_gtsobj = FALSE; } if(o!=NULL) { PyDict_DelItemString(kwds, "alloc_gtsobj"); } } if(kwds) { Py_INCREF(Py_False); PyDict_SetItemString(kwds,"alloc_gtsobj", Py_False); } /* Allocate the gtsobj (if needed) */ if( alloc_gtsobj ) { /* Parse the args */ if( (N = PyTuple_Size(args)) < 3 ) { PyErr_SetString(PyExc_TypeError,"expected three Edges or three Vertices"); return NULL; } o1_ = PyTuple_GET_ITEM(args,0); o2_ = PyTuple_GET_ITEM(args,1); o3_ = PyTuple_GET_ITEM(args,2); /* Convert to PygtsObjects */ if( pygts_edge_check(o1_) ) { e1 = PYGTS_EDGE_AS_GTS_EDGE(o1_); } else { if( pygts_vertex_check(o1_) ) { v1 = PYGTS_VERTEX_AS_GTS_VERTEX(o1_); flag = TRUE; } } if( pygts_edge_check(o2_) ) { e2 = PYGTS_EDGE_AS_GTS_EDGE(o2_); } else { if( pygts_vertex_check(o2_) ) { v2 = PYGTS_VERTEX_AS_GTS_VERTEX(o2_); flag = TRUE; } } if( pygts_edge_check(o3_) ) { e3 = PYGTS_EDGE_AS_GTS_EDGE(o3_); } else { if(pygts_vertex_check(o3_)) { v3 = PYGTS_VERTEX_AS_GTS_VERTEX(o3_); flag = TRUE; } } /* Check for three edges or three vertices */ if( !((e1!=NULL && e2!=NULL && e3!=NULL) || (v1!=NULL && v2!=NULL && v3!=NULL)) ) { PyErr_SetString(PyExc_TypeError, "three Edge or three Vertex objects expected"); return NULL; } if(flag) { /* Create gts edges */ if( (e1 = gts_edge_new(gts_edge_class(),v1,v2)) == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Edge"); return NULL; } if( (e2 = gts_edge_new(gts_edge_class(),v2,v3)) == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Edge"); gts_object_destroy(GTS_OBJECT(e1)); return NULL; } if( (e3 = gts_edge_new(gts_edge_class(),v3,v1)) == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Edge"); gts_object_destroy(GTS_OBJECT(e1)); gts_object_destroy(GTS_OBJECT(e2)); return NULL; } /* Check for duplicates */ if( (e = gts_edge_is_duplicate(e1)) != NULL ) { gts_object_destroy(GTS_OBJECT(e1)); e1 = e; } if( (e = gts_edge_is_duplicate(e2)) != NULL ) { gts_object_destroy(GTS_OBJECT(e2)); e2 = e; } if( (e = gts_edge_is_duplicate(e3)) != NULL ) { gts_object_destroy(GTS_OBJECT(e3)); e3 = e; } } /* Check that edges connect */ s1 = GTS_SEGMENT(e1); s2 = GTS_SEGMENT(e2); s3 = GTS_SEGMENT(e3); if( !((s1->v1==s3->v2 && s1->v2==s2->v1 && s2->v2==s3->v1) || (s1->v1==s3->v2 && s1->v2==s2->v2 && s2->v1==s3->v1) || (s1->v1==s3->v1 && s1->v2==s2->v1 && s2->v2==s3->v2) || (s1->v2==s3->v2 && s1->v1==s2->v1 && s2->v2==s3->v1) || (s1->v1==s3->v1 && s1->v2==s2->v2 && s2->v1==s3->v2) || (s1->v2==s3->v2 && s1->v1==s2->v2 && s2->v1==s3->v1) || (s1->v2==s3->v1 && s1->v1==s2->v1 && s2->v2==s3->v2) || (s1->v2==s3->v1 && s1->v1==s2->v2 && s2->v1==s3->v2)) ) { PyErr_SetString(PyExc_RuntimeError, "Edges in face must connect"); if(!g_hash_table_lookup(obj_table,GTS_OBJECT(e1))) { gts_object_destroy(GTS_OBJECT(e1)); } if(!g_hash_table_lookup(obj_table,GTS_OBJECT(e1))) { gts_object_destroy(GTS_OBJECT(e2)); } if(!g_hash_table_lookup(obj_table,GTS_OBJECT(e1))) { gts_object_destroy(GTS_OBJECT(e3)); } return NULL; } /* Create the GtsFace */ if( (f = gts_face_new(gts_face_class(),e1,e2,e3)) == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Face"); if(!g_hash_table_lookup(obj_table,GTS_OBJECT(e1))) { gts_object_destroy(GTS_OBJECT(e1)); } if(!g_hash_table_lookup(obj_table,GTS_OBJECT(e1))) { gts_object_destroy(GTS_OBJECT(e2)); } if(!g_hash_table_lookup(obj_table,GTS_OBJECT(e1))) { gts_object_destroy(GTS_OBJECT(e3)); } return NULL; } /* Check for duplicate */ t = gts_triangle_is_duplicate(GTS_TRIANGLE(f)); if( t != NULL ) { gts_object_destroy(GTS_OBJECT(f)); if(!GTS_IS_FACE(t)) { PyErr_SetString(PyExc_TypeError, "expected a Face (internal error)"); } f = GTS_FACE(t); } /* If corresponding PyObject found in object table, we are done */ if( (obj=g_hash_table_lookup(obj_table,GTS_OBJECT(f))) != NULL ) { Py_INCREF(obj); return (PyObject*)obj; } } /* Chain up */ obj = PYGTS_OBJECT(PygtsTriangleType.tp_new(type,args,kwds)); if( alloc_gtsobj ) { obj->gtsobj = GTS_OBJECT(f); /* Create the parent GtsSurface */ if( (obj->gtsobj_parent = parent(GTS_FACE(obj->gtsobj))) == NULL ) { gts_object_destroy(obj->gtsobj); obj->gtsobj = NULL; return NULL; } pygts_object_register(PYGTS_OBJECT(obj)); } return (PyObject*)obj; } static int init(PygtsFace *self, PyObject *args, PyObject *kwds) { gint ret; /* Chain up */ if( (ret=PygtsTriangleType.tp_init((PyObject*)self,args,kwds)) != 0 ){ return ret; } return 0; } /* Methods table */ PyTypeObject PygtsFaceType = { PyObject_HEAD_INIT(NULL) 0, /* ob_size */ "gts.Face", /* tp_name */ sizeof(PygtsFace), /* tp_basicsize */ 0, /* tp_itemsize */ 0, /* tp_dealloc */ 0, /* tp_print */ 0, /* tp_getattr */ 0, /* tp_setattr */ 0, /* tp_compare */ 0, /* tp_repr */ 0, /* tp_as_number */ 0, /* tp_as_sequence */ 0, /* tp_as_mapping */ 0, /* tp_hash */ 0, /* tp_call */ 0, /* tp_str */ 0, /* tp_getattro */ 0, /* tp_setattro */ 0, /* tp_as_buffer */ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ "Face object", /* tp_doc */ 0, /* tp_traverse */ 0, /* tp_clear */ 0, /* tp_richcompare */ 0, /* tp_weaklistoffset */ 0, /* tp_iter */ 0, /* tp_iternext */ methods, /* tp_methods */ 0, /* tp_members */ 0, /* tp_getset */ 0, /* tp_base */ 0, /* tp_dict */ 0, /* tp_descr_get */ 0, /* tp_descr_set */ 0, /* tp_dictoffset */ (initproc)init, /* tp_init */ 0, /* tp_alloc */ (newfunc)new /* tp_new */ }; /*-------------------------------------------------------------------------*/ /* Pygts functions */ gboolean pygts_face_check(PyObject* o) { if(! PyObject_TypeCheck(o, &PygtsFaceType)) { return FALSE; } else { #if PYGTS_DEBUG return pygts_face_is_ok(PYGTS_FACE(o)); #else return TRUE; #endif } } gboolean pygts_face_is_ok(PygtsFace *f) { GSList *parent; PygtsObject *obj; obj = PYGTS_OBJECT(f); if(!pygts_triangle_is_ok(PYGTS_TRIANGLE(f))) return FALSE; /* Check for a valid parent */ g_return_val_if_fail(obj->gtsobj_parent!=NULL,FALSE); g_return_val_if_fail(GTS_IS_SURFACE(obj->gtsobj_parent),FALSE); parent = g_slist_find(GTS_FACE(obj->gtsobj)->surfaces, obj->gtsobj_parent); g_return_val_if_fail(parent!=NULL,FALSE); return TRUE; } static GtsObject * parent(GtsFace *face) { GtsSurface *p; p = gts_surface_new(gts_surface_class(), gts_face_class(), gts_edge_class(), gts_vertex_class()); if( p == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create parent"); return NULL; } gts_surface_add_face(p,face); return GTS_OBJECT(p); } PygtsFace * pygts_face_new(GtsFace *f) { PyObject *args, *kwds; PygtsObject *face; /* Check for Face in the object table */ if( (face=PYGTS_OBJECT(g_hash_table_lookup(obj_table,GTS_OBJECT(f)))) != NULL ) { Py_INCREF(face); return PYGTS_FACE(face); } /* Build a new Face */ args = Py_BuildValue("OOO",Py_None,Py_None,Py_None); kwds = Py_BuildValue("{s:O}","alloc_gtsobj",Py_False); face = PYGTS_OBJECT(PygtsFaceType.tp_new(&PygtsFaceType, args, kwds)); Py_DECREF(args); Py_DECREF(kwds); if( face == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Face"); return NULL; } face->gtsobj = GTS_OBJECT(f); /* Attach the parent */ if( (face->gtsobj_parent = parent(f)) == NULL ) { Py_DECREF(face); return NULL; } /* Register and return */ pygts_object_register(face); return PYGTS_FACE(face); } trunk-2017.01a/py/3rd-party/pygts-0.3.1/face.h000066400000000000000000000030651304022710500203150ustar00rootroot00000000000000/* pygts - python package for the manipulation of triangulated surfaces * * Copyright (C) 2009 Thomas J. Duck * All rights reserved. * * Thomas J. Duck * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ #ifndef __PYGTS_FACE_H__ #define __PYGTS_FACE_H__ #ifndef gts_face_is_unattached #define gts_face_is_unattached(f) ((f)->surfaces == NULL ? TRUE : FALSE) #endif typedef struct _PygtsObject PygtsFace; #define PYGTS_FACE(obj) ((PygtsFace*)obj) #define PYGTS_FACE_AS_GTS_FACE(o) (GTS_FACE(PYGTS_OBJECT(o)->gtsobj)) extern PyTypeObject PygtsFaceType; gboolean pygts_face_check(PyObject* o); gboolean pygts_face_is_ok(PygtsFace *f); PygtsFace* pygts_face_new(GtsFace *f); #endif /* __PYGTS_FACE_H__ */ trunk-2017.01a/py/3rd-party/pygts-0.3.1/object.c000066400000000000000000000145061304022710500206620ustar00rootroot00000000000000/* pygts - python package for the manipulation of triangulated surfaces * * Copyright (C) 2009 Thomas J. Duck * All rights reserved. * * Thomas J. Duck * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ #include "pygts.h" /*-------------------------------------------------------------------------*/ /* Methods exported to python */ static PyObject* is_unattached(PygtsObject *self, PyObject *args, PyObject *kwds) { /* Objects are unattached by default */ Py_INCREF(Py_False); return Py_False; } /* Methods table */ static PyMethodDef methods[] = { {"is_unattached", (PyCFunction)is_unattached, METH_NOARGS, "True if this Object o is not attached to another Object.\n" "Otherwise False.\n" "\n" "Trace: o.is_unattached().\n" }, {NULL} /* Sentinel */ }; /*-------------------------------------------------------------------------*/ /* Attributes exported to python */ static PyObject * id(PygtsObject *self, void *closure) { if( self->gtsobj == NULL) { PyErr_SetString(PyExc_RuntimeError, "GTS object does not exist!"); return NULL; } /* Use the pointer of the gtsobj */ return Py_BuildValue("i",(long)(self->gtsobj)); } /* Methods table */ static PyGetSetDef getset[] = { {"id", (getter)id, NULL, "GTS object id", NULL}, {NULL} /* Sentinel */ }; /*-------------------------------------------------------------------------*/ /* Python type methods */ static void dealloc(PygtsObject* self) { /* De-register entry from the object table */ pygts_object_deregister(self); if(self->gtsobj_parent!=NULL) { /* Free the parent; GTS will free the child unless it is attached * to something else. */ gts_object_destroy(self->gtsobj_parent); self->gtsobj_parent=NULL; } else { /* We have the only reference, and so it is safe to destroy the gtsobj * (unless it was never created in the first place). */ if(self->gtsobj!=NULL) { gts_object_destroy(self->gtsobj); self->gtsobj=NULL; } } self->ob_type->tp_free((PyObject*)self); } static PyObject * new(PyTypeObject *type, PyObject *args, PyObject *kwds) { PygtsObject *self; /* Chain up object allocation */ self = PYGTS_OBJECT(type->tp_alloc(type, 0)); if( self == NULL ) return NULL; /* Object initialization */ self->gtsobj = NULL; self->gtsobj_parent = NULL; return (PyObject *)self; } static int init(PygtsObject *self, PyObject *args, PyObject *kwds) { if( self->gtsobj == NULL ) { PyErr_SetString(PyExc_RuntimeError, "Cannot create abstract Object"); return -1; } return 0; } static int compare(PygtsObject *o1, PygtsObject *o2) { if(o1->gtsobj==o2->gtsobj) { return 0; } else { return -1; } } /* Methods table */ PyTypeObject PygtsObjectType = { PyObject_HEAD_INIT(NULL) 0, /* ob_size */ "gts.Object" , /* tp_name */ sizeof(PygtsObject), /* tp_basicsize */ 0, /* tp_itemsize */ (destructor)dealloc, /* tp_dealloc */ 0, /* tp_print */ 0, /* tp_getattr */ 0, /* tp_setattr */ (cmpfunc)compare, /* tp_compare */ 0, /* tp_repr */ 0, /* tp_as_number */ 0, /* tp_as_sequence */ 0, /* tp_as_mapping */ 0, /* tp_hash */ 0, /* tp_call */ 0, /* tp_str */ 0, /* tp_getattro */ 0, /* tp_setattro */ 0, /* tp_as_buffer */ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ "Base object", /* tp_doc */ 0, /* tp_traverse */ 0, /* tp_clear */ 0, /* tp_richcompare */ 0, /* tp_weaklistoffset */ 0, /* tp_iter */ 0, /* tp_iternext */ methods, /* tp_methods */ 0, /* tp_members */ getset, /* tp_getset */ 0, /* tp_base: attached in pygts.c */ 0, /* tp_dict */ 0, /* tp_descr_get */ 0, /* tp_descr_set */ 0, /* tp_dictoffset */ (initproc)init, /* tp_init */ 0, /* tp_alloc */ (newfunc)new /* tp_new */ }; /*-------------------------------------------------------------------------*/ /* Pygts functions */ gboolean pygts_object_check(PyObject* o) { if(! PyObject_TypeCheck(o, &PygtsObjectType)) { return FALSE; } else { #if PYGTS_DEBUG return pygts_object_is_ok(PYGTS_OBJECT(o)); #else return TRUE; #endif } } gboolean pygts_object_is_ok(PygtsObject *o) { g_return_val_if_fail(o->gtsobj!=NULL,FALSE); g_return_val_if_fail(g_hash_table_lookup(obj_table,o->gtsobj)!=NULL,FALSE); return TRUE; } /*-------------------------------------------------------------------------*/ /* Object table functions */ GHashTable *obj_table; /* GtsObject key, associated PyObject value */ void pygts_object_register(PygtsObject *o) { if( g_hash_table_lookup(obj_table,o->gtsobj) == NULL ) { g_hash_table_insert(obj_table,o->gtsobj,o); } } void pygts_object_deregister(PygtsObject *o) { if(o->gtsobj!=NULL) { if(g_hash_table_lookup(obj_table,o->gtsobj)==o) { g_hash_table_remove(obj_table,o->gtsobj); } } } trunk-2017.01a/py/3rd-party/pygts-0.3.1/object.h000066400000000000000000000034231304022710500206630ustar00rootroot00000000000000/* pygts - python package for the manipulation of triangulated surfaces * * Copyright (C) 2009 Thomas J. Duck * All rights reserved. * * Thomas J. Duck * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ #ifndef __PYGTS_OBJECT_H__ #define __PYGTS_OBJECT_H__ typedef struct _PygtsObject PygtsObject; typedef struct _PygtsMethods PygtsMethods; #define PYGTS_OBJECT(obj) ((PygtsObject*)obj) struct _PygtsObject { PyObject_HEAD GtsObject *gtsobj; /* Encapsulated GtsObject */ GtsObject *gtsobj_parent; /* A parent object to ensure persistence */ }; extern PyTypeObject PygtsObjectType; extern PygtsMethods PygtsObjectMethods; gboolean pygts_object_check(PyObject* o); gboolean pygts_object_is_ok(PygtsObject *o); extern GHashTable *obj_table; /* GtsObject key, associated PyObject value */ void pygts_object_register(PygtsObject *o); void pygts_object_deregister(PygtsObject *o); #endif /* __PYGTS_OBJECT_H__ */ trunk-2017.01a/py/3rd-party/pygts-0.3.1/point.c000066400000000000000000000706351304022710500205520ustar00rootroot00000000000000/* pygts - python point for the manipulation of triangulated surfaces * * Copyright (C) 2009 Thomas J. Duck * All rights reserved. * * Thomas J. Duck * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ #include "pygts.h" #if PYGTS_DEBUG #define SELF_CHECK if(!pygts_point_check((PyObject*)self)) { \ PyErr_SetString(PyExc_RuntimeError, \ "problem with self object (internal error)"); \ return NULL; \ } #else #define SELF_CHECK #endif /*-------------------------------------------------------------------------*/ /* Methods exported to python */ static PyObject* is_ok(PygtsPoint *self, PyObject *args) { if(pygts_point_is_ok(self)) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* set(PygtsPoint *self, PyObject *args) { gdouble x=0,y=0,z=0; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "|ddd", &x,&y,&z)) { return NULL; } gts_point_set(PYGTS_POINT_AS_GTS_POINT(self),x,y,z); Py_INCREF(Py_None); return Py_None; } static PyObject* coords(PygtsPoint *self, PyObject *args) { SELF_CHECK return Py_BuildValue("ddd",PYGTS_POINT_AS_GTS_POINT(self)->x, PYGTS_POINT_AS_GTS_POINT(self)->y, PYGTS_POINT_AS_GTS_POINT(self)->z); } static PyObject* is_in_rectangle(PygtsPoint* self, PyObject *args) { PyObject *o1_,*o2_; PygtsPoint *p1, *p2; gboolean flag = FALSE; gdouble x,y; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "OO", &o1_, &o2_) ) { return NULL; } /* Convert to PygtsObjects */ if(!(pygts_point_check(o1_) && pygts_point_check(o2_))) { PyErr_SetString(PyExc_TypeError,"expected two Points"); return NULL; } p1 = PYGTS_POINT(o1_); p2 = PYGTS_POINT(o2_); /* Test if point *may* be on rectangle perimeter */ x = PYGTS_POINT_AS_GTS_POINT(self)->x; y = PYGTS_POINT_AS_GTS_POINT(self)->y; if( PYGTS_POINT_AS_GTS_POINT(p1)->x == x || PYGTS_POINT_AS_GTS_POINT(p1)->y == y || PYGTS_POINT_AS_GTS_POINT(p2)->x == x || PYGTS_POINT_AS_GTS_POINT(p2)->y == y ) { flag = TRUE; } if( gts_point_is_in_rectangle(PYGTS_POINT_AS_GTS_POINT(self), PYGTS_POINT_AS_GTS_POINT(p1), PYGTS_POINT_AS_GTS_POINT(p2)) ) { if(flag) { return Py_BuildValue("i",0); } else { return Py_BuildValue("i",1); } } else { if( flag && gts_point_is_in_rectangle(PYGTS_POINT_AS_GTS_POINT(self), PYGTS_POINT_AS_GTS_POINT(p2), PYGTS_POINT_AS_GTS_POINT(p1))) { return Py_BuildValue("i",0); } else { return Py_BuildValue("i",-1); } } } static PyObject* distance(PygtsPoint* self, PyObject *args) { PyObject *o_; PygtsPoint *p=NULL; PygtsSegment *s=NULL; PygtsTriangle *t=NULL; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &o_) ) { return NULL; } /* Convert to PygtsObjects */ if(pygts_point_check(o_)) { p = PYGTS_POINT(o_); } else { if(pygts_segment_check(o_)) { s = PYGTS_SEGMENT(o_); } else { if(pygts_triangle_check(o_)) { t = PYGTS_TRIANGLE(o_); } else { PyErr_SetString(PyExc_TypeError, "expected a Point, Segment or Triangle"); return NULL; } } } if(p!=NULL) { return Py_BuildValue("d", gts_point_distance(PYGTS_POINT_AS_GTS_POINT(self), PYGTS_POINT_AS_GTS_POINT(p))); } else { if(s!=NULL) { return Py_BuildValue("d", gts_point_segment_distance(PYGTS_POINT_AS_GTS_POINT(self), PYGTS_SEGMENT_AS_GTS_SEGMENT(s) ) ); } else { return Py_BuildValue("d", gts_point_triangle_distance(PYGTS_POINT_AS_GTS_POINT(self), PYGTS_TRIANGLE_AS_GTS_TRIANGLE(t) ) ); } } } static PyObject* distance2(PygtsPoint* self, PyObject *args) { PyObject *o_; PygtsPoint *p=NULL; PygtsSegment *s=NULL; PygtsTriangle *t=NULL; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &o_) ) { return NULL; } /* Convert to PygtsObjects */ if(pygts_point_check(o_)) { p = PYGTS_POINT(o_); } else { if(pygts_segment_check(o_)) { s = PYGTS_SEGMENT(o_); } else { if(pygts_triangle_check(o_)) { t = PYGTS_TRIANGLE(o_); } else { PyErr_SetString(PyExc_TypeError, "expected a Point, Segment or Triangle"); return NULL; } } } if(p!=NULL) { return Py_BuildValue("d", gts_point_distance2(PYGTS_POINT_AS_GTS_POINT(self), PYGTS_POINT_AS_GTS_POINT(p))); } else { if(s!=NULL) { return Py_BuildValue("d", gts_point_segment_distance2(PYGTS_POINT_AS_GTS_POINT(self), PYGTS_SEGMENT_AS_GTS_SEGMENT(s) ) ); } else { return Py_BuildValue("d", gts_point_triangle_distance2(PYGTS_POINT_AS_GTS_POINT(self), PYGTS_TRIANGLE_AS_GTS_TRIANGLE(t) ) ); } } } static PyObject* orientation_3d(PygtsPoint* self, PyObject *args) { PyObject *p1_,*p2_,*p3_; PygtsPoint *p1,*p2,*p3; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "OOO", &p1_, &p2_, &p3_) ) { return NULL; } /* Convert to PygtsObjects */ if(!pygts_point_check(p1_)) { PyErr_SetString(PyExc_TypeError,"expected three Points"); return NULL; } if(!pygts_point_check(p2_)) { PyErr_SetString(PyExc_TypeError,"expected three Points"); return NULL; } if(!pygts_point_check(p3_)) { PyErr_SetString(PyExc_TypeError,"expected three Points"); return NULL; } p1 = PYGTS_POINT(p1_); p2 = PYGTS_POINT(p2_); p3 = PYGTS_POINT(p3_); return Py_BuildValue("d", gts_point_orientation_3d(PYGTS_POINT_AS_GTS_POINT(p1), PYGTS_POINT_AS_GTS_POINT(p2), PYGTS_POINT_AS_GTS_POINT(p3), PYGTS_POINT_AS_GTS_POINT(self))); } static PyObject* orientation_3d_sos(PygtsPoint* self, PyObject *args) { PyObject *p1_,*p2_,*p3_; PygtsPoint *p1,*p2,*p3; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "OOO", &p1_, &p2_, &p3_) ) { return NULL; } /* Convert to PygtsObjects */ if(!pygts_point_check(p1_)) { PyErr_SetString(PyExc_TypeError,"expected three Points"); return NULL; } if(!pygts_point_check(p2_)) { PyErr_SetString(PyExc_TypeError,"expected three Points"); return NULL; } if(!pygts_point_check(p3_)) { PyErr_SetString(PyExc_TypeError,"expected three Points"); return NULL; } p1 = PYGTS_POINT(p1_); p2 = PYGTS_POINT(p2_); p3 = PYGTS_POINT(p3_); return Py_BuildValue("i",gts_point_orientation_3d_sos( PYGTS_POINT_AS_GTS_POINT(p1), PYGTS_POINT_AS_GTS_POINT(p2), PYGTS_POINT_AS_GTS_POINT(p3), PYGTS_POINT_AS_GTS_POINT(self))); } static PyObject* is_in_circle(PygtsPoint* self, PyObject *args) { PyObject *o1_=NULL,*o2_=NULL,*o3_=NULL; PygtsPoint *p1=NULL, *p2=NULL, *p3=NULL; PygtsTriangle *t=NULL; gdouble result; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O|OO", &o1_, &o2_, &o3_) ) { return NULL; } if( (o2_==NULL && o3_!=NULL) || (o2_!=NULL && o3_==NULL) ) { PyErr_SetString(PyExc_TypeError,"expected three Points or one Triangle"); return NULL; } /* Convert to PygtsObjects */ if(o2_==NULL && o3_==NULL) { if(!pygts_triangle_check(o1_)) { PyErr_SetString(PyExc_TypeError,"expected three Points or one Triangle"); return NULL; } t = PYGTS_TRIANGLE(o1_); } else { if(!pygts_point_check(o1_)) { PyErr_SetString(PyExc_TypeError,"expected three Points or one Triangle"); return NULL; } if(!pygts_point_check(o2_)) { PyErr_SetString(PyExc_TypeError,"expected three Points or one Triangle"); return NULL; } if(!pygts_point_check(o3_)) { PyErr_SetString(PyExc_TypeError,"expected three Points or one Triangle"); return NULL; } p1 = PYGTS_POINT(o1_); p2 = PYGTS_POINT(o2_); p3 = PYGTS_POINT(o3_); } if(t!=NULL){ result=gts_point_in_triangle_circle(PYGTS_POINT_AS_GTS_POINT(self), PYGTS_TRIANGLE_AS_GTS_TRIANGLE(t)); } else { result = gts_point_in_circle(PYGTS_POINT_AS_GTS_POINT(self), PYGTS_POINT_AS_GTS_POINT(p1), PYGTS_POINT_AS_GTS_POINT(p2), PYGTS_POINT_AS_GTS_POINT(p3)); } if(result>0) return Py_BuildValue("i",1); if(result==0) return Py_BuildValue("i",0); return Py_BuildValue("i",-1); } static PyObject* is_in(PygtsPoint* self, PyObject *args) { PyObject *t_; PygtsTriangle *t; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &t_) ) { return NULL; } /* Convert to PygtsObjects */ if(!pygts_triangle_check(t_)) { PyErr_SetString(PyExc_TypeError,"expected a Triangle"); return NULL; } t = PYGTS_TRIANGLE(t_); return Py_BuildValue("i", gts_point_is_in_triangle(PYGTS_POINT_AS_GTS_POINT(self), PYGTS_TRIANGLE_AS_GTS_TRIANGLE(t))); } static PyObject* is_inside(PygtsPoint* self, PyObject *args) { PyObject *s_; PygtsSurface *s; GNode *tree; gboolean is_open=FALSE, ret; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &s_) ) { return NULL; } /* Convert to PygtsObjects */ if(!pygts_surface_check(s_)) { PyErr_SetString(PyExc_TypeError,"expected a Surface"); return NULL; } s = PYGTS_SURFACE(s_); /* Error check */ if(!gts_surface_is_closed(PYGTS_SURFACE_AS_GTS_SURFACE(s))) { PyErr_SetString(PyExc_RuntimeError,"Surface is not closed"); return NULL; } /* Determing is_open parameter; note the meaning is different from the * error check above. */ if( gts_surface_volume(PYGTS_SURFACE_AS_GTS_SURFACE(s))<0. ) { is_open = TRUE; } /* Construct the tree */ if((tree=gts_bb_tree_surface(PYGTS_SURFACE_AS_GTS_SURFACE(s))) == NULL) { PyErr_SetString(PyExc_MemoryError,"could not create GTree"); return NULL; } /* Make the call */ ret = gts_point_is_inside_surface(PYGTS_POINT_AS_GTS_POINT(self), tree, is_open); g_node_destroy(tree); if(ret) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* closest(PygtsPoint* self, PyObject *args) { PyObject *o1_,*o2_; PygtsPoint *p=NULL; PygtsSegment *s=NULL; PygtsTriangle *t=NULL; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "OO", &o1_, &o2_) ) { return NULL; } /* Convert to PygtsObjects */ if(pygts_segment_check(o1_)) { s = PYGTS_SEGMENT(o1_); } else { if(pygts_triangle_check(o1_)) { t = PYGTS_TRIANGLE(o1_); } else { PyErr_SetString(PyExc_TypeError, "expected a Segment or Triangle, and a Point"); return NULL; } } if(pygts_point_check(o2_)) { p = PYGTS_POINT(o2_); } else { PyErr_SetString(PyExc_TypeError, "expected a Segment or Triangle, and a Point"); return NULL; } if(s!=NULL) { gts_point_segment_closest(PYGTS_POINT_AS_GTS_POINT(p), PYGTS_SEGMENT_AS_GTS_SEGMENT(s), PYGTS_POINT_AS_GTS_POINT(self)); } else { gts_point_triangle_closest(PYGTS_POINT_AS_GTS_POINT(p), PYGTS_TRIANGLE_AS_GTS_TRIANGLE(t), PYGTS_POINT_AS_GTS_POINT(self)); } Py_INCREF(self); return (PyObject*)self; } /* Helper for rotate() */ gint pygts_point_rotate(GtsPoint* p, gdouble dx, gdouble dy, gdouble dz, gdouble a) { GtsMatrix *m; GtsVector v; v[0] = dx; v[1] = dy; v[2] = dz; if( (m = gts_matrix_rotate(NULL,v,a)) == NULL ) { PyErr_SetString(PyExc_MemoryError,"could not create matrix"); return -1; } gts_point_transform(p,m); gts_matrix_destroy(m); return 0; } static PyObject* rotate(PygtsPoint* self, PyObject *args, PyObject *keywds) { static char *kwlist[] = {"dx", "dy", "dz", "a", NULL}; gdouble dx=0,dy=0,dz=0,a=0; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTupleAndKeywords(args, keywds,"|dddd", kwlist, &dx, &dy, &dz, &a) ) { return NULL; } if(pygts_point_rotate(PYGTS_POINT_AS_GTS_POINT(self),dx,dy,dz,a)==-1) return NULL; Py_INCREF(Py_None); return Py_None; } /* Helper for scale() */ gint pygts_point_scale(GtsPoint* p, gdouble dx, gdouble dy, gdouble dz) { GtsMatrix *m; GtsVector v; v[0] = dx; v[1] = dy; v[2] = dz; if( (m = gts_matrix_scale(NULL,v)) == NULL ) { PyErr_SetString(PyExc_MemoryError,"could not create matrix"); return -1; } gts_point_transform(p,m); gts_matrix_destroy(m); return 0; } static PyObject* scale(PygtsPoint* self, PyObject *args, PyObject *keywds) { static char *kwlist[] = {"dx", "dy", "dz", NULL}; gdouble dx=1,dy=1,dz=1; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTupleAndKeywords(args, keywds,"|ddd", kwlist, &dx, &dy, &dz) ) { return NULL; } if(pygts_point_scale(PYGTS_POINT_AS_GTS_POINT(self),dx,dy,dz)==-1) return NULL; Py_INCREF(Py_None); return Py_None; } /* Helper for translate() */ gint pygts_point_translate(GtsPoint* p, gdouble dx, gdouble dy, gdouble dz) { GtsMatrix *m; GtsVector v; v[0] = dx; v[1] = dy; v[2] = dz; if( (m = gts_matrix_translate(NULL,v)) == NULL ) { PyErr_SetString(PyExc_MemoryError,"could not create matrix"); return -1; } gts_point_transform(p,m); gts_matrix_destroy(m); return 0; } static PyObject* translate(PygtsPoint* self, PyObject *args, PyObject *keywds) { static char *kwlist[] = {"dx", "dy", "dz", NULL}; gdouble dx=0,dy=0,dz=0; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTupleAndKeywords(args, keywds,"|ddd", kwlist, &dx, &dy, &dz) ) { return NULL; } if(pygts_point_translate(PYGTS_POINT_AS_GTS_POINT(self),dx,dy,dz)==-1) return NULL; Py_INCREF(Py_None); return Py_None; } /* Methods table */ static PyMethodDef methods[] = { {"is_ok", (PyCFunction)is_ok, METH_NOARGS, "True if this Point p is OK. False otherwise.\n" "This method is useful for unit testing and debugging.\n" "\n" "Signature: p.is_ok().\n" }, {"set", (PyCFunction)set, METH_VARARGS, "Sets x, y, and z coordinates of this Point p.\n" "\n" "Signature: p.set(x,y,z)\n" }, {"coords", (PyCFunction)coords, METH_VARARGS, "Returns a tuple of the x, y, and z coordinates for this Point p.\n" "\n" "Signature: p.coords(x,y,z)\n" }, {"is_in_rectangle", (PyCFunction)is_in_rectangle, METH_VARARGS, "True if this Point p is in box with bottom-left and upper-right\n" "Points p1 and p2.\n" "\n" "Signature: p.is_in_rectange(p1,p2)\n" }, {"distance", (PyCFunction)distance, METH_VARARGS, "Returns Euclidean distance between this Point p and other Point p2,\n" "Segment s, or Triangle t." "\n" "Signature: p.distance(p2), p.distance(s) or p.distance(t)\n" }, {"distance2", (PyCFunction)distance2, METH_VARARGS, "Returns squared Euclidean distance between Point p and Point p2,\n" "Segment s, or Triangle t.\n" "\n" "Signature: p.distance2(p2), p.distance2(s), or p.distance2(t)\n" }, {"orientation_3d", (PyCFunction)orientation_3d, METH_VARARGS, "Determines if this Point p is above, below or on plane of 3 Points\n" "p1, p2 and p3.\n" "\n" "Signature: p.orientation_3d(p1,p2,p3)\n" "\n" "Below is defined so that p1, p2 and p3 appear in counterclockwise\n" "order when viewed from above the plane.\n" "\n" "The return value is positive if p4 lies below the plane, negative\n" "if p4 lies above the plane, and zero if the four points are\n" "coplanar. The value is an approximation of six times the signed\n" "volume of the tetrahedron defined by the four points.\n" }, {"orientation_3d_sos", (PyCFunction)orientation_3d_sos, METH_VARARGS, "Determines if this Point p is above, below or on plane of 3 Points\n" "p1, p2 and p3.\n" "\n" "Signature: p.orientation_3d_sos(p1,p2,p3)\n" "\n" "Below is defined so that p1, p2 and p3 appear in counterclockwise\n" "order when viewed from above the plane.\n" "\n" "The return value is +1 if p4 lies below the plane, and -1 if p4\n" "lies above the plane. Simulation of Simplicity (SoS) is used to\n" "break ties when the orientation is degenerate (i.e. the point lies\n" "on the plane definedby p1, p2 and p3)." }, {"is_in_circle", (PyCFunction)is_in_circle, METH_VARARGS, "Tests if this Point p is inside or outside circumcircle.\n" "The planar projection (x,y) of Point p is tested against the\n" "circumcircle defined by the planar projection of p1, p2 and p3,\n" "or alternatively the Triangle t\n" "\n" "Signature: p.in_circle(p1,p2,p3) or p.in_circle(t) \n" "\n" "Returns +1 if p lies inside, -1 if p lies outside, and 0 if p lies\n" "on the circle. The Points p1, p2, and p3 must be in\n" "counterclockwise order, or the sign of the result will be reversed.\n" }, {"is_in", (PyCFunction)is_in, METH_VARARGS, "Tests if this Point p is inside or outside Triangle t.\n" "The planar projection (x,y) of Point p is tested against the\n" "planar projection of Triangle t.\n" "\n" "Signature: p.in_circle(p1,p2,p3) or p.in_circle(t) \n" "\n" "Returns a +1 if p lies inside, -1 if p lies outside, and 0\n" "if p lies on the triangle.\n" }, {"is_inside", (PyCFunction)is_inside, METH_VARARGS, "True if this Point p is inside or outside Surface s.\n" "False otherwise.\n" "\n" "Signature: p.in_inside(s)\n" }, {"closest", (PyCFunction)closest, METH_VARARGS, "Set the coordinates of Point p to the Point on Segment s\n" "or Triangle t closest to the Point p2\n" "\n" "Signature: p.closest(s,p2) or p.closest(t,p2)\n" "\n" "Returns the (modified) Point p.\n" }, {"rotate", (PyCFunction)rotate, METH_VARARGS | METH_KEYWORDS, "Rotates Point p around vector dx,dy,dz by angle a.\n" "The sense of the rotation is given by the right-hand-rule.\n" "\n" "Signature: p.rotate(dx=0,dy=0,dz=0,a=0)\n" }, {"scale", (PyCFunction)scale, METH_VARARGS | METH_KEYWORDS, "Scales Point p by vector dx,dy,dz.\n" "\n" "Signature: p.scale(dx=1,dy=1,dz=1)\n" }, {"translate", (PyCFunction)translate, METH_VARARGS | METH_KEYWORDS, "Translates Point p by vector dx,dy,dz.\n" "\n" "Signature: p.translate(dx=0,dy=0,dz=0)\n" }, {NULL} /* Sentinel */ }; /*-------------------------------------------------------------------------*/ /* Attributes exported to python */ static PyObject * getx(PygtsPoint *self, void *closure) { SELF_CHECK return Py_BuildValue("d",PYGTS_POINT_AS_GTS_POINT(self)->x); } static int setx(PygtsPoint *self, PyObject *value, void *closure) { if(PyFloat_Check(value)) { PYGTS_POINT_AS_GTS_POINT(self)->x = PyFloat_AsDouble(value); } else if(PyInt_Check(value)) { PYGTS_POINT_AS_GTS_POINT(self)->x = (gdouble)PyInt_AsLong(value); } else { PyErr_SetString(PyExc_TypeError,"expected a float"); return -1; } return 0; } static PyObject * gety(PygtsPoint *self, void *closure) { SELF_CHECK return Py_BuildValue("d",PYGTS_POINT_AS_GTS_POINT(self)->y); } static int sety(PygtsPoint *self, PyObject *value, void *closure) { if(PyFloat_Check(value)) { PYGTS_POINT_AS_GTS_POINT(self)->y = PyFloat_AsDouble(value); } else if(PyInt_Check(value)) { PYGTS_POINT_AS_GTS_POINT(self)->y = (gdouble)PyInt_AsLong(value); } else { PyErr_SetString(PyExc_TypeError,"expected a float"); return -1; } return 0; } static PyObject * getz(PygtsPoint *self, void *closure) { SELF_CHECK return Py_BuildValue("d",PYGTS_POINT_AS_GTS_POINT(self)->z); } static int setz(PygtsPoint *self, PyObject *value, void *closure) { if(PyFloat_Check(value)) { PYGTS_POINT_AS_GTS_POINT(self)->z = PyFloat_AsDouble(value); } else if(PyInt_Check(value)) { PYGTS_POINT_AS_GTS_POINT(self)->z = (gdouble)PyInt_AsLong(value); } else { PyErr_SetString(PyExc_TypeError,"expected a float"); return -1; } return 0; } /* Methods table */ static PyGetSetDef getset[] = { {"x", (getter)getx, (setter)setx, "x value", NULL}, {"y", (getter)gety, (setter)sety, "y value", NULL}, {"z", (getter)getz, (setter)setz, "z value", NULL}, {NULL} /* Sentinel */ }; /*-------------------------------------------------------------------------*/ /* Python type methods */ static PyObject * new(PyTypeObject *type, PyObject *args, PyObject *kwds) { PyObject *o; PygtsObject *obj; guint alloc_gtsobj = TRUE; /* Parse the args */ if(kwds) { o = PyDict_GetItemString(kwds,"alloc_gtsobj"); if(o==Py_False) { alloc_gtsobj = FALSE; } if(o!=NULL) { PyDict_DelItemString(kwds, "alloc_gtsobj"); } } if(kwds) { Py_INCREF(Py_False); PyDict_SetItemString(kwds,"alloc_gtsobj", Py_False); } /* Chain up */ obj = PYGTS_OBJECT(PygtsObjectType.tp_new(type,args,kwds)); /* Allocate the gtsobj (if needed) */ if( alloc_gtsobj ) { obj->gtsobj = GTS_OBJECT(gts_point_new(gts_point_class(),0,0,0)); if( obj->gtsobj == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Point"); return NULL; } pygts_object_register(obj); } return (PyObject*)obj; } static int init(PygtsPoint *self, PyObject *args, PyObject *kwds) { PygtsObject *obj; gdouble x=0,y=0,z=0; guint a; gint ret; static char *kwlist[] = {"x", "y", "z", "alloc_gtsobj", NULL}; obj = PYGTS_OBJECT(self); /* Parse the args */ if(! PyArg_ParseTupleAndKeywords(args, kwds, "|dddi", kwlist, &x,&y,&z,&a)) { return -1; } /* Initialize */ gts_point_set(GTS_POINT(obj->gtsobj),x,y,z); /* Chain up */ if( (ret=PygtsObjectType.tp_init((PyObject*)self,args,kwds)) != 0 ) { return ret; } return 0; } static int compare(PygtsPoint *p1_, PygtsPoint *p2_) { GtsPoint *p1, *p2; #if PYGTS_DEBUG pygts_point_check((PyObject*)p1_); pygts_point_check((PyObject*)p2_); #endif p1 = PYGTS_POINT_AS_GTS_POINT(p1_); p2 = PYGTS_POINT_AS_GTS_POINT(p2_); return pygts_point_compare(p1,p2); } /* Methods table */ PyTypeObject PygtsPointType = { PyObject_HEAD_INIT(NULL) 0, /* ob_size */ "gts.Point" , /* tp_name */ sizeof(PygtsPoint), /* tp_basicsize */ 0, /* tp_itemsize */ 0, /* tp_dealloc */ 0, /* tp_print */ 0, /* tp_getattr */ 0, /* tp_setattr */ (cmpfunc)compare, /* tp_compare */ 0, /* tp_repr */ 0, /* tp_as_number */ 0, /* tp_as_sequence */ 0, /* tp_as_mapping */ 0, /* tp_hash */ 0, /* tp_call */ 0, /* tp_str */ 0, /* tp_getattro */ 0, /* tp_setattro */ 0, /* tp_as_buffer */ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ "Point object", /* tp_doc */ 0, /* tp_traverse */ 0, /* tp_clear */ 0, /* tp_richcompare */ 0, /* tp_weaklistoffset */ 0, /* tp_iter */ 0, /* tp_iternext */ methods, /* tp_methods */ 0, /* tp_members */ getset, /* tp_getset */ 0, /* tp_base: attached in pygts.c */ 0, /* tp_dict */ 0, /* tp_descr_get */ 0, /* tp_descr_set */ 0, /* tp_dictoffset */ (initproc)init, /* tp_init */ 0, /* tp_alloc */ (newfunc)new /* tp_new */ }; /*-------------------------------------------------------------------------*/ /* Pygts functions */ gboolean pygts_point_check(PyObject* o) { gboolean check = FALSE; guint i,N; PyObject *obj; /* Check for a Point */ if( PyObject_TypeCheck(o, &PygtsPointType) ) { check = TRUE; } /* Convert list into tuple */ if(PyList_Check(o)) { o = PyList_AsTuple(o); } else { Py_INCREF(o); } /* Check for a tuple of floats */ if( PyTuple_Check(o) ) { if( (N = PyTuple_Size(o)) <= 3 ) { check = TRUE; for(i=0;igtsobj = GTS_OBJECT(p); /* Register and return */ pygts_object_register(point); return PYGTS_POINT(point); } PygtsPoint * pygts_point_from_sequence(PyObject *tuple) { guint i,N; gdouble x=0,y=0,z=0; PyObject *obj; GtsPoint *p; PygtsPoint *point; /* Convert list into tuple */ if(PyList_Check(tuple)) { tuple = PyList_AsTuple(tuple); } else { Py_INCREF(tuple); } if(!PyTuple_Check(tuple)) { Py_DECREF(tuple); PyErr_SetString(PyExc_TypeError,"expected a list or tuple of vertices"); return NULL; } /* Get the tuple size */ if( (N = PyTuple_Size(tuple)) > 3 ) { PyErr_SetString(PyExc_RuntimeError, "expected a list or tuple of up to three floats"); Py_DECREF(tuple); return NULL; } /* Get the coordinates */ for(i=0;ix==p2->x) && (p1->y==p2->y) && (p1->z==p2->z) ) { return 0; } /* Compare distances from origin */ r1 = sqrt(pow(p1->x,2) + pow(p1->y,2) + pow(p1->z,2)); r2 = sqrt(pow(p2->x,2) + pow(p2->y,2) + pow(p2->z,2)); if(r1r2) return 1; /* Compare horizontal distances from origin */ r1 = sqrt(pow(p1->x,2) + pow(p1->y,2)); r2 = sqrt(pow(p2->x,2) + pow(p2->y,2)); if(r1r2) return 1; /* Compare x */ r1 = p1->x; r2 = p2->x; if(r1r2) return 1; /* Compare y */ r1 = p1->y; r2 = p2->y; if(r1r2) return 1; /* Compare z */ r1 = p1->z; r2 = p2->z; if(r1 * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ #ifndef __PYGTS_POINT_H__ #define __PYGTS_POINT_H__ typedef struct _PygtsObject PygtsPoint; #define PYGTS_POINT(o) ( PyObject_TypeCheck((PyObject*)o, &PygtsPointType) ? \ (PygtsPoint*)o : \ pygts_point_from_sequence((PyObject*)o) ) #define PYGTS_POINT_AS_GTS_POINT(o) (GTS_POINT(PYGTS_OBJECT(o)->gtsobj)) extern PyTypeObject PygtsPointType; gboolean pygts_point_check(PyObject* o); gboolean pygts_point_is_ok(PygtsPoint *o); PygtsPoint* pygts_point_from_sequence(PyObject *tuple); int pygts_point_compare(GtsPoint* p1,GtsPoint* p2); gint pygts_point_rotate(GtsPoint* p,gdouble dx,gdouble dy,gdouble dz,gdouble a); gint pygts_point_scale(GtsPoint* p, gdouble dx, gdouble dy, gdouble dz); gint pygts_point_translate(GtsPoint* p, gdouble dx, gdouble dy, gdouble dz); #endif /* __PYGTS_POINT_H__ */ trunk-2017.01a/py/3rd-party/pygts-0.3.1/pygts.c000066400000000000000000000505301304022710500205570ustar00rootroot00000000000000/* pygts - python package for the manipulation of triangulated surfaces * * Copyright (C) 2009 Thomas J. Duck * All rights reserved. * * Thomas J. Duck * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ #include "pygts.h" #if PYGTS_HAS_NUMPY #include "numpy/arrayobject.h" #endif static PyObject* merge(PyObject *self, PyObject *args) { PyObject *tuple, *obj; guint i,N; GList *vertices=NULL,*v; gdouble epsilon; PygtsVertex *vertex; /* Parse the args */ if(! PyArg_ParseTuple(args, "Od", &tuple, &epsilon) ) { return NULL; } if(PyList_Check(tuple)) { tuple = PyList_AsTuple(tuple); } else { Py_INCREF(tuple); } if(!PyTuple_Check(tuple)) { Py_DECREF(tuple); PyErr_SetString(PyExc_TypeError,"expected a list or tuple of vertices"); return NULL; } /* Assemble the GList */ N = PyTuple_Size(tuple); for(i=N-1;i>0;i--) { obj = PyTuple_GET_ITEM(tuple,i); if(!pygts_vertex_check(obj)) { Py_DECREF(tuple); g_list_free(vertices); PyErr_SetString(PyExc_TypeError,"expected a list or tuple of vertices"); return NULL; } vertices = g_list_prepend(vertices,PYGTS_VERTEX_AS_GTS_VERTEX(obj)); } Py_DECREF(tuple); /* Make the call */ vertices = pygts_vertices_merge(vertices,epsilon,NULL); /* Assemble the return tuple */ N = g_list_length(vertices); if( (tuple=PyTuple_New(N)) == NULL) { PyErr_SetString(PyExc_MemoryError,"could not create tuple"); return NULL; } v = vertices; for(i=0;idata)) )) ==NULL ) { PyErr_SetString(PyExc_RuntimeError, "could not get object from table (internal error)"); g_list_free(vertices); return NULL; } Py_INCREF(vertex); PyTuple_SET_ITEM(tuple,i,(PyObject*)vertex); v = g_list_next(v); } g_list_free(vertices); return tuple; } static PyObject* vertices(PyObject *self, PyObject *args) { PyObject *tuple, *obj; guint i,N; GSList *segments=NULL,*vertices=NULL,*v; PygtsVertex *vertex; /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &tuple) ) { return NULL; } if(PyList_Check(tuple)) { tuple = PyList_AsTuple(tuple); } else { Py_INCREF(tuple); } if(!PyTuple_Check(tuple)) { Py_DECREF(tuple); PyErr_SetString(PyExc_TypeError,"expected a list or tuple of Segments"); return NULL; } /* Assemble the GSList */ N = PyTuple_Size(tuple); for(i=0;idata))) == NULL ) { Py_DECREF(tuple); g_slist_free(vertices); return NULL; } PyTuple_SET_ITEM(tuple,i,(PyObject*)vertex); v = g_slist_next(v); } g_slist_free(vertices); return tuple; } static PyObject* segments(PyObject *self, PyObject *args) { PyObject *tuple, *obj; guint i,n,N; GSList *segments=NULL,*vertices=NULL,*s; PygtsSegment *segment; /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &tuple) ) { return NULL; } if(PyList_Check(tuple)) { tuple = PyList_AsTuple(tuple); } else { Py_INCREF(tuple); } if(!PyTuple_Check(tuple)) { Py_DECREF(tuple); PyErr_SetString(PyExc_TypeError,"expected a list or tuple of vertices"); return NULL; } /* Assemble the GSList */ N = PyTuple_Size(tuple); for(i=0;idata) || PYGTS_IS_PARENT_EDGE(s->data)) { s = g_slist_next(s); segment = NULL; continue; } /* Fill in the tuple */ if(GTS_IS_EDGE(s->data)) { segment = PYGTS_SEGMENT(pygts_edge_new(GTS_EDGE(s->data))); } else { segment = pygts_segment_new(GTS_SEGMENT(s->data)); } if( segment == NULL ) { Py_DECREF(tuple); g_slist_free(segments); return NULL; } PyTuple_SET_ITEM(tuple,n,(PyObject*)segment); s = g_slist_next(s); n += 1; } g_slist_free(segments); if(_PyTuple_Resize(&tuple,n)!=0) { Py_DECREF(tuple); return NULL; } return tuple; } static PyObject* triangles(PyObject *self, PyObject *args) { PyObject *tuple, *obj; guint i,n,N; GSList *edges=NULL,*triangles=NULL,*t; PygtsTriangle *triangle; /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &tuple) ) { return NULL; } if(PyList_Check(tuple)) { tuple = PyList_AsTuple(tuple); } else { Py_INCREF(tuple); } if(!PyTuple_Check(tuple)) { Py_DECREF(tuple); PyErr_SetString(PyExc_TypeError,"expected a list or tuple of edges"); return NULL; } /* Assemble the GSList */ N = PyTuple_Size(tuple); for(i=0;idata)) { t = g_slist_next(t); triangle = NULL; continue; } /* Fill in the tuple */ if(GTS_IS_FACE(t->data)) { triangle = PYGTS_TRIANGLE(pygts_face_new(GTS_FACE(t->data))); } else { triangle = pygts_triangle_new(GTS_TRIANGLE(t->data)); } if( triangle == NULL ) { Py_DECREF(tuple); g_slist_free(triangles); return NULL; } PyTuple_SET_ITEM(tuple,n,(PyObject*)triangle); t = g_slist_next(t); n += 1; } g_slist_free(triangles); if(_PyTuple_Resize(&tuple,n)!=0) { Py_DECREF(tuple); return NULL; } return tuple; } static PyObject* triangle_enclosing(PyObject *self, PyObject *args) { PyObject *tuple, *obj; guint i,N; GSList *points=NULL; GtsTriangle *t; PygtsTriangle *triangle; /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &tuple) ) { return NULL; } if(PyList_Check(tuple)) { tuple = PyList_AsTuple(tuple); } else { Py_INCREF(tuple); } if(!PyTuple_Check(tuple)) { Py_DECREF(tuple); PyErr_SetString(PyExc_TypeError,"expected a list or tuple of points"); return NULL; } /* Assemble the GSList */ N = PyTuple_Size(tuple); for(i=0;ierror); gts_file_destroy(fp); return NULL; } gts_file_destroy(fp); if( (surface = pygts_surface_new(s)) == NULL ) { gts_object_destroy(GTS_OBJECT(s)); return NULL; } /* Clean up the surface */ pygts_edge_cleanup(PYGTS_SURFACE_AS_GTS_SURFACE(surface)); pygts_face_cleanup(PYGTS_SURFACE_AS_GTS_SURFACE(surface)); return (PyObject*)surface; } static PyObject* sphere(PyObject *self, PyObject *args) { PyObject *kwds; PygtsSurface *surface; guint geodesation_order; /* Parse the args */ if(! PyArg_ParseTuple(args, "i", &geodesation_order) ) return NULL; /* Chain up object allocation */ args = Py_BuildValue("()"); kwds = Py_BuildValue("{s:O}","alloc_gtsobj",Py_True); surface = PYGTS_SURFACE(PygtsSurfaceType.tp_new(&PygtsSurfaceType, args, kwds)); Py_DECREF(args); Py_DECREF(kwds); if( surface == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Surface"); return NULL; } gts_surface_generate_sphere(PYGTS_SURFACE_AS_GTS_SURFACE(surface), geodesation_order); pygts_object_register(PYGTS_OBJECT(surface)); return (PyObject*)surface; } #if PYGTS_HAS_NUMPY /* Helper for pygts_iso to fill f with a layer of data from scalar */ static void isofunc(gdouble **f, GtsCartesianGrid g, guint k, gpointer data) { PyArrayObject *scalars = (PyArrayObject *)data; int i, j; for (i = 0; i < scalars->dimensions[0]; i++) { for (j = 0; j < scalars->dimensions[1]; j++) { f[i][j] = *(gdouble *)(scalars->data + i*scalars->strides[0] + \ j*scalars->strides[1] + k*scalars->strides[2]); } } } #define ISO_CLEANUP \ if (scalars) { Py_DECREF(scalars); } \ if (extents) { Py_DECREF(extents); } static PyObject* isosurface(PyObject *self, PyObject *args, PyObject *kwds) { double isoval[1]; PyObject *Oscalars = NULL, *Oextents = NULL; PyArrayObject *scalars = NULL, *extents = NULL; GtsCartesianGrid g; GtsSurface *s; PygtsSurface *surface; char *method = "cubes"; static char *kwlist[] = {"scalars", "isoval", "method", "extents", NULL}; if(!PyArg_ParseTupleAndKeywords(args, kwds, "Od|sO", kwlist, &Oscalars, isoval, &method, &Oextents)) { return NULL; } if(!(scalars = (PyArrayObject *) PyArray_ContiguousFromObject(Oscalars, PyArray_DOUBLE, 3, 3))) { ISO_CLEANUP; return NULL; } if(Oextents && (!(extents = (PyArrayObject *) PyArray_ContiguousFromObject(Oextents, PyArray_DOUBLE, 1, 1)))) { ISO_CLEANUP; return NULL; } if(extents && extents->dimensions[0] < 6) { PyErr_SetString(PyExc_ValueError, "extents must have at least 6 elements"); ISO_CLEANUP; return NULL; } if(extents) { int s = extents->strides[0]; g.x = *(gdouble*)(extents->data + 0*s); g.nx = scalars->dimensions[0]; g.dx = (*(gdouble*)(extents->data + 1*s) - \ *(gdouble*)(extents->data + 0* s))/(g.nx-1); g.y = *(gdouble*)(extents->data + 2*s); g.ny = scalars->dimensions[1]; g.dy = (*(gdouble*)(extents->data + 3*s) - \ *(gdouble*)(extents->data + 2*s))/(g.ny-1); g.z = *(gdouble*)(extents->data + 4*s); g.nz = scalars->dimensions[2]; g.dz = (*(gdouble*)(extents->data + 5*s) - \ *(gdouble*)(extents->data + 4*s))/(g.nz-1); } else { g.x = -1.0; g.nx = scalars->dimensions[0]; g.dx = 2.0/(scalars->dimensions[0]-1); g.y = -1.0; g.ny = scalars->dimensions[1]; g.dy = 2.0/(scalars->dimensions[1]-1); g.z = -1.0; g.nz = scalars->dimensions[2]; g.dz = 2.0/(scalars->dimensions[2]-1); } /* Create the surface */ if((s = gts_surface_new(gts_surface_class(), gts_face_class(), gts_edge_class(), gts_vertex_class())) == NULL ) { PyErr_SetString(PyExc_MemoryError,"could not create Surface"); return NULL; } /* Make the call */ switch(method[0]) { case 'c': /* cubes */ gts_isosurface_cartesian(s, g, isofunc, scalars, isoval[0]); break; case 't': /* tetra */ gts_isosurface_tetra(s, g, isofunc, scalars, isoval[0]); /* *** ATTENTION *** * Isosurface produced is "inside-out", and so we must revert it. * This is a bug in GTS. */ gts_surface_foreach_face(s, (GtsFunc)gts_triangle_revert, NULL); /* *** ATTENTION *** */ break; case 'b': /* tetra bounded */ gts_isosurface_tetra_bounded(s, g, isofunc, scalars, isoval[0]); /* *** ATTENTION *** * Isosurface produced is "inside-out", and so we must revert it. * This is a bug in GTS. */ gts_surface_foreach_face(s, (GtsFunc)gts_triangle_revert, NULL); /* *** ATTENTION *** */ break; case 'd': /* tetra bcl*/ gts_isosurface_tetra_bcl(s, g, isofunc, scalars, isoval[0]); /* *** ATTENTION *** * Isosurface produced is "inside-out", and so we must revert it. * This is a bug in GTS. */ gts_surface_foreach_face(s, (GtsFunc)gts_triangle_revert, NULL); /* *** ATTENTION *** */ break; default: PyErr_SetString(PyExc_ValueError, "unknown method"); ISO_CLEANUP; return NULL; } ISO_CLEANUP; if( (surface = pygts_surface_new(s)) == NULL ) { gts_object_destroy(GTS_OBJECT(s)); return NULL; } return (PyObject*)surface; } #endif /* PYGTS_HAS_NUMPY */ static PyMethodDef gts_methods[] = { {"read", (PyCFunction)pygts_read, METH_VARARGS, "Returns the data read from File f as a Surface.\n" "The File data must be in GTS format (e.g., as written using\n" "Surface.write())\n" "\n" "Signature: read(f)\n" }, { "sphere", sphere, METH_VARARGS, "Returns a unit sphere generated by recursive subdivision.\n" "First approximation is an isocahedron; each level of refinement\n" "(geodesation_order) increases the number of triangles by a factor\n" "of 4.\n" "\n" "Signature: sphere(geodesation_order)\n" }, #if PYGTS_HAS_NUMPY {"isosurface", (PyCFunction)isosurface, METH_VARARGS|METH_KEYWORDS, "Adds to surface new faces defining the isosurface data[x,y,z] = c\n" "\n" "Signature: isosurface(data, c, ...)\n" "\n" "data is a 3D numpy array.\n" "c is the isovalue defining the surface\n" "\n" "Keyword arguments:\n" "extents= [xmin, xmax, ymin, ymax, zmin, zmax]\n" " A numpy array defining the extent of the data cube.\n" " Default is the cube with corners at (-1,-1,-1) and (1,1,1)\n" " Data is assumed to be regularly sampled in the cube.\n" "method= ['cube'|'tetra'|'dual'|'bounded']\n" " String (only the first character counts) specifying the\n" " method.\n" " cube -- marching cubes (default)\n" " tetra -- marching tetrahedra\n" " dual -- maching tetrahedra producing dual 'body-centred'\n" " faces relative to 'tetra'\n" " bounded -- marching tetrahedra ensuring the surface is\n" " bounded by adding a border of large negative\n" " values around the domain.\n" "\n" "By convention, the normals to the surface are pointing towards\n" "positive values of data[x,y,z] - c.\n" }, #endif /* PYGTS_HAS_NUMPY */ { "merge", merge, METH_VARARGS, "Merges list of Vertices that are within a box of side-length\n" "epsilon of each other.\n" "\n" "Signature: merge(list,epsilon)\n" }, { "vertices", vertices, METH_VARARGS, "Returns tuple of Vertices from a list or tuple of Segments.\n" "\n" "Signature: vertices(list)\n" }, { "segments", segments, METH_VARARGS, "Returns tuple of Segments from a list or tuple of Vertices.\n" "\n" "Signature: segments(list)\n" }, { "triangles", triangles, METH_VARARGS, "Returns tuple of Triangles from a list or tuple of Edges.\n" "\n" "Signature: triangles(list)\n" }, { "triangle_enclosing", triangle_enclosing, METH_VARARGS, "Returns a Triangle that encloses the plane projection of a list\n" "or tuple of Points. The Triangle is equilateral and encloses a\n" "rectangle defined by the maximum and minimum x and y coordinates\n" "of the points.\n" "\n" "Signature: triangles(list)\n" }, {NULL} /* Sentinel */ }; #ifndef PyMODINIT_FUNC /* declarations for DLL import/export */ #define PyMODINIT_FUNC void #endif PyMODINIT_FUNC init_gts(void) { PyObject* m; /* Allocate the object table */ if( (obj_table=g_hash_table_new(NULL,NULL)) == NULL ) return; /* Set class base types and make ready (i.e., inherit methods) */ if (PyType_Ready(&PygtsObjectType) < 0) return; PygtsPointType.tp_base = &PygtsObjectType; if (PyType_Ready(&PygtsPointType) < 0) return; PygtsVertexType.tp_base = &PygtsPointType; if (PyType_Ready(&PygtsVertexType) < 0) return; PygtsSegmentType.tp_base = &PygtsObjectType; if (PyType_Ready(&PygtsSegmentType) < 0) return; PygtsEdgeType.tp_base = &PygtsSegmentType; if (PyType_Ready(&PygtsEdgeType) < 0) return; PygtsTriangleType.tp_base = &PygtsObjectType; if (PyType_Ready(&PygtsTriangleType) < 0) return; PygtsFaceType.tp_base = &PygtsTriangleType; if (PyType_Ready(&PygtsFaceType) < 0) return; PygtsSurfaceType.tp_base = &PygtsObjectType; if (PyType_Ready(&PygtsSurfaceType) < 0) return; /* Initialize the module */ m = Py_InitModule3("_gts", gts_methods,"Gnu Triangulated Surface Library"); if (m == NULL) return; /* Add new types to python */ Py_INCREF(&PygtsObjectType); PyModule_AddObject(m, "Object", (PyObject *)&PygtsObjectType); Py_INCREF(&PygtsPointType); PyModule_AddObject(m, "Point", (PyObject *)&PygtsPointType); Py_INCREF(&PygtsVertexType); PyModule_AddObject(m, "Vertex", (PyObject *)&PygtsVertexType); Py_INCREF(&PygtsSegmentType); PyModule_AddObject(m, "Segment", (PyObject *)&PygtsSegmentType); Py_INCREF(&PygtsEdgeType); PyModule_AddObject(m, "Edge", (PyObject *)&PygtsEdgeType); Py_INCREF(&PygtsTriangleType); PyModule_AddObject(m, "Triangle", (PyObject *)&PygtsTriangleType); Py_INCREF(&PygtsFaceType); PyModule_AddObject(m, "Face", (PyObject *)&PygtsFaceType); Py_INCREF(&PygtsSurfaceType); PyModule_AddObject(m, "Surface", (PyObject *)&PygtsSurfaceType); } trunk-2017.01a/py/3rd-party/pygts-0.3.1/pygts.h000066400000000000000000000031601304022710500205610ustar00rootroot00000000000000/* pygts - python package for the manipulation of triangulated surfaces * * Copyright (C) 2009 Thomas J. Duck * All rights reserved. * * Thomas J. Duck * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ #ifndef __PYGTS_H__ #define __PYGTS_H__ #ifndef PYGTS_DEBUG #define PYGTS_DEBUG 1 #endif /* PYGTS_DEBUG */ #include #include #include #include #include /* Defined for arrayobject.h which is only included where needed */ #define PY_ARRAY_UNIQUE_SYMBOL PYGTS #include #include #include "object.h" #include "point.h" #include "vertex.h" #include "segment.h" #include "edge.h" #include "triangle.h" #include "face.h" #include "surface.h" #include "cleanup.h" #endif /* __PYGTS_H__ */ trunk-2017.01a/py/3rd-party/pygts-0.3.1/pygts.py000066400000000000000000000106271304022710500207700ustar00rootroot00000000000000# pygts - python package for the manipulation of triangulated surfaces # # Copyright (C) 2009 Thomas J. Duck # All rights reserved. # # Thomas J. Duck # Department of Physics and Atmospheric Science, # Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 # # NOTICE # # This library is free software; you can redistribute it and/or # modify it under the terms of the GNU Library General Public # License as published by the Free Software Foundation; either # version 2 of the License, or (at your option) any later version. # # This library is distributed in the hope that it will be useful, # but WITHOUT ANY WARRANTY; without even the implied warranty of # MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU # Library General Public License for more details. # # You should have received a copy of the GNU Library General Public # License along with this library; if not, write to the # Free Software Foundation, Inc., 59 Temple Place - Suite 330, # Boston, MA 02111-1307, USA. # added by eudoxos 29.1.2011, fixes https://bugs.launchpad.net/yade/+bug/668329 ## force decimal separator to be always . (decimal point), not , (decimal comma) -- unless LC_ALL is set, then we are stuck ## this was reason for bogus gts imports ## adding to yade main does not solve the problem for some reason import locale locale.setlocale(locale.LC_NUMERIC,'C') from _gts import * def get_coords_and_face_indices(s,unzip=False): """Returns the coordinates and face indices of Surface s. If unzip is True then four tuples are returned. The first three are the x, y, and z coordinates for each Vertex on the Surface. The last is a list of tuples, one for each Face on the Surface, containing 3 indices linking the Face Vertices to the coordinate lists. If unzip is False then the coordinates are given in a single list of 3-tuples. """ vertices = s.vertices() coords = [v.coords() for v in vertices] face_indices = s.face_indices(vertices) if unzip: x,y,z = zip(*coords) return x,y,z,face_indices else: return vertices, coords def cube(): """Returns a cube of side length 2 centered at the origin.""" # # v8 +------+ v5 # / /| # / v1/ | # v4 +------+ | # | | + v6 # |(v7) | / # | |/ # v3 +------+ v2 # v1,v2,v3,v4=Vertex(1,1,1),Vertex(1,1,-1),Vertex(1,-1,-1),Vertex(1,-1,1) v5,v6,v7,v8=Vertex(-1,1,1),Vertex(-1,1,-1),Vertex(-1,-1,-1),Vertex(-1,-1,1) e12,e23,e34,e14 = Edge(v1,v2), Edge(v2,v3), Edge(v3,v4), Edge(v4,v1) e56,e67,e78,e58 = Edge(v5,v6), Edge(v6,v7), Edge(v7,v8), Edge(v8,v5) e15,e26,e37,e48 = Edge(v1,v5), Edge(v2,v6), Edge(v3,v7), Edge(v4,v8) e13,e16,e18 = Edge(v1,v3), Edge(v1,v6), Edge(v1,v8) e27,e47,e57 = Edge(v7,v2), Edge(v7,v4), Edge(v7,v5) faces = [ Face(e12,e23,e13), Face(e13,e34,e14), Face(e12,e26,e16), Face(e15,e56,e16), Face(e15,e58,e18), Face(e14,e48,e18), Face(e58,e78,e57), Face(e56,e67,e57), Face(e26,e67,e27), Face(e37,e23,e27), Face(e37,e47,e34), Face(e78,e48,e47) ] faces[0].revert() # Set the orientation of the first face s = Surface() for face in faces: if not face.is_compatible(s): face.revert() s.add(face) return s def tetrahedron(): """Returns a tetrahedron of side length 2*sqrt(2) centered at origin. The edges of the tetrahedron are perpendicular to the cardinal directions. """ # v4 # + # | \ e6 # e5 '|e4 \ # v1 . +-e3-+ v3 # / . # ./e1. e2 # / . # + # v2 # Create vertices v1 = Vertex(1,1,1) v2 = Vertex(-1,-1,1) v3 = Vertex(-1,1,-1) v4 = Vertex(1,-1,-1) # Create edges e1 = Edge(v1,v2) e2 = Edge(v2,v3) e3 = Edge(v3,v1) e4 = Edge(v1,v4) e5 = Edge(v4,v2) e6 = Edge(v4,v3) # Create faces f1 = Face(e1,e2,e3) # Bottom face f2 = Face(e1,e4,e5) # Left face f3 = Face(e2,e5,e6) # Right face f4 = Face(e3,e4,e6) # Back face # Set orientation of first face f1.revert() # Assemble surface s = Surface() for face in [f1,f2,f3,f4]: if not face.is_compatible(s): face.revert() s.add(face) return s trunk-2017.01a/py/3rd-party/pygts-0.3.1/segment.c000066400000000000000000000335441304022710500210610ustar00rootroot00000000000000/* pygts - python segment for the manipulation of triangulated surfaces * * Copyright (C) 2009 Thomas J. Duck * All rights reserved. * * Thomas J. Duck * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ #include "pygts.h" #if PYGTS_DEBUG #define SELF_CHECK if(!pygts_segment_check((PyObject*)self)) { \ PyErr_SetString(PyExc_RuntimeError, \ "problem with self object (internal error)"); \ return NULL; \ } #else #define SELF_CHECK #endif /*-------------------------------------------------------------------------*/ /* Methods exported to python */ static PyObject* is_ok(PygtsSegment *self, PyObject *args) { if(pygts_segment_is_ok(self)) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* intersects(PygtsSegment *self, PyObject *args) { PyObject *s_; GtsSegment *s; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &s_) ) { return NULL; } /* Convert to PygtsObjects */ if(!pygts_segment_check(s_)) { PyErr_SetString(PyExc_TypeError,"expected a Segment"); return NULL; } s = PYGTS_SEGMENT_AS_GTS_SEGMENT(s_); return Py_BuildValue("i", gts_segments_are_intersecting(PYGTS_SEGMENT_AS_GTS_SEGMENT(self),s)); } static PyObject* connects(PygtsSegment *self, PyObject *args) { PyObject *v1_,*v2_; GtsVertex *v1,*v2; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "OO", &v1_, &v2_) ) { return NULL; } /* Convert to PygtsObjects */ if(!pygts_vertex_check(v1_)) { PyErr_SetString(PyExc_TypeError,"expected a Vertex"); return NULL; } v1 = PYGTS_VERTEX_AS_GTS_VERTEX(v1_); if(!pygts_vertex_check(v2_)) { PyErr_SetString(PyExc_TypeError,"expected a Vertex"); return NULL; } v2 = PYGTS_VERTEX_AS_GTS_VERTEX(v2_); if(gts_segment_connect(PYGTS_SEGMENT_AS_GTS_SEGMENT(self),v1,v2)) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* touches(PygtsSegment *self, PyObject *args) { PyObject *s_; GtsSegment *s; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &s_) ) { return NULL; } /* Convert to PygtsObjects */ if(!pygts_segment_check(s_)) { PyErr_SetString(PyExc_TypeError,"expected a Segment"); return NULL; } s = PYGTS_SEGMENT_AS_GTS_SEGMENT(s_); if(gts_segments_touch(PYGTS_SEGMENT_AS_GTS_SEGMENT(self),s)) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* midvertex(PygtsSegment *self, PyObject *args) { PygtsVertex *vertex; GtsVertex *v; SELF_CHECK v = gts_segment_midvertex(PYGTS_SEGMENT_AS_GTS_SEGMENT(self), gts_vertex_class()); if( (vertex = pygts_vertex_new(v)) == NULL ) { return NULL; } return (PyObject*)vertex; } static PyObject* intersection(PygtsSegment *self, PyObject *args) { PyObject *t_,*boundary_=NULL; PygtsTriangle *t; gboolean boundary=TRUE; GtsVertex *v; PygtsObject *vertex; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O|O", &t_, &boundary_) ) { return NULL; } /* Convert to PygtsObjects */ if(!pygts_triangle_check(t_)) { PyErr_SetString(PyExc_TypeError,"expected a Triangle and boolean"); return NULL; } t = PYGTS_TRIANGLE(t_); if( boundary_ != NULL ) { if(PyBool_Check(boundary_)==FALSE) { PyErr_SetString(PyExc_TypeError,"expected a Triangle and boolean"); return NULL; } if( boundary_ == Py_False ){ /* Default TRUE */ boundary = FALSE; } } v = GTS_VERTEX( gts_segment_triangle_intersection( PYGTS_SEGMENT_AS_GTS_SEGMENT(self), PYGTS_TRIANGLE_AS_GTS_TRIANGLE(t), boundary, GTS_POINT_CLASS(gts_vertex_class())) ); if( v == NULL ) { Py_INCREF(Py_None); return Py_None; } if( (vertex = pygts_vertex_new(v)) == NULL ) { return NULL; } return (PyObject *)vertex; } /* Methods table */ static PyMethodDef methods[] = { {"is_ok", (PyCFunction)is_ok, METH_NOARGS, "True if this Segment s is not degenerate or duplicate.\n" "False otherwise. Degeneracy implies s.v1.id == s.v2.id.\n" "\n" "Signature: s.is_ok().\n" }, {"intersects", (PyCFunction)intersects, METH_VARARGS, "Checks if this Segment s1 intersects with Segment s2.\n" "Returns 1 if they intersect, 0 if an endpoint of one Segment lies\n" "on the other Segment, -1 otherwise\n" "\n" "Signature: s1.intersects(s2).\n" }, {"connects", (PyCFunction)connects, METH_VARARGS, "Returns True if this Segment s1 connects Vertices v1 and v2.\n" "False otherwise.\n" "\n" "Signature: s1.connects(v1,v2).\n" }, {"touches", (PyCFunction)touches, METH_VARARGS, "Returns True if this Segment s1 touches Segment s2\n" "(i.e., they share a common Vertex). False otherwise.\n" "\n" "Signature: s1.touches(s2).\n" }, {"midvertex", (PyCFunction)midvertex, METH_NOARGS, "Returns a new Vertex at the mid-point of this Segment s.\n" "\n" "Signature: s.midvertex().\n" }, {"intersection", (PyCFunction)intersection, METH_VARARGS, "Returns the intersection of Segment s with Triangle t\n" "\n" "This function is geometrically robust in the sense that it will\n" "return None if s and t do not intersect and will return a\n" "Vertex if they do. However, the point coordinates are subject\n" "to round-off errors. None will be returned if s is contained\n" "in the plane defined by t.\n" "\n" "Signature: s.intersection(t) or s.intersection(t,boundary).\n" "\n" "If boundary is True (default), the boundary of s is taken into\n" "account.\n" "\n" "Returns a summit of t (if boundary is True), one of the endpoints\n" "of s, a new Vertex at the intersection of s with t, or None if\n" "s and t don't intersect.\n" }, {NULL} /* Sentinel */ }; /*-------------------------------------------------------------------------*/ /* Attributes exported to python */ static PyObject * get_v1(PygtsSegment *self, void *closure) { PygtsObject *v1; SELF_CHECK if( (v1=pygts_vertex_new(PYGTS_SEGMENT_AS_GTS_SEGMENT(self)->v1)) == NULL ) { return NULL; } return (PyObject *)v1; } static PyObject * get_v2(PygtsSegment *self, void *closure) { PygtsObject *v2; SELF_CHECK if( (v2=pygts_vertex_new(PYGTS_SEGMENT_AS_GTS_SEGMENT(self)->v2)) == NULL ) { return NULL; } return (PyObject *)v2; } /* Methods table */ static PyGetSetDef getset[] = { {"v1", (getter)get_v1, NULL, "Vertex 1", NULL}, {"v2", (getter)get_v2, NULL, "Vertex 2", NULL}, {NULL} /* Sentinel */ }; /*-------------------------------------------------------------------------*/ /* Python type methods */ static PyObject * new(PyTypeObject *type, PyObject *args, PyObject *kwds) { PyObject *o; PygtsObject *obj; GtsSegment *tmp; GtsObject *segment=NULL; PyObject *v1_=NULL,*v2_=NULL; PygtsVertex *v1,*v2; guint alloc_gtsobj = TRUE; guint N; /* Parse the args */ if(kwds) { o = PyDict_GetItemString(kwds,"alloc_gtsobj"); if(o==Py_False) { alloc_gtsobj = FALSE; } if(o!=NULL) { PyDict_DelItemString(kwds, "alloc_gtsobj"); } } if(kwds) { Py_INCREF(Py_False); PyDict_SetItemString(kwds,"alloc_gtsobj", Py_False); } /* Allocate the gtsobj (if needed) */ if( alloc_gtsobj ) { /* Parse the args */ if( (N = PyTuple_Size(args)) < 2 ) { PyErr_SetString(PyExc_TypeError,"expected two Vertices"); return NULL; } v1_ = PyTuple_GET_ITEM(args,0); v2_ = PyTuple_GET_ITEM(args,1); /* Convert to PygtsObjects */ if(!pygts_vertex_check(v1_)) { PyErr_SetString(PyExc_TypeError,"expected two Vertices"); return NULL; } if(!pygts_vertex_check(v2_)) { PyErr_SetString(PyExc_TypeError,"expected two Vertices"); return NULL; } v1 = PYGTS_VERTEX(v1_); v2 = PYGTS_VERTEX(v2_); /* Error check */ if(PYGTS_OBJECT(v1)->gtsobj == PYGTS_OBJECT(v2)->gtsobj) { PyErr_SetString(PyExc_ValueError,"Vertices are identical"); return NULL; } /* Create the GtsSegment */ segment = GTS_OBJECT(gts_segment_new(gts_segment_class(), GTS_VERTEX(v1->gtsobj), GTS_VERTEX(v2->gtsobj))); if( segment == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Segment"); return NULL; } /* Check for duplicate */ tmp = gts_segment_is_duplicate(GTS_SEGMENT(segment)); if( tmp != NULL ) { gts_object_destroy(segment); segment = GTS_OBJECT(tmp); } /* If corresponding PyObject found in object table, we are done */ if( (obj=g_hash_table_lookup(obj_table,segment)) != NULL ) { Py_INCREF(obj); return (PyObject*)obj; } } /* Chain up */ obj = PYGTS_OBJECT(PygtsObjectType.tp_new(type,args,kwds)); if( alloc_gtsobj ) { obj->gtsobj = segment; pygts_object_register(PYGTS_OBJECT(obj)); } return (PyObject*)obj; } static int init(PygtsSegment *self, PyObject *args, PyObject *kwds) { gint ret; /* Chain up */ if( (ret=PygtsObjectType.tp_init((PyObject*)self,args,kwds)) != 0 ){ return ret; } return 0; } static int compare(PygtsSegment *s1_, PygtsSegment *s2_) { GtsSegment *s1, *s2; #if PYGTS_DEBUG pygts_segment_check((PyObject*)s1_); pygts_segment_check((PyObject*)s2_); #endif s1 = PYGTS_SEGMENT_AS_GTS_SEGMENT(s1_); s2 = PYGTS_SEGMENT_AS_GTS_SEGMENT(s2_); return pygts_segment_compare(s1,s2); } /* Methods table */ PyTypeObject PygtsSegmentType = { PyObject_HEAD_INIT(NULL) 0, /* ob_size */ "gts.Segment", /* tp_name */ sizeof(PygtsSegment), /* tp_basicsize */ 0, /* tp_itemsize */ 0, /* tp_dealloc */ 0, /* tp_print */ 0, /* tp_getattr */ 0, /* tp_setattr */ (cmpfunc)compare, /* tp_compare */ 0, /* tp_repr */ 0, /* tp_as_number */ 0, /* tp_as_sequence */ 0, /* tp_as_mapping */ 0, /* tp_hash */ 0, /* tp_call */ 0, /* tp_str */ 0, /* tp_getattro */ 0, /* tp_setattro */ 0, /* tp_as_buffer */ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ "Segment object", /* tp_doc */ 0, /* tp_traverse */ 0, /* tp_clear */ 0, /* tp_richcompare */ 0, /* tp_weaklistoffset */ 0, /* tp_iter */ 0, /* tp_iternext */ methods, /* tp_methods */ 0, /* tp_members */ getset, /* tp_getset */ 0, /* tp_base */ 0, /* tp_dict */ 0, /* tp_descr_get */ 0, /* tp_descr_set */ 0, /* tp_dictoffset */ (initproc)init, /* tp_init */ 0, /* tp_alloc */ (newfunc)new /* tp_new */ }; /*-------------------------------------------------------------------------*/ /* Pygts functions */ gboolean pygts_segment_check(PyObject* o) { if(! PyObject_TypeCheck(o, &PygtsSegmentType)) { return FALSE; } else { #if PYGTS_DEBUG return pygts_segment_is_ok(PYGTS_SEGMENT(o)); #else return TRUE; #endif } } gboolean pygts_segment_is_ok(PygtsSegment *s) { if(!pygts_object_is_ok(PYGTS_OBJECT(s))) return FALSE; return gts_segment_is_ok(PYGTS_SEGMENT_AS_GTS_SEGMENT(s)); } PygtsSegment * pygts_segment_new(GtsSegment *s) { PyObject *args, *kwds; PygtsObject *segment; /* Check for Segment in the object table */ if( (segment=PYGTS_OBJECT(g_hash_table_lookup(obj_table,GTS_OBJECT(s)))) != NULL ) { Py_INCREF(segment); return PYGTS_FACE(segment); } /* Build a new Segment */ args = Py_BuildValue("OO",Py_None,Py_None); kwds = Py_BuildValue("{s:O}","alloc_gtsobj",Py_False); segment = PYGTS_SEGMENT(PygtsSegmentType.tp_new(&PygtsSegmentType, args, kwds)); Py_DECREF(args); Py_DECREF(kwds); if( segment == NULL ) { PyErr_SetString(PyExc_MemoryError,"could not create Segment"); return NULL; } segment->gtsobj = GTS_OBJECT(s); /* Register and return */ pygts_object_register(segment); return PYGTS_SEGMENT(segment); } int pygts_segment_compare(GtsSegment* s1,GtsSegment* s2) { if( (pygts_point_compare(GTS_POINT(s1->v1),GTS_POINT(s2->v1))==0 && pygts_point_compare(GTS_POINT(s1->v2),GTS_POINT(s2->v2))==0) || (pygts_point_compare(GTS_POINT(s1->v1),GTS_POINT(s2->v2))==0 && pygts_point_compare(GTS_POINT(s1->v2),GTS_POINT(s2->v1))==0) ) { return 0; } return -1; } trunk-2017.01a/py/3rd-party/pygts-0.3.1/segment.h000066400000000000000000000030601304022710500210540ustar00rootroot00000000000000/* pygts - python package for the manipulation of triangulated surfaces * * Copyright (C) 2009 Thomas J. Duck * All rights reserved. * * Thomas J. Duck * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ #ifndef __PYGTS_SEGMENT_H__ #define __PYGTS_SEGMENT_H__ typedef struct _PygtsObject PygtsSegment; #define PYGTS_SEGMENT(obj) ((PygtsSegment*)obj) #define PYGTS_SEGMENT_AS_GTS_SEGMENT(o) (GTS_SEGMENT(PYGTS_OBJECT(o)->gtsobj)) extern PyTypeObject PygtsSegmentType; gboolean pygts_segment_check(PyObject* o); gboolean pygts_segment_is_ok(PygtsSegment *t); PygtsSegment* pygts_segment_new(GtsSegment *f); int pygts_segment_compare(GtsSegment* s1,GtsSegment* s2); #endif /* __PYGTS_SEGMENT_H__ */ trunk-2017.01a/py/3rd-party/pygts-0.3.1/surface.c000066400000000000000000001565711304022710500210550ustar00rootroot00000000000000/* pygts - python package for the manipulation of triangulated surfaces * * Copyright (C) 2009 Thomas J. Duck * All rights reserved. * * Thomas J. Duck * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ #include "pygts.h" #if PYGTS_DEBUG #define SELF_CHECK if(!pygts_surface_check((PyObject*)self)) { \ PyErr_SetString(PyExc_RuntimeError, \ "problem with self object (internal error)"); \ return NULL; \ } #else #define SELF_CHECK #endif /*-------------------------------------------------------------------------*/ /* Methods exported to python */ static PyObject* is_ok(PygtsSurface *self, PyObject *args) { if(pygts_surface_is_ok(self)) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* add(PygtsSurface *self, PyObject *args) { PyObject *o_; PygtsFace *f; PygtsSurface *s; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &o_) ) return NULL; /* Convert to PygtsObjects */ if(pygts_face_check(o_)) { f = PYGTS_FACE(o_); gts_surface_add_face(PYGTS_SURFACE_AS_GTS_SURFACE(self), PYGTS_FACE_AS_GTS_FACE(f)); } else if(pygts_surface_check(o_)) { s = PYGTS_SURFACE(o_); /* Make the call */ gts_surface_merge(PYGTS_SURFACE_AS_GTS_SURFACE(self), PYGTS_SURFACE_AS_GTS_SURFACE(s)); } else { PyErr_SetString(PyExc_TypeError,"expected a Face or a Surface"); return NULL; } Py_INCREF(Py_None); return Py_None; } static PyObject* pygts_remove(PygtsSurface *self, PyObject *args) { PyObject *f_; PygtsFace *f; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &f_) ) return NULL; /* Convert to PygtsObjects */ if(!pygts_face_check(f_)) { PyErr_SetString(PyExc_TypeError,"expected a Face"); return NULL; } f = PYGTS_FACE(f_); /* Make the call */ gts_surface_remove_face(PYGTS_SURFACE_AS_GTS_SURFACE(self), PYGTS_FACE_AS_GTS_FACE(f)); Py_INCREF(Py_None); return Py_None; } static PyObject* copy(PygtsSurface *self, PyObject *args) { PyObject *s_; PygtsSurface *s; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &s_) ) return NULL; /* Convert to PygtsObjects */ if(!pygts_surface_check(s_)) { PyErr_SetString(PyExc_TypeError,"expected a Surface"); return NULL; } s = PYGTS_SURFACE(s_); /* Make the call */ gts_surface_copy(PYGTS_SURFACE_AS_GTS_SURFACE(self), PYGTS_SURFACE_AS_GTS_SURFACE(s)); Py_INCREF((PyObject*)self); return (PyObject*)self; } static PyObject* is_manifold(PygtsSurface *self, PyObject *args) { SELF_CHECK if( gts_surface_is_manifold(PYGTS_SURFACE_AS_GTS_SURFACE(self)) ) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* manifold_faces(PygtsSurface *self, PyObject *args) { PyObject *e_; PygtsEdge *e; GtsFace *f1,*f2; PygtsFace *face1,*face2; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &e_) ) return NULL; /* Convert to PygtsObjects */ if(!pygts_edge_check(e_)) { PyErr_SetString(PyExc_TypeError,"expected an Edge"); return NULL; } e = PYGTS_EDGE(e_); /* Make the call */ if(!gts_edge_manifold_faces(PYGTS_EDGE_AS_GTS_EDGE(e), PYGTS_SURFACE_AS_GTS_SURFACE(self), &f1, &f2)) { Py_INCREF(Py_None); return Py_None; } if( (face1 = pygts_face_new(f1)) == NULL ) { return NULL; } if( (face2 = pygts_face_new(f2)) == NULL ) { Py_DECREF(face1); return NULL; } return Py_BuildValue("OO",face1,face2); } static PyObject* is_orientable(PygtsSurface *self, PyObject *args) { SELF_CHECK if(gts_surface_is_orientable(PYGTS_SURFACE_AS_GTS_SURFACE(self))) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* is_closed(PygtsSurface *self, PyObject *args) { SELF_CHECK if(gts_surface_is_closed(PYGTS_SURFACE_AS_GTS_SURFACE(self))) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* boundary(PyObject *self, PyObject *args) { PyObject *tuple; guint i,N; GSList *edges=NULL,*e; PygtsEdge *edge; SELF_CHECK /* Make the call */ if( (edges = gts_surface_boundary(PYGTS_SURFACE_AS_GTS_SURFACE(self))) == NULL ) { PyErr_SetString(PyExc_RuntimeError,"could not retrieve edges"); return NULL; } /* Assemble the return tuple */ N = g_slist_length(edges); if( (tuple=PyTuple_New(N)) == NULL) { PyErr_SetString(PyExc_MemoryError,"could not create tuple"); return NULL; } e = edges; for(i=0;idata))) == NULL ) { Py_DECREF(tuple); g_slist_free(edges); } PyTuple_SET_ITEM(tuple,i,(PyObject*)edge); e = g_slist_next(e); } g_slist_free(edges); return tuple; } static PyObject* area(PygtsSurface *self, PyObject *args) { GtsSurface *s; SELF_CHECK s = PYGTS_SURFACE_AS_GTS_SURFACE(self); return Py_BuildValue("d",gts_surface_area(s)); } static PyObject* volume(PygtsSurface *self, PyObject *args) { GtsSurface *s; SELF_CHECK s = PYGTS_SURFACE_AS_GTS_SURFACE(self); if(!gts_surface_is_closed(s)) { PyErr_SetString(PyExc_RuntimeError,"Surface is not closed"); return NULL; } if(!gts_surface_is_orientable(s)) { PyErr_SetString(PyExc_RuntimeError,"Surface is not orientable"); return NULL; } return Py_BuildValue("d",gts_surface_volume(s)); } static PyObject* center_of_mass(PygtsSurface *self, PyObject *args) { GtsSurface *s; GtsVector cm; SELF_CHECK s = PYGTS_SURFACE_AS_GTS_SURFACE(self); gts_surface_center_of_mass(s,cm); return Py_BuildValue("ddd",cm[0],cm[1],cm[2]); } static PyObject* center_of_area(PygtsSurface *self, PyObject *args) { GtsSurface *s; GtsVector cm; SELF_CHECK s = PYGTS_SURFACE_AS_GTS_SURFACE(self); gts_surface_center_of_area(s,cm); return Py_BuildValue("ddd",cm[0],cm[1],cm[2]); } static PyObject* pygts_write(PygtsSurface *self, PyObject *args) { PyObject *f_; FILE *f; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &f_) ) return NULL; /* Convert to PygtsObjects */ if(!PyFile_Check(f_)) { PyErr_SetString(PyExc_TypeError,"expected a File"); return NULL; } f = PyFile_AsFile(f_); /* Write to the file */ gts_surface_write(PYGTS_SURFACE_AS_GTS_SURFACE(self),f); Py_INCREF(Py_None); return Py_None; } static PyObject* pygts_write_oogl(PygtsSurface *self, PyObject *args) { PyObject *f_; FILE *f; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &f_) ) return NULL; /* Convert to PygtsObjects */ if(!PyFile_Check(f_)) { PyErr_SetString(PyExc_TypeError,"expected a File"); return NULL; } f = PyFile_AsFile(f_); /* Write to the file */ gts_surface_write_oogl(PYGTS_SURFACE_AS_GTS_SURFACE(self),f); Py_INCREF(Py_None); return Py_None; } static PyObject* pygts_write_oogl_boundary(PygtsSurface *self, PyObject *args) { PyObject *f_; FILE *f; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &f_) ) return NULL; /* Convert to PygtsObjects */ if(!PyFile_Check(f_)) { PyErr_SetString(PyExc_TypeError,"expected a File"); return NULL; } f = PyFile_AsFile(f_); /* Write to the file */ gts_surface_write_oogl_boundary(PYGTS_SURFACE_AS_GTS_SURFACE(self),f); Py_INCREF(Py_None); return Py_None; } static PyObject* pygts_write_vtk(PygtsSurface *self, PyObject *args) { PyObject *f_; FILE *f; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &f_) ) return NULL; /* Convert to PygtsObjects */ if(!PyFile_Check(f_)) { PyErr_SetString(PyExc_TypeError,"expected a File"); return NULL; } f = PyFile_AsFile(f_); /* Write to the file */ gts_surface_write_vtk(PYGTS_SURFACE_AS_GTS_SURFACE(self),f); Py_INCREF(Py_None); return Py_None; } static PyObject* fan_oriented(PygtsSurface *self, PyObject *args) { PyObject *v_; PygtsVertex *v; GSList *edges=NULL, *e; guint i,N; PyObject *tuple; PygtsEdge *edge; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &v_) ) return NULL; /* Convert to PygtsObjects */ if(!pygts_vertex_check(v_)) { PyErr_SetString(PyExc_TypeError,"expected a Vertex"); return NULL; } v = PYGTS_VERTEX(v_); /* Check that the Surface is orientable; the calculation will * fail otherwise. */ if(!gts_surface_is_orientable(PYGTS_SURFACE_AS_GTS_SURFACE(self))) { PyErr_SetString(PyExc_RuntimeError,"Surface must be orientable"); return NULL; } /* Make the call */ edges = gts_vertex_fan_oriented(PYGTS_VERTEX_AS_GTS_VERTEX(v), PYGTS_SURFACE_AS_GTS_SURFACE(self)); /* Build the return tuple */ N = g_slist_length(edges); if( (tuple=PyTuple_New(N)) == NULL) { PyErr_SetString(PyExc_MemoryError,"Could not create tuple"); return NULL; } e = edges; for(i=0;idata))) == NULL ) { Py_DECREF(tuple); g_slist_free(edges); return NULL; } PyTuple_SET_ITEM(tuple,i,(PyObject*)edge); e = g_slist_next(e); } return tuple; } static PyObject* split(PygtsSurface *self, PyObject *args) { GSList *surfaces, *s; PyObject *tuple; PygtsSurface *surface; guint n,N; SELF_CHECK surfaces = gts_surface_split(PYGTS_SURFACE_AS_GTS_SURFACE(self)); /* Create a tuple to put the Surfaces into */ N = g_slist_length(surfaces); if( (tuple=PyTuple_New(N)) == NULL) { PyErr_SetString(PyExc_MemoryError,"could not create tuple"); return NULL; } /* Put PygtsSurface objects into the tuple */ s = surfaces; for(n=0;ndata))) == NULL ) { Py_DECREF(tuple); return NULL; } surface->traverse = NULL; PyTuple_SET_ITEM(tuple, n, (PyObject*)surface); s = g_slist_next(s); } return tuple; } /* Helper function for vertices() */ static void get_vertex(GtsVertex *vertex, GtsVertex ***v) { **v = vertex; *v += 1; } static PyObject* vertices(PygtsSurface *self, PyObject *args) { PyObject *tuple; PygtsVertex *vertex; PygtsVertex **vertices,**v; guint i,N=0; SELF_CHECK /* Get the number of vertices */ N = gts_surface_vertex_number(PYGTS_SURFACE_AS_GTS_SURFACE(self)); /* Retrieve all of the vertex pointers into a temporary array */ if( (vertices = (PygtsVertex**)malloc(N*sizeof(PygtsVertex*))) == NULL ) { PyErr_SetString(PyExc_MemoryError,"could not create array"); return NULL; } v = vertices; gts_surface_foreach_vertex(PYGTS_SURFACE_AS_GTS_SURFACE(self), (GtsFunc)get_vertex,&v); /* Create a tuple to put the vertices into */ if( (tuple=PyTuple_New(N)) == NULL) { PyErr_SetString(PyExc_MemoryError,"could not create tuple"); return NULL; } /* Put PygtsVertex objects into the tuple */ v = vertices; for(i=0;idata))) == NULL ) { Py_DECREF(tuple); g_slist_free(edges); return NULL; } PyTuple_SET_ITEM(tuple,i,(PyObject*)edge); e = g_slist_next(e); } g_slist_free(edges); return tuple; } /* Helper function for edges() */ static void get_face(GtsFace *face, GSList **faces) { *faces = g_slist_prepend(*faces,face); } static PyObject* faces(PyObject *self, PyObject *args) { PyObject *tuple=NULL, *obj; guint i,N; GSList *edges=NULL,*faces=NULL,*f; PygtsFace *face; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "|O", &tuple) ) { return NULL; } if(tuple) { if(PyList_Check(tuple)) { tuple = PyList_AsTuple(tuple); } else { Py_INCREF(tuple); } if(!PyTuple_Check(tuple)) { Py_DECREF(tuple); PyErr_SetString(PyExc_TypeError,"expected a list or tuple of edges"); return NULL; } /* Assemble the GSList */ N = PyTuple_Size(tuple); for(i=0;idata))) == NULL ) { Py_DECREF(tuple); g_slist_free(faces); return NULL; } PyTuple_SET_ITEM(tuple,i,(PyObject*)face); f = g_slist_next(f); } g_slist_free(faces); return tuple; } /* Helper for face_indices() */ typedef struct { PyObject *vertices,*indices; /* Vertex and indices tuples */ guint Nv,Ni; /* Number of vertices and indices */ guint n; /* Current face index */ gboolean errflag; } IndicesData; /* Helper for face_indices() */ static void get_indices(GtsFace *face, IndicesData *data) { PyObject *t; GtsVertex *v[3]; guint i,j; gboolean flag; if(data->errflag) return; /* Put the vertex pointers in an array */ gts_triangle_vertices( GTS_TRIANGLE(face), &(v[0]), &(v[1]), &(v[2]) ); /* Create a tuple to put the indices into */ if( (t=PyTuple_New(3)) == NULL) { PyErr_SetString(PyExc_MemoryError,"could not create tuple"); data->errflag = TRUE; return; } PyTuple_SET_ITEM(data->indices, data->n, t); /* Determine the indices */ for(i=0;i<3;i++) { flag = FALSE; for(j=0;jNv;j++) { if( PYGTS_VERTEX_AS_GTS_VERTEX(PyTuple_GET_ITEM(data->vertices,j)) ==v[i] ) { PyTuple_SET_ITEM(t, i, PyInt_FromLong(j)); flag = TRUE; break; } } if(!flag) { PyErr_SetString(PyExc_RuntimeError, "Could not initialize tuple (internal error)"); data->errflag = TRUE; return; } } data->n += 1; } static PyObject* face_indices(PygtsSurface *self, PyObject *args) { PyObject *vertices,*indices; IndicesData data; guint Nv,Nf; guint i; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &vertices) ) return NULL; /* Make sure that the tuple contains only vertices */ Nv = PyTuple_Size(vertices); for(i=0;idata); n = g_slist_length(f); if( (tuples[i]=PyTuple_New(n)) == NULL) { PyErr_SetString(PyExc_MemoryError,"could not create tuple"); Py_DECREF(tuple); free(tuples); return NULL; } PyTuple_SET_ITEM(tuple, i, tuples[i]); s = g_slist_next(s); } /* Put PygtsFace objects into the tuple */ s = strips; for(i=0;idata); n = g_slist_length(f); for(j=0;jdata))) == NULL ) { } PyTuple_SET_ITEM(tuples[i], j, (PyObject*)face); f = g_slist_next(f); } s = g_slist_next(s); } free(tuples); return tuple; } static PyObject* stats(PygtsSurface *self, PyObject *args) { GtsSurfaceStats stats; PyObject *dict, *edges_per_vertex, *faces_per_edge; SELF_CHECK /* Make the call */ gts_surface_stats(PYGTS_SURFACE_AS_GTS_SURFACE(self),&stats); /* Create the dictionaries */ if( (dict = PyDict_New()) == NULL ) { PyErr_SetString(PyExc_MemoryError,"cannot create dict"); return NULL; } if( (edges_per_vertex = PyDict_New()) == NULL ) { PyErr_SetString(PyExc_MemoryError,"cannot create dict"); Py_DECREF(dict); return NULL; } if( (faces_per_edge = PyDict_New()) == NULL ) { PyErr_SetString(PyExc_MemoryError,"cannot create dict"); Py_DECREF(dict); Py_DECREF(edges_per_vertex); return NULL; } /* Populate the edges_per_vertex dict */ PyDict_SetItemString(edges_per_vertex,"min", Py_BuildValue("d",stats.edges_per_vertex.min)); PyDict_SetItemString(edges_per_vertex,"max", Py_BuildValue("d",stats.edges_per_vertex.max)); PyDict_SetItemString(edges_per_vertex,"sum", Py_BuildValue("d",stats.edges_per_vertex.sum)); PyDict_SetItemString(edges_per_vertex,"sum2", Py_BuildValue("d",stats.edges_per_vertex.sum2)); PyDict_SetItemString(edges_per_vertex,"mean", Py_BuildValue("d",stats.edges_per_vertex.mean)); PyDict_SetItemString(edges_per_vertex,"stddev", Py_BuildValue("d",stats.edges_per_vertex.stddev)); PyDict_SetItemString(edges_per_vertex,"n", Py_BuildValue("i",stats.edges_per_vertex.n)); /* Populate the faces_per_edge dict */ PyDict_SetItemString(faces_per_edge,"min", Py_BuildValue("d",stats.faces_per_edge.min)); PyDict_SetItemString(faces_per_edge,"max", Py_BuildValue("d",stats.faces_per_edge.max)); PyDict_SetItemString(faces_per_edge,"sum", Py_BuildValue("d",stats.faces_per_edge.sum)); PyDict_SetItemString(faces_per_edge,"sum2", Py_BuildValue("d",stats.faces_per_edge.sum2)); PyDict_SetItemString(faces_per_edge,"mean", Py_BuildValue("d",stats.faces_per_edge.mean)); PyDict_SetItemString(faces_per_edge,"stddev", Py_BuildValue("d",stats.faces_per_edge.stddev)); PyDict_SetItemString(faces_per_edge,"n", Py_BuildValue("i",stats.faces_per_edge.n)); /* Populate the main dict */ PyDict_SetItemString(dict,"n_faces", Py_BuildValue("i",stats.n_faces)); PyDict_SetItemString(dict,"n_incompatible_faces", Py_BuildValue("i",stats.n_incompatible_faces)); PyDict_SetItemString(dict,"n_boundary_edges", Py_BuildValue("i",stats.n_boundary_edges)); PyDict_SetItemString(dict,"n_non_manifold_edges", Py_BuildValue("i",stats.n_non_manifold_edges)); PyDict_SetItemString(dict,"edges_per_vertex", edges_per_vertex); PyDict_SetItemString(dict,"faces_per_edge", faces_per_edge); return dict; } static PyObject* quality_stats(PygtsSurface *self, PyObject *args) { GtsSurfaceQualityStats stats; PyObject *dict, *face_quality, *face_area, *edge_length, *edge_angle; SELF_CHECK /* Make the call */ gts_surface_quality_stats(PYGTS_SURFACE_AS_GTS_SURFACE(self),&stats); /* Create the dictionaries */ if( (dict = PyDict_New()) == NULL ) { PyErr_SetString(PyExc_MemoryError,"cannot create dict"); return NULL; } if( (face_quality = PyDict_New()) == NULL ) { PyErr_SetString(PyExc_MemoryError,"cannot create dict"); Py_DECREF(dict); return NULL; } if( (face_area = PyDict_New()) == NULL ) { PyErr_SetString(PyExc_MemoryError,"cannot create dict"); Py_DECREF(dict); Py_DECREF(face_quality); return NULL; } if( (edge_length = PyDict_New()) == NULL ) { PyErr_SetString(PyExc_MemoryError,"cannot create dict"); Py_DECREF(dict); Py_DECREF(face_quality); Py_DECREF(face_area); return NULL; } if( (edge_angle = PyDict_New()) == NULL ) { PyErr_SetString(PyExc_MemoryError,"cannot create dict"); Py_DECREF(dict); Py_DECREF(face_quality); Py_DECREF(face_area); Py_DECREF(edge_length); return NULL; } /* Populate the face_quality dict */ PyDict_SetItemString(face_quality,"min", Py_BuildValue("d",stats.face_quality.min)); PyDict_SetItemString(face_quality,"max", Py_BuildValue("d",stats.face_quality.max)); PyDict_SetItemString(face_quality,"sum", Py_BuildValue("d",stats.face_quality.sum)); PyDict_SetItemString(face_quality,"sum2", Py_BuildValue("d",stats.face_quality.sum2)); PyDict_SetItemString(face_quality,"mean", Py_BuildValue("d",stats.face_quality.mean)); PyDict_SetItemString(face_quality,"stddev", Py_BuildValue("d",stats.face_quality.stddev)); PyDict_SetItemString(face_quality,"n", Py_BuildValue("i",stats.face_quality.n)); /* Populate the face_area dict */ PyDict_SetItemString(face_area,"min", Py_BuildValue("d",stats.face_area.min)); PyDict_SetItemString(face_area,"max", Py_BuildValue("d",stats.face_area.max)); PyDict_SetItemString(face_area,"sum", Py_BuildValue("d",stats.face_area.sum)); PyDict_SetItemString(face_area,"sum2", Py_BuildValue("d",stats.face_area.sum2)); PyDict_SetItemString(face_area,"mean", Py_BuildValue("d",stats.face_area.mean)); PyDict_SetItemString(face_area,"stddev", Py_BuildValue("d",stats.face_area.stddev)); PyDict_SetItemString(face_area,"n", Py_BuildValue("i",stats.face_area.n)); /* Populate the edge_length dict */ PyDict_SetItemString(edge_length,"min", Py_BuildValue("d",stats.edge_length.min)); PyDict_SetItemString(edge_length,"max", Py_BuildValue("d",stats.edge_length.max)); PyDict_SetItemString(edge_length,"sum", Py_BuildValue("d",stats.edge_length.sum)); PyDict_SetItemString(edge_length,"sum2", Py_BuildValue("d",stats.edge_length.sum2)); PyDict_SetItemString(edge_length,"mean", Py_BuildValue("d",stats.edge_length.mean)); PyDict_SetItemString(edge_length,"stddev", Py_BuildValue("d",stats.edge_length.stddev)); PyDict_SetItemString(edge_length,"n", Py_BuildValue("i",stats.edge_length.n)); /* Populate the edge_angle dict */ PyDict_SetItemString(edge_angle,"min", Py_BuildValue("d",stats.edge_angle.min)); PyDict_SetItemString(edge_angle,"max", Py_BuildValue("d",stats.edge_angle.max)); PyDict_SetItemString(edge_angle,"sum", Py_BuildValue("d",stats.edge_angle.sum)); PyDict_SetItemString(edge_angle,"sum2", Py_BuildValue("d",stats.edge_angle.sum2)); PyDict_SetItemString(edge_angle,"mean", Py_BuildValue("d",stats.edge_angle.mean)); PyDict_SetItemString(edge_angle,"stddev", Py_BuildValue("d",stats.edge_angle.stddev)); PyDict_SetItemString(edge_angle,"n", Py_BuildValue("i",stats.edge_angle.n)); /* Populate the main dict */ PyDict_SetItemString(dict,"face_quality", face_quality); PyDict_SetItemString(dict,"face_area", face_area); PyDict_SetItemString(dict,"edge_length", edge_length); PyDict_SetItemString(dict,"edge_angle", edge_angle); return dict; } static PyObject* tessellate(PygtsSurface *self, PyObject *args) { SELF_CHECK gts_surface_tessellate(PYGTS_SURFACE_AS_GTS_SURFACE(self),NULL,NULL); Py_INCREF(Py_None); return Py_None; } /* Helper function for inter() */ void get_largest_coord(GtsVertex *v,gdouble *val) { if( fabs(GTS_POINT(v)->x) > *val ) *val = fabs(GTS_POINT(v)->x); if( fabs(GTS_POINT(v)->y) > *val ) *val = fabs(GTS_POINT(v)->y); if( fabs(GTS_POINT(v)->z) > *val ) *val = fabs(GTS_POINT(v)->z); } /* Helper function for intersection operations */ static PyObject* inter(PygtsSurface *self, PyObject *args, GtsBooleanOperation op1, GtsBooleanOperation op2) { PyObject *obj; PyObject *s_; PygtsSurface *s; GtsSurface *surface; GtsVector cm1, cm2; gdouble area1, area2; GtsSurfaceInter *si; GNode *tree1, *tree2; gboolean is_open1, is_open2, closed; gdouble eps=0.; /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &s_) ) return NULL; /* Convert to PygtsObjects */ if(!pygts_surface_check(s_)) { PyErr_SetString(PyExc_TypeError,"expected a Surface"); return NULL; } s = PYGTS_SURFACE(s_); /* Make sure that we don't have two pointers to the same surface */ if( self == s ) { PyErr_SetString(PyExc_RuntimeError, "can't determine intersection with self"); return NULL; } /* *** ATTENTION *** * Eliminate any active gts traverse objects. They appear to interfere * with the intersection calculation. I would guess that this is due * to the use of the "reserved" field (i.e., it doesn't get properly * reset until the traverse is destroyed). * * I don't expect this to cause problems here, but a bug report should be * filed. */ if(self->traverse!=NULL) { gts_surface_traverse_destroy(self->traverse); self->traverse = NULL; } if(s->traverse!=NULL) { gts_surface_traverse_destroy(s->traverse); s->traverse = NULL; } /* *** ATTENTION *** */ /* Check for self-intersections in either surface */ if( gts_surface_is_self_intersecting(PYGTS_SURFACE_AS_GTS_SURFACE(self)) != NULL ) { PyErr_SetString(PyExc_RuntimeError,"Surface is self-intersecting"); return NULL; } if( gts_surface_is_self_intersecting(PYGTS_SURFACE_AS_GTS_SURFACE(s)) != NULL ) { PyErr_SetString(PyExc_RuntimeError,"Surface is self-intersecting"); return NULL; } /* Avoid complete self-intersection of two surfaces*/ if( (gts_surface_face_number(PYGTS_SURFACE_AS_GTS_SURFACE(self)) == gts_surface_face_number(PYGTS_SURFACE_AS_GTS_SURFACE(s))) && (gts_surface_edge_number(PYGTS_SURFACE_AS_GTS_SURFACE(self)) == gts_surface_edge_number(PYGTS_SURFACE_AS_GTS_SURFACE(s))) && (gts_surface_vertex_number(PYGTS_SURFACE_AS_GTS_SURFACE(self)) == gts_surface_vertex_number(PYGTS_SURFACE_AS_GTS_SURFACE(s))) && (gts_surface_area(PYGTS_SURFACE_AS_GTS_SURFACE(self)) == gts_surface_area(PYGTS_SURFACE_AS_GTS_SURFACE(s))) ) { area1 = \ gts_surface_center_of_area(PYGTS_SURFACE_AS_GTS_SURFACE(self),cm1); area2 = \ gts_surface_center_of_area(PYGTS_SURFACE_AS_GTS_SURFACE(s),cm2); if( (area1==area2) && (cm1[0]==cm2[0]) && (cm1[1]==cm2[1]) && (cm1[2]==cm2[2]) ) { PyErr_SetString(PyExc_RuntimeError,"Surfaces mutually intersect"); return NULL; } } /* Get bounding boxes */ if( (tree1=gts_bb_tree_surface(PYGTS_SURFACE_AS_GTS_SURFACE(self))) ==NULL ) { PyErr_SetString(PyExc_MemoryError,"could not create tree"); return NULL; } is_open1 = !gts_surface_is_closed(PYGTS_SURFACE_AS_GTS_SURFACE(self)); if( (tree2=gts_bb_tree_surface(PYGTS_SURFACE_AS_GTS_SURFACE(s))) ==NULL ) { gts_bb_tree_destroy(tree1, TRUE); PyErr_SetString(PyExc_MemoryError,"could not create tree"); return NULL; } is_open2 = !gts_surface_is_closed(PYGTS_SURFACE_AS_GTS_SURFACE(s)); /* Get the surface intersection object */ if( (si = gts_surface_inter_new(gts_surface_inter_class(), PYGTS_SURFACE_AS_GTS_SURFACE(self), PYGTS_SURFACE_AS_GTS_SURFACE(s), tree1, tree2, is_open1, is_open2))==NULL) { gts_bb_tree_destroy(tree1, TRUE); gts_bb_tree_destroy(tree2, TRUE); PyErr_SetString(PyExc_RuntimeError,"could not create GtsSurfaceInter"); return NULL; } gts_bb_tree_destroy(tree1, TRUE); gts_bb_tree_destroy(tree2, TRUE); /* Check that the surface intersection object is closed */ gts_surface_inter_check(si,&closed); if( closed == FALSE ) { gts_object_destroy(GTS_OBJECT(si)); PyErr_SetString(PyExc_RuntimeError,"result is not closed"); return NULL; } /* Create the surface */ if( (surface = gts_surface_new(gts_surface_class(), gts_face_class(), gts_edge_class(), gts_vertex_class())) == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Surface"); return NULL; } /* Calculate the new surface */ gts_surface_inter_boolean(si, surface ,op1); gts_surface_inter_boolean(si, surface ,op2); gts_object_destroy(GTS_OBJECT(si)); /* Clean up the result */ gts_surface_foreach_vertex(surface, (GtsFunc)get_largest_coord, &eps); eps *= pow(2.,-50); pygts_vertex_cleanup(surface,1.e-9); pygts_edge_cleanup(surface); pygts_face_cleanup(surface); /* Check for self-intersection */ if( gts_surface_is_self_intersecting(surface) != NULL ) { gts_object_destroy(GTS_OBJECT(surface)); PyErr_SetString(PyExc_RuntimeError,"result is self-intersecting surface"); return NULL; } /* Create the return Surface */ if( (obj = (PyObject*)pygts_surface_new(surface)) == NULL ) { gts_object_destroy(GTS_OBJECT(surface)); return NULL; } return obj; } static PyObject* intersection(PygtsSurface *self, PyObject *args, GtsBooleanOperation op1, GtsBooleanOperation op2) { SELF_CHECK return inter(self,args,GTS_1_IN_2,GTS_2_IN_1); } static PyObject* pygts_union(PygtsSurface *self, PyObject *args) { SELF_CHECK return inter(self,args,GTS_1_OUT_2,GTS_2_OUT_1); } static PyObject* difference(PygtsSurface *self, PyObject *args) { SELF_CHECK return inter(self,args,GTS_1_OUT_2,GTS_2_IN_1); } /* Helper for rotate(), scale() and translate() transforms */ typedef struct { double dx, dy, dz, a; gboolean errflag; } TransformData; /* Helper for rotate() */ static void rotate_point(GtsPoint *p, TransformData *data) { if(data->errflag) return; if(pygts_point_rotate(p,data->dx,data->dy,data->dz,data->a)==-1) data->errflag=TRUE; } static PyObject* rotate(PygtsSurface* self, PyObject *args, PyObject *keywds) { TransformData data; static char *kwlist[] = {"dx", "dy", "dz", "a", NULL}; SELF_CHECK data.dx=0; data.dy=0; data.dz=0; data.a=0; data.errflag = FALSE; /* Parse the args */ if(! PyArg_ParseTupleAndKeywords(args, keywds,"|dddd", kwlist, &(data.dx), &(data.dy), &(data.dz), &(data.a)) ) { return NULL; } gts_surface_foreach_vertex(PYGTS_SURFACE_AS_GTS_SURFACE(self), (GtsFunc)rotate_point,&data); if(data.errflag) return NULL; Py_INCREF(Py_None); return Py_None; } /* Helper for scale() */ static void scale_point(GtsPoint *p, TransformData *data) { if(data->errflag) return; if(pygts_point_scale(p,data->dx,data->dy,data->dz)==-1) data->errflag=TRUE; } static PyObject* scale(PygtsSurface* self, PyObject *args, PyObject *keywds) { TransformData data; static char *kwlist[] = {"dx", "dy", "dz", NULL}; SELF_CHECK data.dx=1; data.dy=1; data.dz=1; data.a=0; data.errflag = FALSE; /* Parse the args */ if(! PyArg_ParseTupleAndKeywords(args, keywds,"|ddd", kwlist, &(data.dx), &(data.dy), &(data.dz)) ) { return NULL; } gts_surface_foreach_vertex(PYGTS_SURFACE_AS_GTS_SURFACE(self), (GtsFunc)scale_point,&data); if(data.errflag) return NULL; Py_INCREF(Py_None); return Py_None; } /* Helper for translate() */ static void translate_point(GtsPoint *p, TransformData *data) { if(data->errflag) return; if(pygts_point_translate(p,data->dx,data->dy,data->dz)==-1) data->errflag=TRUE; } static PyObject* translate(PygtsSurface* self, PyObject *args, PyObject *keywds) { TransformData data; static char *kwlist[] = {"dx", "dy", "dz", NULL}; SELF_CHECK data.dx=0; data.dy=0; data.dz=0; data.a=0; data.errflag = FALSE; /* Parse the args */ if(! PyArg_ParseTupleAndKeywords(args, keywds,"|ddd", kwlist, &(data.dx), &(data.dy), &(data.dz)) ) { return NULL; } /* Make the call */ gts_surface_foreach_vertex(PYGTS_SURFACE_AS_GTS_SURFACE(self), (GtsFunc)translate_point,&data); if(data.errflag) return NULL; Py_INCREF(Py_None); return Py_None; } static PyObject* is_self_intersecting(PygtsSurface *self, PyObject *args) { GtsSurface *s; gboolean ret = FALSE; SELF_CHECK if( (s=gts_surface_is_self_intersecting(PYGTS_SURFACE_AS_GTS_SURFACE(self))) != NULL) { gts_object_destroy(GTS_OBJECT(s)); ret = TRUE; } if(ret) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* cleanup(PygtsSurface *self, PyObject *args) { GtsSurface *s; gdouble threshold = 0.; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args,"|d", &threshold) ) { return NULL; } s = PYGTS_SURFACE_AS_GTS_SURFACE(self); /* Do the cleanup */ if( threshold != 0. ) { pygts_vertex_cleanup(s,threshold); } pygts_edge_cleanup(s); pygts_face_cleanup(s); Py_INCREF(Py_None); return Py_None; } static PyObject* coarsen(PygtsSurface *self, PyObject *args) { guint n; gdouble amin=0.; GtsVolumeOptimizedParams params = {0.5,0.5,1.e-10}; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args,"i|d", &n, &amin) ) { return NULL; } /* Make the call */ gts_surface_coarsen(PYGTS_SURFACE_AS_GTS_SURFACE(self), (GtsKeyFunc)gts_volume_optimized_cost, ¶ms, (GtsCoarsenFunc)gts_volume_optimized_vertex, ¶ms, (GtsStopFunc)gts_coarsen_stop_number, &n, amin); Py_INCREF(Py_None); return Py_None; } /* Methods table */ static PyMethodDef methods[] = { {"is_ok", (PyCFunction)is_ok, METH_NOARGS, "True if this Surface s is OK. False otherwise.\n" "\n" "Signature: s.is_ok()\n" }, {"add", (PyCFunction)add, METH_VARARGS, "Adds a Face f or Surface s2 to Surface s1.\n" "\n" "Signature: s1.add(f) or s2.add(f)\n" }, {"remove", (PyCFunction)pygts_remove, METH_VARARGS, "Removes Face f from this Surface s.\n" "\n" "Signature: s.remove(f)\n" }, {"copy", (PyCFunction)copy, METH_VARARGS, "Copys all Faces, Edges and Vertices of Surface s2 to Surface s1.\n" "\n" "Signature: s1.copy(s2)\n" "\n" "Returns s1.\n" }, {"is_manifold", (PyCFunction)is_manifold, METH_NOARGS, "True if Surface s is a manifold, False otherwise.\n" "\n" "Signature: s.is_manifold()\n" }, {"manifold_faces", (PyCFunction)manifold_faces, METH_VARARGS, "Returns the 2 manifold Faces of Edge e on this Surface s\n" "if they exist, or None.\n" "\n" "Signature: s.manifold_faces(e)\n" }, {"is_orientable", (PyCFunction)is_orientable, METH_NOARGS, "True if Faces in Surface s have compatible orientation,\n" "False otherwise.\n" "Note that a closed surface is also a manifold. Note that an\n" "orientable surface is also a manifold.\n" "\n" "Signature: s.is_orientable()\n" }, {"is_closed", (PyCFunction)is_closed, METH_NOARGS, "True if Surface s is closed, False otherwise.\n" "Note that a closed Surface is also a manifold.\n" "\n" "Signature: s.is_closed()\n" }, {"boundary", (PyCFunction)boundary, METH_NOARGS, "Returns a tuple of boundary Edges of Surface s.\n" "\n" "Signature: s.boundary()\n" }, {"area", (PyCFunction)area, METH_NOARGS, "Returns the area of Surface s.\n" "The area is taken as the sum of the signed areas of the Faces of s.\n" "\n" "Signature: s.area()\n" }, {"volume", (PyCFunction)volume, METH_NOARGS, "Returns the signed volume of the domain bounded by the Surface s.\n" "\n" "Signature: s.volume()\n" }, {"center_of_mass", (PyCFunction)center_of_mass, METH_NOARGS, "Returns the coordinates of the center of mass of Surface s.\n" "\n" "Signature: s.center_of_mass()\n" }, {"center_of_area", (PyCFunction)center_of_area, METH_NOARGS, "Returns the coordinates of the center of area of Surface s.\n" "\n" "Signature: s.center_of_area()\n" }, {"write", (PyCFunction)pygts_write, METH_VARARGS, "Saves Surface s to File f in GTS ascii format.\n" "All the lines beginning with #! are ignored.\n" "\n" "Signature: s.write(f)\n" }, {"write_oogl", (PyCFunction)pygts_write_oogl, METH_VARARGS, "Saves Surface s to File f in OOGL (Geomview) format.\n" "\n" "Signature: s.write_oogl(f)\n" }, {"write_oogl_boundary", (PyCFunction)pygts_write_oogl_boundary, METH_VARARGS, "Saves boundary of Surface s to File f in OOGL (Geomview) format.\n" "\n" "Signature: s.write_oogl_boundary(f)\n" }, {"write_vtk", (PyCFunction)pygts_write_vtk, METH_VARARGS, "Saves Surface s to File f in VTK format.\n" "\n" "Signature: s.write_vtk(f)\n" }, {"fan_oriented", (PyCFunction)fan_oriented, METH_VARARGS, "Returns a tuple of outside Edges of the Faces fanning from\n" "Vertex v on this Surface s. The Edges are given in \n" "counter-clockwise order.\n" "\n" "Signature: s.fan_oriented(v)\n" }, {"split", (PyCFunction)split, METH_NOARGS, "Splits a surface into a tuple of connected and manifold components.\n" "\n" "Signature: s.split()\n" }, {"distance", (PyCFunction)distance, METH_VARARGS, "Calculates the distance between the faces of this Surface s1 and\n" "the nearest Faces of other s2, and (if applicable) the distance\n" "between the boundary of this Surface s1 and the nearest boundary\n" "Edges of other s2.\n" "\n" "One or two dictionaries are returned (where applicable), the first\n" "for the face range and the second for the boundary range. The\n" "fields in each dictionary describe statistical results for each\n" "population: {min,max,sum,sum2,mean,stddev,n}.\n" "\n" "Signature: s1.distance(s2) or s1.distance(s2,delta)\n" "\n" "The value delta is a spatial increment defined as the percentage\n" "of the diagonal of the bounding box of s2 (default 0.1).\n" }, {"strip", (PyCFunction)strip, METH_NOARGS, "Returns a tuple of strips, where each strip is a tuple of Faces\n" "that are successive and have one edge in common.\n" "\n" "Signature: s.split()\n" }, {"stats", (PyCFunction)stats, METH_NOARGS, "Returns statistics for this Surface f in a dict.\n" "The stats include n_faces, n_incompatible_faces,, n_boundary_edges,\n" "n_non_manifold_edges, and the statisics {min, max, sum, sum2, mean,\n" "stddev, and n} for populations of edges_per_vertex and\n" "faces_per_edge. Each of these names are dictionary keys.\n" "\n" "Signature: s.stats()\n" }, {"quality_stats", (PyCFunction)quality_stats, METH_NOARGS, "Returns quality statistics for this Surface f in a dict.\n" "The statistics include the {min, max, sum, sum2, mean, stddev,\n" "and n} for populations of face_quality, face_area, edge_length,\n" "and edge_angle. Each of these names are dictionary keys.\n" "See Triangle.quality() for an explanation of the face_quality.\n" "\n" "Signature: s.quality_stats()\n" }, {"tessellate", (PyCFunction)tessellate, METH_NOARGS, "Tessellate each face of this Surface s with 4 triangles.\n" "The number of triangles is increased by a factor of 4.\n" "\n" "Signature: s.tessellate()\n" }, {"vertices", (PyCFunction)vertices, METH_NOARGS, "Returns a tuple containing the vertices of Surface s.\n" "\n" "Signature: s.vertices()\n" }, {"parent", (PyCFunction)parent, METH_VARARGS, "Returns Face on this Surface s that has Edge e, or None\n" "if the Edge is not on this Surface.\n" "\n" "Signature: s.parent(e)\n" }, {"edges", (PyCFunction)edges, METH_VARARGS, "Returns tuple of Edges on Surface s that have Vertex in list.\n" "If a list is not given then all of the Edges are returned.\n" "\n" "Signature: s.edges(list) or s.edges()\n" }, {"faces", (PyCFunction)faces, METH_VARARGS, "Returns tuple of Faces on Surface s that have Edge in list.\n" "If a list is not given then all of the Faces are returned.\n" "\n" "Signature: s.faces(list) s.faces()\n" }, {"face_indices", (PyCFunction)face_indices, METH_VARARGS, "Returns a tuple of 3-tuples containing Vertex indices for each Face\n" "in Surface s. The index for each Vertex in a face corresponds to\n" "where it is found in the Vertex tuple vs.\n" "\n" "Signature: s.face_indices(vs)\n" }, {"intersection", (PyCFunction)intersection, METH_VARARGS, "Returns the intersection of this Surface s1 with Surface s2.\n" "\n" "Signature: s1.intersection(s2)\n" }, {"union", (PyCFunction)pygts_union, METH_VARARGS, "Returns the union of this Surface s1 with Surface s2.\n" "\n" "Signature: s1.union(s2)\n" }, {"difference", (PyCFunction)difference, METH_VARARGS, "Returns the difference of this Surface s1 with Surface s2.\n" "\n" "Signature: s1.difference(s2)\n" }, {"rotate", (PyCFunction)rotate, METH_VARARGS | METH_KEYWORDS, "Rotates Surface s about vector dx,dy,dz and angle a.\n" "The sense of the rotation is given by the right-hand-rule.\n" "\n" "Signature: s.rotate(dx,dy,dz,a)\n" }, {"scale", (PyCFunction)scale, METH_VARARGS | METH_KEYWORDS, "Scales Surface s by vector dx,dy,dz.\n" "\n" "Signature: s.scale(dx=1,dy=1,dz=1)\n" }, {"translate", (PyCFunction)translate, METH_VARARGS | METH_KEYWORDS, "Translates Surface s by vector dx,dy,dz.\n" "\n" "Signature: s.translate(dx=0,dy=0,dz=0)\n" }, {"is_self_intersecting", (PyCFunction)is_self_intersecting, METH_NOARGS, "Returns True if this Surface s is self-intersecting.\n" "False otherwise.\n" "\n" "Signature: s.is_self_intersecting()\n" }, {"cleanup", (PyCFunction)cleanup, METH_VARARGS, "Cleans up the Vertices, Edges, and Faces on a Surface s.\n" "\n" "Signature: s.cleanup() or s.cleanup(threhold)\n" "\n" "If threhold is given, then Vertices that are spaced less than\n" "the threshold are merged. Degenerate Edges and Faces are also\n" "removed.\n" }, {"coarsen", (PyCFunction)coarsen, METH_VARARGS, "Reduces the number of vertices on Surface s.\n" "\n" "Signature: s.coarsen(n) and s.coarsen(amin)\n" "\n" "n is the smallest number of desired edges (but you may get fewer).\n" "amin is the smallest angle between Faces.\n" }, {NULL} /* Sentinel */ }; /*-------------------------------------------------------------------------*/ /* Attributes exported to python */ static PyObject * get_Nvertices(PygtsSurface *self, void *closure) { SELF_CHECK return Py_BuildValue("i", gts_surface_vertex_number(PYGTS_SURFACE_AS_GTS_SURFACE(self))); } static PyObject * get_Nedges(PygtsSurface *self, void *closure) { SELF_CHECK return Py_BuildValue("i", gts_surface_edge_number(PYGTS_SURFACE_AS_GTS_SURFACE(self))); } static PyObject * get_Nfaces(PygtsSurface *self, void *closure) { SELF_CHECK return Py_BuildValue("i", gts_surface_face_number(PYGTS_SURFACE_AS_GTS_SURFACE(self))); } /* Methods table */ static PyGetSetDef getset[] = { { "Nvertices", (getter)get_Nvertices, NULL, "The number of unique vertices", NULL }, { "Nedges", (getter)get_Nedges, NULL, "The number of unique edges", NULL }, { "Nfaces", (getter)get_Nfaces, NULL, "The number of unique faces", NULL }, {NULL} /* Sentinel */ }; /*-------------------------------------------------------------------------*/ /* Python type methods */ static void dealloc(PygtsSurface* self) { if(self->traverse!=NULL) { gts_surface_traverse_destroy(self->traverse); } self->traverse = NULL; /* Chain up */ PygtsObjectType.tp_dealloc((PyObject*)self); } static PyObject * new(PyTypeObject *type, PyObject *args, PyObject *kwds) { PyObject *o; PygtsObject *obj; guint alloc_gtsobj = TRUE; /* Parse the args */ if(kwds) { o = PyDict_GetItemString(kwds,"alloc_gtsobj"); if(o==Py_False) { alloc_gtsobj = FALSE; } if(o!=NULL) { PyDict_DelItemString(kwds, "alloc_gtsobj"); } } if(kwds) { Py_INCREF(Py_False); PyDict_SetItemString(kwds,"alloc_gtsobj", Py_False); } /* Chain up */ obj = PYGTS_OBJECT(PygtsObjectType.tp_new(type,args,kwds)); PYGTS_SURFACE(obj)->traverse = NULL; /* Allocate the gtsobj (if needed) */ if( alloc_gtsobj ) { obj->gtsobj = GTS_OBJECT(gts_surface_new(gts_surface_class(), gts_face_class(), gts_edge_class(), gts_vertex_class())); if( obj->gtsobj == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Surface"); return NULL; } pygts_object_register(obj); } return (PyObject*)obj; } static int init(PygtsSurface *self, PyObject *args, PyObject *kwds) { gint ret; if( (ret = PygtsObjectType.tp_init((PyObject*)self,args,kwds)) != 0 ) { return ret; } return 0; } /* Helper function for iter */ static void get_f0(GtsFace *f,GtsFace **f0) { if(*f0==NULL) *f0 = f; } PyObject* iter(PygtsSurface *self) { GtsFace* f0=NULL; SELF_CHECK if(self->traverse!=NULL) { gts_surface_traverse_destroy(self->traverse); self->traverse = NULL; } /* Assign a "first" face */ gts_surface_foreach_face(PYGTS_SURFACE_AS_GTS_SURFACE(self), (GtsFunc)get_f0,&f0); if(f0==NULL) { PyErr_SetString(PyExc_RuntimeError, "No faces to traverse"); return NULL; } if( (self->traverse=gts_surface_traverse_new( PYGTS_SURFACE_AS_GTS_SURFACE(self),f0)) == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Traverse"); return NULL; } Py_INCREF((PyObject*)self); return (PyObject*)self; } PyObject* iternext(PygtsSurface *self) { PygtsFace *face; GtsFace *f; SELF_CHECK if( self->traverse == NULL ) { PyErr_SetString(PyExc_RuntimeError, "iterator not initialized"); return NULL; } /* Get the next face */ if( (f = gts_surface_traverse_next(self->traverse,NULL)) == NULL ) { gts_surface_traverse_destroy(self->traverse); self->traverse = NULL; PyErr_SetString(PyExc_StopIteration, "No more faces"); return NULL; } if( (face = pygts_face_new(f)) == NULL ) { return NULL; } return (PyObject*)face; } /* Methods table */ PyTypeObject PygtsSurfaceType = { PyObject_HEAD_INIT(NULL) 0, /* ob_size */ "gts.Surface", /* tp_name */ sizeof(PygtsSurface), /* tp_basicsize */ 0, /* tp_itemsize */ (destructor)dealloc, /* tp_dealloc */ 0, /* tp_print */ 0, /* tp_getattr */ 0, /* tp_setattr */ 0, /* tp_compare */ 0, /* tp_repr */ 0, /* tp_as_number */ 0, /* tp_as_sequence */ 0, /* tp_as_mapping */ 0, /* tp_hash */ 0, /* tp_call */ 0, /* tp_str */ 0, /* tp_getattro */ 0, /* tp_setattro */ 0, /* tp_as_buffer */ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE | Py_TPFLAGS_HAVE_ITER, /* tp_flags */ "Surface object", /* tp_doc */ 0, /* tp_traverse */ 0, /* tp_clear */ 0, /* tp_richcompare */ 0, /* tp_weaklistoffset */ (getiterfunc)iter, /* tp_iter */ (iternextfunc)iternext, /* tp_iternext */ methods, /* tp_methods */ 0, /* tp_members */ getset, /* tp_getset */ 0, /* tp_base */ 0, /* tp_dict */ 0, /* tp_descr_get */ 0, /* tp_descr_set */ 0, /* tp_dictoffset */ (initproc)init, /* tp_init */ 0, /* tp_alloc */ (newfunc)new /* tp_new */ }; /*-------------------------------------------------------------------------*/ /* Pygts functions */ gboolean pygts_surface_check(PyObject* o) { if(! PyObject_TypeCheck(o, &PygtsSurfaceType)) { return FALSE; } else { #if PYGTS_DEBUG return pygts_surface_is_ok(PYGTS_SURFACE(o)); #else return TRUE; #endif } } /* Helper function */ static void face_is_ok(GtsFace *f,gboolean *ret) { if( !pygts_gts_triangle_is_ok(GTS_TRIANGLE(f)) ) { *ret = FALSE; } } gboolean pygts_surface_is_ok(PygtsSurface *s) { PygtsObject *obj; gboolean ret=TRUE; obj = PYGTS_OBJECT(s); if(!pygts_object_is_ok(PYGTS_OBJECT(s))) return FALSE; g_return_val_if_fail(obj->gtsobj_parent==NULL,FALSE); /* Check all of the faces this surface contains */ gts_surface_foreach_face(GTS_SURFACE(obj->gtsobj),(GtsFunc)face_is_ok,&ret); if( ret == FALSE ) return FALSE; return TRUE; } PygtsSurface * pygts_surface_new(GtsSurface *s) { PyObject *args, *kwds; PygtsObject *surface; /* Check for Surface in the object table */ if( (surface = PYGTS_OBJECT(g_hash_table_lookup(obj_table,GTS_OBJECT(s)))) !=NULL ) { Py_INCREF(surface); return PYGTS_SURFACE(surface); } /* Build a new Surface */ args = Py_BuildValue("()"); kwds = Py_BuildValue("{s:O}","alloc_gtsobj",Py_False); surface = PYGTS_OBJECT(PygtsSurfaceType.tp_new(&PygtsSurfaceType,args,kwds)); Py_DECREF(args); Py_DECREF(kwds); if( surface == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Surface"); return NULL; } surface->gtsobj = GTS_OBJECT(s); /* Register and return */ pygts_object_register(surface); return PYGTS_SURFACE(surface); } trunk-2017.01a/py/3rd-party/pygts-0.3.1/surface.h000066400000000000000000000030751304022710500210500ustar00rootroot00000000000000/* pygts - python package for the manipulation of triangulated surfaces * * Copyright (C) 2009 Thomas J. Duck * All rights reserved. * * Thomas J. Duck * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ #ifndef __PYGTS_SURFACE_H__ #define __PYGTS_SURFACE_H__ typedef struct _PygtsSurface PygtsSurface; #define PYGTS_SURFACE(o) ((PygtsSurface*)o) #define PYGTS_SURFACE_AS_GTS_SURFACE(o) (GTS_SURFACE(PYGTS_OBJECT(o)->gtsobj)) struct _PygtsSurface { PygtsObject o; GtsSurfaceTraverse* traverse; }; extern PyTypeObject PygtsSurfaceType; gboolean pygts_surface_check(PyObject* o); gboolean pygts_surface_is_ok(PygtsSurface *s); PygtsSurface* pygts_surface_new(GtsSurface *s); #endif /* __PYGTS_SURFACE_H__ */ trunk-2017.01a/py/3rd-party/pygts-0.3.1/triangle.c000066400000000000000000000644401304022710500212230ustar00rootroot00000000000000/* pygts - python package for the manipulation of triangulated surfaces * * Copyright (C) 2009 Thomas J. Duck * All rights reserved. * * Thomas J. Duck * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ #include "pygts.h" #if PYGTS_DEBUG #define SELF_CHECK if(!pygts_triangle_check((PyObject*)self)) { \ PyErr_SetString(PyExc_RuntimeError, \ "problem with self object (internal error)"); \ return NULL; \ } #else #define SELF_CHECK #endif /*-------------------------------------------------------------------------*/ /* Methods exported to python */ static PyObject* is_ok(PygtsTriangle *self, PyObject *args) { if(pygts_triangle_is_ok(self)) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* area(PygtsTriangle *self, PyObject *args) { SELF_CHECK return Py_BuildValue("d", gts_triangle_area(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self))); } static PyObject* perimeter(PygtsTriangle *self, PyObject *args) { SELF_CHECK return Py_BuildValue("d", gts_triangle_perimeter(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self))); } static PyObject* quality(PygtsTriangle *self, PyObject *args) { SELF_CHECK return Py_BuildValue("d", gts_triangle_quality(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self))); } static PyObject* normal(PygtsTriangle *self, PyObject *args) { gdouble x,y,z; SELF_CHECK gts_triangle_normal(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self),&x,&y,&z); return Py_BuildValue("ddd",x,y,z); } static PyObject* revert(PygtsTriangle *self, PyObject *args) { SELF_CHECK gts_triangle_revert(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self)); Py_INCREF(Py_None); return Py_None; } static PyObject* orientation(PygtsTriangle *self, PyObject *args) { SELF_CHECK return Py_BuildValue("d", gts_triangle_orientation(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self))); } static PyObject* angle(PygtsTriangle* self, PyObject *args) { PyObject *t_; PygtsTriangle *t; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &t_) ) { return NULL; } /* Convert to PygtsObjects */ if(!pygts_triangle_check(t_)) { PyErr_SetString(PyExc_TypeError,"expected a Triangle"); return NULL; } t = PYGTS_TRIANGLE(t_); return Py_BuildValue("d", gts_triangles_angle(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self), PYGTS_TRIANGLE_AS_GTS_TRIANGLE(t))); } static PyObject* is_compatible(PygtsTriangle *self, PyObject *args) { PyObject *t2_; PygtsTriangle *t2; GtsEdge *e; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &t2_) ) { return NULL; } /* Convert to PygtsObjects */ if(!pygts_triangle_check(t2_)) { PyErr_SetString(PyExc_TypeError,"expected a Triangle"); return NULL; } t2 = PYGTS_TRIANGLE(t2_); /* Get the common edge */ if( (e = gts_triangles_common_edge(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self), PYGTS_TRIANGLE_AS_GTS_TRIANGLE(t2))) == NULL ) { PyErr_SetString(PyExc_RuntimeError,"Triangles do not share common edge"); return NULL; } if( gts_triangles_are_compatible(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self), PYGTS_TRIANGLE_AS_GTS_TRIANGLE(t2),e) ) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* common_edge(PygtsTriangle *self, PyObject *args) { PyObject *t2_; PygtsTriangle *t2; GtsEdge *e; PygtsEdge *edge; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &t2_) ) { return NULL; } /* Convert to PygtsObjects */ if(!pygts_triangle_check(t2_)) { PyErr_SetString(PyExc_TypeError,"expected a Triangle"); return NULL; } t2 = PYGTS_TRIANGLE(t2_); /* Get the common edge */ if( (e = gts_triangles_common_edge(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self), PYGTS_TRIANGLE_AS_GTS_TRIANGLE(t2))) == NULL ) { Py_INCREF(Py_None); return Py_None; } if( (edge = pygts_edge_new(GTS_EDGE(e))) == NULL ) { return NULL; } return (PyObject*)edge; } static PyObject* opposite(PygtsTriangle *self, PyObject *args) { PyObject *o_; PygtsEdge *e=NULL; PygtsVertex *v=NULL; GtsVertex *vertex=NULL,*v1,*v2,*v3; GtsEdge *edge=NULL; GtsTriangle *triangle; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &o_) ) { return NULL; } /* Convert to PygtsObjects */ if(pygts_edge_check(o_)) { e = PYGTS_TRIANGLE(o_); } else { if(pygts_vertex_check(o_)) { v = PYGTS_TRIANGLE(o_); } else { PyErr_SetString(PyExc_TypeError,"expected an Edge or a Vertex"); return NULL; } } /* Error check */ triangle = PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self); if( e!=NULL ) { edge = PYGTS_EDGE_AS_GTS_EDGE(e); if(! ((triangle->e1==edge)||(triangle->e2==edge)||(triangle->e3==edge)) ) { PyErr_SetString(PyExc_RuntimeError,"Edge not in Triangle"); return NULL; } } else { vertex = PYGTS_VERTEX_AS_GTS_VERTEX(v); gts_triangle_vertices(triangle,&v1,&v2,&v3); if(! ((vertex==v1)||(vertex==v2)||(vertex==v3)) ) { PyErr_SetString(PyExc_RuntimeError,"Vertex not in Triangle"); return NULL; } } /* Get the opposite and return */ if( e!=NULL) { vertex = gts_triangle_vertex_opposite(triangle, edge); if( (v = pygts_vertex_new(vertex)) == NULL ) { return NULL; } return (PyObject*)v; } else{ edge = gts_triangle_edge_opposite(triangle, vertex); if( (e = pygts_edge_new(edge)) == NULL ) { return NULL; } return (PyObject*)e; } } static PyObject * vertices(PygtsTriangle *self,PyObject *args) { GtsVertex *v1_,*v2_,*v3_; PygtsObject *v1,*v2,*v3; SELF_CHECK /* Get the vertices */ gts_triangle_vertices(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self), &v1_, &v2_, &v3_); if( (v1 = pygts_vertex_new(v1_)) == NULL ) { return NULL; } if( (v2 = pygts_vertex_new(v2_)) == NULL ) { Py_DECREF(v1); return NULL; } if( (v3 = pygts_vertex_new(v3_)) == NULL ) { Py_DECREF(v1); Py_DECREF(v2); return NULL; } return Py_BuildValue("OOO",v1,v2,v3); } static PyObject * vertex(PygtsTriangle *self,PyObject *args) { GtsVertex *v1_; PygtsObject *v1; SELF_CHECK /* Get the vertices */ v1_ = gts_triangle_vertex(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self)); if( (v1 = pygts_vertex_new(v1_)) == NULL ) { return NULL; } return (PyObject*)v1; } static PyObject * circumcenter(PygtsTriangle *self,PyObject *args) { PygtsVertex *v; GtsVertex *vertex; SELF_CHECK /* Get the Vertex */ vertex = GTS_VERTEX( gts_triangle_circumcircle_center( PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self), GTS_POINT_CLASS(gts_vertex_class()))); if( vertex == NULL ) { Py_INCREF(Py_None); return Py_None; } if( (v = pygts_vertex_new(vertex)) == NULL ) { return NULL; } return (PyObject*)v; } static PyObject * is_stabbed(PygtsTriangle *self,PyObject *args) { PyObject *p_; PygtsVertex *p; GtsObject *obj; PygtsVertex *vertex; PygtsEdge *edge; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &p_) ) { return NULL; } /* Convert to PygtsObjects */ if(!pygts_point_check(p_)) { PyErr_SetString(PyExc_TypeError,"expected a Point"); return NULL; } p = PYGTS_POINT(p_); obj = gts_triangle_is_stabbed(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self), GTS_POINT(PYGTS_OBJECT(p)->gtsobj), NULL); if( obj == NULL ) { Py_INCREF(Py_None); return Py_None; } if(GTS_IS_VERTEX(obj)) { if( (vertex = pygts_vertex_new(GTS_VERTEX(obj))) == NULL ) { return NULL; } return (PyObject*)vertex; } if(GTS_IS_EDGE(obj)) { if( (edge = pygts_edge_new(GTS_EDGE(obj))) == NULL ) { return NULL; } return (PyObject*)edge; } Py_INCREF(self); return (PyObject*)self; } static PyObject * interpolate_height(PygtsTriangle *self,PyObject *args) { PyObject *p_; PygtsPoint *p; GtsPoint point; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &p_) ) { return NULL; } /* Convert to PygtsObjects */ if(!pygts_point_check(p_)) { PyErr_SetString(PyExc_TypeError,"expected a Point"); return NULL; } p = PYGTS_POINT(p_); point.x = PYGTS_POINT_AS_GTS_POINT(p)->x; point.y = PYGTS_POINT_AS_GTS_POINT(p)->y; gts_triangle_interpolate_height(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self), &point); return Py_BuildValue("d",point.z); } /* Methods table */ static PyMethodDef methods[] = { {"is_ok", (PyCFunction)is_ok, METH_NOARGS, "True if this Triangle t is non-degenerate and non-duplicate.\n" "False otherwise.\n" "\n" "Signature: t.is_ok()\n" }, {"area", (PyCFunction)area, METH_NOARGS, "Returns the area of Triangle t.\n" "\n" "Signature: t.area()\n" }, {"perimeter", (PyCFunction)perimeter, METH_NOARGS, "Returns the perimeter of Triangle t.\n" "\n" "Signature: t.perimeter()\n" }, {"quality", (PyCFunction)quality, METH_NOARGS, "Returns the quality of Triangle t.\n" "\n" "The quality of a triangle is defined as the ratio of the square\n" "root of its surface area to its perimeter relative to this same\n" "ratio for an equilateral triangle with the same area. The quality\n" "is then one for an equilateral triangle and tends to zero for a\n" "very stretched triangle." "\n" "Signature: t.quality()\n" }, {"normal", (PyCFunction)normal, METH_NOARGS, "Returns a tuple of coordinates of the oriented normal of Triangle t\n" "as the cross-product of two edges, using the left-hand rule. The\n" "normal is not normalized. If this triangle is part of a closed and\n" "oriented surface, the normal points to the outside of the surface.\n" "\n" "Signature: t.normal()\n" }, {"revert", (PyCFunction)revert, METH_NOARGS, "Changes the orientation of triangle t, turning it inside out.\n" "\n" "Signature: t.revert()\n" }, {"orientation", (PyCFunction)orientation, METH_NOARGS, "Determines orientation of the plane (x,y) projection of Triangle t\n" "\n" "Signature: t.orientation()\n" "\n" "Returns a positive value if Points p1, p2 and p3 in Triangle t\n" "appear in counterclockwise order, a negative value if they appear\n" "in clockwise order and zero if they are colinear.\n" }, {"angle", (PyCFunction)angle, METH_VARARGS, "Returns the angle (radians) between Triangles t1 and t2\n" "\n" "Signature: t1.angle(t2)\n" }, {"is_compatible", (PyCFunction)is_compatible, METH_VARARGS, "True if this triangle t1 and other t2 are compatible;\n" "otherwise False.\n" "\n" "Checks if this triangle t1 and other t2, which share a common\n" "Edge, can be part of the same surface without conflict in the\n" "surface normal orientation.\n" "\n" "Signature: t1.is_compatible(t2)\n" }, {"common_edge", (PyCFunction)common_edge, METH_VARARGS, "Returns Edge common to both this Triangle t1 and other t2.\n" "Returns None if the triangles do not share an Edge.\n" "\n" "Signature: t1.common_edge(t2)\n" }, {"opposite", (PyCFunction)opposite, METH_VARARGS, "Returns Vertex opposite to Edge e or Edge opposite to Vertex v\n" "for this Triangle t.\n" "\n" "Signature: t.opposite(e) or t.opposite(v)\n" }, {"vertices", (PyCFunction)vertices, METH_NOARGS, "Returns the three oriented set of vertices in Triangle t.\n" "\n" "Signature: t.vertices()\n" }, {"vertex", (PyCFunction)vertex, METH_NOARGS, "Returns the Vertex of this Triangle t not in t.e1.\n" "\n" "Signature: t.vertex()\n" }, {"circumcenter", (PyCFunction)circumcenter, METH_NOARGS, "Returns a Vertex at the center of the circumscribing circle of\n" "this Triangle t, or None if the circumscribing circle is not\n" "defined.\n" "\n" "Signature: t.circumcircle_center()\n" }, {"is_stabbed", (PyCFunction)is_stabbed, METH_VARARGS, "Returns the component of this Triangle t that is stabbed by a\n" "ray projecting from Point p to z=infinity. The result\n" "can be this Triangle t, one of its Edges or Vertices, or None.\n" "If the ray is contained in the plan of this Triangle then None is\n" "also returned.\n" "\n" "Signature: t.is_stabbed(p)\n" }, {"interpolate_height", (PyCFunction)interpolate_height, METH_VARARGS, "Returns the height of the plane defined by Triangle t at Point p.\n" "Only the x- and y-coordinates of p are considered.\n" "\n" "Signature: t.interpolate_height(p)\n" }, {NULL} /* Sentinel */ }; /*-------------------------------------------------------------------------*/ /* Attributes exported to python */ static PyObject * get_e1(PygtsTriangle *self, void *closure) { PygtsEdge *e1; SELF_CHECK if( (e1=pygts_edge_new(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self)->e1)) == NULL ) { return NULL; } return (PyObject *)e1; } static PyObject * get_e2(PygtsTriangle *self, void *closure) { PygtsEdge *e2; SELF_CHECK if( (e2=pygts_edge_new(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self)->e2)) == NULL ) { return NULL; } return (PyObject *)e2; } static PyObject * get_e3(PygtsTriangle *self, void *closure) { PygtsEdge *e3; SELF_CHECK if( (e3=pygts_edge_new(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(self)->e3)) == NULL ) { return NULL; } return (PyObject *)e3; } /* Methods table */ static PyGetSetDef getset[] = { {"e1", (getter)get_e1, NULL, "Edge 1", NULL}, {"e2", (getter)get_e2, NULL, "Edge 2", NULL}, {"e3", (getter)get_e3, NULL, "Edge 3", NULL}, {NULL} /* Sentinel */ }; /*-------------------------------------------------------------------------*/ /* Python type methods */ static PyObject * new(PyTypeObject *type, PyObject *args, PyObject *kwds) { PyObject *o; PygtsObject *obj; guint alloc_gtsobj = TRUE; PyObject *o1_,*o2_,*o3_; GtsVertex *v1=NULL, *v2=NULL, *v3=NULL; GtsEdge *e1=NULL,*e2=NULL,*e3=NULL,*e; GtsSegment *s1,*s2,*s3; gboolean flag=FALSE; /* Flag when the args are gts.Point objects */ GtsTriangle *t,*t_; guint N; /* Parse the args */ if(kwds) { o = PyDict_GetItemString(kwds,"alloc_gtsobj"); if(o==Py_False) { alloc_gtsobj = FALSE; } if(o!=NULL) { PyDict_DelItemString(kwds, "alloc_gtsobj"); } } if(kwds) { Py_INCREF(Py_False); PyDict_SetItemString(kwds,"alloc_gtsobj", Py_False); } /* Allocate the gtsobj (if needed) */ if( alloc_gtsobj ) { /* Parse the args */ if( (N = PyTuple_Size(args)) < 3 ) { PyErr_SetString(PyExc_TypeError,"expected three Edges or three Vertices"); return NULL; } o1_ = PyTuple_GET_ITEM(args,0); o2_ = PyTuple_GET_ITEM(args,1); o3_ = PyTuple_GET_ITEM(args,2); /* Convert to PygtsObjects */ if( pygts_edge_check(o1_) ) { e1 = PYGTS_EDGE_AS_GTS_EDGE(o1_); } else { if( pygts_vertex_check(o1_) ) { v1 = PYGTS_VERTEX_AS_GTS_VERTEX(o1_); flag = TRUE; } } if( pygts_edge_check(o2_) ) { e2 = PYGTS_EDGE_AS_GTS_EDGE(o2_); } else { if( pygts_vertex_check(o2_) ) { v2 = PYGTS_VERTEX_AS_GTS_VERTEX(o2_); flag = TRUE; } } if( pygts_edge_check(o3_) ) { e3 = PYGTS_EDGE_AS_GTS_EDGE(o3_); } else { if(pygts_vertex_check(o3_)) { v3 = PYGTS_VERTEX_AS_GTS_VERTEX(o3_); flag = TRUE; } } /* Check for three edges or three vertices */ if( !((e1!=NULL && e2!=NULL && e3!=NULL) || (v1!=NULL && v2!=NULL && v3!=NULL)) ) { PyErr_SetString(PyExc_TypeError,"expected three Edges or three Vertices"); return NULL; } if( (v1==v2 || v2==v3 || v1==v3) && v1!=NULL ) { PyErr_SetString(PyExc_ValueError,"three Vertices must be different"); return NULL; } /* Get gts edges */ if(flag) { /* Create gts edges */ if( (e1 = gts_edge_new(gts_edge_class(),v1,v2)) == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Edge"); return NULL; } if( (e2 = gts_edge_new(gts_edge_class(),v2,v3)) == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Edge"); gts_object_destroy(GTS_OBJECT(e1)); return NULL; } if( (e3 = gts_edge_new(gts_edge_class(),v3,v1)) == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Edge"); gts_object_destroy(GTS_OBJECT(e1)); gts_object_destroy(GTS_OBJECT(e2)); return NULL; } /* Check for duplicates */ if( (e = gts_edge_is_duplicate(e1)) != NULL ) { gts_object_destroy(GTS_OBJECT(e1)); e1 = e; } if( (e = gts_edge_is_duplicate(e2)) != NULL ) { gts_object_destroy(GTS_OBJECT(e2)); e2 = e; } if( (e = gts_edge_is_duplicate(e3)) != NULL ) { gts_object_destroy(GTS_OBJECT(e3)); e3 = e; } } /* Check that edges connect with common vertices */ s1 = GTS_SEGMENT(e1); s2 = GTS_SEGMENT(e2); s3 = GTS_SEGMENT(e3); if( !((s1->v1==s3->v2 && s1->v2==s2->v1 && s2->v2==s3->v1) || (s1->v1==s3->v2 && s1->v2==s2->v2 && s2->v1==s3->v1) || (s1->v1==s3->v1 && s1->v2==s2->v1 && s2->v2==s3->v2) || (s1->v2==s3->v2 && s1->v1==s2->v1 && s2->v2==s3->v1) || (s1->v1==s3->v1 && s1->v2==s2->v2 && s2->v1==s3->v2) || (s1->v2==s3->v2 && s1->v1==s2->v2 && s2->v1==s3->v1) || (s1->v2==s3->v1 && s1->v1==s2->v1 && s2->v2==s3->v2) || (s1->v2==s3->v1 && s1->v1==s2->v2 && s2->v1==s3->v2)) ) { PyErr_SetString(PyExc_RuntimeError, "Edges in triangle must connect"); if(!g_hash_table_lookup(obj_table,GTS_OBJECT(e1))) { gts_object_destroy(GTS_OBJECT(e1)); } if(!g_hash_table_lookup(obj_table,GTS_OBJECT(e1))) { gts_object_destroy(GTS_OBJECT(e2)); } if(!g_hash_table_lookup(obj_table,GTS_OBJECT(e1))) { gts_object_destroy(GTS_OBJECT(e3)); } return NULL; } /* Create the GtsTriangle */ if( (t = gts_triangle_new(gts_triangle_class(),e1,e2,e3)) == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Face"); if(!g_hash_table_lookup(obj_table,GTS_OBJECT(e1))) { gts_object_destroy(GTS_OBJECT(e1)); } if(!g_hash_table_lookup(obj_table,GTS_OBJECT(e1))) { gts_object_destroy(GTS_OBJECT(e2)); } if(!g_hash_table_lookup(obj_table,GTS_OBJECT(e1))) { gts_object_destroy(GTS_OBJECT(e3)); } return NULL; } /* Check for duplicate */ t_ = gts_triangle_is_duplicate(GTS_TRIANGLE(t)); if( t_ != NULL ) { gts_object_destroy(GTS_OBJECT(t)); t = t_; } /* If corresponding PyObject found in object table, we are done */ if( (obj=g_hash_table_lookup(obj_table,GTS_OBJECT(t))) != NULL ) { Py_INCREF(obj); return (PyObject*)obj; } } /* Chain up */ obj = PYGTS_OBJECT(PygtsObjectType.tp_new(type,args,kwds)); if( alloc_gtsobj ) { obj->gtsobj = GTS_OBJECT(t); pygts_object_register(PYGTS_OBJECT(obj)); } return (PyObject*)obj; } static int init(PygtsTriangle *self, PyObject *args, PyObject *kwds) { gint ret; /* Chain up */ if( (ret=PygtsObjectType.tp_init((PyObject*)self,args,kwds)) != 0 ){ return ret; } #if PYGTS_DEBUG if(!pygts_triangle_check((PyObject*)self)) { PyErr_SetString(PyExc_RuntimeError, "problem with self object (internal error)"); return -1; } #endif return 0; } static int compare(PyObject *o1, PyObject *o2) { GtsTriangle *t1, *t2; if( !(pygts_triangle_check(o1) && pygts_triangle_check(o2)) ) { return -1; } t1 = PYGTS_TRIANGLE_AS_GTS_TRIANGLE(o1); t2 = PYGTS_TRIANGLE_AS_GTS_TRIANGLE(o2); return pygts_triangle_compare(t1,t2); } /* Methods table */ PyTypeObject PygtsTriangleType = { PyObject_HEAD_INIT(NULL) 0, /* ob_size */ "gts.Triangle", /* tp_name */ sizeof(PygtsTriangle), /* tp_basicsize */ 0, /* tp_itemsize */ 0, /* tp_dealloc */ 0, /* tp_print */ 0, /* tp_getattr */ 0, /* tp_setattr */ (cmpfunc)compare, /* tp_compare */ 0, /* tp_repr */ 0, /* tp_as_number */ 0, /* tp_as_sequence */ 0, /* tp_as_mapping */ 0, /* tp_hash */ 0, /* tp_call */ 0, /* tp_str */ 0, /* tp_getattro */ 0, /* tp_setattro */ 0, /* tp_as_buffer */ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ "Triangle object", /* tp_doc */ 0, /* tp_traverse */ 0, /* tp_clear */ 0, /* tp_richcompare */ 0, /* tp_weaklistoffset */ 0, /* tp_iter */ 0, /* tp_iternext */ methods, /* tp_methods */ 0, /* tp_members */ getset, /* tp_getset */ 0, /* tp_base */ 0, /* tp_dict */ 0, /* tp_descr_get */ 0, /* tp_descr_set */ 0, /* tp_dictoffset */ (initproc)init, /* tp_init */ 0, /* tp_alloc */ (newfunc)new /* tp_new */ }; /*-------------------------------------------------------------------------*/ /* Pygts functions */ gboolean pygts_triangle_check(PyObject* o) { if(! PyObject_TypeCheck(o, &PygtsTriangleType)) { return FALSE; } else { #if PYGTS_DEBUG return pygts_triangle_is_ok(PYGTS_TRIANGLE(o)); #else return TRUE; #endif } } gboolean pygts_triangle_is_ok(PygtsTriangle *t) { if(!pygts_object_is_ok(PYGTS_OBJECT(t))) return FALSE; return pygts_gts_triangle_is_ok(PYGTS_TRIANGLE_AS_GTS_TRIANGLE(t)); } PygtsTriangle * pygts_triangle_new(GtsTriangle *t) { PyObject *args, *kwds; PygtsObject *triangle; /* Check for Triangle in the object table */ if( (triangle = PYGTS_OBJECT(g_hash_table_lookup(obj_table,GTS_OBJECT(t)))) !=NULL ) { Py_INCREF(triangle); return PYGTS_TRIANGLE(triangle); } /* Build a new Triangle */ args = Py_BuildValue("OOO",Py_None,Py_None,Py_None); kwds = Py_BuildValue("{s:O}","alloc_gtsobj",Py_False); triangle = PYGTS_OBJECT(PygtsTriangleType.tp_new(&PygtsTriangleType, args, kwds)); Py_DECREF(args); Py_DECREF(kwds); if( triangle == NULL ) { PyErr_SetString(PyExc_MemoryError,"could not create Triangle"); return NULL; } triangle->gtsobj = GTS_OBJECT(t); /* Register and return */ pygts_object_register(triangle); return PYGTS_TRIANGLE(triangle); } int pygts_triangle_compare(GtsTriangle* t1,GtsTriangle* t2) { if( (pygts_segment_compare(GTS_SEGMENT(t1->e1),GTS_SEGMENT(t2->e1))==0 && pygts_segment_compare(GTS_SEGMENT(t1->e2),GTS_SEGMENT(t2->e2))==0 && pygts_segment_compare(GTS_SEGMENT(t1->e3),GTS_SEGMENT(t2->e3))==0) || (pygts_segment_compare(GTS_SEGMENT(t1->e1),GTS_SEGMENT(t2->e3))==0 && pygts_segment_compare(GTS_SEGMENT(t1->e2),GTS_SEGMENT(t2->e1))==0 && pygts_segment_compare(GTS_SEGMENT(t1->e3),GTS_SEGMENT(t2->e2))==0) || (pygts_segment_compare(GTS_SEGMENT(t1->e1),GTS_SEGMENT(t2->e2))==0 && pygts_segment_compare(GTS_SEGMENT(t1->e2),GTS_SEGMENT(t2->e3))==0 && pygts_segment_compare(GTS_SEGMENT(t1->e3),GTS_SEGMENT(t2->e1))==0) || (pygts_segment_compare(GTS_SEGMENT(t1->e1),GTS_SEGMENT(t2->e3))==0 && pygts_segment_compare(GTS_SEGMENT(t1->e2),GTS_SEGMENT(t2->e2))==0 && pygts_segment_compare(GTS_SEGMENT(t1->e3),GTS_SEGMENT(t2->e1))==0) || (pygts_segment_compare(GTS_SEGMENT(t1->e1),GTS_SEGMENT(t2->e2))==0 && pygts_segment_compare(GTS_SEGMENT(t1->e2),GTS_SEGMENT(t2->e1))==0 && pygts_segment_compare(GTS_SEGMENT(t1->e3),GTS_SEGMENT(t2->e3))==0) || (pygts_segment_compare(GTS_SEGMENT(t1->e1),GTS_SEGMENT(t2->e1))==0 && pygts_segment_compare(GTS_SEGMENT(t1->e2),GTS_SEGMENT(t2->e3))==0 && pygts_segment_compare(GTS_SEGMENT(t1->e3),GTS_SEGMENT(t2->e2))==0) ) { return 0; } return -1; } /** * gts_triangle_is_ok: * @t: a #GtsTriangle. * * Returns: %TRUE if @t is a non-degenerate, non-duplicate triangle, * %FALSE otherwise. */ gboolean pygts_gts_triangle_is_ok (GtsTriangle * t) { g_return_val_if_fail (t != NULL, FALSE); g_return_val_if_fail (t->e1 != NULL, FALSE); g_return_val_if_fail (t->e2 != NULL, FALSE); g_return_val_if_fail (t->e3 != NULL, FALSE); g_return_val_if_fail (t->e1 != t->e2 && t->e1 != t->e3 && t->e2 != t->e3, FALSE); g_return_val_if_fail (gts_segments_touch (GTS_SEGMENT (t->e1), GTS_SEGMENT (t->e2)), FALSE); g_return_val_if_fail (gts_segments_touch (GTS_SEGMENT (t->e1), GTS_SEGMENT (t->e3)), FALSE); g_return_val_if_fail (gts_segments_touch (GTS_SEGMENT (t->e2), GTS_SEGMENT (t->e3)), FALSE); g_return_val_if_fail (GTS_SEGMENT (t->e1)->v1 != GTS_SEGMENT (t->e1)->v2, FALSE); g_return_val_if_fail (GTS_SEGMENT (t->e2)->v1 != GTS_SEGMENT (t->e2)->v2, FALSE); g_return_val_if_fail (GTS_SEGMENT (t->e3)->v1 != GTS_SEGMENT (t->e3)->v2, FALSE); /* g_return_val_if_fail (GTS_OBJECT (t)->reserved == NULL, FALSE); */ g_return_val_if_fail (!gts_triangle_is_duplicate (t), FALSE); return TRUE; } trunk-2017.01a/py/3rd-party/pygts-0.3.1/triangle.h000066400000000000000000000040111304022710500212140ustar00rootroot00000000000000/* pygts - python package for the manipulation of triangulated surfaces * * Copyright (C) 2009 Thomas J. Duck * All rights reserved. * * Thomas J. Duck * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ #ifndef __PYGTS_TRIANGLE_H__ #define __PYGTS_TRIANGLE_H__ typedef struct _PygtsObject PygtsTriangle; #define PYGTS_TRIANGLE(obj) ((PygtsTriangle*)obj) #define PYGTS_TRIANGLE_AS_GTS_TRIANGLE(o) \ (GTS_TRIANGLE(PYGTS_OBJECT(o)->gtsobj)) extern PyTypeObject PygtsTriangleType; gboolean pygts_triangle_check(PyObject* o); gboolean pygts_triangle_is_ok(PygtsTriangle *t); PygtsTriangle* pygts_triangle_new(GtsTriangle *t); int pygts_triangle_compare(GtsTriangle* t1,GtsTriangle* t2); /* Replacement for gts_triangle_is_ok(). The problem is that sometimes the * "reserved" variable is set in a face by gts, and so this function fails. * e.g., The error occurs when gts_triangle_is_ok() is called during * iteration over faces in a surface. This function ignores that check so * that there is no failure when PYGTS_DEBUG is set. A bug report should be * submitted. */ gboolean pygts_gts_triangle_is_ok(GtsTriangle *t); #endif /* __PYGTS_TRIANGLE_H__ */ trunk-2017.01a/py/3rd-party/pygts-0.3.1/vertex.c000066400000000000000000000476231304022710500207370ustar00rootroot00000000000000/* pygts - python package for the manipulation of triangulated surfaces * * Copyright (C) 2009 Thomas J. Duck * All rights reserved. * * Thomas J. Duck * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ #include "pygts.h" #if PYGTS_DEBUG #define SELF_CHECK if(!pygts_vertex_check((PyObject*)self)) { \ PyErr_SetString(PyExc_RuntimeError, \ "problem with self object (internal error)"); \ return NULL; \ } #else #define SELF_CHECK #endif /*-------------------------------------------------------------------------*/ /* Methods exported to python */ static PyObject* is_ok(PygtsVertex *self, PyObject *args) { if(pygts_vertex_is_ok(self)) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* is_unattached(PygtsVertex *self, PyObject *args) { guint n; SELF_CHECK /* Check for attachments other than to the gtsobj_parent */ n = g_slist_length(PYGTS_VERTEX_AS_GTS_VERTEX(self)->segments); if( n > 1 ) { Py_INCREF(Py_False); return Py_False; } else { Py_INCREF(Py_True); return Py_True; } } static PyObject* is_boundary(PygtsVertex* self, PyObject *args) { PyObject *s_; PygtsObject *s; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &s_) ) { return NULL; } /* Convert to PygtsObjects */ if(!pygts_surface_check(s_)) { PyErr_SetString(PyExc_TypeError,"expected a Surface"); return NULL; } s = PYGTS_OBJECT(s_); if( gts_vertex_is_boundary(PYGTS_VERTEX_AS_GTS_VERTEX(self), PYGTS_SURFACE_AS_GTS_SURFACE(s)) ) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* contacts(PygtsVertex* self, PyObject *args) { PyObject *sever_=NULL; gboolean sever=FALSE; guint n; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "|O", &sever_) ) { return NULL; } /* Convert to PygtsObjects */ if( sever_ != NULL ) { if(!PyBool_Check(sever_)) { PyErr_SetString(PyExc_TypeError,"expected a Boolean"); return NULL; } if( sever_ == Py_True ) { sever = TRUE; } } n = gts_vertex_is_contact(PYGTS_VERTEX_AS_GTS_VERTEX(self),sever); return Py_BuildValue("i",n); } static PyObject* is_connected(PygtsVertex *self, PyObject *args) { PyObject *v_; PygtsVertex *v; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &v_) ) { return NULL; } /* Convert to PygtsObjects */ if(!pygts_vertex_check(v_)) { PyErr_SetString(PyExc_TypeError,"expected a Vertex"); return NULL; } v = PYGTS_VERTEX(v_); if( gts_vertices_are_connected(PYGTS_VERTEX_AS_GTS_VERTEX(self), PYGTS_VERTEX_AS_GTS_VERTEX(v)) != NULL ) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* replace(PygtsVertex *self, PyObject *args) { PyObject *p2_; PygtsVertex *p2; GSList *parents=NULL, *i, *cur; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &p2_) ) { return NULL; } /* Convert to PygtsObjects */ if(!pygts_vertex_check(p2_)) { PyErr_SetString(PyExc_TypeError,"expected a Vertex"); return NULL; } p2 = PYGTS_VERTEX(p2_); if( self != p2 ) { /* (Ignore self-replacement) */ /* Detach and save any parent segments */ i = PYGTS_VERTEX_AS_GTS_VERTEX(self)->segments; while(i!=NULL) { cur = i; i = g_slist_next(i); if(PYGTS_IS_PARENT_SEGMENT(cur->data)) { PYGTS_VERTEX_AS_GTS_VERTEX(self)->segments = g_slist_remove_link(PYGTS_VERTEX_AS_GTS_VERTEX(self)->segments, cur); parents = g_slist_prepend(parents,cur->data); g_slist_free_1(cur); } } /* Perform the replace operation */ gts_vertex_replace(PYGTS_VERTEX_AS_GTS_VERTEX(self), PYGTS_VERTEX_AS_GTS_VERTEX(p2)); /* Reattach the parent segments */ i = parents; while(i!=NULL) { PYGTS_VERTEX_AS_GTS_VERTEX(self)->segments = g_slist_prepend(PYGTS_VERTEX_AS_GTS_VERTEX(self)->segments,i->data); i = g_slist_next(i); } g_slist_free(parents); } Py_INCREF(Py_None); return Py_None; } static PyObject* neighbors(PygtsVertex* self, PyObject *args) { PyObject *s_=NULL; GtsSurface *s=NULL; GSList *vertices,*v; PygtsVertex *vertex; PyObject *tuple; guint n,N; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "|O", &s_) ) { return NULL; } /* Convert */ if( s_ != NULL ) { if(!pygts_surface_check(s_)) { PyErr_SetString(PyExc_TypeError,"expected a Surface"); return NULL; } s = PYGTS_SURFACE_AS_GTS_SURFACE(s_); } /* Get the neighbors */ vertices = gts_vertex_neighbors(PYGTS_VERTEX_AS_GTS_VERTEX(self), NULL,s); N = g_slist_length(vertices); /* Create the tuple */ if( (tuple=PyTuple_New(N)) == NULL) { PyErr_SetString(PyExc_MemoryError,"could not create tuple"); return NULL; } /* Put PygtsVertex objects into the tuple */ v = vertices; for(n=0;ndata)) ) { v = g_slist_next(v); } if( v==NULL ) break; if( (vertex = pygts_vertex_new(GTS_VERTEX(v->data))) == NULL ) { Py_DECREF((PyObject*)tuple); return NULL; } PyTuple_SET_ITEM(tuple, n, (PyObject*)vertex); v = g_slist_next(v); } if(_PyTuple_Resize(&tuple,n)!=0) { Py_DECREF(tuple); return NULL; } return tuple; } static PyObject* faces(PygtsVertex* self, PyObject *args) { PyObject *s_=NULL; GtsSurface *s=NULL; GSList *faces,*f; PygtsFace *face; PyObject *tuple; guint n,N; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "|O", &s_) ) { return NULL; } /* Convert */ if( s_ != NULL ) { if(!pygts_surface_check(s_)) { PyErr_SetString(PyExc_TypeError,"expected a Surface"); return NULL; } s = PYGTS_SURFACE_AS_GTS_SURFACE(s_); } /* Get the faces */ faces = gts_vertex_faces(PYGTS_VERTEX_AS_GTS_VERTEX(self),s,NULL); N = g_slist_length(faces); /* Create the tuple */ if( (tuple=PyTuple_New(N)) == NULL) { PyErr_SetString(PyExc_MemoryError,"expected a tuple"); return NULL; } /* Put PygtsVertex objects into the tuple */ f = faces; for(n=0;ndata))) == NULL ) { Py_DECREF(tuple); return NULL; } PyTuple_SET_ITEM(tuple, n, (PyObject*)face); f = g_slist_next(f); } return tuple; } static PyObject* encroaches(PygtsVertex *self, PyObject *args) { PyObject *e_; PygtsEdge *e; SELF_CHECK /* Parse the args */ if(! PyArg_ParseTuple(args, "O", &e_) ) { return NULL; } /* Convert to PygtsObjects */ if(!pygts_edge_check(e_)) { PyErr_SetString(PyExc_TypeError,"expected an Edge"); return NULL; } e = PYGTS_EDGE(e_); if(gts_vertex_encroaches_edge(PYGTS_VERTEX_AS_GTS_VERTEX(self), PYGTS_EDGE_AS_GTS_EDGE(e))) { Py_INCREF(Py_True); return Py_True; } else { Py_INCREF(Py_False); return Py_False; } } static PyObject* triangles(PygtsVertex *self, PyObject *args) { GSList *triangles, *t; PygtsTriangle *triangle; guint i,N; PyObject *tuple; SELF_CHECK triangles = gts_vertex_triangles(PYGTS_VERTEX_AS_GTS_VERTEX(self),NULL); N = g_slist_length(triangles); /* Create the tuple */ if( (tuple=PyTuple_New(N)) == NULL) { PyErr_SetString(PyExc_MemoryError,"could not create tuple"); return NULL; } /* Put PygtsVertex objects into the tuple */ t = triangles; for(i=0;idata))) == NULL ) { Py_DECREF(tuple); return NULL; } PyTuple_SET_ITEM(tuple, i, (PyObject*)triangle); t = g_slist_next(t); } return tuple; } /* Methods table */ static PyMethodDef methods[] = { {"is_ok", (PyCFunction)is_ok, METH_NOARGS, "True if this Vertex v is OK. False otherwise.\n" "This method is useful for unit testing and debugging.\n" "\n" "Signature: v.is_ok().\n" }, {"is_unattached", (PyCFunction)is_unattached, METH_NOARGS, "True if this Vertex v is not the endpoint of any Segment.\n" "\n" "Signature: v.is_unattached().\n" }, {"is_boundary", (PyCFunction)is_boundary, METH_VARARGS, "True if this Vertex v is used by a boundary Edge of Surface s.\n" "\n" "Signature: v.is_boundary().\n" }, {"contacts", (PyCFunction)contacts, METH_VARARGS, "Returns the number of sets of connected Triangles sharing this\n" "Vertex v.\n" "\n" "Signature: v.contacts().\n" "\n" "If sever is True (default: False) and v is a contact vertex then\n" "the vertex is replaced in each Triangle with clones.\n" }, {"is_connected", (PyCFunction)is_connected, METH_VARARGS, "Return True if this Vertex v1 is connected to Vertex v2\n" "by a Segment.\n" "\n" "Signature: v1.is_connected().\n" }, {"replace", (PyCFunction)replace, METH_VARARGS, "Replaces this Vertex v1 with Vertex v2 in all Segments that have v1.\n" "Vertex v1 itself is left unchanged.\n" "\n" "Signature: v1.replace(v2).\n" }, {"neighbors", (PyCFunction)neighbors, METH_VARARGS, "Returns a tuple of Vertices attached to this Vertex v\n" "by a Segment.\n" "\n" "If a Surface s is given, only Vertices on s are considered.\n" "\n" "Signature: v.neighbors() or v.neighbors(s).\n" }, {"faces", (PyCFunction)faces, METH_VARARGS, "Returns a tuple of Faces that have this Vertex v.\n" "\n" "If a Surface s is given, only Vertices on s are considered.\n" "\n" "Signature: v.faces() or v.faces(s).\n" }, {"encroaches", (PyCFunction)encroaches, METH_VARARGS, "Returns True if this Vertex v is strictly contained in the\n" "diametral circle of Edge e. False otherwise.\n" "\n" "Only the projection onto the x-y plane is considered.\n" "\n" "Signature: v.encroaches(e)\n" }, {"triangles", (PyCFunction)triangles, METH_NOARGS, "Returns a list of Triangles that have this Vertex v.\n" "\n" "Signature: v.triangles()\n" }, {NULL} /* Sentinel */ }; /*-------------------------------------------------------------------------*/ /* Python type methods */ static GtsObject * parent(GtsVertex *v1); static PyObject * new(PyTypeObject *type, PyObject *args, PyObject *kwds) { PyObject *o; PygtsObject *obj; guint alloc_gtsobj = TRUE; /* Parse the args */ if(kwds) { o = PyDict_GetItemString(kwds,"alloc_gtsobj"); if(o==Py_False) { alloc_gtsobj = FALSE; } if(o!=NULL) { PyDict_DelItemString(kwds, "alloc_gtsobj"); } } if(kwds) { Py_INCREF(Py_False); PyDict_SetItemString(kwds,"alloc_gtsobj", Py_False); } /* Chain up */ obj = PYGTS_OBJECT(PygtsPointType.tp_new(type,args,kwds)); /* Allocate the gtsobj (if needed) */ if( alloc_gtsobj ) { obj->gtsobj = GTS_OBJECT(gts_vertex_new(gts_vertex_class(),0,0,0)); if( obj->gtsobj == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create Vertex"); return NULL; } /* Create the parent GtsSegment */ if( (obj->gtsobj_parent=parent(GTS_VERTEX(obj->gtsobj))) == NULL ) { gts_object_destroy(obj->gtsobj); obj->gtsobj = NULL; return NULL; } pygts_object_register(obj); } return (PyObject*)obj; } static int init(PygtsVertex *self, PyObject *args, PyObject *kwds) { gint ret; /* Chain up */ if( (ret=PygtsPointType.tp_init((PyObject*)self,args,kwds)) != 0 ) { return ret; } return 0; } /* Methods table */ PyTypeObject PygtsVertexType = { PyObject_HEAD_INIT(NULL) 0, /* ob_size */ "gts.Vertex", /* tp_name */ sizeof(PygtsVertex), /* tp_basicsize */ 0, /* tp_itemsize */ 0, /* tp_dealloc */ 0, /* tp_print */ 0, /* tp_getattr */ 0, /* tp_setattr */ 0, /* tp_compare */ 0, /* tp_repr */ 0, /* tp_as_number */ 0, /* tp_as_sequence */ 0, /* tp_as_mapping */ 0, /* tp_hash */ 0, /* tp_call */ 0, /* tp_str */ 0, /* tp_getattro */ 0, /* tp_setattro */ 0, /* tp_as_buffer */ Py_TPFLAGS_DEFAULT | Py_TPFLAGS_BASETYPE, /* tp_flags */ "Vertex object", /* tp_doc */ 0, /* tp_traverse */ 0, /* tp_clear */ 0, /* tp_richcompare */ 0, /* tp_weaklistoffset */ 0, /* tp_iter */ 0, /* tp_iternext */ methods, /* tp_methods */ 0, /* tp_members */ 0, /* tp_getset */ 0, /* tp_base: attached in pygts.c */ 0, /* tp_dict */ 0, /* tp_descr_get */ 0, /* tp_descr_set */ 0, /* tp_dictoffset */ (initproc)init, /* tp_init */ 0, /* tp_alloc */ (newfunc)new /* tp_new */ }; /*-------------------------------------------------------------------------*/ /* Pygts functions */ gboolean pygts_vertex_check(PyObject* o) { gboolean check = FALSE; guint i,N; PyObject *obj; /* Check for a Vertex */ if( PyObject_TypeCheck(o, &PygtsVertexType) ) { check = TRUE; } /* Convert list into tuple */ if(PyList_Check(o)) { o = PyList_AsTuple(o); } else { Py_INCREF(o); } /* Check for a tuple of floats */ if( PyTuple_Check(o) ) { if( (N = PyTuple_Size(o)) <= 3 ) { check = TRUE; for(i=0;igtsobj_parent!=NULL,FALSE); g_return_val_if_fail(PYGTS_IS_PARENT_SEGMENT(obj->gtsobj_parent),FALSE); parent = g_slist_find(GTS_VERTEX(obj->gtsobj)->segments, obj->gtsobj_parent); g_return_val_if_fail(parent!=NULL,FALSE); return TRUE; } static GtsObject * parent(GtsVertex *v1) { GtsPoint *p1; GtsVertex *v2; GtsSegment *p; /* Create another Vertex */ p1 = GTS_POINT(v1); if( (v2 = gts_vertex_new(pygts_parent_vertex_class(),p1->x,p1->y,p1->z+1)) == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create parent"); return NULL; } /* Create and return the parent */ if( (p = gts_segment_new(pygts_parent_segment_class(),v1,v2)) == NULL ) { PyErr_SetString(PyExc_MemoryError, "could not create parent"); gts_object_destroy(GTS_OBJECT(v2)); return NULL; } return GTS_OBJECT(p); } PygtsVertex * pygts_vertex_new(GtsVertex *v) { PyObject *args, *kwds; PygtsObject *vertex; /* Check for Vertex in the object table */ if( (vertex = PYGTS_OBJECT(g_hash_table_lookup(obj_table,GTS_OBJECT(v)))) !=NULL ) { Py_INCREF(vertex); return PYGTS_VERTEX(vertex); } /* Build a new Vertex */ args = Py_BuildValue("ddd",0,0,0); kwds = Py_BuildValue("{s:O}","alloc_gtsobj",Py_False); vertex = PYGTS_VERTEX(PygtsVertexType.tp_new(&PygtsVertexType, args, kwds)); Py_DECREF(args); Py_DECREF(kwds); if( vertex == NULL ) { PyErr_SetString(PyExc_MemoryError,"could not create Vertex"); return NULL; } vertex->gtsobj = GTS_OBJECT(v); /* Attach the parent */ if( (vertex->gtsobj_parent=parent(v)) == NULL ) { Py_DECREF(vertex); return NULL; } /* Register and return */ pygts_object_register(vertex); return PYGTS_VERTEX(vertex); } PygtsVertex * pygts_vertex_from_sequence(PyObject *tuple) { guint i,N; gdouble x=0,y=0,z=0; PyObject *obj; GtsVertex *v; PygtsVertex *vertex; /* Convert list into tuple */ if(PyList_Check(tuple)) { tuple = PyList_AsTuple(tuple); } else { Py_INCREF(tuple); } if(!PyTuple_Check(tuple)) { Py_DECREF(tuple); PyErr_SetString(PyExc_TypeError,"expected a list or tuple of vertices"); return NULL; } /* Get the tuple size */ if( (N = PyTuple_Size(tuple)) > 3 ) { PyErr_SetString(PyExc_RuntimeError, "expected a list or tuple of up to three floats"); Py_DECREF(tuple); return NULL; } /* Get the coordinates */ for(i=0;iinfo.class_init_func), (GtsObjectInitFunc)(super->info.object_init_func), (GtsArgSetFunc) NULL, (GtsArgGetFunc) NULL }; klass = gts_object_class_new(gts_object_class(), &pygts_parent_segment_info); } return klass; } GtsVertexClass* pygts_parent_vertex_class(void) { static GtsVertexClass *klass = NULL; GtsObjectClass *super = NULL; if (klass == NULL) { super = GTS_OBJECT_CLASS(gts_vertex_class()); GtsObjectClassInfo pygts_parent_vertex_info = { "PygtsParentVertex", sizeof(PygtsParentVertex), sizeof(GtsVertexClass), (GtsObjectClassInitFunc)(super->info.class_init_func), (GtsObjectInitFunc)(super->info.object_init_func), (GtsArgSetFunc) NULL, (GtsArgGetFunc) NULL }; klass = gts_object_class_new(gts_object_class(), &pygts_parent_vertex_info); } return klass; } trunk-2017.01a/py/3rd-party/pygts-0.3.1/vertex.h000066400000000000000000000057011304022710500207330ustar00rootroot00000000000000/* pygts - python package for the manipulation of triangulated surfaces * * Copyright (C) 2009 Thomas J. Duck * All rights reserved. * * Thomas J. Duck * Department of Physics and Atmospheric Science, * Dalhousie University, Halifax, Nova Scotia, Canada, B3H 3J5 * * NOTICE * * This library is free software; you can redistribute it and/or * modify it under the terms of the GNU Library General Public * License as published by the Free Software Foundation; either * version 2 of the License, or (at your option) any later version. * * This library is distributed in the hope that it will be useful, * but WITHOUT ANY WARRANTY; without even the implied warranty of * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU * Library General Public License for more details. * * You should have received a copy of the GNU Library General Public * License along with this library; if not, write to the * Free Software Foundation, Inc., 59 Temple Place - Suite 330, * Boston, MA 02111-1307, USA. */ #ifndef __PYGTS_VERTEX_H__ #define __PYGTS_VERTEX_H__ typedef struct _PygtsObject PygtsVertex; #define PYGTS_VERTEX(o) \ ( PyObject_TypeCheck((PyObject*)o, &PygtsVertexType) ? \ (PygtsVertex*)o : \ pygts_vertex_from_sequence((PyObject*)o) ) #define PYGTS_VERTEX_AS_GTS_VERTEX(o) \ ( PyObject_TypeCheck((PyObject*)o, &PygtsVertexType) ? \ GTS_VERTEX(PYGTS_OBJECT(o)->gtsobj) : \ GTS_VERTEX(PYGTS_OBJECT(PYGTS_VERTEX(o))->gtsobj) ) extern PyTypeObject PygtsVertexType; gboolean pygts_vertex_check(PyObject* o); gboolean pygts_vertex_is_ok(PygtsVertex *v); PygtsVertex* pygts_vertex_new(GtsVertex *f); PygtsVertex* pygts_vertex_from_sequence(PyObject *tuple); /*-------------------------------------------------------------------------*/ /* Parent GTS segment for GTS vertices */ /* Define a GtsSegment subclass that can be readily identified as the parent * of an encapsulated GtsVertex. The pygts_parent_segment_class() function * is defined at the bottom, and is what ultimately allows the distinction * to be made. This capability is used for vertex replacement operations. */ typedef struct _GtsSegment PygtsParentSegment; #define PYGTS_PARENT_SEGMENT(obj) GTS_OBJECT_CAST(obj,\ GtsSegment,\ pygts_parent_segment_class()) #define PYGTS_IS_PARENT_SEGMENT(obj)(gts_object_is_from_class(obj,\ pygts_parent_segment_class())) GtsSegmentClass* pygts_parent_segment_class(void); /* GTS vertices in parent segments */ typedef struct _GtsVertex PygtsParentVertex; #define PYGTS_PARENT_VERTEX(obj) GTS_OBJECT_CAST(obj,\ GtsVertex,\ pygts_parent_vertex_class()) #define PYGTS_IS_PARENT_VERTEX(obj)(gts_object_is_from_class(obj,\ pygts_parent_vertex_class())) GtsVertexClass *pygts_parent_vertex_class(void); #endif /* __PYGTS_VERTEX_H__ */ trunk-2017.01a/py/CMakeLists.txt000066400000000000000000000071011304022710500163510ustar00rootroot00000000000000#==================pygts========================================= IF(ENABLE_GTS) find_python_module(gts) IF (PY_gts) MESSAGE(STATUS "Use system gts version") ELSE (PY_gts) MESSAGE(STATUS "Use embedded version of gts. Please, consider installing the corresponding package") FILE(GLOB SRC_PYGTS "${CMAKE_CURRENT_SOURCE_DIR}/3rd-party/pygts-0.3.1/*.c") ADD_LIBRARY(_gts SHARED ${SRC_PYGTS}) SET_TARGET_PROPERTIES(_gts PROPERTIES PREFIX "") TARGET_LINK_LIBRARIES(_gts gts) INSTALL(FILES 3rd-party/pygts-0.3.1/__init__.py DESTINATION ${YADE_LIB_PATH}/py/gts) INSTALL(FILES 3rd-party/pygts-0.3.1/pygts.py DESTINATION ${YADE_LIB_PATH}/py/gts) INSTALL(TARGETS _gts DESTINATION ${YADE_LIB_PATH}/py/gts) ENDIF (PY_gts) ENDIF(ENABLE_GTS) #==================pygts========================================= #==================pyModules========================================= FILE(GLOB filesPY "${CMAKE_CURRENT_SOURCE_DIR}/*.py") SET(filesPY "${filesPY};${CMAKE_CURRENT_SOURCE_DIR}/pack/pack.py") INSTALL(FILES ${filesPY} DESTINATION ${YADE_PY_PATH}/yade) INSTALL(FILES 3rd-party/mtTkinter-0.4/mtTkinter.py DESTINATION ${YADE_LIB_PATH}/py) FILE(GLOB filesPYTests "${CMAKE_CURRENT_SOURCE_DIR}/tests/*.py") INSTALL(FILES ${filesPYTests} DESTINATION ${YADE_PY_PATH}/yade/tests) FILE(GLOB filesPYPerf "${CMAKE_CURRENT_SOURCE_DIR}/../examples/test/performance/*") INSTALL(FILES ${filesPYPerf} DESTINATION ${YADE_PY_PATH}/yade/tests/checks/performance) FILE(GLOB filesFEMxDEM "${CMAKE_CURRENT_SOURCE_DIR}/FEMxDEM/*.py") INSTALL(FILES ${filesFEMxDEM} DESTINATION ${YADE_PY_PATH}/yade/FEMxDEM) ADD_LIBRARY(WeightedAverage2d SHARED "${CMAKE_CURRENT_SOURCE_DIR}/WeightedAverage2d.cpp") SET_TARGET_PROPERTIES(WeightedAverage2d PROPERTIES PREFIX "") INSTALL(TARGETS WeightedAverage2d DESTINATION "${YADE_PY_PATH}/yade/") ADD_LIBRARY(_utils SHARED "${CMAKE_CURRENT_SOURCE_DIR}/_utils.cpp") SET_TARGET_PROPERTIES(_utils PROPERTIES PREFIX "") TARGET_LINK_LIBRARIES(_utils yade) INSTALL(TARGETS _utils DESTINATION "${YADE_PY_PATH}/yade/") ADD_LIBRARY(_polyhedra_utils SHARED "${CMAKE_CURRENT_SOURCE_DIR}/_polyhedra_utils.cpp") SET_TARGET_PROPERTIES(_polyhedra_utils PROPERTIES PREFIX "") TARGET_LINK_LIBRARIES(_polyhedra_utils) INSTALL(TARGETS _polyhedra_utils DESTINATION "${YADE_PY_PATH}/yade/") ADD_LIBRARY(_packPredicates SHARED "${CMAKE_CURRENT_SOURCE_DIR}/pack/_packPredicates.cpp") SET_TARGET_PROPERTIES(_packPredicates PROPERTIES PREFIX "") TARGET_LINK_LIBRARIES(_packPredicates yade) IF(ENABLE_GTS AND NOT(PY_gts)) TARGET_LINK_LIBRARIES(_packPredicates _gts) ENDIF(ENABLE_GTS AND NOT(PY_gts)) INSTALL(TARGETS _packPredicates DESTINATION "${YADE_PY_PATH}/yade/") ADD_LIBRARY(_packSpheres SHARED "${CMAKE_CURRENT_SOURCE_DIR}/pack/_packSpheres.cpp") SET_TARGET_PROPERTIES(_packSpheres PROPERTIES PREFIX "") TARGET_LINK_LIBRARIES(_packSpheres yade) INSTALL(TARGETS _packSpheres DESTINATION "${YADE_PY_PATH}/yade/") ADD_LIBRARY(_packObb SHARED "${CMAKE_CURRENT_SOURCE_DIR}/pack/_packObb.cpp") SET_TARGET_PROPERTIES(_packObb PROPERTIES PREFIX "") INSTALL(TARGETS _packObb DESTINATION "${YADE_PY_PATH}/yade/") ADD_LIBRARY(wrapper SHARED "${CMAKE_CURRENT_SOURCE_DIR}/wrapper/yadeWrapper.cpp") SET_TARGET_PROPERTIES(wrapper PROPERTIES PREFIX "") TARGET_LINK_LIBRARIES(wrapper yade) INSTALL(TARGETS wrapper DESTINATION "${YADE_PY_PATH}/yade/") ADD_LIBRARY(_customConverters SHARED "${CMAKE_CURRENT_SOURCE_DIR}/wrapper/customConverters.cpp") SET_TARGET_PROPERTIES(_customConverters PROPERTIES PREFIX "") TARGET_LINK_LIBRARIES(_customConverters yade) INSTALL(TARGETS _customConverters DESTINATION "${YADE_PY_PATH}/yade/") trunk-2017.01a/py/FEMxDEM/000077500000000000000000000000001304022710500147375ustar00rootroot00000000000000trunk-2017.01a/py/FEMxDEM/mpipool.py000066400000000000000000000041031304022710500167660ustar00rootroot00000000000000__contributor__="Lisandro Dalcín" """ MPIPool wrapped using mpi4py """ #import mpi4py #mpi4py.rc.threaded = False from mpi4py import MPI class MPIPool(object): def __init__(self, comm=None, master=0): self.comm = MPI.COMM_WORLD if comm is None else comm self.master = master self.workers = set(range(self.comm.size)) self.workers.discard(self.master) def is_master(self): return self.master == self.comm.rank def is_worker(self): return self.comm.rank in self.workers def map(self, function, iterable): assert self.is_master() comm = self.comm workerset = self.workers.copy() tasklist = [(tid, (function, arg)) for tid, arg in enumerate(iterable)] resultlist = [None] * len(tasklist) pending = len(tasklist) while pending: if workerset and tasklist: worker = workerset.pop() taskid, task = tasklist.pop() comm.send(task, dest=worker, tag=taskid) if tasklist: flag = comm.Iprobe(source=MPI.ANY_SOURCE, tag=MPI.ANY_TAG) if not flag: continue else: comm.Probe(source=MPI.ANY_SOURCE, tag=MPI.ANY_TAG) status = MPI.Status() result = comm.recv(source=MPI.ANY_SOURCE, tag=MPI.ANY_TAG, status=status) worker = status.source workerset.add(worker) taskid = status.tag resultlist[taskid] = result pending -= 1 return resultlist def start(self): if not self.is_worker(): return comm = self.comm master = self.master status = MPI.Status() while True: task = comm.recv(source=master, tag=MPI.ANY_TAG, status=status) if task is None: break function, arg = task result = function(arg) comm.ssend(result, master, status.tag) def close(self): if not self.is_master(): return for worker in self.workers: self.comm.send(None, worker, 0) trunk-2017.01a/py/FEMxDEM/msFEM2D.py000066400000000000000000000240141304022710500164470ustar00rootroot00000000000000__author__="Ning Guo, ceguo@connect.ust.hk" __supervisor__="Jidong Zhao, jzhao@ust.hk" __institution__="The Hong Kong University of Science and Technology" """ 2D model for multiscale simulation which implements a Newton-Raphson scheme into FEM framework to solve the nonlinear problem where the tangent operator is obtained from DEM simulation by calling simDEM modules""" # import Escript modules import esys.escript as escript from esys.escript import util from esys.escript.linearPDEs import LinearPDE,SolverOptions # import YADE modules from simDEM import * # other python modules from itertools import repeat """ function to return pool for parallelization supporting both MPI (experimental) on distributed memory and multiprocessing on shared memory. """ def get_pool(mpi=False,threads=1): if mpi: # using MPI from mpipool import MPIPool pool = MPIPool() pool.start() if not pool.is_master(): sys.exit(0) elif threads>1: # using multiprocessing from multiprocessing import Pool pool = Pool(processes=threads) else: raise RuntimeError,"Wrong arguments: either mpi=True or threads>1." return pool class MultiScale(object): """ problem description: -(A_{ijkl} u_{k,l})_{,j} = -X_{ij,j} + Y_i Neumann boundary: n_j A_{ijkl} u_{k,l} = n_j X_{ij} + y_i Dirichlet boundary: u_i = r_i where q_i > 0 :var u: unknown vector, displacement :var A: elastic tensor / tangent operator :var X: old/current stress tensor :var Y: vector, body force :var y: vector, Neumann bc traction :var q: vector, Dirichlet bc mask :var r: vector, Dirichlet bc value """ def __init__(self,domain,ng=1,useMPI=False,np=1,random=False,rtol=1.e-2,usePert=False,pert=-2.e-6,verbose=False): """ initialization of the problem, i.e. model constructor :param domain: type Domain, domain of the problem :param ng: type integer, number of Gauss points :param useMPI: type boolean, use MPI or not :param np: type integer, number of processors :param random: type boolean, if or not use random density field :param rtol: type float, relevative tolerance for global convergence :param usePert: type boolean, if or not use perturbation method :param pert: type float, perturbated strain applied to DEM to obtain tangent operator :param verbose: type boolean, if or not print messages during calculation """ self.__domain=domain self.__pde=LinearPDE(domain,numEquations=self.__domain.getDim(),numSolutions=self.__domain.getDim()) self.__pde.getSolverOptions().setSolverMethod(SolverOptions.DIRECT) self.__pde.setSymmetryOn() #self.__pde.getSolverOptions().setTolerance(rtol**2) #self.__pde.getSolverOptions().setPackage(SolverOptions.UMFPACK) self.__numGaussPoints=ng self.__rtol=rtol self.__usepert=usePert self.__pert=pert self.__verbose=verbose self.__pool=get_pool(mpi=useMPI,threads=np) self.__scenes=self.__pool.map(initLoad,range(ng)) self.__strain=escript.Tensor(0,escript.Function(self.__domain)) self.__stress=escript.Tensor(0,escript.Function(self.__domain)) self.__S=escript.Tensor4(0,escript.Function(self.__domain)) if self.__usepert: s = self.__pool.map(getStressTensor,self.__scenes) t = self.__pool.map(getTangentOperator,zip(self.__scenes,repeat(pert))) for i in xrange(ng): self.__stress.setValueOfDataPoint(i,s[i]) self.__S.setValueOfDataPoint(i,t[i]) else: st = self.__pool.map(getStressAndTangent2D,self.__scenes) for i in xrange(ng): self.__stress.setValueOfDataPoint(i,st[i][0]) self.__S.setValueOfDataPoint(i,st[i][1]) def initialize(self, b=escript.Data(), f=escript.Data(), specified_u_mask=escript.Data(), specified_u_val=escript.Data()): """ initialize the model for each time step, e.g. assign parameters :param b: type vector, body force on FunctionSpace, e.g. gravity :param f: type vector, boundary traction on FunctionSpace (FunctionOnBoundary) :param specified_u_mask: type vector, mask of location for Dirichlet boundary :param specified_u_val: type vector, specified displacement for Dirichlet boundary """ self.__pde.setValue(Y=b,y=f,q=specified_u_mask,r=specified_u_val) def getDomain(self): """ return model domain """ return self.__domain def getRelTolerance(self): """ return relative tolerance for convergence type float """ return self.__rtol def getCurrentPacking(self,pos=(),time=0,prefix=''): if len(pos) == 0: # output all Gauss points packings self.__pool.map(outputPack,zip(self.__scenes,repeat(time),repeat(prefix))) else: # output selected Gauss points packings scene = [self.__scenes[i] for i in pos] self.__pool.map(outputPack,zip(scene,repeat(time),repeat(prefix))) def getLocalVoidRatio(self): void=escript.Scalar(0,escript.Function(self.__domain)) e = self.__pool.map(getVoidRatio2D,self.__scenes) for i in xrange(self.__numGaussPoints): void.setValueOfDataPoint(i,e[i]) return void def getLocalAvgRotation(self): rot=escript.Scalar(0,escript.Function(self.__domain)) r = self.__pool.map(avgRotation2D,self.__scenes) for i in xrange(self.__numGaussPoints): rot.setValueOfDataPoint(i,r[i]) return rot def getLocalFabric(self): fabric=escript.Tensor(0,escript.Function(self.__domain)) f = self.__pool.map(getFabric2D,self.__scenes) for i in xrange(self.__numGaussPoints): fabric.setValueOfDataPoint(i,f[i]) return fabric """ used for clumped particle model only def getLocalParOriFab(self): fabric=escript.Tensor(0,escript.Function(self.__domain)) f = self.__pool.map(getParOriFabric,self.__scenes) for i in xrange(self.__numGaussPoints): fabric.setValueOfDataPoint(i,f[i]) return fabric """ """ used for cohesive particle model only def getLocalBondBreakage(self,oriIntr=[]): debond = escript.Scalar(0,escript.Function(self.__domain)) num = self.__pool.map(getDebondingNumber,zip(self.__scenes,repeat(oriIntr))) for i in xrange(self.__numGaussPoints): debond.setValueOfDataPoint(i,num[i]) return debond """ def getCurrentTangent(self): """ return current tangent operator type Tensor4 on FunctionSpace """ return self.__S def getCurrentStress(self): """ return current stress type: Tensor on FunctionSpace """ return self.__stress def getCurrentStrain(self): """ return current strain type: Tensor on FunctionSpace """ return self.__strain def exitSimulation(self): """finish the whole simulation, exit""" self.__pool.close() def solve(self, iter_max=100): """ solve the equation using Newton-Ralphson scheme """ iterate=0 rtol=self.getRelTolerance() stress=self.getCurrentStress() s=self.getCurrentTangent() x_safe=self.__domain.getX() self.__pde.setValue(A=s, X=-stress) #residual0=util.L2(self.__pde.getRightHandSide()) # using force error u=self.__pde.getSolution() # trial solution, displacement D=util.grad(u) # trial strain tensor # !!!!!! obtain stress and tangent operator from DEM part update_stress,update_s,update_scenes=self.applyStrain_getStressTangentDEM(st=D) err=1.0 # initial error before iteration converged=(errrtol*0.001: # only update DEM parts when error is large enough self.__domain.setX(x_safe) D=util.grad(u) update_stress,update_s,update_scenes=self.applyStrain_getStressTangentDEM(st=D) #if err>err_safe: # to ensure consistent convergence, however this may not be achieved due to fluctuation! # raise RuntimeError,"No improvement of convergence with iterations! Relative error: %e"%err """ update 'domain geometry', 'stress', 'tangent operator', 'accumulated strain' and 'simulation scenes'. """ self.__domain.setX(x_safe+u) self.__stress=update_stress self.__S=update_s self.__strain+=D self.__scenes=update_scenes if self.__verbose: print "Convergence reached after %d iteration(s)! Relative error: %e"%(iterate,err) return u """ apply strain to DEM packing, get stress and tangent operator (including two methods) """ def applyStrain_getStressTangentDEM(self,st=escript.Data()): st = st.toListOfTuples() st = numpy.array(st).reshape(-1,4) stress = escript.Tensor(0,escript.Function(self.__domain)) S = escript.Tensor4(0,escript.Function(self.__domain)) scenes = self.__pool.map(shear2D,zip(self.__scenes,st)) if self.__usepert: s = self.__pool.map(getStressTensor,scenes) t = self.__pool.map(getTangentOperator,zip(scenes,repeat(self.__pert))) for i in xrange(self.__numGaussPoints): stress.setValueOfDataPoint(i,s[i]) S.setValueOfDataPoint(i,t[i]) else: ST = self.__pool.map(getStressAndTangent2D,scenes) for i in xrange(self.__numGaussPoints): stress.setValueOfDataPoint(i,ST[i][0]) S.setValueOfDataPoint(i,ST[i][1]) return stress,S,scenes trunk-2017.01a/py/FEMxDEM/msFEM3D.py000066400000000000000000000206721304022710500164560ustar00rootroot00000000000000__author__="Ning Guo, ceguo@connect.ust.hk" __supervisor__="Jidong Zhao, jzhao@ust.hk" __institution__="The Hong Kong University of Science and Technology" """ 3D model for multiscale simulation which implements a Newton-Raphson scheme into FEM framework to solve the nonlinear problem where the tangent operator is obtained from DEM simulation by calling simDEM modules""" """ import Escript modules """ import esys.escript as escript from esys.escript import util from esys.escript.linearPDEs import LinearPDE,SolverOptions from simDEM import * from itertools import repeat """ function to return pool for parallelization supporting both MPI (experimental) on distributed memory and multiprocessing on shared memory. """ def get_pool(mpi=False,threads=1): if mpi: # using MPI from mpipool import MPIPool pool = MPIPool() pool.start() if not pool.is_master(): sys.exit(0) elif threads>1: # using multiprocessing from multiprocessing import Pool pool = Pool(processes=threads) else: raise RuntimeError,"Wrong arguments: either mpi=True or threads>1." return pool class MultiScale(object): """ problem description: -(A_{ijkl} u_{k,l})_{,j} = -X_{ij,j} + Y_i Neumann boundary: n_j A_{ijkl} u_{k,l} = n_j X_{ij} + y_i Dirichlet boundary: u_i = r_i where q_i > 0 :var u: unknown vector, displacement :var A: elastic tensor / tangent operator :var X: old/current stress tensor :var Y: vector, body force :var y: vector, Neumann bc traction :var q: vector, Dirichlet bc mask :var r: vector, Dirichlet bc value """ def __init__(self,domain,ng=1,useMPI=False,np=1,random=False,rtol=1.e-2,verbose=False): """ initialization of the problem, i.e. model constructor :param domain: type Domain, domain of the problem :param ng: type integer, number of Gauss points :param useMPI: type boolean, use MPI or not :param np: type integer, number of processors :param random: type boolean, if or not use random density field :param rtol: type float, relevant tolerance for global convergence :param verbose: type boolean, if or not print messages during calculation """ self.__domain=domain self.__pde=LinearPDE(domain,numEquations=self.__domain.getDim(),numSolutions=self.__domain.getDim()) self.__pde.getSolverOptions().setSolverMethod(SolverOptions.DIRECT) self.__pde.setSymmetryOn() #self.__pde.getSolverOptions().setTolerance(rtol**2) #self.__pde.getSolverOptions().setPackage(SolverOptions.UMFPACK) self.__numGaussPoints=ng self.__rtol=rtol self.__verbose=verbose self.__pool=get_pool(mpi=useMPI,threads=np) self.__scenes=self.__pool.map(initLoad,range(ng)) self.__strain=escript.Tensor(0,escript.Function(self.__domain)) self.__stress=escript.Tensor(0,escript.Function(self.__domain)) self.__S=escript.Tensor4(0,escript.Function(self.__domain)) st = self.__pool.map(getStressAndTangent,self.__scenes) for i in xrange(ng): self.__stress.setValueOfDataPoint(i,st[i][0]) self.__S.setValueOfDataPoint(i,st[i][1]) def initialize(self, b=escript.Data(), f=escript.Data(), specified_u_mask=escript.Data(), specified_u_val=escript.Data()): """ initialize the model for each time step, e.g. assign parameters :param b: type vector, body force on FunctionSpace, e.g. gravity :param f: type vector, boundary traction on FunctionSpace (FunctionOnBoundary) :param specified_u_mask: type vector, mask of location for Dirichlet boundary :param specified_u_val: type vector, specified displacement for Dirichlet boundary """ self.__pde.setValue(Y=b,y=f,q=specified_u_mask,r=specified_u_val) def getDomain(self): """ return model domain """ return self.__domain def getRelTolerance(self): """ return relative tolerance for convergence type float """ return self.__rtol def getCurrentPacking(self,pos=(),time=0,prefix=''): if len(pos) == 0: # output all Gauss points packings self.__pool.map(outputPack,zip(self.__scenes,repeat(time),repeat(prefix))) else: # output selected Gauss points packings scene = [self.__scenes[i] for i in pos] self.__pool.map(outputPack,zip(scene,repeat(time),repeat(prefix))) def getLocalVoidRatio(self): void=escript.Scalar(0,escript.Function(self.__domain)) e = self.__pool.map(getVoidRatio,self.__scenes) for i in xrange(self.__numGaussPoints): void.setValueOfDataPoint(i,e[i]) return void def getLocalAvgRotation(self): rot=escript.Vector(0,escript.Function(self.__domain)) r = self.__pool.map(avgRotation,self.__scenes) for i in xrange(self.__numGaussPoints): rot.setValueOfDataPoint(i,r[i]) return rot def getLocalFabric(self): fabric=escript.Tensor(0,escript.Function(self.__domain)) f = self.__pool.map(getFabric,self.__scenes) for i in xrange(self.__numGaussPoints): fabric.setValueOfDataPoint(i,f[i]) return fabric def getCurrentTangent(self): """ return current tangent operator type Tensor4 on FunctionSpace """ return self.__S def getCurrentStress(self): """ return current stress type: Tensor on FunctionSpace """ return self.__stress def getCurrentStrain(self): """ return current strain type: Tensor on FunctionSpace """ return self.__strain def exitSimulation(self): """finish the whole simulation, exit""" self.__pool.close() def solve(self, iter_max=100): """ solve the equation using Newton-Ralphson scheme """ iterate=0 rtol=self.getRelTolerance() stress=self.getCurrentStress() s=self.getCurrentTangent() x_safe=self.__domain.getX() self.__pde.setValue(A=s, X=-stress) #residual0=util.L2(self.__pde.getRightHandSide()) # using force error u=self.__pde.getSolution() # trial solution, displacement D=util.grad(u) # trial strain tensor # !!!!!! obtain stress and tangent operator from DEM part update_stress,update_s,update_scenes=self.applyStrain_getStressTangentDEM(st=D) err=1.0 # initial error before iteration converged=(errrtol*0.001: # only update DEM parts when error is large enough self.__domain.setX(x_safe) D=util.grad(u) update_stress,update_s,update_scenes=self.applyStrain_getStressTangentDEM(st=D) #if err>err_safe: # to ensure consistent convergence, however this may not be achieved due to fluctuation! # raise RuntimeError,"No improvement of convergence with iterations! Relative error: %e"%err """ update 'domain geometry', 'stress', 'tangent operator', 'accumulated strain' and 'simulation scenes'. """ self.__domain.setX(x_safe+u) self.__stress=update_stress self.__S=update_s self.__strain+=D self.__scenes=update_scenes if self.__verbose: print "Convergence reached after %d iteration(s)! Relative error: %e"%(iterate,err) return u """ apply strain to DEM packing, get stress and tangent operator (including two methods) """ def applyStrain_getStressTangentDEM(self,st=escript.Data()): st = st.toListOfTuples() st = numpy.array(st).reshape(-1,9) stress = escript.Tensor(0,escript.Function(self.__domain)) S = escript.Tensor4(0,escript.Function(self.__domain)) scenes = self.__pool.map(shear,zip(self.__scenes,st)) st = self.__pool.map(getStressAndTangent,scenes) for i in xrange(self.__numGaussPoints): stress.setValueOfDataPoint(i,st[i][0]) S.setValueOfDataPoint(i,st[i][1]) return stress,S,scenes trunk-2017.01a/py/FEMxDEM/msFEMup.py000066400000000000000000000263441304022710500166360ustar00rootroot00000000000000__author__="Ning Guo, ceguo@connect.ust.hk" __supervisor__="Jidong Zhao, jzhao@ust.hk" __institution__="The Hong Kong University of Science and Technology" """ 2D model for multiscale simulation of a hydromechanical system based on u-p formulation; iterative scheme (fixed-stress split) is used for the coupled PDEs; Newton-Raphson scheme is used to solve the nonlinear PDE for displacement, pore pressure is solved from the mass conservation equation; total stress is a superposition of the effective stress and pore pressure.""" # import Escript modules import esys.escript as escript from esys.escript import util from esys.escript.linearPDEs import LinearPDE,SolverOptions from simDEM import * from itertools import repeat """ function to return pool for parallelization supporting both MPI (experimental) on distributed memory and multiprocessing on shared memory. """ def get_pool(mpi=False,threads=1): if mpi: # using MPI from mpipool import MPIPool pool = MPIPool() pool.start() if not pool.is_master(): sys.exit(0) elif threads>1: # using multiprocessing from multiprocessing import Pool pool = Pool(processes=threads) else: raise RuntimeError,"Wrong arguments: either mpi=True or threads>1." return pool class MultiScale(object): """ problem description 1. displacement: -(A_{ijkl} u_{k,l})_{,j} = -X_{ij,j} + Y_i Neumann boundary: n_j A_{ijkl} u_{k,l} = n_j X_{ij} + y_i Dirichlet boundary: u_i = r_i where q_i > 0 :var u: unknown vector, displacement :var A: elastic tensor / tangent operator :var X: tensor, minus old stress :var Y: vector, gamma - grad(p) :var y: vector, Neumann bc traction :var q: vector, Dirichlet bc mask :var r: vector, Dirichlet bc value 2. pore pressure: -(A_{ij} p_{,j})_{,i} + D p = Y Neumann boundary: n_j A_{jl} p_{,l} = y Dirichlet boundary: p = r where q > 0 :var p: unknown scalar, pore pressure :var A: permeability tensor :var D: scalar, n / (K_f dt) :var Y: scalar, -dot(u)_{i,i} + n p_pre / (K_f dt) :var y: scalar, Neumann bc flux :var q: scalar, Dirichlet bc mask :var r: scalar, Dirichlet bc value """ def __init__(self,domain,pore0=0.,perm=1.e-5,kf=2.2e9,dt=0.001,ng=1,useMPI=False,np=1,rtol=1.e-2): """ initialization of the problem, i.e. model constructor :param domain: type Domain, domain of the problem :param pore0: type float, initial pore pressure :param perm: type float, d^2/(150 mu_f) in KC equation :param kf: type float, bulk modulus of the fluid :param dt: type float, time step for calculation :param ng: type integer, number of Gauss points :param useMPI: type boolean, use MPI or not :param np: type integer, number of processors :param rtol: type float, relevative tolerance for global convergence """ self.__domain=domain self.__upde=LinearPDE(domain,numEquations=domain.getDim(),numSolutions=domain.getDim()) self.__ppde=LinearPDE(domain,numEquations=1,numSolutions=1) # use reduced interpolation for pore pressure self.__ppde.setReducedOrderOn() self.__upde.getSolverOptions().setSolverMethod(SolverOptions.DIRECT) self.__ppde.getSolverOptions().setSolverMethod(SolverOptions.DIRECT) self.__upde.setSymmetryOn() self.__ppde.setSymmetryOn() self.__dt=dt self.__bulkFluid=kf self.__numGaussPoints=ng self.__rtol=rtol self.__stress=escript.Tensor(0,escript.Function(domain)) self.__S=escript.Tensor4(0,escript.Function(domain)) self.__pool=get_pool(mpi=useMPI,threads=np) self.__scenes=self.__pool.map(initLoad,range(ng)) st = self.__pool.map(getStressAndTangent2D,self.__scenes) for i in xrange(ng): self.__stress.setValueOfDataPoint(i,st[i][0]) self.__S.setValueOfDataPoint(i,st[i][1]) self.__strain=escript.Tensor(0,escript.Function(domain)) self.__pore=escript.Scalar(pore0,escript.ReducedSolution(domain)) self.__pgauss=util.interpolate(pore0,escript.Function(domain)) self.__permeability=perm self.__meanStressRate=escript.Scalar(0,escript.Function(domain)) self.__r=escript.Vector(0,escript.Solution(domain)) #Dirichlet BC for u def initialize(self, b=escript.Data(), f=escript.Data(), umsk=escript.Data(), uvalue=escript.Data(), flux=escript.Data(), pmsk=escript.Data(), pvalue=escript.Data()): """ initialize the model for each time step, e.g. assign parameters :param b: type vector, body force on FunctionSpace, e.g. gravity :param f: type vector, boundary traction on FunctionSpace (FunctionOnBoundary) :param umsk: type vector, mask of location for Dirichlet boundary :param uvalue: type vector, specified displacement for Dirichlet boundary """ self.__upde.setValue(Y=b,y=f,q=umsk,r=uvalue) self.__ppde.setValue(y=flux,q=pmsk,r=pvalue) self.__r=uvalue def getDomain(self): """ return model domain """ return self.__domain def setTimeStep(self,dt=1.0): self.__dt = dt def getCurrentPacking(self,pos=(),time=0,prefix=''): if len(pos) == 0: # output all Gauss points packings self.__pool.map(outputPack,zip(self.__scenes,repeat(time),repeat(prefix))) else: # output selected Gauss points packings scene = [self.__scenes[i] for i in pos] self.__pool.map(outputPack,zip(scene,repeat(time),repeat(prefix))) def getEquivalentPorosity(self): porosity=escript.Scalar(0,escript.Function(self.__domain)) p = self.__pool.map(getEquivalentPorosity,self.__scenes) for i in xrange(self.__numGaussPoints): porosity.setValueOfDataPoint(i,p[i]) return porosity def getLocalAvgRotation(self): rot=escript.Scalar(0,escript.Function(self.__domain)) r = self.__pool.map(avgRotation2D,self.__scenes) for i in xrange(self.__numGaussPoints): rot.setValueOfDataPoint(i,r[i]) return rot def getLocalFabric(self): fabric=escript.Tensor(0,escript.Function(self.__domain)) f = self.__pool.map(getFabric2D,self.__scenes) for i in xrange(self.__numGaussPoints): fabric.setValueOfDataPoint(i,f[i]) return fabric def getCurrentTangent(self): """ return current tangent operator type Tensor4 on FunctionSpace """ return self.__S def getCurrentStress(self): """ return current stress (effective) type: Tensor on FunctionSpace """ return self.__stress def getCurrentPore(self): """ return current pore pressure type: Scalar on ReducedSolution """ return self.__pore def getCurrentStrain(self): """ return current strain type: Tensor on FunctionSpace """ return self.__strain def getCurrentFlux(self): """ return current Darcy flux type: Vector on FunctionSpace """ n=self.getEquivalentPorosity() perm=self.__permeability*n**3/(1.-n)**2 flux=-perm*util.grad(self.__pore) return flux def exitSimulation(self): """finish the whole simulation, exit""" self.__pool.close() def solveSolid(self, p_iter_gauss=escript.Data(), iter_max=50): """ solve the pde for displacement using Newton-Ralphson scheme """ k=util.kronecker(self.__domain) p=p_iter_gauss*k iterate=0 rtol=self.__rtol stress_safe=self.__stress s_safe=self.__S x_safe=self.__domain.getX() self.__upde.setValue(A=s_safe, X=-stress_safe+p, r=self.__r) #residual0=util.L2(self.__pde.getRightHandSide()) # using force error u=self.__upde.getSolution() # trial solution, displacement D=util.grad(u) # trial strain tensor # !!!!!! obtain stress and tangent operator from DEM part update_stress,update_s,update_scenes=self.applyStrain_getStressTangentDEM(st=D) err=util.Lsup(u) # initial error before iteration converged=(err<1.e-12) while (not converged) and (iterateiter_max: # raise RuntimeError,"Convergence for Newton-Raphson failed after %s steps."%(iter_max) iterate+=1 self.__domain.setX(x_safe+u) self.__upde.setValue(A=update_s,X=-update_stress+p,r=escript.Data()) #residual=util.L2(self.__pde.getRightHandSide()) du=self.__upde.getSolution() u+=du l,d=util.L2(u),util.L2(du) err=d/l # displacement error, alternatively using force error 'residual' converged=(errrtol**3: # only update DEM parts when error is large enough self.__domain.setX(x_safe) D=util.grad(u) update_stress,update_s,update_scenes=self.applyStrain_getStressTangentDEM(st=D) """reset domain geometry to original until global convergence""" self.__domain.setX(x_safe) return u,D,update_stress,update_s,update_scenes def solve(self, globalIter=10, solidIter=50): """ solve the coupled PDE using fixed-stress split method, call solveSolid to get displacement """ rtol=self.__rtol x_safe=self.__domain.getX() k=util.kronecker(self.__domain) kdr=util.inner(k,util.tensor_mult(self.__S,k))/4. n=self.getEquivalentPorosity() perm=self.__permeability*n**3/(1.-n)**2*k kf=self.__bulkFluid dt=self.__dt self.__ppde.setValue(A=perm,D=(n/kf+1./kdr)/dt,Y=(n/kf+1./kdr)/dt*self.__pgauss-self.__meanStressRate/kdr) p_iter_old=self.__ppde.getSolution() p_iter_gauss=util.interpolate(p_iter_old,escript.Function(self.__domain)) u_old,D,sig,s,scene=self.solveSolid(p_iter_gauss=p_iter_gauss,iter_max=solidIter) converge=False iterate=0 while (not converge) and (iterate """ def saveGauss2D(name='',pos=(),**kwargs): fout = file(name,'w') for key in kwargs: data = kwargs[key].toListOfTuples() if len(pos)==0: fout.write('%s '%key+str(len(data))+'\n') for i in xrange(len(data)): fout.write(' '.join('%s %s'%x for x in data[i])+'\n') else: fout.write('%s '%key+str(len(pos))+'\n') for i in pos: fout.write(' '.join('%s %s'%x for x in data[i])+'\n') fout.close() def saveGauss3D(name='',pos=(),**kwargs): fout = file(name,'w') for key in kwargs: data = kwargs[key].toListOfTuples() if len(pos)==0: fout.write('%s '%key+str(len(data))+'\n') for i in xrange(len(data)): fout.write(' '.join('%s %s %s'%x for x in data[i])+'\n') else: fout.write('%s '%key+str(len(pos))+'\n') for i in pos: fout.write(' '.join('%s %s %s'%x for x in data[i])+'\n') fout.close() trunk-2017.01a/py/FEMxDEM/simDEM.py000066400000000000000000000233541304022710500164360ustar00rootroot00000000000000__author__="Ning Guo, ceguo@connect.ust.hk" __supervisor__="Jidong Zhao, jzhao@ust.hk" __institution__="The Hong Kong University of Science and Technology" """ DEM part for multiscale simulation which sets up a packing representing a material point (RVE) at the Gauss point of the FEM domain and returns constitutive responses (updated stress and tangent operator) at this point. """ # import yade modules import sys from os.path import expanduser sys.path.append(expanduser('~')+'/yade/bin') # path where you have yadeimport.py # yadeimport.py is generated by `ln yade-versionNo yadeimport.py` from yadeimport import * import numpy def initLoad(ID=0): # where ID identifies the Gauss point location if 1: # All Gauss points import 0.yade.gz resulting in a uniform sample (default) Omega().load('0.yade.gz') else: # Otherwise load different packings to generate random field # resulting in an inherently heterogeneous sample Omega().load(str(ID)+'.yade.gz') Omega().tags['id']=str(ID) return Omega().sceneToString() def outputPack(param): if len(param) != 3: raise RuntimeError,"No. of param. should be exactly 3. 0: RVE scene; 1: step count; 2: name prefix" Omega().stringToScene(param[0]) pos = Omega().tags['id'] Omega().save(param[2]+'packing_'+pos+'_'+str(param[1])+'.yade.gz') def numOfParticles(scene): Omega().stringToScene(scene) return len(Omega().bodies) # !!! for spherical particle packing only # Apply deformation on 2D DEM packing def shear2D(param): if len(param) != 2: raise RuntimeError,"No. of param. should be exactly 2. 0: RVE scene; 1: strain." Omega().stringToScene(param[0]) ns=int(max(1e5*numpy.max(numpy.abs(param[1])),2)) dstrain = utils.Matrix3(param[1][0],param[1][1],0, param[1][2],param[1][3],0, 0,0,0) Omega().cell.velGrad=dstrain/(ns*Omega().dt) Omega().run(ns,True) Omega().cell.velGrad=utils.Matrix3.Zero return Omega().sceneToString() # Apply deformation on 3D DEM packing def shear3D(param): if len(param) != 2: raise RuntimeError,"No. of param. should be exactly 2. 0: RVE scene; 1: strain." Omega().stringToScene(param[0]) ns=int(max(1e5*numpy.max(numpy.abs(param[1])),2)) dstrain = utils.Matrix3(param[1][0],param[1][1],param[1][2], param[1][3],param[1][4],param[1][5], param[1][6],param[1][7],param[1][8]) Omega().cell.velGrad=dstrain/(ns*Omega().dt) Omega().run(ns,True) Omega().cell.velGrad=utils.Matrix3.Zero return Omega().sceneToString() """ Used for perturbation method only (2D), deprecated def getStressTensor(scene): Omega().stringToScene(scene) stress = utils.getStress() stress = .5*(stress+stress.transpose()) return [[stress[0],stress[1]],[stress[3],stress[4]]] """ # get contact normal based fabric tensor def getFabric2D(scene): Omega().stringToScene(scene) f = utils.fabricTensor(splitTensor=False)[0] return [[f[0,0],f[0,1]],[f[1,0],f[1,1]]] def getFabric3D(scene): Omega().stringToScene(scene) f = utils.fabricTensor(splitTensor=False)[0] return [[f[0,0],f[0,1],f[0,2]],[f[1,0],f[1,1],f[1,2]],[f[2,0],f[2,1],f[2,2]]] """ # Used for clumped particle model only # get particle orientation based fabric tensor def getParOriFabric(scene): Omega().stringToScene(scene) fab = utils.Matrix3.Zero numPar = 0 for b in Omega().bodies: if b.isClump: numPar += 1 keys = b.shape.members.keys() pos1 = Omega().bodies[keys[0]].state.pos pos2 = Omega().bodies[keys[1]].state.pos ori = (pos1-pos2).normalized() fab += ori.outer(ori) fab /= numPar return [[fab[0],fab[1]],[fab[3],fab[4]]] """ """ # Used for cohesive particle model only # get the bond breakage number within a packing def getDebondingNumber(param): Omega().stringToScene(param[0]) num = 0 for id1,id2 in param[1]: try: i = Omega().interactions[id1,id2] if not i.isReal(): num += 1 elif i.phys.cohesionBroken: num += 1 except IndexError: num += 1 return num """ # get updated stress tensor and tangent operator as a tuple # utils.getStressAndTangent() is implemented in Shop.cpp def getStressAndTangent2D(scene): Omega().stringToScene(scene) st = utils.getStressAndTangent(symmetry=True) s = st[0] s = .5*(s+s.transpose()) t=[[[[0,0],[0,0]],[[0,0],[0,0]]],[[[0,0],[0,0]],[[0,0],[0,0]]]] t[0][0][0][0]=st[1][0,0] t[1][1][0][0]=t[0][0][1][1]=st[1][0,1] t[0][1][0][0]=t[0][0][0][1]=t[1][0][0][0]=t[0][0][1][0]=st[1][0,5] t[1][1][1][1]=st[1][1,1] t[1][1][0][1]=t[0][1][1][1]=t[1][1][1][0]=t[1][0][1][1]=st[1][1,5] t[0][1][0][1]=t[0][1][1][0]=t[1][0][0][1]=t[1][0][1][0]=st[1][5,5] return [[s[0,0],s[0,1]],[s[1,0],s[1,1]]],t def getStressAndTangent3D(scene): Omega().stringToScene(scene) st = utils.getStressAndTangent(symmetry=True) s = st[0] s = .5*(s+s.transpose()) t = numpy.zeros((3,3,3,3)) t[0][0][0][0]=st[1][0,0] t[0][0][1][1]=t[1][1][0][0]=st[1][0,1] t[0][0][2][2]=t[2][2][0][0]=st[1][0,2] t[0][0][1][2]=t[0][0][2][1]=t[1][2][0][0]=t[2][1][0][0]=st[1][0,3] t[0][0][0][2]=t[0][0][2][0]=t[0][2][0][0]=t[2][0][0][0]=st[1][0,4] t[0][0][0][1]=t[0][0][1][0]=t[0][1][0][0]=t[1][0][0][0]=st[1][0,5] t[1][1][1][1]=st[1][1,1] t[1][1][2][2]=t[2][2][1][1]=st[1][1,2] t[1][1][1][2]=t[1][1][2][1]=t[1][2][1][1]=t[2][1][1][1]=st[1][1,3] t[1][1][0][2]=t[1][1][2][0]=t[0][2][1][1]=t[2][0][1][1]=st[1][1,4] t[1][1][0][1]=t[1][1][1][0]=t[0][1][1][1]=t[1][0][1][1]=st[1][1,5] t[2][2][2][2]=st[1][2,2] t[2][2][1][2]=t[2][2][2][1]=t[1][2][2][2]=t[2][1][2][2]=st[1][2,3] t[2][2][0][2]=t[2][2][2][0]=t[0][2][2][2]=t[2][0][2][2]=st[1][2,4] t[2][2][0][1]=t[2][2][1][0]=t[0][1][2][2]=t[1][0][2][2]=st[1][2,5] t[1][2][1][2]=t[1][2][2][1]=t[2][1][1][2]=t[2][1][2][1]=st[1][3,3] t[1][2][0][2]=t[1][2][2][0]=t[2][1][0][2]=t[2][1][2][0]=t[0][2][1][2]=t[2][0][1][2]=t[0][2][2][1]=t[2][0][2][1]=st[1][3,4] t[1][2][0][1]=t[1][2][1][0]=t[2][1][0][1]=t[2][1][1][0]=t[0][1][1][2]=t[1][0][1][2]=t[0][1][2][1]=t[1][0][2][1]=st[1][3,5] t[0][2][0][2]=t[2][0][0][2]=t[0][2][2][0]=t[2][0][2][0]=st[1][4,4] t[0][2][0][1]=t[0][2][1][0]=t[2][0][0][1]=t[2][0][1][0]=t[0][1][0][2]=t[1][0][0][2]=t[0][1][2][0]=t[1][0][2][0]=st[1][4,5] t[0][1][0][1]=t[0][1][1][0]=t[1][0][0][1]=t[1][0][1][0]=st[1][5,5] return [[s[0,0],s[0,1],s[0,2]],[s[1,0],s[1,1],s[1,2]],[s[2,0],s[2,1],s[2,2]]],t # utils.voidratio2D() is implemented in Shop.cpp # to get plane void ratio (for 2D test only) def getVoidRatio2D(scene): Omega().stringToScene(scene) zSize = Omega().cell.hSize[2,2] return utils.voidratio2D(zlen=zSize) def getEquivalentPorosity(scene): Omega().stringToScene(scene) zSize = Omega().cell.hSize[2,2] e = utils.voidratio2D(zlen=zSize) return e/(1.+e) def getVoidRatio3D(scene): Omega().stringToScene(scene) p = utils.porosity() return p/(1.0-p) # get average rotation of the particles within a packing def avgRotation2D(scene): Omega().stringToScene(scene) rot = 0.0 for b in Omega().bodies: rot += b.state.rot()[2] rot /= len(Omega().bodies) return rot def avgRotation3D(scene): Omega().stringToScene(scene) rot = utils.Vector3.Zero for b in Omega().bodies: rot += b.state.rot() rot /= len(Omega().bodies) return [rot[0],rot[1],rot[2]] """ Used for perturbation method only (2D), deprecated def getTangentOperator(param): if len(param)!=2: raise RuntimeError,"No. of param. should be exactly 2. 0: RVE scene; 1: perturbation." Omega().stringToScene(param[0]) pos = Omega().tags['id'] perturbation = param[1] t=[[[[0,0],[0,0]],[[0,0],[0,0]]],[[[0,0],[0,0]],[[0,0],[0,0]]]] ns=int(max(1e5*abs(perturbation),2)) stress0 = utils.getStress() stress0 = .5*(stress0+stress0.transpose()) #00 strain=utils.Matrix3(perturbation,0,0, 0,0,0, 0,0,0) Omega().cell.velGrad=strain/(ns*Omega().dt) Omega().run(ns,True) stress1 = utils.getStress() stress1 = .5*(stress1+stress1.transpose()) t[0][0][0][0]=(stress1[0]-stress0[0])/perturbation t[1][1][0][0]=(stress1[4]-stress0[4])/perturbation t[0][1][0][0]=t[1][0][0][0]=(stress1[1]-stress0[1])/perturbation Omega().stringToScene(param[0]) #11 strain=utils.Matrix3(0,0,0, 0,perturbation,0, 0,0,0) Omega().cell.velGrad=strain/(ns*Omega().dt) Omega().run(ns,True) stress1=utils.getStress() stress1=.5*(stress1+stress1.transpose()) t[0][0][1][1]=(stress1[0]-stress0[0])/perturbation t[1][1][1][1]=(stress1[4]-stress0[4])/perturbation t[0][1][1][1]=t[1][0][1][1]=(stress1[1]-stress0[1])/perturbation Omega().stringToScene(param[0]) #01 strain=utils.Matrix3(0,perturbation,0, 0,0,0, 0,0,0) Omega().cell.velGrad=strain/(ns*Omega().dt) Omega().run(ns,True) stress1=utils.getStress() stress1=.5*(stress1+stress1.transpose()) t[0][0][0][1]=(stress1[0]-stress0[0])/perturbation t[1][1][0][1]=(stress1[4]-stress0[4])/perturbation t[0][1][0][1]=t[1][0][0][1]=(stress1[1]-stress0[1])/perturbation Omega().stringToScene(param[0]) #10 strain=utils.Matrix3(0,0,0, perturbation,0,0, 0,0,0) Omega().cell.velGrad=strain/(ns*Omega().dt) Omega().run(ns,True) stress1=utils.getStress() stress1=.5*(stress1+stress1.transpose()) t[0][0][1][0]=(stress1[0]-stress0[0])/perturbation t[1][1][1][0]=(stress1[4]-stress0[4])/perturbation t[0][1][1][0]=t[1][0][1][0]=(stress1[1]-stress0[1])/perturbation #symmetrize t[0][0][1][1]=t[1][1][0][0]=(t[0][0][1][1]+t[1][1][0][0])*0.5 t[0][1][0][0]=t[1][0][0][0]=t[0][0][1][0]=t[0][0][0][1]=(t[0][1][0][0]*2+t[0][0][0][1]+t[0][0][1][0])*0.25 t[0][1][0][1]=t[0][1][1][0]=t[1][0][0][1]=t[1][0][1][0]=(t[0][1][1][0]+t[0][1][0][1])*0.5 t[0][1][1][1]=t[1][0][1][1]=t[1][1][0][1]=t[1][1][1][0]=(t[0][1][1][1]*2+t[1][1][0][1]+t[1][1][1][0])*0.25 return t """ trunk-2017.01a/py/WeightedAverage2d.cpp000066400000000000000000000036061304022710500176040ustar00rootroot00000000000000#include /* Tell whether point is inside polygon * * See _utils.cpp: pointInsidePolygon for docs and license. */ bool pyGaussAverage::pointInsidePolygon(const Vector2r& pt, const vector& vertices){ int i /*current node*/, j/*previous node*/; bool inside=false; int rows=(int)vertices.size(); const Real& testx=pt[0],testy=pt[1]; for(i=0,j=rows-1; itesty)!=(vy_j>testy)) && (testx < (vx_j-vx_i) * (testy-vy_i) / (vy_j-vy_i) + vx_i) ) inside=!inside; } return inside; } BOOST_PYTHON_MODULE(WeightedAverage2d) { boost::python::scope().attr("__doc__")="Smoothing (2d gauss-weighted average) for postprocessing scalars in 2d."; boost::python::class_("GaussAverage",boost::python::init >(boost::python::args("min","max","nCells","stDev","relThreshold"),"Create empty container for data, which can be added using add and later retrieved using avg.")) .def("add",&pyGaussAverage::addPt) .def("avg",&pyGaussAverage::avg) .def("avgPerUnitArea",&pyGaussAverage::avgPerUnitArea) .def("cellNum",&pyGaussAverage::cellNum) .def("cellSum",&pyGaussAverage::cellSum) .def("cellAvg",&pyGaussAverage::cellAvg) .add_property("stDev",&pyGaussAverage::stDev_get,&pyGaussAverage::stDev_set) .add_property("relThreshold",&pyGaussAverage::relThreshold_get,&pyGaussAverage::relThreshold_set) .add_property("clips",&pyGaussAverage::clips_get,&pyGaussAverage::clips_set) .add_property("data",&pyGaussAverage::data_get) .add_property("aabb",&pyGaussAverage::aabb_get) .add_property("nCells",&pyGaussAverage::nCells_get) .add_property("cellArea",&pyGaussAverage::cellArea) .add_property("cellDim",&pyGaussAverage::cellDim) ; }; trunk-2017.01a/py/__init__.py.in000066400000000000000000000065401304022710500163350ustar00rootroot00000000000000# 1. it tells python that yade (this directory) is package of python modules # see http://http://www.python.org/doc/2.1.3/tut/node8.html#SECTION008400000000000000000 # # 2. import the runtime namespace (will be populated from within c++) # """Common initialization core for yade. This file is executed when anything is imported from yade for the first time. It loads yade plugins and injects c++ class constructors to the __builtins__ (that might change in the future, though) namespace, making them available everywhere. """ import ctypes,sys try: import dl except ImportError: import DLFCN as dl if True: # not eval('${mono}'): # see file:///usr/share/doc/python2.6/html/library/sys.html#sys.setdlopenflags # and various web posts on the topic, e.g. # * http://gcc.gnu.org/faq.html#dso # * http://www.code-muse.com/blog/?p=58 # * http://wiki.python.org/moin/boost.python/CrossExtensionModuleDependencies sys.setdlopenflags(dl.RTLD_NOW | dl.RTLD_GLOBAL) else: sys.setdlopenflags(dl.RTLD_NOW) # important: initialize c++ by importing libstdc++ directly # see http://www.abclinuxu.cz/poradna/programovani/show/286322 # https://bugs.launchpad.net/bugs/490744 # # This is already fixed in systems, newer, than Ubuntu 10.04. anyway for # back-compatibility we will keep it. libstdcxx='${libstdcxx}' # substituted by scons try: ctypes.cdll.LoadLibrary(libstdcxx) except: pass # # now ready for c++ imports # find plugin directory import os,os.path import config # find plugins recursively plugins=[] # might add followlinks=True to os.walk, for python>=2.6 for root,dirs,files in os.walk(config.libDir): # skip any directory named 'dbg' in the non-debug build if 'dbg' in dirs: dirs.remove('dbg') for f in files: # ouch, ugly! #if not config.debug and '/dbg/' in root: continue if not (f.startswith('lib') and f.endswith('.so')): continue plugin=os.path.join(config.libDir,root,f) plugins.append(plugin) if 'YADE_DEBUG' in os.environ: print 'The following plugins will be loaded:' for p in plugins: print '\t'+p # c++ initialization code import boot boot.initialize(plugins,config.confDir) import system # create proxies for deprecated classes deprecatedTypes=system.cxxCtorsDict() # insert those in the module namespace globals().update(deprecatedTypes) # declare what should be imported for "from yade import *" __all__=deprecatedTypes.keys()+['O'] from minieigen import * from wrapper import * # import to separate namespace to be able to call dir(miniEigen) and dir(wrapper) below import wrapper # out-of-class docstrings for some classes import _extraDocs # import a few "important" modules along with * import utils # some others? __all__+=['utils',]+dir(wrapper) # make O and wrapper.Omega part of __builtin__ (equvialent to global) import __builtin__ __builtin__.__dict__['O'] = O __builtin__.__dict__['Omega'] = wrapper.Omega # define a default list of engine O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb(),Bo1_Box_Aabb()],label="collider"), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], #for linear model only [Law2_ScGeom_FrictPhys_CundallStrack(label="law")], #for linear model only label="interactionLoop" ), GlobalStiffnessTimeStepper(timeStepUpdateInterval=10,label="timeStepper"), NewtonIntegrator(label="newton") ] trunk-2017.01a/py/_extraDocs.py000066400000000000000000000553751304022710500162760ustar00rootroot00000000000000# encoding: utf-8 # 2010 © Václav Šmilauer # # This module is imported at startup. It is meant to update # docstrings of wrapper classes, which are not practical to document # in the c++ source itself, due to the necessity of writing # \n for newlines and having everything as "string". # # PLEASE: # # 1. provide at least brief description of the class # in the c++ code (for those who read it) and # # 2. Add something like # # "Full documentation of this class is in py/_extraDocs.py." # # to the c++ documentation. import wrapper # Update docstring of your class/function like this: # # wrapper.YourClass.__doc__=""" # This class is documented from _extraDocs.py. Yay! # # .. note:: # The c++ documentation will be overwritten by this string. # """ wrapper.TriaxialTest.__doc__=''' Create a scene for triaxal test. **Introduction** Yade includes tools to simulate triaxial tests on particles assemblies. This pre-processor (and variants like e.g. :yref:`CapillaryTriaxialTest`) illustrate how to use them. It generates a scene which will - by default - go through the following steps : * generate random loose packings in a parallelepiped. * compress the packing isotropicaly, either squeezing the packing between moving rigid boxes or expanding the particles while boxes are fixed (depending on flag :yref:`internalCompaction`). The confining pressure in this stage is defined via :yref:`sigmaIsoCompaction`. * when the packing is dense and stable, simulate a loading path and get the mechanical response as a result. The default loading path corresponds to a constant lateral stress (:yref:`sigmaLateralConfinement`) in 2 directions and constant strain rate on the third direction. This default loading path is performed when the flag :yref:`autoCompressionActivation` it ``True``, otherwise the simulation stops after isotropic compression. Different loading paths might be performed. In order to define them, the user can modify the flags found in engine :yref:`TriaxialStressController` at any point in the simulation (in c++). If ``TriaxialStressController.wall_X_activated`` is ``true`` boundary X is moved automatically to maintain the defined stress level *sigmaN* (see axis conventions below). If ``false`` the boundary is not controlled by the engine at all. In that case the user is free to prescribe fixed position, constant velocity, or more complex conditions. .. note:: *Axis conventions.* Boundaries perpendicular to the *x* axis are called "left" and "right", *y* corresponds to "top" and "bottom", and axis *z* to "front" and "back". In the default loading path, strain rate is assigned along *y*, and constant stresses are assigned on *x* and *z*. **Essential engines** #. The :yref:`TriaxialCompressionEngine` is used for controlling the state of the sample and simulating loading paths. :yref:`TriaxialCompressionEngine` inherits from :yref:`TriaxialStressController`, which computes stress- and strain-like quantities in the packing and maintain a constant level of stress at each boundary. :yref:`TriaxialCompressionEngine` has few more members in order to impose constant strain rate and control the transition between isotropic compression and triaxial test. Transitions are defined by changing some flags of the :yref:`TriaxialStressController`, switching from/to imposed strain rate to/from imposed stress. #. The class :yref:`TriaxialStateRecorder` is used to write to a file the history of stresses and strains. #. :yref:`TriaxialTest` is using :yref:`GlobalStiffnessTimeStepper` to compute an appropriate $\Dt$ for the numerical scheme. .. note:: ``TriaxialStressController::ComputeUnbalancedForce`` returns a value that can be useful for evaluating the stability of the packing. It is defined as (mean force on particles)/(mean contact force), so that it tends to 0 in a stable packing. This parameter is checked by :yref:`TriaxialCompressionEngine` to switch from one stage of the simulation to the next one (e.g. stop isotropic confinment and start axial loading) .. admonition:: Frequently Asked Questions #. How is generated the packing? How to change particles sizes distribution? Why do I have a message "Exceeded 3000 tries to insert non-overlapping sphere? The initial positioning of spheres is done by generating random (x,y,z) in a box and checking if a sphere of radius R (R also randomly generated with respect to a uniform distribution between mean*(1-std_dev) and mean*(1+std_dev) can be inserted at this location without overlaping with others. If the sphere overlaps, new (x,y,z)'s are generated until a free position for the new sphere is found. This explains the message you have: after 3000 trial-and-error, the sphere couldn't be placed, and the algorithm stops. You get the message above if you try to generate an initialy dense packing, which is not possible with this algorithm. It can only generate clouds. You should keep the default value of porosity (n~0.7), or even increase if it is still to low in some cases. The dense state will be obtained in the second step (compaction, see below). #. How is the compaction done, what are the parameters :yref:`maxWallVelocity` and :yref:`finalMaxMultiplier`? Compaction is done #. by moving rigid boxes or #. by increasing the sizes of the particles (decided using the option :yref:`internalCompaction` ⇒ size increase). Both algorithm needs numerical parameters to prevent instabilities. For instance, with the method (1) :yref:`maxWallVelocity` is the maximum wall velocity, with method (2) :yref:`finalMaxMultiplier` is the max value of the multiplier applied on sizes at each iteration (always something like 1.00001). #. During the simulation of triaxial compression test, the wall in one direction moves with an increment of strain while the stresses in other two directions are adjusted to :yref:`sigma_iso`. How the stresses in other directions are maintained constant to :yref:`sigma_iso`? What is the mechanism? Where is it implemented in Yade? The control of stress on a boundary is based on the total stiffness *K* of all contacts between the packing and this boundary. In short, at each step, displacement=stress_error/K. This algorithm is implemented in :yref:`TriaxialStressController`, and the control itself is in ``TriaxialStressController::ControlExternalStress``. The control can be turned off independently for each boundary, using the flags ``wall_XXX_activated``, with *XXX*\ ∈{*top*, *bottom*, *left*, *right*, *back*, *front*}. The imposed sress is a unique value (:yref:`sigma_iso`) for all directions if :yref:`TriaxialStressController.isAxisymetric`, or 3 independent values :yref:`sigma1`, :yref:`sigma2`, :yref:`sigma3`. #. Which value of friction angle do you use during the compaction phase of the Triaxial Test? The friction during the compaction (whether you are using the expansion method or the compression one for the specimen generation) can be anything between 0 and the final value used during the Triaxial phase. Note that higher friction than the final one would result in volumetric collapse at the beginning of the test. The purpose of using a different value of friction during this phase is related to the fact that the final porosity you get at the end of the sample generation essentially depends on it as well as on the assumed Particle Size Distribution. Changing the initial value of friction will get to a different value of the final porosity. #. Which is the aim of the ``bool isRadiusControlIteration``? This internal variable (updated automatically) is true each *N* timesteps (with *N*\ =\ :yref:`radiusControlInterval`). For other timesteps, there is no expansion. Cycling without expanding is just a way to speed up the simulation, based on the idea that 1% increase each 10 iterations needs less operations than 0.1% at each iteration, but will give similar results. #. How comes the unbalanced force reaches a low value only after many timesteps in the compaction phase? The value of unbalanced force (dimensionless) is expected to reach low value (i.e. identifying a static-equilibrium condition for the specimen) only at the end of the compaction phase. The code is not aiming at simulating a quasistatic isotropic compaction process, it is only giving a stable packing at the end of it. ''' wrapper.Peri3dController.__doc__=r''' Class for controlling independently all 6 components of "engineering" :yref:`stress` and :yref:`strain` of periodic :yref:`Cell`. :yref:`goal` are the goal values, while :yref:`stressMask` determines which components prescribe stress and which prescribe strain. If the strain is prescribed, appropriate strain rate is directly applied. If the stress is prescribed, the strain predictor is used: from stress values in two previous steps the value of strain rate is prescribed so as the value of stress in the next step is as close as possible to the ideal one. Current algorithm is extremly simple and probably will be changed in future, but is roboust enough and mostly works fine. Stress error (difference between actual and ideal stress) is evaluated in current and previous steps ($\mathrm{d}\sigma_i,\mathrm{d}\sigma_{i-1}$). Linear extrapolation is used to estimate error in the next step .. math:: \mathrm{d}\sigma_{i+1}=2\mathrm{d}\sigma_i - \mathrm{d}\sigma_{i-1} According to this error, the strain rate is modified by :yref:`mod` parameter .. math:: \mathrm{d}\sigma_{i+1}\left\{\begin{array}{c} >0 \rightarrow \dot{\varepsilon}_{i+1} = \dot{\varepsilon}_i - \max(\mathrm{abs}(\dot{\boldsymbol{\varepsilon}}_i))\cdot\mathrm{mod} \\ <0 \rightarrow \dot{\varepsilon}_{i+1} = \dot{\varepsilon}_i + \max(\mathrm{abs}(\dot{\boldsymbol{\varepsilon}}_i))\cdot\mathrm{mod} \end{array}\right. According to this fact, the prescribed stress will (almost) never have exact prescribed value, but the difference would be very small (and decreasing for increasing :yref:`nSteps`. This approach works good if one of the dominant strain rates is prescribed. If all stresses are prescribed or if all goal strains is prescribed as zero, a good estimation is needed for the first step, therefore the compliance matrix is estimated (from user defined estimations of macroscopic material parameters :yref:`youngEstimation` and :yref:`poissonEstimation`) and respective strain rates is computed form prescribed stress rates and compliance matrix (the estimation of compliance matrix could be computed autamatically avoiding user inputs of this kind). The simulation on rotated periodic cell is also supported. Firstly, the `polar decomposition `_ is performed on cell's transformation matrix :yref:`trsf` $\mathcal{T}=\mat{U}\mat{P}$, where $\mat{U}$ is orthogonal (unitary) matrix representing rotation and $\mat{P}$ is a positive semi-definite Hermitian matrix representing strain. A logarithm of $\mat{P}$ should be used to obtain realistic values at higher strain values (not implemented yet). A prescribed strain increment in global coordinates $\mathrm{d}t\cdot\dot{\boldsymbol{\varepsilon}}$ is properly rotated to cell's local coordinates and added to $\mat{P}$ .. math:: \mat{P}_{i+1}=\mat{P}+\mat{U}^{\mathsf{T}}\mathrm{d}t\cdot\dot{\boldsymbol{\varepsilon}}\mat{U} The new value of :yref:`trsf` is computed at $\mat{T}_{i+1}=\mat{UP}_{i+1}$. From current and next :yref:`trsf` the cell's velocity gradient :yref:`velGrad` is computed (according to its definition) as .. math:: \mat{V} = (\mat{T}_{i+1}\mat{T}^{-1}-\mat{I})/\mathrm{d}t Current implementation allow user to define independent loading "path" for each prescribed component. i.e. define the prescribed value as a function of time (or :yref:`progress` or steps). See :yref:`Paths`. Examples :ysrc:`examples/test/peri3dController_example1.py` and :ysrc:`examples/test/peri3dController_triaxialCompression.py` explain usage and inputs of Peri3dController, :ysrc:`examples/test/peri3dController_shear.py` is an example of using shear components and also simulation on rotated cell. ''' wrapper.Ig2_Sphere_Sphere_L3Geom.__doc__=r'''Functor for computing incrementally configuration of 2 :yref:`Spheres` stored in :yref:`L3Geom`; the configuration is positioned in global space by local origin $\vec{c}$ (contact point) and rotation matrix $\mat{T}$ (orthonormal transformation matrix), and its degrees of freedom are local displacement $\vec{u}$ (in one normal and two shear directions); with :yref:`Ig2_Sphere_Sphere_L6Geom` and :yref:`L6Geom`, there is additionally $\vec{\phi}$. The first row of $\mat{T}$, i.e. local $x$-axis, is the contact normal noted $\vec{n}$ for brevity. Additionally, quasi-constant values of $\vec{u}_0$ (and $\vec{\phi}_0$) are stored as shifted origins of $\vec{u}$ (and $\vec{\phi}$); therefore, current value of displacement is always $\curr{\vec{u}}-\vec{u}_0$. Suppose two spheres with radii $r_i$, positions $\vec{x}_i$, velocities $\vec{v}_i$, angular velocities $\vec{\omega}_i$. When there is not yet contact, it will be created if $u_N=|\curr{\vec{x}}_2-\curr{\vec{x}}_1|-|f_d|(r_1+r2)<0$, where $f_d$ is :yref:`distFactor` (sometimes also called \`\`interaction radius''). If $f_d>0$, then $\vec{u}_{0x}$ will be initalized to $u_N$, otherwise to 0. In another words, contact will be created if spheres enlarged by $|f_d|$ touch, and the \`\`equilibrium distance'' (where $\vec{u}_x-\vec{u}-{0x}$ is zero) will be set to the current distance if $f_d$ is positive, and to the geometrically-touching distance if negative. Local axes (rows of $\mat{T}$) are initially defined as follows: * local $x$-axis is $\vec{n}=\vec{x}_l=\normalized{\vec{x}_2-\vec{x}_1}$; * local $y$-axis positioned arbitrarily, but in a deterministic manner: aligned with the $xz$ plane (if $\vec{n}_y<\vec{n}_z$) or $xy$ plane (otherwise); * local $z$-axis $\vec{z}_l=\vec{x}_l\times\vec{y}_l$. If there has already been contact between the two spheres, it is updated to keep track of rigid motion of the contact (one that does not change mutual configuration of spheres) and mutual configuration changes. Rigid motion transforms local coordinate system and can be decomposed in rigid translation (affecting $\vec{c}$), and rigid rotation (affecting $\mat{T}$), which can be split in rotation $\vec{o}_r$ perpendicular to the normal and rotation $\vec{o}_t$ (\`\`twist'') parallel with the normal: .. math:: \pprev{\vec{o}_r}=\prev{\vec{n}}\times\curr{\vec{n}}. Since velocities are known at previous midstep ($t-\Dt/2$), we consider mid-step normal .. math:: \pprev{\vec{n}}=\frac{\prev{\vec{n}}+\curr{\vec{n}}}{2}. For the sake of numerical stability, $\pprev{\vec{n}}$ is re-normalized after being computed, unless prohibited by :yref:`approxMask`. If :yref:`approxMask` has the appropriate bit set, the mid-normal is not compute, and we simply use $\pprev{\vec{n}}\approx\prev{\vec{n}}$. Rigid rotation parallel with the normal is .. math:: \pprev{\vec{o}_t}=\pprev{\vec{n}}\left(\pprev{\vec{n}}\cdot\frac{\pprev{\vec{\omega}}_1+\pprev{\vec{\omega}}_2}{2}\right)\Dt. *Branch vectors* $\vec{b}_1$, $\vec{b}_2$ (connecting $\curr{\vec{x}}_1$, $\curr{\vec{x}}_2$ with $\curr{\vec{c}}$ are computed depending on :yref:`noRatch` (see :yref:`here`). .. math:: :nowrap: \begin{align*} \vec{b}_1&=\begin{cases} r_1 \curr{\vec{n}} & \mbox{with \texttt{noRatch}} \\ \curr{\vec{c}}-\curr{\vec{x}}_1 & \mbox{otherwise} \end{cases} \\ \vec{b}_2&=\begin{cases} -r_2\curr{\vec{n}} & \mbox{with \texttt{noRatch}} \\ \curr{\vec{c}}-\curr{\vec{x}}_2 & \mbox{otherwise} \end{cases} \\ \end{align*} Relative velocity at $\curr{\vec{c}}$ can be computed as .. math:: \pprev{\vec{v}_r}=(\pprev{\vec{\tilde{v}}_2}+\vec{\omega}_2\times\vec{b}_2)-(\vec{v}_1+\vec{\omega}_1\times\vec{b}_1) where $\vec{\tilde{v}}_2$ is $\vec{v}_2$ without mean-field velocity gradient in periodic boundary conditions (see :yref:`Cell.homoDeform`). In the numerial implementation, the normal part of incident velocity is removed (since it is computed directly) with $\pprev{\vec{v}_{r2}}=\pprev{\vec{v}_r}-(\pprev{\vec{n}}\cdot\pprev{\vec{v}_r})\pprev{\vec{n}}$. Any vector $\vec{a}$ expressed in global coordinates transforms during one timestep as .. math:: \curr{\vec{a}}=\prev{\vec{a}}+\pprev{\vec{v}_r}\Dt-\prev{\vec{a}}\times\pprev{\vec{o}_r}-\prev{\vec{a}}\times{\pprev{\vec{t}_r}} where the increments have the meaning of relative shear, rigid rotation normal to $\vec{n}$ and rigid rotation parallel with $\vec{n}$. Local coordinate system orientation, rotation matrix $\mat{T}$, is updated by rows, i.e. .. math:: \curr{\mat{T}}=\begin{pmatrix} \curr{\vec{n}_x} & \curr{\vec{n}_y} & \curr{\vec{n}_z} \\ \multicolumn{3}{c}{\prev{\mat{T}_{1,\bullet}}-\prev{\mat{T}_{1,\bullet}}\times\pprev{\vec{o}_r}-\prev{\mat{T}_{1,\bullet}}\times\pprev{\vec{o}_t}} \\ \multicolumn{3}{c}{\prev{\mat{T}_{2,\bullet}}-\prev{\mat{T}_{2,\bullet}}\times\pprev{\vec{o}_r}-\prev{\mat{T}_{,\bullet}}\times\pprev{\vec{o}_t}} \end{pmatrix} This matrix is re-normalized (unless prevented by :yref:`approxMask`) and mid-step transformation is computed using quaternion spherical interpolation as .. math:: \pprev{\mat{T}}=\mathrm{Slerp}\,\left(\prev{\mat{T}};\curr{\mat{T}};t=1/2\right). Depending on :yref:`approxMask`, this computation can be avoided by approximating $\pprev{\mat{T}}=\prev{\mat{T}}$. Finally, current displacement is evaluated as .. math:: \curr{\vec{u}}=\prev{u}+\pprev{\mat{T}}\pprev{\vec{v}_r}\Dt. For the normal component, non-incremental evaluation is preferred, giving .. math:: \curr{\vec{u}_x}=|\curr{\vec{x}_2}-\curr{\vec{x}_1}|-(r_1+r_2) If this functor is called for :yref:`L6Geom`, local rotation is updated as .. math:: \curr{\vec{\phi}}=\prev{\vec{\phi}}+\pprev{\mat{T}}\Dt(\vec{\omega}_2-\vec{\omega}_1) .. note: TODO: ``distFactor`` is not yet implemented as described above; some formulas mix values at different times, should be checked carefully. ''' wrapper.LawTester.__doc__='''Prescribe and apply deformations of an interaction in terms of local mutual displacements and rotations. The loading path is specified either using :yref:`path` (as sequence of 6-vectors containing generalized displacements $u_x$, $u_y$, $u_z$, $\phi_x$, $\phi_y$, $\phi_z$) or :yref:`disPath` ($u_x$, $u_y$, $u_z$) and :yref:`rotPath` ($\phi_x$, $\phi_y$, $\phi_z$). Time function with time values (step numbers) corresponding to points on loading path is given by :yref:`pathSteps`. Loading values are linearly interpolated between given loading path points, and starting zero-value (the initial configuration) is assumed for both :yref:`path` and :yref:`pathSteps`. :yref:`hooks` can specify python code to run when respective point on the path is reached; when the path is finished, :yref:`doneHook` will be run. LawTester should be placed between :yref:`InteractionLoop` and :yref:`NewtonIntegrator` in the simulation loop, since it controls motion via setting linear/angular velocities on particles; those velocities are integrated by :yref:`NewtonIntegrator` to yield an actual position change, which in turn causes :yref:`IGeom` to be updated (and :yref:`contact law` applied) when :yref:`InteractionLoop` is executed. Constitutive law generating forces on particles will not affect prescribed particle motion, since both particles have all :yref:`DoFs blocked` when first used with LawTester. LawTester uses, as much as possible, :yref:`IGeom` to provide useful data (such as local coordinate system), but is able to compute those independently if absent in the respective :yref:`IGeom`: =================== ===== ================================== :yref:`IGeom` #DoFs LawTester support level =================== ===== ================================== :yref:`L3Geom` 3 full :yref:`L6Geom` 6 full :yref:`ScGeom` 3 emulate local coordinate system :yref:`ScGeom6D` 6 emulate local coordinate system =================== ===== ================================== Depending on :yref:`IGeom`, 3 ($u_x$, $u_y$, $u_z$) or 6 ($u_x$, $u_y$, $u_z$, $\phi_x$, $\phi_y$, $\phi_z$) degrees of freedom (DoFs) are controlled with LawTester, by prescribing linear and angular velocities of both particles in contact. All DoFs controlled with LawTester are orthogonal (fully decoupled) and are controlled independently. When 3 DoFs are controlled, :yref:`rotWeight` controls whether local shear is applied by moving particle on arc around the other one, or by rotating without changing position; although such rotation induces mutual rotation on the interaction, it is ignored with :yref:`IGeom` with only 3 DoFs. When 6 DoFs are controlled, only arc-displacement is applied for shear, since otherwise mutual rotation would occur. :yref:`idWeight` distributes prescribed motion between both particles (resulting local deformation is the same if ``id1`` is moved towards ``id2`` or ``id2`` towards ``id1``). This is true only for $u_x$, $u_y$, $u_z$, $\phi_x$ however ; bending rotations $\phi_y$, $\phi_z$ are nevertheless always distributed regardless of ``idWeight`` to both spheres in inverse proportion to their radii, so that there is no shear induced. LawTester knows current contact deformation from 2 sources: from its own internal data (which are used for prescribing the displacement at every step), which can be accessed in :yref:`uTest`, and from :yref:`IGeom` itself (depending on which data it provides), which is stored in :yref:`uGeom`. These two values should be identical (disregarding numerical percision), and it is a way to test whether :yref:`IGeom` and related functors compute what they are supposed to compute. LawTester-operated interactions can be rendered with :yref:`GlExtra_LawTester` renderer. See :ysrc:`scripts/test/law-test.py` for an example. ''' trunk-2017.01a/py/_polyhedra_utils.cpp000066400000000000000000000522451304022710500176740ustar00rootroot00000000000000// © 2013 Jan Elias, http://www.fce.vutbr.cz/STM/elias.j/, elias.j@fce.vutbr.cz // https://www.vutbr.cz/www_base/gigadisk.php?i=95194aa9a #ifdef YADE_CGAL #include "pkg/dem/Polyhedra.hpp" #include #include #include #include #include #include #include namespace py = boost::python; //********************************************************************************** //print polyhedron in basic position void PrintPolyhedra(const shared_ptr& shape){ Polyhedra* A = static_cast(shape.get()); Polyhedron PA = A->GetPolyhedron(); A->Initialize(); PrintPolyhedron(PA); } //********************************************************************************** //print polyhedron in actual position void PrintPolyhedraActualPos(const shared_ptr& cm1,const State& state1){ const Se3r& se3=state1.se3; Polyhedra* A = static_cast(cm1.get()); A->Initialize(); //move and rotate CGAL structure Polyhedron Matrix3r rot_mat = (se3.orientation).toRotationMatrix(); Vector3r trans_vec = se3.position; Transformation t_rot_trans(rot_mat(0,0),rot_mat(0,1),rot_mat(0,2), trans_vec[0],rot_mat(1,0),rot_mat(1,1),rot_mat(1,2),trans_vec[1],rot_mat(2,0),rot_mat(2,1),rot_mat(2,2),trans_vec[2],1.); Polyhedron PA = A->GetPolyhedron(); std::transform( PA.points_begin(), PA.points_end(), PA.points_begin(), t_rot_trans); PrintPolyhedron(PA); } //********************************************************************************** //test of polyhedron intersection callable from python shell bool do_Polyhedras_Intersect(const shared_ptr& cm1,const shared_ptr& cm2,const State& state1,const State& state2){ const Se3r& se31=state1.se3; const Se3r& se32=state2.se3; Polyhedra* A = static_cast(cm1.get()); Polyhedra* B = static_cast(cm2.get()); //move and rotate 1st the CGAL structure Polyhedron Matrix3r rot_mat = (se31.orientation).toRotationMatrix(); Vector3r trans_vec = se31.position; Transformation t_rot_trans(rot_mat(0,0),rot_mat(0,1),rot_mat(0,2), trans_vec[0],rot_mat(1,0),rot_mat(1,1),rot_mat(1,2),trans_vec[1],rot_mat(2,0),rot_mat(2,1),rot_mat(2,2),trans_vec[2],1.); Polyhedron PA = A->GetPolyhedron(); std::transform( PA.points_begin(), PA.points_end(), PA.points_begin(), t_rot_trans); //move and rotate 2st the CGAL structure Polyhedron rot_mat = (se32.orientation).toRotationMatrix(); trans_vec = se32.position; t_rot_trans = Transformation(rot_mat(0,0),rot_mat(0,1),rot_mat(0,2), trans_vec[0],rot_mat(1,0),rot_mat(1,1),rot_mat(1,2),trans_vec[1],rot_mat(2,0),rot_mat(2,1),rot_mat(2,2),trans_vec[2],1.); Polyhedron PB = B->GetPolyhedron(); std::transform( PB.points_begin(), PB.points_end(), PB.points_begin(), t_rot_trans); //calculate plane equations std::transform( PA.facets_begin(), PA.facets_end(), PA.planes_begin(),Plane_equation()); std::transform( PB.facets_begin(), PB.facets_end(), PB.planes_begin(),Plane_equation()); //call test return do_intersect(PA,PB); } //********************************************************************************** //determination of critical time step for polyhedrons & spheres (just rough estimation) Real PWaveTimeStep(){ const shared_ptr _rb=shared_ptr(); shared_ptr rb=(_rb?_rb:Omega::instance().getScene()); Real dt=std::numeric_limits::infinity(); FOREACH(const shared_ptr& b, *rb->bodies){ if(!b || !b->material || !b->shape) continue; shared_ptr s=YADE_PTR_DYN_CAST(b->shape); shared_ptr p=YADE_PTR_DYN_CAST(b->shape); if(!s && !p) continue; if(!p){ //spheres shared_ptr ebp=YADE_PTR_DYN_CAST(b->material); if(!ebp) continue; Real density=b->state->mass/((4./3.)*Mathr::PI*pow(s->radius,3)); dt=min(dt,s->radius/sqrt(ebp->young/density)); }else{ //polyhedrons shared_ptr ebp=YADE_PTR_DYN_CAST(b->material); if(!ebp) continue; Real density=b->state->mass/p->GetVolume(); //get equivalent radius and use same equation as for sphere Real equi_radius=pow(p->GetVolume()/((4./3.)*Mathr::PI),1./3.); dt=min(dt,equi_radius/sqrt(ebp->young*equi_radius/density)); } } if (dt==std::numeric_limits::infinity()) { dt = 1.0; LOG_WARN("PWaveTimeStep has not found any suitable spherical or polyhedral body to calculate dt. dt is set to 1.0"); } return dt; } //********************************************************************************** //returns approximate sieve size of polyhedron Real SieveSize(const shared_ptr& cm1){ Polyhedra* A = static_cast(cm1.get()); double phi = M_PI/4.; double x,y; double minx = 0, maxx = 0, miny = 0, maxy = 0; for (vector::iterator i=A->v.begin(); i!=A->v.end(); ++i){ x = cos(phi)*(*i)[1] + sin(phi)*(*i)[2]; y = -sin(phi)*(*i)[1] + cos(phi)*(*i)[2]; minx = min(minx,x); maxx = max(maxx,x); miny = min(miny,y); maxy = max(maxy,y); } return max(maxx-minx, maxy-miny); } //********************************************************************************** //returns approximate size of polyhedron Vector3r SizeOfPolyhedra(const shared_ptr& cm1){ Polyhedra* A = static_cast(cm1.get()); double minx = 0, maxx = 0, miny = 0, maxy = 0, minz = 0, maxz = 0; for (vector::iterator i=A->v.begin(); i!=A->v.end(); ++i){ minx = min(minx,(*i)[0]); maxx = max(maxx,(*i)[0]); miny = min(miny,(*i)[1]); maxy = max(maxy,(*i)[1]); minz = min(minz,(*i)[2]); maxz = max(maxz,(*i)[2]); } return Vector3r(maxx-minx, maxy-miny, maxz-minz); } //********************************************************************************** //save sieve curve points into a file void SieveCurve(){ const shared_ptr _rb=shared_ptr(); shared_ptr rb=(_rb?_rb:Omega::instance().getScene()); std::vector< std::pair > sieve_volume; double total_volume = 0; FOREACH(const shared_ptr& b, *rb->bodies){ if(!b || !b->shape) continue; shared_ptr p=YADE_PTR_DYN_CAST(b->shape); if(p){ sieve_volume.push_back(std::pair(SieveSize(p),p->GetVolume())); total_volume += p->GetVolume(); } } std::sort(sieve_volume.begin(), sieve_volume.end()) ; double cumul_vol = 0; ofstream myfile; myfile.open ("sieve_curve.dat"); for(std::vector< std::pair > :: iterator i = sieve_volume.begin(); i != sieve_volume.end(); ++i) { cumul_vol += i->second/total_volume; myfile << i->first << "\t" << cumul_vol << endl; } myfile.close(); } //********************************************************************************** //save size of polyhedrons into a file void SizeRatio(){ const shared_ptr _rb=shared_ptr(); shared_ptr rb=(_rb?_rb:Omega::instance().getScene()); ofstream myfile; myfile.open ("sizes.dat"); FOREACH(const shared_ptr& b, *rb->bodies){ if(!b || !b->shape) continue; shared_ptr p=YADE_PTR_DYN_CAST(b->shape); if(p){ myfile << SizeOfPolyhedra(p) << endl; } } myfile.close(); } //********************************************************************************** //returns max coordinates Vector3r MaxCoord(const shared_ptr& cm1,const State& state1){ const Se3r& se3=state1.se3; Polyhedra* A = static_cast(cm1.get()); //move and rotate CGAL structure Polyhedron Matrix3r rot_mat = (se3.orientation).toRotationMatrix(); Vector3r trans_vec = se3.position; Transformation t_rot_trans(rot_mat(0,0),rot_mat(0,1),rot_mat(0,2), trans_vec[0],rot_mat(1,0),rot_mat(1,1),rot_mat(1,2),trans_vec[1],rot_mat(2,0),rot_mat(2,1),rot_mat(2,2),trans_vec[2],1.); Polyhedron PA = A->GetPolyhedron(); std::transform( PA.points_begin(), PA.points_end(), PA.points_begin(), t_rot_trans); Vector3r maxccord = trans_vec; for(Polyhedron::Vertex_iterator vi = PA.vertices_begin(); vi != PA.vertices_end(); ++vi){ if (vi->point()[0]>maxccord[0]) maxccord[0]=vi->point()[0]; if (vi->point()[1]>maxccord[1]) maxccord[1]=vi->point()[1]; if (vi->point()[2]>maxccord[2]) maxccord[2]=vi->point()[2]; } return maxccord; } //********************************************************************************** //returns min coordinates Vector3r MinCoord(const shared_ptr& cm1,const State& state1){ const Se3r& se3=state1.se3; Polyhedra* A = static_cast(cm1.get()); //move and rotate CGAL structure Polyhedron Matrix3r rot_mat = (se3.orientation).toRotationMatrix(); Vector3r trans_vec = se3.position; Transformation t_rot_trans(rot_mat(0,0),rot_mat(0,1),rot_mat(0,2), trans_vec[0],rot_mat(1,0),rot_mat(1,1),rot_mat(1,2),trans_vec[1],rot_mat(2,0),rot_mat(2,1),rot_mat(2,2),trans_vec[2],1.); Polyhedron PA = A->GetPolyhedron(); std::transform( PA.points_begin(), PA.points_end(), PA.points_begin(), t_rot_trans); Vector3r minccord = trans_vec; for(Polyhedron::Vertex_iterator vi = PA.vertices_begin(); vi != PA.vertices_end(); ++vi){ if (vi->point()[0]point()[0]; if (vi->point()[1]point()[1]; if (vi->point()[2]point()[2]; } return minccord; } //********************************************************************************** //generate "packing" of non-overlapping polyhedrons vector fillBox_cpp(Vector3r minCoord, Vector3r maxCoord, Vector3r sizemin, Vector3r sizemax, Vector3r ratio, int seed, shared_ptr mat){ vector v; Polyhedra trialP; Polyhedron trial, trial_moved; srand(seed); int it = 0; vector polyhedrons; vector > vv; Vector3r position; bool intersection; int count = 0; bool fixed_ratio = 0; if (ratio[0] > 0 && ratio[1] > 0 && ratio[2]>0){ fixed_ratio = 1; sizemax[0] = min(min(sizemax[0]/ratio[0], sizemax[1]/ratio[1]), sizemax[2]/ratio[2]); sizemin[0] = max(max(sizemin[0]/ratio[0], sizemin[1]/ratio[1]), sizemin[2]/ratio[2]); } //it - number of trials to make packing possibly more/less dense Vector3r random_size; while (it<1000){ it = it+1; if (it == 1){ trialP.Clear(); trialP.seed = rand(); if(fixed_ratio) trialP.size = (rand()*(sizemax[0]-sizemin[0])/RAND_MAX + sizemin[0])*ratio; else trialP.size = Vector3r(rand()*(sizemax[0]-sizemin[0]),rand()*(sizemax[1]-sizemin[1]),rand()*(sizemax[2]-sizemin[2]))/RAND_MAX + sizemin; trialP.Initialize(); trial = trialP.GetPolyhedron(); Matrix3r rot_mat = (trialP.GetOri()).toRotationMatrix(); Transformation t_rot(rot_mat(0,0),rot_mat(0,1),rot_mat(0,2),rot_mat(1,0),rot_mat(1,1),rot_mat(1,2),rot_mat(2,0),rot_mat(2,1),rot_mat(2,2),1.); std::transform( trial.points_begin(), trial.points_end(), trial.points_begin(), t_rot); } position = Vector3r(rand()*(maxCoord[0]-minCoord[0]),rand()*(maxCoord[1]-minCoord[1]),rand()*(maxCoord[2]-minCoord[2]))/RAND_MAX + minCoord; //move CGAL structure Polyhedron Transformation transl(CGAL::TRANSLATION, ToCGALVector(position)); trial_moved = trial; std::transform( trial_moved.points_begin(), trial_moved.points_end(), trial_moved.points_begin(), transl); //calculate plane equations std::transform( trial_moved.facets_begin(), trial_moved.facets_end(), trial_moved.planes_begin(),Plane_equation()); intersection = false; //call test with boundary for(Polyhedron::Vertex_iterator vi = trial_moved.vertices_begin(); (vi != trial_moved.vertices_end()) && (!intersection); vi++){ intersection = (vi->point().x()point().x()>maxCoord[0]) || (vi->point().y()point().y()>maxCoord[1]) || (vi->point().z()point().z()>maxCoord[2]); } //call test with other polyhedrons for(vector::iterator a = polyhedrons.begin(); (a != polyhedrons.end()) && (!intersection); a++){ intersection = do_intersect(*a,trial_moved); if (intersection) break; } if (!intersection){ polyhedrons.push_back(trial_moved); v.clear(); for(Polyhedron::Vertex_iterator vi = trial_moved.vertices_begin(); vi != trial_moved.vertices_end(); vi++){ v.push_back(FromCGALPoint(vi->point())); } vv.push_back(v); it = 0; count ++; } } cout << "generated " << count << " polyhedrons"<< endl; //can't be used - no information about material Scene* scene=Omega::instance().getScene().get(); for(vector >::iterator p=vv.begin(); p!=vv.end(); ++p){ shared_ptr BP = NewPolyhedra(*p, mat); BP->shape->color = Vector3r(double(rand())/RAND_MAX,double(rand())/RAND_MAX,double(rand())/RAND_MAX); scene->bodies->insert(BP); } return v; } //************************************************************************** /* Generate truncated icosahedron*/ vector TruncIcosaHedPoints(Vector3r radii){ vector v; double p = (1.+sqrt(5.))/2.; Vector3r f,c,b; f = radii/sqrt(9.*p + 1.); vector A,B; A.push_back(Vector3r(0.,1.,3.*p)); A.push_back(Vector3r(2.,1.+2.*p,p)); A.push_back(Vector3r(1.,2.+p,2.*p)); for(int i=0;i<(int) A.size() ;i++){ B.clear(); c = Vector3r(A[i][0]*f[0],A[i][1]*f[1],A[i][2]*f[2]); B.push_back(c); B.push_back(Vector3r(c[1],c[2],c[0])); B.push_back(Vector3r(c[2],c[0],c[1])); for(int j=0;j<(int) B.size() ;j++){ b = B[j]; v.push_back(b); if (b[0] != 0.){ v.push_back(Vector3r(-b[0], b[1], b[2])); if (b[1] != 0.){ v.push_back(Vector3r(-b[0],-b[1], b[2])); if (b[2] != 0.) v.push_back(Vector3r(-b[0],-b[1],-b[2])); } if (b[2] != 0.) v.push_back(Vector3r(-b[0], b[1],-b[2])); } if (b[1] != 0.){ v.push_back(Vector3r( b[0],-b[1], b[2])); if (b[2] != 0.) v.push_back(Vector3r( b[0],-b[1],-b[2])); } if (b[2] != 0.) v.push_back(Vector3r( b[0], b[1],-b[2])); } } return v; } //************************************************************************** /* Generate SnubCube*/ vector SnubCubePoints(Vector3r radii){ vector v; double c1 = 0.337754; double c2 = 1.14261; double c3 = 0.621226; Vector3r f,b; f = radii/1.3437133737446; vector A; A.push_back(Vector3r(c2,c1,c3)); A.push_back(Vector3r(c1,c3,c2)); A.push_back(Vector3r(c3,c2,c1)); A.push_back(Vector3r(-c1,-c2,-c3)); A.push_back(Vector3r(-c2,-c3,-c1)); A.push_back(Vector3r(-c3,-c1,-c2)); for(int i=0;i<(int) A.size();i++){ b = Vector3r(A[i][0]*f[0],A[i][1]*f[1],A[i][2]*f[2]); v.push_back(b); v.push_back(Vector3r(-b[0],-b[1], b[2])); v.push_back(Vector3r(-b[0], b[1],-b[2])); v.push_back(Vector3r( b[0],-b[1],-b[2])); } return v; } //************************************************************************** /* Generate ball*/ vector BallPoints(Vector3r radii, int NumFacets,int seed){ vector v; if (NumFacets == 60) v = TruncIcosaHedPoints(radii); if (NumFacets == 24) v = SnubCubePoints(radii); else{ double inc = Mathr::PI * (3. - pow(5.,0.5)); double off = 2. / double(NumFacets); double y,r,phi; for(int k=0; k fillBoxByBalls_cpp(Vector3r minCoord, Vector3r maxCoord, Vector3r sizemin, Vector3r sizemax, Vector3r ratio, int seed, shared_ptr mat, int NumPoints){ vector v; Polyhedra trialP; Polyhedron trial, trial_moved; srand(seed); int it = 0; vector polyhedrons; vector > vv; Vector3r position; bool intersection; int count = 0; Vector3r radii; bool fixed_ratio = 0; if (ratio[0] > 0 && ratio[1] > 0 && ratio[2]>0){ fixed_ratio = 1; sizemax[0] = min(min(sizemax[0]/ratio[0], sizemax[1]/ratio[1]), sizemax[2]/ratio[2]); sizemin[0] = max(max(sizemin[0]/ratio[0], sizemin[1]/ratio[1]), sizemin[2]/ratio[2]); } fixed_ratio = 1; //force spherical //it - number of trials to make packing possibly more/less dense Vector3r random_size; while (it<1000){ it = it+1; if (it == 1){ if (fixed_ratio) { double rrr = (rand()*(sizemax[0]-sizemin[0])/RAND_MAX + sizemin[0])/2.; radii = Vector3r(rrr,rrr,rrr); }else { radii = Vector3r(rand()*(sizemax[0]-sizemin[0])/2.,rand()*(sizemax[1]-sizemin[1])/2.,rand()*(sizemax[2]-sizemin[2])/2.)/RAND_MAX + sizemin/2.; } trialP.v = BallPoints(radii,NumPoints,rand()); trialP.Initialize(); trial = trialP.GetPolyhedron(); Matrix3r rot_mat = (trialP.GetOri()).toRotationMatrix(); Transformation t_rot(rot_mat(0,0),rot_mat(0,1),rot_mat(0,2),rot_mat(1,0),rot_mat(1,1),rot_mat(1,2),rot_mat(2,0),rot_mat(2,1),rot_mat(2,2),1.); std::transform( trial.points_begin(), trial.points_end(), trial.points_begin(), t_rot); } position = Vector3r(rand()*(maxCoord[0]-minCoord[0]),rand()*(maxCoord[1]-minCoord[1]),rand()*(maxCoord[2]-minCoord[2]))/RAND_MAX + minCoord; //move CGAL structure Polyhedron Transformation transl(CGAL::TRANSLATION, ToCGALVector(position)); trial_moved = trial; std::transform( trial_moved.points_begin(), trial_moved.points_end(), trial_moved.points_begin(), transl); //calculate plane equations std::transform( trial_moved.facets_begin(), trial_moved.facets_end(), trial_moved.planes_begin(),Plane_equation()); intersection = false; //call test with boundary for(Polyhedron::Vertex_iterator vi = trial_moved.vertices_begin(); (vi != trial_moved.vertices_end()) && (!intersection); vi++){ intersection = (vi->point().x()point().x()>maxCoord[0]) || (vi->point().y()point().y()>maxCoord[1]) || (vi->point().z()point().z()>maxCoord[2]); } //call test with other polyhedrons for(vector::iterator a = polyhedrons.begin(); (a != polyhedrons.end()) && (!intersection); a++){ intersection = do_intersect(*a,trial_moved); if (intersection) break; } if (!intersection){ polyhedrons.push_back(trial_moved); v.clear(); for(Polyhedron::Vertex_iterator vi = trial_moved.vertices_begin(); vi != trial_moved.vertices_end(); vi++){ v.push_back(FromCGALPoint(vi->point())); } vv.push_back(v); it = 0; count ++; } } cout << "generated " << count << " polyhedrons"<< endl; //can't be used - no information about material Scene* scene=Omega::instance().getScene().get(); for(vector >::iterator p=vv.begin(); p!=vv.end(); ++p){ shared_ptr BP = NewPolyhedra(*p, mat); BP->shape->color = Vector3r(double(rand())/RAND_MAX,double(rand())/RAND_MAX,double(rand())/RAND_MAX); scene->bodies->insert(BP); } return v; } //********************************************************************************** //split polyhedra void Split(const shared_ptr body, Vector3r direction, Vector3r point){ SplitPolyhedra(body, direction, point); } //********************************************************************************** //distace of point from a plane (squared) with sign double Oriented_squared_distance2(Plane P, CGALpoint x){ double h = P.a()*x.x()+P.b()*x.y()+P.c()*x.z()+P.d(); return ((h>0.)-(h<0.))*pow(h,2)/(CGALvector(P.a(),P.b(),P.c())).squared_length(); } //********************************************************************************** bool convexHull(vector points){ vector pointsCGAL; for(int i=0;i<(int) points.size() ;i++) { pointsCGAL.push_back(ToCGALPoint(points[i])); } Polyhedron P; CGAL::convex_hull_3(pointsCGAL.begin(), pointsCGAL.end(), P); return true; } BOOST_PYTHON_MODULE(_polyhedra_utils){ YADE_SET_DOCSTRING_OPTS; py::def("PrintPolyhedra",PrintPolyhedra,"Print list of vertices sorted according to polyhedrons facets."); py::def("PrintPolyhedraActualPos",PrintPolyhedraActualPos,"Print list of vertices sorted according to polyhedrons facets."); py::def("PWaveTimeStep",PWaveTimeStep,"Get timestep accoring to the velocity of P-Wave propagation; computed from sphere radii, rigidities and masses."); py::def("do_Polyhedras_Intersect",do_Polyhedras_Intersect,"check polyhedras intersection"); py::def("fillBox_cpp",fillBox_cpp,"Generate non-overlaping polyhedrons in box"); py::def("fillBoxByBalls_cpp",fillBoxByBalls_cpp,"Generate non-overlaping 'spherical' polyhedrons in box"); py::def("MinCoord",MinCoord,"returns min coordinates"); py::def("MaxCoord",MaxCoord,"returns max coordinates"); py::def("SieveSize",SieveSize,"returns approximate sieve size of polyhedron"); py::def("SieveCurve",SieveCurve,"save sieve curve coordinates into file"); py::def("SizeOfPolyhedra",SizeOfPolyhedra,"returns max, middle an min size in perpendicular directions"); py::def("SizeRatio",SizeRatio,"save sizes of polyhedra into file"); py::def("convexHull",convexHull,"TODO"); py::def("Split",Split,"split polyhedron perpendicularly to given direction through given point"); } #endif // YADE_CGAL trunk-2017.01a/py/_utils.cpp000066400000000000000000001261751304022710500156310ustar00rootroot00000000000000#include #include bool isInBB(Vector3r p, Vector3r bbMin, Vector3r bbMax){return p[0]>bbMin[0] && p[0]bbMin[1] && p[1]bbMin[2] && p[2](extrema[0][axis])(),maxCoord=py::extract(extrema[1][axis])(); py::list minIds,maxIds; FOREACH(const shared_ptr& b, *Omega::instance().getScene()->bodies){ shared_ptr s=YADE_PTR_DYN_CAST(b->shape); if(!s) continue; if(b->state->pos[axis]-s->radius*distFactor<=minCoord) minIds.append(b->getId()); if(b->state->pos[axis]+s->radius*distFactor>=maxCoord) maxIds.append(b->getId()); } return py::make_tuple(minIds,maxIds); } py::tuple coordsAndDisplacements(int axis,py::tuple Aabb){ Vector3r bbMin(Vector3r::Zero()), bbMax(Vector3r::Zero()); bool useBB=py::len(Aabb)>0; if(useBB){bbMin=py::extract(Aabb[0])();bbMax=py::extract(Aabb[1])();} py::list retCoord,retDispl; FOREACH(const shared_ptr&b, *Omega::instance().getScene()->bodies){ if(useBB && !isInBB(b->state->pos,bbMin,bbMax)) continue; retCoord.append(b->state->pos[axis]); retDispl.append(b->state->pos[axis]-b->state->refPos[axis]); } return py::make_tuple(retCoord,retDispl); } void setRefSe3(){ Scene* scene=Omega::instance().getScene().get(); FOREACH(const shared_ptr& b, *scene->bodies){ b->state->refPos=b->state->pos; b->state->refOri=b->state->ori; } if(scene->isPeriodic){ scene->cell->refHSize=scene->cell->hSize; } } Real PWaveTimeStep(){return Shop::PWaveTimeStep();}; Real RayleighWaveTimeStep(){return Shop::RayleighWaveTimeStep();}; py::tuple interactionAnglesHistogram(int axis, int mask, size_t bins, py::tuple aabb, bool sphSph, Real minProjLen){ if(axis<0||axis>2) throw invalid_argument("Axis must be from {0,1,2}=x,y,z."); Vector3r bbMin(Vector3r::Zero()), bbMax(Vector3r::Zero()); bool useBB=py::len(aabb)>0; if(useBB){bbMin=py::extract(aabb[0])();bbMax=py::extract(aabb[1])();} Real binStep=Mathr::PI/bins; int axis2=(axis+1)%3, axis3=(axis+2)%3; vector cummProj(bins,0.); shared_ptr rb=Omega::instance().getScene(); FOREACH(const shared_ptr& i, *rb->interactions){ if(!i->isReal()) continue; const shared_ptr& b1=Body::byId(i->getId1(),rb), b2=Body::byId(i->getId2(),rb); if(!b1->maskOk(mask) || !b2->maskOk(mask)) continue; if(useBB && !isInBB(b1->state->pos,bbMin,bbMax) && !isInBB(b2->state->pos,bbMin,bbMax)) continue; if (sphSph && ( !dynamic_cast(b1->shape.get()) || !dynamic_cast(b2->shape.get()) ) ) continue; GenericSpheresContact* geom=dynamic_cast(i->geom.get()); if(!geom) continue; Vector3r n(geom->normal); n[axis]=0.; Real nLen=n.norm(); if(nLen0?1:-1); if(theta<0) theta+=Mathr::PI; int binNo=theta/binStep; cummProj[binNo]+=nLen; } py::list val,binMid; for(size_t i=0; i<(size_t)bins; i++){ val.append(cummProj[i]); binMid.append(i*binStep);} return py::make_tuple(binMid,val); } py::tuple bodyNumInteractionsHistogram(py::tuple aabb){ Vector3r bbMin(Vector3r::Zero()), bbMax(Vector3r::Zero()); bool useBB=py::len(aabb)>0; if(useBB){bbMin=py::extract(aabb[0])();bbMax=py::extract(aabb[1])();} const shared_ptr& rb=Omega::instance().getScene(); vector bodyNumIntr; bodyNumIntr.resize(rb->bodies->size(),0); int maxIntr=0; FOREACH(const shared_ptr& i, *rb->interactions){ if(!i->isReal()) continue; const Body::id_t id1=i->getId1(), id2=i->getId2(); const shared_ptr& b1=Body::byId(id1,rb), b2=Body::byId(id2,rb); if((useBB && isInBB(b1->state->pos,bbMin,bbMax)) || !useBB) { if (b1->isClumpMember()) bodyNumIntr[b1->clumpId]+=1; //count bodyNumIntr for the clump, not for the member else bodyNumIntr[id1]+=1; } if((useBB && isInBB(b2->state->pos,bbMin,bbMax)) || !useBB) { if (b2->isClumpMember()) bodyNumIntr[b2->clumpId]+=1; //count bodyNumIntr for the clump, not for the member else bodyNumIntr[id2]+=1; } maxIntr=max(max(maxIntr,bodyNumIntr[b1->getId()]),bodyNumIntr[b2->getId()]); if (b1->isClumpMember()) maxIntr=max(maxIntr,bodyNumIntr[b1->clumpId]); if (b2->isClumpMember()) maxIntr=max(maxIntr,bodyNumIntr[b2->clumpId]); } vector bins; bins.resize(maxIntr+1,0); for(size_t id=0; id& b=Body::byId(id,rb); if (b) { if(bodyNumIntr[id]>0) bins[bodyNumIntr[id]]+=1; // 0 is handled specially: add body to the 0 bin only if it is inside the bb requested (if applicable) // otherwise don't do anything, since it is outside the volume of interest else if(((useBB && isInBB(b->state->pos,bbMin,bbMax)) || !useBB) && !(b->isClumpMember())) bins[0]+=1; } } py::list count,num; for(size_t n=0; n b = shared_ptr(new ViscElMat()); Shop::getViscoelasticFromSpheresInteraction(tc,en,es,b); py::dict d; d["kn"]=b->kn; d["cn"]=b->cn; d["ks"]=b->ks; d["cs"]=b->cs; return d; } /* reset highlight of all bodies */ void highlightNone(){ FOREACH(const shared_ptr& b, *Omega::instance().getScene()->bodies){ if(!b->shape) continue; b->shape->highlight=false; } } /*!Sum moments acting on given bodies * * @param ids is the calculated bodies ids * @param axis is the direction of axis with respect to which the moment is calculated. * @param axisPt is a point on the axis. * * The computation is trivial: moment from force is is by definition r×F, where r * is position relative to axisPt; moment from moment is m; such moment per body is * projected onto axis. */ Real sumTorques(py::list ids, const Vector3r& axis, const Vector3r& axisPt){ shared_ptr rb=Omega::instance().getScene(); rb->forces.sync(); Real ret=0; size_t len=py::len(ids); for(size_t i=0; ibodies)[py::extract(ids[i])].get(); const Vector3r& m=rb->forces.getTorque(b->getId()); const Vector3r& f=rb->forces.getForce(b->getId()); Vector3r r=b->state->pos-axisPt; ret+=axis.dot(m+r.cross(f)); } return ret; } /* Sum forces acting on bodies within mask. * * @param ids list of ids * @param direction direction in which forces are summed * */ Real sumForces(py::list ids, const Vector3r& direction){ shared_ptr rb=Omega::instance().getScene(); rb->forces.sync(); Real ret=0; size_t len=py::len(ids); for(size_t i=0; i(ids[i]); const Vector3r& f=rb->forces.getForce(id); ret+=direction.dot(f); } return ret; } /* Sum force acting on facets given by their ids in the sense of their respective normals. If axis is given, it will sum forces perpendicular to given axis only (not the the facet normals). */ Real sumFacetNormalForces(vector ids, int axis){ shared_ptr rb=Omega::instance().getScene(); rb->forces.sync(); Real ret=0; FOREACH(const Body::id_t id, ids){ Facet* f=YADE_CAST(Body::byId(id,rb)->shape.get()); if(axis<0) ret+=rb->forces.getForce(id).dot(f->normal); else { Vector3r ff=rb->forces.getForce(id); ff[axis]=0; ret+=ff.dot(f->normal); } } return ret; } /* Set wire display of all/some/none bodies depending on the filter. */ void wireSome(string filter){ enum{none,all,noSpheres,unknown}; int mode=(filter=="none"?none:(filter=="all"?all:(filter=="noSpheres"?noSpheres:unknown))); if(mode==unknown) { LOG_WARN("Unknown wire filter `"<& b, *Omega::instance().getScene()->bodies){ if(!b->shape) return; bool wire; switch(mode){ case none: wire=false; break; case all: wire=true; break; case noSpheres: wire=!(bool)(YADE_PTR_DYN_CAST(b->shape)); break; default: throw logic_error("No such case possible"); } b->shape->wire=wire; } } void wireAll(){wireSome("all");} void wireNone(){wireSome("none");} void wireNoSpheres(){wireSome("noSpheres");} /* Tell us whether a point lies in polygon given by array of points. * @param xy is the point that is being tested * @param vertices is Numeric.array (or list or tuple) of vertices of the polygon. * Every row of the array is x and y coordinate, numer of rows is >= 3 (triangle). * * Copying the algorithm from http://www.ecse.rpi.edu/Homepages/wrf/Research/Short_Notes/pnpoly.html * is gratefully acknowledged: * * License to Use: * Copyright (c) 1970-2003, Wm. Randolph Franklin * Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: * 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimers. * 2. Redistributions in binary form must reproduce the above copyright notice in the documentation and/or other materials provided with the distribution. * 3. The name of W. Randolph Franklin may not be used to endorse or promote products derived from this Software without specific prior written permission. * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. * * http://numpy.scipy.org/numpydoc/numpy-13.html told me how to use Numeric.array from c */ bool pointInsidePolygon(py::tuple xy, py::object vertices){ Real testx=py::extract(xy[0])(),testy=py::extract(xy[1])(); char** vertData; int rows, cols; PyArrayObject* vert=(PyArrayObject*)vertices.ptr(); int result=PyArray_As2D((PyObject**)&vert /* is replaced */ ,&vertData,&rows,&cols,PyArray_DOUBLE); if(result!=0) throw invalid_argument("Unable to cast vertices to 2d array"); if(cols!=2 || rows<3) throw invalid_argument("Vertices must have 2 columns (x and y) and at least 3 rows."); int i /*current node*/, j/*previous node*/; bool inside=false; for(i=0,j=rows-1; idata+i*vert->strides[0]), vy_i=*(double*)(vert->data+i*vert->strides[0]+vert->strides[1]), vx_j=*(double*)(vert->data+j*vert->strides[0]), vy_j=*(double*)(vert->data+j*vert->strides[0]+vert->strides[1]); if (((vy_i>testy)!=(vy_j>testy)) && (testx < (vx_j-vx_i) * (testy-vy_i) / (vy_j-vy_i) + vx_i) ) inside=!inside; } Py_DECREF(vert); return inside; } /* Compute area of convex hull when when taking (swept) spheres crossing the plane at coord, perpendicular to axis. All spheres that touch the plane are projected as hexagons on their circumference to the plane. Convex hull from this cloud is computed. The area of the hull is returned. */ Real approxSectionArea(Real coord, int axis){ std::list cloud; if(axis<0 || axis>2) throw invalid_argument("Axis must be ∈ {0,1,2}"); const int ax1=(axis+1)%3, ax2=(axis+2)%3; const Real sqrt3=sqrt(3); Vector2r mm,mx; int i=0; FOREACH(const shared_ptr& b, *Omega::instance().getScene()->bodies){ Sphere* s=dynamic_cast(b->shape.get()); if(!s) continue; const Vector3r& pos(b->state->pos); const Real r(s->radius); if((pos[axis]>coord && (pos[axis]-r)>coord) || (pos[axis] hull=ch2d(); return simplePolygonArea2d(hull); } /* Find all interactions deriving from NormShearPhys that cross plane given by a point and normal (the normal may not be normalized in this case, though) and sum forces (both normal and shear) on them. Returns a 3-tuple with the components along global x,y,z axes, which can be viewed as "action from lower part, towards upper part" (lower and upper parts with respect to the plane's normal). (This could be easily extended to return sum of only normal forces or only of shear forces.) */ Vector3r forcesOnPlane(const Vector3r& planePt, const Vector3r& normal){ Vector3r ret(Vector3r::Zero()); Scene* scene=Omega::instance().getScene().get(); FOREACH(const shared_ptr&I, *scene->interactions){ if(!I->isReal()) continue; NormShearPhys* nsi=dynamic_cast(I->phys.get()); if(!nsi) continue; Vector3r pos1,pos2; pos1=Body::byId(I->getId1(),scene)->state->pos; pos2=Body::byId(I->getId2(),scene)->state->pos; Real dot1=(pos1-planePt).dot(normal), dot2=(pos2-planePt).dot(normal); if(dot1*dot2>0) continue; // both (centers of) bodies are on the same side of the plane=> this interaction has to be disregarded // if pt1 is on the negative plane side, d3dg->normal.Dot(normal)>0, the force is well oriented; // otherwise, reverse its contribution. So that we return finally // Sum [ ( normal(plane) dot normal(interaction= from 1 to 2) ) "nsi->force" ] ret+=(dot1<0.?1.:-1.)*(nsi->normalForce+nsi->shearForce); } return ret; } /* Less general than forcesOnPlane, computes force on plane perpendicular to axis, passing through coordinate coord. */ Vector3r forcesOnCoordPlane(Real coord, int axis){ Vector3r planePt(Vector3r::Zero()); planePt[axis]=coord; Vector3r normal(Vector3r::Zero()); normal[axis]=1; return forcesOnPlane(planePt,normal); } py::tuple spiralProject(const Vector3r& pt, Real dH_dTheta, int axis, Real periodStart, Real theta0){ Real r,h,theta; boost::tie(r,h,theta)=Shop::spiralProject(pt,dH_dTheta,axis,periodStart,theta0); return py::make_tuple(py::make_tuple(r,h),theta); } shared_ptr Shop__createExplicitInteraction(Body::id_t id1, Body::id_t id2){ return Shop::createExplicitInteraction(id1,id2,/*force*/true);} Real Shop__unbalancedForce(bool useMaxForce /*false by default*/){return Shop::unbalancedForce(useMaxForce);} py::tuple Shop__totalForceInVolume(){Real stiff; Vector3r ret=Shop::totalForceInVolume(stiff); return py::make_tuple(ret,stiff); } Real Shop__getSpheresVolume(int mask){ return Shop::getSpheresVolume(Omega::instance().getScene(), mask);} Real Shop__getSpheresMass(int mask){ return Shop::getSpheresMass(Omega::instance().getScene(), mask);} py::object Shop__kineticEnergy(bool findMaxId){ if(!findMaxId) return py::object(Shop::kineticEnergy()); Body::id_t maxId; Real E=Shop::kineticEnergy(NULL,&maxId); return py::make_tuple(E,maxId); } Real maxOverlapRatio(){ Scene* scene=Omega::instance().getScene().get(); Real ret=-1; FOREACH(const shared_ptr I, *scene->interactions){ if(!I->isReal()) continue; Sphere *s1(dynamic_cast(Body::byId(I->getId1(),scene)->shape.get())), *s2(dynamic_cast(Body::byId(I->getId2(),scene)->shape.get())); if((!s1) || (!s2)) continue; ScGeom* geom=dynamic_cast(I->geom.get()); if(!geom) continue; Real rEq=2*s1->radius*s2->radius/(s1->radius+s2->radius); ret=max(ret,geom->penetrationDepth/rEq); } return ret; } Real Shop__getPorosity(Real volume){ return Shop::getPorosity(Omega::instance().getScene(),volume); } Real Shop__getVoxelPorosity(int resolution, Vector3r start,Vector3r end){ return Shop::getVoxelPorosity(Omega::instance().getScene(),resolution,start,end); } //Matrix3r Shop__stressTensorOfPeriodicCell(bool smallStrains=false){return Shop::stressTensorOfPeriodicCell(smallStrains);} py::tuple Shop__fabricTensor(Real cutoff, bool splitTensor, Real thresholdForce){return Shop::fabricTensor(cutoff, splitTensor,thresholdForce);} py::tuple Shop__normalShearStressTensors(bool compressionPositive, bool splitNormalTensor, Real thresholdForce){return Shop::normalShearStressTensors(compressionPositive,splitNormalTensor,thresholdForce);} py::list Shop__getStressLWForEachBody(){return Shop::getStressLWForEachBody();} py::list Shop__getBodyIdsContacts(Body::id_t bodyID){return Shop::getBodyIdsContacts(bodyID);} Real shiftBodies(py::list ids, const Vector3r& shift){ shared_ptr rb=Omega::instance().getScene(); size_t len=py::len(ids); for(size_t i=0; ibodies)[py::extract(ids[i])].get(); if(!b) continue; b->state->pos+=shift; } return 1; } void Shop__calm(int mask){ return Shop::calm(Omega::instance().getScene(), mask);} void setNewVerticesOfFacet(const shared_ptr& b, const Vector3r& v1, const Vector3r& v2, const Vector3r& v3) { Vector3r center = inscribedCircleCenter(v1,v2,v3); Facet* facet = YADE_CAST(b->shape.get()); facet->vertices[0] = v1 - center; facet->vertices[1] = v2 - center; facet->vertices[2] = v3 - center; b->state->pos = center; } py::list intrsOfEachBody() { py::list ret, temp; shared_ptr rb=Omega::instance().getScene(); size_t n = rb->bodies->size(); // create list of size len(O.bodies) full of zeros for (size_t i=0; i& i, *rb->interactions) { if (!i->isReal()) { continue; } temp = py::extract(ret[i->getId1()]); temp.append( i ); temp = py::extract(ret[i->getId2()]); temp.append( i ); } return ret; } py::list numIntrsOfEachBody() { py::list ret; shared_ptr rb=Omega::instance().getScene(); size_t n = rb->bodies->size(); // create list of size len(O.bodies) full of zeros for (size_t i=0; i& i, *rb->interactions) { if (!i->isReal()) continue; ret[i->getId1()] += 1; ret[i->getId2()] += 1; } return ret; } Real Shop__getSpheresVolume2D(int mask=-1){ return Shop::getSpheresVolume2D(Omega::instance().getScene(), mask);} Real Shop__getVoidRatio2D(Real zlen=1){ return Shop::getVoidRatio2D(Omega::instance().getScene(),zlen);} py::tuple Shop__getStressAndTangent(Real volume=0, bool symmetry=true){return Shop::getStressAndTangent(volume,symmetry);} void setBodyPosition(int id, Vector3r newPos, string axis){ shared_ptr rb=Omega::instance().getScene(); const Body* b=(*rb->bodies)[id].get(); for (char c : axis){ if(c=='x') {b->state->pos[0] = newPos[0];continue;} if(c=='y') {b->state->pos[1] = newPos[1];continue;} if(c=='z') {b->state->pos[2] = newPos[2];continue;} } } void setBodyVelocity(int id, Vector3r newVel, string axis){ shared_ptr rb=Omega::instance().getScene(); const Body* b=(*rb->bodies)[id].get(); for (char c : axis){ if(c=='x') {b->state->vel[0] = newVel[0];continue;} if(c=='y') {b->state->vel[1] = newVel[1];continue;} if(c=='z') {b->state->vel[2] = newVel[2];continue;} } } void setBodyOrientation(int id, Quaternionr newOri){ shared_ptr rb=Omega::instance().getScene(); const Body* b=(*rb->bodies)[id].get(); b->state->ori=newOri; } void setBodyAngularVelocity(int id, Vector3r newAngVel){ shared_ptr rb=Omega::instance().getScene(); const Body* b=(*rb->bodies)[id].get(); b->state->angVel=newAngVel; } void setBodyColor(int id, Vector3r newColor){ shared_ptr rb=Omega::instance().getScene(); const Body* b=(*rb->bodies)[id].get(); b->shape->color=newColor; } BOOST_PYTHON_MODULE(_utils){ YADE_SET_DOCSTRING_OPTS; py::def("PWaveTimeStep",PWaveTimeStep,"Get timestep accoring to the velocity of P-Wave propagation; computed from sphere radii, rigidities and masses."); py::def("RayleighWaveTimeStep",RayleighWaveTimeStep,"Determination of time step according to Rayleigh wave speed of force propagation."); py::def("getSpheresVolume",Shop__getSpheresVolume,(py::arg("mask")=-1),"Compute the total volume of spheres in the simulation, mask parameter is considered"); py::def("getSpheresMass",Shop__getSpheresMass,(py::arg("mask")=-1),"Compute the total mass of spheres in the simulation, mask parameter is considered"); py::def("porosity",Shop__getPorosity,(py::arg("volume")=-1),"Compute packing porosity $\\frac{V-V_s}{V}$ where $V$ is overall volume and $V_s$ is volume of spheres.\n\n:param float volume: overall volume $V$. For periodic simulations, current volume of the :yref:`Cell` is used. For aperiodic simulations, the value deduced from utils.aabbDim() is used. For compatibility reasons, positive values passed by the user are also accepted in this case.\n"); py::def("voxelPorosity",Shop__getVoxelPorosity,(py::arg("resolution")=200,py::arg("start")=Vector3r(0,0,0),py::arg("end")=Vector3r(0,0,0)),"Compute packing porosity $\\frac{V-V_v}{V}$ where $V$ is a specified volume (from start to end) and $V_v$ is volume of voxels that fall inside any sphere. The calculation method is to divide whole volume into a dense grid of voxels (at given resolution), and count the voxels that fall inside any of the spheres. This method allows one to calculate porosity in any given sub-volume of a whole sample. It is properly excluding part of a sphere that does not fall inside a specified volume.\n\n:param int resolution: voxel grid resolution, values bigger than resolution=1600 require a 64 bit operating system, because more than 4GB of RAM is used, a resolution=800 will use 500MB of RAM.\n:param Vector3 start: start corner of the volume.\n:param Vector3 end: end corner of the volume.\n"); py::def("aabbExtrema",Shop::aabbExtrema,(py::arg("cutoff")=0.0,py::arg("centers")=false),"Return coordinates of box enclosing all bodies\n\n:param bool centers: do not take sphere radii in account, only their centroids\n:param float∈〈0…1〉 cutoff: relative dimension by which the box will be cut away at its boundaries.\n\n\n:return: (lower corner, upper corner) as (Vector3,Vector3)\n\n"); py::def("ptInAABB",isInBB,"Return True/False whether the point p is within box given by its min and max corners"); py::def("negPosExtremeIds",negPosExtremeIds,(py::arg("axis"),py::arg("distFactor")),"Return list of ids for spheres (only) that are on extremal ends of the specimen along given axis; distFactor multiplies their radius so that sphere that do not touch the boundary coordinate can also be returned."); py::def("approxSectionArea",approxSectionArea,"Compute area of convex hull when when taking (swept) spheres crossing the plane at coord, perpendicular to axis."); py::def("coordsAndDisplacements",coordsAndDisplacements,(py::arg("axis"),py::arg("Aabb")=py::tuple()),"Return tuple of 2 same-length lists for coordinates and displacements (coordinate minus reference coordinate) along given axis (1st arg); if the Aabb=((x_min,y_min,z_min),(x_max,y_max,z_max)) box is given, only bodies within this box will be considered."); py::def("setRefSe3",setRefSe3,"Set reference :yref:`positions` and :yref:`orientations` of all :yref:`bodies` equal to their current :yref:`positions` and :yref:`orientations`."); py::def("interactionAnglesHistogram",interactionAnglesHistogram,(py::arg("axis"),py::arg("mask")=0,py::arg("bins")=20,py::arg("aabb")=py::tuple(),py::arg("sphSph")=0,py::arg("minProjLen")=1e-6)); py::def("bodyNumInteractionsHistogram",bodyNumInteractionsHistogram,(py::arg("aabb"))); py::def("inscribedCircleCenter",inscribedCircleCenter,(py::arg("v1"),py::arg("v2"),py::arg("v3")),"Return center of inscribed circle for triangle given by its vertices *v1*, *v2*, *v3*."); py::def("unbalancedForce",&Shop__unbalancedForce,(py::args("useMaxForce")=false),"Compute the ratio of mean (or maximum, if *useMaxForce*) summary force on bodies and mean force magnitude on interactions. For perfectly static equilibrium, summary force on all bodies is zero (since forces from interactions cancel out and induce no acceleration of particles); this ratio will tend to zero as simulation stabilizes, though zero is never reached because of finite precision computation. Sufficiently small value can be e.g. 1e-2 or smaller, depending on how much equilibrium it should be."); py::def("kineticEnergy",Shop__kineticEnergy,(py::args("findMaxId")=false),"Compute overall kinetic energy of the simulation as\n\n.. math:: \\sum\\frac{1}{2}\\left(m_i\\vec{v}_i^2+\\vec{\\omega}(\\mat{I}\\vec{\\omega}^T)\\right).\n\nFor :yref:`aspherical` bodies, the inertia tensor $\\mat{I}$ is transformed to global frame, before multiplied by $\\vec{\\omega}$, therefore the value should be accurate.\n"); py::def("sumForces",sumForces,(py::arg("ids"),py::arg("direction")),"Return summary force on bodies with given *ids*, projected on the *direction* vector."); py::def("sumTorques",sumTorques,(py::arg("ids"),py::arg("axis"),py::arg("axisPt")),"Sum forces and torques on bodies given in *ids* with respect to axis specified by a point *axisPt* and its direction *axis*."); py::def("sumFacetNormalForces",sumFacetNormalForces,(py::arg("ids"),py::arg("axis")=-1),"Sum force magnitudes on given bodies (must have :yref:`shape` of the :yref:`Facet` type), considering only part of forces perpendicular to each :yref:`facet's` face; if *axis* has positive value, then the specified axis (0=x, 1=y, 2=z) will be used instead of facet's normals."); py::def("forcesOnPlane",forcesOnPlane,(py::arg("planePt"),py::arg("normal")),"Find all interactions deriving from :yref:`NormShearPhys` that cross given plane and sum forces (both normal and shear) on them.\n\n:param Vector3 planePt: a point on the plane\n:param Vector3 normal: plane normal (will be normalized).\n"); py::def("forcesOnCoordPlane",forcesOnCoordPlane); py::def("totalForceInVolume",Shop__totalForceInVolume,"Return summed forces on all interactions and average isotropic stiffness, as tuple (Vector3,float)"); py::def("createInteraction",Shop__createExplicitInteraction,(py::arg("id1"),py::arg("id2")),"Create interaction between given bodies by hand.\n\nCurrent engines are searched for :yref:`IGeomDispatcher` and :yref:`IPhysDispatcher` (might be both hidden in :yref:`InteractionLoop`). Geometry is created using ``force`` parameter of the :yref:`geometry dispatcher`, wherefore the interaction will exist even if bodies do not spatially overlap and the functor would return ``false`` under normal circumstances. \n\n.. warning:: This function will very likely behave incorrectly for periodic simulations (though it could be extended it to handle it farily easily)."); py::def("spiralProject",spiralProject,(py::arg("pt"),py::arg("dH_dTheta"),py::arg("axis")=2,py::arg("periodStart")=std::numeric_limits::quiet_NaN(),py::arg("theta0")=0)); py::def("pointInsidePolygon",pointInsidePolygon); py::def("scalarOnColorScale",Shop::scalarOnColorScale); py::def("highlightNone",highlightNone,"Reset :yref:`highlight` on all bodies."); py::def("wireAll",wireAll,"Set :yref:`Shape::wire` on all bodies to True, rendering them with wireframe only."); py::def("wireNone",wireNone,"Set :yref:`Shape::wire` on all bodies to False, rendering them as solids."); py::def("wireNoSpheres",wireNoSpheres,"Set :yref:`Shape::wire` to True on non-spherical bodies (:yref:`Facets`, :yref:`Walls`)."); py::def("flipCell",&Shop::flipCell,(py::arg("flip")=Matrix3r(Matrix3r::Zero())),"Flip periodic cell so that angles between $R^3$ axes and transformed axes are as small as possible. This function relies on the fact that periodic cell defines by repetition or its corners regular grid of points in $R^3$; however, all cells generating identical grid are equivalent and can be flipped one over another. This necessiatates adjustment of :yref:`Interaction.cellDist` for interactions that cross boundary and didn't before (or vice versa), and re-initialization of collider. The *flip* argument can be used to specify desired flip: integers, each column for one axis; if zero matrix, best fit (minimizing the angles) is computed automatically.\n\nIn c++, this function is accessible as ``Shop::flipCell``.\n\n.. warning:: This function is currently broken and should not be used."); py::def("getViscoelasticFromSpheresInteraction",getViscoelasticFromSpheresInteraction,(py::arg("tc"),py::arg("en"),py::arg("es")),"Attention! The function is deprecated! Compute viscoelastic interaction parameters from analytical solution of a pair spheres collision problem:\n\n.. math:: k_n=\\frac{m}{t_c^2}\\left(\\pi^2+(\\ln e_n)^2\\right) \\\\ c_n=-\\frac{2m}{t_c}\\ln e_n \\\\ k_t=\\frac{2}{7}\\frac{m}{t_c^2}\\left(\\pi^2+(\\ln e_t)^2\\right) \\\\ c_t=-\\frac{2}{7}\\frac{m}{t_c}\\ln e_t \n\n\nwhere $k_n$, $c_n$ are normal elastic and viscous coefficients and $k_t$, $c_t$ shear elastic and viscous coefficients. For details see [Pournin2001]_.\n\n:param float m: sphere mass $m$\n:param float tc: collision time $t_c$\n:param float en: normal restitution coefficient $e_n$\n:param float es: tangential restitution coefficient $e_s$\n:return: dictionary with keys ``kn`` (the value of $k_n$), ``cn`` ($c_n$), ``kt`` ($k_t$), ``ct`` ($c_t$)."); py::def("stressTensorOfPeriodicCell",Shop::getStress,(py::args("volume")=0),"Deprecated, use utils.getStress instead |ydeprecated|"); py::def("normalShearStressTensors",Shop__normalShearStressTensors,(py::args("compressionPositive")=false,py::args("splitNormalTensor")=false,py::args("thresholdForce")=NaN),"Compute overall stress tensor of the periodic cell decomposed in 2 parts, one contributed by normal forces, the other by shear forces. The formulation can be found in [Thornton2000]_, eq. (3):\n\n.. math:: \\tens{\\sigma}_{ij}=\\frac{2}{V}\\sum R N \\vec{n}_i \\vec{n}_j+\\frac{2}{V}\\sum R T \\vec{n}_i\\vec{t}_j\n\nwhere $V$ is the cell volume, $R$ is \"contact radius\" (in our implementation, current distance between particle centroids), $\\vec{n}$ is the normal vector, $\\vec{t}$ is a vector perpendicular to $\\vec{n}$, $N$ and $T$ are norms of normal and shear forces.\n\n:param bool splitNormalTensor: if true the function returns normal stress tensor split into two parts according to the two subnetworks of strong an weak forces.\n\n:param Real thresholdForce: threshold value according to which the normal stress tensor can be split (e.g. a zero value would make distinction between tensile and compressive forces)."); py::def("fabricTensor",Shop__fabricTensor,(py::args("cutoff")=0.0,py::args("splitTensor")=false,py::args("thresholdForce")=NaN),"Computes the fabric tensor $F_{ij}=\\frac{1}{n_c}\\sum_c n_i n_j$ [Satake1982]_, for all interactions $c$.\n\n:param Real cutoff: intended to disregard boundary effects: to define in [0;1] to focus on the interactions located in the centered inner (1-cutoff)^3*$V$ part of the spherical packing $V$.\n\n:param bool splitTensor: split the fabric tensor into two parts related to the strong (greatest compressive normal forces) and weak contact forces respectively.\n\n:param Real thresholdForce: if the fabric tensor is split into two parts, a threshold value can be specified otherwise the mean contact force is considered by default. Use negative signed values for compressive states. To note that this value could be set to zero if one wanted to make distinction between compressive and tensile forces."); py::def("bodyStressTensors",Shop__getStressLWForEachBody,"Compute and return a table with per-particle stress tensors. Each tensor represents the average stress in one particle, obtained from the contour integral of applied load as detailed below. This definition is considering each sphere as a continuum. It can be considered exact in the context of spheres at static equilibrium, interacting at contact points with negligible volume changes of the solid phase (this last assumption is not restricting possible deformations and volume changes at the packing scale).\n\nProof: \n\nFirst, we remark the identity: $\\sigma_{ij}=\\delta_{ik}\\sigma_{kj}=x_{i,k}\\sigma_{kj}=(x_{i}\\sigma_{kj})_{,k}-x_{i}\\sigma_{kj,k}$.\n\nAt equilibrium, the divergence of stress is null: $\\sigma_{kj,k}=\\vec{0}$. Consequently, after divergence theorem: $\\frac{1}{V}\\int_V \\sigma_{ij}dV = \\frac{1}{V}\\int_V (x_{i}\\sigma_{kj})_{,k}dV = \\frac{1}{V}\\int_{\\partial V}x_i\\sigma_{kj}n_kdS = \\frac{1}{V}\\sum_bx_i^bf_j^b$.\n\nThe last equality is implicitely based on the representation of external loads as Dirac distributions whose zeros are the so-called *contact points*: 0-sized surfaces on which the *contact forces* are applied, located at $x_i$ in the deformed configuration.\n\nA weighted average of per-body stresses will give the average stress inside the solid phase. There is a simple relation between the stress inside the solid phase and the stress in an equivalent continuum in the absence of fluid pressure. For porosity $n$, the relation reads: $\\sigma_{ij}^{equ.}=(1-n)\\sigma_{ij}^{solid}$.\n\nThis last relation may not be very useful if porosity is not homogeneous. If it happens, one can define the equivalent bulk stress a the particles scale by assigning a volume to each particle. This volume can be obtained from :yref:`TesselationWrapper` (see e.g. [Catalano2014a]_)"); py::def("getStress",Shop::getStress,(py::args("volume")=0),"Compute and return Love-Weber stress tensor:\n\n $\\sigma_{ij}=\\frac{1}{V}\\sum_b f_i^b l_j^b$, where the sum is over all interactions, with $f$ the contact force and $l$ the branch vector (joining centers of the bodies). Stress is negativ for repulsive contact forces, i.e. compression. $V$ can be passed to the function. If it is not, it will be equal to the volume of the cell in periodic cases, or to the one deduced from utils.aabbDim() in non-periodic cases."); py::def("getStressProfile",Shop::getStressProfile,(py::args("volume"),py::args("nCell"),py::args("dz"),py::args("zRef"),py::args("vPartAverageX"),py::args("vPartAverageY"),py::args("vPartAverageZ")),"Compute and return the stress tensor depth profile, including the contribution from Love-Weber stress tensor and the dynamic stress tensor taking into account the effect of particles inertia. For each defined cell z, the stress tensor reads: \n\n $\\sigma_{ij}^z= \\frac{1}{V}\\sum_c f_i^c l_j^{c,z} - \\frac{1}{V}\\sum_p m^p u'^p_i u'^p_j$,\n\n where the first sum is made over the contacts which are contained or cross the cell z, f^c is the contact force from particle 1 to particle 2, and l^{c,z} is the part of the branch vector from particle 2 to particle 1, contained in the cell. The second sum is made over the particles, and u'^p is the velocity fluctuations of the particle p with respect to the spatial averaged particle velocity at this point (given as input parameters). The expression of the stress tensor is the same as the one given in getStress plus the inertial contribution. Apart from that, the main difference with getStress stands in the fact that it gives a depth profile of stress tensor, i.e. from the reference horizontal plane at elevation zRef (input parameter) until the plane of elevation zRef+nCell*dz (input parameters), it is computing the stress tensor for each cell of height dz. For the love-Weber stress contribution, the branch vector taken into account in the calculations is only the part of the branch vector contained in the cell considered.\n To validate the formulation, it has been checked that activating only the Love-Weber stress tensor, and suming all the contributions at the different altitude, we recover the same stress tensor as when using getStress. For my own use, I have troubles with strong overlap between fixed object, so that I made a condition to exclude the contribution to the stress tensor of the fixed objects, this can be desactivated easily if needed (and should be desactivated for the comparison with getStress)." ); py::def("getDepthProfiles",Shop::getDepthProfiles,(py::args("volume"),py::args("nCell"),py::args("dz"),py::args("zRef"),py::args("activateCond"),py::args("radiusPy")),"Compute and return the particle velocity and solid volume fraction (porosity) depth profile. For each defined cell z, the k component of the average particle velocity reads: \n\n $^z= \\sum_p V^p v_k^p/\\sum_p V^p$,\n\n where the sum is made over the particles contained in the cell, $v_k^p$ is the k component of the velocity associated to particle p, and $V^p$ is the part of the volume of the particle p contained inside the cell. This definition allows to smooth the averaging, and is equivalent to taking into account the center of the particles only when there is a lot of particles in each cell. As for the solid volume fraction, it is evaluated in the same way: for each defined cell z, it reads: \n\n $<\\phi>^z= \\frac{1}{V_{cell}}\\sum_p V^p$, where $V_{cell}$ is the volume of the cell considered, and $V^p$ is the volume of particle p contained in cell z.\n This function gives depth profiles of average velocity and solid volume fraction, returning the average quantities in each cell of height dz, from the reference horizontal plane at elevation zRef (input parameter) until the plane of elevation zRef+nCell*dz (input parameters). If the argument activateCond is set to true, do the average only on particles of radius equal to radiusPy (input parameter)" ); py::def("getCapillaryStress",Shop::getCapillaryStress,(py::args("volume")=0,py::args("mindlin")=false),"Compute and return Love-Weber capillary stress tensor:\n\n $\\sigma^{cap}_{ij}=\\frac{1}{V}\\sum_b l_i^b f^{cap,b}_j$, where the sum is over all interactions, with $l$ the branch vector (joining centers of the bodies) and $f^{cap}$ is the capillary force. $V$ can be passed to the function. If it is not, it will be equal to one in non-periodic cases, or equal to the volume of the cell in periodic cases. Only the CapillaryPhys interaction type is supported presently. Using this function with physics MindlinCapillaryPhys needs to pass True as second argument."); py::def("getBodyIdsContacts",Shop__getBodyIdsContacts,(py::args("bodyID")=0),"Get a list of body-ids, which contacts the given body."); py::def("maxOverlapRatio",maxOverlapRatio,"Return maximum overlap ration in interactions (with :yref:`ScGeom`) of two :yref:`spheres`. The ratio is computed as $\\frac{u_N}{2(r_1 r_2)/r_1+r_2}$, where $u_N$ is the current overlap distance and $r_1$, $r_2$ are radii of the two spheres in contact."); py::def("shiftBodies",shiftBodies,(py::arg("ids"),py::arg("shift")),"Shifts bodies listed in ids without updating their velocities."); py::def("calm",Shop__calm,(py::arg("mask")=-1),"Set translational and rotational velocities of bodies to zero. Applied to all bodies by default. To calm only some bodies, use mask parameter, it will calm only bodies with groupMask compatible to given value"); py::def("setNewVerticesOfFacet",setNewVerticesOfFacet,(py::arg("b"),py::arg("v1"),py::arg("v2"),py::arg("v3")),"Sets new vertices (in global coordinates) to given facet."); py::def("setContactFriction",Shop::setContactFriction,py::arg("angleRad"),"Modify the friction angle (in radians) inside the material classes and existing contacts. The friction for non-dynamic bodies is not modified."); py::def("growParticles",Shop::growParticles,(py::args("multiplier"), py::args("updateMass")=true, py::args("dynamicOnly")=true), "Change the size of spheres and sphere clumps by the multiplier. If updateMass=True, then the mass and inertia are updated. dynamicOnly=True will select dynamic bodies."); py::def("growParticle",Shop::growParticle,(py::args("bodyID"),py::args("multiplier"), py::args("updateMass")=true), "Change the size of a single sphere (to be implemented: single clump). If updateMass=True, then the mass is updated."); py::def("intrsOfEachBody",intrsOfEachBody,"returns list of lists of interactions of each body"); py::def("numIntrsOfEachBody",numIntrsOfEachBody,"returns list of number of interactions of each body"); py::def("TetrahedronSignedVolume",static_cast&)>(&TetrahedronSignedVolume),"TODO"); py::def("TetrahedronVolume",static_cast&)>(&TetrahedronVolume),"TODO"); py::def("TetrahedronInertiaTensor",TetrahedronInertiaTensor,"TODO"); py::def("TetrahedronCentralInertiaTensor",TetrahedronCentralInertiaTensor,"TODO"); py::def("TetrahedronWithLocalAxesPrincipal",TetrahedronWithLocalAxesPrincipal,"TODO"); py::def("momentum",Shop::momentum,"TODO"); py::def("angularMomentum",Shop::angularMomentum,(py::args("origin")=Vector3r(Vector3r::Zero())),"TODO"); py::def("getSpheresVolume2D",Shop__getSpheresVolume2D,(py::arg("mask")=-1),"Compute the total volume of discs in the simulation, mask parameter is considered"); py::def("voidratio2D",Shop__getVoidRatio2D,(py::arg("zlen")=1),"Compute 2D packing void ratio $\\frac{V-V_s}{V_s}$ where $V$ is overall volume and $V_s$ is volume of disks.\n\n:param float zlen: length in the third direction.\n"); py::def("getStressAndTangent",Shop__getStressAndTangent,(py::args("volume")=0,py::args("symmetry")=true),"Compute overall stress of periodic cell using the same equation as function getStress. In addition, the tangent operator is calculated using the equation published in [Kruyt and Rothenburg1998]_:\n\n.. math:: S_{ijkl}=\\frac{1}{V}\\sum_{c}(k_n n_i l_j n_k l_l + k_t t_i l_j t_k l_l)\n\n:param float volume: same as in function getStress\n:param bool symmetry: make the tensors symmetric.\n\n:return: macroscopic stress tensor and tangent operator as py::tuple"); py::def("setBodyPosition",setBodyPosition,(py::args("id"),py::args("pos"),py::args("axis")="xyz"),"Set a body position from its id and a new vector3r.\n\n:param int id: the body id.\n:param Vector3 pos: the desired updated position.\n:param str axis: the axis along which the position has to be updated (ex: if axis==\"xy\" and pos==Vector3r(r0,r1,r2), r2 will be ignored and the position along z will not be updated)."); py::def("setBodyVelocity",setBodyVelocity,(py::args("id"),py::args("vel"),py::args("axis")="xyz"),"Set a body velocity from its id and a new vector3r.\n\n:param int id: the body id.\n:param Vector3 vel: the desired updated velocity.\n:param str axis: the axis along which the velocity has to be updated (ex: if axis==\"xy\" and vel==Vector3r(r0,r1,r2), r2 will be ignored and the velocity along z will not be updated)."); py::def("setBodyOrientation",setBodyOrientation,(py::args("id"),py::args("ori")),"Set a body orientation from its id and a new Quaternionr.\n\n:param int id: the body id.\n:param Quaternion ori: the desired updated orientation."); py::def("setBodyAngularVelocity",setBodyAngularVelocity,(py::args("id"),py::args("angVel")),"Set a body angular velocity from its id and a new Vector3r.\n\n:param int id: the body id.\n:param Vector3 angVel: the desired updated angular velocity."); py::def("setBodyColor",setBodyColor,(py::args("id"),py::args("color")),"Set a body color from its id and a new Vector3r.\n\n:param int id: the body id.\n:param Vector3 color: the desired updated color."); } trunk-2017.01a/py/_utils.hpp000066400000000000000000000204341304022710500156250ustar00rootroot00000000000000#include #include #include #include #include #include #include #include #include #include #include #include namespace py = boost::python; bool isInBB(Vector3r p, Vector3r bbMin, Vector3r bbMax); py::tuple negPosExtremeIds(int axis, Real distFactor=1.1); py::tuple coordsAndDisplacements(int axis,py::tuple Aabb=py::tuple()); void setRefSe3(); Real PWaveTimeStep(); Real RayleighWaveTimeStep(); py::tuple interactionAnglesHistogram(int axis, int mask=0, size_t bins=20, py::tuple aabb=py::tuple(), bool sphSph=0, Real minProjLen=1e-6); py::tuple bodyNumInteractionsHistogram(py::tuple aabb=py::tuple()); Vector3r inscribedCircleCenter(const Vector3r& v0, const Vector3r& v1, const Vector3r& v2); py::dict getViscoelasticFromSpheresInteraction(Real tc, Real en, Real es); /* reset highlight of all bodies */ void highlightNone(); /*!Sum moments acting on given bodies * * @param ids is the calculated bodies ids * @param axis is the direction of axis with respect to which the moment is calculated. * @param axisPt is a point on the axis. * * The computation is trivial: moment from force is is by definition r×F, where r * is position relative to axisPt; moment from moment is m; such moment per body is * projected onto axis. */ Real sumTorques(py::list ids, const Vector3r& axis, const Vector3r& axisPt); /* Sum forces acting on bodies within mask. * * @param ids list of ids * @param direction direction in which forces are summed * */ Real sumForces(py::list ids, const Vector3r& direction); /* Sum force acting on facets given by their ids in the sense of their respective normals. If axis is given, it will sum forces perpendicular to given axis only (not the the facet normals). */ Real sumFacetNormalForces(vector ids, int axis=-1); /* Set wire display of all/some/none bodies depending on the filter. */ void wireSome(string filter); void wireAll(); void wireNone(); void wireNoSpheres(); /* Tell us whether a point lies in polygon given by array of points. * @param xy is the point that is being tested * @param vertices is Numeric.array (or list or tuple) of vertices of the polygon. * Every row of the array is x and y coordinate, numer of rows is >= 3 (triangle). * * Copying the algorithm from http://www.ecse.rpi.edu/Homepages/wrf/Research/Short_Notes/pnpoly.html * is gratefully acknowledged: * * License to Use: * Copyright (c) 1970-2003, Wm. Randolph Franklin * Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions: * 1. Redistributions of source code must retain the above copyright notice, this list of conditions and the following disclaimers. * 2. Redistributions in binary form must reproduce the above copyright notice in the documentation and/or other materials provided with the distribution. * 3. The name of W. Randolph Franklin may not be used to endorse or promote products derived from this Software without specific prior written permission. * THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE. * * http://numpy.scipy.org/numpydoc/numpy-13.html told me how to use Numeric.array from c */ bool pointInsidePolygon(py::tuple xy, py::object vertices); /* Compute area of convex hull when when taking (swept) spheres crossing the plane at coord, perpendicular to axis. All spheres that touch the plane are projected as hexagons on their circumference to the plane. Convex hull from this cloud is computed. The area of the hull is returned. */ Real approxSectionArea(Real coord, int axis); /* Find all interactions deriving from NormShearPhys that cross plane given by a point and normal (the normal may not be normalized in this case, though) and sum forces (both normal and shear) on them. Returns a 3-tuple with the components along global x,y,z axes, which can be viewed as "action from lower part, towards upper part" (lower and upper parts with respect to the plane's normal). (This could be easily extended to return sum of only normal forces or only of shear forces.) */ Vector3r forcesOnPlane(const Vector3r& planePt, const Vector3r& normal); /* Less general than forcesOnPlane, computes force on plane perpendicular to axis, passing through coordinate coord. */ Vector3r forcesOnCoordPlane(Real coord, int axis); py::tuple spiralProject(const Vector3r& pt, Real dH_dTheta, int axis=2, Real periodStart=std::numeric_limits::quiet_NaN(), Real theta0=0); shared_ptr Shop__createExplicitInteraction(Body::id_t id1, Body::id_t id2); Real Shop__unbalancedForce(bool useMaxForce /*false by default*/); py::tuple Shop__totalForceInVolume(); Real Shop__getSpheresVolume(int mask=-1); Real Shop__getSpheresMass(int mask=-1); py::object Shop__kineticEnergy(bool findMaxId=false); Real maxOverlapRatio(); Real Shop__getPorosity(Real volume=-1); Real Shop__getVoxelPorosity(int resolution=200, Vector3r start=Vector3r(0,0,0),Vector3r end=Vector3r(0,0,0)); //Matrix3r Shop__stressTensorOfPeriodicCell(bool smallStrains=false){return Shop::stressTensorOfPeriodicCell(smallStrains);} py::tuple Shop__fabricTensor(Real cutoff=0.0,bool splitTensor=false, Real thresholdForce=NaN); py::tuple Shop__normalShearStressTensors(bool compressionPositive=false, bool splitNormalTensor=false, Real thresholdForce=NaN); py::list Shop__getStressLWForEachBody(); py::list Shop__getBodyIdsContacts(Body::id_t bodyID=-1); Real shiftBodies(py::list ids, const Vector3r& shift); void Shop__calm(int mask=-1); void setNewVerticesOfFacet(const shared_ptr& b, const Vector3r& v1, const Vector3r& v2, const Vector3r& v3); py::list intrsOfEachBody(); py::list numIntrsOfEachBody(); /* The 5 following setters are used to workaround a long-standing bug in the c++/python binding which produces a memory leak (see two links below). * https://bugs.launchpad.net/yade/+bug/1041084 * https://answers.launchpad.net/yade/+question/253112 * It is not in the spirit of Yade Python binding but you can use them if you massively update bodies attributes. * TODO : remove them as soon as the bug is solved. */ /* Set a body position from its id and a new vector3r. * @param id is the body id * @param newPos is the desired updated position * @param axis is the axis along which the position has to be updated (ex: if axis=="xy" and newPos==Vector3r(r0,r1,r2), r2 will be ignored and the position along z will not be updated). */ void setBodyPosition(int id, Vector3r newPos, string axis="xyz"); /* Set a body velocity from its id and a new vector3r. * @param id is the body id * @param newPos is the desired updated velocity * @param axis is the axis along which the velocity has to be updated (ex: if axis=="xy" and newVel==Vector3r(r0,r1,r2), r2 will be ignored and the velocity along z will not be updated). */ void setBodyVelocity(int id, Vector3r newVel, string axis="xyz"); /* Set a body orientation from its id and a new Quaternionr. * @param id is the body id * @param newOri is the desired updated orientation */ void setBodyOrientation(int id, Quaternionr newOri); /* Set a body angular velocity from its id and a new Vector3r. * @param id is the body id * @param newAngVel is the desired updated angular velocity */ void setBodyAngularVelocity(int id, Vector3r newAngVel); /* Set a body color from its id and a new Vector3r. * @param id is the body id * @param newColor is the desired rgb color */ void setBodyColor(int id, Vector3r newColor);trunk-2017.01a/py/bodiesHandling.py000066400000000000000000000201751304022710500171030ustar00rootroot00000000000000# encoding: utf-8 """ Miscellaneous functions, which are useful for handling bodies. """ from yade.wrapper import * import utils,math,numpy from minieigen import * #spheresPackDimensions================================================== def spheresPackDimensions(idSpheres=[],mask=-1): """The function accepts the list of spheres id's or list of bodies and calculates max and min dimensions, geometrical center. :param list idSpheres: list of spheres :param int mask: :yref:`Body.mask` for the checked bodies :return: dictionary with keys ``min`` (minimal dimension, Vector3), ``max`` (maximal dimension, Vector3), ``minId`` (minimal dimension sphere Id, Vector3), ``maxId`` (maximal dimension sphere Id, Vector3), ``center`` (central point of bounding box, Vector3), ``extends`` (sizes of bounding box, Vector3), ``volume`` (volume of spheres, Real), ``mass`` (mass of spheres, Real), ``number`` (number of spheres, int), """ idSpheresIter=[] if (len(idSpheres)<1): #check mask ifSpherMask=[] if (mask>-1): #The case, when only the mask was given, without list of ids for i in O.bodies: if ((i.mask&mask)<>0): ifSpherMask.append(i.id) if (len(ifSpherMask)<2): raise RuntimeWarning("Not enough bodies to analyze with given mask") else: idSpheresIter=ifSpherMask else: raise RuntimeWarning("Only a list of particles with length > 1 can be analyzed") else: idSpheresIter=idSpheres minVal = Vector3.Zero maxVal = Vector3.Zero minId = Vector3.Zero maxId = Vector3.Zero counter = 0 volume = 0.0 mass = 0.0 for i in idSpheresIter: if (type(i).__name__=='int'): b = O.bodies[i] #We have received a list of ID's elif (type(i).__name__=='Body'): b = i #We have recevied a list of bodies else: raise TypeError("Unknow type of data, should be list of int's or bodies's") if (b): spherePosition=b.state.pos #skip non-existent spheres try: sphereRadius=b.shape.radius #skip non-spheres except AttributeError: continue if (mask>-1) and ((mask&b.mask)==0): continue #skip bodies with wrong mask sphereRadiusVec3 = Vector3(sphereRadius,sphereRadius,sphereRadius) sphereMax = spherePosition + sphereRadiusVec3 sphereMin = spherePosition - sphereRadiusVec3 for dim in range(0,3): if ((sphereMax[dim]>maxVal[dim]) or (counter==0)): maxVal[dim]=sphereMax[dim] maxId[dim] = b.id if ((sphereMin[dim]-1): #The case, when only the mask was given, without list of ids for i in O.bodies: if ((i.mask&mask)<>0): ifFacetMask.append(i.id) if (len(ifFacetMask)<2): raise RuntimeWarning("Not enough bodies to analyze with given mask") else: idFacetsIter=ifFacetMask else: raise RuntimeWarning("Only a list of particles with length > 1 can be analyzed") else: idFacetsIter=idFacets minVal = Vector3.Zero maxVal = Vector3.Zero minId = Vector3.Zero maxId = Vector3.Zero counter = 0 for i in idFacetsIter: if (type(i).__name__=='int'): b = O.bodies[i] #We have received a list of ID's elif (type(i).__name__=='Body'): b = i #We have recevied a list of bodies else: raise TypeError("Unknow type of data, should be list of int's or bodies's") if (b): p = b.state.pos o = b.state.ori s = b.shape pt1 = p + o*s.vertices[0] pt2 = p + o*s.vertices[1] pt3 = p + o*s.vertices[2] if (mask>-1) and ((mask&b.mask)==0): continue #skip bodies with wrong mask facetMax = Vector3(max(pt1[0], pt2[0], pt3[0]), max(pt1[1], pt2[1], pt3[1]), max(pt1[2], pt2[2], pt3[2])) facetMin = Vector3(min(pt1[0], pt2[0], pt3[0]), min(pt1[1], pt2[1], pt3[1]), min(pt1[2], pt2[2], pt3[2])) for dim in range(0,3): if ((facetMax[dim]>maxVal[dim]) or (counter==0)): maxVal[dim]=facetMax[dim] maxId[dim] = b.id if ((facetMin[dim]-1): #The case, when only the mask was given, without list of ids for i in O.bodies: if ((i.mask&mask)<>0): ifSpherMask.append(i.id) if (len(ifSpherMask)==0): raise RuntimeWarning("No bodies to modify with given mask") else: idSpheresIter=ifSpherMask else: raise RuntimeWarning("No bodies to modify") else: idSpheresIter=idSpheres dims = spheresPackDimensions(idSpheresIter) ret=[] for i in idSpheresIter: if (type(i).__name__=='int'): b = O.bodies[i] #We have received a list of ID's elif (type(i).__name__=='Body'): b = i #We have recevied a list of bodies else: raise TypeError("Unknown type of data, should be list of int's or bodies") try: sphereRadius=b.shape.radius #skip non-spheres except AttributeError: continue if (mask>-1) and ((mask&b.mask)==0): continue #skip bodies with wrong mask if (copy): b=sphereDuplicate(b) b.state.pos=orientation*(b.state.pos-dims['center'])+dims['center'] b.shape.radius*=scale b.state.mass*=pow(scale, 3) b.state.inertia*=pow(scale, 5) b.state.pos=(b.state.pos-dims['center'])*scale + dims['center'] b.state.pos+=shift if (copy): ret.append(b) if (copy): return ret else: return True #spheresDublicate======================================================= def sphereDuplicate(idSphere): """The functions makes a copy of sphere""" i=idSphere if (type(i).__name__=='int'): b = O.bodies[i] #We have received a list of ID's elif (type(i).__name__=='Body'): b = i #We have recevied a list of bodies else: raise TypeError("Unknown type of data, should be list of int's or bodies") try: sphereRadius=b.shape.radius #skip non-spheres except AttributeError: return False addedBody = utils.sphere(center=b.state.pos,radius=b.shape.radius,fixed=not(b.dynamic),wire=b.shape.wire,color=b.shape.color,highlight=b.shape.highlight,material=b.material,mask=b.mask) return addedBody trunk-2017.01a/py/config.py.in000066400000000000000000000043631304022710500160440ustar00rootroot00000000000000# encoding: utf-8 """ Compile-time configuration for yade. Template file is processed by cmake to create the actual configuration at build-time. """ import os,datetime,os.path prefix='${runtimePREFIX}' if not os.environ.has_key('YADE_PREFIX') else os.environ['YADE_PREFIX'] suffix='${SUFFIX}' libPATH='${LIBRARY_OUTPUT_PATH}' if (libPATH[1:] == '{LIBRARY_OUTPUT_PATH}'): libPATH='lib' libDir=os.path.abspath(prefix+'/'+libPATH+'/yade${SUFFIX}') confDir=os.environ['HOME']+'/.yade${SUFFIX}' libstdcxx='${libstdcxx}' features='${CONFIGURED_FEATS}'.split(' ') if (features[0]==''): features=features[1:] revision='${realVersion}' version='${version}' sourceRoot='${sourceRoot}' # project metadata metadata=dict( short_desc='open-source platform for dynamic computations', long_desc='Extensible open-source framework for discrete numerical models, focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, allowing independent implementation of new alogrithms and interfaces. Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging.\n\n\n\nSee http://www.yade-dem.org/ for documentation and http://www.launchpad.net/yade for the project itself.\n\nThis is version %s with features %s.'%(version,','.join(features)), author='Yade Developers Team', website='http://www.yade-dem.org', author_contact='http://www.launchpad.net/~yade-dev', mailinglist='yade-users@lists.launchpad.net', bugtracker='http://bugs.launchpad.net/yade', copyright='© 2003--%s'%(datetime.date.today().year), license='''This program is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version. This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU General Public License for more details. You should have received a copy of the GNU General Public License along with this program; if not, write to the Free Software Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307 USA. ''', ) trunk-2017.01a/py/deformableelementsutils.py000066400000000000000000000301741304022710500211070ustar00rootroot00000000000000# encoding: utf-8 # # utility functions for deformable cohesive elements # # burak er buraker88@yandex.com import math,random,doctest,geom,numpy from yade import * from yade.wrapper import * from yade.utils import * try: # use psyco if available import psyco psyco.full() except ImportError: pass from minieigen import * # c++ implementations for performance reasons from yade._utils import * from yade.utils import _commonBodySetup #Deformable Element Node def node(center,radius,dynamic=None,fixed=True,wire=False,color=None,highlight=False,material=-1,mask=1): """Create sphere with given parameters; mass and inertia computed automatically. Last assigned material is used by default (*material* = -1), and utils.defaultMaterial() will be used if no material is defined at all. :param Vector3 center: center :param float radius: radius :param float dynamic: deprecated, see "fixed" :param float fixed: generate the body with all DOFs blocked? :param material: specify :yref:`Body.material`; different types are accepted: * int: O.materials[material] will be used; as a special case, if material==-1 and there is no shared materials defined, utils.defaultMaterial() will be assigned to O.materials[0] * string: label of an existing material that will be used * :yref:`Material` instance: this instance will be used * callable: will be called without arguments; returned Material value will be used (Material factory object, if you like) :param int mask: :yref:`Body.mask` for the body :param wire: display as wire sphere? :param highlight: highlight this body in the viewer? :param Vector3-or-None: body's color, as normalized RGB; random color will be assigned if ``None``. :return: A Body instance with desired characteristics. Creating default shared material if none exists neither is given:: >>> O.reset() >>> from yade import utils >>> len(O.materials) 0 >>> s0=utils.sphere([2,0,0],1) >>> len(O.materials) 1 Instance of material can be given:: >>> s1=utils.sphere([0,0,0],1,wire=False,color=(0,1,0),material=ElastMat(young=30e9,density=2e3)) >>> s1.shape.wire False >>> s1.shape.color Vector3(0,1,0) >>> s1.mat.density 2000.0 Material can be given by label:: >>> O.materials.append(FrictMat(young=10e9,poisson=.11,label='myMaterial')) 1 >>> s2=utils.sphere([0,0,2],1,material='myMaterial') >>> s2.mat.label 'myMaterial' >>> s2.mat.poisson 0.11 Finally, material can be a callable object (taking no arguments), which returns a Material instance. Use this if you don't call this function directly (for instance, through yade.pack.randomDensePack), passing only 1 *material* parameter, but you don't want material to be shared. For instance, randomized material properties can be created like this: >>> import random >>> def matFactory(): return ElastMat(young=1e10*random.random(),density=1e3+1e3*random.random()) ... >>> s3=utils.sphere([0,2,0],1,material=matFactory) >>> s4=utils.sphere([1,2,0],1,material=matFactory) """ b=Body() b.shape=Node(radius=radius,color=color if color else randomColor(),wire=wire,highlight=highlight) V=(4./3)*math.pi*radius**3 geomInert=(2./5.)*V*radius**2 _commonBodySetup(b,V,Vector3(geomInert,geomInert,geomInert),material,pos=center,dynamic=dynamic,fixed=fixed,blockedDOFs='XYZ') b.aspherical=False b.mask=mask b.bounded=True return b def randomColor(): """Return random Vector3 with each component in interval 0…1 (uniform distribution)""" return Vector3(random.random(),random.random(),random.random()) # Meshing def clear_mesh(gmshmeshhandle_): sceneelements=gmshmeshhandle_[1]; #first remove elements and nodes from the scene for elem in sceneelements: bdy=elem[0]; nodes=elem[1]; O.bodies.erase(bdy.id); for node in nodes: O.bodies.erase(node.id); def tetrahedronvolume(nodes): V =0.166666666*numpy.linalg.det([[nodes[0][0], nodes[1][0] ,nodes[2][0] ,nodes[3][0]],[nodes[0][1], nodes[1][1], nodes[2][1] ,nodes[3][1]], [nodes[0][2] ,nodes[1][2], nodes[2][2], nodes[3][2]], [ 1,1,1,1]]); return V def tetrahedral_mesh_generator(filename,tetrahedralelementshape,elementmat,interfaceelementshape,interfacemat): [nodeList,elementList,interactionList]=mshreader(filename) nodes=nodeList meshelements=elementList interfacepairs=interactionList scenebodies=[] for elem in elementList: #Create the corresponding mesh element nodesofelement=[nodes[elem[0]],nodes[elem[1]],nodes[elem[2]],nodes[elem[3]]] noderadius=0.1*(0.75*tetrahedronvolume(nodesofelement))**0.33333333; [elbody, nodebodies]=tetrahedral_element(elementmat,nodesofelement,tetrahedralelementshape,radius=noderadius) scenebodies.append([elbody,nodebodies]) #Create the interfacing element pairs for interpair in interfacepairs: #get element pair elementpair=interpair[0]; #get node pairs pairofnodes=interpair[1] interfaceelementpairs=[] for pair in pairofnodes: firstid=pair[0]; secondid=pair[1]; el1nodebodies=scenebodies[elementpair[0]][1]; el2nodebodies=scenebodies[elementpair[1]][1]; node1=el1nodebodies[firstid] node2=el2nodebodies[secondid] interfaceelementpairs.append([node1, node2]) [elbody, nodebodies]=interaction_element(interfacemat,interfaceelementpairs,interfaceelementshape); scenebodies.append([elbody,nodebodies]) return scenebodies #Read mesh file and get elements nodes and interactions def mshreader(meshfile="file.mesh",shift=Vector3.Zero,scale=1.0,orientation=Quaternion.Identity,**kw): """ Imports volume mesh from gmsh2 file :Parameters: `shift`: [float,float,float] [X,Y,Z] parameter moves the specimen. `scale`: float factor scales the given data. `orientation`: quaternion orientation of the imported mesh `**kw`: (unused keyword arguments) is passed to :yref:`yade.utils.facet` :Returns: list of nodes and elements for the specimen. """ infile = open(meshfile,"r") lines = infile.readlines() infile.close() nodelistVector3=[] elementList=[] interactionList=[] findVerticesString=0 while (lines[findVerticesString].split()[0]<>'$Nodes'): #Find the string with the number of Vertices findVerticesString+=1 findVerticesString+=1 numNodes = int(lines[findVerticesString].split()[0]) for line in lines[findVerticesString+1:numNodes+findVerticesString+1]: data = line.split() nodelistVector3.append(orientation*Vector3(float(data[1])*scale,float(data[2])*scale,float(data[3])*scale)+shift) findElementString=findVerticesString+numNodes while (lines[findElementString].split()[0]<>'$Elements'): #Find the string with the number of Elements findElementString+=1 findElementString+=1 numElements = int(lines[findElementString].split()[0]) for line in lines[findElementString+1:findElementString+numElements+1]: data = line.split() numberofnodes=data[1] if(int(numberofnodes)==4):#tetrahedral element id1 = int(data[5])-1 id2 = int(data[6])-1 id3 = int(data[7])-1 id4 = int(data[8])-1 elementList.append([id1,id2,id3,id4]) #Create the interaction list i=0 numVolElements=elementList.__len__() for elem in elementList: j=i+1 while j0): interactionList.append([Vector2i(i,j),pair]) j=j+1 i=i+1 return [nodelistVector3,elementList,interactionList] def check_coinciding_nodes(element1,element2): pairstemp=[] #for each node of the element1 i=0 j=0 for node1 in element1: for node2 in element2: if(node1==node2): pairstemp.append([i,j]) j=j+1 i=i+1 j=0 if(3<=pairstemp.__len__()): pairs=pairstemp else: pairs=[] return pairs def interaction_element(material,nodepairs,elementshape,radius=0.0015,dynamic=None,fixed=True,wire=False,color=Vector3(1,0,0),highlight=False,mask=1): # triangles for drawing(node indices) #faces=[Vector3(0,1,3),Vector3(1,2,3),Vector3(2,0,3),Vector3(0,1,2)] faces=[]; shape=elementshape() shape.color=color if color else randomColor(); [body_,nodes_]=finite_element(material,shape,nodepairs,faces,radius,interface=True) return [body_,nodes_] def tetrahedral_element(material,nodes,elementshape,radius=0.0015,dynamic=None,fixed=True,wire=False,color=Vector3(1,0,0),highlight=False,mask=1): # triangles for drawing(node indices) #faces are in the format [face_vertex0,face_vertex1,face_vertex2,opposite_vertex] faces=[Vector3(1,2,0),Vector3(2,1,3),Vector3(2,0,3),Vector3(3,1,0)] shape=elementshape() shape.color=color if color else randomColor(); [body_,nodes_]=finite_element(material,shape,nodes,faces,radius) return [body_,nodes_] def finite_element(material,shape,nodes,faces,radius,dynamic=None,fixed=True,wire=False,Color=None,highlight=False,mask=1,interface=False): """Create sphere with given parameters; mass and inertia computed automatically. Last assigned material is used by default (*material* = -1), and utils.defaultMaterial() will be used if no material is defined at all. :param Vector3 center: center :param float radius: radius :param float dynamic: deprecated, see "fixed" :param float fixed: generate the body with all DOFs blocked? :param material: specify :yref:`Body.material`; different types are accepted: * int: O.materials[material] will be used; as a special case, if material==-1 and there is no shared materials defined, utils.defaultMaterial() will be assigned to O.materials[0] * string: label of an existing material that will be used * :yref:`Material` instance: this instance will be used * callable: will be called without arguments; returned Material value will be used (Material factory object, if you like) :param int mask: :yref:`Body.mask` for the body :param wire: display as wire sphere? :param highlight: highlight this body in the viewer? :param Vector3-or-None: body's color, as normalized RGB; random color will be assigned if ``None``. :return: A Body instance with desired characteristics. Creating default shared material if none exists neither is given:: >>> O.reset() >>> from yade import utils >>> len(O.materials) 0 >>> s0=utils.sphere([2,0,0],1) >>> len(O.materials) 1 Instance of material can be given:: >>> s1=utils.sphere([0,0,0],1,wire=False,color=(0,1,0),material=ElastMat(young=30e9,density=2e3)) >>> s1.shape.wire False >>> s1.shape.color Vector3(0,1,0) >>> s1.mat.density 2000.0 Material can be given by label:: >>> O.materials.append(FrictMat(young=10e9,poisson=.11,label='myMaterial')) 1 >>> s2=utils.sphere([0,0,2],1,material='myMaterial') >>> s2.mat.label 'myMaterial' >>> s2.mat.poisson 0.11 Finally, material can be a callable object (taking no arguments), which returns a Material instance. Use this if you don't call this function directly (for instance, through yade.pack.randomDensePack), passing only 1 *material* parameter, but you don't want material to be shared. For instance, randomized material properties can be created like this: >>> import random >>> def matFactory(): return ElastMat(young=1e10*random.random(),density=1e3+1e3*random.random()) ... >>> s3=utils.sphere([0,2,0],1,material=matFactory) >>> s4=utils.sphere([1,2,0],1,material=matFactory) """ b=Body(); b.shape=shape; O.bodies.append(b) nodes_ret=[]; #b.shape.color=Color; #add nodes to the scene and keep them in the nodes list if(interface==False): #Deformable Element for vec in nodes: # Second Example nod=node(vec,radius) O.bodies.append(nod) b.shape.addNode(nod) nodes_ret.append(nod) #add faces for drawing purposes for face in faces: b.shape.addFace(face) else: #Deformable Cohesive Element for nodepair in nodes: # Second Example b.shape.addPair(nodepair[0],nodepair[1]) #add faces for drawing purposes for face in faces: b.shape.addFace(face) V=1;#For symbolical geomInert=Vector3(1,1,1)#For symbolical #Only add body to draw it not for integration, therefore block all dof _commonBodySetup(b,V,geomInert,material,pos=Vector3(0,0,0),dynamic=False,fixed=True,blockedDOFs='xyzXYZ') b.aspherical=False b.mask=mask b.bounded=False return [b,nodes_ret] ##**********************End of Deformable Elements********************************* trunk-2017.01a/py/export.py000066400000000000000000001262301304022710500155110ustar00rootroot00000000000000# encoding: utf-8 """ Export (not only) geometry to various formats. """ from yade.wrapper import * from yade import utils,Matrix3,Vector3 #textExt=============================================================== def textExt(filename, format='x_y_z_r', comment='',mask=-1,attrs=[]): """Save sphere coordinates and other parameters into a text file in specific format. Non-spherical bodies are silently skipped. Users can add here their own specific format, giving meaningful names. The first file row will contain the format name. Be sure to add the same format specification in ymport.textExt. :param string filename: the name of the file, where sphere coordinates will be exported. :param string format: the name of output format. Supported 'x_y_z_r'(default), 'x_y_z_r_matId', 'x_y_z_r_attrs' (use proper comment) :param string comment: the text, which will be added as a comment at the top of file. If you want to create several lines of text, please use '\\\\n#' for next lines. With 'x_y_z_r_attrs' format, the last (or only) line should consist of column headers of quantities passed as attrs (1 comment word for scalars, 3 comment words for vectors and 9 comment words for matrices) :param int mask: export only spheres with the corresponding mask export only spheres with the corresponding mask :param [str] attrs: attributes to be exported with 'x_y_z_r_attrs' format. Each str in the list is evaluated for every body exported with body=b (i.e. 'b.state.pos.norm()' would stand for distance of body from coordinate system origin) :return: number of spheres which were written. :rtype: int """ O=Omega() try: out=open(filename,'w') except: raise RuntimeError("Problem to write into the file") count=0 # TODO use output=[] instrad of ''??? output = '' outputVel='' if (format<>'liggghts_in'): output = '#format ' + format + '\n' if (comment): if format=='x_y_z_r_attrs': cmts = comment.split('\n') for cmt in cmts[:-1]: output += cmt output += '# x y z r ' + cmts[-1] + '\n' else: output += '# ' + comment + '\n' minCoord= Vector3.Zero maxCoord= Vector3.Zero maskNumber = [] for b in O.bodies: try: if (isinstance(b.shape,Sphere) and ((mask<0) or ((mask&b.mask)>0))): if (format=='x_y_z_r'): output+=('%g\t%g\t%g\t%g\n'%(b.state.pos[0],b.state.pos[1],b.state.pos[2],b.shape.radius)) elif (format=='x_y_z_r_matId'): output+=('%g\t%g\t%g\t%g\t%d\n'%(b.state.pos[0],b.state.pos[1],b.state.pos[2],b.shape.radius,b.material.id)) elif (format=='x_y_z_r_attrs'): output+=('%g\t%g\t%g\t%g'%(b.state.pos[0],b.state.pos[1],b.state.pos[2],b.shape.radius)) for cmd in attrs: v = eval(cmd) if isinstance(v,(int,float)): output+='\t%g'%v elif isinstance(v,Vector3): output+='\t%g\t%g\t%g'%tuple(v[i] for i in xrange(3)) elif isinstance(v,Matrix3): output+='\t%g'%tuple(v[i] for i in xrange(9)) output += '\n' elif (format=='id_x_y_z_r_matId'): output+=('%d\t%g\t%g\t%g\t%g\t%d\n'%(b.id,b.state.pos[0],b.state.pos[1],b.state.pos[2],b.shape.radius,b.material.id)) elif (format=='jointedPM'): output+=('%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\t%g\n'%(b.id,b.state.onJoint,b.state.joint,b.state.jointNormal1[0],b.state.jointNormal1[1],b.state.jointNormal1[2],b.state.jointNormal2[0],b.state.jointNormal2[1],b.state.jointNormal2[2],b.state.jointNormal3[0],b.state.jointNormal3[1],b.state.jointNormal3[2])) elif (format=='liggghts_in'): output+=('%g %g %g %g %g %g %g\n'%(count+1,b.mask,b.shape.radius,b.material.density,b.state.pos[0],b.state.pos[1],b.state.pos[2])) outputVel+=('%g %g %g %g %g %g %g\n'%(count+1,b.state.vel[0],b.state.vel[1],b.state.vel[2],b.state.angVel[0],b.state.angVel[1],b.state.angVel[2])) else: raise RuntimeError("Please, specify a correct format output!"); count+=1 if (count==1): minCoord = b.state.pos - Vector3(b.shape.radius,b.shape.radius,b.shape.radius) maxCoord = b.state.pos + Vector3(b.shape.radius,b.shape.radius,b.shape.radius) else: minCoord = Vector3(min(minCoord[0], b.state.pos[0]-b.shape.radius),min(minCoord[1], b.state.pos[1]-b.shape.radius),min(minCoord[2], b.state.pos[2]-b.shape.radius)) maxCoord = Vector3(max(maxCoord[0], b.state.pos[0]+b.shape.radius),max(maxCoord[1], b.state.pos[1]+b.shape.radius),max(minCoord[2], b.state.pos[2]+b.shape.radius)) if b.mask not in maskNumber: maskNumber.append(b.mask) except AttributeError: pass if (format=='liggghts_in'): outputHeader = 'LIGGGHTS Description\n\n' outputHeader += '%d atoms\n%d atom types\n\n'%(count,len(maskNumber)) outputHeader += '%g %g xlo xhi\n%g %g ylo yhi\n%g %g zlo zhi\n\n'%(minCoord[0],maxCoord[0],minCoord[1],maxCoord[1],minCoord[2],maxCoord[2]) output=outputHeader + 'Atoms\n\n' + output + '\nVelocities\n\n' + outputVel out.write(output) out.close() return count bodies = [b for b in O.bodies if isinstance(b.shape,Sphere) and (True if mask==-1 else b.msak==mask)] data = [] for b in bodies: pos = b.state.pos d = [pos[i] for i in (0,1,2)] for name,command in what: val = eval(command) if isinstance(val,Matrix3): d.extend((val[0,0],val[0,1],val[0,2],val[1,0],val[1,1],val[1,2],val[2,0],val[2,1],val[2,2])) elif isinstance(val,Vector3): d.extend((v[0],v[1],v[2])) elif isinstance(val,(int,float)): d.append(val) else: print "WARNING: export.text: wrong 'what' parameter, output might be corrupted" return 0 data.append(d) dataw = [' '.join('%e'%v for v in d) for d in data] outFile = open(filename,'w') outFile.writelines(dataw) outFile.close() return len(bodies) #textClumps=============================================================== def textClumps(filename, format='x_y_z_r_clumpId', comment='',mask=-1): """Save clumps-members into a text file. Non-clumps members are bodies are silently skipped. :param string filename: the name of the file, where sphere coordinates will be exported. :param string comment: the text, which will be added as a comment at the top of file. If you want to create several lines of text, please use '\\\\n#' for next lines. :param int mask: export only spheres with the corresponding mask export only spheres with the corresponding mask :return: number of clumps, number of spheres which were written. :rtype: int """ O=Omega() try: out=open(filename,'w') except: raise RuntimeError("Problem to write into the file") count=0 countClumps=0 output = '' output = '#format x_y_z_r_clumpId\n' if (comment): output += '# ' + comment + '\n' minCoord= Vector3.Zero maxCoord= Vector3.Zero maskNumber = [] for bC in O.bodies: if bC.isClump: keys = bC.shape.members.keys() countClumps+=1 for ii in keys: try: b = O.bodies[ii] if (isinstance(b.shape,Sphere) and ((mask<0) or ((mask&b.mask)>0))): output+=('%g\t%g\t%g\t%g\t%g\n'%(b.state.pos[0],b.state.pos[1],b.state.pos[2],b.shape.radius,bC.id)) count+=1 except AttributeError: pass out.write(output) out.close() return countClumps,count #textPolyhedra=============================================================== def textPolyhedra(fileName, comment='',mask=-1, explanationComment=True,attrs=[]): """Save polyhedra into a text file. Non-polyhedra bodies are silently skipped. :param string filename: the name of the output file :param string comment: the text, which will be added as a comment at the top of file. If you want to create several lines of text, please use '\\\\n#' for next lines. :param int mask: export only polyhedra with the corresponding mask :param str explanationComment: inclde explanation of format to the beginning of file :return: number of polyhedra which were written. :rtype: int """ count = 0 f = open(fileName,'w') f.writelines('# %s\n'%l for l in [ 'YADE export of polyhedra.', 'Each polyhedron export contains first line with id, nuber of vertices and number of surfaces.', 'x,y,z coordinates of each vertex follows (each vertex on separate line).', 'ids if vertices of individual surfaces follows (numbering from 0, each surface on separate line).', '', 'Example of tetrahedron and cube with random ids:', '23 4 4', '0.1 0.2 0.3','1.3 0.1 -0.1','-0.2 1.2 0','0 -0.1 1.5', '0 2 1','0 3 2','0 1 3','1 2 3', '65 8 6', '4 0 0','5 0 0','4 1 0','5 1 0','4 0 1','5 0 1','4 1 1','5 1 1', '0 2 3 1','0 1 5 4','1 3 7 5','3 2 6 7','2 0 4 6','4 5 7 6', '', ]) if comment: f.write('#\n# %s\n'%comment) for b in O.bodies: if not isinstance(b.shape,Polyhedra) or not mask & b.mask: continue count += 1 vertices = [b.state.pos + b.state.ori*v for v in b.shape.v] surfaces = b.shape.GetSurfaces() strAttrs = '' if attrs: for cmd in attrs: v = eval(cmd) if isinstance(v,(int,float)): strAttrs+=' %g'%v elif isinstance(v,Vector3): strAttrs+=' %g %g %g'%tuple(v[i] for i in xrange(3)) elif isinstance(v,Matrix3): strAttrs+=' %g'%tuple(v[i] for i in xrange(9)) f.write('%d %d %d%s\n'%(b.id,len(vertices),len(surfaces),strAttrs)) f.writelines('%.8e %.8e %.8e\n'%(v[0],v[1],v[2]) for v in vertices) f.writelines(' '.join(str(i) for i in surface)+'\n' for surface in surfaces) f.close() return count #VTKWriter=============================================================== class VTKWriter: """ USAGE: create object vtk_writer = VTKWriter('base_file_name'), add to engines PyRunner with command='vtk_writer.snapshot()' """ def __init__(self,baseName='snapshot',startSnap=0): self.snapCount = startSnap self.baseName=baseName def snapshot(self): import xml.dom.minidom #import xml.dom.ext # python 2.5 and later positions=[]; radii=[] for b in Omega().bodies: if b.mold.name=='Sphere': positions.append(b.phys['se3'][0]) radii.append(b.mold['radius']) # Document and root element doc = xml.dom.minidom.Document() root_element = doc.createElementNS("VTK", "VTKFile") root_element.setAttribute("type", "UnstructuredGrid") root_element.setAttribute("version", "0.1") root_element.setAttribute("byte_order", "LittleEndian") doc.appendChild(root_element) # Unstructured grid element unstructuredGrid = doc.createElementNS("VTK", "UnstructuredGrid") root_element.appendChild(unstructuredGrid) # Piece 0 (only one) piece = doc.createElementNS("VTK", "Piece") piece.setAttribute("NumberOfPoints", str(len(positions))) piece.setAttribute("NumberOfCells", "0") unstructuredGrid.appendChild(piece) ### Points #### points = doc.createElementNS("VTK", "Points") piece.appendChild(points) # Point location data point_coords = doc.createElementNS("VTK", "DataArray") point_coords.setAttribute("type", "Float32") point_coords.setAttribute("format", "ascii") point_coords.setAttribute("NumberOfComponents", "3") points.appendChild(point_coords) string = str() for x,y,z in positions: string += repr(x) + ' ' + repr(y) + ' ' + repr(z) + ' ' point_coords_data = doc.createTextNode(string) point_coords.appendChild(point_coords_data) #### Cells #### cells = doc.createElementNS("VTK", "Cells") piece.appendChild(cells) # Cell locations cell_connectivity = doc.createElementNS("VTK", "DataArray") cell_connectivity.setAttribute("type", "Int32") cell_connectivity.setAttribute("Name", "connectivity") cell_connectivity.setAttribute("format", "ascii") cells.appendChild(cell_connectivity) # Cell location data connectivity = doc.createTextNode("0") cell_connectivity.appendChild(connectivity) cell_offsets = doc.createElementNS("VTK", "DataArray") cell_offsets.setAttribute("type", "Int32") cell_offsets.setAttribute("Name", "offsets") cell_offsets.setAttribute("format", "ascii") cells.appendChild(cell_offsets) offsets = doc.createTextNode("0") cell_offsets.appendChild(offsets) cell_types = doc.createElementNS("VTK", "DataArray") cell_types.setAttribute("type", "UInt8") cell_types.setAttribute("Name", "types") cell_types.setAttribute("format", "ascii") cells.appendChild(cell_types) types = doc.createTextNode("1") cell_types.appendChild(types) #### Data at Points #### point_data = doc.createElementNS("VTK", "PointData") piece.appendChild(point_data) # Particle radii if len(radii) > 0: radiiNode = doc.createElementNS("VTK", "DataArray") radiiNode.setAttribute("Name", "radii") radiiNode.setAttribute("type", "Float32") radiiNode.setAttribute("format", "ascii") point_data.appendChild(radiiNode) string = str() for r in radii: string += repr(r) + ' ' radiiData = doc.createTextNode(string) radiiNode.appendChild(radiiData) #### Cell data (dummy) #### cell_data = doc.createElementNS("VTK", "CellData") piece.appendChild(cell_data) # Write to file and exit outFile = open(self.baseName+'%08d'%self.snapCount+'.vtu', 'w') # xml.dom.ext.PrettyPrint(doc, file) doc.writexml(outFile, newl='\n') outFile.close() self.snapCount+=1 #text=============================================================== def text(filename,mask=-1): """Save sphere coordinates into a text file; the format of the line is: x y z r. Non-spherical bodies are silently skipped. Example added to examples/regular-sphere-pack/regular-sphere-pack.py :param string filename: the name of the file, where sphere coordinates will be exported. :param int mask: export only spheres with the corresponding mask :return: number of spheres which were written. :rtype: int """ return (textExt(filename=filename, format='x_y_z_r',mask=mask)) #VTKExporter=============================================================== class VTKExporter: """Class for exporting data to VTK Simple Legacy File (for example if, for some reason, you are not able to use VTKRecorder). Export of spheres, facets, interactions and polyhedra is supported. USAGE: create object vtkExporter = VTKExporter('baseFileName'), add to engines PyRunner with command='vtkExporter.exportSomething(params)' alternatively just use vtkExporter.exportSomething(...) at the end of the script for instance Example: :ysrc:`examples/test/vtk-exporter/vtkExporter.py`, :ysrc:`examples/test/unv-read/unvReadVTKExport.py`. :param string baseName: name of the exported files. The files would be named baseName-spheres-snapNb.vtk or baseName-facets-snapNb.vtk :param int startSnap: the numbering of files will start form startSnap """ # TODO comments def __init__(self,baseName,startSnap=0): self.spheresSnapCount = startSnap self.facetsSnapCount = startSnap self.intrsSnapCount = startSnap self.polyhedraSnapCount = startSnap self.contactPointsSnapCount = startSnap self.baseName = baseName # auxiliary functions def _warn(self,msg): print "Warning (yade.export.VTKExporter): " + msg def _error(self,msg): print "ERROR (yade.export.VTKExporter): " + msg def _getBodies(self,ids,type): allIds = False if isinstance(ids,str) and ids.lower()=='all': ids=xrange(len(O.bodies)) allIds = True bodies = [] for i in ids: b = O.bodies[i] if not b: continue if not isinstance(b.shape,type): if not allIds: self._warn("body %d is not of type %s"%(i,type)) continue bodies.append(b) if not bodies: self._warn("no bodies...") return bodies def _getInteractions(self,ids): if isinstance(ids,str) and ids.lower()=='all': ids = [(i.id1,i.id2) for i in O.interactions] intrs = [(i,j) for i,j in ids] if not intrs: self._warn("no interactions ...") return intrs def exportSpheres(self,ids='all',what=[],comment="comment",numLabel=None,useRef=False): """exports spheres (positions and radius) and defined properties. :param [int]|"all" ids: if "all", then export all spheres, otherwise only spheres from integer list :param [tuple(2)] what: what other than then position and radius export. parameter is list of couple (name,command). Name is string under which it is save to vtk, command is string to evaluate. Note that the bodies are labeled as b in this function. Scalar, vector and tensor variables are supported. For example, to export velocity (with name particleVelocity) and the distance form point (0,0,0) (named as dist) you should write: ... what=[('particleVelocity','b.state.vel'),('dist','b.state.pos.norm()', ... :param string comment: comment to add to vtk file :param int numLabel: number of file (e.g. time step), if unspecified, the last used value + 1 will be used :param bool useRef: if False (default), use current position of the spheres for export, use reference position otherwise """ # get list of bodies to export bodies = self._getBodies(ids,Sphere) if not bodies: return nBodies = len(bodies) # output file fName = self.baseName+'-spheres-%08d'%(numLabel if numLabel else self.spheresSnapCount)+'.vtk' outFile = open(fName, 'w') # head outFile.write("# vtk DataFile Version 3.0.\n%s\nASCII\n\nDATASET POLYDATA\nPOINTS %d double\n"%(comment,nBodies)) # write position of spheres for b in bodies: pos = b.state.refPos if useRef else b.state.pos if not O.periodic else O.cell.wrap(b.state.pos) outFile.write("%g %g %g\n"%(pos[0],pos[1],pos[2])) # write radius outFile.write("\nPOINT_DATA %d\nSCALARS radius double 1\nLOOKUP_TABLE default\n"%(nBodies)) for b in bodies: outFile.write("%g\n"%(b.shape.radius)) # write additional data from 'what' param for name,command in what: # for each name... test = eval(command) # ... eval one example to see what type (float, Vector3, Matrix3) the result is ... # ... and write appropriate header line and loop over all bodies and write appropriate vtk line(s) if isinstance(test,Matrix3): outFile.write("\nTENSORS %s double\n"%(name)) for b in bodies: t = eval(command) outFile.write("%g %g %g\n%g %g %g\n%g %g %g\n\n"%(t[0,0],t[0,1],t[0,2],t[1,0],t[1,1],t[1,2],t[2,0],t[2,1],t[2,2])) elif isinstance(test,Vector3): outFile.write("\nVECTORS %s double\n"%(name)) for b in bodies: v = eval(command) outFile.write("%g %g %g\n"%(v[0],v[1],v[2])) elif isinstance(test,(int,float)): outFile.write("\nSCALARS %s double 1\nLOOKUP_TABLE default\n"%(name)) for b in bodies: outFile.write("%g\n"%(eval(command))) else: self._warn("exportSpheres: wrong 'what' parameter, vtk output might be corrupted'") outFile.close() self.spheresSnapCount += 1 def exportFacets(self,ids='all',what=[],comment="comment",numLabel=None): """ exports facets (positions) and defined properties. Facets are exported with multiplicated nodes :param [int]|"all" ids: if "all", then export all facets, otherwise only facets from integer list :param [tuple(2)] what: see exportSpheres :param string comment: comment to add to vtk file :param int numLabel: number of file (e.g. time step), if unspecified, the last used value + 1 will be used """ # get list of bodies to export bodies = self._getBodies(ids,Facet) if not bodies: return nBodies = len(bodies) # output file fName = self.baseName+'-facets-%08d'%(numLabel if numLabel else self.facetsSnapCount)+'.vtk' outFile = open(fName, 'w') # head outFile.write("# vtk DataFile Version 3.0.\n%s\nASCII\n\nDATASET POLYDATA\nPOINTS %d double\n"%(comment,3*nBodies)) # write vertices for b in bodies: p = b.state.pos o = b.state.ori s = b.shape pt1 = p + o*s.vertices[0] pt2 = p + o*s.vertices[1] pt3 = p + o*s.vertices[2] outFile.write("%g %g %g\n"%(pt1[0],pt1[1],pt1[2])) outFile.write("%g %g %g\n"%(pt2[0],pt2[1],pt2[2])) outFile.write("%g %g %g\n"%(pt3[0],pt3[1],pt3[2])) # write facets outFile.write("\nPOLYGONS %d %d\n"%(nBodies,4*nBodies)) i = 0 for b in bodies: outFile.write("3 %d %d %d\n"%(i,i+1,i+2)) i += 3 # write additional data from 'what' param if what: outFile.write("\nCELL_DATA %d"%(nBodies)) # see exportSpheres for explanation of this code block for name,command in what: test = eval(command) if isinstance(test,Matrix3): outFile.write("\nTENSORS %s double\n"%(name)) for b in bodies: t = eval(command) outFile.write("%g %g %g\n%g %g %g\n%g %g %g\n\n"%(t[0,0],t[0,1],t[0,2],t[1,0],t[1,1],t[1,2],t[2,0],t[2,1],t[2,2])) if isinstance(test,Vector3): outFile.write("\nVECTORS %s double\n"%(name)) for b in bodies: v = eval(command) outFile.write("%g %g %g\n"%(v[0],v[1],v[2])) else: outFile.write("\nSCALARS %s double 1\nLOOKUP_TABLE default\n"%(name)) for b in bodies: outFile.write("%g\n"%(eval(command))) outFile.close() self.facetsSnapCount += 1 def exportFacetsAsMesh(self,ids='all',connectivityTable=None,what=[],comment="comment",numLabel=None): """ exports facets (positions) and defined properties. Facets are exported as mesh (not with multiplicated nodes). Therefore additional parameters connectivityTable is needed :param [int]|"all" ids: if "all", then export all facets, otherwise only facets from integer list :param [tuple(2)] what: see exportSpheres :param string comment: comment to add to vtk file :param int numLabel: number of file (e.g. time step), if unspecified, the last used value + 1 will be used :param [(float,float,float)|Vector3] nodes: list of coordinates of nodes :param [(int,int,int)] connectivityTable: list of node ids of individual elements (facets) """ # get list of bodies to export bodies = self._getBodies(ids,Facet) ids = [b.id for b in bodies] if not bodies: return nBodies = len(bodies) if connectivityTable is None: self._error("'connectivityTable' not specified") return if nBodies != len(connectivityTable): self._error("length of 'connectivityTable' does not match length of 'ids', no export") return # nodes nodes = [Vector3.Zero for i in xrange(max(max(e) for e in connectivityTable)+1)] for id,e in zip(ids,connectivityTable): b = bodies[id] p = b.state.pos o = b.state.ori s = b.shape pt1 = p + o*s.vertices[0] pt2 = p + o*s.vertices[1] pt3 = p + o*s.vertices[2] nodes[e[0]] = pt1 nodes[e[1]] = pt2 nodes[e[2]] = pt3 # output file fName = self.baseName+'-facets-%08d'%(numLabel if numLabel else self.facetsSnapCount)+'.vtk' outFile = open(fName, 'w') # head outFile.write("# vtk DataFile Version 3.0.\n%s\nASCII\n\nDATASET POLYDATA\nPOINTS %d double\n"%(comment,len(nodes))) # write vertices for node in nodes: outFile.write("%g %g %g\n"%(node[0],node[1],node[2])) # write facets outFile.write("\nPOLYGONS %d %d\n"%(len(connectivityTable),4*len(connectivityTable))) for e in connectivityTable: outFile.write("3 %d %d %d\n"%e) # write additional data from 'what' param if what: outFile.write("\nCELL_DATA %d"%(nBodies)) # see exportSpheres for explanation of this code block for name,command in what: test = eval(command) if isinstance(test,Matrix3): outFile.write("\nTENSORS %s double\n"%(name)) for b in bodies: t = eval(command) outFile.write("%g %g %g\n%g %g %g\n%g %g %g\n\n"%(t[0,0],t[0,1],t[0,2],t[1,0],t[1,1],t[1,2],t[2,0],t[2,1],t[2,2])) if isinstance(test,Vector3): outFile.write("\nVECTORS %s double\n"%(name)) for b in bodies: v = eval(command) outFile.write("%g %g %g\n"%(v[0],v[1],v[2])) else: outFile.write("\nSCALARS %s double 1\nLOOKUP_TABLE default\n"%(name)) for b in bodies: outFile.write("%g\n"%(eval(command))) outFile.close() self.facetsSnapCount += 1 def exportInteractions(self,ids='all',what=[],verticesWhat=[],comment="comment",numLabel=None,useRef=False): """exports interactions and defined properties. :param [(int,int)]|"all" ids: if "all", then export all interactions, otherwise only interactions from (int,int) list :param [tuple(2)] what: what to export. parameter is list of couple (name,command). Name is string under which it is save to vtk, command is string to evaluate. Note that the interactions are labeled as i in this function. Scalar, vector and tensor variables are supported. For example, to export stiffness difference from certain value (1e9) (named as dStiff) you should write: ... what=[('dStiff','i.phys.kn-1e9'), ... :param [tuple(2|3)] verticesWhat: what to export on connected bodies. Bodies are labeled as 'b' (or 'b1' and 'b2' if you need treat both bodies differently) :param string comment: comment to add to vtk file :param int numLabel: number of file (e.g. time step), if unspecified, the last used value + 1 will be used """ # get list of interactions to export intrs = self._getInteractions(ids) if not intrs: return nIntrs = len(intrs) # output file fName = self.baseName+'-intrs-%08d'%(numLabel if numLabel else self.intrsSnapCount)+'.vtk' outFile = open(fName, 'w') # head outFile.write("# vtk DataFile Version 3.0.\n%s\nASCII\n\nDATASET POLYDATA\nPOINTS %d double\n"%(comment,2*nIntrs)) # write coords of intrs bodies (also taking into account possible periodicity for ii,jj in intrs: i = O.interactions[ii,jj] pos = O.bodies[ii].state.refPos if useRef else O.bodies[ii].state.pos outFile.write("%g %g %g\n"%(pos[0],pos[1],pos[2])) pos = (O.bodies[jj].state.refPos if useRef else O.bodies[jj].state.pos) + (O.cell.hSize*i.cellDist if O.periodic else Vector3.Zero) outFile.write("%g %g %g\n"%(pos[0],pos[1],pos[2])) # write interactions as lines outFile.write("LINES %d %d\n"%(nIntrs,3*nIntrs)) for j,i in enumerate(intrs): outFile.write("2 %d %d\n"%(2*j,2*j+1)) # write additional data from 'what' param if what: outFile.write("\nCELL_DATA %d\n"%(nIntrs)) for i in O.interactions: if i.isReal: break # see exportSpheres for explanation of this code block for name,command in what: test = eval(command) if isinstance(test,Matrix3): outFile.write("\nTENSORS %s double\n"%(name)) for ii,jj in intrs: i = O.interactions[ii,jj] t = eval(command) outFile.write("%g %g %g\n%g %g %g\n%g %g %g\n\n"%(t[0,0],t[0,1],t[0,2],t[1,0],t[1,1],t[1,2],t[2,0],t[2,1],t[2,2])) elif isinstance(test,Vector3): outFile.write("\nVECTORS %s double\n"%(name)) for ii,jj in intrs: i = O.interactions[ii,jj] v = eval(command) outFile.write("%g %g %g\n"%(v[0],v[1],v[2])) elif isinstance(test,(int,float)): outFile.write("\nSCALARS %s double 1\nLOOKUP_TABLE default\n"%(name)) for ii,jj in intrs: i = O.interactions[ii,jj] outFile.write("%g\n"%(eval(command))) else: self._warn("exportInteractions: wrong 'what' parameter, vtk output might be corrupted") # write additional data of bodies if verticesWhat: outFile.write("\nPOINT_DATA %d\n"%(2*nIntrs)) b = b1 = b2 = O.bodies[0] # see exportSpheres for explanation of this code block for vWhat in verticesWhat: lw = len(vWhat) if lw == 2: name,command = vWhat test = eval(command) elif lw == 3: name,command1,command2 = vWhat test = eval(command1) if isinstance(test,Matrix3): outFile.write("\nTENSORS %s double\n"%(name)) for ii,jj in intrs: i = O.interactions[ii,jj] b1 = O.bodies[ii] b2 = O.bodies[jj] if lw==2: for b in (b1,b2): t = eval(command) outFile.write("%g %g %g\n%g %g %g\n%g %g %g\n\n"%(t[0,0],t[0,1],t[0,2],t[1,0],t[1,1],t[1,2],t[2,0],t[2,1],t[2,2])) elif lw==3: t1 = eval(command1) t2 = eval(command2) outFile.write("%g %g %g\n%g %g %g\n%g %g %g\n\n"%(t1[0,0],t1[0,1],t1[0,2],t1[1,0],t1[1,1],t1[1,2],t1[2,0],t1[2,1],t1[2,2])) outFile.write("%g %g %g\n%g %g %g\n%g %g %g\n\n"%(t2[0,0],t2[0,1],t2[0,2],t2[1,0],t2[1,1],t2[1,2],t2[2,0],t2[2,1],t2[2,2])) elif isinstance(test,Vector3): outFile.write("\nVECTORS %s double\n"%(name)) for ii,jj in intrs: i = O.interactions[ii,jj] b1 = O.bodies[ii] b2 = O.bodies[jj] if lw==2: for b in (b1,b2): v = eval(command) outFile.write("%g %g %g\n"%(v[0],v[1],v[2])) elif lw==3: v1 = eval(command1) v2 = eval(command2) outFile.write("%g %g %g\n"%(v1[0],v1[1],v1[2])) outFile.write("%g %g %g\n"%(v2[0],v2[1],v2[2])) elif isinstance(test,(int,float)): outFile.write("\nSCALARS %s double 1\nLOOKUP_TABLE default\n"%(name)) for ii,jj in intrs: i = O.interactions[ii,jj] b1 = O.bodies[ii] b2 = O.bodies[jj] if lw==2: for b in (b1,b2): outFile.write("%g\n"%(eval(command))) elif lw==3: outFile.write("%g\n"%(eval(command1))) outFile.write("%g\n"%(eval(command2))) else: self._warn("exportInteractions: wrong 'what' parameter, vtk output might be corrupted") outFile.close() self.intrsSnapCount += 1 def exportContactPoints(self,ids='all',what=[],useRef={},comment="comment",numLabel=None): """exports constact points and defined properties. :param [(int,int)] ids: see exportInteractions :param [tuple(2)] what: what to export. parameter is list of couple (name,command). Name is string under which it is save to vtk, command is string to evaluate. Note that the CPs are labeled as i in this function (sccording to their interaction). Scalar, vector and tensor variables are supported. For example, to export stiffness difference from certain value (1e9) (named as dStiff) you should write: ... what=[('dStiff','i.phys.kn-1e9'), ... :param {Interaction:Vector3} useRef: if not specified, current position used. Otherwise use position from dict using interactions as keys. Interactions not in dict are not exported :param string comment: comment to add to vtk file :param int numLabel: number of file (e.g. time step), if unspecified, the last used value + 1 will be used """ # get list of interactions to export if useRef: useRef = dict(((i.id1,i.id2),v) for i,v in useRef.iteritems()) intrs = useRef.keys() else: intrs = self._getInteractions(ids) if not intrs: return nIntrs = len(intrs) # output file fName = self.baseName+'-cps-%08d'%(numLabel if numLabel else self.contactPointsSnapCount)+'.vtk' outFile = open(fName, 'w') # head outFile.write("# vtk DataFile Version 3.0.\n%s\nASCII\n\nDATASET POLYDATA\nPOINTS %d double\n"%(comment,nIntrs)) # write coords of contact points for ii,jj in intrs: if useRef: pos = useRef[(ii,jj)] else: i = O.interactions[ii,jj] pos = i.geom.contactPoint outFile.write("%g %g %g\n"%(pos[0],pos[1],pos[2])) # see exportSpheres for explanation of this code block if what: outFile.write("\nPOINT_DATA %d\n"%(nIntrs)) for i in O.interactions: if i.isReal: break for name,command in what: test = eval(command) if isinstance(test,Matrix3): outFile.write("\nTENSORS %s double\n"%(name)) for ii,jj in intrs: try: i = O.interactions[ii,jj] t = eval(command) except IndexError: t = Matrix3.Zero # TODO? outFile.write("%g %g %g\n%g %g %g\n%g %g %g\n\n"%(t[0,0],t[0,1],t[0,2],t[1,0],t[1,1],t[1,2],t[2,0],t[2,1],t[2,2])) elif isinstance(test,Vector3): outFile.write("\nVECTORS %s double\n"%(name)) for ii,jj in intrs: try: i = O.interactions[ii,jj] v = eval(command) except IndexError: v = Vector3.Zero # TODO? outFile.write("%g %g %g\n"%(v[0],v[1],v[2])) elif isinstance(test,(int,float)): outFile.write("\nSCALARS %s double 1\nLOOKUP_TABLE default\n"%(name)) for ii,jj in intrs: try: i = O.interactions[ii,jj] f = eval(command) except IndexError: f = 0. # TODO? outFile.write("%g\n"%(f)) else: self._warn("exportContacPoints: wrong 'what' parameter, vtk output might be corrupted'") outFile.close() self.contactPointsSnapCount += 1 def exportPeriodicCell(self,comment="comment",numLabel=None): """exports spheres (positions and radius) and defined properties. :param string comment: comment to add to vtk file :param int numLabel: number of file (e.g. time step), if unspecified, the last used value + 1 will be used """ if not O.periodic: self._warn("exportPeriodicCell: scene is not periodic, no export...") return hSize = O.cell.hSize fName = self.baseName+'-periCell-%08d'%(numLabel if numLabel else self.intrsSnapCount)+'.vtk' outFile = open(fName, 'w') outFile.write("# vtk DataFile Version 3.0.\n%s\nASCII\n\nDATASET UNSTRUCTURED_GRID\nPOINTS 8 double\n"%(comment)) vertices = [ hSize*Vector3(0,0,1), hSize*Vector3(0,1,1), hSize*Vector3(1,1,1), hSize*Vector3(1,0,1), hSize*Vector3(0,0,0), hSize*Vector3(0,1,0), hSize*Vector3(1,1,0), hSize*Vector3(1,0,0), ] for v in vertices: outFile.write('%g %g %g\n'%(v[0],v[1],v[2])) outFile.write('\nCELLS 1 9\n') outFile.write('8 0 1 2 3 4 5 6 7\n') outFile.write('\nCELL_TYPES 1\n12\n') outFile.close() def exportPolyhedra(self,ids='all',what=[],comment="comment",numLabel=None,useRef=False): """Exports polyhedrons and defined properties. :param ids: if "all", then export all polyhedrons, otherwise only polyhedrons from integer list :type ids: [int] | "all" :param what: what other than then position to export. parameter is list of couple (name,command). Name is string under which it is save to vtk, command is string to evaluate. Note that the bodies are labeled as b in this function. Scalar, vector and tensor variables are supported. For example, to export velocity (with name particleVelocity) and the distance form point (0,0,0) (named as dist) you should write: ... what=[('particleVelocity','b.state.vel'),('dist','b.state.pos.norm()', ... :type what: [tuple(2)] :param string comment: comment to add to vtk file :param int numLabel: number of file (e.g. time step), if unspecified, the last used value + 1 will be used """ # TODO useRef? # get list of bodies to export bodies = self._getBodies(ids,Polyhedra) # TODO if not bodies: return # number of vertices nVertices = sum(len(b.shape.v) for b in bodies) # export polyherda as a set of triangle faces bodyFaces = [] for b in bodies: ff = [] f = b.shape.GetSurfaceTriangulation() for i in xrange(len(f)/3): ff.append([f[3*i+j] for j in (0,1,2)]) bodyFaces.append(ff) # output file nFaces = sum(len(f) for f in bodyFaces) fName = self.baseName+'-polyhedra-%08d'%(numLabel if numLabel else self.polyhedraSnapCount)+'.vtk' outFile = open(fName, 'w') # head outFile.write("# vtk DataFile Version 3.0.\n%s\nASCII\n\nDATASET POLYDATA\nPOINTS %d double\n"%(comment,nVertices)) # write position of vertices if useRef: dspls = [] for b in bodies: bPos = b.state.pos bOri = b.state.ori brPos = b.state.refPos brOri = b.state.refOri for v in b.shape.v: rPos = brPos + brOri*v pos = bPos + bOri*v outFile.write("%g %g %g\n"%(rPos[0],rPos[1],rPos[2])) dspls.append(pos-rPos) else: for b in bodies: bPos = b.state.pos bOri = b.state.ori for v in b.shape.v: pos = bPos + bOri*v outFile.write("%g %g %g\n"%(pos[0],pos[1],pos[2])) # write triangle faces outFile.write("\nPOLYGONS %d %d\n"%(nFaces,4*nFaces)) j = 0 for i,b in enumerate(bodies): faces = bodyFaces[i] for face in faces: t = tuple([j+ii for ii in face]) outFile.write("3 %d %d %d\n"%t) j += len(b.shape.v) # write additional data from 'what' param if useRef: outFile.write("\nPOINT_DATA %d\n"%(len(dspls))) outFile.write("\nVECTORS displacement double\n") for v in dspls: outFile.write("%g %g %g\n"%(v[0],v[1],v[2])) if what: outFile.write("\nCELL_DATA %d"%(nFaces)) # see exportSpheres for explanation of this code block for name,command in what: test = eval(command) if isinstance(test,Matrix3): outFile.write("\nTENSORS %s double\n"%(name)) for i,b in enumerate(bodies): t = eval(command) for f in bodyFaces[i]: outFile.write("%g %g %g\n%g %g %g\n%g %g %g\n\n"%(t[0,0],t[0,1],t[0,2],t[1,0],t[1,1],t[1,2],t[2,0],t[2,1],t[2,2])) elif isinstance(test,Vector3): outFile.write("\nVECTORS %s double\n"%(name)) for i,b in enumerate(bodies): v = eval(command) for f in bodyFaces[i]: outFile.write("%g %g %g\n"%(v[0],v[1],v[2])) elif isinstance(test,(int,float)): outFile.write("\nSCALARS %s double 1\nLOOKUP_TABLE default\n"%(name)) for i,b in enumerate(bodies): e = eval(command) for f in bodyFaces[i]: outFile.write("%g\n"%e) else: self._warn("exportPolyhedra: wrong 'what' parameter, vtk output might be corrupted") outFile.close() self.polyhedraSnapCount += 1 #gmshGeoExport=============================================================== def gmshGeo(filename, comment='',mask=-1,accuracy=-1): """Save spheres in geo-file for the following using in GMSH (http://www.geuz.org/gmsh/doc/texinfo/) program. The spheres can be there meshed. :param string filename: the name of the file, where sphere coordinates will be exported. :param int mask: export only spheres with the corresponding mask export only spheres with the corresponding mask :param float accuracy: the accuracy parameter, which will be set for the poinst in geo-file. By default: 1./10. of the minimal sphere diameter. :return: number of spheres which were exported. :rtype: int """ O=Omega() try: out=open(filename,'w') except: raise RuntimeError("Problem to write into the file") count=0 #out.write('#format \n') # Find the minimal diameter if (accuracy<0.0): dMin = -1.0 for b in O.bodies: try: if (isinstance(b.shape,Sphere) and ((mask<0) or ((mask&b.mask)>0))): if (((dMin>0.0) and (dMin>b.shape.radius*2.0)) or (dMin<0.0)): dMin = b.shape.radius*2.0 except AttributeError: pass accuracy = dMin/10.0 # Export bodies PTS = 0 CRS = 0 out.write('Acc = %g;\n'%(accuracy)) for b in O.bodies: try: if (isinstance(b.shape,Sphere) and ((mask<0) or ((mask&b.mask)>0))): r = b.shape.radius x = b.state.pos[0] y = b.state.pos[1] z = b.state.pos[2] out.write('Rad = %g;\n'%(r)) out.write('Point(%d) = {%g, %g, %g, Acc};\n\ Point(%d) = {%g, %g, %g, Acc};\n\ Point(%d) = {%g, %g, %g, Acc};\n\ Point(%d) = {%g, %g, %g, Acc};\n\ Point(%d) = {%g, %g, %g, Acc};\n\ Point(%d) = {%g, %g, %g, Acc};\n\ Point(%d) = {%g, %g, %g, Acc};\n\n'%( PTS+1, x, y, z, PTS+2, r+x, y, z, PTS+3, -r+x, y, z, PTS+4, x, y, r+z, PTS+5, x, y, -r+z, PTS+6, x, r+y, z, PTS+7, x, -r+y, z )) out.write('\n\ Circle(%d) = {%d, %d, %d};\n\ Circle(%d) = {%d, %d, %d};\n\ Circle(%d) = {%d, %d, %d};\n\ Circle(%d) = {%d, %d, %d};\n\ Circle(%d) = {%d, %d, %d};\n\ Circle(%d) = {%d, %d, %d};\n\ Circle(%d) = {%d, %d, %d};\n\ Circle(%d) = {%d, %d, %d};\n\ Circle(%d) = {%d, %d, %d};\n\ Circle(%d) = {%d, %d, %d};\n\ Circle(%d) = {%d, %d, %d};\n\ Circle(%d) = {%d, %d, %d};\n'%( CRS+1, PTS+4, PTS+1, PTS+6, CRS+2, PTS+6, PTS+1, PTS+5, CRS+3, PTS+6, PTS+1, PTS+3, CRS+4, PTS+3, PTS+1, PTS+7, CRS+5, PTS+7, PTS+1, PTS+5, CRS+6, PTS+7, PTS+1, PTS+2, CRS+7, PTS+2, PTS+1, PTS+6, CRS+8, PTS+7, PTS+1, PTS+4, CRS+9, PTS+2, PTS+1, PTS+5, CRS+10, PTS+5, PTS+1, PTS+3, CRS+11, PTS+3, PTS+1, PTS+4, CRS+12, PTS+4, PTS+1, PTS+2, )) out.write('\n\ Line Loop(%d) = {%d, %d, %d}; Ruled Surface(%d) = {%d};\n\ Line Loop(%d) = {%d, %d, %d}; Ruled Surface(%d) = {%d};\n\ Line Loop(%d) = {%d, %d, %d}; Ruled Surface(%d) = {%d};\n\ Line Loop(%d) = {%d, %d, %d}; Ruled Surface(%d) = {%d};\n\ Line Loop(%d) = {%d, %d, %d}; Ruled Surface(%d) = {%d};\n\ Line Loop(%d) = {%d, %d, %d}; Ruled Surface(%d) = {%d};\n\ Line Loop(%d) = {%d, %d, %d}; Ruled Surface(%d) = {%d};\n\ Line Loop(%d) = {%d, %d, %d}; Ruled Surface(%d) = {%d};\n\n\ '%( (CRS+13), +(CRS+1), -(CRS+7), -(CRS+12), (CRS+14), (CRS+13), (CRS+15), +(CRS+7), +(CRS+2), -(CRS+9), (CRS+16), (CRS+15), (CRS+17), +(CRS+2), +(CRS+10), -(CRS+3), (CRS+18), (CRS+17), (CRS+19), +(CRS+3), +(CRS+11), +(CRS+1), (CRS+20), (CRS+19), (CRS+21), +(CRS+8), +(CRS+12), -(CRS+6), (CRS+22), (CRS+21), (CRS+23), +(CRS+4), +(CRS+8), -(CRS+11), (CRS+24), (CRS+23), (CRS+25), +(CRS+5), +(CRS+10), (CRS+4), (CRS+26), (CRS+25), (CRS+27), +(CRS+6), +(CRS+9), -(CRS+5), (CRS+28), (CRS+27), )) PTS+=7 CRS+=28 count+=1 except AttributeError: pass out.close() return count # external vtk manipulation =============================================================== def text2vtk(inFileName,outFileName): """Converts text file (created by :yref:`yade.export.textExt` function) into vtk file. See :ysrc:`examples/test/paraview-spheres-solid-section/export_text.py` example :param str inFileName: name of input text file :param str outFileName: name of output vtk file """ fin = open(inFileName) fout = open(outFileName,'w') lastLine = None line = '#' while line.startswith('#'): lastLine = line line = fin.readline() columns = lastLine.split()[5:] data = [line.split() for line in fin] fin.close() n = len(data) fout.write('# vtk DataFile Version 3.0.\ncomment\nASCII\n\nDATASET POLYDATA\nPOINTS %d double\n'%(n)) fout.writelines('%s %s %s\n'%(d[0],d[1],d[2]) for d in data) fout.write("\nPOINT_DATA %d\nSCALARS radius double 1\nLOOKUP_TABLE default\n"%(n)) fout.writelines('%s\n'%(d[3]) for d in data) for i,c in enumerate(columns): fout.write("\nSCALARS %s double 1\nLOOKUP_TABLE default\n"%(c)) fout.writelines('%s\n'%(d[4+i]) for d in data) fout.close() def text2vtkSection(inFileName,outFileName,point,normal=(1,0,0)): """Converts section through spheres from text file (created by :yref:`yade.export.textExt` function) into vtk file. See :ysrc:`examples/test/paraview-spheres-solid-section/export_text.py` example :param str inFileName: name of input text file :param str outFileName: name of output vtk file :param Vector3|(float,float,float) point: coordinates of a point lying on the section plane :param Vector3|(float,float,float) normal: normal vector of the section plane """ from math import sqrt norm = sqrt(pow(normal[0],2)+pow(normal[1],2)+pow(normal[2],2)) normal = (normal[0]/norm,normal[1]/norm,normal[2]/norm) # def computeD(point,normal): # from point and normal computes parameter d in plane equation ax+by+cz+d=0 return -normal[0]*point[0] - normal[1]*point[1] - normal[2]*point[2] def computeDistanceFromPlane(dat,point,normal,d=None): # computes distance of sphere dat from plane (point,normal) x,y,z = computeProjectionOnPlane(dat,point,normal,d) cx,cy,cz = dat[0],dat[1],dat[2] return sqrt(pow(x-cx,2)+pow(y-cy,2)+pow(z-cz,2)) def computeProjectionOnPlane(self,point,normal,d=None): # computes projection of sphere dat on plane (point,normal) if d is None: d = computeD(point,normal) nx,ny,nz = normal[0],normal[1],normal[2] cx,cy,cz = dat[0],dat[1],dat[2] t = (-d-nx*cx-ny*cy-nz*cz) / (nx*nx+ny*ny+nz*nz) x,y,z = cx+t*nx, cy+t*ny, cz+t*nz return x,y,z # fin = open(inFileName) lastLine = None line = '#' while line.startswith('#'): lastLine = line line = fin.readline() columns = lastLine.split()[4:] data = [[float(w) for w in line.split()] for line in fin] fin.close() # d = computeD(point,normal) circs = [] for dat in data: r = dat[3] dst = computeDistanceFromPlane(dat,point,normal,d) if dst > r: continue x,y,z = computeProjectionOnPlane(dat,point,normal,d) rNew = sqrt(r*r-dst*dst) dNew = [x,y,z,rNew,r] dNew.extend(dat[4:]) circs.append(dNew) n = len(circs) fout = open(outFileName,'w') fout.write('# vtk DataFile Version 3.0.\ncomment\nASCII\n\nDATASET POLYDATA\nPOINTS %d double\n'%(n)) fout.writelines('%g %g %g\n'%(c[0],c[1],c[2]) for c in circs) fout.write("\nPOINT_DATA %d\nSCALARS radius double 1\nLOOKUP_TABLE default\n"%(n)) fout.writelines('%g\n'%(c[3]) for c in circs) fout.write("\nSCALARS radiusOrig double 1\nLOOKUP_TABLE default\n") fout.writelines('%g\n'%(c[4]) for c in circs) fout.write("\nVECTORS normal double\n") fout.writelines("%g %g %g\n"%normal for i in circs) for i,c in enumerate(columns): fout.write("\nSCALARS %s double 1\nLOOKUP_TABLE default\n"%(c)) fout.writelines('%s\n'%(c[4+i]) for c in circs) fout.close() trunk-2017.01a/py/geom.py000066400000000000000000000571321304022710500151230ustar00rootroot00000000000000# encoding: utf-8 """ Creates geometry objects from facets. """ from yade.wrapper import * import utils,math,numpy from minieigen import * #facetBox=============================================================== def facetBox(center,extents,orientation=Quaternion((0,1,0),0.0),wallMask=63,**kw): """ Create arbitrarily-aligned box composed of facets, with given center, extents and orientation. If any of the box dimensions is zero, corresponding facets will not be created. The facets are oriented outwards from the box. :param Vector3 center: center of the box :param Vector3 extents: lengths of the box sides :param Quaternion orientation: orientation of the box :param bitmask wallMask: determines which walls will be created, in the order -x (1), +x (2), -y (4), +y (8), -z (16), +z (32). The numbers are ANDed; the default 63 means to create all walls :param \*\*kw: (unused keyword arguments) passed to :yref:`yade.utils.facet` :returns: list of facets forming the box """ return facetParallelepiped(center=center, extents=extents, height=extents[2], orientation=orientation, wallMask=wallMask, **kw) #facetParallelepiped=============================================================== def facetParallelepiped(center,extents,height,orientation=Quaternion((0,1,0),0.0),wallMask=63,**kw): """ Create arbitrarily-aligned Parallelepiped composed of facets, with given center, extents, height and orientation. If any of the parallelepiped dimensions is zero, corresponding facets will not be created. The facets are oriented outwards from the parallelepiped. :param Vector3 center: center of the parallelepiped :param Vector3 extents: lengths of the parallelepiped sides :param Real height: height of the parallelepiped (along axis z) :param Quaternion orientation: orientation of the parallelepiped :param bitmask wallMask: determines which walls will be created, in the order -x (1), +x (2), -y (4), +y (8), -z (16), +z (32). The numbers are ANDed; the default 63 means to create all walls :param \*\*kw: (unused keyword arguments) passed to :yref:`yade.utils.facet` :returns: list of facets forming the parallelepiped """ if (height<0): raise RuntimeError("The height should have the positive value"); if (height>extents[2]): raise RuntimeError("The height should be smaller or equal as extents[2]"); #Defense from zero dimensions if (wallMask>63): print "wallMask must be 63 or less" wallMask=63 if (extents[0]==0): wallMask=1 elif (extents[1]==0): wallMask=4 elif (extents[2]==0 or height==0): wallMask=16 if (((extents[0]==0) and (extents[1]==0)) or ((extents[0]==0) and (extents[2]==0)) or ((extents[1]==0) and (extents[2]==0))): raise RuntimeError("Please, specify at least 2 none-zero dimensions in extents!"); # ___________________________ #inclination angle beta = 0; dx = 0 if (height>0): beta = math.asin(height/extents[2]) dx = math.cos(beta)*extents[2] mn,mx=[-extents[i] for i in 0,1,2],[extents[i] for i in 0,1,2] def doWall(a,b,c,d): return [utils.facet((a,b,c),**kw),utils.facet((a,c,d),**kw)] ret=[] mn[2] = -height mx[2] = +height A=orientation*Vector3(mn[0],mn[1],mn[2])+center B=orientation*Vector3(mx[0],mn[1],mn[2])+center C=orientation*Vector3(mx[0],mx[1],mn[2])+center D=orientation*Vector3(mn[0],mx[1],mn[2])+center E=orientation*Vector3(mn[0]+dx,mn[1],mx[2])+center F=orientation*Vector3(mx[0]+dx,mn[1],mx[2])+center G=orientation*Vector3(mx[0]+dx,mx[1],mx[2])+center H=orientation*Vector3(mn[0]+dx,mx[1],mx[2])+center if wallMask&1: ret+=doWall(A,D,H,E) if wallMask&2: ret+=doWall(B,F,G,C) if wallMask&4: ret+=doWall(A,E,F,B) if wallMask&8: ret+=doWall(D,C,G,H) if wallMask&16: ret+=doWall(A,B,C,D) if wallMask&32: ret+=doWall(E,H,G,F) return ret #facetCylinder========================================================== def facetCylinder(center,radius,height,orientation=Quaternion((0,1,0),0.0), segmentsNumber=10,wallMask=7,angleRange=None,closeGap=False, radiusTopInner=-1, radiusBottomInner=-1, **kw): """ Create arbitrarily-aligned cylinder composed of facets, with given center, radius, height and orientation. Return List of facets forming the cylinder; :param Vector3 center: center of the created cylinder :param float radius: cylinder radius :param float height: cylinder height :param float radiusTopInner: inner radius of cylinders top, -1 by default :param float radiusBottomInner: inner radius of cylinders bottom, -1 by default :param Quaternion orientation: orientation of the cylinder; the reference orientation has axis along the $+x$ axis. :param int segmentsNumber: number of edges on the cylinder surface (>=5) :param bitmask wallMask: determines which walls will be created, in the order up (1), down (2), side (4). The numbers are ANDed; the default 7 means to create all walls :param (θmin,Θmax) angleRange: allows one to create only part of bunker by specifying range of angles; if ``None``, (0,2*pi) is assumed. :param bool closeGap: close range skipped in angleRange with triangular facets at cylinder bases. :param \*\*kw: (unused keyword arguments) passed to utils.facet; """ # check zero dimentions if (radius<=0): raise RuntimeError("The radius should have the positive value"); if (height<=0): wallMask = 1; return facetCylinderConeGenerator(center=center,radiusTop=radius,height=height, orientation=orientation,segmentsNumber=segmentsNumber,wallMask=wallMask, angleRange=angleRange,closeGap=closeGap, radiusTopInner=radiusTopInner, radiusBottomInner=radiusBottomInner, **kw) #facetSphere========================================================== def facetSphere(center,radius,thetaResolution=8,phiResolution=8,returnElementMap=False,**kw): """ Create arbitrarily-aligned sphere composed of facets, with given center, radius and orientation. Return List of facets forming the sphere. Parameters inspired by ParaView sphere glyph :param Vector3 center: center of the created sphere :param float radius: sphere radius :param int thetaResolution: number of facets around "equator" :param int phiResolution: number of facets between "poles" + 1 :param bool returnElementMap: returns also tuple of nodes ((x1,y1,z1),(x2,y2,z2),...) and elements ((id01,id02,id03),(id11,id12,id13),...) if true, only facets otherwise :param \*\*kw: (unused keyword arguments) passed to utils.facet; """ # check zero dimentions if (radius<=0): raise RuntimeError("The radius should have the positive value"); if (thetaResolution<3): raise RuntimeError("thetaResolution must be > 3"); if (phiResolution<3): raise RuntimeError("phiResolution must be > 3"); r,c0,c1,c2 = radius,center[0],center[1],center[2] nodes = [Vector3(c0,c1,c2+radius)] phis = numpy.linspace(math.pi/(phiResolution-1),math.pi,phiResolution-2,endpoint=False) thetas = numpy.linspace(0,2*math.pi,thetaResolution,endpoint=False) nodes.extend((Vector3(c0+r*math.cos(theta)*math.sin(phi),c1+r*math.sin(theta)*math.sin(phi),c2+r*math.cos(phi)) for phi in phis for theta in thetas)) nodes.append(Vector3(c0,c1,c2-radius)) n = len(nodes)-1 elements = [(0,i+1,i+2) for i in xrange(thetaResolution-1)] elements.append((0,1,thetaResolution)) for j in xrange(0,phiResolution-3): k = j*thetaResolution + 1 elements.extend((k+i,k+i+1,k+i+thetaResolution) for i in xrange(thetaResolution-1)) elements.append((k,k+thetaResolution-1,k+2*thetaResolution-1)) elements.extend((k+i+thetaResolution,k+i+1+thetaResolution,k+i+1) for i in xrange(thetaResolution-1)) elements.append((k+2*thetaResolution-1,k+thetaResolution,k)) elements.extend((n,n-i-1,n-i-2) for i in xrange(thetaResolution-1)) elements.append((n,n-1,n-thetaResolution)) facets = [utils.facet(tuple(nodes[node] for node in elem),**kw) for elem in elements] if returnElementMap: return facets,nodes,elements return facets #facetCone============================================================== def facetCone(center,radiusTop,radiusBottom,height,orientation=Quaternion((0,1,0),0.0), segmentsNumber=10,wallMask=7,angleRange=None,closeGap=False, radiusTopInner=-1, radiusBottomInner=-1, **kw): """ Create arbitrarily-aligned cone composed of facets, with given center, radius, height and orientation. Return List of facets forming the cone; :param Vector3 center: center of the created cylinder :param float radiusTop: cone top radius :param float radiusBottom: cone bottom radius :param float radiusTopInner: inner radius of cones top, -1 by default :param float radiusBottomInner: inner radius of cones bottom, -1 by default :param float height: cone height :param Quaternion orientation: orientation of the cone; the reference orientation has axis along the $+x$ axis. :param int segmentsNumber: number of edges on the cone surface (>=5) :param bitmask wallMask: determines which walls will be created, in the order up (1), down (2), side (4). The numbers are ANDed; the default 7 means to create all walls :param (θmin,Θmax) angleRange: allows one to create only part of cone by specifying range of angles; if ``None``, (0,2*pi) is assumed. :param bool closeGap: close range skipped in angleRange with triangular facets at cylinder bases. :param \*\*kw: (unused keyword arguments) passed to utils.facet; """ # check zero dimentions if ((radiusBottom<=0) and (radiusTop<=0)): raise RuntimeError("The radiusBottom or radiusTop should have the positive value"); return facetCylinderConeGenerator(center=center,radiusTop=radiusTop, radiusBottom=radiusBottom,height=height,orientation=orientation,segmentsNumber=segmentsNumber, wallMask=wallMask,angleRange=angleRange,closeGap=closeGap, radiusTopInner=radiusTopInner, radiusBottomInner=radiusBottomInner, **kw) #facetPolygon=========================================================== def facetPolygon(center,radiusOuter,orientation=Quaternion((0,1,0),0.0),segmentsNumber=10,angleRange=None,radiusInner=0,**kw): """ Create arbitrarily-aligned polygon composed of facets, with given center, radius (outer and inner) and orientation. Return List of facets forming the polygon; :param Vector3 center: center of the created cylinder :param float radiusOuter: outer radius :param float radiusInner: inner height (can be 0) :param Quaternion orientation: orientation of the polygon; the reference orientation has axis along the $+x$ axis. :param int segmentsNumber: number of edges on the polygon surface (>=3) :param (θmin,Θmax) angleRange: allows one to create only part of polygon by specifying range of angles; if ``None``, (0,2*pi) is assumed. :param \*\*kw: (unused keyword arguments) passed to utils.facet; """ # check zero dimentions if (abs(angleRange[1]-angleRange[0])>2.0*math.pi): raise RuntimeError("The |angleRange| cannot be larger 2.0*math.pi"); return facetPolygonHelixGenerator(center=center,radiusOuter=radiusOuter,orientation=orientation,segmentsNumber=segmentsNumber,angleRange=angleRange,radiusInner=radiusInner,**kw) #facetHelix=========================================================== def facetHelix(center,radiusOuter,pitch,orientation=Quaternion((0,1,0),0.0),segmentsNumber=10,angleRange=None,radiusInner=0,**kw): """ Create arbitrarily-aligned helix composed of facets, with given center, radius (outer and inner), pitch and orientation. Return List of facets forming the helix; :param Vector3 center: center of the created cylinder :param float radiusOuter: outer radius :param float radiusInner: inner height (can be 0) :param Quaternion orientation: orientation of the helix; the reference orientation has axis along the $+x$ axis. :param int segmentsNumber: number of edges on the helix surface (>=3) :param (θmin,Θmax) angleRange: range of angles; if ``None``, (0,2*pi) is assumed. :param \*\*kw: (unused keyword arguments) passed to utils.facet; """ # check zero dimentions if (pitch<=0): raise RuntimeError("The pitch should have the positive value"); return facetPolygonHelixGenerator(center=center,radiusOuter=radiusOuter,orientation=orientation,segmentsNumber=segmentsNumber,angleRange=angleRange,radiusInner=radiusInner,pitch=pitch,**kw) #facetBunker============================================================ def facetBunker(center,dBunker,dOutput,hBunker,hOutput,hPipe=0.0,orientation=Quaternion((0,1,0),0.0),segmentsNumber=10,wallMask=4,angleRange=None,closeGap=False,**kw): """ Create arbitrarily-aligned bunker, composed of facets, with given center, radii, heights and orientation. Return List of facets forming the bunker; .. code-block:: none dBunker ______________ | | | | | | hBunker | | | | | | |____________| \ / \ / \ / hOutput \ / \____/ | | |____| hPipe dOutput :param Vector3 center: center of the created bunker :param float dBunker: bunker diameter, top :param float dOutput: bunker output diameter :param float hBunker: bunker height :param float hOutput: bunker output height :param float hPipe: bunker pipe height :param Quaternion orientation: orientation of the bunker; the reference orientation has axis along the $+x$ axis. :param int segmentsNumber: number of edges on the bunker surface (>=5) :param bitmask wallMask: determines which walls will be created, in the order up (1), down (2), side (4). The numbers are ANDed; the default 7 means to create all walls :param (θmin,Θmax) angleRange: allows one to create only part of bunker by specifying range of angles; if ``None``, (0,2*pi) is assumed. :param bool closeGap: close range skipped in angleRange with triangular facets at cylinder bases. :param \*\*kw: (unused keyword arguments) passed to utils.facet; """ # check zero dimentions if (dBunker<=0): raise RuntimeError("The diameter dBunker should have the positive value"); if (dOutput<=0): raise RuntimeError("The diameter dOutput should have the positive value"); if (hBunker<0): raise RuntimeError("The height hBunker should have the positive or or zero"); if (hOutput<=0): raise RuntimeError("The height hOutput should have the positive value"); if (hPipe<0): raise RuntimeError("The height hPipe should have the positive value or zero"); ret=[] if ((hPipe>0) or (wallMask&2)): centerPipe = Vector3(0,0,hPipe/2.0) ret+=facetCylinder(center=centerPipe,radius=dOutput/2.0,height=hPipe,segmentsNumber=segmentsNumber,wallMask=wallMask&6,angleRange=angleRange,closeGap=closeGap,**kw) centerOutput = Vector3(0.0,0.0,hPipe+hOutput/2.0) ret+=facetCone(center=centerOutput,radiusTop=dBunker/2.0,radiusBottom=dOutput/2.0,height=hOutput,segmentsNumber=segmentsNumber,wallMask=wallMask&4,angleRange=angleRange,closeGap=closeGap,**kw) if (hBunker>0): centerBunker = Vector3(0.0,0.0,hPipe+hOutput+hBunker/2.0) ret+=facetCylinder(center=centerBunker,radius=dBunker/2.0,height=hBunker,segmentsNumber=segmentsNumber,wallMask=wallMask&5,angleRange=angleRange,closeGap=closeGap,**kw) for i in ret: i.state.pos=orientation*(i.state.pos)+Vector3(center) i.state.ori=orientation return ret #facetPolygonHelixGenerator================================================== def facetPolygonHelixGenerator(center,radiusOuter,pitch=0,orientation=Quaternion((0,1,0),0.0),segmentsNumber=10,angleRange=None,radiusInner=0,**kw): """ Please, do not use this function directly! Use geom.facetPloygon and geom.facetHelix instead. This is the base function for generating polygons and helixes from facets. """ # check zero dimentions if (segmentsNumber<3): raise RuntimeError("The segmentsNumber should be at least 3"); if (radiusOuter<=0): raise RuntimeError("The radiusOuter should have the positive value"); if (radiusInner<0): raise RuntimeError("The radiusInner should have the positive value or 0"); if angleRange==None: angleRange=(0,2*math.pi) anglesInRad = numpy.linspace(angleRange[0], angleRange[1], segmentsNumber+1, endpoint=True) heightsInRad = numpy.linspace(0, pitch*(abs(angleRange[1]-angleRange[0])/(2.0*math.pi)), segmentsNumber+1, endpoint=True) POuter=[]; PInner=[]; PCenter=[]; z=0; for i in anglesInRad: XOuter=radiusOuter*math.cos(i); YOuter=radiusOuter*math.sin(i); POuter.append(Vector3(XOuter,YOuter,heightsInRad[z])) PCenter.append(Vector3(0,0,heightsInRad[z])) if (radiusInner<>0): XInner=radiusInner*math.cos(i); YInner=radiusInner*math.sin(i); PInner.append(Vector3(XInner,YInner,heightsInRad[z])) z+=1 for i in range(0,len(POuter)): POuter[i]=orientation*POuter[i]+center PCenter[i]=orientation*PCenter[i]+center if (radiusInner<>0): PInner[i]=orientation*PInner[i]+center ret=[] for i in range(1,len(POuter)): if (radiusInner==0): ret.append(utils.facet((PCenter[i],POuter[i],POuter[i-1]),**kw)) else: ret.append(utils.facet((PInner[i-1],POuter[i-1],POuter[i]),**kw)) ret.append(utils.facet((PInner[i],PInner[i-1],POuter[i]),**kw)) return ret #facetCylinderConeGenerator============================================= def facetCylinderConeGenerator(center,radiusTop,height,orientation=Quaternion((0,1,0),0.0), segmentsNumber=10,wallMask=7,angleRange=None,closeGap=False, radiusBottom=-1, radiusTopInner=-1, radiusBottomInner=-1, **kw): """ Please, do not use this function directly! Use geom.facetCylinder and geom.facetCone instead. This is the base function for generating cylinders and cones from facets. :param float radiusTop: top radius :param float radiusBottom: bottom radius :param \*\*kw: (unused keyword arguments) passed to utils.facet; """ #For cylinders top and bottom radii are equal if (radiusBottom == -1): radiusBottom = radiusTop if ((radiusTopInner > 0 and radiusTopInner > radiusTop) or (radiusBottomInner > 0 and radiusBottomInner > radiusBottom)): raise RuntimeError("The internal radius cannot be larger than outer"); # check zero dimentions if (segmentsNumber<3): raise RuntimeError("The segmentsNumber should be at least 3"); if (height<0): raise RuntimeError("The height should have the positive value"); if angleRange==None: angleRange=(0,2*math.pi) if (abs(angleRange[1]-angleRange[0])>2.0*math.pi): raise RuntimeError("The |angleRange| cannot be larger 2.0*math.pi"); if (angleRange[1] 0): XTopIn=radiusTopInner*math.cos(i); YTopIn=radiusTopInner*math.sin(i); PTopIn.append(Vector3(XTopIn,YTopIn,+height/2)) XBottom=radiusBottom*math.cos(i); YBottom=radiusBottom*math.sin(i); PBottom.append(Vector3(XBottom,YBottom,-height/2)) if (radiusBottomInner > 0): XBottomIn=radiusBottomInner*math.cos(i); YBottomIn=radiusBottomInner*math.sin(i); PBottomIn.append(Vector3(XBottomIn,YBottomIn,-height/2)) for i in range(0,len(PTop)): PTop[i]=orientation*PTop[i]+center PBottom[i]=orientation*PBottom[i]+center if (len(PTopIn)>1): PTopIn[i]=orientation*PTopIn[i]+center if (len(PBottomIn)>1): PBottomIn[i]=orientation*PBottomIn[i]+center ret=[] for i in range(2,len(PTop)): if (wallMask&1)and(radiusTop!=0): if (len(PTopIn)>1): ret.append(utils.facet((PTop[i-1],PTopIn[i],PTopIn[i-1]),**kw)) ret.append(utils.facet((PTop[i-1],PTop[i],PTopIn[i]),**kw)) else: ret.append(utils.facet((PTop[0],PTop[i],PTop[i-1]),**kw)) if (wallMask&2)and(radiusBottom!=0): if (len(PBottomIn)>1): ret.append(utils.facet((PBottom[i-1],PBottomIn[i],PBottomIn[i-1]),**kw)) ret.append(utils.facet((PBottom[i-1],PBottom[i],PBottomIn[i]),**kw)) else: ret.append(utils.facet((PBottom[0],PBottom[i-1],PBottom[i]),**kw)) if wallMask&4: if (radiusBottom!=0): ret.append(utils.facet((PTop[i],PBottom[i],PBottom[i-1]),**kw)) if (radiusTop!=0): ret.append(utils.facet((PBottom[i-1],PTop[i-1],PTop[i]),**kw)) if (closeGap): if (wallMask&1)and(radiusTop!=0)and(abs(((angleRange[1]-angleRange[0])) > math.pi)): pts=[(radiusTop*math.cos(angleRange[i]),radiusTop*math.sin(angleRange[i])) for i in (0,1)] pp=[(pts[0][0],pts[0][1],+height/2.0), (pts[1][0],pts[1][1],+height/2.0), (0,0,+height/2.0)] pp=[orientation*p+center for p in pp] ret.append(utils.facet(pp,**kw)) if (wallMask&2)and(radiusBottom!=0)and(abs(((angleRange[1]-angleRange[0])) > math.pi)): pts=[(radiusBottom*math.cos(angleRange[i]),radiusBottom*math.sin(angleRange[i])) for i in (0,1)] pp=[(0,0,-height/2.0), (pts[1][0],pts[1][1],-height/2.0), (pts[0][0],pts[0][1],-height/2.0)] pp=[orientation*p+center for p in pp] ret.append(utils.facet(pp,**kw)) if (wallMask&4): ptsBottom=[(radiusBottom*math.cos(angleRange[i]),radiusBottom*math.sin(angleRange[i])) for i in (0,1)] ptsTop=[(radiusTop*math.cos(angleRange[i]),radiusTop*math.sin(angleRange[i])) for i in (0,1)] if (abs(((angleRange[1]-angleRange[0])) >= math.pi)): if (radiusBottom!=0)and(radiusTop!=0): #Cylinder pp=[(ptsBottom[0][0],ptsBottom[0][1],-height/2.0),(ptsBottom[1][0],ptsBottom[1][1],-height/2.0),(ptsTop[0][0],ptsTop[0][1],height/2.0)] pp=[orientation*p+center for p in pp] ret.append(utils.facet(pp,**kw)) pp=[(ptsBottom[1][0],ptsBottom[1][1],-height/2.0), (ptsTop[1][0],ptsTop[1][1],height/2.0), (ptsTop[0][0],ptsTop[0][1],height/2.0)] pp=[orientation*p+center for p in pp] ret.append(utils.facet(pp,**kw)) elif (radiusBottom==0)and(radiusTop!=0): #ConeTop pp=[(ptsTop[1][0],ptsTop[1][1],height/2.0), (ptsTop[0][0],ptsTop[0][1],height/2.0), (0,0,-height/2.0)] pp=[orientation*p+center for p in pp] ret.append(utils.facet(pp,**kw)) elif (radiusTop==0)and(radiusBottom!=0): #ConeBottom pp=[(0,0,height/2.0),(ptsBottom[0][0],ptsBottom[0][1],-height/2.0),(ptsBottom[1][0],ptsBottom[1][1],-height/2.0)] pp=[orientation*p+center for p in pp] ret.append(utils.facet(pp,**kw)) else: if (radiusBottom!=0)and(radiusTop!=0): #Cylinder pp=[(ptsBottom[0][0],ptsBottom[0][1],-height/2.0),(0,0,-height/2.0),(ptsTop[0][0],ptsTop[0][1],height/2.0)] pp=[orientation*p+center for p in pp] ret.append(utils.facet(pp,**kw)) pp=[(0,0,-height/2.0), (0,0,height/2.0), (ptsTop[0][0],ptsTop[0][1],height/2.0)] pp=[orientation*p+center for p in pp] ret.append(utils.facet(pp,**kw)) pp=[(0,0,-height/2.0),(ptsBottom[1][0],ptsBottom[1][1],-height/2.0),(0,0,height/2.0)] pp=[orientation*p+center for p in pp] ret.append(utils.facet(pp,**kw)) pp=[(ptsBottom[1][0],ptsBottom[1][1],-height/2.0), (ptsTop[1][0],ptsTop[1][1],height/2.0), (0,0,height/2.0)] pp=[orientation*p+center for p in pp] ret.append(utils.facet(pp,**kw)) elif (radiusBottom==0)and(radiusTop!=0): #ConeTop pp=[(0,0,height/2.0), (ptsTop[0][0],ptsTop[0][1],height/2.0), (0,0,-height/2.0)] pp=[orientation*p+center for p in pp] ret.append(utils.facet(pp,**kw)) pp=[(ptsTop[1][0],ptsTop[1][1],height/2.0), (0,0,height/2.0), (0,0,-height/2.0)] pp=[orientation*p+center for p in pp] ret.append(utils.facet(pp,**kw)) elif (radiusTop==0)and(radiusBottom!=0): #ConeBottom pp=[(0,0,height/2.0),(ptsBottom[0][0],ptsBottom[0][1],-height/2.0),(0,0,-height/2.0)] pp=[orientation*p+center for p in pp] ret.append(utils.facet(pp,**kw)) pp=[(0,0,height/2.0),(0,0,-height/2.0),(ptsBottom[1][0],ptsBottom[1][1],-height/2.0)] pp=[orientation*p+center for p in pp] ret.append(utils.facet(pp,**kw)) return ret trunk-2017.01a/py/gridpfacet.py000066400000000000000000000541031304022710500162770ustar00rootroot00000000000000# encoding: utf-8 # # 2015 © Bruno Chareyre # 2015 © Anna Effeindzourou # 2015 © François Kneib # 2015 © Klaus Thoeni """ Helper functions for creating cylinders, grids and membranes. For more details on this type of elements see [Effeindzourou2016]_, [Effeindzourou2015a]_, [Bourrier2013]_,. For examples using :yref:`GridConnections`, see * :ysrc:`examples/grids/CohesiveGridConnectionSphere.py` * :ysrc:`examples/grids/GridConnection_Spring.py` * :ysrc:`examples/grids/Simple_Grid_Falling.py` * :ysrc:`examples/grids/Simple_GridConnection_Falling.py` For examples using :yref:`PFacets`, see * :ysrc:`examples/pfacet/gts-pfacet.py` * :ysrc:`examples/pfacet/mesh-pfacet.py` * :ysrc:`examples/pfacet/pfacetcreators.py` """ import math,random,doctest,geom,numpy from yade.wrapper import * try: # use psyco if available import psyco psyco.full() except ImportError: pass from yade import utils from yade._utils import createInteraction from minieigen import * def chainedCylinder(begin=Vector3(0,0,0),end=Vector3(1.,0.,0.),radius=0.2,dynamic=None,fixed=False,wire=False,color=None,highlight=False,material=-1,mask=1): """ Create and connect a chainedCylinder with given parameters. The shape generated by repeted calls of this function is the Minkowski sum of polyline and sphere. :param Real radius: radius of sphere in the Minkowski sum. :param Vector3 begin: first point positioning the line in the Minkowski sum :param Vector3 last: last point positioning the line in the Minkowski sum In order to build a correct chain, last point of element of rank N must correspond to first point of element of rank N+1 in the same chain (with some tolerance, since bounding boxes will be used to create connections. :return: Body object with the :yref:`ChainedCylinder` :yref:`shape`. .. note:: :yref:`ChainedCylinder` is deprecated and will be removed in the future, use :yref:`GridConnection` instead. See :yref:`yade.gridpfacet.cylinder` and :yref:`yade.gridpfacet.cylinderConnection`. """ import warnings warnings.warn('\033[1;31mchainedCylinder is deprecated and will be removed in the future, use GridConnection instead.\033[1;0m',category=UserWarning) segment=end-begin b=Body() b.shape=ChainedCylinder(radius=radius,length=segment.norm(),color=color if color else utils.randomColor(),wire=wire,highlight=highlight) b.shape.segment=segment V=2*(4./3)*math.pi*radius**3 geomInert=(2./5.)*V*radius**2+b.shape.length*b.shape.length*2*(4./3)*math.pi*radius**3 b.state=ChainedState() b.state.addToChain(O.bodies.append(b)) utils._commonBodySetup(b,V,Vector3(geomInert,geomInert,geomInert),material,pos=begin,resetState=False,dynamic=dynamic,fixed=fixed) b.mask=mask b.bound=Aabb(color=[0,1,0]) b.state.ori.setFromTwoVectors(Vector3(0.,0.,1.),segment) if (end == begin): b.state.ori = Quaternion((1,0,0),0) return b def gridNode(center,radius,dynamic=None,fixed=False,wire=False,color=None,highlight=False,material=-1): """ Create a :yref:`GridNode` which is needed to set up :yref:`GridConnections`. See documentation of :yref:`yade.utils.sphere` for meaning of parameters. :return: Body object with the :yref:`gridNode` :yref:`shape`. """ b=Body() b.shape=GridNode(radius=radius,color=color if color else utils.randomColor(),wire=wire,highlight=highlight) #V=(4./3)*math.pi*radius**3 # will be overwritten by the connection V=0. geomInert=(2./5.)*V*radius**2 # will be overwritten by the connection utils._commonBodySetup(b,V,Vector3(geomInert,geomInert,geomInert),material,pos=center,dynamic=dynamic,fixed=fixed) b.aspherical=False b.bounded=False b.mask=0 # avoid contact detection with the nodes. Manual interaction will be set for them in "gridConnection" below. return b def gridConnection(id1,id2,radius,wire=False,color=None,highlight=False,material=-1,mask=1,cellDist=None): """ Create a :yref:`GridConnection` by connecting two :yref:`GridNodes`. :param id1,id2: the two :yref:`GridNodes` forming the cylinder. :param float radius: radius of the cylinder. Note that the radius needs to be the same as the one for the :yref:`GridNodes`. :param Vector3 cellDist: for periodic boundary conditions, see :yref:`Interaction.cellDist`. Note: periodic boundary conditions for gridConnections are not yet implemented! See documentation of :yref:`yade.utils.sphere` for meaning of other parameters. :return: Body object with the :yref:`GridConnection` :yref:`shape`. .. note:: The material of the :yref:`GridNodes` will be used to set the constitutive behaviour of the internal connection, i.e., the constitutive behaviour of the cylinder. The material of the :yref:`GridConnection` is used for interactions with other (external) bodies. """ b=Body() b.shape=GridConnection(radius=radius,color=color if color else utils.randomColor(),wire=wire,highlight=highlight) sph1=O.bodies[id1] ; sph2=O.bodies[id2] i=createInteraction(id1,id2) nodeMat=sph1.material b.shape.node1=sph1 ; b.shape.node2=sph2 sph1.shape.addConnection(b) ; sph2.shape.addConnection(b) if(O.periodic): if(cellDist!=None): i.cellDist=cellDist segt=sph2.state.pos + O.cell.hSize*i.cellDist - sph1.state.pos else: segt=sph2.state.pos - sph1.state.pos L=segt.norm() V=0.5*L*math.pi*radius**2 geomInert=(2./5.)*V*radius**2 utils._commonBodySetup(b,V,Vector3(geomInert,geomInert,geomInert),material,pos=sph1.state.pos,dynamic=False,fixed=True) sph1.state.mass = sph1.state.mass + V*nodeMat.density sph2.state.mass = sph2.state.mass + V*nodeMat.density for k in [0,1,2]: sph1.state.inertia[k] = sph1.state.inertia[k] + geomInert*nodeMat.density sph2.state.inertia[k] = sph2.state.inertia[k] + geomInert*nodeMat.density b.aspherical=False if O.periodic: i.phys.unp= -(sph2.state.pos + O.cell.hSize*i.cellDist - sph1.state.pos).norm() + sph1.shape.radius + sph2.shape.radius b.shape.periodic=True b.shape.cellDist=i.cellDist else: i.phys.unp= -(sph2.state.pos - sph1.state.pos).norm() + sph1.shape.radius + sph2.shape.radius i.geom.connectionBody=b I=math.pi*(2.*radius)**4/64. E=nodeMat.young i.phys.kn=E*math.pi*(radius**2)/L i.phys.kr=E*I/L i.phys.ks=12.*E*I/(L**3) G=E/(2.*(1+nodeMat.poisson)) i.phys.ktw=2.*I*G/L b.mask=mask return b #TODO: find a better way of handling the Id lists for checking duplicated gridNodes or gridConnections with the same coordinates etc. It would be better to handle this globally, maybe implement something like O.bodies.getGridNodes def cylinder(begin=Vector3(0,0,0),end=Vector3(1.,0.,0.),radius=0.2,nodesIds=[],cylIds=[],dynamic=None,fixed=False,wire=False,color=None,highlight=False,intMaterial=-1,extMaterial=-1,mask=1): """ Create a cylinder with given parameters. The shape corresponds to the Minkowski sum of line-segment and sphere, hence, the cylinder has rounded vertices. The cylinder (:yref:`GridConnection`) and its corresponding nodes (yref:`GridNodes`) are automatically added to the simulation. The lists with nodes and cylinder ids will be updated automatically. :param Vector3 begin: first point of the Minkowski sum in the global coordinate system. :param Vector3 end: last point of the Minkowski sum in the global coordinate system. :param Real radius: radius of sphere in the Minkowski sum. :param list nodesIds: list with ids of already existing :yref:`GridNodes`. New ids will be added. :param list cylIds: list with ids of already existing :yref:`GridConnections`. New id will be added. :param intMaterial: :yref:`Body.material` used to create the interaction physics between the two GridNodes :param extMaterial: :yref:`Body.material` used to create the interaction physics between the Cylinder (GridConnection) and other bodies (e.g., spheres interaction with the cylinder) See :yref:`yade.utils.sphere`'s documentation for meaning of other parameters. """ id1 = O.bodies.append( gridNode(begin,radius,dynamic=dynamic,fixed=fixed,wire=wire,color=color,highlight=highlight,material=intMaterial) ) nodesIds.append(id1) id2 = O.bodies.append( gridNode(end,radius,dynamic=dynamic,fixed=fixed,wire=wire,color=color,highlight=highlight,material=intMaterial) ) nodesIds.append(id2) cylIds.append(O.bodies.append( gridConnection(id1,id2,radius=radius,wire=wire,color=color,highlight=highlight,material=extMaterial,mask=mask,cellDist=None) )) def cylinderConnection(vertices,radius=0.2,nodesIds=[],cylIds=[],dynamic=None,fixed=False,wire=False,color=None,highlight=False,intMaterial=-1,extMaterial=-1,mask=1): """ Create a chain of cylinders with given parameters. The cylinders (:yref:`GridConnection`) and its corresponding nodes (yref:`GridNodes`) are automatically added to the simulation. The lists with nodes and cylinder ids will be updated automatically. :param [[Vector3]] vertices: coordinates of vertices to connect in the global coordinate system. See :yref:`yade.gridpfacet.cylinder` documentation for meaning of other parameters. """ # create all gridNodes first nodesIdsCC=[] for i in vertices: nodesIdsCC.append( O.bodies.append(gridNode(i,radius=radius, dynamic=dynamic,fixed=fixed,wire=wire,color=color,highlight=highlight,material=intMaterial)) ) nodesIds.extend(nodesIdsCC) # now create connection between the gridNodes for i,j in zip( nodesIdsCC[:-1], nodesIdsCC[1:]): cylIds.append( O.bodies.append( gridConnection(i,j,radius=radius, wire=wire,color=color,highlight=highlight,material=intMaterial,mask=mask,cellDist=None)) ) def pfacet(id1,id2,id3,wire=True,color=None,highlight=False,material=-1,mask=1,cellDist=None): """ Create a :yref:`PFacet` element from 3 :yref:`GridNodes` which are already connected via 3 :yref:`GridConnections`: :param id1,id2,id3: already with :yref:`GridConnections` connected :yref:`GridNodes` :param bool wire: if ``True``, top and bottom facet are shown as skeleton; otherwise facets are filled. :param Vector3-or-None color: color of the PFacet; random color will be assigned if ``None``. :param Vector3 cellDist: for periodic boundary conditions, see :yref:`Interaction.cellDist`. Note: periodic boundary conditions are not yet implemented for PFacets! See documentation of :yref:`yade.utils.sphere` for meaning of other parameters. :return: Body object with the :yref:`PFacet` :yref:`shape`. .. note:: :yref:`GridNodes` and :yref:`GridConnections` need to have the same radius. This is also the radius used to create the :yref:`PFacet` """ b=Body() GridN1=O.bodies[id1]; GridN2=O.bodies[id2]; GridN3=O.bodies[id3] b.shape=PFacet(color=color if color else randomColor(),wire=wire,highlight=highlight,node1=GridN1,node2=GridN2,node3=GridN3) GridN1.bounded=False; GridN2.bounded=False; GridN3.bounded=False GridC1=O.bodies[O.interactions[id1,id2].geom.connectionBody.id] GridC2=O.bodies[O.interactions[id2,id3].geom.connectionBody.id] GridC3=O.bodies[O.interactions[id1,id3].geom.connectionBody.id] GridC1.bounded=False GridC2.bounded=False GridC3.bounded=False b.shape.conn1=GridC1 b.shape.conn2=GridC2 b.shape.conn3=GridC3 b.shape.radius=GridN1.shape.radius GridC1.shape.addPFacet(b) GridC2.shape.addPFacet(b) GridC3.shape.addPFacet(b) GridN1.shape.addPFacet(b); GridN2.shape.addPFacet(b); GridN3.shape.addPFacet(b) V=0 utils._commonBodySetup(b,V,Vector3(0,0,0),material,pos=GridN1.state.pos,dynamic=False,fixed=True) b.aspherical=False # mass and inertia are lumped into the GridNodes b.mask=mask return b #TODO: find a better way of handling the Id lists for checking duplicated gridNodes or gridConnections with the same coordinates etc. It would be better to handle this globally, maybe implement something like O.bodies.getGridNodes def pfacetCreator1(vertices,radius,nodesIds=[],cylIds=[],pfIds=[],wire=False,fixed=True,materialNodes=-1,material=-1,color=None): """ Create a :yref:`PFacet` element from 3 vertices and automatically append to simulation. The function uses the vertices to create :yref:`GridNodes` and automatically checks for existing nodes. :param [Vector3,Vector3,Vector3] vertices: coordinates of vertices in the global coordinate system. :param float radius: radius used to create the :yref:`PFacets`. :param list nodesIds: list with ids of already existing :yref:`GridNodes`. New ids will be added. :param list cylIds: list with ids of already existing :yref:`GridConnections`. New ids will be added. :param list pfIds: list with ids of already existing :yref:`PFacets`. New ids will be added. :param materialNodes: specify :yref:`Body.material` of :yref:`GridNodes`. This material is used to make the internal connections. :param material: specify :yref:`Body.material` of :yref:`PFacets`. This material is used for interactions with external bodies. See documentation of :yref:`yade.utils.sphere` for meaning of other parameters. """ n=len(nodesIds) k=[0,0,0] f=[0,0,0] u=0 nod=0 for i in vertices: u=0 for j in nodesIds: if(i==O.bodies[j].state.pos): f[nod]=j k[nod]=1 u+=1 nod+=1 test=True #if(u==0): for GN in nodesIds: if(i==O.bodies[GN].state.pos): u=1 if(u==0): nodesIds.append( O.bodies.append(gridNode(i,radius,wire=wire,fixed=fixed,material=materialNodes,color=color)) ) if(k==[0,0,0]): pfacetCreator3(nodesIds[n],nodesIds[n+1],nodesIds[n+2],cylIds=cylIds,pfIds=pfIds,wire=wire,material=material,color=color,fixed=fixed ) if(k==[1,0,0]): pfacetCreator3(f[0],nodesIds[n],nodesIds[n+1],cylIds=cylIds,pfIds=pfIds,wire=wire,material=material,color=color,fixed=fixed ) if(k==[0,1,0]): pfacetCreator3(nodesIds[n],f[1],nodesIds[n+1],cylIds=cylIds,pfIds=pfIds,wire=wire,material=material,color=color,fixed=fixed ) if(k==[0,0,1]): pfacetCreator3(nodesIds[n],nodesIds[n+1],f[2],cylIds=cylIds,pfIds=pfIds,wire=wire,material=material,color=color,fixed=fixed ) if(k==[1,1,0]): pfacetCreator3(f[0],f[1],nodesIds[n],cylIds=cylIds,pfIds=pfIds,wire=wire,material=material,color=color,fixed=fixed ) if(k==[0,1,1]): pfacetCreator3(nodesIds[n],f[1],f[2],cylIds=cylIds,pfIds=pfIds,wire=wire,material=material,color=color,fixed=fixed ) if(k==[1,0,1]): pfacetCreator3(f[0],nodesIds[n],f[2],cylIds=cylIds,pfIds=pfIds,wire=wire,material=material,color=color,fixed=fixed ) if(k==[1,1,1]): pfacetCreator3(f[0],f[1],f[2],cylIds=cylIds,pfIds=pfIds,wire=wire,material=material,color=color,fixed=fixed ) def pfacetCreator2(id1,id2,vertex,radius,nodesIds=[],wire=True,materialNodes=-1,material=-1,color=None,fixed=True): """ Create a :yref:`PFacet` element from 2 already existing and connected :yref:`GridNodes` and one vertex. The element is automatically appended to the simulation. :param int id1,id2: ids of already with :yref:`GridConnection` connected :yref:`GridNodes`. :param Vector3 vertex: coordinates of the vertex in the global coordinate system. See documentation of :yref:`yade.gridpfacet.pfacetCreator1` for meaning of other parameters. """ n=len(nodesIds) nodesIds.append( O.bodies.append(gridNode(vertex,radius,wire=wire,fixed=fixed,material=materialNodes,color=color)) ) O.bodies.append(gridConnection(id1,nodesIds[n],radius=radius,material=materialNodes,color=color,wire=wire)) O.bodies.append(gridConnection(id2,nodesIds[n],radius=radius,material=materialNodes,color=color,wire=wire)) O.bodies.append(pfacet(id1,id2,nodesIds[n],wire=wire,material=material,color=color)) def pfacetCreator3(id1,id2,id3,cylIds=[],pfIds=[],wire=True,material=-1,color=None,fixed=True,mask=-1): """ Create a :yref:`PFacet` element from 3 already existing :yref:`GridNodes` which are not yet connected. The element is automatically appended to the simulation. :param int id1,id2,id3: id of the 3 :yref:`GridNodes` forming the :yref:`PFacet`. See documentation of :yref:`yade.gridpfacet.pfacetCreator1` for meaning of other parameters. """ radius=O.bodies[id1].shape.radius try: cylIds.append(O.bodies.append(gridConnection(id1,id2,radius=radius,material=material,color=color,wire=wire,mask=mask))) except: pass try: cylIds.append(O.bodies.append(gridConnection(id2,id3,radius=radius,material=material,color=color,wire=wire,mask=mask))) except: pass try: cylIds.append(O.bodies.append(gridConnection(id3,id1,radius=radius,material=material,color=color,wire=wire,mask=mask))) except: pass pfIds.append(O.bodies.append(pfacet(id1,id2,id3,wire=wire,material=material,color=color,mask=mask))) def pfacetCreator4(id1,id2,id3,pfIds=[],wire=True,material=-1,color=None,fixed=True,mask=-1): """ Create a :yref:`PFacet` element from 3 already existing :yref:`GridConnections`. The element is automatically appended to the simulation. :param int id1,id2,id3: id of the 3 :yref:`GridConnections` forming the :yref:`PFacet`. See documentation of :yref:`yade.gridpfacet.pfacetCreator1` for meaning of other parameters. """ radius=O.bodies[id1].shape.radius GridN=[] GridN1=O.bodies[id1].shape.node1.id GridN2=O.bodies[id1].shape.node2.id GridN.append(GridN1) GridN.append(GridN2) GridN1=O.bodies[id2].shape.node1.id if(GridN1 not in GridN): GridN.append(GridN1) GridN2=O.bodies[id2].shape.node2.id if(GridN2 not in GridN): GridN.append(GridN2) GridN1=O.bodies[id3].shape.node1.id if(GridN1 not in GridN): GridN.append(GridN1) GridN2=O.bodies[id3].shape.node2.id if(GridN2 not in GridN): GridN.append(GridN2) pfIds.append(O.bodies.append(pfacet(GridN[0],GridN[1],GridN[2],wire=wire,material=material,color=color,mask=mask))) def gtsPFacet(meshfile,shift=Vector3.Zero,scale=1.0, radius=1,wire=True,fixed=True,materialNodes=-1,material=-1,color=None): """ Imports mesh geometry from .gts file and automatically creates connected :yref:`PFacet3` elements. For an example see :ysrc:`examples/pfacet/gts-pfacet.py`. :param string filename: .gts file to read. :param [float,float,float] shift: [X,Y,Z] parameter shifts the mesh. :param float scale: factor scales the mesh. :param float radius: radius used to create the :yref:`PFacets`. :param materialNodes: specify :yref:`Body.material` of :yref:`GridNodes`. This material is used to make the internal connections. :param material: specify :yref:`Body.material` of :yref:`PFacets`. This material is used for interactions with external bodies. See documentation of :yref:`yade.utils.sphere` for meaning of other parameters. :returns: lists of :yref:`GridNode` ids `nodesIds`, :yref:`GridConnection` ids `cylIds`, and :yref:`PFacet` ids `pfIds` """ import gts,yade.pack surf=gts.read(open(meshfile)) surf.scale(scale,scale,scale) surf.translate(shift[0],shift[1],shift[2]) nodesIds=[]; cylIds=[]; pfIds=[] for face in surf.faces(): a=face.vertices()[0].coords() b=face.vertices()[1].coords() c=face.vertices()[2].coords() pfacetCreator1([a,b,c],radius=radius,nodesIds=nodesIds,cylIds=cylIds,pfIds=pfIds,wire=wire,fixed=fixed,materialNodes=materialNodes,material=material,color=color) #print a,b,c return nodesIds,cylIds,pfIds def gmshPFacet(meshfile="file.mesh",shift=Vector3.Zero,scale=1.0,orientation=Quaternion.Identity, radius=1.0,wire=True,fixed=True,materialNodes=-1,material=-1,color=None): """ Imports mesh geometry from .mesh file and automatically creates connected PFacet elements. For an example see :ysrc:`examples/pfacet/mesh-pfacet.py`. :param string filename: .gts file to read. :param [float,float,float] shift: [X,Y,Z] parameter shifts the mesh. :param float scale: factor scales the mesh. :param quaternion orientation: orientation of the imported geometry. :param float radius: radius used to create the :yref:`PFacets`. :param materialNodes: specify :yref:`Body.material` of :yref:`GridNodes`. This material is used to make the internal connections. :param material: specify :yref:`Body.material` of :yref:`PFacets`. This material is used for interactions with external bodies. See documentation of :yref:`yade.utils.sphere` for meaning of other parameters. :returns: lists of :yref:`GridNode` ids `nodesIds`, :yref:`GridConnection` ids `cylIds`, and :yref:`PFacet` ids `pfIds` mesh files can easily be created with `GMSH `_. Additional examples of mesh-files can be downloaded from http://www-roc.inria.fr/gamma/download/download.php """ infile = open(meshfile,"r") lines = infile.readlines() infile.close() nodelistVector3=[] findVerticesString=0 while (lines[findVerticesString].split()[0]<>'Vertices'): # find the string with the number of Vertices findVerticesString+=1 findVerticesString+=1 numNodes = int(lines[findVerticesString].split()[0]) for i in range(numNodes): nodelistVector3.append(Vector3(0.0,0.0,0.0)) id = 0 for line in lines[findVerticesString+1:numNodes+findVerticesString+1]: data = line.split() nodelistVector3[id] = orientation*Vector3(float(data[0])*scale,float(data[1])*scale,float(data[2])*scale)+shift id += 1 findTriangleString=findVerticesString+numNodes while (lines[findTriangleString].split()[0]<>'Triangles'): # find the string with the number of Triangles findTriangleString+=1 findTriangleString+=1 numTriangles = int(lines[findTriangleString].split()[0]) triList = [] for i in range(numTriangles): triList.append([0,0,0,0]) tid = 0 for line in lines[findTriangleString+1:findTriangleString+numTriangles+1]: data = line.split() id1 = int(data[0])-1 id2 = int(data[1])-1 id3 = int(data[2])-1 triList[tid][0] = tid triList[tid][1] = id1 triList[tid][2] = id2 triList[tid][3] = id3 tid += 1 nodesIds=[]; cylIds=[]; pfIds=[] for i in triList: a=nodelistVector3[i[1]] b=nodelistVector3[i[2]] c=nodelistVector3[i[3]] #print 'i',i #print 'a',a #print 'b',b #print 'c',c try: pfacetCreator1([a,b,c],radius=radius,nodesIds=nodesIds,cylIds=cylIds,pfIds=pfIds, wire=wire,fixed=fixed,materialNodes=materialNodes,material=material,color=color) except: pass return nodesIds,cylIds,pfIds trunk-2017.01a/py/linterpolation.py000066400000000000000000000070001304022710500172240ustar00rootroot00000000000000# encoding: utf-8 # # © 2009 Václav Šmilauer # """ Module for rudimentary support of manipulation with piecewise-linear functions (which are usually interpolations of higher-order functions, whence the module name). Interpolation is always given as two lists of the same length, where the x-list must be increasing. Periodicity is supported by supposing that the interpolation can wrap from the last x-value to the first x-value (which should be 0 for meaningful results). Non-periodic interpolation can be converted to periodic one by padding the interpolation with constant head and tail using the sanitizeInterpolation function. There is a c++ template function for interpolating on such sequences in pkg/common/Engine/PartialEngine/LinearInterpolate.hpp (stateful, therefore fast for sequential reads). TODO: Interpolating from within python is not (yet) supported. """ def revIntegrateLinear(I,x0,y0,x1,y1): """Helper function, returns value of integral variable x for linear function f passing through (x0,y0),(x1,y1) such that 1. x∈[x0,x1] 2. ∫_x0^x f dx=I and raise exception if such number doesn't exist or the solution is not unique (possible?) """ from math import sqrt dx,dy=x1-x0,y1-y0 if dy==0: # special case, degenerates to linear equation return (x0*y0+I)/y0 a=dy/dx; b=2*(y0-x0*dy/dx); c=x0**2*dy/dx-2*x0*y0-2*I det=b**2-4*a*c; assert(det>0) p,q=(-b+sqrt(det))/(2*a),(-b-sqrt(det))/(2*a) pOK,qOK=x0<=p<=x1,x0<=q<=x1 if pOK and qOK: raise ValueError("Both radices within interval!?") if not pOK and not qOK: raise ValueError("No radix in given interval!") return p if pOK else q def integral(x,y): """Return integral of piecewise-linear function given by points x0,x1,… and y0,y1,… """ assert(len(x)==len(y)) sum=0 for i in range(1,len(x)): sum+=(x[i]-x[i-1])*.5*(y[i]+y[i-1]) return sum def xFractionalFromIntegral(integral,x,y): """Return x within range x0…xn such that ∫_x0^x f dx==integral. Raises error if the integral value is not reached within the x-range. """ sum=0 for i in range(1,len(x)): diff=(x[i]-x[i-1])*.5*(y[i]+y[i-1]) if sum+diff>integral: return revIntegrateLinear(integral-sum,x[i-1],y[i-1],x[i],y[i]) else: sum+=diff raise "Integral not reached within the interpolation range!" def xFromIntegral(integralValue,x,y): """Return x such that ∫_x0^x f dx==integral. x wraps around at xn. For meaningful results, therefore, x0 should == 0 """ from math import floor period=x[-1]-x[0] periodIntegral=integral(x,y) numPeriods=floor(integralValue/periodIntegral) xFrac=xFractionalFromIntegral(integralValue-numPeriods*periodIntegral,x,y) #print '### wanted _%g; period=%g; periodIntegral=_%g (numPeriods=%g); rests _%g (xFrac=%g)'%(integralValue,period,periodIntegral,numPeriods,integralValue-numPeriods*periodIntegral,xFrac) #print '### returning %g*%g+%g=%g'%(period,numPeriods,xFrac,period*numPeriods+xFrac) return period*numPeriods+xFrac def sanitizeInterpolation(x,y,x0,x1): """Extends piecewise-linear function in such way that it spans at least the x0…x1 interval, by adding constant padding at the beginning (using y0) and/or at the end (using y1) or not at all.""" xx,yy=[],[] if x0x[-1]: xx+=[x1]; yy+=[y[-1]] return xx,yy if __name__=="main": xx,yy=sanitizeInterpolation([1,2,3],[1,1,2],0,4) print xx,yy print integral(xx,yy) # 5.5 print revIntegrateLinear(.625,1,1,2,2) # 1.5 print xFractionalFromIntegral(1.625,xx,yy) # 1.625 print xFractionalFromIntegral(2.625,xx,yy) # 2.5 trunk-2017.01a/py/pack/000077500000000000000000000000001304022710500145305ustar00rootroot00000000000000trunk-2017.01a/py/pack/_packObb.cpp000066400000000000000000000050721304022710500167400ustar00rootroot00000000000000// many thanks to http://codesuppository.blogspot.com/2006_06_01_archive.html // the code written after http://www.amillionpixels.us/bestfitobb.cpp // which is MIT-licensed #include #include #include // compute minimum bounding for a cloud of points // returns volume Real computeOBB(const std::vector& pts, const Matrix3r& rot, Vector3r& center, Vector3r& halfSize){ const Real inf=std::numeric_limits::infinity(); Vector3r mn(inf,inf,inf), mx(-inf,-inf,-inf); FOREACH(const Vector3r& pt, pts){ Vector3r ptT=rot*pt; mn=mn.cwiseMin(ptT); mx=mx.cwiseMax(ptT); } halfSize=.5*(mx-mn); center=.5*(mn+mx); return 8*halfSize[0]*halfSize[1]*halfSize[2]; } void bestFitOBB(const std::vector& pts, Vector3r& center, Vector3r& halfSize, Quaternionr& rot){ Vector3r angle0(Vector3r::Zero()), angle(Vector3r::Zero()); Vector3r center0; Vector3r halfSize0; Real bestVolume=std::numeric_limits::infinity(); Real sweep=Mathr::PI/4; Real steps=7.; while(sweep>=Mathr::PI/180.){ bool found=false; Real stepSize=sweep/steps; for(Real x=angle0[0]-sweep; x<=angle0[0]+sweep; x+=stepSize){ for(Real y=angle0[1]-sweep; y pts; pts.resize(l); for(int i=0; i(_pts[i]); Quaternionr rot; Vector3r halfSize, center; bestFitOBB(pts,center,halfSize,rot); return boost::python::make_tuple(center,halfSize,rot); } BOOST_PYTHON_MODULE(_packObb){ YADE_SET_DOCSTRING_OPTS; boost::python::scope().attr("__doc__")="Computation of oriented bounding box for cloud of points."; boost::python::def("cloudBestFitOBB",bestFitOBB_py,"Return (Vector3 center, Vector3 halfSize, Quaternion orientation) of\nbest-fit oriented bounding-box for given tuple of points\n(uses brute-force velome minimization, do not use for very large clouds)."); }; trunk-2017.01a/py/pack/_packPredicates.cpp000066400000000000000000000446611304022710500203300ustar00rootroot00000000000000// 2009 © Václav Šmilauer #include #include #include namespace py=boost::python; /* This file contains various predicates that say whether a given point is within the solid, or, not closer than "pad" to its boundary, if pad is nonzero Besides the (point,pad) operator, each predicate defines aabb() method that returns (min,max) tuple defining minimum and maximum point of axis-aligned bounding box for the predicate. These classes are primarily used for yade.pack.* functions creating packings. See examples/regular-sphere-pack/regular-sphere-pack.py for an example. */ // aux functions void ttuple2vvec(const py::tuple& t, Vector3r& v1, Vector3r& v2){ v1=py::extract(t[0])(); v2=py::extract(t[1])(); } // do not use make_tuple directly on vector ops, since their type can be something like Eigen::CwiseBinaryOp<...> py::tuple vvec2tuple(const Vector3r& a, const Vector3r& b){ return py::make_tuple(a,b); } struct Predicate{ public: virtual bool operator() (const Vector3r& pt,Real pad=0.) const = 0; virtual py::tuple aabb() const = 0; Vector3r dim() const { Vector3r mn,mx; ttuple2vvec(aabb(),mn,mx); return (mx-mn).eval(); } Vector3r center() const { Vector3r mn,mx; ttuple2vvec(aabb(),mn,mx); return .5*(mn+mx); } }; struct PredicateWrap: Predicate, py::wrapper{ bool operator()(const Vector3r& pt, Real pad=0.) const { return this->get_override("__call__")(pt,pad);} py::tuple aabb() const { return this->get_override("aabb")(); } }; /********************************************************************************* ****************** Boolean operations on predicates ****************************** *********************************************************************************/ const Predicate& obj2pred(py::object obj){ return py::extract(obj)();} class PredicateBoolean: public Predicate{ protected: const py::object A,B; public: PredicateBoolean(const py::object _A, const py::object _B): A(_A), B(_B){} const py::object getA(){ return A;} const py::object getB(){ return B;} }; // http://www.linuxtopia.org/online_books/programming_books/python_programming/python_ch16s03.html class PredicateUnion: public PredicateBoolean{ public: PredicateUnion(const py::object _A, const py::object _B): PredicateBoolean(_A,_B){} virtual bool operator()(const Vector3r& pt,Real pad) const {return obj2pred(A)(pt,pad)||obj2pred(B)(pt,pad);} virtual py::tuple aabb() const { Vector3r minA,maxA,minB,maxB; ttuple2vvec(obj2pred(A).aabb(),minA,maxA); ttuple2vvec(obj2pred(B).aabb(),minB,maxB); return vvec2tuple(minA.cwiseMin(minB),maxA.cwiseMax(maxB)); } }; PredicateUnion makeUnion(const py::object& A, const py::object& B){ return PredicateUnion(A,B);} class PredicateIntersection: public PredicateBoolean{ public: PredicateIntersection(const py::object _A, const py::object _B): PredicateBoolean(_A,_B){} virtual bool operator()(const Vector3r& pt,Real pad) const {return obj2pred(A)(pt,pad) && obj2pred(B)(pt,pad);} virtual py::tuple aabb() const { Vector3r minA,maxA,minB,maxB; ttuple2vvec(obj2pred(A).aabb(),minA,maxA); ttuple2vvec(obj2pred(B).aabb(),minB,maxB); return vvec2tuple(minA.cwiseMax(minB),maxA.cwiseMin(maxB)); } }; PredicateIntersection makeIntersection(const py::object& A, const py::object& B){ return PredicateIntersection(A,B);} class PredicateDifference: public PredicateBoolean{ public: PredicateDifference(const py::object _A, const py::object _B): PredicateBoolean(_A,_B){} virtual bool operator()(const Vector3r& pt,Real pad) const {return obj2pred(A)(pt,pad) && !obj2pred(B)(pt,-pad);} virtual py::tuple aabb() const { return obj2pred(A).aabb(); } }; PredicateDifference makeDifference(const py::object& A, const py::object& B){ return PredicateDifference(A,B);} class PredicateSymmetricDifference: public PredicateBoolean{ public: PredicateSymmetricDifference(const py::object _A, const py::object _B): PredicateBoolean(_A,_B){} virtual bool operator()(const Vector3r& pt,Real pad) const {bool inA=obj2pred(A)(pt,pad), inB=obj2pred(B)(pt,pad); return (inA && !inB) || (!inA && inB);} virtual py::tuple aabb() const { Vector3r minA,maxA,minB,maxB; ttuple2vvec(obj2pred(A).aabb(),minA,maxA); ttuple2vvec(obj2pred(B).aabb(),minB,maxB); return vvec2tuple(minA.cwiseMin(minB),maxA.cwiseMax(maxB)); } }; PredicateSymmetricDifference makeSymmetricDifference(const py::object& A, const py::object& B){ return PredicateSymmetricDifference(A,B);} /********************************************************************************* ****************************** Primitive predicates ****************************** *********************************************************************************/ /*! Sphere predicate */ class inSphere: public Predicate { Vector3r center; Real radius; public: inSphere(const Vector3r& _center, Real _radius){center=_center; radius=_radius;} virtual bool operator()(const Vector3r& pt, Real pad=0.) const { return ((pt-center).norm()<=radius-pad); } virtual py::tuple aabb() const {return vvec2tuple(Vector3r(center[0]-radius,center[1]-radius,center[2]-radius),Vector3r(center[0]+radius,center[1]+radius,center[2]+radius));} }; /*! Axis-aligned box predicate */ class inAlignedBox: public Predicate{ Vector3r mn, mx; public: inAlignedBox(const Vector3r& _mn, const Vector3r& _mx): mn(_mn), mx(_mx) {} virtual bool operator()(const Vector3r& pt, Real pad=0.) const { return mn[0]+pad<=pt[0] && mx[0]-pad>=pt[0] && mn[1]+pad<=pt[1] && mx[1]-pad>=pt[1] && mn[2]+pad<=pt[2] && mx[2]-pad>=pt[2]; } virtual py::tuple aabb() const { return vvec2tuple(mn,mx); } }; class inParallelepiped: public Predicate{ Vector3r n[6]; // outer normals, for -x, +x, -y, +y, -z, +z Vector3r pts[6]; // points on planes Vector3r mn,mx; public: inParallelepiped(const Vector3r& o, const Vector3r& a, const Vector3r& b, const Vector3r& c){ Vector3r A(o), B(a), C(a+(b-o)), D(b), E(c), F(c+(a-o)), G(c+(a-o)+(b-o)), H(c+(b-o)); Vector3r x(B-A), y(D-A), z(E-A); n[0]=-y.cross(z).normalized(); n[1]=-n[0]; pts[0]=A; pts[1]=B; n[2]=-z.cross(x).normalized(); n[3]=-n[2]; pts[2]=A; pts[3]=D; n[4]=-x.cross(y).normalized(); n[5]=-n[4]; pts[4]=A; pts[5]=E; // bounding box Vector3r vertices[8]={A,B,C,D,E,F,G,H}; mn=mx=vertices[0]; for(int i=1; i<8; i++){ mn=mn.cwiseMin(vertices[i]); mx=mx.cwiseMax(vertices[i]); } } virtual bool operator()(const Vector3r& pt, Real pad=0.) const { for(int i=0; i<6; i++) if((pt-pts[i]).dot(n[i])>-pad) return false; return true; } virtual py::tuple aabb() const { return vvec2tuple(mn,mx); } }; /*! Arbitrarily oriented cylinder predicate */ class inCylinder: public Predicate{ Vector3r c1,c2,c12; Real radius,ht; public: inCylinder(const Vector3r& _c1, const Vector3r& _c2, Real _radius){c1=_c1; c2=_c2; c12=c2-c1; radius=_radius; ht=c12.norm(); } bool operator()(const Vector3r& pt, Real pad=0.) const { Real u=(pt.dot(c12)-c1.dot(c12))/(ht*ht); // normalized coordinate along the c1--c2 axis if((u*ht<0+pad) || (u*ht>ht-pad)) return false; // out of cylinder along the axis Real axisDist=((pt-c1).cross(pt-c2)).norm()/ht; if(axisDist>radius-pad) return false; return true; } py::tuple aabb() const { // see http://www.gamedev.net/community/forums/topic.asp?topic_id=338522&forum_id=20&gforum_id=0 for the algorithm const Vector3r& A(c1); const Vector3r& B(c2); Vector3r k( sqrt((pow(A[1]-B[1],2)+pow(A[2]-B[2],2)))/ht, sqrt((pow(A[0]-B[0],2)+pow(A[2]-B[2],2)))/ht, sqrt((pow(A[0]-B[0],2)+pow(A[1]-B[1],2)))/ht); Vector3r mn=A.cwiseMin(B), mx=A.cwiseMax(B); return vvec2tuple((mn-radius*k).eval(),(mx+radius*k).eval()); } }; /*! Oriented hyperboloid predicate (cylinder as special case). See http://mathworld.wolfram.com/Hyperboloid.html for the parametrization and meaning of symbols */ class inHyperboloid: public Predicate{ Vector3r c1,c2,c12; Real R,a,ht,c; public: inHyperboloid(const Vector3r& _c1, const Vector3r& _c2, Real _R, Real _r){ c1=_c1; c2=_c2; R=_R; a=_r; c12=c2-c1; ht=c12.norm(); Real uMax=sqrt(pow(R/a,2)-1); c=ht/(2*uMax); } // WARN: this is not accurate, since padding is taken as perpendicular to the axis, not the the surface bool operator()(const Vector3r& pt, Real pad=0.) const { Real v=(pt.dot(c12)-c1.dot(c12))/(ht*ht); // normalized coordinate along the c1--c2 axis if((v*ht<0+pad) || (v*ht>ht-pad)) return false; // out of cylinder along the axis Real u=(v-.5)*ht/c; // u from the wolfram parametrization; u is 0 in the center Real rHere=a*sqrt(1+u*u); // pad is taken perpendicular to the axis, not to the surface (inaccurate) Real axisDist=((pt-c1).cross(pt-c2)).norm()/ht; if(axisDist>rHere-pad) return false; return true; } py::tuple aabb() const { // the lazy way return inCylinder(c1,c2,R).aabb(); } }; /*! Axis-aligned ellipsoid predicate */ class inEllipsoid: public Predicate{ Vector3r c, abc; public: inEllipsoid(const Vector3r& _c, const Vector3r& _abc) {c=_c; abc=_abc;} bool operator()(const Vector3r& pt, Real pad=0.) const { //Define the ellipsoid X-coordinate of given Y and Z Real x = sqrt((1-pow((pt[1]-c[1]),2)/((abc[1]-pad)*(abc[1]-pad))-pow((pt[2]-c[2]),2)/((abc[2]-pad)*(abc[2]-pad)))*((abc[0]-pad)*(abc[0]-pad)))+c[0]; Vector3r edgeEllipsoid(x,pt[1],pt[2]); // create a vector of these 3 coordinates //check whether given coordinates lie inside ellipsoid or not if ((pt-c).norm()<=(edgeEllipsoid-c).norm()) return true; else return false; } py::tuple aabb() const { const Vector3r& center(c); const Vector3r& ABC(abc); return vvec2tuple(Vector3r(center[0]-ABC[0],center[1]-ABC[1],center[2]-ABC[2]),Vector3r(center[0]+ABC[0],center[1]+ABC[1],center[2]+ABC[2])); } }; /*! Negative notch predicate. Use intersection (& operator) of another predicate with notInNotch to create notched solid. geometry explanation: c: the center normalHalfHt (in constructor): A-C inside: perpendicular to notch edge, points inside the notch (unit vector) normal: perpendicular to inside, perpendicular to both notch planes edge: unit vector in the direction of the edge ↑ distUp A ------------------------- | C inside(unit) ← * → distInPlane | ------------------------- ↓ distDown B */ class notInNotch: public Predicate{ Vector3r c, edge, normal, inside; Real aperture; public: notInNotch(const Vector3r& _c, const Vector3r& _edge, const Vector3r& _normal, Real _aperture){ c=_c; edge=_edge; edge.normalize(); normal=_normal; normal-=edge*edge.dot(normal); normal.normalize(); inside=edge.cross(normal); aperture=_aperture; // LOG_DEBUG("edge="< *bb) { GtsPoint *_p=GTS_POINT(vertex); Vector3r p(_p->x,_p->y,_p->z); bb->first=bb->first.cwiseMin(p); bb->second=bb->second.cwiseMax(p); } /* This class plays tricks getting around pyGTS to get GTS objects and cache bb tree to speed up point inclusion tests. For this reason, we have to link with _gts.so (see corresponding SConscript file), which is at the same time the python module. */ class inGtsSurface: public Predicate{ py::object pySurf; // to hold the reference so that surf is valid GtsSurface *surf; bool is_open, noPad, noPadWarned; GNode* tree; public: inGtsSurface(py::object _surf, bool _noPad=false): pySurf(_surf), noPad(_noPad), noPadWarned(false) { if(!pygts_surface_check(_surf.ptr())) throw std::invalid_argument("Ctor must receive a gts.Surface() instance."); surf=PYGTS_SURFACE_AS_GTS_SURFACE(PYGTS_SURFACE(_surf.ptr())); if(!gts_surface_is_closed(surf)) throw std::invalid_argument("Surface is not closed."); is_open=gts_surface_volume(surf)<0.; if((tree=gts_bb_tree_surface(surf))==NULL) throw std::runtime_error("Could not create GTree."); } ~inGtsSurface(){g_node_destroy(tree);} py::tuple aabb() const { Real inf=std::numeric_limits::infinity(); std::pair bb; bb.first=Vector3r(inf,inf,inf); bb.second=Vector3r(-inf,-inf,-inf); gts_surface_foreach_vertex(surf,(GtsFunc)vertex_aabb,&bb); return vvec2tuple(bb.first,bb.second); } bool ptCheck(const Vector3r& pt) const{ GtsPoint gp; gp.x=pt[0]; gp.y=pt[1]; gp.z=pt[2]; return (bool)gts_point_is_inside_surface(&gp,tree,is_open); } bool operator()(const Vector3r& pt, Real pad=0.) const { if(noPad){ if(pad!=0. && noPadWarned) LOG_WARN("inGtsSurface constructed with noPad; requested non-zero pad set to zero."); return ptCheck(pt); } return ptCheck(pt) && ptCheck(pt-Vector3r(pad,0,0)) && ptCheck(pt+Vector3r(pad,0,0)) && ptCheck(pt-Vector3r(0,pad,0))&& ptCheck(pt+Vector3r(0,pad,0)) && ptCheck(pt-Vector3r(0,0,pad))&& ptCheck(pt+Vector3r(0,0,pad)); } py::object surface() const {return pySurf;} }; #endif BOOST_PYTHON_MODULE(_packPredicates){ py::scope().attr("__doc__")="Spatial predicates for volumes (defined analytically or by triangulation)."; YADE_SET_DOCSTRING_OPTS; // base predicate class py::class_("Predicate") .def("__call__",py::pure_virtual(&Predicate::operator())) .def("aabb",py::pure_virtual(&Predicate::aabb)) .def("dim",&Predicate::dim) .def("center",&Predicate::center) .def("__or__",makeUnion).def("__and__",makeIntersection).def("__sub__",makeDifference).def("__xor__",makeSymmetricDifference); // boolean operations py::class_,boost::noncopyable>("PredicateBoolean","Boolean operation on 2 predicates (abstract class)",py::no_init) .add_property("A",&PredicateBoolean::getA).add_property("B",&PredicateBoolean::getB); py::class_ >("PredicateUnion","Union (non-exclusive disjunction) of 2 predicates. A point has to be inside any of the two predicates to be inside. Can be constructed using the ``|`` operator on predicates: ``pred1 | pred2``.",py::init()); py::class_ >("PredicateIntersection","Intersection (conjunction) of 2 predicates. A point has to be inside both predicates. Can be constructed using the ``&`` operator on predicates: ``pred1 & pred2``.",py::init()); py::class_ >("PredicateDifference","Difference (conjunction with negative predicate) of 2 predicates. A point has to be inside the first and outside the second predicate. Can be constructed using the ``-`` operator on predicates: ``pred1 - pred2``.",py::init()); py::class_ >("PredicateSymmetricDifference","SymmetricDifference (exclusive disjunction) of 2 predicates. A point has to be in exactly one predicate of the two. Can be constructed using the ``^`` operator on predicates: ``pred1 ^ pred2``.",py::init()); // primitive predicates py::class_ >("inSphere","Sphere predicate.",py::init(py::args("center","radius"),"Ctor taking center (as a 3-tuple) and radius")); py::class_ >("inAlignedBox","Axis-aligned box predicate",py::init(py::args("minAABB","maxAABB"),"Ctor taking minumum and maximum points of the box (as 3-tuples).")); py::class_ >("inParallelepiped","Parallelepiped predicate",py::init(py::args("o","a","b","c"),"Ctor taking four points: ``o`` (for origin) and then ``a``, ``b``, ``c`` which define endpoints of 3 respective edges from ``o``.")); py::class_ >("inCylinder","Cylinder predicate",py::init(py::args("centerBottom","centerTop","radius"),"Ctor taking centers of the lateral walls (as 3-tuples) and radius.")); py::class_ >("inHyperboloid","Hyperboloid predicate",py::init(py::args("centerBottom","centerTop","radius","skirt"),"Ctor taking centers of the lateral walls (as 3-tuples), radius at bases and skirt (middle radius).")); py::class_ >("inEllipsoid","Ellipsoid predicate",py::init(py::args("centerPoint","abc"),"Ctor taking center of the ellipsoid (3-tuple) and its 3 radii (3-tuple).")); py::class_ >("notInNotch","Outside of infinite, rectangle-shaped notch predicate",py::init(py::args("centerPoint","edge","normal","aperture"),"Ctor taking point in the symmetry plane, vector pointing along the edge, plane normal and aperture size.\nThe side inside the notch is edge×normal.\nNormal is made perpendicular to the edge.\nAll vectors are normalized at construction time.")); #ifdef YADE_GTS py::class_ >("inGtsSurface","GTS surface predicate",py::init >(py::args("surface","noPad"),"Ctor taking a gts.Surface() instance, which must not be modified during instance lifetime.\nThe optional noPad can disable padding (if set to True), which speeds up calls several times.\nNote: padding checks inclusion of 6 points along +- cardinal directions in the pad distance from given point, which is not exact.")) .add_property("surf",&inGtsSurface::surface,"The associated gts.Surface object."); #endif } trunk-2017.01a/py/pack/_packSpheres.cpp000066400000000000000000000265041304022710500176520ustar00rootroot00000000000000// 2009 © Václav Šmilauer #include #include #include BOOST_PYTHON_MODULE(_packSpheres){ boost::python::scope().attr("__doc__")="Creation, manipulation, IO for generic sphere packings."; YADE_SET_DOCSTRING_OPTS; boost::python::class_("SpherePack","Set of spheres represented as centers and radii. This class is returned by :yref:`yade.pack.randomDensePack`, :yref:`yade.pack.randomPeriPack` and others. The object supports iteration over spheres, as in \n\n\t>>> sp=SpherePack()\n\t>>> for center,radius in sp: print center,radius\n\n\t>>> for sphere in sp: print sphere[0],sphere[1] ## same, but without unpacking the tuple automatically\n\n\t>>> for i in range(0,len(sp)): print sp[i][0], sp[i][1] ## same, but accessing spheres by index\n\n\n.. admonition:: Special constructors\n\n\tConstruct from list of ``[(c1,r1),(c2,r2),…]``. To convert two same-length lists of ``centers`` and ``radii``, construct with ``zip(centers,radii)``.\n",boost::python::init >(boost::python::args("list"),"Empty constructor, optionally taking list [ ((cx,cy,cz),r), … ] for initial data." )) .def("add",&SpherePack::add,"Add single sphere to packing, given center as 3-tuple and radius") .def("toList",&SpherePack::toList,"Return packing data as python list.") .def("fromList",&SpherePack::fromList,"Make packing from given list, same format as for constructor. Discards current data.") .def("fromList",&SpherePack::fromLists,(boost::python::arg("centers"),boost::python::arg("radii")),"Make packing from given list, same format as for constructor. Discards current data.") .def("load",&SpherePack::fromFile,(boost::python::arg("fileName")),"Load packing from external text file (current data will be discarded).") .def("save",&SpherePack::toFile,(boost::python::arg("fileName")),"Save packing to external text file (will be overwritten).") .def("fromSimulation",&SpherePack::fromSimulation,"Make packing corresponding to the current simulation. Discards current data.") //The basic sphere generator .def("makeCloud",&SpherePack::makeCloud,(boost::python::arg("minCorner")=Vector3r(Vector3r::Zero()),boost::python::arg("maxCorner")=Vector3r(Vector3r::Zero()),boost::python::arg("rMean")=-1,boost::python::arg("rRelFuzz")=0,boost::python::arg("num")=-1,boost::python::arg("periodic")=false,boost::python::arg("porosity")=0.65,boost::python::arg("psdSizes")=vector(),boost::python::arg("psdCumm")=vector(),boost::python::arg("distributeMass")=false,boost::python::arg("seed")=0,boost::python::arg("hSize")=Matrix3r(Matrix3r::Zero())),"Create random very loose packing enclosed in a parallelepiped (also works in 2D if minCorner[k]=maxCorner[k] for one coordinate). The resulting packing conforms in fact a gas-like state (see Cloud denomination) with no contacts between particles. Usually used as a first step for packing generation, before subsequent mechanical loading that will confer a solid-like nature to the packing." "\nSphere radius distribution can be specified using one of the following ways:\n\n#. *rMean*, *rRelFuzz* and *num* gives uniform radius distribution in *rMean×(1 ± rRelFuzz)*. Less than *num* spheres can be generated if it is too high.\n#. *rRelFuzz*, *num* and (optional) *porosity*, which estimates mean radius so that *porosity* is attained at the end. *rMean* must be less than 0 (default). *porosity* is only an initial guess for the generation algorithm, which will retry with higher porosity until the prescibed *num* is obtained.\n#. *psdSizes* and *psdCumm*, two arrays specifying points of the `particle size distribution `__ function. As many spheres as possible are generated.\n#. *psdSizes*, *psdCumm*, *num*, and (optional) *porosity*, like above but if *num* is not obtained, *psdSizes* will be scaled down uniformly, until *num* is obtained (see :yref:`appliedPsdScaling`).\n\nBy default (with ``distributeMass==False``), the distribution is applied to particle radii. The usual sense of \"particle size distribution\" is the distribution of *mass fraction* (rather than particle count); this can be achieved with ``distributeMass=True``." "\n\nIf *num* is defined, then sizes generation is deterministic, giving the best fit of target distribution. It enables spheres placement in descending size order, thus giving lower porosity than the random generation." "\n\n:param Vector3 minCorner: lower corner of an axis-aligned box\n:param Vector3 maxCorner: upper corner of an axis-aligned box\n:param Matrix3 hSize: base vectors of a generalized box (arbitrary parallelepiped, typically :yref:`Cell::hSize`), superseeds minCorner and maxCorner if defined. For periodic boundaries only.\n:param float rMean: mean radius or spheres\n:param float rRelFuzz: dispersion of radius relative to rMean\n:param int num: number of spheres to be generated. If negavite (default), generate as many as possible with stochastic sizes, ending after a fixed number of tries to place the sphere in space, else generate exactly *num* spheres with deterministic size distribution.\n:param bool periodic: whether the packing to be generated should be periodic\n:param float porosity: initial guess for the iterative generation procedure (if *num*>1). The algorithm will be retrying until the number of generated spheres is *num*. The first iteration tries with the provided porosity, but next iterations increase it if necessary (hence an initialy high porosity can speed-up the algorithm). If *psdSizes* is not defined, *rRelFuzz* ($z$) and *num* ($N$) are used so that the porosity given ($\\rho$) is approximately achieved at the end of generation, $r_m=\\sqrt[3]{\\frac{V(1-\\rho)}{\\frac{4}{3}\\pi(1+z^2)N}}$. The default is $\\rho$=0.5. The optimal value depends on *rRelFuzz* or *psdSizes*.\n:param psdSizes: sieve sizes (particle diameters) when particle size distribution (PSD) is specified\n:param psdCumm: cummulative fractions of particle sizes given by *psdSizes*; must be the same length as *psdSizes* and should be non-decreasing\n:param bool distributeMass: if ``True``, given distribution will be used to distribute sphere's mass rather than radius of them.\n:param seed: number used to initialize the random number generator.\n:returns: number of created spheres, which can be lower than *num* depending on the method used.\n") .def("psd",&SpherePack::psd,(boost::python::arg("bins")=50,boost::python::arg("mass")=true),"Return `particle size distribution `__ of the packing.\n:param int bins: number of bins between minimum and maximum diameter\n:param mass: Compute relative mass rather than relative particle count for each bin. Corresponds to :yref:`distributeMass parameter for makeCloud`.\n:returns: tuple of ``(cumm,edges)``, where ``cumm`` are cummulative fractions for respective diameters and ``edges`` are those diameter values. Dimension of both arrays is equal to ``bins+1``.") //The variant for clumps .def("makeClumpCloud",&SpherePack::makeClumpCloud,(boost::python::arg("minCorner"),boost::python::arg("maxCorner"),boost::python::arg("clumps"),boost::python::arg("periodic")=false,boost::python::arg("num")=-1,boost::python::arg("seed")=0),"Create random loose packing of clumps within box given by *minCorner* and *maxCorner*. Clumps are selected with equal probability. At most *num* clumps will be positioned if *num* is positive; otherwise, as many clumps as possible will be put in space, until maximum number of attempts to place a new clump randomly is attained.\n:param seed: number used to initialize the random number generator.") // old unmaintained stuff, kept for the moment so it at least returns an error message .def("particleSD",&SpherePack::particleSD,(boost::python::arg("minCorner"),boost::python::arg("maxCorner"),boost::python::arg("rMean"),boost::python::arg("periodic")=false,boost::python::arg("name"),boost::python::arg("numSph"),boost::python::arg("radii")=vector(),boost::python::arg("passing")=vector(),boost::python::arg("passingIsNotPercentageButCount")=false, boost::python::arg("seed")=0),"Not working. Use makeCloud instead.") .def("particleSD2",&SpherePack::particleSD2,(boost::python::arg("radii"),boost::python::arg("passing"),boost::python::arg("numSph"),boost::python::arg("periodic")=false,boost::python::arg("cloudPorosity")=.8,boost::python::arg("seed")=0),"Not working. Use makeCloud instead.") .def("particleSD_2d",&SpherePack::particleSD_2d,(boost::python::arg("minCorner"),boost::python::arg("maxCorner"),boost::python::arg("rMean"),boost::python::arg("periodic")=false,boost::python::arg("name"),boost::python::arg("numSph"),boost::python::arg("radii")=vector(),boost::python::arg("passing")=vector(),boost::python::arg("passingIsNotPercentageButCount")=false,boost::python::arg("seed")=0),"Not working. Use makeCloud instead.") // .def("aabb",&SpherePack::aabb_py,"Get axis-aligned bounding box coordinates, as 2 3-tuples.") .def("dim",&SpherePack::dim,"Return dimensions of the packing in terms of aabb(), as a 3-tuple.") .def("center",&SpherePack::midPt,"Return coordinates of the bounding box center.") .def_readwrite("cellSize",&SpherePack::cellSize,"Size of periodic cell; is Vector3(0,0,0) if not periodic. (Change this property only if you know what you're doing).") .def_readwrite("isPeriodic",&SpherePack::isPeriodic,"was the packing generated in periodic boundaries?") .def("cellFill",&SpherePack::cellFill,"Repeat the packing (if periodic) so that the results has dim() >= given size. The packing retains periodicity, but changes cellSize. Raises exception for non-periodic packing.") .def("cellRepeat",&SpherePack::cellRepeat,"Repeat the packing given number of times in each dimension. Periodicity is retained, cellSize changes. Raises exception for non-periodic packing.") .def("relDensity",&SpherePack::relDensity,"Relative packing density, measured as sum of spheres' volumes / aabb volume.\n(Sphere overlaps are ignored.)") .def("translate",&SpherePack::translate,"Translate all spheres by given vector.") .def("rotate",&SpherePack::rotate,(boost::python::arg("axis"),boost::python::arg("angle")),"Rotate all spheres around packing center (in terms of aabb()), given axis and angle of the rotation.") .def("scale",&SpherePack::scale,"Scale the packing around its center (in terms of aabb()) by given factor (may be negative).") .def("hasClumps",&SpherePack::hasClumps,"Whether this object contains clumps.") .def("getClumps",&SpherePack::getClumps,"Return lists of sphere ids sorted by clumps they belong to. The return value is (standalones,[clump1,clump2,…]), where each item is list of id's of spheres.") .def("__len__",&SpherePack::len,"Get number of spheres in the packing") .def("__getitem__",&SpherePack::getitem,"Get entry at given index, as tuple of center and radius.") .def("__iter__",&SpherePack::getIterator,"Return iterator over spheres.") .def_readonly("appliedPsdScaling",&SpherePack::appliedPsdScaling,"A factor between 0 and 1, uniformly applied on all sizes of of the PSD.") ; boost::python::class_("SpherePackIterator",boost::python::init()) .def("__iter__",&SpherePack::_iterator::iter) .def("next",&SpherePack::_iterator::next) ; } trunk-2017.01a/py/pack/pack.py000066400000000000000000001007721304022710500160270ustar00rootroot00000000000000# encoding: utf-8 # 2009 © Václav Šmilauer """ Creating packings and filling volumes defined by boundary representation or constructive solid geometry. For examples, see * :ysrc:`scripts/test/gts-operators.py` * :ysrc:`scripts/test/gts-random-pack-obb.py` * :ysrc:`scripts/test/gts-random-pack.py` * :ysrc:`scripts/test/pack-cloud.py` * :ysrc:`scripts/test/pack-predicates.py` * :ysrc:`examples/packs/packs.py` * :ysrc:`examples/gts-horse/gts-horse.py` * :ysrc:`examples/WireMatPM/wirepackings.py` """ import itertools,warnings from numpy import arange from math import sqrt from yade import utils from yade.wrapper import * from minieigen import * ## compatibility hack for python 2.5 (21/8/2009) ## can be safely removed at some point if 'product' not in dir(itertools): def product(*args, **kwds): "http://docs.python.org/library/itertools.html#itertools.product" pools = map(tuple, args) * kwds.get('repeat', 1); result = [[]] for pool in pools: result = [x+[y] for x in result for y in pool] for prod in result: yield tuple(prod) itertools.product=product # for now skip the import, but try in inGtsSurface constructor again, to give error if we really use it try: import gts except ImportError: pass # make c++ predicates available in this module noPredicate = False try: from _packPredicates import * ## imported in randomDensePack as well except ImportError: pass; noPredicate = True # import SpherePack from _packSpheres import * from _packObb import * ## # extend _packSphere.SpherePack c++ class by this method ## if not (noPredicate): def SpherePack_toSimulation(self,rot=Matrix3.Identity,**kw): """Append spheres directly to the simulation. In addition calling :yref:`O.bodies.append`, this method also appropriately sets periodic cell information of the simulation. >>> from yade import pack; from math import * >>> sp=pack.SpherePack() Create random periodic packing with 20 spheres: >>> sp.makeCloud((0,0,0),(5,5,5),rMean=.5,rRelFuzz=.5,periodic=True,num=20) 20 Virgin simulation is aperiodic: >>> O.reset() >>> O.periodic False Add generated packing to the simulation, rotated by 45° along +z >>> sp.toSimulation(rot=Quaternion((0,0,1),pi/4),color=(0,0,1)) [0, 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19] Periodic properties are transferred to the simulation correctly, including rotation (this could be avoided by explicitly passing "hSize=O.cell.hSize" as an argument): >>> O.periodic True >>> O.cell.refSize Vector3(5,5,5) """ #The following 2 lines do not work, because of accuaracy #>>> O.cell.hSize #Matrix3(3.53553,-3.53553,0, 3.53553,3.53553,0, 0,0,5) """ The current state (even if rotated) is taken as mechanically undeformed, i.e. with identity transformation: >>> O.cell.trsf Matrix3(1,0,0, 0,1,0, 0,0,1) :param Quaternion/Matrix3 rot: rotation of the packing, which will be applied on spheres and will be used to set :yref:`Cell.trsf` as well. :param \*\*kw: passed to :yref:`yade.utils.sphere` :return: list of body ids added (like :yref:`O.bodies.append`) """ if isinstance(rot,Quaternion): rot=rot.toRotationMatrix() assert(isinstance(rot,Matrix3)) if self.isPeriodic: O.periodic=True if self.cellSize!=Vector3.Zero and self.isPeriodic: O.cell.hSize=rot*Matrix3(self.cellSize[0],0,0, 0,self.cellSize[1],0, 0,0,self.cellSize[2]) O.cell.trsf=Matrix3.Identity if not self.hasClumps(): return O.bodies.append([utils.sphere(rot*c,r,**kw) for c,r in self]) else: standalone,clumps=self.getClumps() ids=O.bodies.append([utils.sphere(rot*c,r,**kw) for c,r in self]) # append all spheres first clumpIds=[] userColor='color' in kw for clump in clumps: clumpIds.append(O.bodies.clump([ids[i] for i in clump])) # clump spheres with given ids together, creating the clump object as well # make all spheres within one clump a single color, unless color was specified by the user if not userColor: for i in clump[1:]: O.bodies[ids[i]].shape.color=O.bodies[ids[clump[0]]].shape.color return ids+clumpIds SpherePack.toSimulation=SpherePack_toSimulation class inGtsSurface_py(Predicate): """This class was re-implemented in c++, but should stay here to serve as reference for implementing Predicates in pure python code. C++ allows us to play dirty tricks in GTS which are not accessible through pygts itself; the performance penalty of pygts comes from fact that if constructs and destructs bb tree for the surface at every invocation of gts.Point().is_inside(). That is cached in the c++ code, provided that the surface is not manipulated with during lifetime of the object (user's responsibility). --- Predicate for GTS surfaces. Constructed using an already existing surfaces, which must be closed. import gts surf=gts.read(open('horse.gts')) inGtsSurface(surf) .. note:: Padding is optionally supported by testing 6 points along the axes in the pad distance. This must be enabled in the ctor by saying doSlowPad=True. If it is not enabled and pad is not zero, warning is issued. """ def __init__(self,surf,noPad=False): # call base class ctor; necessary for virtual methods to work as expected. # see comments in _packPredicates.cpp for struct PredicateWrap. super(inGtsSurface,self).__init__() if not surf.is_closed(): raise RuntimeError("Surface for inGtsSurface predicate must be closed.") self.surf=surf self.noPad=noPad inf=float('inf') mn,mx=[inf,inf,inf],[-inf,-inf,-inf] for v in surf.vertices(): c=v.coords() mn,mx=[min(mn[i],c[i]) for i in 0,1,2],[max(mx[i],c[i]) for i in 0,1,2] self.mn,self.mx=tuple(mn),tuple(mx) import gts def aabb(self): return self.mn,self.mx def __call__(self,_pt,pad=0.): p=gts.Point(*_pt) if self.noPad: if pad!=0: warnings.warn("Padding disabled in ctor, using 0 instead.") return p.is_inside(self.surf) pp=[gts.Point(_pt[0]-pad,_pt[1],_pt[2]),gts.Point(_pt[0]+pad,_pt[1],_pt[2]),gts.Point(_pt[0],_pt[1]-pad,_pt[2]),gts.Point(_pt[0],_pt[1]+pad,_pt[2]),gts.Point(_pt[0],_pt[1],_pt[2]-pad),gts.Point(_pt[0],_pt[1],_pt[2]+pad)] return p.is_inside(self.surf) and pp[0].is_inside(self.surf) and pp[1].is_inside(self.surf) and pp[2].is_inside(self.surf) and pp[3].is_inside(self.surf) and pp[4].is_inside(self.surf) and pp[5].is_inside(self.surf) class inSpace(Predicate): """Predicate returning True for any points, with infinite bounding box.""" def __init__(self, _center=Vector3().Zero): self._center=_center def aabb(self): inf=float('inf'); return Vector3(-inf,-inf,-inf),Vector3(inf,inf,inf) def center(self): return self._center def dim(self): inf=float('inf'); return Vector3(inf,inf,inf) def __call__(self,pt,pad): return True class inHalfSpace(Predicate): """Predicate returning True any points, with infinite bounding box.""" def __init__(self, _center=Vector3().Zero, _dir=Vector3(1,0,0)): self._center = Vector3(_center) self._dir = Vector3(_dir) assert self._dir.norm() > 0., "Direction has to be nonzero vector" self._dir.normalize() self._d = -self._dir.dot(self._center) def aabb(self): d,c = self._dir, self._center inf=float('inf') min = Vector3(-inf,-inf,-inf) max = Vector3(+inf,+inf,+inf) for i in xrange(3): j = (i+1)%3 k = (i+2)%3 if d[i]==0 and d[j]==0: if d[k] > 0: min[k] = c[k] else: max[k] = c[k] return min,max def center(self): return self._center def dim(self): inf=float('inf') return Vector3(inf,inf,inf) def __call__(self,pt,pad): v = self._dir.dot(pt) + self._d return v > pad class inConvexPolyhedron(Predicate): def __init__(self,planes): self._inHalfSpaces = [inHalfSpace(c,d) for c,d in planes] self._min, self._max = self._computeAabb() def _computeAabb(self): try: import scipy.optimize except ImportError: raise ImportError, "scipy (package python-scipy) needed for pack.inConvexPolyhedron" min,max = Vector3.Zero, Vector3.Zero A,b = [],[] for h in self._inHalfSpaces: A.append(tuple(-h._dir)) b.append(h._d) inf = float('inf') for i in xrange(3): c = Vector3.Zero # c[i] = 1 opt = scipy.optimize.linprog(c,A_ub=A,b_ub=b,bounds=(-inf,inf)) errmsg = "Something wrong in pack.inConvexPolyhedron defining planes.\nThe scipy.optimize.linprog output:\n{}\n" if not opt.success: raise ValueError, errmsg.format(opt) min[i] = opt.x[i] # c[i] = -1 opt = scipy.optimize.linprog(c,A_ub=A,b_ub=b,bounds=(-inf,inf)) if not opt.success: raise ValueError, errmsg.format(opt) max[i] = opt.x[i] return min,max def aabb(self): return Vector3(self._min), Vector3(self._max) def center(self): return .5*(self._min + self._max) def dim(self): return self._max - self._min def __call__(self,pt,pad): for p in self._inHalfSpaces: if not p(pt,pad): return False return True ##### ## surface construction and manipulation ##### def gtsSurface2Facets(surf,**kw): """Construct facets from given GTS surface. \*\*kw is passed to utils.facet.""" import gts return [utils.facet([v.coords() for v in face.vertices()],**kw) for face in surf.faces()] def sweptPolylines2gtsSurface(pts,threshold=0,capStart=False,capEnd=False): """Create swept suface (as GTS triangulation) given same-length sequences of points (as 3-tuples). If threshold is given (>0), then * degenerate faces (with edges shorter than threshold) will not be created * gts.Surface().cleanup(threshold) will be called before returning, which merges vertices mutually closer than threshold. In case your pts are closed (last point concident with the first one) this will the surface strip of triangles. If you additionally have capStart==True and capEnd==True, the surface will be closed. .. note:: capStart and capEnd make the most naive polygon triangulation (diagonals) and will perhaps fail for non-convex sections. .. warning:: the algorithm connects points sequentially; if two polylines are mutually rotated or have inverse sense, the algorithm will not detect it and connect them regardless in their given order. """ import gts # will raise an exception in gts-less builds if not len(set([len(pts1) for pts1 in pts]))==1: raise RuntimeError("Polylines must be all of the same length!") vtxs=[[gts.Vertex(x,y,z) for x,y,z in pts1] for pts1 in pts] sectEdges=[[gts.Edge(vtx[i],vtx[i+1]) for i in xrange(0,len(vtx)-1)] for vtx in vtxs] interSectEdges=[[] for i in range(0,len(vtxs)-1)] for i in range(0,len(vtxs)-1): for j in range(0,len(vtxs[i])): interSectEdges[i].append(gts.Edge(vtxs[i][j],vtxs[i+1][j])) if j0: # replace edges of zero length with None; their faces will be skipped def fixEdges(edges): for i,e in enumerate(edges): if (Vector3(e.v1.x,e.v1.y,e.v1.z)-Vector3(e.v2.x,e.v2.y,e.v2.z)).norm()0: surf.cleanup(threshold) return surf def gtsSurfaceBestFitOBB(surf): """Return (Vector3 center, Vector3 halfSize, Quaternion orientation) describing best-fit oriented bounding box (OBB) for the given surface. See cloudBestFitOBB for details.""" import gts pts=[Vector3(v.x,v.y,v.z) for v in surf.vertices()] return cloudBestFitOBB(tuple(pts)) def revolutionSurfaceMeridians(sects,angles,origin=Vector3().Zero,orientation=Quaternion().Identity): """Revolution surface given sequences of 2d points and sequence of corresponding angles, returning sequences of 3d points representing meridian sections of the revolution surface. The 2d sections are turned around z-axis, but they can be transformed using the origin and orientation arguments to give arbitrary orientation.""" import math def toGlobal(x,y,z): return tuple(origin+orientation*(Vector3(x,y,z))) return [[toGlobal(x2d*math.cos(angles[i]),x2d*math.sin(angles[i]),y2d) for x2d,y2d in sects[i]] for i in range(0,len(sects))] ######## ## packing generators ######## def regularOrtho(predicate,radius,gap,**kw): """Return set of spheres in regular orthogonal grid, clipped inside solid given by predicate. Created spheres will have given radius and will be separated by gap space.""" ret=[] mn,mx=predicate.aabb() if(max([mx[i]-mn[i] for i in 0,1,2])==float('inf')): raise ValueError("Aabb of the predicate must not be infinite (didn't you use union | instead of intersection & for unbounded predicate such as notInNotch?"); xx,yy,zz=[arange(mn[i]+radius,mx[i]-radius,2*radius+gap) for i in 0,1,2] for xyz in itertools.product(xx,yy,zz): if predicate(xyz,radius): ret+=[utils.sphere(xyz,radius=radius,**kw)] if (len(ret)==0): warnings.warn('No spheres are produced by regularOrtho-function',category=RuntimeWarning) return ret def regularHexa(predicate,radius,gap,**kw): """Return set of spheres in regular hexagonal grid, clipped inside solid given by predicate. Created spheres will have given radius and will be separated by gap space.""" ret=[] a=2*radius+gap hy,hz=a*sqrt(3)/2.,a*sqrt(6)/3. mn,mx=predicate.aabb() dim=[mx[i]-mn[i] for i in 0,1,2] if(max(dim)==float('inf')): raise ValueError("Aabb of the predicate must not be infinite (didn't you use union | instead of intersection & for unbounded predicate such as notInNotch?"); ii,jj,kk=[range(0,int(dim[0]/a)+1),range(0,int(dim[1]/hy)+1),range(0,int(dim[2]/hz)+1)] for i,j,k in itertools.product(ii,jj,kk): #Simple HCP-lattice packing #http://en.wikipedia.org/wiki/Close-packing_of_equal_spheres#Simple_hcp_lattice coordSph = Vector3((2*i + ((j + k) % 2 ) ), (sqrt(3.)*(j + 1./3.*(k % 2))), (2.*sqrt(6.)/3.*k))*(a/2.0) + mn if predicate(coordSph,radius): ret+=[utils.sphere(coordSph,radius=radius,**kw)] if (len(ret)==0): warnings.warn('No spheres are produced by regularHexa-function',category=RuntimeWarning) return ret def filterSpherePack(predicate,spherePack,returnSpherePack=None,**kw): """Using given SpherePack instance, return spheres that satisfy predicate. It returns either a :yref:`yade._packSpheres.SpherePack` (if returnSpherePack) or a list. The packing will be recentered to match the predicate and warning is given if the predicate is larger than the packing.""" if returnSpherePack==None: warnings.warn('The default behavior will change; specify returnSpherePack=True for the new behavior, and False to get rid of this warning (your code will break in the future, however). The returned SpherePack object can be added to the simulation using SpherePack.toSimulation()',category=FutureWarning) returnSpherePack=False mn,mx=predicate.aabb() dimP,centP=predicate.dim(),predicate.center() dimS,centS=spherePack.dim(),spherePack.center() if dimP[0]>dimS[0] or dimP[1]>dimS[1] or dimP[2]>dimS[2]: warnings.warn("Packing's dimension (%s) doesn't fully contain dimension of the predicate (%s)."%(dimS,dimP)) spherePack.translate(centP-centS) if returnSpherePack: ret=SpherePack() for c,r in spherePack: if predicate(c,r): ret.add(c,r) return ret else: # return particles to be added to O.bodies ret=[] for s in spherePack: if predicate(s[0],s[1]): ret+=[utils.sphere(s[0],radius=s[1],**kw)] return ret def _memoizePacking(memoizeDb,sp,radius,rRelFuzz,wantPeri,fullDim,noPrint=False): if not memoizeDb: return import cPickle,sqlite3,time,os if os.path.exists(memoizeDb): conn=sqlite3.connect(memoizeDb) else: conn=sqlite3.connect(memoizeDb) c=conn.cursor() c.execute('create table packings (radius real, rRelFuzz real, dimx real, dimy real, dimz real, N integer, timestamp real, periodic integer, pack blob)') c=conn.cursor() packBlob=buffer(cPickle.dumps(sp.toList(),cPickle.HIGHEST_PROTOCOL)) packDim=sp.cellSize if wantPeri else fullDim c.execute('insert into packings values (?,?,?,?,?,?,?,?,?)',(radius,rRelFuzz,packDim[0],packDim[1],packDim[2],len(sp),time.time(),wantPeri,packBlob,)) c.close() conn.commit() if not noPrint: print "Packing saved to the database",memoizeDb def _getMemoizedPacking(memoizeDb,radius,rRelFuzz,x1,y1,z1,fullDim,wantPeri,fillPeriodic,spheresInCell,memoDbg=False,noPrint=False): """Return suitable SpherePack read from *memoizeDb* if found, None otherwise. :param fillPeriodic: whether to fill fullDim by repeating periodic packing :param wantPeri: only consider periodic packings """ import os,os.path,sqlite3,time,cPickle,sys if memoDbg and not noPrint: def memoDbgMsg(s): print s else: def memoDbgMsg(s): pass if not memoizeDb or not os.path.exists(memoizeDb): if memoizeDb: memoDbgMsg("Database %s does not exist."%memoizeDb) return None # find suitable packing and return it directly conn=sqlite3.connect(memoizeDb); c=conn.cursor(); try: c.execute('select radius,rRelFuzz,dimx,dimy,dimz,N,timestamp,periodic from packings order by N') except sqlite3.OperationalError: raise RuntimeError("ERROR: database `"+memoizeDb+"' not compatible with randomDensePack (corrupt, deprecated format or not a db created by randomDensePack)") for row in c: R,rDev,X,Y,Z,NN,timestamp,isPeri=row[0:8]; scale=radius/R rDev*=scale; X*=scale; Y*=scale; Z*=scale memoDbgMsg("Considering packing (radius=%g±%g,N=%g,dim=%g×%g×%g,%s,scale=%g), created %s"%(R,.5*rDev,NN,X,Y,Z,"periodic" if isPeri else "non-periodic",scale,time.asctime(time.gmtime(timestamp)))) if not isPeri and wantPeri: memoDbgMsg("REJECT: is not periodic, which is requested."); continue if wantPeri and (X/x1>0.9 or X/x1<0.6): memoDbgMsg("REJECT: initSize differs too much from scaled packing size."); continue if (rRelFuzz==0 and rDev!=0) or (rRelFuzz!=0 and rDev==0) or (rRelFuzz!=0 and abs((rDev-rRelFuzz)/rRelFuzz)>1e-2): memoDbgMsg("REJECT: radius fuzz differs too much (%g, %g desired)"%(rDev,rRelFuzz)); continue # radius fuzz differs too much if isPeri and wantPeri: if spheresInCell>NN and spheresInCell>0: memoDbgMsg("REJECT: Number of spheres in the packing too small"); continue if abs((y1/x1)/(Y/X)-1)>0.3 or abs((z1/x1)/(Z/X)-1)>0.3: memoDbgMsg("REJECT: proportions (y/x=%g, z/x=%g) differ too much from what is desired (%g, %g)."%(Y/X,Z/X,y1/x1,z1/x1)); continue else: if (X0) if 'inGtsSurface' in dir(_packPredicates) and type(predicate)==inGtsSurface and useOBB: center,dim,orientation=gtsSurfaceBestFitOBB(predicate.surf) print "Best-fit oriented-bounding-box computed for GTS surface, orientation is",orientation dim*=2 # gtsSurfaceBestFitOBB returns halfSize else: if not dim: dim=predicate.dim() if max(dim)==float('inf'): raise RuntimeError("Infinite predicate and no dimension of packing requested.") center=predicate.center() orientation=None if not wantPeri: fullDim=tuple([dim[i]+4*cropLayers*radius for i in 0,1,2]) else: # compute cell dimensions now, as they will be compared to ones stored in the db # they have to be adjusted to not make the cell to small WRT particle radius fullDim=dim cloudPorosity=0.25 # assume this number for the initial cloud (can be underestimated) beta,gamma=fullDim[1]/fullDim[0],fullDim[2]/fullDim[0] # ratios β=y₀/x₀, γ=z₀/x₀ N100=spheresInCell/cloudPorosity # number of spheres for cell being filled by spheres without porosity x1=radius*(1/(beta*gamma)*N100*(4/3.)*pi)**(1/3.) y1,z1=beta*x1,gamma*x1; vol0=x1*y1*z1 maxR=radius*(1+rRelFuzz) x1=max(x1,8*maxR); y1=max(y1,8*maxR); z1=max(z1,8*maxR); vol1=x1*y1*z1 N100*=vol1/vol0 # volume might have been increased, increase number of spheres to keep porosity the same sp=_getMemoizedPacking(memoizeDb,radius,rRelFuzz,x1,y1,z1,fullDim,wantPeri,fillPeriodic=True,spheresInCell=spheresInCell,memoDbg=False) if sp: if orientation: sp.cellSize=(0,0,0) # resetting cellSize avoids warning when rotating sp.rotate(*orientation.toAxisAngle()) return filterSpherePack(predicate,sp,material=material,returnSpherePack=returnSpherePack) else: print "No suitable packing in database found, running",'PERIODIC compression' if wantPeri else 'triaxial' sys.stdout.flush() O.switchScene(); O.resetThisScene() ### !! if wantPeri: # x1,y1,z1 already computed above sp=SpherePack() O.periodic=True #O.cell.refSize=(x1,y1,z1) O.cell.setBox((x1,y1,z1)) #print cloudPorosity,beta,gamma,N100,x1,y1,z1,O.cell.refSize #print x1,y1,z1,radius,rRelFuzz O.materials.append(FrictMat(young=3e10,density=2400)) num=sp.makeCloud(Vector3().Zero,O.cell.refSize,radius,rRelFuzz,spheresInCell,True) O.engines=[ForceResetter(),InsertionSortCollider([Bo1_Sphere_Aabb()],verletDist=.05*radius),InteractionLoop([Ig2_Sphere_Sphere_ScGeom()],[Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_ScGeom_FrictPhys_CundallStrack()]),PeriIsoCompressor(charLen=2*radius,stresses=[-100e9,-1e8],maxUnbalanced=1e-2,doneHook='O.pause();',globalUpdateInt=5,keepProportions=True),NewtonIntegrator(damping=.6)] O.materials.append(FrictMat(young=30e9,frictionAngle=.5,poisson=.3,density=1e3)) for s in sp: O.bodies.append(utils.sphere(s[0],s[1])) O.dt=utils.PWaveTimeStep() O.run(); O.wait() sp=SpherePack(); sp.fromSimulation() #print 'Resulting cellSize',sp.cellSize,'proportions',sp.cellSize[1]/sp.cellSize[0],sp.cellSize[2]/sp.cellSize[0] # repetition to the required cell size will be done below, after memoizing the result else: assumedFinalDensity=0.6 V=(4.0/3.0)*pi*radius**3.0; N=assumedFinalDensity*fullDim[0]*fullDim[1]*fullDim[2]/V; TriaxialTest( numberOfGrains=int(N),radiusMean=radius,radiusStdDev=rRelFuzz, # upperCorner is just size ratio, if radiusMean is specified upperCorner=fullDim, ## no need to touch any the following noFiles=True,lowerCorner=[0,0,0],sigmaIsoCompaction=-1e7,sigmaLateralConfinement=-1e5,compactionFrictionDeg=1,StabilityCriterion=.05,strainRate=.2,thickness=-1,maxWallVelocity=.1,wallOversizeFactor=1.5,autoUnload=True,autoCompressionActivation=False).load() while ( numpy.isnan(utils.unbalancedForce()) or utils.unbalancedForce()>0.005 ) : O.run(100,True) sp=SpherePack(); sp.fromSimulation() O.switchScene() ### !! _memoizePacking(memoizeDb,sp,radius,rRelFuzz,wantPeri,fullDim) if wantPeri: sp.cellFill(Vector3(fullDim[0],fullDim[1],fullDim[2])) if orientation: sp.cellSize=(0,0,0); # reset periodicity to avoid warning when rotating periodic packing sp.rotate(*orientation.toAxisAngle()) return filterSpherePack(predicate,sp,material=material,color=color,returnSpherePack=returnSpherePack) def randomPeriPack(radius,initSize,rRelFuzz=0.0,memoizeDb=None,noPrint=False): """Generate periodic dense packing. A cell of initSize is stuffed with as many spheres as possible, then we run periodic compression with PeriIsoCompressor, just like with randomDensePack. :param radius: mean sphere radius :param rRelFuzz: relative fuzz of sphere radius (equal distribution); see the same param for randomDensePack. :param initSize: initial size of the periodic cell. :return: SpherePack object, which also contains periodicity information. """ from math import pi sp=_getMemoizedPacking(memoizeDb,radius,rRelFuzz,initSize[0],initSize[1],initSize[2],fullDim=Vector3(0,0,0),wantPeri=True,fillPeriodic=False,spheresInCell=-1,memoDbg=True,noPrint=noPrint) if sp: return sp O.switchScene(); O.resetThisScene() sp=SpherePack() O.periodic=True #O.cell.refSize=initSize O.cell.setBox(initSize) sp.makeCloud(Vector3().Zero,O.cell.refSize,radius,rRelFuzz,-1,True) O.engines=[ForceResetter(),InsertionSortCollider([Bo1_Sphere_Aabb()],verletDist=.05*radius),InteractionLoop([Ig2_Sphere_Sphere_ScGeom()],[Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_ScGeom_FrictPhys_CundallStrack()]),PeriIsoCompressor(charLen=2*radius,stresses=[-100e9,-1e8],maxUnbalanced=1e-2,doneHook='O.pause();',globalUpdateInt=20,keepProportions=True),NewtonIntegrator(damping=.8)] O.materials.append(FrictMat(young=30e9,frictionAngle=.1,poisson=.3,density=1e3)) for s in sp: O.bodies.append(utils.sphere(s[0],s[1])) O.dt=utils.PWaveTimeStep() O.timingEnabled=True O.run(); O.wait() ret=SpherePack() ret.fromSimulation() _memoizePacking(memoizeDb,ret,radius,rRelFuzz,wantPeri=True,fullDim=Vector3(0,0,0),noPrint=noPrint) # fullDim unused O.switchScene() return ret def hexaNet( radius, cornerCoord=[0,0,0], xLength=1., yLength=0.5, mos=0.08, a=0.04, b=0.04, startAtCorner=True, isSymmetric=False, **kw ): """Definition of the particles for a hexagonal wire net in the x-y-plane for the WireMatPM. :param radius: radius of the particle :param cornerCoord: coordinates of the lower left corner of the net :param xLenght: net length in x-direction :param yLenght: net length in y-direction :param mos: mesh opening size (horizontal distance between the double twists) :param a: length of double-twist :param b: height of single wire section :param startAtCorner: if true the generation starts with a double-twist at the lower left corner :param isSymmetric: defines if the net is symmetric with respect to the y-axis :return: set of spheres which defines the net (net) and exact dimensions of the net (lx,ly). .. note:: This packing works for the WireMatPM only. The particles at the corner are always generated first. For examples on how to use this packing see examples/WireMatPM. In order to create the proper interactions for the net the interaction radius has to be adapted in the simulation. """ # check input dimension if(xLength """ Module containing utility functions for plotting inside yade. See :ysrc:`examples/simple-scene/simple-scene-plot.py` or :ysrc:`examples/concrete/uniax.py` for example of usage. """ ## all exported names __all__=['data','plots','labels','live','liveInterval','autozoom','plot','reset','resetData','splitData','reverseData','addData','addAutoData','saveGnuplot','saveDataTxt','savePlotSequence'] # multi-threaded support for Tk # safe to import even if Tk will not be used import mtTkinter as Tkinter try: import Image except: try: import PIL.Image except: import warnings warnings.warn("PIL (python-imaging package) must be installed to use yade.plot") import matplotlib,os,time,math,itertools # running in batch # # If GtkAgg is the default, X must be working, which is not the case # with batches (DISPLAY is unset in such case) and importing pylab fails then. # # Agg does not require the GUI part and works without any DISPLAY active # just fine. # # see http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg04320.html # and https://lists.launchpad.net/yade-users/msg03289.html # import yade.runtime if not yade.runtime.hasDisplay: matplotlib.use('Agg') from minieigen import * #matplotlib.use('TkAgg') #matplotlib.use('GTKAgg') ##matplotlib.use('QtAgg') matplotlib.rc('axes',grid=True) # put grid in all figures import pylab data={} "Global dictionary containing all data values, common for all plots, in the form {'name':[value,...],...}. Data should be added using plot.addData function. All [value,...] columns have the same length, they are padded with NaN if unspecified." imgData={} "Dictionary containing lists of strings, which have the meaning of images corresponding to respective :yref:`yade.plot.data` rows. See :yref:`yade.plot.plots` on how to plot images." plots={} # dictionary x-name -> (yspec,...), where yspec is either y-name or (y-name,'line-specification') "dictionary x-name -> (yspec,...), where yspec is either y-name or (y-name,'line-specification'). If ``(yspec,...)`` is ``None``, then the plot has meaning of image, which will be taken from respective field of :yref:`yade.plot.imgData`." labels={} "Dictionary converting names in data to human-readable names (TeX names, for instance); if a variable is not specified, it is left untranslated." xylabels={} "Dictionary of 2-tuples specifying (xlabel,ylabel) for respective plots; if either of them is None, the default auto-generated title is used." legendLoc=('upper left','upper right') "Location of the y1 and y2 legends on the plot, if y2 is active." live=True if yade.runtime.hasDisplay else False "Enable/disable live plot updating. Disabled by default for now, since it has a few rough edges." liveInterval=1 "Interval for the live plot updating, in seconds." autozoom=True "Enable/disable automatic plot rezooming after data update." scientific=True if hasattr(pylab,'ticklabel_format') else False ## safe default for older matplotlib versions "Use scientific notation for axes ticks." axesWd=0 "Linewidth (in points) to make *x* and *y* axes better visible; not activated if non-positive." current=-1 "Point that is being tracked with a scatter point. -1 is for the last point, set to *nan* to disable." afterCurrentAlpha=.2 "Color alpha value for part of lines after :yref:`yade.plot.current`, between 0 (invisible) to 1 (full color)" scatterMarkerKw=dict(verts=[(0.,0.),(-30.,10.),(-25,0),(-30.,-10.)],marker=None) "Parameters for the current position marker" componentSeparator='_' componentSuffixes={Vector2:{0:'x',1:'y'},Vector3:{0:'x',1:'y',2:'z'},Matrix3:{(0,0):'xx',(1,1):'yy',(2,2):'zz',(0,1):'xy',(0,2):'xz',(1,2):'yz',(1,0):'yz',(2,0):'zx',(2,1):'zy'}} # if a type with entry in componentSuffixes is given in addData, columns for individual components are synthesized using indices and suffixes given for each type, e.g. foo=Vector3r(1,2,3) will result in columns foox=1,fooy=2,fooz=3 def reset(): "Reset all plot-related variables (data, plots, labels)" global data, plots, labels # plotLines data={}; plots={}; imgData={} # plotLines={}; pylab.close('all') def resetData(): "Reset all plot data; keep plots and labels intact." global data data={} from yade.wrapper import * def splitData(): "Make all plots discontinuous at this point (adds nan's to all data fields)" addData({}) def reverseData(): """Reverse yade.plot.data order. Useful for tension-compression test, where the initial (zero) state is loaded and, to make data continuous, last part must *end* in the zero state. """ for k in data: data[k].reverse() def addDataColumns(dd): '''Add new columns with NaN data, without adding anything to other columns. Does nothing for columns that already exist''' numSamples=len(data[data.keys()[0]]) if len(data)>0 else 0 for d in dd: if d in data.keys(): continue data[d]=[nan for i in range(numSamples)] def addAutoData(): """Add data by evaluating contents of :yref:`yade.plot.plots`. Expressions rasing exceptions will be handled gracefully, but warning is printed for each. >>> from yade import plot >>> from pprint import pprint >>> O.reset() >>> plot.resetData() >>> plot.plots={'O.iter':('O.time',None,'numParticles=len(O.bodies)')} >>> plot.addAutoData() >>> pprint(plot.data) {'O.iter': [0], 'O.time': [0.0], 'numParticles': [0]} Note that each item in :yref:`yade.plot.plots` can be * an expression to be evaluated (using the ``eval`` builtin); * ``name=expression`` string, where ``name`` will appear as label in plots, and expression will be evaluated each time; * a dictionary-like object -- current keys are labels of plots and current values are added to :yref:`yade.plot.data`. The contents of the dictionary can change over time, in which case new lines will be created as necessary. A simple simulation with plot can be written in the following way; note how the energy plot is specified. >>> from yade import plot, utils >>> plot.plots={'i=O.iter':(O.energy,None,'total energy=O.energy.total()')} >>> # we create a simple simulation with one ball falling down >>> plot.resetData() >>> O.bodies.append(utils.sphere((0,0,0),1)) 0 >>> O.dt=utils.PWaveTimeStep() >>> O.engines=[ ... ForceResetter(), ... GravityEngine(gravity=(0,0,-10),warnOnce=False), ... NewtonIntegrator(damping=.4,kinSplit=True), ... # get data required by plots at every step ... PyRunner(command='yade.plot.addAutoData()',iterPeriod=1,initRun=True) ... ] >>> O.trackEnergy=True >>> O.run(2,True) >>> pprint(plot.data) #doctest: +ELLIPSIS {'gravWork': [0.0, -25.13274...], 'i': [0, 1], 'kinRot': [0.0, 0.0], 'kinTrans': [0.0, 7.5398...], 'nonviscDamp': [0.0, 10.0530...], 'total energy': [0.0, -7.5398...]} """ # this part of docstring does not work with Sphinx """ .. plot:: from yade import * from yade import plot,utils O.reset() O.engines=[ForceResetter(),GravityEngine(gravity=(0,0,-10),warnOnce=False),NewtonIntegrator(damping=.4,kinSplit=True),PyRunner(command='yade.plot.addAutoData()',iterPeriod=1,initRun=True)] O.bodies.append(utils.sphere((0,0,0),1)); O.dt=utils.PWaveTimeStep() plot.resetData() plot.plots={'i=O.iter':(O.energy,None,'total energy=O.energy.total()')} O.trackEnergy=True O.run(50,True) import pylab; pylab.grid(True) plot.legendLoc=('lower left','upper right') plot.plot(noShow=True) """ def colDictUpdate(col,dic): 'update *dic* with the value from col, which is a "expr" or "name=expr" string; all exceptions from ``eval`` are caught and warning is printed without adding any data.' name,expr=col.split('=',1) if '=' in col else (col,col) try: val=eval(expr) dic.update({name:val}) except: print 'WARN: ignoring exception raised while evaluating auto-column `'+expr+"'%s."%('' if name==expr else ' ('+name+')') cols={} for p in plots: pp=plots[p] colDictUpdate(p.strip(),cols) for y in tuplifyYAxis(plots[p]): # imgplot specifier if y==None: continue yy=addPointTypeSpecifier(y,noSplit=True)[0] # dict-like object if hasattr(yy,'keys'): cols.update(dict(yy)) # callable returning list sequence of expressions to evaluate #elif callable(yy): # for yyy in yy(): colDictUpdate(yyy,cols) # plain value else: colDictUpdate(yy,cols) addData(cols) def addData(*d_in,**kw): """Add data from arguments name1=value1,name2=value2 to yade.plot.data. (the old {'name1':value1,'name2':value2} is deprecated, but still supported) New data will be padded with nan's, unspecified data will be nan (nan's don't appear in graphs). This way, equal length of all data is assured so that they can be plotted one against any other. >>> from yade import plot >>> from pprint import pprint >>> plot.resetData() >>> plot.addData(a=1) >>> plot.addData(b=2) >>> plot.addData(a=3,b=4) >>> pprint(plot.data) {'a': [1, nan, 3], 'b': [nan, 2, 4]} Some sequence types can be given to addData; they will be saved in synthesized columns for individual components. >>> plot.resetData() >>> plot.addData(c=Vector3(5,6,7),d=Matrix3(8,9,10, 11,12,13, 14,15,16)) >>> pprint(plot.data) {'c_x': [5.0], 'c_y': [6.0], 'c_z': [7.0], 'd_xx': [8.0], 'd_xy': [9.0], 'd_xz': [10.0], 'd_yy': [12.0], 'd_yz': [11.0], 'd_zx': [14.0], 'd_zy': [15.0], 'd_zz': [16.0]} """ import numpy if len(data)>0: numSamples=len(data[data.keys()[0]]) else: numSamples=0 # align with imgData, if there is more of them than data if len(imgData)>0 and numSamples==0: numSamples=max(numSamples,len(imgData[imgData.keys()[0]])) d=(d_in[0] if len(d_in)>0 else {}) d.update(**kw) # handle types composed of multiple values (vectors, matrices) dNames=d.keys()[:] # make copy, since dict cannot change size if iterated over directly for name in dNames: if type(d[name]) in componentSuffixes: val=d[name] suffixes=componentSuffixes[type(d[name])] for ix in suffixes: d[name+componentSeparator+suffixes[ix]]=d[name][ix] del d[name] elif hasattr(d[name],'__len__'): raise ValueError('plot.addData given unhandled sequence type (is a '+type(d[name]).__name__+', must be number or '+'/'.join([k.__name__ for k in componentSuffixes])+')') for name in d: if not name in data.keys(): data[name]=[] for name in data: data[name]+=(numSamples-len(data[name]))*[nan] data[name].append(d[name] if name in d else nan) #print [(k,len(data[k])) for k in data.keys()] #numpy.array([nan for i in range(numSamples)]) #numpy.append(data[name],[d[name]],1) def addImgData(**kw): for k in kw: if k not in imgData: imgData[k]=[] # align imgData with data if len(data.keys())>0 and len(imgData.keys())>0: nData,nImgData=len(data[data.keys()[0]]),len(imgData[imgData.keys()[0]]) #if nImgData>nData-1: raise RuntimeError("imgData is already the same length as data?") if nImgData0 else None imgData[k]+=(nData-len(imgData[k])-1)*[lastValue] elif nData0 else nan data[k]+=(nImgData-nData)*[lastValue] # add one more, because we will append to imgData below # add values from kw newLen=(len(imgData[imgData.keys()[0]]) if imgData else 0)+1 # current length plus 1 for k in kw: if k in imgData and len(imgData[k])>0: imgData[k]+=(newLen-len(imgData[k])-1)*[imgData[k][-1]]+[kw[k]] # repeat last element as necessary else: imgData[k]=(newLen-1)*[None]+[kw[k]] # repeat None if no previous value # align values which were not in kw by repeating the last value for k in imgData: if len(imgData[k])current else 0) self.line.set_xdata(self.xdata[:preCurrEnd]); self.line.set_ydata(self.ydata[:preCurrEnd]) self.line2.set_xdata(self.xdata[current:]); self.line2.set_ydata(self.ydata[current:]) try: x,y=self.xdata[current],self.ydata[current] except IndexError: x,y=0,0 # this could be written in a nicer way, very likely try: pt=numpy.ndarray((2,),buffer=numpy.array([float(x),float(y)])) if self.scatter: self.scatter.set_offsets(pt) # change rotation of the marker (possibly incorrect) try: dx,dy=self.xdata[current]-self.xdata[current-1],self.ydata[current]-self.ydata[current-1] # smoothing from last n values, if possible # FIXME: does not show arrow at all if less than window values #try: # window=10 # dx,dy=[numpy.average(numpy.diff(dta[current-window:current])) for dta in self.xdata,self.ydata] #except IndexError: pass # there must be an easier way to find on-screen derivative angle, ask on the matplotlib mailing list axes=self.line.axes() p=axes.patch; xx,yy=p.get_verts()[:,0],p.get_verts()[:,1]; size=max(xx)-min(xx),max(yy)-min(yy) aspect=(size[1]/size[0])*(1./axes.get_data_ratio()) angle=math.atan(aspect*dy/dx) if dx<0: angle-=math.pi self.scatter.set_transform(matplotlib.transforms.Affine2D().rotate(angle)) except IndexError: pass except TypeError: pass # this happens at i386 with empty data, saying TypeError: buffer is too small for requested array currLineRefs=[] liveTimeStamp=0 # timestamp when live update was started, so that the old thread knows to stop if that changes nan=float('nan') def createPlots(subPlots=True,scatterSize=60,wider=False): global currLineRefs figs=set([l.line.get_axes().get_figure() for l in currLineRefs]) # get all current figures for f in figs: pylab.close(f) # close those currLineRefs=[] # remove older plots (breaks live updates of windows that are still open) if len(plots)==0: return # nothing to plot if subPlots: # compute number of rows and colums for plots we have subCols=int(round(math.sqrt(len(plots)))); subRows=int(math.ceil(len(plots)*1./subCols)) if wider: subRows,subCols=subCols,subRows for nPlot,p in enumerate(plots.keys()): pStrip=p.strip().split('=',1)[0] if not subPlots: pylab.figure() else: pylab.subplot(subRows,subCols,nPlot+1) if plots[p]==None: # image plot if not pStrip in imgData.keys(): imgData[pStrip]=[] # fake (empty) image if no data yet if len(imgData[pStrip])==0 or imgData[pStrip][-1]==None: img=Image.new('RGBA',(1,1),(0,0,0,0)) else: img=Image.open(imgData[pStrip][-1]) img=pylab.imshow(img,origin='lower') currLineRefs.append(LineRef(img,None,None,imgData[pStrip],None,pStrip)) pylab.gca().set_axis_off() continue plots_p=[addPointTypeSpecifier(o) for o in tuplifyYAxis(plots[p])] plots_p_y1,plots_p_y2=[],[]; y1=True missing=set() # missing data columns if pStrip not in data.keys(): missing.add(pStrip) for d in plots_p: if d[0]==None: y1=False; continue if y1: plots_p_y1.append(d) else: plots_p_y2.append(d) if d[0] not in data.keys() and not callable(d[0]) and not hasattr(d[0],'keys'): missing.add(d[0]) if missing: if len(data.keys())==0 or len(data[data.keys()[0]])==0: # no data at all yet, do not add garbage NaNs for m in missing: data[m]=[] else: print 'Missing columns in plot.data, adding NaN: ',','.join(list(missing)) addDataColumns(missing) def createLines(pStrip,ySpecs,isY1=True,y2Exists=False): '''Create data lines from specifications; this code is common for y1 and y2 axes; it handles y-data specified as callables, which might create additional lines when updated with liveUpdate. ''' # save the original specifications; they will be smuggled into the axes object # the live updated will run yNameFuncs to see if there are new lines to be added # and will add them if necessary yNameFuncs=set([d[0] for d in ySpecs if callable(d[0])]) | set([d[0].keys for d in ySpecs if hasattr(d[0],'keys')]) yNames=set() ySpecs2=[] for ys in ySpecs: # ys[0]() must return list of strings, which are added to ySpecs2; line specifier is synthesized by tuplifyYAxis and cannot be specified by the user if callable(ys[0]): ySpecs2+=[(ret,ys[1]) for ret in ys[0]()] elif hasattr(ys[0],'keys'): ySpecs2+=[(yy,'') for yy in ys[0].keys()] else: ySpecs2.append(ys) if len(ySpecs2)==0: print 'yade.plot: creating fake plot, since there are no y-data yet' line,=pylab.plot([nan],[nan]) line2,=pylab.plot([nan],[nan]) currLineRefs.append(LineRef(line,None,line2,[nan],[nan])) # set different color series for y1 and y2 so that they are recognizable if pylab.rcParams.has_key('axes.color_cycle'): pylab.rcParams['axes.color_cycle']='b,g,r,c,m,y,k' if not isY1 else 'm,y,k,b,g,r,c' for d in ySpecs2: yNames.add(d) line,=pylab.plot(data[pStrip],data[d[0]],d[1],label=xlateLabel(d[0])) line2,=pylab.plot([],[],d[1],color=line.get_color(),alpha=afterCurrentAlpha) # use (0,0) if there are no data yet scatterPt=[0,0] if len(data[pStrip])==0 else (data[pStrip][current],data[d[0]][current]) # if current value is NaN, use zero instead scatter=pylab.scatter(scatterPt[0] if not math.isnan(scatterPt[0]) else 0,scatterPt[1] if not math.isnan(scatterPt[1]) else 0,s=scatterSize,color=line.get_color(),**scatterMarkerKw) currLineRefs.append(LineRef(line,scatter,line2,data[pStrip],data[d[0]])) axes=line.axes labelLoc=(legendLoc[0 if isY1 else 1] if y2Exists>0 else 'best') l=pylab.legend(loc=labelLoc) if hasattr(l,'draggable'): l.draggable(True) if scientific: pylab.ticklabel_format(style='sci',scilimits=(0,0),axis='both') # fixes scientific exponent placement for y2: https://sourceforge.net/mailarchive/forum.php?thread_name=20101223174750.GD28779%40ykcyc&forum_name=matplotlib-users if not isY1: axes.yaxis.set_offset_position('right') if isY1: pylab.ylabel((', '.join([xlateLabel(_p[0]) for _p in ySpecs2])) if p not in xylabels or not xylabels[p][1] else xylabels[p][1]) pylab.xlabel(xlateLabel(pStrip) if (p not in xylabels or not xylabels[p][0]) else xylabels[p][0]) else: pylab.ylabel((', '.join([xlateLabel(_p[0]) for _p in ySpecs2])) if (p not in xylabels or len(xylabels[p])<3 or not xylabels[p][2]) else xylabels[p][2]) # if there are callable/dict ySpecs, save them inside the axes object, so that the live updater can use those if yNameFuncs: axes.yadeYNames,axes.yadeYFuncs,axes.yadeXName,axes.yadeLabelLoc=yNames,yNameFuncs,pStrip,labelLoc # prepend yade to avoid clashes createLines(pStrip,plots_p_y1,isY1=True,y2Exists=len(plots_p_y2)>0) if axesWd>0: pylab.axhline(linewidth=axesWd,color='k') pylab.axvline(linewidth=axesWd,color='k') # create y2 lines, if any if len(plots_p_y2)>0: pylab.twinx() # create the y2 axis createLines(pStrip,plots_p_y2,isY1=False,y2Exists=True) if 'title' in O.tags.keys(): pylab.title(O.tags['title']) def liveUpdate(timestamp): global liveTimeStamp liveTimeStamp=timestamp while True: if not live or liveTimeStamp!=timestamp: return figs,axes,linesData=set(),set(),set() for l in currLineRefs: l.update() figs.add(l.line.get_figure()) axes.add(l.line.axes) linesData.add(id(l.ydata)) # find callables in y specifiers, create new lines if necessary for ax in axes: if not hasattr(ax,'yadeYFuncs') or not ax.yadeYFuncs: continue # not defined of empty yy=set(); for f in ax.yadeYFuncs: if callable(f): yy.update(f()) elif hasattr(f,'keys'): yy.update(f.keys()) else: raise ValueError("Internal error: ax.yadeYFuncs items must be callables or dictionary-like objects and nothing else.") #print 'callables y names:',yy news=yy-ax.yadeYNames if not news: continue for new in news: ax.yadeYNames.add(new) if new in data.keys() and id(data[new]) in linesData: continue # do not add when reloaded and the old lines are already there print 'yade.plot: creating new line for',new if not new in data.keys(): data[new]=len(data[ax.yadeXName])*[nan] # create data entry if necessary #print 'data',len(data[ax.yadeXName]),len(data[new]),data[ax.yadeXName],data[new] line,=ax.plot(data[ax.yadeXName],data[new],label=xlateLabel(new)) # no line specifier line2,=ax.plot([],[],color=line.get_color(),alpha=afterCurrentAlpha) scatterPt=(0 if len(data[ax.yadeXName])==0 or math.isnan(data[ax.yadeXName][current]) else data[ax.yadeXName][current]),(0 if len(data[new])==0 or math.isnan(data[new][current]) else data[new][current]) scatter=ax.scatter(scatterPt[0],scatterPt[1],s=60,color=line.get_color(),**scatterMarkerKw) currLineRefs.append(LineRef(line,scatter,line2,data[ax.yadeXName],data[new])) ax.set_ylabel(ax.get_ylabel()+(', ' if ax.get_ylabel() else '')+xlateLabel(new)) # it is possible that the legend has not yet been created l=ax.legend(loc=ax.yadeLabelLoc) if hasattr(l,'draggable'): l.draggable(True) if autozoom: for ax in axes: try: ax.relim() # recompute axes limits ax.autoscale_view() except RuntimeError: pass # happens if data are being updated and have not the same dimension at the very moment for fig in figs: try: fig.canvas.draw() except RuntimeError: pass # happens here too time.sleep(liveInterval) def savePlotSequence(fileBase,stride=1,imgRatio=(5,7),title=None,titleFrames=20,lastFrames=30): '''Save sequence of plots, each plot corresponding to one line in history. It is especially meant to be used for :yref:`yade.utils.makeVideo`. :param stride: only consider every stride-th line of history (default creates one frame per each line) :param title: Create title frame, where lines of title are separated with newlines (``\\n``) and optional subtitle is separated from title by double newline. :param int titleFrames: Create this number of frames with title (by repeating its filename), determines how long the title will stand in the movie. :param int lastFrames: Repeat the last frame this number of times, so that the movie does not end abruptly. :return: List of filenames with consecutive frames. ''' createPlots(subPlots=True,scatterSize=60,wider=True) sqrtFigs=math.sqrt(len(plots)) pylab.gcf().set_size_inches(8*sqrtFigs,5*sqrtFigs) # better readable pylab.subplots_adjust(left=.05,right=.95,bottom=.05,top=.95) # make it more compact if len(plots)==1 and plots[plots.keys()[0]]==None: # only pure snapshot is there pylab.gcf().set_size_inches(5,5) pylab.subplots_adjust(left=0,right=1,bottom=0,top=1) #if not data.keys(): raise ValueError("plot.data is empty.") pltLen=max(len(data[data.keys()[0]]) if data else 0,len(imgData[imgData.keys()[0]]) if imgData else 0) if pltLen==0: raise ValueError("Both plot.data and plot.imgData are empty.") global current, currLineRefs ret=[] print 'Saving %d plot frames, it can take a while...'%(pltLen) for i,n in enumerate(range(0,pltLen,stride)): current=n for l in currLineRefs: l.update() out=fileBase+'-%03d.png'%i pylab.gcf().savefig(out) ret.append(out) if len(ret)==0: raise RuntimeError("No images created?!") if title: titleImgName=fileBase+'-title.png' createTitleFrame(titleImgName,Image.open(ret[-1]).size,title) ret=titleFrames*[titleImgName]+ret if lastFrames>1: ret+=(lastFrames-1)*[ret[-1]] return ret def createTitleFrame(out,size,title): 'create figure with title and save to file; a figure object must be opened to get the right size' pylab.clf(); fig=pylab.gcf() #insize=fig.get_size_inches(); size=insize[1]*fig.get_dpi(),insize[0]*fig.get_dpi() # this gives wrong dimensions... #fig.set_facecolor('blue'); fig.patch.set_color('blue'); fig.patch.set_facecolor('blue'); fig.patch.set_alpha(None) title,subtitle=title.split('\n\n') lines=[(t,True) for t in title.split('\n')]+([(t,False) for t in subtitle.split('\n')] if subtitle else []) nLines=len(lines); fontSizes=size[1]/10.,size[1]/16. import matplotlib.mathtext def writeLine(text,vertPos,fontsize): rgba,depth=matplotlib.mathtext.MathTextParser('Bitmap').to_rgba(text,fontsize=fontsize,dpi=fig.get_dpi(),color='blue') textsize=rgba.shape[1],rgba.shape[0] if textsize[0]>size[0]: rgba,depth=matplotlib.mathtext.MathTextParser('Bitmap').to_rgba(text,fontsize=fontsize*size[0]/textsize[0],dpi=fig.get_dpi(),color='blue') textsize=rgba.shape[1],rgba.shape[0] fig.figimage(rgba.astype(float)/255.,xo=(size[0]-textsize[0])/2.,yo=vertPos-depth) ht=size[1]; y0=ht-2*fontSizes[0]; yStep=(ht-2.5*fontSizes[0])/len(lines) for i,(l,isTitle) in enumerate(lines): writeLine(l,y0-i*yStep,fontSizes[0 if isTitle else 1]) fig.savefig(out) def plot(noShow=False,subPlots=True): """Do the actual plot, which is either shown on screen (and nothing is returned: if *noShow* is ``False`` - note that your yade compilation should present qt4 feature so that figures can be displayed) or, if *noShow* is ``True``, returned as matplotlib's Figure object or list of them. You can use >>> from yade import plot >>> plot.resetData() >>> plot.plots={'foo':('bar',)} >>> plot.plot(noShow=True).savefig('someFile.pdf') >>> import os >>> os.path.exists('someFile.pdf') True >>> os.remove('someFile.pdf') to save the figure to file automatically. .. note:: For backwards compatibility reasons, *noShow* option will return list of figures for multiple figures but a single figure (rather than list with 1 element) if there is only 1 figure. """ createPlots(subPlots=subPlots) global currLineRefs figs=set([l.line.axes.get_figure() for l in currLineRefs]) if not hasattr(list(figs)[0],'show') and not noShow: import warnings warnings.warn('plot.plot not showing figure (matplotlib using headless backend?)') noShow=True if not noShow: if not yade.runtime.hasDisplay: return # would error out with some backends, such as Agg used in batches if live: import thread thread.start_new_thread(liveUpdate,(time.time(),)) # pylab.show() # this blocks for some reason; call show on figures directly for f in figs: f.show() else: figs=list(set([l.line.get_figure() for l in currLineRefs])) if len(figs)==1: return figs[0] else: return figs def saveDataTxt(fileName,vars=None): """Save plot data into a (optionally compressed) text file. The first line contains a comment (starting with ``#``) giving variable name for each of the columns. This format is suitable for being loaded for further processing (outside yade) with ``numpy.genfromtxt`` function, which recognizes those variable names (creating numpy array with named entries) and handles decompression transparently. >>> from yade import plot >>> from pprint import pprint >>> plot.reset() >>> plot.addData(a=1,b=11,c=21,d=31) # add some data here >>> plot.addData(a=2,b=12,c=22,d=32) >>> pprint(plot.data) {'a': [1, 2], 'b': [11, 12], 'c': [21, 22], 'd': [31, 32]} >>> plot.saveDataTxt('/tmp/dataFile.txt.bz2',vars=('a','b','c')) >>> import numpy >>> d=numpy.genfromtxt('/tmp/dataFile.txt.bz2',dtype=None,names=True) >>> d['a'] array([1, 2]) >>> d['b'] array([11, 12]) :param fileName: file to save data to; if it ends with ``.bz2`` / ``.gz``, the file will be compressed using bzip2 / gzip. :param vars: Sequence (tuple/list/set) of variable names to be saved. If ``None`` (default), all variables in :yref:`yade.plot.plot` are saved. """ import bz2,gzip if not vars: vars=data.keys(); vars.sort() if fileName.endswith('.bz2'): f=bz2.BZ2File(fileName,'w') elif fileName.endswith('.gz'): f=gzip.GzipFile(fileName,'w') else: f=open(fileName,'w') f.write("# "+"\t\t".join(vars)+"\n") for i in range(len(data[vars[0]])): f.write("\t".join([str(data[var][i]) for var in vars])+"\n") f.close() def savePylab(baseName,timestamp=False,title=None): '''This function is not finished, do not use it.''' import time if len(data.keys())==0: raise RuntimeError("No data for plotting were saved.") if timestamp: baseName+=_mkTimestamp() baseNameNoPath=baseName.split('/')[-1] saveDataTxt(fileName=baseName+'.data.bz2') if len(plots)==0: raise RuntimeError("No plots to save, only data saved.") py=file(baseName+'.py','w') py.write('#!/usr/bin/env python\n# encoding: utf-8\n# created '+time.asctime()+' ('+time.strftime('%Y%m%d_%H:%M')+')\n#\nimport pylab, numpy\n') py.write("data=numpy.genfromtxt('%s.data.bz2',dtype=None,names=True)\n"%baseName) subCols=int(round(math.sqrt(len(plots)))); subRows=int(math.ceil(len(plots)*1./subCols)) for nPlot,p in enumerate(plots.keys()): pStrip=p.strip().split('=',1)[0] if plots[p]==None: continue # image plots, which is not exported if len(plots)==1: py.write('pylab.figure()\n') else: py.write('pylab.subplot(%d,%d,%d)\n'%(subRows,subCols,nPlots+1)) def _mkTimestamp(): import time return time.strftime('_%Y%m%d_%H:%M') def saveGnuplot(baseName,term='wxt',extension=None,timestamp=False,comment=None,title=None,varData=False): """Save data added with :yref:`yade.plot.addData` into (compressed) file and create .gnuplot file that attempts to mimick plots specified with :yref:`yade.plot.plots`. :param baseName: used for creating baseName.gnuplot (command file for gnuplot), associated ``baseName.data.bz2`` (data) and output files (if applicable) in the form ``baseName.[plot number].extension`` :param term: specify the gnuplot terminal; defaults to ``x11``, in which case gnuplot will draw persistent windows to screen and terminate; other useful terminals are ``png``, ``cairopdf`` and so on :param extension: extension for ``baseName`` defaults to terminal name; fine for png for example; if you use ``cairopdf``, you should also say ``extension='pdf'`` however :param bool timestamp: append numeric time to the basename :param bool varData: whether file to plot will be declared as variable or be in-place in the plot expression :param comment: a user comment (may be multiline) that will be embedded in the control file :return: name of the gnuplot file created. """ if len(data.keys())==0: raise RuntimeError("No data for plotting were saved.") if timestamp: baseName+=_mkTimestamp() baseNameNoPath=baseName.split('/')[-1] vars=data.keys(); vars.sort() saveDataTxt(fileName=baseName+'.data.bz2',vars=vars) fPlot=file(baseName+".gnuplot",'w') fPlot.write('#!/usr/bin/env gnuplot\n#\n# created '+time.asctime()+' ('+time.strftime('%Y%m%d_%H:%M')+')\n#\n') if comment: fPlot.write('# '+comment.replace('\n','\n# ')+'#\n') dataFile='"< bzcat %s.data.bz2"'%(baseNameNoPath) if varData: fPlot.write('dataFile=%s'%dataFile); dataFile='dataFile' if not extension: extension=term i=0 for p in plots: pStrip=p.strip().split('=',1)[0] if plots[p]==None: continue ## this plot is image plot, which is not applicable to gnuplot plots_p=[addPointTypeSpecifier(o) for o in tuplifyYAxis(plots[p])] if term in ['wxt','x11']: fPlot.write("set term %s %d persist\n"%(term,i)) else: fPlot.write("set term %s; set output '%s.%d.%s'\n"%(term,baseNameNoPath,i,extension)) fPlot.write("set xlabel '%s'\n"%xlateLabel(p)) fPlot.write("set grid\n") fPlot.write("set datafile missing 'nan'\n") if title: fPlot.write("set title '%s'\n"%title) y1=True; plots_y1,plots_y2=[],[] # replace callable/dict-like data specifiers by the results, it that particular data exists plots_p2=[] for pp in plots_p: if callable(pp[0]): plots_p2+=[(ppp,'') for ppp in pp[0]() if ppp in data.keys()] elif hasattr(pp[0],'keys'): plots_p2+=[(name,val) for name,val in pp[0].items() if name in data.keys()] else: plots_p2.append((pp[0],pp[1])) plots_p=plots_p2 #plots_p=sum([([(pp,'') for pp in p[0]() if pp in data.keys()] if callable(p[0]) else [(p[0],p[1])] ) for p in plots_p],[]) for d in plots_p: if d[0]==None: y1=False; continue if y1: plots_y1.append(d) else: plots_y2.append(d) fPlot.write("set ylabel '%s'\n"%(','.join([xlateLabel(_p[0]) for _p in plots_y1]))) if len(plots_y2)>0: fPlot.write("set y2label '%s'\n"%(','.join([xlateLabel(_p[0]) for _p in plots_y2]))) fPlot.write("set y2tics\n") ppp=[] for pp in plots_y1: ppp.append(" %s using %d:%d title '← %s(%s)' with lines"%(dataFile,vars.index(pStrip)+1,vars.index(pp[0])+1,xlateLabel(pp[0]),xlateLabel(pStrip),)) for pp in plots_y2: ppp.append(" %s using %d:%d title '%s(%s) →' with lines axes x1y2"%(dataFile,vars.index(pStrip)+1,vars.index(pp[0])+1,xlateLabel(pp[0]),xlateLabel(pStrip),)) fPlot.write("plot "+",".join(ppp)+"\n") i+=1 fPlot.close() return baseName+'.gnuplot' trunk-2017.01a/py/polyhedra_utils.py000066400000000000000000000131561304022710500174010ustar00rootroot00000000000000# 2013 Jan Elias, http://www.fce.vutbr.cz/STM/elias.j/, elias.j@fce.vutbr.cz # https://www.vutbr.cz/www_base/gigadisk.php?i=95194aa9a """ Auxiliary functions for polyhedra """ import math,random,doctest,geom,numpy from yade import Vector3 from yade.wrapper import * try: # use psyco if available import psyco psyco.full() except ImportError: pass # c++ implementations for performance reasons from yade._polyhedra_utils import * #********************************************************************************** def randomColor(seed=None): random.seed(seed); #Return random Vector3 with each component in interval 0...1 (uniform distribution) return Vector3(random.random(),random.random(),random.random()) #********************************************************************************** #create polyhedra, one can specify vertices directly, or leave it empty for random shape def polyhedra(material,size=Vector3(1,1,1),seed=None,v=[],mask=1,fixed=False, color=[-1,-1,-1]): """create polyhedra, one can specify vertices directly, or leave it empty for random shape. :param Material material: material of new body :param Vector3 size: size of new body (see Polyhedra docs) :param float seed: seed for random operations :param [Vector3] v: list of body vertices (see Polyhedra docs) """ b=Body() random.seed(seed); b.aspherical = True if len(v)>0: b.shape = Polyhedra(v=v) else: b.shape = Polyhedra(size = size, seed=random.randint(0,1E6)) if color[0] == -1: b.shape.color = randomColor(seed=random.randint(0,1E6)) else: b.shape.color = color b.mat = material b.state.mass = b.mat.density*b.shape.GetVolume() b.state.inertia = b.shape.GetInertia()*b.mat.density b.state.ori = b.shape.GetOri() b.state.pos = b.shape.GetCentroid() b.mask=mask if fixed: b.state.blockedDOFs = 'xyzXYZ' return b #********************************************************************************** #creates polyhedra having N vertices and resembling sphere def polyhedralBall(radius, N, material, center,mask=1): """creates polyhedra having N vertices and resembling sphere :param float radius: ball radius :param int N: number of vertices :param Material material: material of new body :param Vector3 center: center of the new body """ pts = [] inc = math.pi * (3. - math.sqrt(5.)) off = 2. / float(N) for k in range(0, N): y = k * off - 1. + (off / 2.) r = math.sqrt(1. - y*y) phi = k * inc pts.append([math.cos(phi)*r*radius, y*radius, math.sin(phi)*r*radius]) ball = polyhedra(material,v=pts) ball.state.pos = center return ball #********************************************************************************** def polyhedraTruncIcosaHed(radius, material, centre,mask=1): pts = [] p = (1.+math.sqrt(5.))/2. f = radius/math.sqrt(9.*p + 1.) A = [[0.,1.,3.*p],[2.,1.+2.*p,p],[1.,2.+p,2.*p]] for a in A: a = [a[0]*f,a[1]*f,a[2]*f] B = [a,[a[1],a[2],a[0]],[a[2],a[0],a[1]]] for b in B: pts.append(b) if not b[0] == 0: pts.append([-b[0], b[1], b[2]]) if not b[1] == 0: pts.append([-b[0],-b[1], b[2]]) if not b[2] == 0: pts.append([-b[0],-b[1],-b[2]]) if not b[2] == 0: pts.append([-b[0], b[1],-b[2]]) if not b[1] == 0: pts.append([ b[0],-b[1], b[2]]) if not b[2] == 0: pts.append([ b[0],-b[1],-b[2]]) if not b[2] == 0: pts.append([ b[0], b[1],-b[2]]) ball = polyhedra(material,v=pts) ball.state.pos = centre return ball #********************************************************************************** def polyhedraSnubCube(radius, material, centre, mask=1): pts = [] f = radius/1.3437133737446 c1 = 0.337754 c2 = 1.14261 c3 = 0.621226 A = [[c2,c1,c3],[c1,c3,c2],[c3,c2,c1],[-c1,-c2,-c3],[-c2,-c3,-c1],[-c3,-c1,-c2]] for a in A: a = [a[0]*f,a[1]*f,a[2]*f] pts.append([-a[0],-a[1], a[2]]) pts.append([ a[0],-a[1],-a[2]]) pts.append([-a[0], a[1],-a[2]]) pts.append([ a[0], a[1], a[2]]) ball = polyhedra(material,v=pts) ball.state.pos = centre return ball #********************************************************************************** #fill box [mincoord, maxcoord] by non-overlaping polyhedrons with random geometry and sizes within the range (uniformly distributed) def fillBox(mincoord, maxcoord,material,sizemin=[1,1,1],sizemax=[1,1,1],ratio=[0,0,0],seed=None,mask=1): """fill box [mincoord, maxcoord] by non-overlaping polyhedrons with random geometry and sizes within the range (uniformly distributed) :param Vector3 mincoord: first corner :param Vector3 maxcoord: second corner :param Vector3 sizemin: minimal size of bodies :param Vector3 sizemax: maximal size of bodies :param Vector3 ratio: scaling ratio :param float seed: random seed """ random.seed(seed); v = fillBox_cpp(mincoord, maxcoord, sizemin,sizemax, ratio, random.randint(0,1E6), material) #lastnan = -1 #for i in range(0,len(v)): # if(math.isnan(v[i][0])): # O.bodies.append(polyhedra(material,seed=random.randint(0,1E6),v=v[lastnan+1:i],mask=1,fixed=False)) # lastnan = i #********************************************************************************** #fill box [mincoord, maxcoord] by non-overlaping polyhedrons with random geometry and sizes within the range (uniformly distributed) def fillBoxByBalls(mincoord, maxcoord,material,sizemin=[1,1,1],sizemax=[1,1,1],ratio=[0,0,0],seed=None,mask=1,numpoints=60): random.seed(seed); v = fillBoxByBalls_cpp(mincoord, maxcoord, sizemin,sizemax, ratio, random.randint(0,1E6), material,numpoints) #lastnan = -1 #for i in range(0,len(v)): # if(math.isnan(v[i][0])): # O.bodies.append(polyhedra(material,seed=random.randint(0,1E6),v=v[lastnan+1:i],mask=1,fixed=False)) # lastnan = i trunk-2017.01a/py/post2d.py000066400000000000000000000327531304022710500154110ustar00rootroot00000000000000# encoding: utf-8 # 2009 © Václav Šmilauer """ Module for 2d postprocessing, containing classes to project points from 3d to 2d in various ways, providing basic but flexible framework for extracting arbitrary scalar values from bodies/interactions and plotting the results. There are 2 basic components: flatteners and extractors. The algorithms operate on bodies (default) or interactions, depending on the ``intr`` parameter of post2d.data. Flatteners ========== Instance of classes that convert 3d (model) coordinates to 2d (plot) coordinates. Their interface is defined by the :yref:`yade.post2d.Flatten` class (``__call__``, ``planar``, ``normal``). Extractors ========== Callable objects returning scalar or vector value, given a body/interaction object. If a 3d vector is returned, Flattener.planar is called, which should return only in-plane components of the vector. Example ======= This example can be found in examples/concrete/uniax-post.py :: from yade import post2d import pylab # the matlab-like interface of matplotlib O.load('/tmp/uniax-tension.xml.bz2') # flattener that project to the xz plane flattener=post2d.AxisFlatten(useRef=False,axis=1) # return scalar given a Body instance extractDmg=lambda b: b.state.normDmg # will call flattener.planar implicitly # the same as: extractVelocity=lambda b: flattener.planar(b,b.state.vel) extractVelocity=lambda b: b.state.vel # create new figure pylab.figure() # plot raw damage post2d.plot(post2d.data(extractDmg,flattener)) # plot smooth damage into new figure pylab.figure(); ax,map=post2d.plot(post2d.data(extractDmg,flattener,stDev=2e-3)) # show color scale pylab.colorbar(map,orientation='horizontal') # raw velocity (vector field) plot pylab.figure(); post2d.plot(post2d.data(extractVelocity,flattener)) # smooth velocity plot; data are sampled at regular grid pylab.figure(); ax,map=post2d.plot(post2d.data(extractVelocity,flattener,stDev=1e-3)) # save last (current) figure to file pylab.gcf().savefig('/tmp/foo.png') # show the figures pylab.show() """ from yade.wrapper import * from minieigen import * class Flatten: """Abstract class for converting 3d point into 2d. Used by post2d.data2d.""" def __init__(self): pass def __call__(self,b): "Given a :yref:`Body` / :yref:`Interaction` instance, should return either 2d coordinates as a 2-tuple, or None if the Body should be discarded." pass def planar(self,pos,vec): "Given position and vector value, project the vector value to the flat plane and return its 2 in-plane components." def normal(self,pos,vec): "Given position and vector value, return lenght of the vector normal to the flat plane." class HelixFlatten(Flatten): """Class converting 3d point to 2d based on projection from helix. The y-axis in the projection corresponds to the rotation axis""" def __init__(self,useRef,thetaRange,dH_dTheta,axis=2,periodStart=0): """ :param bool useRef: use reference positions rather than actual positions :param (θmin,θmax) thetaRange: bodies outside this range will be discarded :param float dH_dTheta: inclination of the spiral (per radian) :param {0,1,2} axis: axis of rotation of the spiral :param float periodStart: height of the spiral for zero angle """ self.useRef,self.thetaRange,self.dH_dTheta,self.axis,self.periodStart=useRef,thetaRange,dH_dTheta,axis,periodStart self.ax1,self.ax2=(axis+1)%3,(axis+2)%3 def _getPos(self,b): return b.state.refPos if self.useRef else b.state.pos def __call__(self,b): import yade.utils xy,theta=yade.utils.spiralProject(_getPos(b),self.dH_dTheta,self.axis,self.periodStart) if thetathetaRange[1]: return None return xy def planar(self,b,vec): from math import sqrt pos=_getPos(b) pos[self.axis]=0; pos.Normalize() return pos.Dot(vec),vec[axis] def normal(self,pos,vec): ax=Vector3(0,0,0); ax[axis]=1; pos=_getPos(b) circum=ax.Cross(pos); circum.Normalize() return circum.Dot(vec) class CylinderFlatten(Flatten): """Class for converting 3d point to 2d based on projection onto plane from circle. The y-axis in the projection corresponds to the rotation axis; the x-axis is distance form the axis. """ def __init__(self,useRef,axis=2): """ :param useRef: (bool) use reference positions rather than actual positions :param axis: axis of the cylinder, ∈{0,1,2} """ if axis not in (0,1,2): raise IndexError("axis must be one of 0,1,2 (not %d)"%axis) self.useRef,self.axis=useRef,axis def _getPos(self,b): return b.state.refPos if self.useRef else b.state.pos def __call__(self,b): p=_getPos(b) pp=(p[(self.axis+1)%3],p[(self.axis+2)%3]) import math.sqrt return math.sqrt(pp[0]**2+pp[2]**2),p[self.axis] def planar(self,b,vec): pos=_getPos(b) from math import sqrt pos[self.axis]=0; pos.Normalize() return pos.Dot(vec),vec[axis] def normal(self,b,vec): pos=_getPos(b) ax=Vector3(0,0,0); ax[axis]=1 circum=ax.Cross(pos); circum.Normalize() return circum.Dot(vec) class AxisFlatten(Flatten): def __init__(self,useRef=False,axis=2): """ :param bool useRef: use reference positions rather than actual positions (only meaningful when operating on Bodies) :param {0,1,2} axis: axis normal to the plane; the return value will be simply position with this component dropped. """ if axis not in (0,1,2): raise IndexError("axis must be one of 0,1,2 (not %d)"%axis) self.useRef,self.axis=useRef,axis self.ax1,self.ax2=(self.axis+1)%3,(self.axis+2)%3 def __call__(self,b): p=((b.state.refPos if self.useRef else b.state.pos) if isinstance(b,Body) else b.geom.contactPoint) return (p[self.ax1],p[self.ax2]) def planar(self,pos,vec): return vec[self.ax1],vec[self.ax2] def normal(self,pos,vec): return vec[self.axis] def data(extractor,flattener,intr=False,onlyDynamic=True,stDev=None,relThreshold=3.,perArea=0,div=(50,50),margin=(0,0),radius=1): """Filter all bodies/interactions, project them to 2d and extract required scalar value; return either discrete array of positions and values, or smoothed data, depending on whether the stDev value is specified. The ``intr`` parameter determines whether we operate on bodies or interactions; the extractor provided should expect to receive body/interaction. :param callable extractor: receives :yref:`Body` (or :yref:`Interaction`, if ``intr`` is ``True``) instance, should return scalar, a 2-tuple (vector fields) or None (to skip that body/interaction) :param callable flattener: :yref:`yade.post2d.Flatten` instance, receiving body/interaction, returns its 2d coordinates or ``None`` (to skip that body/interaction) :param bool intr: operate on interactions rather than bodies :param bool onlyDynamic: skip all non-dynamic bodies :param float/None stDev: standard deviation for averaging, enables smoothing; ``None`` (default) means raw mode, where discrete points are returned :param float relThreshold: threshold for the gaussian weight function relative to stDev (smooth mode only) :param int perArea: if 1, compute weightedSum/weightedArea rather than weighted average (weightedSum/sumWeights); the first is useful to compute average stress; if 2, compute averages on subdivision elements, not using weight function :param (int,int) div: number of cells for the gaussian grid (smooth mode only) :param (float,float) margin: x,y margins around bounding box for data (smooth mode only) :param float/callable radius: Fallback value for radius (for raw plotting) for non-spherical bodies or interactions; if a callable, receives body/interaction and returns radius :return: dictionary Returned dictionary always containing keys 'type' (one of 'rawScalar','rawVector','smoothScalar','smoothVector', depending on value of smooth and on return value from extractor), 'x', 'y', 'bbox'. Raw data further contains 'radii'. Scalar fields contain 'val' (value from *extractor*), vector fields have 'valX' and 'valY' (2 components returned by the *extractor*). """ from minieigen import Vector3 xx,yy,dd1,dd2,rr=[],[],[],[],[] nDim=0 objects=O.interactions if intr else O.bodies for b in objects: if not intr and onlyDynamic and not b.dynamic: continue xy,d=flattener(b),extractor(b) if xy==None or d==None: continue if nDim==0: nDim=1 if isinstance(d,float) else 2 if nDim==1: dd1.append(d); elif len(d)==2: dd1.append(d[0]); dd2.append(d[1]) elif len(d)==3: d1,d2=flattener.planar(b,Vector3(d)) dd1.append(d1); dd2.append(d2) else: raise RuntimeError("Extractor must return float or 2 or 3 (not %d) floats"%nDim) if stDev==None: # radii are needed in the raw mode exclusively if not intr and isinstance(b.shape,Sphere): r=b.shape.radius else: r=(radius(b) if callable(radius) else radius) rr.append(r) xx.append(xy[0]); yy.append(xy[1]); if stDev==None: bbox=(min(xx),min(yy)),(max(xx),max(yy)) if nDim==1: return {'type':'rawScalar','x':xx,'y':yy,'val':dd1,'radii':rr,'bbox':bbox} else: return {'type':'rawVector','x':xx,'y':yy,'valX':dd1,'valY':dd2,'radii':rr,'bbox':bbox} from yade.WeightedAverage2d import GaussAverage import numpy lo,hi=(min(xx),min(yy)),(max(xx),max(yy)) llo=lo[0]-margin[0],lo[1]-margin[1]; hhi=hi[0]+margin[0],hi[1]+margin[1] ga=GaussAverage(llo,hhi,div,stDev,relThreshold) ga2=GaussAverage(llo,hhi,div,stDev,relThreshold) for i in range(0,len(xx)): ga.add(dd1[i],(xx[i],yy[i])) if nDim>1: ga2.add(dd2[i],(xx[i],yy[i])) step=[(hhi[i]-llo[i])/float(div[i]) for i in [0,1]] xxx,yyy=[numpy.arange(llo[i]+.5*step[i],hhi[i],step[i]) for i in [0,1]] ddd=numpy.zeros((len(yyy),len(xxx)),float) ddd2=numpy.zeros((len(yyy),len(xxx)),float) # set the type of average we are going to use if perArea==0: def compAvg(gauss,coord,cellCoord): return float(gauss.avg(coord)) elif perArea==1: def compAvg(gauss,coord,cellCoord): return gauss.avgPerUnitArea(coord) elif perArea==2: def compAvg(gauss,coord,cellCoord): s=gauss.cellSum(cellCoord); return (s/gauss.cellArea) if s>0 else float('nan') elif perArea==3: def compAvg(gauss,coord,cellCoord): s=gauss.cellSum(cellCoord); return s if s>0 else float('nan') else: raise RuntimeError('Invalid value of *perArea*, must be one of 0,1,2,3.') # for cx in range(0,div[0]): for cy in range(0,div[1]): ddd[cy,cx]=compAvg(ga,(xxx[cx],yyy[cy]),(cx,cy)) if nDim>1: ddd2[cy,cx]=compAvg(ga2,(xxx[cx],yyy[cy]),(cx,cy)) if nDim==1: return {'type':'smoothScalar','x':xxx,'y':yyy,'val':ddd,'bbox':(llo,hhi),'perArea':perArea,'grid':ga} else: return {'type':'smoothVector','x':xxx,'y':yyy,'valX':ddd,'valY':ddd2,'bbox':(llo,hhi),'grid':ga,'grid2':ga2} def plot(data,axes=None,alpha=.5,clabel=True,cbar=False,aspect='equal',**kw): """Given output from post2d.data, plot the scalar as discrete or smooth plot. For raw discrete data, plot filled circles with radii of particles, colored by the scalar value. For smooth discrete data, plot image with optional contours and contour labels. For vector data (raw or smooth), plot quiver (vector field), with arrows colored by the magnitude. :param axes: matplotlib.axes\ instance where the figure will be plotted; if None, will be created from scratch. :param data: value returned by :yref:`yade.post2d.data` :param bool clabel: show contour labels (smooth mode only), or annotate cells with numbers inside (with perArea==2) :param bool cbar: show colorbar (equivalent to calling pylab.colorbar(mappable) on the returned mappable) :return: tuple of ``(axes,mappable)``; mappable can be used in further calls to pylab.colorbar. """ import pylab,math if not axes: axes=pylab.gca() if data['type']=='rawScalar': from matplotlib.patches import Circle import matplotlib.collections,numpy patches=[] for x,y,d,r in zip(data['x'],data['y'],data['val'],data['radii']): patches.append(Circle(xy=(x,y),radius=r)) coll=matplotlib.collections.PatchCollection(patches,linewidths=0.,**kw) coll.set_array(numpy.array(data['val'])) bb=coll.get_datalim(coll.get_transform()) axes.add_collection(coll) axes.set_xlim(bb.xmin,bb.xmax); axes.set_ylim(bb.ymin,bb.ymax) if cbar: axes.get_figure().colorbar(coll) axes.grid(True); axes.set_aspect(aspect) return axes,coll elif data['type']=='smoothScalar': loHi=data['bbox'] if data['perArea'] in (0,1): img=axes.imshow(data['val'],extent=(loHi[0][0],loHi[1][0],loHi[0][1],loHi[1][1]),origin='lower',aspect=aspect,**kw) ct=axes.contour(data['x'],data['y'],data['val'],colors='k',origin='lower',extend='both') if clabel: axes.clabel(ct,inline=1,fontsize=10) else: img=axes.imshow(data['val'],extent=(loHi[0][0],loHi[1][0],loHi[0][1],loHi[1][1]),origin='lower',aspect=aspect,interpolation='nearest',**kw) xStep=(data['x'][1]-data['x'][0]) if len(data['x'])>1 else 0 for y,valLine in zip(data['y'],data['val']): for x,val in zip(data['x'],valLine): axes.text(x-.4*xStep,y,('-' if math.isnan(val) else '%5g'%val),size=4) axes.update_datalim(loHi) axes.set_xlim(loHi[0][0],loHi[1][0]); axes.set_ylim(loHi[0][1],loHi[1][1]) if cbar: axes.get_figure().colorbar(img) axes.grid(True if data['perArea'] in (0,1) else False); axes.set_aspect(aspect) return axes,img elif data['type'] in ('rawVector','smoothVector'): import numpy loHi=data['bbox'] valX,valY=numpy.array(data['valX']),numpy.array(data['valY']) # rawVector data are plain python lists scalars=numpy.sqrt(valX**2+valY**2) # numpy.sqrt computes element-wise sqrt quiv=axes.quiver(data['x'],data['y'],data['valX'],data['valY'],scalars,**kw) #axes.update_datalim(loHi) axes.set_xlim(loHi[0][0],loHi[1][0]); axes.set_ylim(loHi[0][1],loHi[1][1]) if cbar: axes.get_figure().colorbar(coll) axes.grid(True); axes.set_aspect(aspect) return axes,quiv trunk-2017.01a/py/remote.py000066400000000000000000000216721304022710500154670ustar00rootroot00000000000000# encoding: utf-8 # 2008-2009 © Václav Šmilauer """ Remote connections to yade: authenticated python command-line over telnet and anonymous socket for getting some read-only information about current simulation. These classes are used internally in gui/py/PythonUI_rc.py and are not intended for direct use. """ import SocketServer,xmlrpclib,socket import sys,time,os,math from yade import * import yade.runtime useQThread=False gui='' "Set before using any of our classes to use QThread for background execution instead of the standard thread module. Mixing the two (in case the qt4 UI is running, for instance) does not work well." plotImgFormat,plotImgMimetype='png','image/png' #plotImgFormat,plotImgMimetype='svg','image/svg+xml' # yade 16x16 favicon, encoded with base64 b64favicon='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' bgThreads=[] # needed to keep background threads alive class InfoProvider: def basicInfo(self): ret=dict(iter=O.iter,dt=O.dt,stopAtIter=O.stopAtIter,speed=O.speed,realtime=O.realtime,time=O.time,id=O.tags['id'] if O.tags.has_key('id') else None,threads=os.environ['OMP_NUM_THREADS'] if os.environ.has_key('OMP_NUM_THREADS') else '0',numBodies=len(O.bodies),numIntrs=len(O.interactions)) sys.stdout.flush(); sys.stderr.flush() return ret def plot(self): try: from yade import plot if len(plot.plots)==0: return None fig=plot.plot(subPlots=True,noShow=True) img=O.tmpFilename()+'.'+plotImgFormat sqrtFigs=math.sqrt(len(plot.plots)) fig.set_size_inches(5*sqrtFigs,7*sqrtFigs) fig.savefig(img) f=open(img,'rb'); data=f.read(); f.close(); os.remove(img) #print 'returning '+plotImgFormat return xmlrpclib.Binary(data) except: print 'Error updating plots:' import traceback traceback.print_exc() return None def stop(self): O.pause() return True class PythonConsoleSocketEmulator(SocketServer.BaseRequestHandler): """Class emulating python command-line over a socket connection. The connection is authenticated by requiring a cookie. Only connections from localhost (127.0.0.*) are allowed. """ def setup(self): if not self.client_address[0].startswith('127.0.0'): print "TCP Connection from non-127.0.0.* address %s rejected"%self.client_address[0] return print self.client_address, 'connected!' self.request.send('Enter auth cookie: ') def tryLogin(self): if self.request.recv(1024).rstrip()==self.server.cookie: self.server.authenticated+=[self.client_address] self.request.send("""__ __ ____ __ _____ ____ ____ \ \ / /_ _| _ \ ___ ___ / / |_ _/ ___| _ \ \ V / _` | | | |/ _ \ / _ \ / / | || | | |_) | | | (_| | |_| | __/ | (_) / / | || |___| __/ |_|\__,_|____/ \___| \___/_/ |_| \____|_| (connected from %s:%d) >>> """%(str(self.client_address[0]),self.client_address[1])) return True else: import time time.sleep(5) print "invalid cookie" return False def displayhook(self,s): import pprint self.request.send(pprint.pformat(s)) def handle(self): if self.client_address not in self.server.authenticated and not self.tryLogin(): return import code,cStringIO,traceback buf=[] while True: data = self.request.recv(1024).rstrip() if data=='\x04' or data=='exit' or data=='quit': # \x04 == ^D return buf.append(data) orig_displayhook,orig_stdout=sys.displayhook,sys.stdout sio=cStringIO.StringIO() continuation=False #print "buffer:",buf try: comp=code.compile_command('\n'.join(buf)) if comp: sys.displayhook=self.displayhook sys.stdout=sio exec comp self.request.send(sio.getvalue()) buf=[] else: self.request.send('... '); continuation=True except: self.request.send(traceback.format_exc()) buf=[] finally: sys.displayhook,sys.stdout=orig_displayhook,orig_stdout if not continuation: self.request.send('\n>>> ') def finish(self): print self.client_address, 'disconnected!' self.request.send('\nBye ' + str(self.client_address) + '\n') def _runInBackground(func): if useQThread: if (gui=='qt4'): from PyQt4.QtCore import QThread elif (gui=='qt5'): from PyQt5.QtCore import QThread class WorkerThread(QThread): def __init__(self,func_): QThread.__init__(self); self.func=func_ def run(self): self.func() wt=WorkerThread(func) wt.start() global bgThreads; bgThreads.append(wt) else: import thread; thread.start_new_thread(func,()) class GenericTCPServer: "Base class for socket server, handling port allocation, initial logging and thead backgrounding." def __init__(self,handler,title,cookie=True,minPort=9000,host='',maxPort=65536,background=True): import socket, random, sys self.port=-1 self.host=host tryPort=minPort if maxPort==None: maxPort=minPort while self.port==-1 and tryPort<=maxPort: try: self.server=SocketServer.ThreadingTCPServer((host,tryPort),handler) self.port=tryPort if cookie: self.server.cookie=''.join([i for i in random.sample('yadesucks',6)]) self.server.authenticated=[] sys.stderr.write(title+" on %s:%d, auth cookie `%s'\n"%(host if host else 'localhost',self.port,self.server.cookie)) else: sys.stderr.write(title+" on %s:%d\n"%(host if host else 'localhost',self.port)) if background: _runInBackground(self.server.serve_forever) else: self.server.serve_forever() except socket.error: tryPort+=1 if self.port==-1: raise RuntimeError("No free port to listen on in range %d-%d"%(minPort,maxPort)) def runServers(): """Run python telnet server and info socket. They will be run at localhost on ports 9000 (or higher if used) and 21000 (or higer if used) respectively. The python telnet server accepts only connection from localhost, after authentication by random cookie, which is printed on stdout at server startup. The info socket provides read-only access to several simulation parameters at runtime. Each connection receives pickled dictionary with those values. This socket is primarily used by yade-multi batch scheduler. """ srv=GenericTCPServer(handler=yade.remote.PythonConsoleSocketEmulator,title='TCP python prompt',cookie=True,minPort=9000) yade.runtime.cookie=srv.server.cookie #info=GenericTCPServer(handler=yade.remote.InfoSocketProvider,title='TCP info provider',cookie=False,minPort=21000) ## XMPRPC server for general information: from SimpleXMLRPCServer import SimpleXMLRPCServer port,maxPort=21000,65535 # minimum port number while port """ Functions for accessing yade's internals; only used internally. """ import sys from yade import wrapper from yade._customConverters import * from yade import runtime from yade import config O=wrapper.Omega() def childClasses(base,recurse=True,includeBase=False): """Enumerate classes deriving from given base (as string), recursively by default. Returns set.""" ret=set(O.childClassesNonrecursive(base)); ret2=set(); if includeBase: ret|=set([base]) if not recurse: return ret for bb in ret: ret2|=childClasses(bb) return ret | ret2 _allSerializables=childClasses('Serializable') ## set of classes for which the proxies were created _proxiedClasses=set() ## deprecated classes # if old class name is used, the new object is constructed and a warning is issued about old name being used # keep chronologically ordered, oldest first; script/rename-class.py appends at the end _deprecated={ 'GranularMat':'FrictMat', # Sun Jan 10 09:26:45 2010, vaclav@flux 'SimpleElasticRelationships':'Ip2_FrictMat_FrictMat_NormShearPhys', # Sun Jan 10 09:28:17 2010, vaclav@flux 'NormalInteraction':'NormPhys', # Sun Jan 10 09:28:56 2010, vaclav@flux 'NormalShearInteraction':'NormShearPhys', # Sun Jan 10 09:29:22 2010, vaclav@flux 'ElasticMat':'ElastMat', # Sun Jan 10 09:53:15 2010, vaclav@flux 'ElasticContactInteraction':'FrictPhys', # Sun Jan 10 09:57:59 2010, vaclav@flux 'ef2_Spheres_Elastic_ElasticLaw':'Law2_ScGeom_FrictPhys_Basic', # Sun Jan 10 09:59:42 2010, vaclav@flux 'Ip2_FrictMat_FrictMat_NormShearPhys':'Ip2_FrictMat_FrictMat_FrictPhys', # Sun Jan 10 10:07:40 2010, vaclav@flux 'GLDrawCpmPhys':'Gl1_CpmPhys', # Sat Feb 6 14:46:08 2010, vaclav@flux 'RockJointLawRelationships':'Ip2_2xCohFrictMat_NormalInelasticityPhys', # Mon Feb 8 11:17:59 2010, jduriez@c1solimara-l 'TetraBang':'TTetraGeom', # Tue Feb 9 10:21:24 2010, vaclav@flux 'TetraMold':'Tetra', # Tue Feb 9 10:22:15 2010, vaclav@flux 'TetraAABB':'Bo1_Tetra_Aabb', # Tue Feb 9 10:22:33 2010, vaclav@flux 'Tetra2TetraBang':'Ig2_Tetra_Tetra_TTetraGeom', # Tue Feb 9 10:23:19 2010, vaclav@flux 'TetraLaw':'TetraVolumetricLaw', # Tue Feb 9 10:24:10 2010, vaclav@flux 'DirecResearchEngine':'Disp2DPropLoadEngine', # Wed Mar 10 12:23:42 2010, jduriez@c1solimara-l 'Ip2_BMP_BMP_CSPhys':'Ip2_2xFrictMat_CSPhys', # Wed Mar 10 15:08:56 2010, eudoxos@frigo 'NormalInelasticityLaw':'Law2_ScGeom_NormalInelasticityPhys_NormalInelasticity', # Wed Mar 17 15:50:59 2010, jduriez@c1solimara-l 'CapillaryCohesiveLaw':'CapillaryLaw', # Tue Mar 30 14:11:36 2010, sch50p@fluent-ph 'SimpleElasticRelationshipsWater':'Ip2_Frictmat_FrictMat_CapillaryLawPhys', # Tue Mar 30 14:20:36 2010, sch50p@fluent-ph 'CapillaryLaw':'Law2_ScGeom_CapillaryPhys_Capillarity', # Wed Mar 31 09:23:36 2010, sch50p@fluent-ph 'CapillaryParameters':'CapillaryPhys', # Wed Mar 31 09:25:03 2010, sch50p@fluent-ph 'Ip2_FrictMat_FrictMat_CapillaryLawPhys':'Ip2_FrictMat_FrictMat_CapillaryPhys', # Wed Mar 31 09:26:04 2010, sch50p@fluent-ph 'SimpleViscoelasticMat':'ViscElMat', # Fri Apr 9 19:25:38 2010, vaclav@flux 'SimpleViscoelasticPhys':'ViscElPhys', # Fri Apr 9 19:26:34 2010, vaclav@flux 'Law2_Spheres_Viscoelastic_SimpleViscoelastic':'Law2_ScGeom_ViscElPhys_Basic', # Fri Apr 9 19:28:02 2010, vaclav@flux 'Ip2_SimleViscoelasticMat_SimpleViscoelasticMat_SimpleViscoelasticPhys':'Ip2_ViscElMat_ViscElMat_ViscElPhys', # Fri Apr 9 19:28:48 2010, vaclav@flux 'MomentEngine':'TorqueEngine', # Sun May 2 16:09:34 2010, vaclav@flux 'JumpChangeSe3':'StepDisplacer', # Sun May 2 16:14:21 2010, vaclav@flux 'Ip2_2xCohFrictMat_NormalInelasticityPhys':'Ip2_2xNormalInelasticMat_NormalInelasticityPhys', # Fri Jun 4 15:36:41 2010, jduriez@c1solimara-l 'Ip2_2xCohFrictMat_NormalInelasticityPhys':'Ip2_2xNormalInelasticMat_NormalInelasticityPhys', # Fri Jun 4 15:37:01 2010, jduriez@c1solimara-l 'Ip2_2xCohFrictMat_NormalInelasticityPhys':'Ip2_2xNormalInelasticMat_NormalInelasticityPhys', # Fri Jun 4 15:37:16 2010, jduriez@c1solimara-l 'OpenGLRenderingEngine':'OpenGLRenderer', # Sat Jul 24 06:04:13 2010, vaclav@flux 'PeriodicPythonRunner':'PyRunner', # Wed Sep 1 16:41:50 2010, chia@engs-018373 'InteractionDispatchers':'InteractionLoop', # Mon Sep 27 13:44:54 2010, chia@engs-018373 'InteractionGeometry':'IGeom', # Thu Sep 30 10:39:24 2010, chia@engs-018373 'InteractionPhysics':'IPhys', # Thu Sep 30 10:39:43 2010, chia@engs-018373 'InteractionGeometryFunctor':'IGeomFunctor', # Thu Sep 30 14:27:43 2010, chia@engs-018373 'InteractionPhysicsFunctor':'IPhysFunctor', # Thu Sep 30 14:27:53 2010, chia@engs-018373 'InteractionPhysicsDispatcher':'IPhysDispatcher', # Thu Sep 30 14:28:12 2010, chia@engs-018373 'InteractionGeometryDispatcher':'IGeomDispatcher', # Thu Sep 30 14:28:22 2010, chia@engs-018373 'Law2_ScGeom_FrictPhys_Basic':'Law2_ScGeom_FrictPhys_CundallStrack', # Wed Oct 13 17:40:42 2010, bchareyre@dt-rv020 'Law2_ScGeom_CohFrictPhys_ElasticPlastic':'Law2_ScGeom_CohFrictPhys_CohesionMoment', # Wed Oct 13 17:47:09 2010, bchareyre@dt-rv020 'Law2_ScGeom_NormalInelasticityPhys_NormalInelasticity':'Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity', # Thu Oct 28 18:09:16 2010, jduriez@c1solimara-l 'SpiralEngine':'HelixEngine', # Sat Oct 30 05:52:06 2010, vaclav@flux 'InterpolatingSpiralEngine':'InterpolatingHelixEngine', # Sat Oct 30 05:52:21 2010, vaclav@flux 'SpiralInteractionLocator2d':'HelixInteractionLocator2d', # Sat Oct 30 05:53:04 2010, vaclav@flux 'Law2_ScGeom_CohFrictPhys_CohesionMoment':'Law2_ScGeom6D_CohFrictPhys_CohesionMoment', # Fri Nov 12 18:45:23 2010, bchareyre@dt-rv020 'Ig2_ChainedCylinder_ChainedCylinder_ScGeom':'Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D', # Fri Nov 12 18:47:44 2010, bchareyre@dt-rv020 'Ip2_2xCohFrictMat_CohFrictPhys':'Ip2_CohFrictMat_CohFrictMat_CohFrictPhys', # Tue Dec 21 16:11:28 2010, bchareyre@dt-rv020 'Ig2_Sphere_Sphere_L3Geom_Inc':'Ig2_Sphere_Sphere_L3Geom', # Sun Dec 26 11:11:05 2010, vaclav@flux 'Ig2_Wall_Sphere_L3Geom_Inc':'Ig2_Wall_Sphere_L3Geom', # Sun Dec 26 11:11:30 2010, vaclav@flux 'Ig2_Sphere_Sphere_L6Geom_Inc':'Ig2_Sphere_Sphere_L6Geom', # Sun Dec 26 11:11:53 2010, vaclav@flux ### END_RENAMED_CLASSES_LIST ### (do not delete this line; scripts/rename-class.py uses it } def updateScripts(scripts): ## Thanks goes to http://code.activestate.com/recipes/81330-single-pass-multiple-replace/ from UserDict import UserDict import re,os class Xlator(UserDict): "An all-in-one multiple string substitution class; adapted to match only whole words" def _make_regex(self): "Build a regular expression object based on the keys of the current dictionary" return re.compile(r"(\b%s\b)" % "|".join(self.keys())) ## adapted here def __call__(self, mo): "This handler will be invoked for each regex match" # Count substitutions self.count += 1 # Look-up string return self[mo.string[mo.start():mo.end()]] def xlat(self, text): "Translate text, returns the modified text." # Reset substitution counter self.count = 0 # Process text return self._make_regex().sub(self, text) # use the _deprecated dictionary for translation, but only when matching on words boundary xlator=Xlator(_deprecated) if len(scripts)==0: print "No scripts given to --update. Nothing to do." for s in scripts: if not s.endswith('.py'): raise RuntimeError("Refusing to do --update on file '"+s+"' (not *.py)") txt=open(s).read() txt2=xlator.xlat(txt) if xlator.count==0: print "%s: already up-to-date."%s else: os.rename(s,s+'~') out=open(s,'w'); out.write(txt2); out.close() print "%s: %d subtitution%s made, backup in %s~"%(s,xlator.count,'s' if xlator.count>1 else '',s) def cxxCtorsDict(proxyNamespace=__builtins__): """Return dictionary of class constructors for yade's c++ types, which should be used to update a namespace. Root classes are those that are directly wrapped by boost::python. These are only put to the dict. Derived classes (from these root classes) are faked by creating a callable which invokes appropriate root class constructor with the derived class parameter and passes remaining arguments to it. Classes that are neither root nor derived are exposed via callable object that constructs a Serializable of given type and passes the parameters. """ proxyNamespace={} import yade.wrapper for c in _allSerializables: try: proxyNamespace[c]=yade.wrapper.__dict__[c] except KeyError: pass # not registered properly # deprecated names for oldName in _deprecated.keys(): class warnWrap: def __init__(self,_old,_new): # assert(proxyNamespace.has_key(_new)) self.old,self.new=_old,_new def __call__(self,*args,**kw): import warnings; warnings.warn("Class `%s' was renamed to (or replaced by) `%s', update your code! (you can run 'yade --update script.py' to do that automatically)"%(self.old,self.new),DeprecationWarning,stacklevel=2); return yade.wrapper.__dict__[self.new](*args,**kw) proxyNamespace[oldName]=warnWrap(oldName,_deprecated[oldName]) return proxyNamespace # consistency check # if there are no serializables, then plugins were not loaded yet, probably if(len(_allSerializables)==0): raise ImportError("No classes deriving from Serializable found; you must call yade.boot.initialize to load plugins before importing yade.system.") trunk-2017.01a/py/tests/000077500000000000000000000000001304022710500147545ustar00rootroot00000000000000trunk-2017.01a/py/tests/__init__.py000066400000000000000000000027341304022710500170730ustar00rootroot00000000000000# encoding: utf-8 # 2009 © Václav Šmilauer """All defined functionality tests for yade.""" import unittest,inspect,sys # add any new test suites to the list here, so that they are picked up by testAll allTests=['wrapper','core','pbc','clump','cohesive-chain'] # all yade modules (ugly...) import yade.export,yade.linterpolation,yade.pack,yade.plot,yade.post2d,yade.timing,yade.utils,yade.ymport,yade.geom,yade.gridpfacet allModules=(yade.export,yade.linterpolation,yade.pack,yade.plot,yade.post2d,yade.timing,yade.utils,yade.ymport,yade.geom,yade.gridpfacet) try: import yade.qt allModules+=(yade.qt,) except ImportError: pass # fully qualified module names allTestsFQ=['yade.tests.'+test for test in allTests] def testModule(module): """Run all tests defined in the module specified, return TestResult object (http://docs.python.org/library/unittest.html#unittest.TextTestResult) for further processing. @param module: fully-qualified module name, e.g. yade.tests.wrapper """ suite=unittest.defaultTestLoader.loadTestsFromName(module) return unittest.TextTestRunner(stream=sys.stdout,verbosity=2).run(suite) def testAll(): """Run all tests defined in all yade.tests.* modules and return TestResult object for further examination.""" suite=unittest.defaultTestLoader.loadTestsFromNames(allTestsFQ) import doctest for mod in allModules: suite.addTest(doctest.DocTestSuite(mod)) return unittest.TextTestRunner(stream=sys.stdout,verbosity=2).run(suite) trunk-2017.01a/py/tests/clump.py000066400000000000000000000046351304022710500164560ustar00rootroot00000000000000 ''' Various computations affected by the periodic boundary conditions. ''' import unittest import random from yade.wrapper import * from yade._customConverters import * from yade import utils from yade import * from math import * from minieigen import * class TestSimpleClump(unittest.TestCase): "Test things on a simple clump composed of 2 spheres." def setUp(self): O.reset() r1,r2,p0,p1=1,.5,Vector3.Zero,Vector3(0,0,3) self.idC,(self.id1,self.id2)=O.bodies.appendClumped([ utils.sphere(p0,r1), utils.sphere(p1,r2) ]) def testConsistency(self): "Clump: ids and flags consistency" b1,b2,bC=[O.bodies[id] for id in (self.id1,self.id2,self.idC)] self.assertEqual(b1.clumpId,bC.id) self.assertEqual(b2.clumpId,bC.id) self.assertEqual(bC.clumpId,bC.id) self.assert_(bC.isClump) self.assert_(b1.isClumpMember) self.assert_(b2.isClumpMember) self.assert_(not bC.bounded) def testStaticProperties(self): "Clump: mass, centroid, intertia" b1,b2,bC=[O.bodies[id] for id in (self.id1,self.id2,self.idC)] # mass self.assertEqual(bC.state.mass,b1.state.mass+b2.state.mass) # centroid S=b1.state.mass*b1.state.pos+b2.state.mass*b2.state.pos c=S/bC.state.mass self.assertAlmostEqual(bC.state.pos[0],c[0]); self.assertAlmostEqual(bC.state.pos[1],c[1]); self.assertAlmostEqual(bC.state.pos[2],c[2]); # inertia i1,i2=(8./15)*pi*b1.material.density*b1.shape.radius**5, (8./15)*pi*b2.material.density*b2.shape.radius**5 # inertia of spheres iMax=i1+i2+b1.state.mass*(b1.state.pos-c).norm()**2+b2.state.mass*(b2.state.pos-c).norm()**2 # minimum principal inertia iMin=i1+i2 # perpendicular to the # the order of bC.state.inertia is arbitrary (though must match the orientation) iC=list(bC.state.inertia); iC.sort() self.assertAlmostEqual(iC[0],iMin) self.assertAlmostEqual(iC[1],iMax) self.assertAlmostEqual(iC[2],iMax) # check orientation...? #self.assertAlmostEqual def testVelocity(self): "Clump: velocities of member assigned by NewtonIntegrator" s1,s2,sC=[O.bodies[id].state for id in (self.id1,self.id2,self.idC)] O.dt=0 sC.vel=(1.,.2,.4) sC.angVel=(0,.4,.1) O.engines=[NewtonIntegrator()]; O.step() # update velocities # linear velocities self.assertEqual(s1.vel,sC.vel+sC.angVel.cross(s1.pos-sC.pos)) self.assertEqual(s2.vel,sC.vel+sC.angVel.cross(s2.pos-sC.pos)) # angular velocities self.assertEqual(s1.angVel,sC.angVel); self.assertEqual(s2.angVel,sC.angVel); trunk-2017.01a/py/tests/cohesive-chain.py000066400000000000000000000051461304022710500202210ustar00rootroot00000000000000# encoding: utf-8 # 2010 © Bruno Chareyre ''' Motion of a "sinusoidal" beam made of cylinders. The test checks the position and velocity of the free end of the bending beam subjected to gravitational load. It is similar to scripts/test/chained-cylinder-spring.py but with less elements. positions and velocity are compared during the transient oscillations, only positions are compared for the larger time since residual velocity is compiler-dependent (see https://lists.launchpad.net/yade-dev/msg06178.html). ''' import unittest import random from yade.wrapper import * from yade._customConverters import * from yade.gridpfacet import * from math import * from minieigen import * class TestCohesiveChain(unittest.TestCase): # prefix test names with PBC: def setUp(self): O.reset(); young=1.0e3 poisson=5 density=2.60e3 frictionAngle=radians(30) O.materials.append(CohFrictMat(young=young,poisson=poisson,density=density,frictionAngle=frictionAngle,normalCohesion=1e13,shearCohesion=1e13,momentRotationLaw=True)) O.dt=1e-3 O.engines=[ ForceResetter(), InsertionSortCollider([ Bo1_ChainedCylinder_Aabb(), Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_ChainedCylinder_ChainedCylinder_ScGeom6D(),Ig2_Sphere_ChainedCylinder_CylScGeom()], [Ip2_CohFrictMat_CohFrictMat_CohFrictPhys(setCohesionNow=True,setCohesionOnNewContacts=True)], [Law2_ScGeom6D_CohFrictPhys_CohesionMoment()]), ## Apply gravity ## Motion equation NewtonIntegrator(damping=0.15,gravity=[0,-9.81,0]) ] #Generate a spiral Ne=10 for i in range(0, Ne): omeg=95.0/float(Ne); hy=0.05; hz=0.07; px=float(i)*(omeg/60.0); py=sin(float(i)*omeg)*hy; pz=cos(float(i)*omeg)*hz; px2=float(i+1.)*(omeg/60.0); py2=sin(float(i+1.)*omeg)*hy; pz2=cos(float(i+1.)*omeg)*hz; chainedCylinder(begin=Vector3(pz,py,px), radius=0.005,end=Vector3(pz2,py2,px2),color=Vector3(0.6,0.5,0.5)) O.bodies[Ne-1].state.blockedDOFs='xyzXYZ' def testMotion(self): "CohesiveChain: velocity/positions tested in transient dynamics and equilibrium state" #target values tv1=-0.790576599652;tp1=-0.0483370740415;tv2=-0.000494271551993;tp2=-0.0611987315415; tolerance = 10e-3 O.run(100,True) v1=O.bodies[0].state.vel[1];p1=O.bodies[0].state.pos[1] #print v1,p1 O.run(10000,True) v2=O.bodies[0].state.vel[1];p2=O.bodies[0].state.pos[1] #print v2,p2 self.assertTrue(abs(tv1-v1) """ Core functionality (Scene in c++), such as accessing bodies, materials, interactions. Specific functionality tests should go to engines.py or elsewhere, not here. """ import unittest import random from yade.wrapper import * from yade._customConverters import * from yade import utils from yade import * from math import * from minieigen import * ## TODO tests class TestForce(unittest.TestCase): pass class TestTags(unittest.TestCase): pass class TestInteractions(unittest.TestCase): def setUp(self): O.reset() def testEraseBodiesInInteraction(self): O.reset() id1 = O.bodies.append(utils.sphere([0.5,0.5,0.0+0.095],.1)) id2 = O.bodies.append(utils.sphere([0.5,0.5,0.0+0.250],.1)) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_L3Geom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_L3Geom_FrictPhys_ElPerfPl()] ), NewtonIntegrator(damping=0.1,gravity=(0,0,-9.81)) ] O.dt=.5e-4*utils.PWaveTimeStep() O.step() O.bodies.erase(id1) O.step() class TestLoop(unittest.TestCase): def setUp(self): O.reset() def testSubstepping(self): 'Loop: substepping' O.engines=[ForceResetter(),PyRunner(initRun=True,iterPeriod=1,command='pass')] # value outside the loop self.assert_(O.subStep==-1) # O.subStep is meaningful when substepping O.subStepping=True O.step(); self.assert_(O.subStep==0) O.step(); self.assert_(O.subStep==1) # when substepping is turned off in the middle of the loop, the next step finishes the loop O.subStepping=False O.step(); self.assert_(O.subStep==-1) # subStep==0 inside the loop without substepping O.engines=[PyRunner(initRun=True,iterPeriod=1,command='if O.subStep!=0: raise RuntimeError("O.subStep!=0 inside the loop with O.subStepping==False!")')] O.step() def testEnginesModificationInsideLoop(self): 'Loop: O.engines can be modified inside the loop transparently.' O.engines=[ PyRunner(initRun=True,iterPeriod=1,command='from yade import *; O.engines=[ForceResetter(),GravityEngine(),NewtonIntegrator()]'), # change engines here ForceResetter() # useless engine ] O.subStepping=True # run prologue and the first engine, which modifies O.engines O.step(); O.step(); self.assert_(O.subStep==1) self.assert_(len(O.engines)==3) # gives modified engine sequence transparently self.assert_(len(O._nextEngines)==3) self.assert_(len(O._currEngines)==2) O.step(); O.step(); # run the 2nd ForceResetter, and epilogue self.assert_(O.subStep==-1) # start the next step, nextEngines should replace engines automatically O.step() self.assert_(O.subStep==0) self.assert_(len(O._nextEngines)==0) self.assert_(len(O.engines)==3) self.assert_(len(O._currEngines)==3) def testDead(self): 'Loop: dead engines are not run' O.engines=[PyRunner(dead=True,initRun=True,iterPeriod=1,command='pass')] O.step(); self.assert_(O.engines[0].nDone==0) class TestIO(unittest.TestCase): def testSaveAllClasses(self): 'I/O: All classes can be saved and loaded with boost::serialization' import yade.system failed=set() for c in yade.system.childClasses('Serializable'): O.reset() try: O.miscParams=[eval(c)()] O.saveTmp(quiet=True) O.loadTmp(quiet=True) except (RuntimeError,ValueError): failed.add(c) failed=list(failed); failed.sort() self.assert_(len(failed)==0,'Failed classes were: '+' '.join(failed)) class TestMaterialStateAssociativity(unittest.TestCase): def setUp(self): O.reset() def testThrowsAtBadCombination(self): "Material+State: throws when body has material and state that don't work together." b=Body() b.mat=CpmMat() b.state=State() #should be CpmState() O.bodies.append(b) self.assertRaises(RuntimeError,lambda: O.step()) # throws runtime_error def testThrowsAtNullState(self): "Material+State: throws when body has material but NULL state." b=Body() b.mat=Material() b.state=None # → shared_ptr() by boost::python O.bodies.append(b) self.assertRaises(RuntimeError,lambda: O.step()) def testMaterialReturnsState(self): "Material+State: CpmMat returns CpmState when asked for newAssocState" self.assert_(CpmMat().newAssocState().__class__==CpmState) class TestBodies(unittest.TestCase): def setUp(self): O.reset() self.count=100 O.bodies.append([utils.sphere([random.random(),random.random(),random.random()],random.random()) for i in range(0,self.count)]) random.seed() def testIterate(self): "Bodies: Iteration" counted=0 for b in O.bodies: counted+=1 self.assert_(counted==self.count) def testLen(self): "Bodies: len(O.bodies)" self.assert_(len(O.bodies)==self.count) def testErase(self): "Bodies: erased bodies are None in python" O.bodies.erase(0) self.assert_(O.bodies[0]==None) def testNegativeIndex(self): "Bodies: Negative index counts backwards (like python sequences)." self.assert_(O.bodies[-1]==O.bodies[self.count-1]) def testErasedIterate(self): "Bodies: Iterator silently skips erased ones" removed,counted=0,0 for i in range(0,10): id=random.randint(0,self.count-1) if O.bodies[id]: O.bodies.erase(id);removed+=1 for b in O.bodies: counted+=1 self.assert_(counted==self.count-removed) def testErasedAndNewlyCreatedSphere(self): "Bodies: The bug is described in LP:1001194. If the new body was created after deletion of previous, it has no bounding box" O.reset() id1 = O.bodies.append(utils.sphere([0.0, 0.0, 0.0],0.5)) id2 = O.bodies.append(utils.sphere([0.0, 2.0, 0.0],0.5)) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_L3Geom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_L3Geom_FrictPhys_ElPerfPl()] ), NewtonIntegrator(damping=0.1,gravity=(0,0,-9.81)) ] O.dt=.5e-4*utils.PWaveTimeStep() #Before first step the bodies should not have bounds self.assert_(O.bodies[id1].bound==None and O.bodies[id2].bound==None) O.run(1, True) #After first step the bodies should have bounds self.assert_(O.bodies[id1].bound!=None and O.bodies[id2].bound!=None) #Add 3rd body id3 = O.bodies.append(utils.sphere([0.0, 4.0, 0.0],0.5)) O.run(1, True) self.assert_(O.bodies[id1].bound!=None and O.bodies[id2].bound!=None and O.bodies[id3].bound!=None) #Remove 3rd body O.bodies.erase(id3) O.run(1, True) #Add 4th body id4 = O.bodies.append(utils.sphere([0.0, 6.0, 0.0],0.5)) O.run(1, True) self.assert_(O.bodies[id1].bound!=None and O.bodies[id2].bound!=None and O.bodies[id4].bound!=None) class TestMaterials(unittest.TestCase): def setUp(self): # common setup for all tests in this class O.reset() O.materials.append([ FrictMat(young=1,label='materialZero'), ElastMat(young=100,label='materialOne') ]) O.bodies.append([ utils.sphere([0,0,0],.5,material=0), utils.sphere([1,1,1],.5,material=0), utils.sphere([1,1,1],.5,material=1) ]) def testShared(self): "Material: shared_ptr's makes change in material immediate everywhere" O.bodies[0].mat.young=23423333 self.assert_(O.bodies[0].mat.young==O.bodies[1].mat.young) def testSharedAfterReload(self): "Material: shared_ptr's are preserved when saving/loading" O.saveTmp(quiet=True); O.loadTmp(quiet=True) O.bodies[0].mat.young=9087438484 self.assert_(O.bodies[0].mat.young==O.bodies[1].mat.young) def testLen(self): "Material: len(O.materials)" self.assert_(len(O.materials)==2) def testNegativeIndex(self): "Material: negative index counts backwards." self.assert_(O.materials[-1]==O.materials[1]) def testIterate(self): "Material: iteration over O.materials" counted=0 for m in O.materials: counted+=1 self.assert_(counted==len(O.materials)) def testAccess(self): "Material: find by index or label; KeyError raised for invalid label." self.assertRaises(KeyError,lambda: O.materials['nonexistent label']) self.assert_(O.materials['materialZero']==O.materials[0]) class TestMatchMaker(unittest.TestCase): def setUp(self): O.reset(); def testMatchMakerCollisions(self): fr = 0.5;rho=2000 tc = 0.001; en = 0.5; et = 0.5; mat1 = O.materials.append(ViscElMat(frictionAngle=fr,tc=tc,en=en,et=et,density=rho)) mat2 = O.materials.append(ViscElMat(frictionAngle=fr,tc=tc,en=en,et=et,density=rho)) mat3 = O.materials.append(ViscElMat(frictionAngle=fr,tc=tc,en=en,et=et,density=rho)) r1 = 0.002381 r2 = 0.002381 id11 = O.bodies.append(utils.sphere(center=[0,0,0],radius=r1,material=mat1,fixed=True,color=[0,0,1])) id12 = O.bodies.append(utils.sphere(center=[0,0,(r1+r2)],radius=r2,material=mat2,fixed=False,color=[0,0,1])) id21 = O.bodies.append(utils.sphere(center=[3*r1,0,0],radius=r1,material=mat1,fixed=True,color=[0,1,0])) id22 = O.bodies.append(utils.sphere(center=[3*r1,0,(r1+r2)],radius=r2,material=mat3,fixed=False,color=[0,1,0])) id31 = O.bodies.append(utils.sphere(center=[6*r1,0,0],radius=r1,material=mat2,fixed=True,color=[1,0,0])) id32 = O.bodies.append(utils.sphere(center=[6*r1,0,(r1+r2)],radius=r2,material=mat3,fixed=False,color=[1,0,0])) O.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()],verletDist=r1*10.0), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys( en=MatchMaker(matches=((mat1,mat2,.1),(mat1,mat3,.2),(mat2,mat3,.4))), et=MatchMaker(matches=((mat1,mat2,.7),(mat1,mat3,.8),(mat2,mat3,.9))), frictAngle=MatchMaker(matches=((mat1,mat2,.1),(mat1,mat3,.2),(mat2,mat3,.3))) )], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0,gravity=[0,0,-9.81]), ] O.step() self.assertTrue((atan(O.interactions[id11,id12].phys.tangensOfFrictionAngle)-0.1)==0) self.assertTrue((atan(O.interactions[id21,id22].phys.tangensOfFrictionAngle)-0.2)==0) self.assertTrue((atan(O.interactions[id31,id32].phys.tangensOfFrictionAngle)-0.3)==0) self.assertTrue(round(O.interactions[id11,id12].phys.cn, 3) - 0.26 == 0) self.assertTrue(round(O.interactions[id21,id22].phys.cn, 3) - 0.182 == 0) self.assertTrue(round(O.interactions[id31,id32].phys.cn, 3) - 0.104 == 0) self.assertTrue(round(O.interactions[id11,id12].phys.cs, 3) - 0.012== 0) self.assertTrue(round(O.interactions[id21,id22].phys.cs, 3) - 0.007 == 0) self.assertTrue(round(O.interactions[id31,id32].phys.cs, 3) - 0.003 == 0) trunk-2017.01a/py/tests/engines.py000066400000000000000000000074741304022710500167720ustar00rootroot00000000000000'test functionality of individual engines' import unittest import random from yade.wrapper import * from yade._customConverters import * from yade import utils from yade import * from math import * from minieigen import * class TestKinematicEngines(unittest.TestCase): def testKinematicEngines(self): 'Engines: kinematic engines' tolerance = 1e-5 rotIndex=1.0 angVelTemp = pi/rotIndex O.reset() id_fixed_transl = O.bodies.append(utils.sphere((0.0,0.0,0.0),1.0,fixed=True)) id_nonfixed_transl = O.bodies.append(utils.sphere((0.0,5.0,0.0),1.0,fixed=False)) id_fixed_rot = O.bodies.append(utils.sphere((0.0,10.0,10.0),1.0,fixed=True)) id_nonfixed_rot = O.bodies.append(utils.sphere((0.0,15.0,10.0),1.0,fixed=False)) id_fixed_helix = O.bodies.append(utils.sphere((0.0,20.0,10.0),1.0,fixed=True)) id_nonfixed_helix = O.bodies.append(utils.sphere((0.0,25.0,10.0),1.0,fixed=False)) O.engines=[ TranslationEngine(velocity = 1.0, translationAxis = [1.0,0,0], ids = [id_fixed_transl]), TranslationEngine(velocity = 1.0, translationAxis = [1.0,0,0], ids = [id_nonfixed_transl]), RotationEngine(angularVelocity = pi/angVelTemp, rotationAxis = [0.0,1.0,0.0], rotateAroundZero = True, zeroPoint = [0.0,0.0,0.0], ids = [id_fixed_rot]), RotationEngine(angularVelocity = pi/angVelTemp, rotationAxis = [0.0,1.0,0.0], rotateAroundZero = True, zeroPoint = [0.0,5.0,0.0], ids = [id_nonfixed_rot]), HelixEngine(angularVelocity = pi/angVelTemp, rotationAxis = [0.0,1.0,0.0], linearVelocity = 1.0, zeroPoint = [0.0,0.0,0.0], ids = [id_fixed_helix]), HelixEngine(angularVelocity = pi/angVelTemp, rotationAxis = [0.0,1.0,0.0], linearVelocity = 1.0, zeroPoint = [0.0,5.0,0.0], ids = [id_nonfixed_helix]), ForceResetter(), NewtonIntegrator() ] O.dt = 1.0 for i in range(0,2): O.step() self.assertTrue(abs(O.bodies[id_fixed_transl].state.pos[0] - O.iter) < tolerance) #Check translation of fixed bodies self.assertTrue(abs(O.bodies[id_nonfixed_transl].state.pos[0] - O.iter) < tolerance) #Check translation of nonfixed bodies self.assertTrue(abs(O.bodies[id_fixed_rot].state.pos[0]-10.0*sin(pi/angVelTemp*O.iter)) ''' Various computations affected by the periodic boundary conditions. ''' import unittest import random,math from yade.wrapper import * from yade._customConverters import * from yade import utils from yade import * from minieigen import * class TestPBC(unittest.TestCase): # prefix test names with PBC: def setUp(self): O.reset(); O.periodic=True; O.cell.setBox(2.5,2.5,3) self.cellDist=Vector3i(0,0,10) # how many cells away we go self.relDist=Vector3(0,.999999999999999999,0) # rel position of the 2nd ball within the cell self.initVel=Vector3(0,0,5) O.bodies.append(utils.sphere((1,1,1),.5)) self.initPos=Vector3([O.bodies[0].state.pos[i]+self.relDist[i]+self.cellDist[i]*O.cell.refSize[i] for i in (0,1,2)]) O.bodies.append(utils.sphere(self.initPos,.5)) #print O.bodies[1].state.pos O.bodies[1].state.vel=self.initVel O.engines=[NewtonIntegrator(warnNoForceReset=False)] O.cell.velGrad=Matrix3(0,0,0, 0,0,0, 0,0,-1) O.dt=0 # do not change positions with dt=0 in NewtonIntegrator, but still update velocities from velGrad def testVelGrad(self): 'PBC: velGrad changes hSize, accumulates in trsf' O.dt=1e-3 hSize,trsf=O.cell.hSize,Matrix3.Identity hSize0=hSize O.step() for i in range(0,10): O.step(); hSize+=O.dt*O.cell.velGrad*hSize; trsf+=O.dt*O.cell.velGrad*trsf for i in range(0,len(O.cell.hSize)): self.assertAlmostEqual(hSize[i],O.cell.hSize[i]) self.assertAlmostEqual(trsf[i],O.cell.trsf[i]) def testTrsfChange(self): 'PBC: chaing trsf changes hSize0, but does not modify hSize' O.dt=1e-2 O.step() O.cell.trsf=Matrix3.Identity for i in range(0,len(O.cell.hSize)): self.assertAlmostEqual(O.cell.hSize0[i],O.cell.hSize[i]) def testDegenerate(self): "PBC: degenerate cell raises exception" self.assertRaises(RuntimeError,lambda: setattr(O.cell,'hSize',Matrix3(1,0,0, 0,0,0, 0,0,1))) def testSetBox(self): "PBC: setBox modifies hSize correctly" O.cell.setBox(2.55,11,45) self.assert_(O.cell.hSize==Matrix3(2.55,0,0, 0,11,0, 0,0,45)); def testHomotheticResizeVel(self): "PBC: homothetic cell deformation adjusts particle velocity " O.dt=1e-5 O.step() s1=O.bodies[1].state self.assertAlmostEqual(s1.vel[2],self.initVel[2]+self.initPos[2]*O.cell.velGrad[2,2]) def testScGeomIncidentVelocity(self): "PBC: ScGeom computes incident velocity correctly" O.run(2,1) O.engines=[InteractionLoop([Ig2_Sphere_Sphere_ScGeom()],[Ip2_FrictMat_FrictMat_FrictPhys()],[])] i=utils.createInteraction(0,1) self.assertEqual(self.initVel,i.geom.incidentVel(i,avoidGranularRatcheting=True)) self.assertEqual(self.initVel,i.geom.incidentVel(i,avoidGranularRatcheting=False)) self.assertAlmostEqual(self.relDist[1],1-i.geom.penetrationDepth) def testL3GeomIncidentVelocity(self): "PBC: L3Geom computes incident velocity correctly" O.step() O.engines=[ForceResetter(),InteractionLoop([Ig2_Sphere_Sphere_L3Geom()],[Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_L3Geom_FrictPhys_ElPerfPl(noBreak=True)]),NewtonIntegrator()] i=utils.createInteraction(0,1) O.dt=1e-10; O.step() # tiny timestep, to not move the normal too much self.assertAlmostEqual(self.initVel.norm(),(i.geom.u/O.dt).norm()) def testKineticEnergy(self): "PBC: utils.kineticEnergy considers only fluctuation velocity, not the velocity gradient" O.step() # updates velocity with homotheticCellResize # ½(mv²+ωIω) # #0 is still, no need to add it; #1 has zero angular velocity # we must take self.initVel since O.bodies[1].state.vel now contains the homothetic resize which utils.kineticEnergy is supposed to compensate back Ek=.5*O.bodies[1].state.mass*self.initVel.squaredNorm() self.assertAlmostEqual(Ek,utils.kineticEnergy()) trunk-2017.01a/py/tests/wrapper.py000066400000000000000000000152761304022710500170210ustar00rootroot00000000000000# encoding: utf-8 # 2009 © Václav Šmilauer """ This test module covers python/c++ transitions, for both classes deriving from Serializable, but also for other classes that we wrap (like miniEigen). """ import unittest from yade.wrapper import * from yade._customConverters import * from math import * from yade import system from yade import * from minieigen import * allClasses=system.childClasses('Serializable') class TestObjectInstantiation(unittest.TestCase): def setUp(self): pass # no setup needed for tests here def testClassCtors(self): "Core: correct types are instantiated" # correct instances created with Foo() syntax for r in allClasses: obj=eval(r)(); self.assert_(obj.__class__.__name__==r,'Failed for '+r) def testRootDerivedCtors_attrs_few(self): "Core: class ctor's attributes" # attributes passed when using the Foo(attr1=value1,attr2=value2) syntax gm=Shape(wire=True); self.assert_(gm.wire==True) def testDispatcherCtor(self): "Core: dispatcher ctors with functors" # dispatchers take list of their functors in the ctor # same functors are collapsed in one cld1=LawDispatcher([Law2_ScGeom_FrictPhys_CundallStrack(),Law2_ScGeom_FrictPhys_CundallStrack()]); self.assert_(len(cld1.functors)==1) # two different make two different, right? cld2=LawDispatcher([Law2_ScGeom_FrictPhys_CundallStrack(),Law2_ScGeom6D_CohFrictPhys_CohesionMoment()]); self.assert_(len(cld2.functors)==2) def testInteractionLoopCtor(self): "Core: InteractionLoop special ctor" # InteractionLoop takes 3 lists id=InteractionLoop([Ig2_Facet_Sphere_ScGeom(),Ig2_Sphere_Sphere_ScGeom()],[Ip2_FrictMat_FrictMat_FrictPhys()],[Law2_ScGeom_FrictPhys_CundallStrack()],) self.assert_(len(id.geomDispatcher.functors)==2) self.assert_(id.geomDispatcher.__class__==IGeomDispatcher().__class__) self.assert_(id.physDispatcher.functors[0].__class__==Ip2_FrictMat_FrictMat_FrictPhys().__class__) self.assert_(id.lawDispatcher.functors[0].__class__==Law2_ScGeom_FrictPhys_CundallStrack().__class__) def testParallelEngineCtor(self): "Core: ParallelEngine special ctor" pe=ParallelEngine([InsertionSortCollider(),[BoundDispatcher(),ForceResetter()]]) self.assert_(pe.slaves[0].__class__==InsertionSortCollider().__class__) self.assert_(len(pe.slaves[1])==2) pe.slaves=[] self.assert_(len(pe.slaves)==0) ## ## testing incorrect operations that should raise exceptions ## def testWrongFunctorType(self): "Core: dispatcher and functor type mismatch is detected" # dispatchers accept only correct functors self.assertRaises(TypeError,lambda: LawDispatcher([Bo1_Sphere_Aabb()])) def testInvalidAttr(self): 'Core: invalid attribute access raises AttributeError' # accessing invalid attributes raises AttributeError self.assertRaises(AttributeError,lambda: Sphere(attributeThatDoesntExist=42)) self.assertRaises(AttributeError,lambda: Sphere().attributeThatDoesntExist) ## ## attribute flags ## def testTriggerPostLoad(self): 'Core: Attr::triggerPostLoad' # TranslationEngine normalizes translationAxis automatically # anything else could be tested te=TranslationEngine(); te.translationAxis=(0,2,0) self.assert_(te.translationAxis==(0,1,0)) def testHidden(self): 'Core: Attr::hidden' # hidden attributes are not wrapped in python at all self.assert_(not hasattr(Interaction(),'iterLastSeen')) def testNoSave(self): 'Core: Attr::noSave' # update bound of the particle O.bodies.append(utils.sphere((0,0,0),1)) O.engines=[InsertionSortCollider([Bo1_Sphere_Aabb()]),NewtonIntegrator()] O.step() O.saveTmp(quiet=True) mn0=Vector3(O.bodies[0].bound.min) O.reload(quiet=True) mn1=Vector3(O.bodies[0].bound.min) # check that the minimum is not saved self.assert_(not isnan(mn0[0])) self.assert_(isnan(mn1[0])) def _testReadonly(self): 'Core: Attr::readonly' self.assertRaises(AttributeError,lambda: setattr(Body(),'id',3)) class TestEigenWrapper(unittest.TestCase): def assertSeqAlmostEqual(self,v1,v2): "floating-point comparison of vectors/quaterions" self.assertEqual(len(v1),len(v2)); for i in range(len(v1)): self.assertAlmostEqual(v1[i],v2[i],msg='Component '+str(i)+' of '+str(v1)+' and '+str(v2)) def testVector2(self): "Math: Vector2 operations" v=Vector2(1,2); v2=Vector2(3,4) self.assert_(v+v2==Vector2(4,6)) self.assert_(Vector2().UnitX.dot(Vector2().UnitY)==0) self.assert_(Vector2().Zero.norm()==0) def testVector3(self): "Math: Vector3 operations" v=Vector3(3,4,5); v2=Vector3(3,4,5) self.assert_(v[0]==3 and v[1]==4 and v[2]==5) self.assert_(v.squaredNorm()==50) self.assert_(v==(3,4,5)) # comparison with list/tuple self.assert_(v==[3,4,5]) self.assert_(v==v2) x,y,z,one=Vector3().UnitX,Vector3().UnitY,Vector3().UnitZ,Vector3().Ones self.assert_(x+y+z==one) self.assert_(x.dot(y)==0) self.assert_(x.cross(y)==z) def testQuaternion(self): "Math: Quaternion operations" # construction q1=Quaternion((0,0,1),pi/2) q2=Quaternion(Vector3(0,0,1),pi/2) q1==q2 x,y,z,one=Vector3().UnitX,Vector3().UnitY,Vector3().UnitZ,Vector3().Ones self.assertSeqAlmostEqual(q1*x,y) self.assertSeqAlmostEqual(q1*q1*x,-x) self.assertSeqAlmostEqual(q1*q1.conjugate(),Quaternion().Identity) self.assertSeqAlmostEqual(q1.toAxisAngle()[0],(0,0,1)) self.assertAlmostEqual(q1.toAxisAngle()[1],pi/2) def testMatrix3(self): "Math: Matrix3 operations" #construction m1=Matrix3(1,0,0,0,1,0,0,0,1) # comparison self.assert_(m1==Matrix3().Identity) # rotation matrix from quaternion m1=Quaternion(Vector3(0,0,1),pi/2).toRotationMatrix() # multiplication with vectors self.assertSeqAlmostEqual(m1*Vector3().UnitX,Vector3().UnitY) # determinant m2=Matrix3(-2,2,-3,-1,1,3,2,0,-1) self.assertEqual(m2.determinant(),18) # inverse inv=Matrix3(-0.055555555555556,0.111111111111111,0.5,0.277777777777778,0.444444444444444,0.5,-0.111111111111111,0.222222222222222,0.0) m2inv=m2.inverse() self.assertSeqAlmostEqual(m2inv,inv) # matrix-matrix multiplication self.assertSeqAlmostEqual(Matrix3().Identity*Matrix3().Identity,Matrix3().Identity) m3=Matrix3(1,2,3,4,5,6,-1,0,3) m33=m3*m3 self.assertSeqAlmostEqual(m33,Matrix3(6,12,24,18,33,60,-4,-2,6)) # not really wm3 thing, but closely related # no way to test this currently, as State::se3 is not serialized (State::pos and State::ori are serialized instead...) #def testSe3Conversion(self): # return # pp=State() # pp.se3=(Vector3().Zero,Quaternion().Identity) # self.assert_(pp['se3'][0]==Vector3().Zero) # self.assert_(pp['se3'][1]==Quaternion().Identity) # pp.se3=((1,2,3),Quaternion((1,1,1),pi/4)) # self.assert_(pp['se3'][0]==(1,2,3)) # self.assert_(pp['se3'][0]==pp.pos) # self.assert_(pp['se3'][1]==Quaternion((1,1,1),pi/4)) # self.assert_(pp['se3'][1]==pp.ori) trunk-2017.01a/py/timing.py000066400000000000000000000155111304022710500154560ustar00rootroot00000000000000# encoding: utf-8 # 2008 © Václav Šmilauer """Functions for accessing timing information stored in engines and functors. See :ref:`timing` section of the programmer's manual, `wiki page `_ for some examples. """ from yade.wrapper import * def _resetEngine(e): if e.timingDeltas: e.timingDeltas.reset() if isinstance(e,Functor): return if isinstance(e,Dispatcher): for f in e.functors: _resetEngine(f) elif isinstance(e,ParallelEngine): for s in e.slaves: _resetEngine(s) e.execTime,e.execCount=0,0 def reset(): "Zero all timing data." for e in O.engines: _resetEngine(e) _statCols={'label':40,'count':20,'time':20,'relTime':20} _maxLev=3 def _formatLine(label,time,count,totalTime,level): sp,negSp=' '*level*2,' '*(_maxLev-level)*2 raw=[] raw.append(label) raw.append(str(count) if count>=0 else '') raw.append((str(time/1000)+u'us') if time>=0 else '') raw.append(('%6.2f%%'%(time*100./totalTime)) if totalTime>0 else '') return u' '.join([ (sp+raw[0]).ljust(_statCols['label']), (raw[1]+negSp).rjust(_statCols['count']), (raw[2]+negSp).rjust(_statCols['time']), (raw[3]+negSp).rjust(_statCols['relTime']), ]) def _delta_stats(deltas,totalTime,level): ret=0 deltaTime=sum([d[1] for d in deltas.data]) for d in deltas.data: print _formatLine(d[0],d[1],d[2],totalTime,level); ret+=1 if len(deltas.data)>1: print _formatLine('TOTAL',deltaTime,sum(d[2] for d in deltas.data),totalTime,level); ret+=1 return ret def _engines_stats(engines,totalTime,level): lines=0; hereLines=0 for e in engines: if not isinstance(e,Functor): print _formatLine(u'"'+e.label+'"' if e.label else e.__class__.__name__,e.execTime,e.execCount,totalTime,level); lines+=1; hereLines+=1 if e.timingDeltas: if isinstance(e,Functor): print _formatLine(e.__class__.__name__,sum(d[1] for d in e.timingDeltas.data),sum(d[2] for d in e.timingDeltas.data),totalTime,level); lines+=1; hereLines+=1 execTime=sum([d[1] for d in e.timingDeltas.data]) else: execTime=e.execTime lines+=_delta_stats(e.timingDeltas,execTime,level+1) if isinstance(e,Dispatcher): lines+=_engines_stats(e.functors,e.execTime,level+1) if isinstance(e,InteractionLoop): lines+=_engines_stats(e.geomDispatcher.functors,e.execTime,level+1) lines+=_engines_stats(e.physDispatcher.functors,e.execTime,level+1) lines+=_engines_stats(e.lawDispatcher.functors,e.execTime,level+1) elif isinstance(e,ParallelEngine): lines+=_engines_stats(e.slave,e.execTime,level+1) if hereLines>1 and not isinstance(e,Functor): print _formatLine('TOTAL',totalTime,-1,totalTime,level); lines+=1 return lines def stats(): """Print summary table of timing information from engines and functors. Absolute times as well as percentages are given. Sample output: .. code-block:: none Name Count Time Rel. time ------------------------------------------------------------------------------------------------------- ForceResetter 102 2150us 0.02% "collider" 5 64200us 0.60% InteractionLoop 102 10571887us 98.49% "combEngine" 102 8362us 0.08% "newton" 102 73166us 0.68% "cpmStateUpdater" 1 9605us 0.09% PyRunner 1 136us 0.00% "plotDataCollector" 1 291us 0.00% TOTAL 10733564us 100.00% sample output (compiled with -DENABLE_PROFILING=1 option): .. code-block:: none Name Count Time Rel. time ------------------------------------------------------------------------------------------------------- ForceResetter 102 2150us 0.02% "collider" 5 64200us 0.60% InteractionLoop 102 10571887us 98.49% Ig2_Sphere_Sphere_ScGeom 1222186 1723168us 16.30% Ig2_Sphere_Sphere_ScGeom 1222186 1723168us 100.00% Ig2_Facet_Sphere_ScGeom 753 1157us 0.01% Ig2_Facet_Sphere_ScGeom 753 1157us 100.00% Ip2_CpmMat_CpmMat_CpmPhys 11712 26015us 0.25% end of Ip2_CpmPhys 11712 26015us 100.00% Ip2_FrictMat_CpmMat_FrictPhys 0 0us 0.00% Law2_ScGeom_CpmPhys_Cpm 3583872 4819289us 45.59% GO A 1194624 1423738us 29.54% GO B 1194624 1801250us 37.38% rest 1194624 1594300us 33.08% TOTAL 3583872 4819289us 100.00% Law2_ScGeom_FrictPhys_CundallStrack 0 0us 0.00% "combEngine" 102 8362us 0.08% "newton" 102 73166us 0.68% "cpmStateUpdater" 1 9605us 0.09% PyRunner 1 136us 0.00% "plotDataCollector" 1 291us 0.00% TOTAL 10733564us 100.00% """ print 'Name'.ljust(_statCols['label'])+' '+'Count'.rjust(_statCols['count'])+' '+'Time'.rjust(_statCols['time'])+' '+'Rel. time'.rjust(_statCols['relTime']) print '-'*(sum([_statCols[k] for k in _statCols])+len(_statCols)-1) _engines_stats(O.engines,sum([e.execTime for e in O.engines]),0) print trunk-2017.01a/py/utils.py000066400000000000000000001275241304022710500153370ustar00rootroot00000000000000# encoding: utf-8 # # utility functions for yade # # 2008-2009 © Václav Šmilauer """Heap of functions that don't (yet) fit anywhere else. Devs: please DO NOT ADD more functions here, it is getting too crowded! """ import math,random,doctest,geom,numpy from yade import * from yade.wrapper import * try: # use psyco if available import psyco psyco.full() except ImportError: pass from minieigen import * # c++ implementations for performance reasons from yade._utils import * def saveVars(mark='',loadNow=True,**kw): """Save passed variables into the simulation so that it can be recovered when the simulation is loaded again. For example, variables *a*, *b* and *c* are defined. To save them, use:: >>> saveVars('something',a=1,b=2,c=3) >>> from yade.params.something import * >>> a,b,c (1, 2, 3) those variables will be save in the .xml file, when the simulation itself is saved. To recover those variables once the .xml is loaded again, use ``loadVars('something')`` and they will be defined in the yade.params.\ *mark* module. The *loadNow* parameter calls :yref:`yade.utils.loadVars` after saving automatically. If 'something' already exists, given variables will be inserted. """ import cPickle try: d=cPickle.loads(Omega().tags['pickledPythonVariablesDictionary'+mark]) #load dictionary d for key in kw.keys(): d[key]=kw[key] #insert new variables into d except KeyError: d = kw Omega().tags['pickledPythonVariablesDictionary'+mark]=cPickle.dumps(d) if loadNow: loadVars(mark) def loadVars(mark=None): """Load variables from :yref:`yade.utils.saveVars`, which are saved inside the simulation. If ``mark==None``, all save variables are loaded. Otherwise only those with the mark passed.""" import cPickle, types, sys, warnings def loadOne(d,mark=None): """Load given dictionary into a synthesized module yade.params.name (or yade.params if *name* is not given). Update yade.params.__all__ as well.""" import yade.params if mark: if mark in yade.params.__dict__: warnings.warn('Overwriting yade.params.%s which already exists.'%mark) modName='yade.params.'+mark mod=types.ModuleType(modName) mod.__dict__.update(d) mod.__all__=list(d.keys()) # otherwise params starting with underscore would not be imported sys.modules[modName]=mod yade.params.__all__.append(mark) yade.params.__dict__[mark]=mod else: yade.params.__all__+=list(d.keys()) yade.params.__dict__.update(d) if mark!=None: d=cPickle.loads(Omega().tags['pickledPythonVariablesDictionary'+mark]) loadOne(d,mark) else: # load everything one by one for m in Omega().tags.keys(): if m.startswith('pickledPythonVariablesDictionary'): loadVars(m[len('pickledPythonVariableDictionary')+1:]) def SpherePWaveTimeStep(radius,density,young): r"""Compute P-wave critical timestep for a single (presumably representative) sphere, using formula for P-Wave propagation speed $\Delta t_{c}=\frac{r}{\sqrt{E/\rho}}$. If you want to compute minimum critical timestep for all spheres in the simulation, use :yref:`yade.utils.PWaveTimeStep` instead. >>> SpherePWaveTimeStep(1e-3,2400,30e9) 2.8284271247461903e-07 """ from math import sqrt return radius/sqrt(young/density) def randomColor(): """Return random Vector3 with each component in interval 0…1 (uniform distribution)""" return Vector3(random.random(),random.random(),random.random()) def typedEngine(name): """Return first engine from current O.engines, identified by its type (as string). For example: >>> from yade import utils >>> O.engines=[InsertionSortCollider(),NewtonIntegrator(),GravityEngine()] >>> utils.typedEngine("NewtonIntegrator") == O.engines[1] True """ return [e for e in Omega().engines if e.__class__.__name__==name][0] def defaultMaterial(): """Return default material, when creating bodies with :yref:`yade.utils.sphere` and friends, material is unspecified and there is no shared material defined yet. By default, this function returns:: .. code-block:: python FrictMat(density=1e3,young=1e7,poisson=.3,frictionAngle=.5,label='defaultMat') """ return FrictMat(density=1e3,young=1e7,poisson=.3,frictionAngle=.5,label='defaultMat') def _commonBodySetup(b,volume,geomInertia,material,pos,noBound=False,resetState=True,dynamic=None,fixed=False,blockedDOFs='xyzXYZ'): """Assign common body parameters.""" if isinstance(material,int): if material<0 and len(O.materials)==0: O.materials.append(defaultMaterial()); b.mat=O.materials[material] elif isinstance(material,str): b.mat=O.materials[material] elif isinstance(material,Material): b.mat=material elif callable(material): b.mat=material() else: raise TypeError("The 'material' argument must be None (for defaultMaterial), string (for shared material label), int (for shared material id) or Material instance."); ## resets state (!!) if resetState: b.state=b.mat.newAssocState() mass=volume*b.mat.density b.state.mass,b.state.inertia=mass,geomInertia*b.mat.density b.state.pos=b.state.refPos=pos b.bounded=(not noBound) if dynamic!=None: import warnings warnings.warn('dynamic=%s is deprecated, use fixed=%s instead'%(str(dynamic),str(not dynamic)),category=DeprecationWarning,stacklevel=2) fixed=not dynamic b.state.blockedDOFs=(blockedDOFs if fixed else '') def sphere(center,radius,dynamic=None,fixed=False,wire=False,color=None,highlight=False,material=-1,mask=1): """Create sphere with given parameters; mass and inertia computed automatically. Last assigned material is used by default (*material* = -1), and utils.defaultMaterial() will be used if no material is defined at all. :param Vector3 center: center :param float radius: radius :param float dynamic: deprecated, see "fixed" :param float fixed: generate the body with all DOFs blocked? :param material: specify :yref:`Body.material`; different types are accepted: * int: O.materials[material] will be used; as a special case, if material==-1 and there is no shared materials defined, utils.defaultMaterial() will be assigned to O.materials[0] * string: label of an existing material that will be used * :yref:`Material` instance: this instance will be used * callable: will be called without arguments; returned Material value will be used (Material factory object, if you like) :param int mask: :yref:`Body.mask` for the body :param wire: display as wire sphere? :param highlight: highlight this body in the viewer? :param Vector3-or-None: body's color, as normalized RGB; random color will be assigned if ``None``. :return: A Body instance with desired characteristics. Creating default shared material if none exists neither is given:: >>> O.reset() >>> from yade import utils >>> len(O.materials) 0 >>> s0=utils.sphere([2,0,0],1) >>> len(O.materials) 1 Instance of material can be given:: >>> s1=utils.sphere([0,0,0],1,wire=False,color=(0,1,0),material=ElastMat(young=30e9,density=2e3)) >>> s1.shape.wire False >>> s1.shape.color Vector3(0,1,0) >>> s1.mat.density 2000.0 Material can be given by label:: >>> O.materials.append(FrictMat(young=10e9,poisson=.11,label='myMaterial')) 1 >>> s2=utils.sphere([0,0,2],1,material='myMaterial') >>> s2.mat.label 'myMaterial' >>> s2.mat.poisson 0.11 Finally, material can be a callable object (taking no arguments), which returns a Material instance. Use this if you don't call this function directly (for instance, through yade.pack.randomDensePack), passing only 1 *material* parameter, but you don't want material to be shared. For instance, randomized material properties can be created like this: >>> import random >>> def matFactory(): return ElastMat(young=1e10*random.random(),density=1e3+1e3*random.random()) ... >>> s3=utils.sphere([0,2,0],1,material=matFactory) >>> s4=utils.sphere([1,2,0],1,material=matFactory) """ b=Body() b.shape=Sphere(radius=radius,color=color if color else randomColor(),wire=wire,highlight=highlight) V=(4./3)*math.pi*radius**3 geomInert=(2./5.)*V*radius**2 _commonBodySetup(b,V,Vector3(geomInert,geomInert,geomInert),material,pos=center,dynamic=dynamic,fixed=fixed) b.aspherical=False b.mask=mask return b def box(center,extents,orientation=Quaternion(1,0,0,0),dynamic=None,fixed=False,wire=False,color=None,highlight=False,material=-1,mask=1): """Create box (cuboid) with given parameters. :param Vector3 extents: half-sizes along x,y,z axes See :yref:`yade.utils.sphere`'s documentation for meaning of other parameters.""" b=Body() b.shape=Box(extents=extents,color=color if color else randomColor(),wire=wire,highlight=highlight) V=8*extents[0]*extents[1]*extents[2] # I = m*dim**2/12. = (m=V) = V*(2*extent)**2/12. = V*extent**2*4/12. = V*extent**2/3. geomInert=(V/3.)*Vector3(extents[1]**2+extents[2]**2,extents[0]**2+extents[2]**2,extents[0]**2+extents[1]**2) _commonBodySetup(b,V,geomInert,material,pos=center,dynamic=dynamic,fixed=fixed) b.state.ori=orientation b.mask=mask b.aspherical=True return b def wall(position,axis,sense=0,color=None,material=-1,mask=1): """Return ready-made wall body. :param float-or-Vector3 position: center of the wall. If float, it is the position along given axis, the other 2 components being zero :param ∈{0,1,2} axis: orientation of the wall normal (0,1,2) for x,y,z (sc. planes yz, xz, xy) :param ∈{-1,0,1} sense: sense in which to interact (0: both, -1: negative, +1: positive; see :yref:`Wall`) See :yref:`yade.utils.sphere`'s documentation for meaning of other parameters.""" b=Body() b.shape=Wall(sense=sense,axis=axis,color=color if color else randomColor()) if isinstance(position,(int,long,float)): pos2=Vector3(0,0,0); pos2[axis]=position else: pos2=position _commonBodySetup(b,0,Vector3(0,0,0),material,pos=pos2,fixed=True) b.aspherical=False # wall never moves dynamically b.mask=mask return b def facet(vertices,dynamic=None,fixed=True,wire=True,color=None,highlight=False,noBound=False,material=-1,mask=1,chain=-1): """Create facet with given parameters. :param [Vector3,Vector3,Vector3] vertices: coordinates of vertices in the global coordinate system. :param bool wire: if ``True``, facets are shown as skeleton; otherwise facets are filled :param bool noBound: set :yref:`Body.bounded` :param Vector3-or-None color: color of the facet; random color will be assigned if ``None``. See :yref:`yade.utils.sphere`'s documentation for meaning of other parameters.""" b=Body() center=inscribedCircleCenter(vertices[0],vertices[1],vertices[2]) vertices=Vector3(vertices[0])-center,Vector3(vertices[1])-center,Vector3(vertices[2])-center b.shape=Facet(color=color if color else randomColor(),wire=wire,highlight=highlight,vertices=vertices) _commonBodySetup(b,0,Vector3(0,0,0),material,noBound=noBound,pos=center,fixed=fixed) b.aspherical=False # mass and inertia are 0 anyway; fell free to change to ``True`` if needed b.mask=mask b.chain=chain return b def tetraPoly(vertices,dynamic=True,fixed=False,wire=True,color=None,highlight=False,noBound=False,material=-1,mask=1,chain=-1): """Create tetrahedron (actually simple Polyhedra) with given parameters. :param [Vector3,Vector3,Vector3,Vector3] vertices: coordinates of vertices in the global coordinate system. See :yref:`yade.utils.sphere`'s documentation for meaning of other parameters.""" b=Body() b.shape = Polyhedra(v=vertices,color=color if color else randomColor(),wire=wire,highlight=highlight) volume = b.shape.GetVolume() inertia = b.shape.GetInertia() center = b.shape.GetCentroid() _commonBodySetup(b,volume,inertia,material,noBound=noBound,pos=center,fixed=fixed) b.aspherical=True b.state.ori = b.shape.GetOri() b.mask=mask b.chain=chain return b def tetra(vertices,strictCheck=True,dynamic=True,fixed=False,wire=True,color=None,highlight=False,noBound=False,material=-1,mask=1,chain=-1): """Create tetrahedron with given parameters. :param [Vector3,Vector3,Vector3,Vector3] vertices: coordinates of vertices in the global coordinate system. :param bool strictCheck: checks vertices order, raise RuntimeError for negative volume See :yref:`yade.utils.sphere`'s documentation for meaning of other parameters.""" b=Body() center = .25*sum(vertices,Vector3.Zero) volume = TetrahedronSignedVolume(vertices) if volume < 0: if strictCheck: raise RuntimeError, "tetra: wrong order of vertices" temp = vertices[3] vertices[3] = vertices[2] vertices[2] = temp volume = TetrahedronSignedVolume(vertices) assert(volume>0) b.shape = Tetra(v=vertices,color=color if color else randomColor(),wire=wire,highlight=highlight) # modifies pos, ori and inertia ori = TetrahedronWithLocalAxesPrincipal(b) _commonBodySetup(b,volume,b.state.inertia,material,noBound=noBound,pos=center,fixed=fixed) b.state.ori = b.state.refOri = ori b.aspherical = True b.mask = mask b.chain = chain return b def polyhedron(vertices,dynamic=True,fixed=False,wire=True,color=None,highlight=False,noBound=False,material=-1,mask=1,chain=-1): """Create polyhedron with given parameters. :param [[Vector3]] vertices: coordinates of vertices in the global coordinate system. See :yref:`yade.utils.sphere`'s documentation for meaning of other parameters.""" b=Body() b.shape = Polyhedra(v=vertices,color=color if color else randomColor(),wire=wire,highlight=highlight) volume = b.shape.GetVolume() inertia = b.shape.GetInertia() center = b.shape.GetCentroid() _commonBodySetup(b,volume,inertia,material,noBound=noBound,pos=center,fixed=fixed) b.aspherical=True b.state.ori = b.shape.GetOri() b.mask=mask b.chain=chain return b #def setNewVerticesOfFacet(b,vertices): # center = inscribedCircleCenter(vertices[0],vertices[1],vertices[2]) # vertices = Vector3(vertices[0])-center,Vector3(vertices[1])-center,Vector3(vertices[2])-center # b.shape.vertices = vertices # b.state.pos = center def facetBox(*args,**kw): "|ydeprecated|" _deprecatedUtilsFunction('facetBox','geom.facetBox') return geom.facetBox(*args,**kw) def facetCylinder(*args,**kw): "|ydeprecated|" _deprecatedUtilsFunction('facetCylinder','geom.facetCylinder') return geom.facetCylinder(*args,**kw) def aabbWalls(extrema=None,thickness=0,oversizeFactor=1.5,**kw): """Return 6 boxes that will wrap existing packing as walls from all sides; extrema are extremal points of the Aabb of the packing (will be calculated if not specified) thickness is wall thickness (will be 1/10 of the X-dimension if not specified) Walls will be enlarged in their plane by oversizeFactor. returns list of 6 wall Bodies enclosing the packing, in the order minX,maxX,minY,maxY,minZ,maxZ. """ walls=[] if not extrema: extrema=aabbExtrema() #if not thickness: thickness=(extrema[1][0]-extrema[0][0])/10. for axis in [0,1,2]: mi,ma=extrema center=[(mi[i]+ma[i])/2. for i in range(3)] extents=[.5*oversizeFactor*(ma[i]-mi[i]) for i in range(3)] extents[axis]=thickness/2. for j in [0,1]: center[axis]=extrema[j][axis]+(j-.5)*thickness walls.append(box(center=center,extents=extents,fixed=True,**kw)) walls[-1].shape.wire=True return walls def aabbDim(cutoff=0.,centers=False): """Return dimensions of the axis-aligned bounding box, optionally with relative part *cutoff* cut away.""" a=aabbExtrema(cutoff,centers) return (a[1][0]-a[0][0],a[1][1]-a[0][1],a[1][2]-a[0][2]) def aabbExtrema2d(pts): """Return 2d bounding box for a sequence of 2-tuples.""" inf=float('inf') min,max=[inf,inf],[-inf,-inf] for pt in pts: if pt[0]max[0]: max[0]=pt[0] if pt[1]max[1]: max[1]=pt[1] return tuple(min),tuple(max) def perpendicularArea(axis): """Return area perpendicular to given axis (0=x,1=y,2=z) generated by bodies for which the function consider returns True (defaults to returning True always) and which is of the type :yref:`Sphere`. """ ext=aabbExtrema() other=((axis+1)%3,(axis+2)%3) return (ext[1][other[0]]-ext[0][other[0]])*(ext[1][other[1]]-ext[0][other[1]]) def fractionalBox(fraction=1.,minMax=None): """retrurn (min,max) that is the original minMax box (or aabb of the whole simulation if not specified) linearly scaled around its center to the fraction factor""" if not minMax: minMax=aabbExtrema() half=[.5*(minMax[1][i]-minMax[0][i]) for i in [0,1,2]] return (tuple([minMax[0][i]+(1-fraction)*half[i] for i in [0,1,2]]),tuple([minMax[1][i]-(1-fraction)*half[i] for i in [0,1,2]])) def randomizeColors(onlyDynamic=False): """Assign random colors to :yref:`Shape::color`. If onlyDynamic is true, only dynamic bodies will have the color changed. """ for b in O.bodies: color=(random.random(),random.random(),random.random()) if b.dynamic or not onlyDynamic: b.shape.color=color def avgNumInteractions(cutoff=0.,skipFree=False,considerClumps=False): r"""Return average numer of interactions per particle, also known as *coordination number* $Z$. This number is defined as .. math:: Z=2C/N where $C$ is number of contacts and $N$ is number of particles. When clumps are present, number of particles is the sum of standalone spheres plus the sum of clumps. Clumps are considered in the calculation if cutoff != 0 or skipFree = True. If cutoff=0 (default) and skipFree=False (default) one needs to set considerClumps=True to consider clumps in the calculation. With *skipFree*, particles not contributing to stable state of the packing are skipped, following equation (8) given in [Thornton2000]_: .. math:: Z_m=\frac{2C-N_1}{N-N_0-N_1} :param cutoff: cut some relative part of the sample's bounding box away. :param skipFree: see above. :param considerClumps: also consider clumps if cutoff=0 and skipFree=False; for further explanation see above. """ if cutoff==0 and not skipFree and not considerClumps: return 2*O.interactions.countReal()*1./len(O.bodies) else: nums,counts=bodyNumInteractionsHistogram(aabbExtrema(cutoff)) ## CC is 2*C CC=sum([nums[i]*counts[i] for i in range(len(nums))]); N=sum(counts) if not skipFree: return CC*1./N if N>0 else float('nan') ## find bins with 0 and 1 spheres N0=0 if (0 not in nums) else counts[nums.index(0)] N1=0 if (1 not in nums) else counts[nums.index(1)] NN=N-N0-N1 return (CC-N1)*1./NN if NN>0 else float('nan') def plotNumInteractionsHistogram(cutoff=0.): "Plot histogram with number of interactions per body, optionally cutting away *cutoff* relative axis-aligned box from specimen margin." nums,counts=bodyNumInteractionsHistogram(aabbExtrema(cutoff)) import pylab pylab.bar(nums,counts) pylab.title('Number of interactions histogram, average %g (cutoff=%g)'%(avgNumInteractions(cutoff),cutoff)) pylab.xlabel('Number of interactions') pylab.ylabel('Body count') pylab.ion() pylab.show() def plotDirections(aabb=(),mask=0,bins=20,numHist=True,noShow=False,sphSph=False): """Plot 3 histograms for distribution of interaction directions, in yz,xz and xy planes and (optional but default) histogram of number of interactions per body. If sphSph only sphere-sphere interactions are considered for the 3 directions histograms. :returns: If *noShow* is ``False``, displays the figure and returns nothing. If *noShow*, the figure object is returned without being displayed (works the same way as :yref:`yade.plot.plot`). """ import pylab,math from yade import utils for axis in [0,1,2]: d=utils.interactionAnglesHistogram(axis,mask=mask,bins=bins,aabb=aabb,sphSph=sphSph) fc=[0,0,0]; fc[axis]=1. subp=pylab.subplot(220+axis+1,polar=True); # 1.1 makes small gaps between values (but the column is a bit decentered) pylab.bar(d[0],d[1],width=math.pi/(1.1*bins),fc=fc,alpha=.7,label=['yz','xz','xy'][axis]) #pylab.title(['yz','xz','xy'][axis]+' plane') pylab.text(.5,.25,['yz','xz','xy'][axis],horizontalalignment='center',verticalalignment='center',transform=subp.transAxes,fontsize='xx-large') if numHist: pylab.subplot(224,polar=False) nums,counts=utils.bodyNumInteractionsHistogram(aabb if len(aabb)>0 else utils.aabbExtrema()) avg=sum([nums[i]*counts[i] for i in range(len(nums))])/(1.*sum(counts)) pylab.bar(nums,counts,fc=[1,1,0],alpha=.7,align='center') pylab.xlabel('Interactions per body (avg. %g)'%avg) pylab.axvline(x=avg,linewidth=3,color='r') pylab.ylabel('Body count') if noShow: return pylab.gcf() else: pylab.ion() pylab.show() def encodeVideoFromFrames(*args,**kw): "|ydeprecated|" _deprecatedUtilsFunction('utils.encodeVideoFromFrames','utils.makeVideo') return makeVideo(*args,**kw) def makeVideo(frameSpec,out,renameNotOverwrite=True,fps=24,kbps=6000,bps=None): """Create a video from external image files using `mencoder `__. Two-pass encoding using the default mencoder codec (mpeg4) is performed, running multi-threaded with number of threads equal to number of OpenMP threads allocated for Yade. :param frameSpec: wildcard | sequence of filenames. If list or tuple, filenames to be encoded in given order; otherwise wildcard understood by mencoder's mf:// URI option (shell wildcards such as ``/tmp/snap-*.png`` or and printf-style pattern like ``/tmp/snap-%05d.png``) :param str out: file to save video into :param bool renameNotOverwrite: if True, existing same-named video file will have -*number* appended; will be overwritten otherwise. :param int fps: Frames per second (``-mf fps=…``) :param int kbps: Bitrate (``-lavcopts vbitrate=…``) in kb/s """ import os,os.path,subprocess,warnings if bps!=None: warnings.warn('plot.makeVideo: bps is deprecated, use kbps instead (the significance is the same, but the name is more precise)',stacklevel=2,category=DeprecationWarning) kbps=bps if renameNotOverwrite and os.path.exists(out): i=0 while(os.path.exists(out+"~%d"%i)): i+=1 os.rename(out,out+"~%d"%i); print "Output file `%s' already existed, old file renamed to `%s'"%(out,out+"~%d"%i) if isinstance(frameSpec,list) or isinstance(frameSpec,tuple): frameSpec=','.join(frameSpec) for passNo in (1,2): cmd=['mencoder','mf://%s'%frameSpec,'-mf','fps=%d'%int(fps),'-ovc','lavc','-lavcopts','vbitrate=%d:vpass=%d:threads=%d:%s'%(int(kbps),passNo,O.numThreads,'turbo' if passNo==1 else ''),'-o',('/dev/null' if passNo==1 else out)] print 'Pass %d:'%passNo,' '.join(cmd) ret=subprocess.call(cmd) if ret!=0: raise RuntimeError("Error when running mencoder.") def replaceCollider(colliderEngine): """Replaces collider (Collider) engine with the engine supplied. Raises error if no collider is in engines.""" colliderIdx=-1 for i,e in enumerate(O.engines): if O.isChildClassOf(e.__class__.__name__,"Collider"): colliderIdx=i break if colliderIdx<0: raise RuntimeError("No Collider found within O.engines.") O.engines=O.engines[:colliderIdx]+[colliderEngine]+O.engines[colliderIdx+1:] def _procStatus(name): import os for l in open('/proc/%d/status'%os.getpid()): if l.split(':')[0]==name: return l raise "No such line in /proc/[pid]/status: "+name def vmData(): "Return memory usage data from Linux's /proc/[pid]/status, line VmData." l=_procStatus('VmData'); ll=l.split(); assert(ll[2]=='kB') return int(ll[1]) def uniaxialTestFeatures(filename=None,areaSections=10,axis=-1,distFactor=2.2,**kw): """Get some data about the current packing useful for uniaxial test: #. Find the dimensions that is the longest (uniaxial loading axis) #. Find the minimum cross-section area of the specimen by examining several (areaSections) sections perpendicular to axis, computing area of the convex hull for each one. This will work also for non-prismatic specimen. #. Find the bodies that are on the negative/positive boundary, to which the straining condition should be applied. :param filename: if given, spheres will be loaded from this file (ASCII format); if not, current simulation will be used. :param float areaSection: number of section that will be used to estimate cross-section :param ∈{0,1,2} axis: if given, force strained axis, rather than computing it from predominant length :return: dictionary with keys ``negIds``, ``posIds``, ``axis``, ``area``. .. warning:: The function :yref:`yade.utils.approxSectionArea` uses convex hull algorithm to find the area, but the implementation is reported to be *buggy* (bot works in some cases). Always check this number, or fix the convex hull algorithm (it is documented in the source, see :ysrc:`py/_utils.cpp`). """ if filename: ids=spheresFromFile(filename,**kw) else: ids=[b.id for b in O.bodies] mm,mx=aabbExtrema() dim=aabbDim(); if axis<0: axis=list(dim).index(max(dim)) # list(dim) for compat with python 2.5 which didn't have index defined for tuples yet (appeared in 2.6 first) assert(axis in (0,1,2)) import numpy areas=[approxSectionArea(coord,axis) for coord in numpy.linspace(mm[axis],mx[axis],num=10)[1:-1]] negIds,posIds=negPosExtremeIds(axis=axis,distFactor=distFactor) return {'negIds':negIds,'posIds':posIds,'axis':axis,'area':min(areas)} def voxelPorosityTriaxial(triax,resolution=200,offset=0): """ Calculate the porosity of a sample, given the TriaxialCompressionEngine. A function :yref:`yade.utils.voxelPorosity` is invoked, with the volume of a box enclosed by TriaxialCompressionEngine walls. The additional parameter offset allows using a smaller volume inside the box, where each side of the volume is at offset distance from the walls. By this way it is possible to find a more precise porosity of the sample, since at walls' contact the porosity is usually reduced. A recommended value of offset is bigger or equal to the average radius of spheres inside. The value of resolution depends on size of spheres used. It can be calibrated by invoking voxelPorosityTriaxial with offset=0 and comparing the result with TriaxialCompressionEngine.porosity. After calibration, the offset can be set to radius, or a bigger value, to get the result. :param triax: the TriaxialCompressionEngine handle :param resolution: voxel grid resolution :param offset: offset distance :return: the porosity of the sample inside given volume Example invocation:: from yade import utils rAvg=0.03 TriaxialTest(numberOfGrains=200,radiusMean=rAvg).load() O.dt=-1 O.run(1000) O.engines[4].porosity 0.44007807740143889 utils.voxelPorosityTriaxial(O.engines[4],200,0) 0.44055412500000002 utils.voxelPorosityTriaxial(O.engines[4],200,rAvg) 0.36798199999999998 """ p_bottom = O.bodies[triax.wall_bottom_id].state.se3[0] p_top = O.bodies[triax.wall_top_id ].state.se3[0] p_left = O.bodies[triax.wall_left_id ].state.se3[0] p_right = O.bodies[triax.wall_right_id ].state.se3[0] p_front = O.bodies[triax.wall_front_id ].state.se3[0] p_back = O.bodies[triax.wall_back_id ].state.se3[0] th = (triax.thickness)*0.5+offset x_0 = p_left [0] + th x_1 = p_right [0] - th y_0 = p_bottom[1] + th y_1 = p_top [1] - th z_0 = p_back [2] + th z_1 = p_front [2] - th a=Vector3(x_0,y_0,z_0) b=Vector3(x_1,y_1,z_1) return voxelPorosity(resolution,a,b) def trackPerfomance(updateTime=5): """ Track perfomance of a simulation. (Experimental) Will create new thread to produce some plots. Useful for track perfomance of long run simulations (in bath mode for example). """ def __track_perfomance(updateTime): pid=os.getpid() threadsCpu={} lastTime,lastIter=-1,-1 while 1: time.sleep(updateTime) if not O.running: lastTime,lastIter=-1,-1 continue if lastTime==-1: lastTime=time.time();lastIter=O.iter plot.plots.update({'Iteration':('Perfomance',None,'Bodies','Interactions')}) continue curTime=time.time();curIter=O.iter perf=(curIter-lastIter)/(curTime-lastTime) out=subprocess.Popen(['top','-bH','-n1', ''.join(['-p',str(pid)])],stdout=subprocess.PIPE).communicate()[0].splitlines() for s in out[7:-1]: w=s.split() threadsCpu[w[0]]=float(w[8]) plot.addData(Iteration=curIter,Iter=curIter,Perfomance=perf,Bodies=len(O.bodies),Interactions=len(O.interactions),**threadsCpu) plot.plots.update({'Iter':threadsCpu.keys()}) lastTime=time.time();lastIter=O.iter thread.start_new_thread(__track_perfomance,(updateTime)) def NormalRestitution2DampingRate(en): r"""Compute the normal damping rate as a function of the normal coefficient of restitution $e_n$. For $e_n\in\langle0,1\rangle$ damping rate equals .. math:: -\frac{\log e_n}{\sqrt{e_n^2+\pi^2}} """ if en == 0.0: return 0.999999999 if en == 1.0: return 0.0 from math import sqrt,log,pi ln_en = math.log(en) return (-ln_en/math.sqrt((math.pow(ln_en,2) + math.pi*math.pi))) def xMirror(half): """Mirror a sequence of 2d points around the x axis (changing sign on the y coord). The sequence should start up and then it will wrap from y downwards (or vice versa). If the last point's x coord is zero, it will not be duplicated.""" return list(half)+[(x,-y) for x,y in reversed(half[:-1] if half[-1][1]==0 else half)] ############################# ##### deprecated functions def _deprecatedUtilsFunction(old,new): "Wrapper for deprecated functions, example below." import warnings warnings.warn('Function utils.%s is deprecated, use %s instead.'%(old,new),stacklevel=2,category=UserWarning) # example of _deprecatedUtilsFunction usage: # # def import_mesh_geometry(*args,**kw): # "|ydeprecated|" # _deprecatedUtilsFunction('import_mesh_geometry','yade.import.gmsh') # import yade.ymport # return yade.ymport.stl(*args,**kw) class TableParamReader(): """Class for reading simulation parameters from text file. Each parameter is represented by one column, each parameter set by one line. Colums are separated by blanks (no quoting). First non-empty line contains column titles (without quotes). You may use special column named 'description' to describe this parameter set; if such colum is absent, description will be built by concatenating column names and corresponding values (``param1=34,param2=12.22,param4=foo``) * from columns ending in ``!`` (the ``!`` is not included in the column name) * from all columns, if no columns end in ``!``. Empty lines within the file are ignored (although counted); ``#`` starts comment till the end of line. Number of blank-separated columns must be the same for all non-empty lines. A special value ``=`` can be used instead of parameter value; value from the previous non-empty line will be used instead (works recursively). This class is used by :yref:`yade.utils.readParamsFromTable`. """ def __init__(self,file): "Setup the reader class, read data into memory." import re # read file in memory, remove newlines and comments; the [''] makes lines 1-indexed ll=[re.sub('\s*#.*','',l[:-1]) for l in ['']+open(file,'r').readlines()] # usable lines are those that contain something else than just spaces usableLines=[i for i in range(len(ll)) if not re.match(r'^\s*(#.*)?$',ll[i])] headings=ll[usableLines[0]].split() # use all values of which heading has ! after its name to build up the description string # if there are none, use all columns if not 'description' in headings: bangHeads=[h[:-1] for h in headings if h[-1]=='!'] or headings headings=[(h[:-1] if h[-1]=='!' else h) for h in headings] usableLines=usableLines[1:] # and remove headinds from usableLines values={} for l in usableLines: val={} for i in range(len(headings)): val[headings[i]]=ll[l].split()[i] values[l]=val lines=values.keys(); lines.sort() # replace '=' by previous value of the parameter for i,l in enumerate(lines): for j in values[l].keys(): if values[l][j]=='=': try: values[l][j]=values[lines[i-1]][j] except IndexError,KeyError: raise RuntimeError("The = specifier on line %d refers to nonexistent value on previous line?"%l) #import pprint; pprint.pprint(headings); pprint.pprint(values) # add descriptions, but if they repeat, append line number as well if not 'description' in headings: descs=set() for l in lines: dd=','.join(head.replace('!','')+'='+('%g'%values[head] if isinstance(values[l][head],float) else str(values[l][head])) for head in bangHeads).replace("'",'').replace('"','') if dd in descs: dd+='__line=%d__'%l values[l]['description']=dd descs.add(dd) self.values=values def paramDict(self): """Return dictionary containing data from file given to constructor. Keys are line numbers (which might be non-contiguous and refer to real line numbers that one can see in text editors), values are dictionaries mapping parameter names to their values given in the file. The special value '=' has already been interpreted, ``!`` (bangs) (if any) were already removed from column titles, ``description`` column has already been added (if absent).""" return self.values if __name__=="__main__": tryTable="""head1 important2! !OMP_NUM_THREADS! abcd 1 1.1 1.2 1.3 'a' 'b' 'c' 'd' ### comment # empty line 1 = = g """ file='/tmp/try-tbl.txt' f=open(file,'w') f.write(tryTable) f.close() from pprint import * pprint(TableParamReader(file).paramDict()) def runningInBatch(): 'Tell whether we are running inside the batch or separately.' import os return 'YADE_BATCH' in os.environ def waitIfBatch(): 'Block the simulation if running inside a batch. Typically used at the end of script so that it does not finish prematurely in batch mode (the execution would be ended in such a case).' if runningInBatch(): O.wait() def readParamsFromTable(tableFileLine=None,noTableOk=True,unknownOk=False,**kw): """ Read parameters from a file and assign them to __builtin__ variables. The format of the file is as follows (commens starting with # and empty lines allowed):: # commented lines allowed anywhere name1 name2 … # first non-blank line are column headings # empty line is OK, with or without comment val1 val2 … # 1st parameter set val2 val2 … # 2nd … Assigned tags (the ``description`` column is synthesized if absent,see :yref:`yade.utils.TableParamReader`); O.tags['description']=… # assigns the description column; might be synthesized O.tags['params']="name1=val1,name2=val2,…" # all explicitly assigned parameters O.tags['defaultParams']="unassignedName1=defaultValue1,…" # parameters that were left at their defaults O.tags['d.id']=O.tags['id']+'.'+O.tags['description'] O.tags['id.d']=O.tags['description']+'.'+O.tags['id'] All parameters (default as well as settable) are saved using :yref:`yade.utils.saveVars`\ ``('table')``. :param tableFileLine: string attribute to define which line number (as seen in a text editor) from wich text file (with one value per blank-separated columns) to get the values from. A ':' should appear between the two informations, e.g. 'file.table:4' to read the 4th line from file.table file :param bool noTableOk: if False, raise exception if the file cannot be open; use default values otherwise :param bool unknownOk: do not raise exception if unknown column name is found in the file, and assign it as well :return: number of assigned parameters """ tagsParams=[] # dictParams is what eventually ends up in yade.params.table (default+specified values) dictDefaults,dictParams,dictAssign={},{},{} import os, __builtin__,re,math if not tableFileLine and ('YADE_BATCH' not in os.environ or os.environ['YADE_BATCH']==''): if not noTableOk: raise EnvironmentError("YADE_BATCH is not defined in the environment") O.tags['line']='l!' else: if not tableFileLine: tableFileLine=os.environ['YADE_BATCH'] env=tableFileLine.split(':') tableFile,tableLine=env[0],int(env[1]) allTab=TableParamReader(tableFile).paramDict() if not allTab.has_key(tableLine): raise RuntimeError("Table %s doesn't contain valid line number %d"%(tableFile,tableLine)) vv=allTab[tableLine] O.tags['line']='l%d'%tableLine O.tags['description']=vv['description'] O.tags['id.d']=O.tags['id']+'.'+O.tags['description']; O.tags['d.id']=O.tags['description']+'.'+O.tags['id'] # assign values specified in the table to python vars # !something cols are skipped, those are env vars we don't treat at all (they are contained in description, though) for col in vv.keys(): if col=='description' or col[0]=='!': continue if col not in kw.keys() and (not unknownOk): raise NameError("Parameter `%s' has no default value assigned"%col) if vv[col]=='*': vv[col]=kw[col] # use default value for * in the table elif col in kw.keys(): kw.pop(col) # remove the var from kw, so that it contains only those that were default at the end of this loop #print 'ASSIGN',col,vv[col] tagsParams+=['%s=%s'%(col,vv[col])]; dictParams[col]=eval(vv[col],math.__dict__) # assign remaining (default) keys to python vars defaults=[] for k in kw.keys(): dictDefaults[k]=kw[k] defaults+=["%s=%s"%(k,kw[k])]; O.tags['defaultParams']=",".join(defaults) O.tags['params']=",".join(tagsParams) dictParams.update(dictDefaults) saveVars('table',loadNow=True,**dictParams) return len(tagsParams) def psd(bins=5, mass=True, mask=-1): """Calculates particle size distribution. :param int bins: number of bins :param bool mass: if true, the mass-PSD will be calculated :param int mask: :yref:`Body.mask` for the body :return: * binsSizes: list of bin's sizes * binsProc: how much material (in percents) are in the bin, cumulative * binsSumCum: how much material (in units) are in the bin, cumulative binsSizes, binsProc, binsSumCum """ maxD = 0.0 minD = 0.0 for b in O.bodies: if (isinstance(b.shape,Sphere) and ((mask<0) or ((b.mask&mask)<>0))): if ((2*b.shape.radius) > maxD) : maxD = 2*b.shape.radius if (((2*b.shape.radius) < minD) or (minD==0.0)): minD = 2*b.shape.radius if (minD==maxD): print 'Monodisperse packing with diameter =', minD,'. Not computing psd' return False #All particles are having the same size binsSizes = numpy.linspace(minD, maxD, bins+1) deltaBinD = (maxD-minD)/bins binsMass = numpy.zeros(bins) binsNumbers = numpy.zeros(bins) for b in O.bodies: if (isinstance(b.shape,Sphere) and ((mask<0) or ((b.mask&mask)<>0))): d=2*b.shape.radius basketId = int(math.floor( (d-minD) / deltaBinD ) ) if (d == maxD): basketId = bins-1 #If the diameter equals the maximal diameter, put the particle into the last bin binsMass[basketId] = binsMass[basketId] + b.state.mass #Put masses into the bin binsNumbers[basketId] = binsNumbers[basketId] + 1 #Put numbers into the bin binsProc = numpy.zeros(bins+1) binsSumCum = numpy.zeros(bins+1) i=1 for size in binsSizes[:-1]: if (mass): binsSumCum[i]+=binsSumCum[i-1]+binsMass[i-1] #Calculate mass else: binsSumCum[i]+=binsSumCum[i-1]+binsNumbers[i-1] #Calculate number of particles i+=1 if (binsSumCum[len(binsSumCum)-1] > 0): i=0 for l in binsSumCum: binsProc[i] = binsSumCum[i]/binsSumCum[len(binsSumCum)-1] i+=1 return binsSizes, binsProc, binsSumCum class clumpTemplate: """Create a clump template by a list of relative radii and a list of relative positions. Both lists must have the same length. :param [float,float,...] relRadii: list of relative radii (minimum length = 2) :param [Vector3,Vector3,...] relPositions: list of relative positions (minimum length = 2) """ def __init__(self,relRadii=[],relPositions=[[],[]]): if (len(relRadii) != len(relPositions)): raise ValueError("Given lists must have same length! Given lists does not match clump template structure."); if (len(relRadii) < 2): raise ValueError("One or more of given lists for relative radii have length < 2! Given lists does not match clump template structure."); for ii in range(0,len(relPositions)): if len(relPositions[ii]) != 3: raise ValueError("One or more of given lists for relative positions do not have length of 3! Given lists does not match clump template structure."); for jj in range(ii,len(relPositions)): if ii != jj: if (relPositions[ii] == relPositions[jj]): raise ValueError("Two or more of given lists for relative positions are equal! Given lists does not match clump template structure."); self.numCM = len(relRadii) self.relRadii = relRadii self.relPositions = relPositions class UnstructuredGrid: """EXPERIMENTAL. Class representing triangulated FEM-like unstructured grid. It is used for transfereing data from ad to YADE and external FEM program. The main purpose of this class is to store information about individual grid vertices/nodes coords (since facets stores only coordinates of vertices in local coords) and to avaluate and/or apply nodal forces from contact forces (from actual contact force and contact point the force is distributed to nodes using linear approximation). TODO rewrite to C++ TODO better docs :param dict vertices: dict of {internal vertex label:vertex}, e.g. {5:(0,0,0),22:(0,1,0),23:(1,0,0)} :param dict connectivityTable: dict of {internal element label:[indices of vertices]}, e.g. {88:[5,22,23]} """ def __init__(self,vertices={},connectivityTable={},**kw): self.vertices = vertices self.connectivityTable = connectivityTable self.forces = dict( (i,Vector3(0,0,0)) for i in vertices) self.build(**kw) def setup(self,vertices,connectivityTable,toSimulation=False,bodies=None,**kw): """Sets new information to receiver :param dict vertices: see constructor for explanation :param dict connectivityTable: see constructor for explanation :param bool toSimulation: if new information should be inserted to Yade simulation (create new bodies or not) :param [[int]]|None bodies: list of list of bodies indices to be appended as clumps (thus no contact detection is done within one body) """ self.vertices = dict( (i,v) for i,v in vertices.iteritems()) self.connectivityTable = dict( (i,e) for i,e in connectivityTable.iteritems()) self.build(**kw) if toSimulation: self.toSimulation(bodies) def build(self,**kw): self.elements = {} for i,c in self.connectivityTable.iteritems(): if len(c) == 3: b = facet([self.vertices[j] for j in c],**kw) elif len(c) == 4: b = tetra([self.vertices[j] for j in c],**kw) #b = polyhedron([self.vertices[j] for j in c],**kw) else: raise RuntimeError, "Unsupported cell shape (should be triangle or tetrahedron)" self.elements[i] = b def resetForces(self): for i in self.vertices: self.forces[i] = Vector3(0,0,0) def getForcesOfNodes(self): """Computes forces for each vertex/node. The nodal force is computed from contact force and contact point using linear approximation """ self.resetForces() for i,e in self.elements.iteritems(): ie = self.connectivityTable[i] for i in e.intrs(): fn = i.phys.normalForce fs = i.phys.shearForce if hasattr(i.phys,"shearForce") else Vector3.Zero f = (fn+fs) * (-1 if e.id == i.id1 else +1 if e.id == i.id2 else 'ERROR') cp = i.geom.contactPoint if isinstance(e.shape,Facet): v0,v1,v2 = [Vector3(self.vertices[j]) for j in ie] w0 = ((cp-v1).cross(v2-v1)).norm() w1 = ((cp-v2).cross(v0-v2)).norm() w2 = ((cp-v0).cross(v1-v0)).norm() ww = w0+w1+w2 self.forces[ie[0]] += f*w0/ww self.forces[ie[1]] += f*w1/ww self.forces[ie[2]] += f*w2/ww elif isinstance(e.shape,Tetra): v0,v1,v2,v3 = [Vector3(self.vertices[j]) for j in ie] w0 = TetrahedronVolume((cp,v1,v2,v3)) w1 = TetrahedronVolume((cp,v2,v3,v0)) w2 = TetrahedronVolume((cp,v3,v0,v1)) w3 = TetrahedronVolume((cp,v0,v1,v2)) ww = w0+w1+w2+w3 self.forces[ie[0]] += f*w0/ww self.forces[ie[1]] += f*w1/ww self.forces[ie[2]] += f*w2/ww self.forces[ie[3]] += f*w3/ww else: raise RuntimeError, "TODO" return self.forces def setPositionsOfNodes(self,newPoss): """Sets new position of nodes and also updates all elements in the simulation :param [Vector3] newPoss: list of new positions """ for i in self.vertices: self.vertices[i] = newPoss[i] self.updateElements() def updateElements(self): """Updates positions of all elements in the simulation """ for i,c in self.connectivityTable.iteritems(): e = self.elements[i] e.state.pos = Vector3(0,0,0) e.state.ori = Quaternion((1,0,0),0) if isinstance(e.shape,Facet): #e.shape.vertices = [self.vertices[j] for j in c] vs = [Vector3(self.vertices[j]) for j in c] cc = inscribedCircleCenter(*vs) for v in vs: v -= cc e.state.pos = cc e.shape.setVertices(*vs) elif isinstance(e.shape,Tetra): e.shape.v = [self.vertices[j] for j in c] else: raise RuntimeError, "TODO" def toSimulation(self,bodies=None): """Insert all elements to Yade simulation """ if bodies: e = self.elements.values() for b in bodies: O.bodies.appendClumped([e[i] for i in b]) else: O.bodies.append(self.elements.values()) trunk-2017.01a/py/wrapper/000077500000000000000000000000001304022710500152725ustar00rootroot00000000000000trunk-2017.01a/py/wrapper/customConverters.cpp000066400000000000000000000251601304022710500213670ustar00rootroot00000000000000// 2009 © Václav Šmilauer #include #include #include #include #include #include #include #ifdef YADE_OPENGL #include #include #endif #include // move this to the miniEigen wrapper later /* two-way se3 handling */ struct custom_se3_to_tuple{ static PyObject* convert(const Se3r& se3){ boost::python::tuple ret=boost::python::make_tuple(se3.position,se3.orientation); return boost::python::incref(ret.ptr()); } }; struct custom_Se3r_from_seq{ custom_Se3r_from_seq(){ boost::python::converter::registry::push_back(&convertible,&construct,boost::python::type_id()); } static void* convertible(PyObject* obj_ptr){ if(!PySequence_Check(obj_ptr)) return 0; if(PySequence_Size(obj_ptr)!=2 && PySequence_Size(obj_ptr)!=7) return 0; return obj_ptr; } static void construct(PyObject* obj_ptr, boost::python::converter::rvalue_from_python_stage1_data* data){ void* storage=((boost::python::converter::rvalue_from_python_storage*)(data))->storage.bytes; new (storage) Se3r; Se3r* se3=(Se3r*)storage; if(PySequence_Size(obj_ptr)==2){ // from vector and quaternion se3->position=boost::python::extract(PySequence_GetItem(obj_ptr,0)); se3->orientation=boost::python::extract(PySequence_GetItem(obj_ptr,1)); } else if(PySequence_Size(obj_ptr)==7){ // 3 vector components, 3 axis components, angle se3->position=Vector3r(boost::python::extract(PySequence_GetItem(obj_ptr,0)),boost::python::extract(PySequence_GetItem(obj_ptr,1)),boost::python::extract(PySequence_GetItem(obj_ptr,2))); Vector3r axis=Vector3r(boost::python::extract(PySequence_GetItem(obj_ptr,3)),boost::python::extract(PySequence_GetItem(obj_ptr,4)),boost::python::extract(PySequence_GetItem(obj_ptr,5))); Real angle=boost::python::extract(PySequence_GetItem(obj_ptr,6)); se3->orientation=Quaternionr(AngleAxisr(angle,axis)); } else throw std::logic_error(__FILE__ ": First, the sequence size for Se3r object was 2 or 7, but now is not? (programming error, please report!"); data->convertible=storage; } }; struct custom_OpenMPAccumulator_to_float{ static PyObject* convert(const OpenMPAccumulator& acc){ return boost::python::incref(PyFloat_FromDouble(acc.get())); } }; struct custom_OpenMPAccumulator_from_float{ custom_OpenMPAccumulator_from_float(){ boost::python::converter::registry::push_back(&convertible,&construct,boost::python::type_id >()); } static void* convertible(PyObject* obj_ptr){ return PyFloat_Check(obj_ptr) ? obj_ptr : 0; } static void construct(PyObject* obj_ptr, boost::python::converter::rvalue_from_python_stage1_data* data){ void* storage=((boost::python::converter::rvalue_from_python_storage >*)(data))->storage.bytes; new (storage) OpenMPAccumulator; ((OpenMPAccumulator*)storage)->set(boost::python::extract(obj_ptr)); data->convertible=storage; } }; struct custom_OpenMPAccumulator_to_int { static PyObject* convert(const OpenMPAccumulator& acc){ return boost::python::incref(PyInt_FromLong((long)acc.get())); } }; struct custom_OpenMPAccumulator_from_int{ custom_OpenMPAccumulator_from_int(){ boost::python::converter::registry::push_back(&convertible,&construct,boost::python::type_id >()); } static void* convertible(PyObject* obj_ptr){ return PyInt_Check(obj_ptr) ? obj_ptr : 0; } static void construct(PyObject* obj_ptr, boost::python::converter::rvalue_from_python_stage1_data* data){ void* storage=((boost::python::converter::rvalue_from_python_storage >*)(data))->storage.bytes; new (storage) OpenMPAccumulator; ((OpenMPAccumulator*)storage)->set(boost::python::extract(obj_ptr)); data->convertible=storage; } }; template struct custom_vvector_to_list{ static PyObject* convert(const std::vector >& vv){ boost::python::list ret; FOREACH(const std::vector& v, vv){ boost::python::list ret2; FOREACH(const T& e, v) ret2.append(e); ret.append(ret2); } return boost::python::incref(ret.ptr()); } }; template struct custom_list_to_list{ static PyObject* convert(const std::list& v){ boost::python::list ret; FOREACH(const containedType& e, v) ret.append(e); return boost::python::incref(ret.ptr()); } }; /*** c++-list to python-list */ template struct custom_vector_to_list{ static PyObject* convert(const std::vector& v){ boost::python::list ret; FOREACH(const containedType& e, v) ret.append(e); return boost::python::incref(ret.ptr()); } }; template struct custom_vector_from_seq{ custom_vector_from_seq(){ boost::python::converter::registry::push_back(&convertible,&construct,boost::python::type_id >()); } static void* convertible(PyObject* obj_ptr){ // the second condition is important, for some reason otherwise there were attempted conversions of Body to list which failed afterwards. if(!PySequence_Check(obj_ptr) || !PyObject_HasAttrString(obj_ptr,"__len__")) return 0; return obj_ptr; } static void construct(PyObject* obj_ptr, boost::python::converter::rvalue_from_python_stage1_data* data){ void* storage=((boost::python::converter::rvalue_from_python_storage >*)(data))->storage.bytes; new (storage) std::vector(); std::vector* v=(std::vector*)(storage); int l=PySequence_Size(obj_ptr); if(l<0) abort(); /*std::cerr<<"l="<reserve(l); for(int i=0; ipush_back(boost::python::extract(PySequence_GetItem(obj_ptr,i))); } data->convertible=storage; } }; struct custom_ptrMatchMaker_from_float{ custom_ptrMatchMaker_from_float(){ boost::python::converter::registry::push_back(&convertible,&construct,boost::python::type_id >()); } static void* convertible(PyObject* obj_ptr){ if(!PyNumber_Check(obj_ptr)) { cerr<<"Not convertible to MatchMaker"< >*)(data))->storage.bytes; new (storage) shared_ptr(new MatchMaker); // allocate the object at given address shared_ptr* mm=(shared_ptr*)(storage); // convert that address to our type (*mm)->algo="val"; (*mm)->val=PyFloat_AsDouble(obj_ptr); (*mm)->postLoad(**mm); data->convertible=storage; } }; #ifdef YADE_MASK_ARBITRARY struct custom_mask_to_long{ static PyObject* convert(const mask_t& mask){ return PyLong_FromString(const_cast(mask.to_string().c_str()),NULL,2); } }; struct custom_mask_from_long{ custom_mask_from_long(){ boost::python::converter::registry::push_back(&convertible,&construct,boost::python::type_id()); } static void* convertible(PyObject* obj_ptr){ return (PyLong_Check(obj_ptr) || PyInt_Check(obj_ptr))? obj_ptr : 0; } static void construct(PyObject* obj_ptr, boost::python::converter::rvalue_from_python_stage1_data* data){ void* storage=((boost::python::converter::rvalue_from_python_storage*)(data))->storage.bytes; new (storage) mask_t; mask_t* mask=(mask_t*)storage; if (PyInt_Check(obj_ptr)) obj_ptr = PyLong_FromLong(PyInt_AsLong(obj_ptr)); obj_ptr = _PyLong_Format(obj_ptr,2,0,0); std::string s(PyString_AsString(obj_ptr)); // if (s.substr(0,2).compare("0b")==0) s = s.substr(2); if (s[s.length()-1]=='L') s = s.substr(0,s.length()-1); // TODO? *mask = mask_t(s); data->convertible=storage; } }; #endif BOOST_PYTHON_MODULE(_customConverters){ custom_Se3r_from_seq(); boost::python::to_python_converter(); custom_OpenMPAccumulator_from_float(); boost::python::to_python_converter, custom_OpenMPAccumulator_to_float>(); custom_OpenMPAccumulator_from_int(); boost::python::to_python_converter, custom_OpenMPAccumulator_to_int>(); // todo: OpenMPAccumulator custom_ptrMatchMaker_from_float(); // StrArrayMap (typedef for std::map) → python dictionary //custom_StrArrayMap_to_dict(); // register from-python converter and to-python converter boost::python::to_python_converter >,custom_vvector_to_list >(); boost::python::to_python_converter >,custom_vvector_to_list >(); //boost::python::to_python_converter >, custom_list_to_list > >(); //boost::python::to_python_converter >, custom_list_to_list > >(); #ifdef YADE_MASK_ARBITRARY custom_mask_from_long(); boost::python::to_python_converter(); #endif // register 2-way conversion between c++ vector and python homogeneous sequence (list/tuple) of corresponding type #define VECTOR_SEQ_CONV(Type) custom_vector_from_seq(); boost::python::to_python_converter, custom_vector_to_list >(); VECTOR_SEQ_CONV(int); VECTOR_SEQ_CONV(bool); VECTOR_SEQ_CONV(Real); VECTOR_SEQ_CONV(Se3r); VECTOR_SEQ_CONV(Vector2r); VECTOR_SEQ_CONV(Vector2i); VECTOR_SEQ_CONV(Vector3r); VECTOR_SEQ_CONV(Vector3i); VECTOR_SEQ_CONV(Vector6r); VECTOR_SEQ_CONV(Vector6i); VECTOR_SEQ_CONV(Matrix3r); VECTOR_SEQ_CONV(Matrix6r); VECTOR_SEQ_CONV(std::string); VECTOR_SEQ_CONV(shared_ptr); VECTOR_SEQ_CONV(shared_ptr); VECTOR_SEQ_CONV(shared_ptr); VECTOR_SEQ_CONV(shared_ptr); VECTOR_SEQ_CONV(shared_ptr); VECTOR_SEQ_CONV(shared_ptr); VECTOR_SEQ_CONV(shared_ptr); VECTOR_SEQ_CONV(shared_ptr); VECTOR_SEQ_CONV(shared_ptr); #ifdef YADE_BODY_CALLBACK VECTOR_SEQ_CONV(shared_ptr); #endif VECTOR_SEQ_CONV(shared_ptr); VECTOR_SEQ_CONV(shared_ptr); #ifdef YADE_OPENGL VECTOR_SEQ_CONV(shared_ptr); VECTOR_SEQ_CONV(shared_ptr); VECTOR_SEQ_CONV(shared_ptr); VECTOR_SEQ_CONV(shared_ptr); VECTOR_SEQ_CONV(shared_ptr); VECTOR_SEQ_CONV(shared_ptr); #endif #undef VECTOR_SEQ_CONV } trunk-2017.01a/py/wrapper/yadeWrapper.cpp000066400000000000000000001720741304022710500202740ustar00rootroot00000000000000// 2007,2008 © Václav Šmilauer #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include #include namespace py = boost::python; /* Python normally iterates over object it is has __getitem__ and __len__, which BodyContainer does. However, it will not skip removed bodies automatically, hence this iterator which does just that. */ class pyBodyIterator{ BodyContainer::iterator I, Iend; public: pyBodyIterator(const shared_ptr& bc){ I=bc->begin(); Iend=bc->end(); } pyBodyIterator pyIter(){return *this;} shared_ptr pyNext(){ BodyContainer::iterator ret; while(I!=Iend){ ret=I; ++I; if(*ret) return *ret; } PyErr_SetNone(PyExc_StopIteration); py::throw_error_already_set(); /* never reached, but makes the compiler happier */ throw; } }; class pyBodyContainer{ private: void checkClump(shared_ptr b){ if (!(b->isClump())){ PyErr_SetString(PyExc_TypeError,("Error: Body"+boost::lexical_cast(b->getId())+" is not a clump.").c_str()); py::throw_error_already_set(); } } typedef std::map MemberMap; public: const shared_ptr proxee; pyBodyIterator pyIter(){return pyBodyIterator(proxee);} pyBodyContainer(const shared_ptr& _proxee): proxee(_proxee){} shared_ptr pyGetitem(Body::id_t _id){ int id=(_id>=0 ? _id : proxee->size()+_id); if(id<0 || (size_t)id>=proxee->size()){ PyErr_SetString(PyExc_IndexError, "Body id out of range."); py::throw_error_already_set(); /* make compiler happy; never reached */ return shared_ptr(); } else return (*proxee)[id]; } Body::id_t append(shared_ptr b){ // shoud be >=0, but Body is by default created with id 0... :-| if(b->getId()>=0){ PyErr_SetString(PyExc_IndexError,("Body already has id "+boost::lexical_cast(b->getId())+" set; appending such body (for the second time) is not allowed.").c_str()); py::throw_error_already_set(); } return proxee->insert(b); } vector appendList(vector > bb){ boost::mutex::scoped_lock lock(Omega::instance().renderMutex); vector ret; FOREACH(shared_ptr& b, bb){ret.push_back(append(b));} return ret; } Body::id_t clump(vector ids, unsigned int discretization){ // create and add clump itself Scene* scene(Omega::instance().getScene().get()); shared_ptr clumpBody=shared_ptr(new Body()); shared_ptr clump=shared_ptr(new Clump()); clumpBody->shape=clump; clumpBody->setBounded(false); proxee->insert(clumpBody); // add clump members to the clump FOREACH(Body::id_t id, ids) { if (Body::byId(id,scene)->isClumpMember()){ //Check, whether the body is clumpMember Clump::del(Body::byId(Body::byId(id,scene)->clumpId,scene),Body::byId(id,scene)); //If so, remove it from there } }; FOREACH(Body::id_t id, ids) Clump::add(clumpBody,Body::byId(id,scene)); Clump::updateProperties(clumpBody, discretization); return clumpBody->getId(); } py::tuple appendClump(vector > bb, unsigned int discretization){ // append constituent particles vector ids(appendList(bb)); // clump them together (the clump fcn) and return return py::make_tuple(clump(ids, discretization),ids); } void updateClumpProperties(py::list excludeList,unsigned int discretization){ //convert excludeList to a c++ list vector excludeListC; for (int ii = 0; ii < py::len(excludeList); ii++) excludeListC.push_back(py::extract(excludeList[ii])()); FOREACH(const shared_ptr& b, *proxee){ if ( !(std::find(excludeListC.begin(), excludeListC.end(), b->getId()) != excludeListC.end()) ) { if (b->isClump()) Clump::updateProperties(b, discretization); } } } void deleteClumpMember(shared_ptr clumpBody, shared_ptr memberBody){ //FIXME const shared_ptr clump(YADE_PTR_CAST(clumpBody->shape)); if (clump->members.size()==1 ){ Clump::del(clumpBody,memberBody); //phD was not commented out for (int i=0; iids.size(); i++){ if (clump->ids[i] == memberBody->getId()){ clump->ids.erase(clump->ids.begin()+i); } } proxee->erase(memberBody->getId(),false); proxee->erase(clumpBody->getId(),false); }else{ Clump::del(clumpBody,memberBody); //pHD was not commented out for (int i=0; iids.size(); i++){ if (clump->ids[i] == memberBody->getId()){ clump->ids.erase(clump->ids.begin()+i); } } Clump::updatePropertiesNonSpherical(clumpBody,/*intersecting*/ false); proxee->erase(memberBody->getId(),false); } } void deleteClumpBody(shared_ptr clumpBody){ //FIXME const shared_ptr clump(YADE_PTR_CAST(clumpBody->shape)); //if (clump->members.size()==0 ){ // proxee->erase(clumpBody->getId()); //}else{ Scene* scene(Omega::instance().getScene().get()); int totalNumber = clump->ids.size(); int count = 0; while(countids.size(); i++){ shared_ptr memberBody (YADE_PTR_CAST( Body::byId(clump->ids[/*i */0],scene) )); deleteClumpMember(clumpBody,memberBody); //clump->ids.erase(clump->ids.begin()+i); //proxee->erase(memberBody->getId()); count++; } proxee->erase(clumpBody->getId(),true); //} } void addToClump(vector bids, Body::id_t cid, unsigned int discretization){ Scene* scene(Omega::instance().getScene().get()); // get scene shared_ptr clp = Body::byId(cid,scene); // get clump pointer checkClump(clp); vector eraseList; FOREACH(Body::id_t bid, bids) { shared_ptr bp = Body::byId(bid,scene); // get body pointer if (bp->isClump()){ if (bp == clp) {PyErr_Warn(PyExc_UserWarning,("Warning: Body "+boost::lexical_cast(bid)+" and clump "+boost::lexical_cast(cid)+" are the same bodies. Body was not added.").c_str()); return;} Clump::add(clp,bp);//add clump bid to clump cid eraseList.push_back(bid); } else if (bp->isClumpMember()){ Body::id_t bpClumpId = bp->clumpId; shared_ptr bpClumpPointer = Body::byId(bpClumpId,scene); if (bpClumpPointer == clp) {PyErr_Warn(PyExc_UserWarning,("Warning: Body "+boost::lexical_cast(bid)+" is already a clump member of clump "+boost::lexical_cast(cid)+". Body was not added.").c_str()); return;} Clump::add(clp,bpClumpPointer);//add clump bpClumpId to clump cid eraseList.push_back(bpClumpId); } else Clump::add(clp,bp);// bp must be a standalone! } Clump::updateProperties(clp, discretization); FOREACH(Body::id_t bid, eraseList) proxee->erase(bid,false);//erase old clumps } void releaseFromClump(Body::id_t bid, Body::id_t cid, unsigned int discretization){ Scene* scene(Omega::instance().getScene().get()); // get scene shared_ptr bp = Body::byId(bid,scene); // get body pointer shared_ptr clp = Body::byId(cid,scene); // get clump pointer checkClump(clp); if (bp->isClumpMember()){ Body::id_t bpClumpId = bp->clumpId; if (cid == bpClumpId){ const shared_ptr& clump=YADE_PTR_CAST(clp->shape); std::map& members = clump->members; if (members.size() == 2) {PyErr_Warn(PyExc_UserWarning,("Warning: Body "+boost::lexical_cast(bid)+" not released from clump "+boost::lexical_cast(cid)+", because number of clump members would get < 2!").c_str()); return;} Clump::del(clp,bp);//release bid from cid Clump::updateProperties(clp, discretization); } else { PyErr_Warn(PyExc_UserWarning,("Warning: Body "+boost::lexical_cast(bid)+" must be a clump member of clump "+boost::lexical_cast(cid)+". Body was not released.").c_str()); return;} } else { PyErr_Warn(PyExc_UserWarning,("Warning: Body "+boost::lexical_cast(bid)+" is not a clump member. Body was not released.").c_str()); return;} } py::list replaceByClumps(py::list ctList, vector amounts, unsigned int discretization){ py::list ret; Real checkSum = 0.0; FOREACH(Real amount, amounts) { if (amount < 0.0) { PyErr_SetString(PyExc_ValueError,("Error: One or more of given amounts are negative!")); py::throw_error_already_set(); } else checkSum += amount; } if (checkSum > 1.0){ PyErr_SetString(PyExc_ValueError,("Error: Sum of amounts "+boost::lexical_cast(checkSum)+" should not be bigger than 1.0!").c_str()); py::throw_error_already_set(); } if (py::len(ctList) != (unsigned) amounts.size()) {//avoid unsigned comparison warning PyErr_SetString(PyExc_ValueError,("Error: Length of amounts list ("+boost::lexical_cast(amounts.size())+") differs from length of template list ("+boost::lexical_cast(py::len(ctList))+").").c_str()); py::throw_error_already_set(); } //set a random generator (code copied from pkg/dem/SpherePack.cpp): static boost::minstd_rand randGen((int)TimingInfo::getNow(/* get the number even if timing is disabled globally */ true)); typedef boost::variate_generator > UniRandGen; static UniRandGen rndUnit(randGen,boost::uniform_real<>(-1,1)); //get number of spherical particles and a list of all spheres: vector > sphereList; shared_ptr sph (new Sphere); int Sph_Index = sph->getClassIndexStatic(); FOREACH(const shared_ptr& b, *proxee) if ( (b->shape->getClassIndex() == Sph_Index) && (b->isStandalone()) ) sphereList.push_back(b); int num = sphereList.size(); //loop over templates: int numSphereList = num, numTemplates = amounts.size(); for (int ii = 0; ii < numTemplates; ii++) { //ctList: [,, ...] = [,, ...] //ct: = (python objects) //relRadList: [relRad1,relRad2, ...] (list of doubles) //relPosList: [relPos1,relPos2, ...] (list of vectors) //extract attributes from python objects: py::object ctTmp = ctList[ii]; int numCM = py::extract(ctTmp.attr("numCM"))();// number of clump members py::list relRadListTmp = py::extract(ctTmp.attr("relRadii"))(); py::list relPosListTmp = py::extract(ctTmp.attr("relPositions"))(); //get relative radii and positions; calculate volumes; get balance point: get axis aligned bounding box; get minimum radius; vector relRadTmp(numCM), relVolTmp(numCM); vector relPosTmp(numCM); Vector3r relPosTmpMean = Vector3r::Zero(); Real rMin=1./0.; AlignedBox3r aabb; for (int jj = 0; jj < numCM; jj++) { relRadTmp[jj] = py::extract(relRadListTmp[jj])(); relVolTmp[jj] = (4./3.)*Mathr::PI*pow(relRadTmp[jj],3.); relPosTmp[jj] = py::extract(relPosListTmp[jj])(); relPosTmpMean += relPosTmp[jj]; aabb.extend(relPosTmp[jj] + Vector3r::Constant(relRadTmp[jj])); aabb.extend(relPosTmp[jj] - Vector3r::Constant(relRadTmp[jj])); rMin=min(rMin,relRadTmp[jj]); } relPosTmpMean /= numCM;//balance point //get volume of the clump template using regular cubic cell array inside axis aligned bounding box of the clump: //(some parts are duplicated from intergration algorithm in Clump::updateProperties) Real dx = rMin/5.; //edge length of cell Real dv = pow(dx,3); //volume of a single cell Vector3r x; //position vector (center) of cell Real relVolSumTmp = 0.0; //volume of clump template for(x.x()=aabb.min().x()+dx/2.; x.x() > bpListTmp(numReplaceTmp); int a = 0, c = 0;//counters vector posTmp; FOREACH (const shared_ptr& b, sphereList) { if (c == a*numSphereList/numReplaceTmp) { bpListTmp[a] = b; a++; posTmp.push_back(c);//remember position in sphereList } c++; } for (int jj = 0; jj < a; jj++) { sphereList.erase(sphereList.begin()+posTmp[jj]-jj);//remove bodies from sphereList, that were already found numSphereList--; } //adapt position- and radii-informations and replace spheres from bpListTmp by clumps: FOREACH (const shared_ptr& b, bpListTmp) { //get sphere, that should be replaced: const Sphere* sphere = YADE_CAST (b->shape.get()); shared_ptr matTmp = b->material; //get a random rotation quaternion: Quaternionr randAxisTmp = (Quaternionr) AngleAxisr(2*Mathr::PI*rndUnit(),Vector3r(rndUnit(),rndUnit(),rndUnit())); randAxisTmp.normalize(); //convert geometries in global coordinates (scaling): Real scalingFactorVolume = ((4./3.)*Mathr::PI*pow(sphere->radius,3.))/relVolSumTmp; Real scalingFactor1D = pow(scalingFactorVolume,1./3.);//=((vol. sphere)/(relative clump volume))^(1/3) vector newPosTmp(numCM); vector newRadTmp(numCM); vector idsTmp(numCM); for (int jj = 0; jj < numCM; jj++) { newPosTmp[jj] = relPosTmp[jj] - relPosTmpMean; //shift position, to get balance point at (0,0,0) newPosTmp[jj] = randAxisTmp*newPosTmp[jj]; //rotate around balance point newRadTmp[jj] = relRadTmp[jj] * scalingFactor1D;//scale radii newPosTmp[jj] = newPosTmp[jj] * scalingFactor1D;//scale position newPosTmp[jj] += b->state->pos; //translate new position to spheres center //create spheres: shared_ptr newSphere = shared_ptr(new Body()); newSphere->state->blockedDOFs = State::DOF_NONE; newSphere->state->mass = scalingFactorVolume*relVolTmp[jj]*matTmp->density;//vol. corrected mass for clump members Real inertiaTmp = 2.0/5.0*newSphere->state->mass*newRadTmp[jj]*newRadTmp[jj]; newSphere->state->inertia = Vector3r(inertiaTmp,inertiaTmp,inertiaTmp); newSphere->state->pos = newPosTmp[jj]; newSphere->material = matTmp; shared_ptr sphereTmp = shared_ptr(new Sphere()); sphereTmp->radius = newRadTmp[jj]; sphereTmp->color = Vector3r(Mathr::UnitRandom(),Mathr::UnitRandom(),Mathr::UnitRandom()); sphereTmp->color.normalize(); newSphere->shape = sphereTmp; shared_ptr aabbTmp = shared_ptr(new Aabb()); aabbTmp->color = Vector3r(0,1,0); newSphere->bound = aabbTmp; proxee->insert(newSphere); LOG_DEBUG("New body (sphere) "<id<<" added."); idsTmp[jj] = newSphere->id; } Body::id_t newClumpId = clump(idsTmp, discretization); ret.append(py::make_tuple(newClumpId,idsTmp)); erase(b->id,false); } } return ret; } Real getRoundness(py::list excludeList){ Scene* scene(Omega::instance().getScene().get()); // get scene shared_ptr sph (new Sphere); int Sph_Index = sph->getClassIndexStatic(); // get sphere index for checking if bodies are spheres //convert excludeList to a c++ list vector excludeListC; for (int ii = 0; ii < py::len(excludeList); ii++) excludeListC.push_back(py::extract(excludeList[ii])()); Real RC_sum = 0.0; //sum of local roundnesses Real R1, R2, vol, dens; int c = 0; //counter FOREACH(const shared_ptr& b, *proxee){ if ( !(std::find(excludeListC.begin(), excludeListC.end(), b->getId()) != excludeListC.end()) ) { if ((b->shape->getClassIndex() == Sph_Index) && (b->isStandalone())) { RC_sum += 1.0; c += 1; } if (b->isClump()){ R2 = 0.0; dens = 0.0; vol = 0.0; const shared_ptr& clump=YADE_PTR_CAST(b->shape); std::map& members = clump->members; for(MemberMap::value_type& mm : members){ const Body::id_t& memberId=mm.first; const shared_ptr& member=Body::byId(memberId,scene); assert(member->isClumpMember()); if (member->shape->getClassIndex() == Sph_Index){//clump member should be a sphere const Sphere* sphere = YADE_CAST (member->shape.get()); R2 = max((member->state->pos - b->state->pos).norm() + sphere->radius, R2); //get minimum radius of a sphere, that imbeds clump dens = member->material->density; } } if (dens > 0.) vol = b->state->mass/dens; R1 = pow((3.*vol)/(4.*Mathr::PI),1./3.); //get theoretical radius of a sphere, with same volume as clump if (R2 < R1) {PyErr_Warn(PyExc_UserWarning,("Something went wrong in getRoundness method (R2 < R1 detected).")); return 0;} RC_sum += R1/R2; c += 1; } } } if (c == 0) c = 1; //in case no spheres and no clumps are present in the scene: RC = 0 return RC_sum/c; //return roundness coefficient RC } vector replace(vector > bb){proxee->clear(); return appendList(bb);} long length(){return proxee->size();} void clear(){proxee->clear();} bool erase(Body::id_t id, bool eraseClumpMembers){ return proxee->erase(id,eraseClumpMembers); } }; class pyTags{ public: pyTags(const shared_ptr _mb): mb(_mb){} const shared_ptr mb; bool hasKey(const string& key){ FOREACH(string val, mb->tags){ if(boost::algorithm::starts_with(val,key+"=")){ return true;} } return false; } string getItem(const string& key){ FOREACH(string& val, mb->tags){ if(boost::algorithm::starts_with(val,key+"=")){ string val1(val); boost::algorithm::erase_head(val1,key.size()+1); return val1;} } PyErr_SetString(PyExc_KeyError,("Invalid key: "+key+".").c_str()); py::throw_error_already_set(); /* make compiler happy; never reached */ return string(); } void setItem(const string& key,const string& item){ if(key.find("=")!=string::npos) { PyErr_SetString(PyExc_KeyError, "Key must not contain the '=' character (implementation limitation; sorry)."); py::throw_error_already_set(); } FOREACH(string& val, mb->tags){if(boost::algorithm::starts_with(val,key+"=")){ val=key+"="+item; return; } } mb->tags.push_back(key+"="+item); } py::list keys(){ py::list ret; FOREACH(string val, mb->tags){ size_t i=val.find("="); if(i==string::npos) throw runtime_error("Tags must be in the key=value format (internal error?)"); boost::algorithm::erase_tail(val,val.size()-i); ret.append(val); } return ret; } }; class pyInteractionIterator{ InteractionContainer::iterator I, Iend; public: pyInteractionIterator(const shared_ptr& ic){ I=ic->begin(); Iend=ic->end(); } pyInteractionIterator pyIter(){return *this;} shared_ptr pyNext(){ InteractionContainer::iterator ret; while(I!=Iend){ ret=I; ++I; if((*ret)->isReal()) return *ret; } PyErr_SetNone(PyExc_StopIteration); py::throw_error_already_set(); throw; // to avoid compiler warning; never reached //InteractionContainer::iterator ret=I; ++I; return *ret; } }; class pyInteractionContainer{ public: const shared_ptr proxee; pyInteractionContainer(const shared_ptr& _proxee): proxee(_proxee){} pyInteractionIterator pyIter(){return pyInteractionIterator(proxee);} bool has(Body::id_t id1, Body::id_t id2){return proxee->found(id1,id2);} shared_ptr pyGetitem(vector id12){ //if(!PySequence_Check(id12.ptr())) throw invalid_argument("Key must be a tuple"); //if(py::len(id12)!=2) throw invalid_argument("Key must be a 2-tuple: id1,id2."); if(id12.size()==2){ //if(max(id12[0],id12[1])> shared_ptr i=proxee->find(id12[0],id12[1]); if(i) return i; else { PyErr_SetString(PyExc_IndexError,"No such interaction"); py::throw_error_already_set(); /* make compiler happy; never reached */ return shared_ptr(); } } else if(id12.size()==1){ return (*proxee)[id12[0]];} else throw invalid_argument("2 integers (id1,id2) or 1 integer (nth) required."); } /* return nth _real_ iteration from the container (0-based index); this is to facilitate picking random interaction */ shared_ptr pyNth(long n){ long i=0; FOREACH(shared_ptr I, *proxee){ if(!I->isReal()) continue; if(i++==n) return I; } PyErr_SetString(PyExc_IndexError,(string("Interaction number out of range (")+boost::lexical_cast(n)+">="+boost::lexical_cast(i)+").").c_str()); py::throw_error_already_set(); /* make compiler happy; never reached */ return shared_ptr(); } long len(){return proxee->size();} void clear(){proxee->clear();} py::list withBody(long id){ py::list ret; FOREACH(const shared_ptr& I, *proxee){ if(I->isReal() && (I->getId1()==id || I->getId2()==id)) ret.append(I);} return ret;} py::list withBodyAll(long id){ py::list ret; FOREACH(const shared_ptr& I, *proxee){ if(I->getId1()==id || I->getId2()==id) ret.append(I);} return ret; } py::list getAll(bool onlyReal){ py::list ret; FOREACH(const shared_ptr& I, *proxee){ if(onlyReal && !I->isReal()) continue; ret.append(I);} return ret;} long countReal(){ long ret=0; FOREACH(const shared_ptr& I, *proxee){ if(I->isReal()) ret++; } return ret; } bool serializeSorted_get(){return proxee->serializeSorted;} void serializeSorted_set(bool ss){proxee->serializeSorted=ss;} void eraseNonReal(){ proxee->eraseNonReal(); } void erase(Body::id_t id1, Body::id_t id2){ proxee->requestErase(id1,id2); } }; class pyForceContainer{ shared_ptr scene; public: pyForceContainer(shared_ptr _scene): scene(_scene) { } void checkId(long id){ if(id<0 || (size_t)id>=scene->bodies->size()){ PyErr_SetString(PyExc_IndexError, "Body id out of range."); py::throw_error_already_set(); /* never reached */ throw; } } Vector3r force_get(long id, bool sync){ checkId(id); if (!sync) return scene->forces.getForceSingle(id); scene->forces.sync(); return scene->forces.getForce(id);} Vector3r torque_get(long id, bool sync){ checkId(id); if (!sync) return scene->forces.getTorqueSingle(id); scene->forces.sync(); return scene->forces.getTorque(id);} Vector3r move_get(long id){ checkId(id); return scene->forces.getMoveSingle(id); } Vector3r rot_get(long id){ checkId(id); return scene->forces.getRotSingle(id); } void force_add(long id, const Vector3r& f, bool permanent){ checkId(id); if (!permanent) scene->forces.addForce (id,f); else { LOG_WARN("O.forces.addF(...,permanent=True) is deprecated, use O.forces.setPermF(...) instead"); scene->forces.setPermForce (id,f); } } void torque_add(long id, const Vector3r& t, bool permanent){ checkId(id); if (!permanent) scene->forces.addTorque(id,t); else { LOG_WARN("O.forces.addT(...,permanent=True) is deprecated, use O.forces.setPermT(...) instead"); scene->forces.setPermTorque(id,t); } } void move_add(long id, const Vector3r& t){ checkId(id); scene->forces.addMove(id,t);} void rot_add(long id, const Vector3r& t){ checkId(id); scene->forces.addRot(id,t);} Vector3r permForce_get(long id){ checkId(id); return scene->forces.getPermForce(id);} Vector3r permTorque_get(long id){ checkId(id); return scene->forces.getPermTorque(id);} void permForce_set (long id, const Vector3r& f){ checkId(id); scene->forces.setPermForce (id,f); } void permTorque_set(long id, const Vector3r& t){ checkId(id); scene->forces.setPermTorque(id,t); } void reset(bool resetAll) {scene->forces.reset(scene->iter,resetAll);} long syncCount_get(){ return scene->forces.syncCount;} void syncCount_set(long count){ scene->forces.syncCount=count;} bool getPermForceUsed() {return scene->forces.getPermForceUsed();} }; class pyMaterialContainer{ shared_ptr scene; public: pyMaterialContainer(shared_ptr _scene): scene(_scene) { } shared_ptr getitem_id(int _id){ int id=(_id>=0 ? _id : scene->materials.size()+_id); if(id<0 || (size_t)id>=scene->materials.size()){ PyErr_SetString(PyExc_IndexError, "Material id out of range."); py::throw_error_already_set(); /* never reached */ throw; } return Material::byId(id,scene); } shared_ptr getitem_label(string label){ // translate runtime_error to KeyError (instead of RuntimeError) if the material doesn't exist try { return Material::byLabel(label,scene); } catch (std::runtime_error& e){ PyErr_SetString(PyExc_KeyError,e.what()); py::throw_error_already_set(); /* never reached; avoids warning */ throw; } } int append(shared_ptr m){ scene->materials.push_back(m); m->id=scene->materials.size()-1; return m->id; } vector appendList(vector > mm){ vector ret; FOREACH(shared_ptr& m, mm) ret.push_back(append(m)); return ret; } int len(){ return (int)scene->materials.size(); } int index(const std::string& label){ return Material::byLabelIndex(label,scene.get()); } }; void termHandlerNormal(int sig){cerr<<"Yade: normal exit."< rb=OMEGA.getScene(); if(!rb){ OMEGA.init(); rb=OMEGA.getScene(); } assert(rb); if(!OMEGA.hasSimulationLoop()){ OMEGA.createSimulationLoop(); } }; /* Create variables in python's __builtin__ namespace that correspond to labeled objects. At this moment, only engines and functors can be labeled (not bodies etc). */ void mapLabeledEntitiesToVariables(){ // not sure if we should map materials to variables by default... // a call to this functions would have to be added to pyMaterialContainer::append #if 0 FOREACH(const shared_ptr& m, OMEGA.getScene()->materials){ if(!m->label.empty()) { PyGILState_STATE gstate; gstate = PyGILState_Ensure(); PyRun_SimpleString(("__builtins__."+m->label+"=Omega().materials["+boost::lexical_cast(m->id)+"]").c_str()); PyGILState_Release(gstate); } } #endif FOREACH(const shared_ptr& e, OMEGA.getScene()->engines){ if(!e->label.empty()){ pyRunString("__builtins__."+e->label+"=Omega().labeledEngine('"+e->label+"')"); } #define _DO_FUNCTORS(functors,FunctorT){ FOREACH(const shared_ptr& f, functors){ if(!f->label.empty()){ pyRunString("__builtins__."+f->label+"=Omega().labeledEngine('"+f->label+"')");}} } #define _TRY_DISPATCHER(DispatcherT) { DispatcherT* d=dynamic_cast(e.get()); if(d){ _DO_FUNCTORS(d->functors,DispatcherT::FunctorType); } } _TRY_DISPATCHER(BoundDispatcher); _TRY_DISPATCHER(IGeomDispatcher); _TRY_DISPATCHER(IPhysDispatcher); _TRY_DISPATCHER(LawDispatcher); InteractionLoop* id=dynamic_cast(e.get()); if(id){ _DO_FUNCTORS(id->geomDispatcher->functors,IGeomFunctor); _DO_FUNCTORS(id->physDispatcher->functors,IPhysFunctor); _DO_FUNCTORS(id->lawDispatcher->functors,LawFunctor); } Collider* coll=dynamic_cast(e.get()); if(coll){ _DO_FUNCTORS(coll->boundDispatcher->functors,BoundFunctor); } #undef _DO_FUNCTORS #undef _TRY_DISPATCHER } } py::object labeled_engine_get(string label){ FOREACH(const shared_ptr& e, OMEGA.getScene()->engines){ #define _DO_FUNCTORS(functors,FunctorT){ FOREACH(const shared_ptr& f, functors){ if(f->label==label) return py::object(f); }} #define _TRY_DISPATCHER(DispatcherT) { DispatcherT* d=dynamic_cast(e.get()); if(d){ _DO_FUNCTORS(d->functors,DispatcherT::FunctorType); } } if(e->label==label){ return py::object(e); } _TRY_DISPATCHER(BoundDispatcher); _TRY_DISPATCHER(IGeomDispatcher); _TRY_DISPATCHER(IPhysDispatcher); _TRY_DISPATCHER(LawDispatcher); InteractionLoop* id=dynamic_cast(e.get()); if(id){ _DO_FUNCTORS(id->geomDispatcher->functors,IGeomFunctor); _DO_FUNCTORS(id->physDispatcher->functors,IPhysFunctor); _DO_FUNCTORS(id->lawDispatcher->functors,LawFunctor); } Collider* coll=dynamic_cast(e.get()); if(coll){ _DO_FUNCTORS(coll->boundDispatcher->functors,BoundFunctor); } #undef _DO_FUNCTORS #undef _TRY_DISPATCHER } throw std::invalid_argument(string("No engine labeled `")+label+"'"); } long iter(){ return OMEGA.getScene()->iter;} int subStep(){ return OMEGA.getScene()->subStep; } bool subStepping_get(){ return OMEGA.getScene()->subStepping; } void subStepping_set(bool val){ OMEGA.getScene()->subStepping=val; } double time(){return OMEGA.getScene()->time;} double realTime(){ return OMEGA.getRealTime(); } double speed(){ return OMEGA.getScene()->speed; } double dt_get(){return OMEGA.getScene()->dt;} void dt_set(double dt){ Scene* scene=OMEGA.getScene().get(); // activate timestepper, if possible (throw exception if there is none) if(dt<0){ if(!scene->timeStepperActivate(true)) /* not activated*/ throw runtime_error("No TimeStepper found in O.engines."); } else { scene->dt=dt; } } bool dynDt_get(){return OMEGA.getScene()->timeStepperActive();} bool dynDt_set(bool activate){if(!OMEGA.getScene()->timeStepperActivate(activate)) /* not activated*/ throw runtime_error("No TimeStepper found in O.engines."); return true;} bool dynDtAvailable_get(){ return OMEGA.getScene()->timeStepperPresent(); } long stopAtIter_get(){return OMEGA.getScene()->stopAtIter; } void stopAtIter_set(long s){OMEGA.getScene()->stopAtIter=s; } Real stopAtTime_get(){return OMEGA.getScene()->stopAtTime; } void stopAtTime_set(long s){OMEGA.getScene()->stopAtTime=s; } bool timingEnabled_get(){return TimingInfo::enabled;} void timingEnabled_set(bool enabled){TimingInfo::enabled=enabled;} // deprecated: unsigned long forceSyncCount_get(){ return OMEGA.getScene()->forces.syncCount;} void forceSyncCount_set(unsigned long count){ OMEGA.getScene()->forces.syncCount=count;} void run(long int numIter=-1,bool doWait=false){ Scene* scene=OMEGA.getScene().get(); if(numIter>0) scene->stopAtIter=scene->iter+numIter; OMEGA.run(); // timespec t1,t2; t1.tv_sec=0; t1.tv_nsec=40000000; /* 40 ms */ // while(!OMEGA.isRunning()) nanosleep(&t1,&t2); // wait till we start, so that calling wait() immediately afterwards doesn't return immediately LOG_DEBUG("RUN"<<((scene->stopAtIter-scene->iter)>0?string(" ("+boost::lexical_cast(scene->stopAtIter-scene->iter)+" to go)"):string(""))<<"!"); if(doWait) wait(); } void pause(){Py_BEGIN_ALLOW_THREADS; OMEGA.pause(); Py_END_ALLOW_THREADS; LOG_DEBUG("PAUSE!");} void step() { if(OMEGA.isRunning()) throw runtime_error("Called O.step() while simulation is running."); OMEGA.getScene()->moveToNextTimeStep(); /* LOG_DEBUG("STEP!"); run(1); wait(); */ } void wait(){ if(OMEGA.isRunning()){LOG_DEBUG("WAIT!");} else return; timespec t1,t2; t1.tv_sec=0; t1.tv_nsec=40000000; /* 40 ms */ Py_BEGIN_ALLOW_THREADS; while(OMEGA.isRunning()) nanosleep(&t1,&t2); Py_END_ALLOW_THREADS; if(!OMEGA.simulationLoop->workerThrew) return; LOG_ERROR("Simulation error encountered."); OMEGA.simulationLoop->workerThrew=false; throw OMEGA.simulationLoop->workerException; } bool isRunning(){ return OMEGA.isRunning(); } py::object get_filename(){ string f=OMEGA.sceneFile; if(f.size()>0) return py::object(f); return py::object();} void load(std::string fileName,bool quiet=false) { Py_BEGIN_ALLOW_THREADS; OMEGA.stop(); Py_END_ALLOW_THREADS; OMEGA.loadSimulation(fileName,quiet); OMEGA.createSimulationLoop(); mapLabeledEntitiesToVariables(); } void reload(bool quiet=false){ load(OMEGA.sceneFile,quiet);} void saveTmp(string mark="", bool quiet=false){ save(":memory:"+mark,quiet);} void loadTmp(string mark="", bool quiet=false){ load(":memory:"+mark,quiet);} py::list lsTmp(){ py::list ret; typedef pair strstr; FOREACH(const strstr& sim,OMEGA.memSavedSimulations){ string mark=sim.first; boost::algorithm::replace_first(mark,":memory:",""); ret.append(mark); } return ret; } void tmpToFile(string mark, string filename){ if(OMEGA.memSavedSimulations.count(":memory:"+mark)==0) throw runtime_error("No memory-saved simulation named "+mark); boost::iostreams::filtering_ostream out; if(boost::algorithm::ends_with(filename,".bz2")) out.push(boost::iostreams::bzip2_compressor()); out.push(boost::iostreams::file_sink(filename)); if(!out.good()) throw runtime_error("Error while opening file `"+filename+"' for writing."); LOG_INFO("Saving :memory:"<iter=0; OMEGA.getScene()->time=0; OMEGA.timeInit(); } void switchScene(){ std::swap(OMEGA.scenes[OMEGA.currentSceneNb],OMEGA.sceneAnother); } void resetAllScenes(){Py_BEGIN_ALLOW_THREADS; OMEGA.stop(); Py_END_ALLOW_THREADS; OMEGA.resetAllScenes(); OMEGA.createSimulationLoop();} shared_ptr scene_get(){ return OMEGA.getScene(); } int addScene(){return OMEGA.addScene();} void switchToScene(int i){OMEGA.switchToScene(i);} string sceneToString(){ ostringstream oss; yade::ObjectIO::save(oss,"scene",OMEGA.getScene()); oss.flush(); return oss.str(); } void stringToScene(const string &sstring, string mark=""){ Py_BEGIN_ALLOW_THREADS; OMEGA.stop(); Py_END_ALLOW_THREADS; assertScene(); OMEGA.memSavedSimulations[":memory:"+mark]=sstring; OMEGA.sceneFile=":memory:"+mark; load(OMEGA.sceneFile,true); } int thisScene(){return OMEGA.currentSceneNb;} void save(std::string fileName,bool quiet=false){ assertScene(); OMEGA.saveSimulation(fileName,quiet); // OMEGA.sceneFile=fileName; // done in Omega::saveSimulation; } py::list miscParams_get(){ py::list ret; FOREACH(shared_ptr& s, OMEGA.getScene()->miscParams){ ret.append(s); } return ret; } void miscParams_set(vector > ss){ vector >& miscParams=OMEGA.getScene()->miscParams; miscParams.clear(); FOREACH(shared_ptr s, ss){ miscParams.push_back(s); } } vector > engines_get(void){assertScene(); Scene* scene=OMEGA.getScene().get(); return scene->_nextEngines.empty()?scene->engines:scene->_nextEngines;} void engines_set(const vector >& egs){ assertScene(); Scene* scene=OMEGA.getScene().get(); if(scene->subStep<0) scene->engines=egs; // not inside the engine loop right now, ok to update directly else scene->_nextEngines=egs; // inside the engine loop, update _nextEngines; O.engines picks that up automatically, and Scene::moveToNextTimestep will put them in place of engines at the start of the next loop mapLabeledEntitiesToVariables(); } // raw access to engines/_nextEngines, for debugging vector > currEngines_get(){ return OMEGA.getScene()->engines; } vector > nextEngines_get(){ return OMEGA.getScene()->_nextEngines; } pyBodyContainer bodies_get(void){assertScene(); return pyBodyContainer(OMEGA.getScene()->bodies); } pyInteractionContainer interactions_get(void){assertScene(); return pyInteractionContainer(OMEGA.getScene()->interactions); } pyForceContainer forces_get(void){return pyForceContainer(OMEGA.getScene());} pyMaterialContainer materials_get(void){return pyMaterialContainer(OMEGA.getScene());} py::list listChildClassesNonrecursive(const string& base){ py::list ret; for(map::const_iterator di=Omega::instance().getDynlibsDescriptor().begin();di!=Omega::instance().getDynlibsDescriptor().end();++di) if (Omega::instance().isInheritingFrom((*di).first,base)) ret.append(di->first); return ret; } bool isChildClassOf(const string& child, const string& base){ return (Omega::instance().isInheritingFrom_recursive(child,base)); } py::list plugins_get(){ const map& plugins=Omega::instance().getDynlibsDescriptor(); std::pair p; py::list ret; FOREACH(p, plugins) ret.append(p.first); return ret; } pyTags tags_get(void){assertScene(); return pyTags(OMEGA.getScene());} void interactionContainer_set(string clss){ Scene* rb=OMEGA.getScene().get(); if(rb->interactions->size()>0) throw std::runtime_error("Interaction container not empty, will not change its class."); shared_ptr ic=YADE_PTR_DYN_CAST(ClassFactory::instance().createShared(clss)); rb->interactions=ic; } string interactionContainer_get(string clss){ return OMEGA.getScene()->interactions->getClassName(); } void bodyContainer_set(string clss){ Scene* rb=OMEGA.getScene().get(); if(rb->bodies->size()>0) throw std::runtime_error("Body container not empty, will not change its class."); shared_ptr bc=YADE_PTR_DYN_CAST(ClassFactory::instance().createShared(clss)); rb->bodies=bc; } string bodyContainer_get(string clss){ return OMEGA.getScene()->bodies->getClassName(); } #ifdef YADE_OPENMP int numThreads_get(){ return omp_get_max_threads();} void numThreads_set(int n){ int bcn=OMEGA.getScene()->forces.getNumAllocatedThreads(); if(bcn cell_get(){ if(OMEGA.getScene()->isPeriodic) return OMEGA.getScene()->cell; return shared_ptr(); } bool periodic_get(void){ return OMEGA.getScene()->isPeriodic; } void periodic_set(bool v){ OMEGA.getScene()->isPeriodic=v; } shared_ptr energy_get(){ return OMEGA.getScene()->energy; } bool trackEnergy_get(void){ return OMEGA.getScene()->trackEnergy; } void trackEnergy_set(bool e){ OMEGA.getScene()->trackEnergy=e; } void disableGdb(){ signal(SIGSEGV,SIG_DFL); signal(SIGABRT,SIG_DFL); } void exitNoBacktrace(int status=0){ if(status==0) signal(SIGSEGV,termHandlerNormal); /* unset the handler that runs gdb and prints backtrace */ else signal(SIGSEGV,termHandlerError); // try to clean our mess Omega::instance().cleanupTemps(); // flush all streams (so that in case we crash at exit, unflushed buffers are not lost) fflush(NULL); // attempt exit exit(status); } void runEngine(const shared_ptr& e){ LOG_WARN("Omega().runEngine(): deprecated, use __call__ method of the engine instance directly instead; will be removed in the future."); e->scene=OMEGA.getScene().get(); e->action(); } std::string tmpFilename(){ return OMEGA.tmpFilename(); } }; BOOST_PYTHON_MODULE(wrapper) { py::scope().attr("__doc__")="Wrapper for c++ internals of yade."; YADE_SET_DOCSTRING_OPTS; py::enum_("AttrFlags") .value("noSave",yade::Attr::noSave) .value("readonly",yade::Attr::readonly) .value("triggerPostLoad",yade::Attr::triggerPostLoad) .value("noResize",yade::Attr::noResize) ; py::class_("Omega") .add_property("iter",&pyOmega::iter,"Get current step number") .add_property("subStep",&pyOmega::subStep,"Get the current subStep number (only meaningful if O.subStepping==True); -1 when outside the loop, otherwise either 0 (O.subStepping==False) or number of engine to be run (O.subStepping==True)") .add_property("subStepping",&pyOmega::subStepping_get,&pyOmega::subStepping_set,"Get/set whether subStepping is active.") .add_property("stopAtIter",&pyOmega::stopAtIter_get,&pyOmega::stopAtIter_set,"Get/set number of iteration after which the simulation will stop.") .add_property("stopAtTime",&pyOmega::stopAtTime_get,&pyOmega::stopAtTime_set,"Get/set time after which the simulation will stop.") .add_property("time",&pyOmega::time,"Return virtual (model world) time of the simulation.") .add_property("realtime",&pyOmega::realTime,"Return clock (human world) time the simulation has been running.") .add_property("speed",&pyOmega::speed,"Return current calculation speed [iter/sec].") .add_property("dt",&pyOmega::dt_get,&pyOmega::dt_set,"Current timestep (Δt) value.") .add_property("dynDt",&pyOmega::dynDt_get,&pyOmega::dynDt_set,"Whether a :yref:`TimeStepper` is used for dynamic Δt control. See :yref:`dt` on how to enable/disable :yref:`TimeStepper`.") .add_property("dynDtAvailable",&pyOmega::dynDtAvailable_get,"Whether a :yref:`TimeStepper` is amongst :yref:`O.engines`, activated or not.") .def("load",&pyOmega::load,(py::arg("file"),py::arg("quiet")=false),"Load simulation from file. The file should be :yref:`saved` in the same version of Yade, otherwise compatibility is not guaranteed.") .def("reload",&pyOmega::reload,(py::arg("quiet")=false),"Reload current simulation") .def("save",&pyOmega::save,(py::arg("file"),py::arg("quiet")=false),"Save current simulation to file (should be .xml or .xml.bz2 or .yade or .yade.gz). .xml files are bigger than .yade, but can be more or less easily (due to their size) opened and edited, e.g. with text editors. .bz2 and .gz correspond both to compressed versions. All saved files should be :yref:`loaded` in the same version of Yade, otherwise compatibility is not guaranteed.") .def("loadTmp",&pyOmega::loadTmp,(py::arg("mark")="",py::arg("quiet")=false),"Load simulation previously stored in memory by saveTmp. *mark* optionally distinguishes multiple saved simulations") .def("saveTmp",&pyOmega::saveTmp,(py::arg("mark")="",py::arg("quiet")=false),"Save simulation to memory (disappears at shutdown), can be loaded later with loadTmp. *mark* optionally distinguishes different memory-saved simulations.") .def("lsTmp",&pyOmega::lsTmp,"Return list of all memory-saved simulations.") .def("tmpToFile",&pyOmega::tmpToFile,(py::arg("fileName"),py::arg("mark")=""),"Save XML of :yref:`saveTmp`'d simulation into *fileName*.") .def("tmpToString",&pyOmega::tmpToString,(py::arg("mark")=""),"Return XML of :yref:`saveTmp`'d simulation as string.") .def("run",&pyOmega::run,(py::arg("nSteps")=-1,py::arg("wait")=false),"Run the simulation. *nSteps* how many steps to run, then stop (if positive); *wait* will cause not returning to python until simulation will have stopped.") .def("pause",&pyOmega::pause,"Stop simulation execution. (May be called from within the loop, and it will stop after the current step).") .def("step",&pyOmega::step,"Advance the simulation by one step. Returns after the step will have finished.") .def("wait",&pyOmega::wait,"Don't return until the simulation will have been paused. (Returns immediately if not running).") .add_property("running",&pyOmega::isRunning,"Whether background thread is currently running a simulation.") .add_property("filename",&pyOmega::get_filename,"Filename under which the current simulation was saved (None if never saved).") .def("reset",&pyOmega::reset,"Reset simulations completely (including another scenes!).") .def("resetThisScene",&pyOmega::resetThisScene,"Reset current scene.") .def("resetCurrentScene",&pyOmega::resetCurrentScene,"Reset current scene.") .def("resetAllScenes",&pyOmega::resetAllScenes,"Reset all scenes.") .def("addScene",&pyOmega::addScene,"Add new scene to Omega, returns its number") .def("switchToScene",&pyOmega::switchToScene,"Switch to defined scene. Default scene has number 0, other scenes have to be created by addScene method.") .def("switchScene",&pyOmega::switchScene,"Switch to alternative simulation (while keeping the old one). Calling the function again switches back to the first one. Note that most variables from the first simulation will still refer to the first simulation even after the switch\n(e.g. b=O.bodies[4]; O.switchScene(); [b still refers to the body in the first simulation here])") .add_property("thisScene",&pyOmega::thisScene,"Return current scene's id.") .def("sceneToString",&pyOmega::sceneToString,"Return the entire scene as a string. Equivalent to using O.save(...) except that the scene goes to a string instead of a file. (see also stringToScene())") .def("stringToScene",&pyOmega::stringToScene,(py::arg("mark")=""),"Load simulation from a string passed as argument (see also sceneToString).") .def("labeledEngine",&pyOmega::labeled_engine_get,"Return instance of engine/functor with the given label. This function shouldn't be called by the user directly; every ehange in O.engines will assign respective global python variables according to labels.\n\nFor example:\n\n\t *O.engines=[InsertionSortCollider(label='collider')]*\n\n\t *collider.nBins=5 # collider has become a variable after assignment to O.engines automatically*") .def("resetTime",&pyOmega::resetTime,"Reset simulation time: step number, virtual and real time. (Doesn't touch anything else, including timings).") .def("plugins",&pyOmega::plugins_get,"Return list of all plugins registered in the class factory.") .def("_sceneObj",&pyOmega::scene_get,"Return the :yref:`scene ` object. Debugging only, all (or most) :yref:`Scene` functionality is proxies through :yref:`Omega`.") .add_property("engines",&pyOmega::engines_get,&pyOmega::engines_set,"List of engines in the simulation (corresponds to Scene::engines in C++ source code).") .add_property("_currEngines",&pyOmega::currEngines_get,"Currently running engines; debugging only!") .add_property("_nextEngines",&pyOmega::nextEngines_get,"Engines for the next step, if different from the current ones, otherwise empty; debugging only!") .add_property("miscParams",&pyOmega::miscParams_get,&pyOmega::miscParams_set,"MiscParams in the simulation (Scene::mistParams), usually used to save serializables that don't fit anywhere else, like GL functors") .add_property("bodies",&pyOmega::bodies_get,"Bodies in the current simulation (container supporting index access by id and iteration)") .add_property("interactions",&pyOmega::interactions_get,"Access to :yref:`interactions` of simulation, by using \n\n#. id's of both :yref:`Bodies` of the interactions, e.g. ``O.interactions[23,65]``\n#. iteraction over the whole container::\n\n\tfor i in O.interactions: print i.id1,i.id2\n\n.. note::\n\tIteration silently skips interactions that are not :yref:`real`.") .add_property("materials",&pyOmega::materials_get,"Shared materials; they can be accessed by id or by label") .add_property("forces",&pyOmega::forces_get,":yref:`ForceContainer` (forces, torques, displacements) in the current simulation.") .add_property("energy",&pyOmega::energy_get,":yref:`EnergyTracker` of the current simulation. (meaningful only with :yref:`O.trackEnergy`)") .add_property("trackEnergy",&pyOmega::trackEnergy_get,&pyOmega::trackEnergy_set,"When energy tracking is enabled or disabled in this simulation.") .add_property("tags",&pyOmega::tags_get,"Tags (string=string dictionary) of the current simulation (container supporting string-index access/assignment)") .def("childClassesNonrecursive",&pyOmega::listChildClassesNonrecursive,"Return list of all classes deriving from given class, as registered in the class factory") .def("isChildClassOf",&pyOmega::isChildClassOf,"Tells whether the first class derives from the second one (both given as strings).") .add_property("timingEnabled",&pyOmega::timingEnabled_get,&pyOmega::timingEnabled_set,"Globally enable/disable timing services (see documentation of the :yref:`timing module`).") .add_property("forceSyncCount",&pyOmega::forceSyncCount_get,&pyOmega::forceSyncCount_set,"Counter for number of syncs in ForceContainer, for profiling purposes.") .add_property("numThreads",&pyOmega::numThreads_get /* ,&pyOmega::numThreads_set*/ ,"Get maximum number of threads openMP can use.") .add_property("cell",&pyOmega::cell_get,"Periodic cell of the current scene (None if the scene is aperiodic).") .add_property("periodic",&pyOmega::periodic_get,&pyOmega::periodic_set,"Get/set whether the scene is periodic or not (True/False).") .def("exitNoBacktrace",&pyOmega::exitNoBacktrace,(py::arg("status")=0),"Disable SEGV handler and exit, optionally with given status number.") .def("disableGdb",&pyOmega::disableGdb,"Revert SEGV and ABRT handlers to system defaults.") .def("runEngine",&pyOmega::runEngine,"Run given engine exactly once; simulation time, step number etc. will not be incremented (use only if you know what you do).") .def("tmpFilename",&pyOmega::tmpFilename,"Return unique name of file in temporary directory which will be deleted when yade exits.") ; py::class_("TagsWrapper","Container emulating dictionary semantics for accessing tags associated with simulation. Tags are accesed by strings.",py::init()) .def("__getitem__",&pyTags::getItem) .def("__setitem__",&pyTags::setItem) .def("keys",&pyTags::keys) .def("has_key",&pyTags::hasKey); py::class_("BodyContainer",py::init()) .def("__getitem__",&pyBodyContainer::pyGetitem) .def("__len__",&pyBodyContainer::length) .def("__iter__",&pyBodyContainer::pyIter) .def("append",&pyBodyContainer::append,"Append one Body instance, return its id.") .def("append",&pyBodyContainer::appendList,"Append list of Body instance, return list of ids") .def("appendClumped",&pyBodyContainer::appendClump,(py::arg("discretization")=0),"Append given list of bodies as a clump (rigid aggregate); returns a tuple of ``(clumpId,[memberId1,memberId2,...])``. Clump masses and inertia are adapted automatically (for details see :yref:`clump()`).") .def("clump",&pyBodyContainer::clump,(py::arg("discretization")=0),"Clump given bodies together (creating a rigid aggregate); returns ``clumpId``. Clump masses and inertia are adapted automatically when discretization>0. If clump members are overlapping this is done by integration/summation over mass points using a regular grid of cells (grid cells length is defined as $R_{min}/discretization$, where $R_{min}$ is minimum clump member radius). For non-overlapping members inertia of the clump is the sum of inertias from members. If discretization<=0 sum of inertias from members is used (faster, but inaccurate).") .def("updateClumpProperties",&pyBodyContainer::updateClumpProperties,(py::arg("excludeList")=py::list(),py::arg("discretization")=5),"Manually force Yade to update clump properties mass, volume and inertia (for details of 'discretization' value see :yref:`clump()`). Can be used, when clumps are modified or erased during a simulation. Clumps can be excluded from the calculation by giving a list of ids: *O.bodies.updateProperties([ids])*.") .def("deleteClumpMember", &pyBodyContainer::deleteClumpMember,"Erase clump member.") //FIXME .def("deleteClumpBody", &pyBodyContainer::deleteClumpBody,"Erase clump member.")//FIXME .def("addToClump",&pyBodyContainer::addToClump,(py::arg("discretization")=0),"Add body b (or a list of bodies) to an existing clump c. c must be clump and b may not be a clump member of c. Clump masses and inertia are adapted automatically (for details see :yref:`clump()`).\n\nSee :ysrc:`examples/clumps/addToClump-example.py` for an example script.\n\n.. note:: If b is a clump itself, then all members will be added to c and b will be deleted. If b is a clump member of clump d, then all members from d will be added to c and d will be deleted. If you need to add just clump member b, :yref:`release` this member from d first.") .def("releaseFromClump",&pyBodyContainer::releaseFromClump,(py::arg("discretization")=0),"Release body b from clump c. b must be a clump member of c. Clump masses and inertia are adapted automatically (for details see :yref:`clump()`).\n\nSee :ysrc:`examples/clumps/releaseFromClump-example.py` for an example script.\n\n.. note:: If c contains only 2 members b will not be released and a warning will appear. In this case clump c should be :yref:`erased`.") .def("replaceByClumps",&pyBodyContainer::replaceByClumps,(py::arg("discretization")=0),"Replace spheres by clumps using a list of clump templates and a list of amounts; returns a list of tuples: ``[(clumpId1,[memberId1,memberId2,...]),(clumpId2,[memberId1,memberId2,...]),...]``. A new clump will have the same volume as the sphere, that was replaced. Clump masses and inertia are adapted automatically (for details see :yref:`clump()`). \n\n\t *O.bodies.replaceByClumps( [utils.clumpTemplate([1,1],[.5,.5])] , [.9] ) #will replace 90 % of all standalone spheres by 'dyads'*\n\nSee :ysrc:`examples/clumps/replaceByClumps-example.py` for an example script.") .def("getRoundness",&pyBodyContainer::getRoundness,(py::arg("excludeList")=py::list()),"Returns roundness coefficient RC = R2/R1. R1 is the equivalent sphere radius of a clump. R2 is the minimum radius of a sphere, that imbeds the clump. If just spheres are present RC = 1. If clumps are present 0 < RC < 1. Bodies can be excluded from the calculation by giving a list of ids: *O.bodies.getRoundness([ids])*.\n\nSee :ysrc:`examples/clumps/replaceByClumps-example.py` for an example script.") .def("clear", &pyBodyContainer::clear,"Remove all bodies (interactions not checked)") .def("erase", &pyBodyContainer::erase,(py::arg("eraseClumpMembers")=0),"Erase body with the given id; all interaction will be deleted by InteractionLoop in the next step. If a clump is erased use *O.bodies.erase(clumpId,True)* to erase the clump AND its members.") .def("replace",&pyBodyContainer::replace); py::class_("BodyIterator",py::init()) .def("__iter__",&pyBodyIterator::pyIter) .def("next",&pyBodyIterator::pyNext); py::class_("InteractionContainer","Access to :yref:`interactions` of simulation, by using \n\n#. id's of both :yref:`Bodies` of the interactions, e.g. ``O.interactions[23,65]``\n#. iteraction over the whole container::\n\n\tfor i in O.interactions: print i.id1,i.id2\n\n.. note::\n\tIteration silently skips interactions that are not :yref:`real`.",py::init()) .def("__iter__",&pyInteractionContainer::pyIter) .def("__getitem__",&pyInteractionContainer::pyGetitem) .def("__len__",&pyInteractionContainer::len) .def("has",&pyInteractionContainer::has,"Tell if a pair of ids corresponds to an existing interaction (real or not)") .def("countReal",&pyInteractionContainer::countReal,"Return number of interactions that are \"real\", i.e. they have phys and geom.") .def("nth",&pyInteractionContainer::pyNth,"Return n-th interaction from the container (usable for picking random interaction).") .def("withBody",&pyInteractionContainer::withBody,"Return list of real interactions of given body.") .def("withBodyAll",&pyInteractionContainer::withBodyAll,"Return list of all (real as well as non-real) interactions of given body.") .def("all",&pyInteractionContainer::getAll,(py::arg("onlyReal")=false),"Return list of all interactions. Virtual interaction are filtered out if onlyReal=True, else (default) it dumps the full content.") .def("eraseNonReal",&pyInteractionContainer::eraseNonReal,"Erase all interactions that are not :yref:`real `.") .def("erase",&pyInteractionContainer::erase,"Erase one interaction, given by id1, id2 (internally, ``requestErase`` is called -- the interaction might still exist as potential, if the :yref:`Collider` decides so).") .add_property("serializeSorted",&pyInteractionContainer::serializeSorted_get,&pyInteractionContainer::serializeSorted_set) .def("clear",&pyInteractionContainer::clear,"Remove all interactions, and invalidate persistent collider data (if the collider supports it)."); py::class_("InteractionIterator",py::init()) .def("__iter__",&pyInteractionIterator::pyIter) .def("next",&pyInteractionIterator::pyNext); py::class_("ForceContainer",py::init()) .def("f",&pyForceContainer::force_get,(py::arg("id"),py::arg("sync")=false),"Force applied on body. For clumps in openMP, synchronize the force container with sync=True, else the value will be wrong.") .def("t",&pyForceContainer::torque_get,(py::arg("id"),py::arg("sync")=false),"Torque applied on body. For clumps in openMP, synchronize the force container with sync=True, else the value will be wrong.") .def("m",&pyForceContainer::torque_get,(py::arg("id"),py::arg("sync")=false),"Deprecated alias for t (torque).") .def("move",&pyForceContainer::move_get,(py::arg("id")),"Displacement applied on body.") .def("rot",&pyForceContainer::rot_get,(py::arg("id")),"Rotation applied on body.") .def("addF",&pyForceContainer::force_add,(py::arg("id"),py::arg("f"),py::arg("permanent")=false),"Apply force on body (accumulates). The force applies for one iteration, then it is reset by ForceResetter. \n # permanent parameter is deprecated, instead of addF(...,permanent=True) use setPermF(...).") .def("addT",&pyForceContainer::torque_add,(py::arg("id"),py::arg("t"),py::arg("permanent")=false),"Apply torque on body (accumulates). The torque applies for one iteration, then it is reset by ForceResetter. \n # permanent parameter is deprecated, instead of addT(...,permanent=True) use setPermT(...).") .def("permF",&pyForceContainer::permForce_get,(py::arg("id")),"read the value of permanent force on body (set with setPermF()).") .def("permT",&pyForceContainer::permTorque_get,(py::arg("id")),"read the value of permanent torque on body (set with setPermT()).") .def("setPermF",&pyForceContainer::permForce_set, "set the value of permanent force on body.") .def("setPermT",&pyForceContainer::permTorque_set,"set the value of permanent torque on body.") .def("addMove",&pyForceContainer::move_add,(py::arg("id"),py::arg("m")),"Apply displacement on body (accumulates).") .def("addRot",&pyForceContainer::rot_add,(py::arg("id"),py::arg("r")),"Apply rotation on body (accumulates).") .def("reset",&pyForceContainer::reset,(py::arg("resetAll")=true),"Reset the force container, including user defined permanent forces/torques. resetAll=False will keep permanent forces/torques unchanged.") .def("getPermForceUsed",&pyForceContainer::getPermForceUsed,"Check wether permanent forces are present.") .add_property("syncCount",&pyForceContainer::syncCount_get,&pyForceContainer::syncCount_set,"Number of synchronizations of ForceContainer (cummulative); if significantly higher than number of steps, there might be unnecessary syncs hurting performance.") ; py::class_("MaterialContainer","Container for :yref:`Materials`. A material can be accessed using \n\n #. numerical index in range(0,len(cont)), like cont[2]; \n #. textual label that was given to the material, like cont['steel']. This etails traversing all materials and should not be used frequently.",py::init()) .def("append",&pyMaterialContainer::append,"Add new shared :yref:`Material`; changes its id and return it.") .def("append",&pyMaterialContainer::appendList,"Append list of :yref:`Material` instances, return list of ids.") .def("index",&pyMaterialContainer::index,"Return id of material, given its label.") .def("__getitem__",&pyMaterialContainer::getitem_id) .def("__getitem__",&pyMaterialContainer::getitem_label) .def("__len__",&pyMaterialContainer::len); py::class_("STLImporter").def("ymport",&STLImporter::import); ////////////////////////////////////////////////////////////// ///////////// proxyless wrappers Serializable().pyRegisterClass(py::scope()); py::class_, boost::noncopyable >("TimingDeltas").add_property("data",&TimingDeltas::pyData,"Get timing data as list of tuples (label, execTime[nsec], execCount) (one tuple per checkpoint)").def("reset",&TimingDeltas::reset,"Reset timing information"); py::scope().attr("O")=pyOmega(); } trunk-2017.01a/py/ymport.py000066400000000000000000000426761304022710500155350ustar00rootroot00000000000000""" Import geometry from various formats ('import' is python keyword, hence the name 'ymport'). """ from yade.wrapper import * from yade import utils from minieigen import * def textExt(fileName,format='x_y_z_r',shift=Vector3.Zero,scale=1.0,attrs=[],**kw): """Load sphere coordinates from file in specific format, returns a list of corresponding bodies; that may be inserted to the simulation with O.bodies.append(). :param str filename: file name :param str format: the name of output format. Supported `x_y_z_r`(default), `x_y_z_r_matId`, 'x_y_z_r_attrs' :param [float,float,float] shift: [X,Y,Z] parameter moves the specimen. :param float scale: factor scales the given data. :param list attrs: attrs read from file if export.textExt(format='x_y_z_r_attrs') were used ('passed by refernece' style) :param \*\*kw: (unused keyword arguments) is passed to :yref:`yade.utils.sphere` :returns: list of spheres. Lines starting with # are skipped """ infile = open(fileName,"r") lines = infile.readlines() infile.close() ret=[] for line in lines: data = line.split() if (data[0] == "#format"): format=data[1] continue elif (data[0][0] == "#"): continue if (format=='x_y_z_r'): pos = Vector3(float(data[0]),float(data[1]),float(data[2])) ret.append(utils.sphere(shift+scale*pos,scale*float(data[3]),**kw)) elif (format=='x_y_z_r_matId'): pos = Vector3(float(data[0]),float(data[1]),float(data[2])) ret.append(utils.sphere(shift+scale*pos,scale*float(data[3]),material=int(data[4]),**kw)) elif (format=='id_x_y_z_r_matId'): pos = Vector3(float(data[1]),float(data[2]),float(data[3])) ret.append(utils.sphere(shift+scale*pos,scale*float(data[4]),material=int(data[5]),**kw)) elif (format=='x_y_z_r_attrs'): pos = Vector3(float(data[0]),float(data[1]),float(data[2])) s = utils.sphere(shift+scale*pos,scale*float(data[3]),**kw) ret.append(s) attrs.append(data[4:]) else: raise RuntimeError("Please, specify a correct format output!"); return ret def textClumps(fileName,shift=Vector3.Zero,discretization=0,orientation=Quaternion((0,1,0),0.0),scale=1.0,**kw): """Load clumps-members from file, insert them to the simulation. :param str filename: file name :param str format: the name of output format. Supported `x_y_z_r`(default), `x_y_z_r_clumpId` :param [float,float,float] shift: [X,Y,Z] parameter moves the specimen. :param float scale: factor scales the given data. :param \*\*kw: (unused keyword arguments) is passed to :yref:`yade.utils.sphere` :returns: list of spheres. Lines starting with # are skipped """ infile = open(fileName,"r") lines = infile.readlines() infile.close() ret=[] curClump=[] newClumpId = -1 for line in lines: data = line.split() if (data[0][0] == "#"): continue pos = orientation*Vector3(float(data[0]),float(data[1]),float(data[2])) if (newClumpId<0 or newClumpId==int(data[4])): idD = curClump.append(utils.sphere(shift+scale*pos,scale*float(data[3]),**kw)) newClumpId = int(data[4]) else: newClumpId = int(data[4]) ret.append(O.bodies.appendClumped(curClump,discretization=discretization)) curClump=[] idD = curClump.append(utils.sphere(shift+scale*pos,scale*float(data[3]),**kw)) if (len(curClump)<>0): ret.append(O.bodies.appendClumped(curClump,discretization=discretization)) # Set the mask to a clump the same as the first member of it for i in range(len(ret)): O.bodies[ret[i][0]].mask = O.bodies[ret[i][1][0]].mask return ret def text(fileName,shift=Vector3.Zero,scale=1.0,**kw): """Load sphere coordinates from file, returns a list of corresponding bodies; that may be inserted to the simulation with O.bodies.append(). :param string filename: file which has 4 colums [x, y, z, radius]. :param [float,float,float] shift: [X,Y,Z] parameter moves the specimen. :param float scale: factor scales the given data. :param \*\*kw: (unused keyword arguments) is passed to :yref:`yade.utils.sphere` :returns: list of spheres. Lines starting with # are skipped """ return textExt(fileName=fileName,format='x_y_z_r',shift=shift,scale=scale,**kw) def stl(file, dynamic=None,fixed=True,wire=True,color=None,highlight=False,noBound=False,material=-1): """ Import geometry from stl file, return list of created facets.""" imp = STLImporter() facets=imp.ymport(file) for b in facets: b.shape.color=color if color else utils.randomColor() b.shape.wire=wire b.shape.highlight=highlight pos=b.state.pos utils._commonBodySetup(b,0,Vector3(0,0,0),material=material,pos=pos,noBound=noBound,dynamic=dynamic,fixed=fixed) b.aspherical=False return facets def gts(meshfile,shift=Vector3.Zero,scale=1.0,**kw): """ Read given meshfile in gts format. :Parameters: `meshfile`: string name of the input file. `shift`: [float,float,float] [X,Y,Z] parameter moves the specimen. `scale`: float factor scales the given data. `**kw`: (unused keyword arguments) is passed to :yref:`yade.utils.facet` :Returns: list of facets. """ import gts,yade.pack surf=gts.read(open(meshfile)) surf.scale(scale,scale,scale) surf.translate(shift[0],shift[1],shift[2]) yade.pack.gtsSurface2Facets(surf,**kw) def gmsh(meshfile="file.mesh",shift=Vector3.Zero,scale=1.0,orientation=Quaternion((0,1,0),0.0),**kw): """ Imports geometry from .mesh file and creates facets. :Parameters: `shift`: [float,float,float] [X,Y,Z] parameter moves the specimen. `scale`: float factor scales the given data. `orientation`: quaternion orientation of the imported mesh `**kw`: (unused keyword arguments) is passed to :yref:`yade.utils.facet` :Returns: list of facets forming the specimen. mesh files can easily be created with `GMSH `_. Example added to :ysrc:`examples/packs/packs.py` Additional examples of mesh-files can be downloaded from http://www-roc.inria.fr/gamma/download/download.php """ infile = open(meshfile,"r") lines = infile.readlines() infile.close() nodelistVector3=[] elementlistVector3=[] # for deformable elements findVerticesString=0 while (lines[findVerticesString].split()[0]<>'Vertices'): #Find the string with the number of Vertices findVerticesString+=1 findVerticesString+=1 numNodes = int(lines[findVerticesString].split()[0]) for i in range(numNodes): nodelistVector3.append(Vector3(0.0,0.0,0.0)) id = 0 for line in lines[findVerticesString+1:numNodes+findVerticesString+1]: data = line.split() nodelistVector3[id] = orientation*Vector3(float(data[0])*scale,float(data[1])*scale,float(data[2])*scale)+shift id += 1 findTriangleString=findVerticesString+numNodes while (lines[findTriangleString].split()[0]<>'Triangles'): #Find the string with the number of Triangles findTriangleString+=1 findTriangleString+=1 numTriangles = int(lines[findTriangleString].split()[0]) triList = [] for i in range(numTriangles): triList.append([0,0,0,0]) tid = 0 for line in lines[findTriangleString+1:findTriangleString+numTriangles+1]: data = line.split() id1 = int(data[0])-1 id2 = int(data[1])-1 id3 = int(data[2])-1 triList[tid][0] = tid triList[tid][1] = id1 triList[tid][2] = id2 triList[tid][3] = id3 tid += 1 ret=[] for i in triList: a=nodelistVector3[i[1]] b=nodelistVector3[i[2]] c=nodelistVector3[i[3]] ret.append(utils.facet((nodelistVector3[i[1]],nodelistVector3[i[2]],nodelistVector3[i[3]]),**kw)) return ret def gengeoFile(fileName="file.geo",shift=Vector3.Zero,scale=1.0,orientation=Quaternion((0,1,0),0.0),**kw): """ Imports geometry from LSMGenGeo .geo file and creates spheres. Since 2012 the package is available in Debian/Ubuntu and known as python-demgengeo http://packages.qa.debian.org/p/python-demgengeo.html :Parameters: `filename`: string file which has 4 colums [x, y, z, radius]. `shift`: Vector3 Vector3(X,Y,Z) parameter moves the specimen. `scale`: float factor scales the given data. `orientation`: quaternion orientation of the imported geometry `**kw`: (unused keyword arguments) is passed to :yref:`yade.utils.sphere` :Returns: list of spheres. LSMGenGeo library allows one to create pack of spheres with given [Rmin:Rmax] with null stress inside the specimen. Can be useful for Mining Rock simulation. Example: :ysrc:`examples/packs/packs.py`, usage of LSMGenGeo library in :ysrc:`examples/test/genCylLSM.py`. * https://answers.launchpad.net/esys-particle/+faq/877 * http://www.access.edu.au/lsmgengeo_python_doc/current/pythonapi/html/GenGeo-module.html * https://svn.esscc.uq.edu.au/svn/esys3/lsm/contrib/LSMGenGeo/""" from yade.utils import sphere infile = open(fileName,"r") lines = infile.readlines() infile.close() numSpheres = int(lines[6].split()[0]) ret=[] for line in lines[7:numSpheres+7]: data = line.split() pos = orientation*Vector3(float(data[0]),float(data[1]),float(data[2])) ret.append(utils.sphere(shift+scale*pos,scale*float(data[3]),**kw)) return ret def gengeo(mntable,shift=Vector3.Zero,scale=1.0,**kw): """ Imports geometry from LSMGenGeo library and creates spheres. Since 2012 the package is available in Debian/Ubuntu and known as python-demgengeo http://packages.qa.debian.org/p/python-demgengeo.html :Parameters: `mntable`: mntable object, which creates by LSMGenGeo library, see example `shift`: [float,float,float] [X,Y,Z] parameter moves the specimen. `scale`: float factor scales the given data. `**kw`: (unused keyword arguments) is passed to :yref:`yade.utils.sphere` LSMGenGeo library allows one to create pack of spheres with given [Rmin:Rmax] with null stress inside the specimen. Can be useful for Mining Rock simulation. Example: :ysrc:`examples/packs/packs.py`, usage of LSMGenGeo library in :ysrc:`examples/test/genCylLSM.py`. * https://answers.launchpad.net/esys-particle/+faq/877 * http://www.access.edu.au/lsmgengeo_python_doc/current/pythonapi/html/GenGeo-module.html * https://svn.esscc.uq.edu.au/svn/esys3/lsm/contrib/LSMGenGeo/""" try: from GenGeo import MNTable3D,Sphere except ImportError: from gengeo import MNTable3D,Sphere ret=[] sphereList=mntable.getSphereListFromGroup(0) for i in range(0, len(sphereList)): r=sphereList[i].Radius() c=sphereList[i].Centre() ret.append(utils.sphere([shift[0]+scale*float(c.X()),shift[1]+scale*float(c.Y()),shift[2]+scale*float(c.Z())],scale*float(r),**kw)) return ret def unv(fileName,shift=(0,0,0),scale=1.0,returnConnectivityTable=False,**kw): """ Import geometry from unv file, return list of created facets. :param string fileName: name of unv file :param (float,float,float)|Vector3 shift: (X,Y,Z) parameter moves the specimen. :param float scale: factor scales the given data. :param \*\*kw: (unused keyword arguments) is passed to :yref:`yade.utils.facet` :param bool returnConnectivityTable: if True, apart from facets returns also nodes (list of (x,y,z) nodes coordinates) and elements (list of (id1,id2,id3) element nodes ids). If False (default), returns only facets unv files are mainly used for FEM analyses (are used by `OOFEM `_ and `Abaqus `_), but triangular elements can be imported as facets. These files cen be created e.g. with open-source free software `Salome `_. Example: :ysrc:`examples/test/unv-read/unvRead.py`.""" class UNVReader: # class used in ymport.unv function # reads and evaluate given unv file and extracts all triangles # can be extended to read tetrahedrons as well def __init__(self,fileName,shift=(0,0,0),scale=1.0,returnConnectivityTable=False,**kw): self.shift = shift self.scale = scale self.unvFile = open(fileName,'r') self.flag = 0 self.line = self.unvFile.readline() self.lineSplit = self.line.split() self.nodes = [] self.elements = [] self.read(**kw) def readLine(self): self.line = self.unvFile.readline() self.lineSplit = self.line.split() def read(self,**kw): while self.line: self.evalLine() self.line = self.unvFile.readline() self.unvFile.close() self.createFacets(**kw) def evalLine(self): self.lineSplit = self.line.split() if len(self.lineSplit) <= 1: # eval special unv format if self.lineSplit[0] == '-1': pass elif self.lineSplit[0] == '2411': self.flag = 1; # nodes elif self.lineSplit[0] == '2412': self.flag = 2; # edges (lines) else: self.flag = 4; # volume elements or other, not interesting for us (at least yet) elif self.flag == 1: self.evalNodes() elif self.flag == 2: self.evalEdge() elif self.flag == 3: self.evalFacet() #elif self.flag == 4: self.evalGroup() def evalNodes(self): self.readLine() self.nodes.append(( self.shift[0]+self.scale*float(self.lineSplit[0]), self.shift[1]+self.scale*float(self.lineSplit[1]), self.shift[2]+self.scale*float(self.lineSplit[2]))) def evalEdge(self): if self.lineSplit[1]=='41': self.flag = 3 self.evalFacet() else: self.readLine() self.readLine() def evalFacet(self): if self.lineSplit[1]=='41': # triangle self.readLine() self.elements.append(( int(self.lineSplit[0])-1, int(self.lineSplit[1])-1, int(self.lineSplit[2])-1)) else: # is not triangle self.readLine() self.flag = 4 # can be added function to handle tetrahedrons def createFacets(self,**kw): self.facets = [utils.facet(tuple(self.nodes[i] for i in e),**kw) for e in self.elements] # unvReader = UNVReader(fileName,shift,scale,returnConnectivityTable,**kw) if returnConnectivityTable: return unvReader.facets, unvReader.nodes, unvReader.elements return facets def iges(fileName,shift=(0,0,0),scale=1.0,returnConnectivityTable=False,**kw): """ Import triangular mesh from .igs file, return list of created facets. :param string fileName: name of iges file :param (float,float,float)|Vector3 shift: (X,Y,Z) parameter moves the specimen. :param float scale: factor scales the given data. :param \*\*kw: (unused keyword arguments) is passed to :yref:`yade.utils.facet` :param bool returnConnectivityTable: if True, apart from facets returns also nodes (list of (x,y,z) nodes coordinates) and elements (list of (id1,id2,id3) element nodes ids). If False (default), returns only facets """ nodes,elems = [],[] f = open(fileName) for line in f: if line.startswith('134,'): # read nodes coordinates ls = line.split(',') v = Vector3( float(ls[1])*scale + shift[0], float(ls[2])*scale + shift[1], float(ls[3])*scale + shift[2] ) nodes.append(v) if line.startswith('136,'): # read elements ls = line.split(',') i1,i2,i3 = int(ls[3])/2, int(ls[4])/2, int(ls[5])/2 # the numbering of nodes is 1,3,5,7,..., hence this int(ls[*])/2 elems.append( (i1,i2,i3) ) facets = [utils.facet( ( nodes[e[0]], nodes[e[1]], nodes[e[2]] ), **kw) for e in elems] if returnConnectivityTable: return facets, nodes, elems return facets def ele(nodeFileName,eleFileName,shift=(0,0,0),scale=1.0,**kw): """ Import tetrahedral mesh from .ele file, return list of created tetrahedrons. :param string nodeFileName: name of .node file :param string eleFileName: name of .ele file :param (float,float,float)|Vector3 shift: (X,Y,Z) parameter moves the specimen. :param float scale: factor scales the given data. :param \*\*kw: (unused keyword arguments) is passed to :yref:`yade.utils.polyhedron` """ f = open(nodeFileName) line = f.readline() while line.startswith('#'): line = f.readline() ls = line.split() nVertices = int(ls[0]) if int(ls[1])!=3: raise RuntimeError, "wrong .node file, number of dimensions should be 3" vertices = [None for i in xrange(nVertices)] shift = Vector3(shift) for i in xrange(nVertices): line = f.readline() while line.startswith('#'): line = f.readline() ls = line.split() if not ls: continue v = shift + scale*Vector3(tuple(float(ls[j]) for j in (1,2,3))) vertices[int(ls[0])-1] = v f.close() # f = open(eleFileName) line = f.readline() while line.startswith('#'): line = f.readline() ls = line.split() if int(ls[1])!=4: raise RuntimeError, "wrong .ele file, unsupported tetrahedra's number of nodes" nTetras = int(ls[0]) tetras = [None for i in xrange(nTetras)] for i in xrange(nTetras): ls = f.readline().split() tetras[int(ls[0])-1] = utils.polyhedron([vertices[int(ls[j])-1] for j in (1,2,3,4)],**kw) f.close() return tetras def textPolyhedra(fileName,material,shift=Vector3.Zero,scale=1.0,orientation=Quaternion((0,1,0),0.0),**kw): from yade import polyhedra_utils """Load polyhedra from a text file. :param str filename: file name :param [float,float,float] shift: [X,Y,Z] parameter moves the specimen. :param float scale: factor scales the given data. :param quaternion orientation: orientation of the imported polyhedra :param \*\*kw: (unused keyword arguments) is passed to :yref:`yade.polyhedra_utils.polyhedra` :returns: list of polyhedras. Lines starting with # are skipped """ infile = open(fileName,"r") lines = infile.readlines() infile.close() ret=[] i=-1 while (i < (len(lines)-1)): i+=1 line = lines[i] data = line.split() if (data[0][0] == "#"): continue if (len(data)!=3): raise RuntimeError("Check polyhedra input file! Number of parameters in the first line is not 3!"); else: vertLoad = [] ids = int(data[0]) verts = int(data[1]) surfs = int(data[2]) i+=1 for d in range(verts): dataV = lines[i].split() pos = orientation*Vector3(float(dataV[0])*scale,float(dataV[1])*scale,float(dataV[2])*scale)+shift vertLoad.append(pos) i+=1 polR = polyhedra_utils.polyhedra(material=material,v=vertLoad,**kw) ret.append(polR) i= i + surfs - 1 return ret trunk-2017.01a/scripts/000077500000000000000000000000001304022710500146515ustar00rootroot00000000000000trunk-2017.01a/scripts/README000066400000000000000000000001071304022710500155270ustar00rootroot00000000000000In this directory are placed scripts that help managing yade project. trunk-2017.01a/scripts/RPM_packaging/000077500000000000000000000000001304022710500173135ustar00rootroot00000000000000trunk-2017.01a/scripts/RPM_packaging/exclude-rpath-patch000066400000000000000000000056501304022710500231060ustar00rootroot00000000000000=== modified file 'SConstruct' --- SConstruct 2011-02-02 10:39:58 +0000 +++ SConstruct 2011-02-12 15:20:51 +0000 @@ -436,12 +436,12 @@ ### LINKER ## libs for all plugins env.Append(LIBS=[],SHLINKFLAGS=['-rdynamic']) -env.Append(LINKFLAGS=['-rdynamic','-Wl,-z,origin']) +env.Append(LINKFLAGS=['-rdynamic']) if not env['debug']: env.Append(SHLINKFLAGS=['-W,--strip-all']) # makes dynamic library loading easier (no LD_LIBRARY_PATH) and perhaps faster -env.Append(RPATH=runtimeLibDirs) +#env.Append(RPATH=runtimeLibDirs) # find already compiled but not yet installed libraries for linking env.Append(LIBPATH=instLibDirs) # this is if we link to libs that are installed, which is the case now === modified file 'core/main/main.py.in' --- core/main/main.py.in 2011-01-29 23:02:30 +0000 +++ core/main/main.py.in 2011-02-12 20:56:17 +0000 @@ -11,6 +11,16 @@ ## find available builds nonDebugLibDir=prefix+'/lib/yade'+suffix debugLibDir=nonDebugLibDir+'/dbg' + +try: + os.environ["LD_LIBRARY_PATH"] +except KeyError: + #UGLY!!! Need to change it. + os.environ["LD_LIBRARY_PATH"] = nonDebugLibDir + "/lib:" + nonDebugLibDir + "/plugins:" + nonDebugLibDir + "/py:" + nonDebugLibDir + "/py/gts:" + nonDebugLibDir + "/py/yade/:" + nonDebugLibDir + "/py/yade/qt" + debugLibDir + "/lib:" + debugLibDir + "/plugins:" + debugLibDir + "/py:" + debugLibDir + "/py/gts:" + debugLibDir + "/py/yade/:" + debugLibDir + "/py/yade/qt" + os.execve(sys.argv[0], sys.argv, os.environ) + + + hasDebug,hasNonDebug=os.path.exists(debugLibDir+'/py/yade/__init__.py'),os.path.exists(nonDebugLibDir+'/py/yade/__init__.py') if hasDebug and hasNonDebug: buildsAvailable='both non-debug and debug build' elif hasDebug and not hasNonDebug: buildsAvailable='debug build only' === modified file 'gui/SConscript' --- gui/SConscript 2010-10-12 12:28:40 +0000 +++ gui/SConscript 2011-02-12 15:09:00 +0000 @@ -11,7 +11,7 @@ env.File('qt4/SerializableEditor.py'), env.File('qt4/Inspector.py'), env.File('qt4/__init__.py'), - env.SharedLibrary('_GLViewer',['qt4/GLViewer.cpp','qt4/_GLViewer.cpp','qt4/OpenGLManager.cpp'],SHLIBPREFIX='',LIBS=env['LIBS']+[env['QGLVIEWER_LIB']]+linkPlugins(['PeriodicEngines']),RPATH=env['RPATH']+[env.Literal('\\$$ORIGIN/../../../gui')],CXX=env['QT4CXX'] if haveQt4Cxx else env['CXX'],CXXFLAGS=[f for f in env['CXXFLAGS'] if not f.startswith('-Q')] if haveQt4Cxx else env['CXXFLAGS']) + env.SharedLibrary('_GLViewer',['qt4/GLViewer.cpp','qt4/_GLViewer.cpp','qt4/OpenGLManager.cpp'],SHLIBPREFIX='',LIBS=env['LIBS']+[env['QGLVIEWER_LIB']]+linkPlugins(['PeriodicEngines']),CXX=env['QT4CXX'] if haveQt4Cxx else env['CXX'],CXXFLAGS=[f for f in env['CXXFLAGS'] if not f.startswith('-Q')] if haveQt4Cxx else env['CXXFLAGS']) ]) env.Command('qt4/img_rc.py','qt4/img.qrc','pyrcc4 -o $buildDir/gui/qt4/img_rc.py gui/qt4/img.qrc') env.Command('qt4/ui_controller.py','qt4/controller.ui','pyuic4 -o $buildDir/gui/qt4/ui_controller.py gui/qt4/controller.ui') trunk-2017.01a/scripts/RPM_packaging/exclude-rpath-patch-060000066400000000000000000000056641304022710500234160ustar00rootroot00000000000000=== modified file 'SConstruct' --- SConstruct 2011-02-02 13:41:00 +0000 +++ SConstruct 2011-02-12 21:12:28 +0000 @@ -480,12 +480,12 @@ ## libs for all plugins if not env['mono']: env.Append(LIBS=[],SHLINKFLAGS=['-rdynamic']) - env.Append(LINKFLAGS=['-rdynamic','-Wl,-z,origin']) + env.Append(LINKFLAGS=['-rdynamic']) if not env['debug']: env.Append(SHLINKFLAGS=['-W,--strip-all']) # makes dynamic library loading easier (no LD_LIBRARY_PATH) and perhaps faster -env.Append(RPATH=runtimeLibDirs) +#env.Append(RPATH=runtimeLibDirs) # find already compiled but not yet installed libraries for linking env.Append(LIBPATH=instLibDirs) # this is if we link to libs that are installed, which is the case now === modified file 'core/main/main.py.in' --- core/main/main.py.in 2011-01-22 21:30:51 +0000 +++ core/main/main.py.in 2011-02-12 21:11:07 +0000 @@ -11,6 +11,16 @@ ## find available builds nonDebugLibDir=prefix+'/lib/yade'+suffix debugLibDir=nonDebugLibDir+'/dbg' + +try: + os.environ["LD_LIBRARY_PATH"] +except KeyError: + #UGLY!!! Need to change it. + os.environ["LD_LIBRARY_PATH"] = nonDebugLibDir + "/lib:" + nonDebugLibDir + "/plugins:" + nonDebugLibDir + "/py:" + nonDebugLibDir + "/py/gts:" + nonDebugLibDir + "/py/yade/:" + nonDebugLibDir + "/py/yade/qt" + debugLibDir + "/lib:" + debugLibDir + "/plugins:" + debugLibDir + "/py:" + debugLibDir + "/py/gts:" + debugLibDir + "/py/yade/:" + debugLibDir + "/py/yade/qt" + os.execve(sys.argv[0], sys.argv, os.environ) + + + hasDebug,hasNonDebug=os.path.exists(debugLibDir+'/py/yade/__init__.py'),os.path.exists(nonDebugLibDir+'/py/yade/__init__.py') if hasDebug and hasNonDebug: buildsAvailable='both non-debug and debug build' elif hasDebug and not hasNonDebug: buildsAvailable='debug build only' === modified file 'gui/SConscript' --- gui/SConscript 2010-10-12 12:28:40 +0000 +++ gui/SConscript 2011-02-12 21:11:07 +0000 @@ -11,7 +11,7 @@ env.File('qt4/SerializableEditor.py'), env.File('qt4/Inspector.py'), env.File('qt4/__init__.py'), - env.SharedLibrary('_GLViewer',['qt4/GLViewer.cpp','qt4/_GLViewer.cpp','qt4/OpenGLManager.cpp'],SHLIBPREFIX='',LIBS=env['LIBS']+[env['QGLVIEWER_LIB']]+linkPlugins(['PeriodicEngines']),RPATH=env['RPATH']+[env.Literal('\\$$ORIGIN/../../../gui')],CXX=env['QT4CXX'] if haveQt4Cxx else env['CXX'],CXXFLAGS=[f for f in env['CXXFLAGS'] if not f.startswith('-Q')] if haveQt4Cxx else env['CXXFLAGS']) + env.SharedLibrary('_GLViewer',['qt4/GLViewer.cpp','qt4/_GLViewer.cpp','qt4/OpenGLManager.cpp'],SHLIBPREFIX='',LIBS=env['LIBS']+[env['QGLVIEWER_LIB']]+linkPlugins(['PeriodicEngines']),CXX=env['QT4CXX'] if haveQt4Cxx else env['CXX'],CXXFLAGS=[f for f in env['CXXFLAGS'] if not f.startswith('-Q')] if haveQt4Cxx else env['CXXFLAGS']) ]) env.Command('qt4/img_rc.py','qt4/img.qrc','pyrcc4 -o $buildDir/gui/qt4/img_rc.py gui/qt4/img.qrc') env.Command('qt4/ui_controller.py','qt4/controller.ui','pyuic4 -o $buildDir/gui/qt4/ui_controller.py gui/qt4/controller.ui') trunk-2017.01a/scripts/RPM_packaging/yade.spec000066400000000000000000000077031304022710500211200ustar00rootroot00000000000000Name: yade-0.60 Version: 0.60 Release: 1%{?dist} Summary: Platform for discrete element modeling Group: Applications/Engineering License: GPLv2 URL: https://launchpad.net/yade Source0: http://launchpad.net/yade/trunk/0.60/+download/yade-0.60.1.tar.bz2 patch0: exclude-rpath-patch-060 patch1: disable-info.patch BuildRoot: %{_tmppath}/%{name}-%{version} BuildRequires: scons, freeglut-devel, boost-devel >= 1.35, boost-date-time >= 1.35, boost-filesystem >= 1.35, boost-thread >= 1.35, boost-regex >= 1.35, fakeroot, gcc, gcc-c++ > 4.0, boost-iostreams >= 1.35, log4cxx, log4cxx-devel, python-devel, boost-python >= 1.35, ipython, python-matplotlib, sqlite-devel, python-numeric, graphviz-python, vtk-devel, ScientificPython, bzr, eigen2-devel, libQGLViewer-devel, loki-lib-devel, python-xlib, PyQt4, PyQt4-devel, ScientificPython-tk, gnuplot, doxygen, gts-devel, texlive-xetex, texlive-latex Requires: ScientificPython, python-numeric, ipython, ScientificPython-tk, PyQt4, gnuplot Requires(post): info Requires(preun): info %description Platform for discrete element modeling. Yet Another Dynamic Engine. Extensible open-source framework for discrete numerical models, focused on Discrete Element Method. The computation parts are written in c++ using flexible object model, allowing independent implementation of new algorithms and interfaces. Python is used for rapid and concise scene construction, simulation control, postprocessing and debugging. %package dbg Summary: Debug Yade version %description dbg This package contains debug-libraries for yade %package doc Summary: Documentation for Yade %description doc This package contains examples, test scripts and documentation. %prep %setup -q %patch1 %build %install rm -f scons.profile-rpm rm -rf %{buildroot}/* #Compile and install optimized version scons profile=rpm PREFIX=%{buildroot}/usr runtimePREFIX=/usr buildPrefix=rpm march= brief=0 chunkSize=5 jobs=1 version=0.60 features=vtk,gts,opengl,openmp,qt4 optimize=1 debug=0 variant='' #Compile and install debug version scons profile=rpm brief=0 chunkSize=5 jobs=1 optimize=0 debug=1 variant='' %{buildroot}%_libdir #Copy a library "by hand" (not sure, why the symling is not working in RPMs) rm %{buildroot}%_libdir/%{name}/lib/lib_gts__python-module.so cp %{buildroot}%_libdir/%{name}/py/gts/_gts.so %{buildroot}%_libdir/%{name}/lib/lib_gts__python-module.so #Generate documentation cd %_builddir/%{name}-%{version}/doc/sphinx PYTHONPATH=. YADE_PREFIX=%{buildroot}/usr %{buildroot}/usr/bin/%{name} yadeSphinx.py cd _build/latex; xelatex Yade.tex; xelatex Yade.tex; xelatex Yade.tex; YADE_PREFIX=%{buildroot}/usr %{buildroot}/usr/bin/%{name} --generate-manpage yade-%{version}.1 YADE_PREFIX=%{buildroot}/usr %{buildroot}/usr/bin/%{name}-batch --generate-manpage yade-%{version}-batch.1 cd ../..; mkdir -p %{buildroot}%{_docdir}/%{name} mkdir -p %{buildroot}%{_mandir}/man1 mv %_builddir/%{name}-%{version}/doc/sphinx/_build/html %{buildroot}%{_docdir}/%{name} mv %_builddir/%{name}-%{version}/doc/sphinx/_build/latex/Yade.pdf %{buildroot}%{_docdir}/%{name} mv %_builddir/%{name}-%{version}/examples %{buildroot}%{_docdir}/%{name} mv %_builddir/%{name}-%{version}/doc/sphinx/_build/latex/yade-%{version}.1 %{buildroot}%{_mandir}/man1/ mv %_builddir/%{name}-%{version}/doc/sphinx/_build/latex/yade-%{version}-batch.1 %{buildroot}%{_mandir}/man1/ %clean rm -rf %{buildroot} rm -rf %{_builddir}/* %files %defattr(-,root,root,-) %{_bindir}/* %{_libdir}/%{name}/lib/* %{_libdir}/%{name}/plugins/* %{_libdir}/%{name}/py/* %doc %{_mandir}/* %files dbg %defattr(-,root,root,-) %{_libdir}/%{name}/dbg/* %files doc %defattr(-,root,root,-) %doc %{_docdir}/%{name}/* %check YADE_PREFIX=%{buildroot}/usr %{buildroot}/usr/bin/%{name} --test YADE_PREFIX=%{buildroot}/usr %{buildroot}/usr/bin/%{name} --debug --test %changelog * Wed Feb 23 2011 Anton Gladky 0.60-1 - Initial packaging trunk-2017.01a/scripts/RPM_packaging/yade_old.spec000066400000000000000000000046671304022710500217640ustar00rootroot00000000000000# # This needs to be tuned by hand # %define REVISION 0.11 %define _REVISION -0.11 %define SNAPSHOT -stable # do not strip files after compilation %define __spec_install_post /usr/lib/rpm/brp-compress # do not generate debug package %define debug_package %{nil} Name: yade%{_REVISION} Provides: yade%{SNAPSHOT} Version: 1 Release: a Summary: Platform for discrete numerical modeling License: GPL Requires: boost python libQGLViewer BuildRequires: qt-devel boost-devel scons libXmu libXmu-devel glut-devel ScientificPython python-devel Url: http://yade.wikia.com Source: http://download.berlios.de/yade/yade-0.11.0.tar.gz Group: Applications/Engineering BuildRoot: %{_tmppath}/%{name}-buildroot %package dbg Summary: Platform for discrete numerical modeling, debugging version. Group: Applications/Engineering Provides: yade%{SNAPSHOT}-dbg %package devel Summary: Platform for discrete numerical modeling, development files. Group: Applications/Engineering Provides: yade%{SNAPSHOT}-devel Requires: boost-devel python-devel qt-devel libQGLViewer-devel glut-devel %description YADE is an Open Source GNU/GPL Software framework designed with dynamic libraries in a way that it is easy to add new numerical models for simulation. It aims to provide versatile means to perform discrete modelling. %description dbg YADE is an Open Source GNU/GPL Software framework designed with dynamic libraries in a way that it is easy to add new numerical models for simulation. It aims to provide versatile means to perform discrete modelling. This packages is built with debugging support. %description devel YADE is an Open Source GNU/GPL Software framework designed with dynamic libraries in a way that it is easy to add new numerical models for simulation. It aims to provide versatile means to perform discrete modelling. This package contains development files. %prep %setup -n yade-0.11.0 %build %install #optimized build (main package) scons buildPrefix=${RPM_BUILD_DIR} PREFIX=%{RPM_BUILD_ROOT}/usr runtimePREFIX=/usr version=%{REVISION} useMiniWm3=1 exclude=realtime-rigidbody variant='' optimize=1 debug=0 #debug build (-dbg) scons variant=-dbg optimize=0 debug=1 # install headers (-devel) scons %{RPM_BUILD_ROOT}/usr/include %{RPM_BUILD_ROOT}/usr/lib/pkgconfig %files %defattr(-,root,root) /usr/lib/%name /usr/bin/%name %files dbg %defattr(-,root,root) /usr/lib/%name-dbg /usr/bin/%name-dbg %files devel %defattr(-,root,root) /usr/include/%name /usr/lib/pkgconfig/%{name}*.pc trunk-2017.01a/scripts/build-infrastructure/000077500000000000000000000000001304022710500210265ustar00rootroot00000000000000trunk-2017.01a/scripts/build-infrastructure/build-farm000077500000000000000000000053051304022710500230010ustar00rootroot00000000000000#!/usr/bin/python # encoding: utf-8 #Initial script to create build-bot import sys,os,shutil,glob,argparse revNo = 0 parser = argparse.ArgumentParser(description='Build packages for different distributions') parser.add_argument('--buildpath', metavar=os.path.normpath(sys.path[0]), default = os.path.normpath(sys.path[0]) , help ='path, where all files for building will be stored ) [default: current directory]') parser.add_argument('--distributions', metavar="lucid maverick natty sid", default = "lucid maverick natty sid" , help ='distributions for building [default: lucid maverick]') parser.add_argument('--architectures', metavar="i386 amd64", default = "i386 amd64" , help ='architectures to building [default: i386 amd64]') args = parser.parse_args() defaultPath = args.buildpath distributionsNames = args.distributions.split() distributionsArch = args.architectures.split() # Check, whether base files for building exist for distrName in distributionsNames: for archName in distributionsArch: distr_plus_arch = distrName+'_'+archName if not(os.path.exists('/var/cache/pbuilder/'+distr_plus_arch+'.tgz')): os.system('sudo pbuilder --create --basetgz /var/cache/pbuilder/'+distr_plus_arch+'.tgz --aptcache /var/cache/pbuilder/aptcache_'+archName+'/ --distribution '+distrName+' --architecture '+archName+' --components "main universe" --debootstrapopts --variant=buildd') os.system('sudo pbuilder --update --basetgz /var/cache/pbuilder/'+distr_plus_arch+'.tgz') #Update to the latest revision or checkout if os.path.exists(defaultPath+'/cleanBzr'): print "CleanBZR folder exists" print "Updating to the latest bzr version" os.chdir(defaultPath+'/cleanBzr/yade') os.system('bzr up') revNo=os.popen("LC_ALL=C bzr revno 2>/dev/null").readlines()[0][:-1] else: os.mkdir(defaultPath+'/cleanBzr') print "CleanBZR created" print "Checking out the latest bzr version" os.chdir(defaultPath+'/cleanBzr/') os.system('bzr checkout lp:yade --lightweight') os.chdir('yade') revNo=os.popen("LC_ALL=C bzr revno 2>/dev/null").readlines()[0][:-1] os.chdir(defaultPath) VERSION = 'bzr'+str(revNo) # Prepare .dsc files for pbuilder for distrName in distributionsNames: if os.path.exists(distrName) and (os.path.isdir(distrName)): shutil.rmtree(distrName) os.mkdir(distrName) os.chdir(distrName) shutil.copytree('../cleanBzr/yade','yade') os.chdir('yade') os.system('scripts/debian-prep ' + distrName) os.chdir('..') os.system('dpkg-source -b -I yade-'+VERSION) dscFile = glob.glob('*.dsc')[0] for archName in distributionsArch: os.mkdir(archName) os.system('sudo pbuilder --build --basetgz /var/cache/pbuilder/'+distr_plus_arch+'.tgz --buildresult '+defaultPath+'/'+distrName+'/'+archName+' '+dscFile) os.chdir('..') trunk-2017.01a/scripts/build-infrastructure/master.cfg000066400000000000000000000302061304022710500230030ustar00rootroot00000000000000# -*- python -*- # ex: set syntax=python: # This is a sample buildmaster config file. It must be installed as # 'master.cfg' in your buildmaster's base directory (although the filename # can be changed with the --basedir option to 'mktap buildbot master'). # It has one job: define a dictionary named BuildmasterConfig. This # dictionary has a variety of keys to control different aspects of the # buildmaster. They are documented in docs/config.xhtml . # This is the dictionary that the buildmaster pays attention to. We also use # a shorter alias to save typing. c = BuildmasterConfig = {} ####### BUILDSLAVES # the 'slaves' list defines the set of allowable buildslaves. Each element is # a BuildSlave object, which is created with bot-name, bot-password. These # correspond to values given to the buildslave's mktap invocation. from buildbot.buildslave import BuildSlave c['slaves'] = [BuildSlave("r0calcul5", "1MotDePasse!"), BuildSlave("r0calcul6", "1MotDePasse!"), BuildSlave("r0calcul7", "1MotDePasse!"), BuildSlave("r0calcul8", "1MotDePasse!"), BuildSlave("r0calcul9", "1MotDePasse!"), BuildSlave("r0calcul10", "1MotDePasse!")] c['slavePortnum'] = 9989 ####### CHANGESOURCES #bm = {'lp:yade' : 'defaultBranch' } from buildbot.changes.mail import BzrLaunchpadEmailMaildirSource c['change_source'] = BzrLaunchpadEmailMaildirSource("/var/lib/buildbot/Maildir", defaultBranch = None) ####### SCHEDULERS ## configure the Schedulers from buildbot.scheduler import Scheduler, Nightly c['schedulers'] = [] c['schedulers'].append(Scheduler(name="full", branch=None, treeStableTimer=5*60, builderNames=["yade-full"])) c['schedulers'].append(Nightly(name="nightly", branch=None, hour=01,minute=23, builderNames=["yade-full"])) #c['schedulers'].append(Nightly(name="nightly", branch=None, # hour=16,minute=55, # builderNames=["yade-full-test"])) # #c['schedulers'].append(Nightly(name="lucid64", branch=None, # hour=01,minute=23, # builderNames=["yade-full-lucid64"])) # ####### BUILDERS # the 'builders' list defines the Builders. Each one is configured with a # dictionary, using the following keys: # name (required): the name used to describe this builder # slavename (required): which slave to use (must appear in c['bots']) # builddir (required): which subdirectory to run the builder in # factory (required): a BuildFactory to define how the build is run # periodicBuildTime (optional): if set, force a build every N seconds from buildbot.process import factory from buildbot.process.properties import WithProperties from buildbot.steps.source import Bzr from buildbot.steps.python_twisted import Trial from buildbot.steps.shell import Compile from buildbot.steps.shell import ShellCommand, RemoteCommand from buildbot.steps.shell import Test from buildbot.steps.transfer import DirectoryUpload, FileUpload from buildbot.steps.master import MasterShellCommand ## nextSlave : choose the best buildslave ## we use nagios probe do determine which hosts is the bets. import os import subprocess def nextSlave(builder, slaves): best = 0 for slave in slaves: print slave mem = float(subprocess.Popen(["/usr/local/bin/check_nrpe", "-H", slave.slave.slavename, "-c", "check_freemem"], stdout=subprocess.PIPE).communicate()[0].split("(")[1].split(")")[0].strip("M")) load = float(subprocess.Popen(["/usr/local/bin/check_nrpe", "-H", slave.slave.slavename, "-c", "check_load_buildbot"], stdout=subprocess.PIPE).communicate()[0].split()[1].rstrip(',')) + 0.01 score = mem/load if score > best : best = score selected = slave return selected bzrurl = "lp:yade" f1 = factory.BuildFactory() # EIGEN3 prefix = "/home/buildbot/yade/yade-full" f1.addStep(Bzr(repourl=bzrurl, mode="update")) f1.addStep(Compile(description="Compiling with eigen3", command=["scons", "features=opengl,gts,openmp,vtk,qt4,cgal", "chunkSize=20", "jobs=4", "PREFIX=" + prefix])) f1.addStep(Test(command=[WithProperties(prefix + "/bin/yade-bzr%(got_revision)s"), "--test"])) f1.addStep(Test(command=[WithProperties(prefix + "/bin/yade-bzr%(got_revision)s"), "--checks"], description="checking eigen3 build", descriptionDone="checking eigen3 build done")) # EIGEN3 - DEBUG #f1.addStep(Compile(description="Compiling debug with eigen3", command=["scons", "features=opengl,gts,openmp,vtk,qt4,cgal", # "chunkSize=20", "jobs=4","debug=true", "PREFIX=" + prefix])) #f1.addStep(Test(command=[WithProperties(prefix + "/bin/yade-bzr%(got_revision)s"), "--test"])) #f1.addStep(Test(command=[WithProperties(prefix + "/bin/yade-bzr%(got_revision)s"), "--checks"], # description="checking eigen3 debug build", descriptionDone="checking eigen3 debug build done")) # # EIGEN2 f1.addStep(Compile(description="Compiling with eigen2", command=["scons", "features=opengl,gts,openmp,vtk,qt4,cgal", "chunkSize=20", "jobs=4", "PREFIX=" + prefix, "eigen2=true"])) f1.addStep(Test(command=[WithProperties(prefix + "/bin/yade-bzr%(got_revision)s"), "--test"])) f1.addStep(Test(command=[WithProperties(prefix + "/bin/yade-bzr%(got_revision)s"), "--checks"], description="checking eigen2 build", descriptionDone="checks eigen2 build done")) # doc wdir = prefix + "/build/doc/sphinx/" texdir = wdir+"_build/latex/" f1.addStep(ShellCommand(workdir=wdir, env={'PYTHONPATH':wdir}, command=["xvfb-run", WithProperties(prefix + "/bin/yade-bzr%(got_revision)s"), "yadeSphinx.py"], description="compiling html doc", descriptionDone="html doc", haltOnFailure=True)) f1.addStep(ShellCommand(workdir= texdir, command=["xelatex", "Yade.tex"], description="compiling pdf doc 1st pass", descriptionDone="pdf doc", haltOnFailure=True)) f1.addStep(ShellCommand(workdir= texdir, command=["xelatex", "Yade.tex"], description="compiling pdf doc 2nd pass", descriptionDone="pdf doc (2)", haltOnFailure=True)) f1.addStep(DirectoryUpload(slavesrc="doc/sphinx/_build/html", masterdest=WithProperties("/var/www/doc"))) f1.addStep(DirectoryUpload(slavesrc="doc/sphinx/_build/html", masterdest=WithProperties("/var/www/doc/%(got_revision)s"))) f1.addStep(FileUpload(slavesrc=texdir+"Yade.pdf", masterdest="/var/www/doc/Yade.pdf")) f1.addStep(MasterShellCommand(command="chmod -R a-x+rX /var/www/doc")) # tarball f1.addStep(ShellCommand(workdir= prefix + "/build", command="/usr/bin/bzr export /tmp/yade")) f1.addStep(ShellCommand(workdir="/tmp",command=["tar", "cvzf", "yade-src.tgz", "yade"])) f1.addStep(FileUpload(slavesrc="/tmp/yade-src.tgz", masterdest=WithProperties("/var/www/source/yade_r%(got_revision)s.tgz"))) f1.addStep(MasterShellCommand(command=["ln", "-sf", WithProperties("/var/www/source/yade_r%(got_revision)s.tgz") ,"/var/www/source/yade_latest_trunk.tgz"])) # clean f1.addStep(ShellCommand(command=["rm","-rf", WithProperties(prefix + "/build-bzr%(got_revision)s"), WithProperties(prefix + "/bin/yade-bzr%(got_revision)s"), "/tmp/yade", WithProperties(prefix + "/bin/yade-bzr%(got_revision)s-batch"), WithProperties(prefix + "/lib/yade-bzr%(got_revision)s")], alwaysRun=True, description="cleaning", descriptionDone="clean")) b1 = {'name': "yade-full", 'slavenames': ["r0calcul5", "r0calcul8", "r0calcul9", "r0calcul10"], 'builddir': "yade-full", 'factory': f1, 'nextSlave': nextSlave, } #b1-test = {'name': "yade-full-test", # 'slavenames': ["r0calcul5", "r0calcul8", "r0calcul9", "r0calcul10"], # 'builddir': "yade-full-test", # 'factory': f2, # 'nextSlave': nextSlave, # } # c['builders'] = [b1] ####### STATUS TARGETS # 'status' is a list of Status Targets. The results of each build will be # pushed to these targets. buildbot/status/*.py has a variety to choose from, # including web pages, email senders, and IRC bots. c['status'] = [] # Use allowForce=True (boolean, not a string. ie: not 'True') to allow # Forcing Builds in the Web User Interface. The default is False. # from buildbot.status import html # c['status'].append(html.WebStatus(http_port=8010,allowForce=True)) from buildbot.status import html c['status'].append(html.WebStatus(http_port=8010,allowForce=True)) from zope.interface import implements from buildbot.interfaces import IEmailLookup import re class MailLookup(): implements(IEmailLookup) def getAddress(self,user): found = set() mailsrch = re.compile("[a-zA-Z0-9\.\_\%\-\+]+@[a-zA-Z0-9\.\_\%\-]+.[a-zA-Z]{2,6}") found.update(mailsrch.findall(user)) if len(found) : return found.pop() else : return None email_lookup = MailLookup() from buildbot.status import mail c['status'].append(mail.MailNotifier(fromaddr="buildbot@yade-dem.org", extraRecipients=["remi.cailletaud@hmg.inpg.fr"], sendToInterestedUsers=True, lookup=email_lookup)) c['status'].append(mail.MailNotifier(fromaddr="buildbot@yade-dem.org", mode="failing", extraRecipients=["yade-dev@lists.launchpad.net"], sendToInterestedUsers=False)) #from buildbot.status import words #irc = words.IRC("chat.eu.freenode.net", "ybb", # channels=["#yade-dev"], # port=8000, # password="1MotDePasse!", # notify_events={ # 'started': 1, # 'finished': 1, # 'exception': 1, # 'successToFailure': 1, # 'failureToSuccess': 1, # }) #c['status'].append(irc) # # #c['status'].append(mail.MailNotifier(fromaddr="buildbot@yade-dem.org",builders=["yade-full-test"], # extraRecipients=["remi.cailletaud@hmg.inpg.fr"], # sendToInterestedUsers=True)) # from buildbot.status import client # c['status'].append(client.PBListener(9988)) ####### DEBUGGING OPTIONS # if you set 'debugPassword', then you can connect to the buildmaster with # the diagnostic tool in contrib/debugclient.py . From this tool, you can # manually force builds and inject changes, which may be useful for testing # your buildmaster without actually committing changes to your repository (or # before you have a functioning 'sources' set up). The debug tool uses the # same port number as the slaves do: 'slavePortnum'. #c['debugPassword'] = "debugpassword" # if you set 'manhole', you can ssh into the buildmaster and get an # interactive python shell, which may be useful for debugging buildbot # internals. It is probably only useful for buildbot developers. You can also # use an authorized_keys file, or plain telnet. #from buildbot import manhole #c['manhole'] = manhole.PasswordManhole("tcp:9999:interface=127.0.0.1", # "admin", "password") ####### PROJECT IDENTITY # the 'projectName' string will be used to describe the project that this # buildbot is working on. For example, it is used as the title of the # waterfall HTML page. The 'projectURL' string will be used to provide a link # from buildbot HTML pages to your project's home page. c['projectName'] = "Yade" c['projectURL'] = "http://yade-dem.org" # the 'buildbotURL' string should point to the location where the buildbot's # internal web server (usually the html.Waterfall page) is visible. This # typically uses the port number set in the Waterfall 'status' entry, but # with an externally-visible host name which the buildbot cannot figure out # without some help. c['buildbotURL'] = "http://yade-dem.org/buildbot/" trunk-2017.01a/scripts/checks-and-tests/000077500000000000000000000000001304022710500200115ustar00rootroot00000000000000trunk-2017.01a/scripts/checks-and-tests/checks/000077500000000000000000000000001304022710500212515ustar00rootroot00000000000000trunk-2017.01a/scripts/checks-and-tests/checks/DEM-PFV-check.py000066400000000000000000000125161304022710500237410ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Here, we are testing bulk modulus, then permeability, then the consolidation of a specimen. # the test is based on examples/FluidCouplingPFV/oedometer.py, only slightly simplified and using less particles if ('PFVFLOW' in features): errors=0 toleranceWarning =0.01 toleranceCritical=0.10 from yade import pack num_spheres=100# number of spheres young=1e6 compFricDegree = 3 # initial contact friction during the confining phase finalFricDegree = 30 # contact friction during the deviatoric loading mn,mx=Vector3(0,0,0),Vector3(1,1,1) # corners of the initial packing O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=radians(compFricDegree),density=2600,label='spheres')) O.materials.append(FrictMat(young=young,poisson=0.5,frictionAngle=0,density=0,label='walls')) walls=aabbWalls([mn,mx],thickness=0,material='walls') wallIds=O.bodies.append(walls) sp=pack.SpherePack() sp.makeCloud(mn,mx,-1,0.3333,num_spheres,False, 0.95,seed=0) #"seed" is not enough for portable determinism it seems, let us use a data file sp.load(checksPath+'/data/100spheres') sp.toSimulation(material='spheres') triax=TriaxialStressController( maxMultiplier=1.+2e4/young, # spheres growing factor (fast growth) finalMaxMultiplier=1.+2e3/young, # spheres growing factor (slow growth) thickness = 0, stressMask = 7, max_vel = 0.005, internalCompaction=True, # If true the confining pressure is generated by growing particles ) newton=NewtonIntegrator(damping=0.2) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Box_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Box_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()],label="iloop" ), FlowEngine(dead=1,label="flow"),#introduced as a dead engine for the moment, see 2nd section GlobalStiffnessTimeStepper(active=1,timeStepUpdateInterval=100,timestepSafetyCoefficient=0.8), triax, newton ] triax.goal1=triax.goal2=triax.goal3=-10000 while 1: O.run(200, True) unb=unbalancedForce() if unb<0.01 and abs(-10000-triax.meanStress)/10000<0.01: break setContactFriction(radians(finalFricDegree)) ## ______________ Oedometer section _________________ #A. Check bulk modulus of the dry material from load/unload cycles triax.stressMask=2 triax.goal1=triax.goal3=0 triax.internalCompaction=False triax.wall_bottom_activated=False triax.goal2=-11000; O.run(2000,1) triax.goal2=-10000; O.run(2000,1) triax.goal2=-11000; O.run(2000,1) e22=triax.strain[1] triax.goal2=-10000; O.run(2000,1) e22=e22-triax.strain[1] modulus = 1000./abs(e22) target=252759.905803 if abs((modulus-target)/target)>toleranceWarning: print "DEM-PFV: difference in bulk modulus:", modulus, "vs. target ",target if (abs((modulus-target)/target)>toleranceCritical): errors+=1 print "The difference is more, than the critical tolerance!" #B. Activate flow engine and set boundary conditions in order to get permeability flow.dead=0 flow.defTolerance=0.3 flow.meshUpdateInterval=200 flow.useSolver=3 flow.viscosity=10 flow.bndCondIsPressure=[0,0,1,1,0,0] flow.bndCondValue=[0,0,1,0,0,0] flow.boundaryUseMaxMin=[0,0,0,0,0,0] O.dt=0.1e-3 O.dynDt=False O.run(1,1) Qin = flow.getBoundaryFlux(2) Qout = flow.getBoundaryFlux(3) permeability = abs(Qin)/1.e-4 #size is one, we compute K=V/∇H if abs(Qin+Qout)>1e-10 : print "DEM-PFV: unbalanced Qin vs. Qout (",Qin," vs. ",Qout,")" errors+=1 target=0.040399916554 if abs((permeability-target)/target)>toleranceWarning: print "DEM-PFV: difference in permeability:",permeability," vs. target ",target if (abs((permeability-target)/target)>toleranceCritical): errors+=1 print "The difference is more, than the critical tolerance!" #C. now the oedometer test, drained at the top, impermeable at the bottom plate flow.bndCondIsPressure=[0,0,0,1,0,0] flow.bndCondValue=[0,0,0,0,0,0] newton.damping=0 zeroTime=O.time zeroe22 = triax.strain[1] triax.goal2=-11000 O.timingEnabled=1 from yade import timing O.run(3000,1) target=628.314160434 if abs((flow.getPorePressure((0.5,0.1,0.5))-target)/target)>toleranceWarning: print "DEM-PFV: difference in final pressure:",flow.getPorePressure((0.5,0.1,0.5))," vs. target ",target if (abs((flow.getPorePressure((0.5,0.1,0.5))-target)/target)>toleranceCritical): errors+=1 print "The difference is more, than the critical tolerance!" target=-0.00258113045083 if abs((triax.strain[1]-zeroe22-target)/target)>toleranceWarning: print "DEM-PFV: difference in final deformation",triax.strain[1]-zeroe22," vs. target ",target if (abs((triax.strain[1]-zeroe22-target)/target)>toleranceCritical): errors+=1 print "The difference is more, than the critical tolerance!" if (float(flow.execTime)/float(sum([e.execTime for e in O.engines])))>0.6 : print "(INFO) DEM-PFV: More than 60\% of cpu time in FlowEngine (",100.*(float(flow.execTime)/float(sum([e.execTime for e in O.engines]))) ,"%). Should not happen with efficient libraries (check blas/lapack/cholmod implementations)" flow.forceMetis=True O.run(201,1) if not flow.metisUsed(): print "DEM-PFV: Metis is not used during cholmod's reordering although explicitly enabled, something wrong with libraries" #errors+=1 if (errors): resultStatus +=1 #Test is failed else: print "skip DEM-PFV check, FlowEngine not available" trunk-2017.01a/scripts/checks-and-tests/checks/README000066400000000000000000000041571304022710500221400ustar00rootroot00000000000000=== Checktesting === 1. Check tests perform comparisons of simulation results between different versions of yade, as discussed in http://www.mail-archive.com/yade-dev@lists.launchpad.net/msg05784.html and the whole thread. They differ with regression tests in the sense that they simulate more complex situations and combinations of different engines, and usually don't have a mathematical proof (though there is no restriction on the latest). 2. They compare the values obtained in version N with values obtained in a previous version or any other "expected" results. The reference values must be hardcoded in the script itself or in data files provided with the script. 3. Check tests are based on regular yade scripts, so that users can easily commit their own scripts to trunk in order to get some automatized testing after commits. 4. Since the check tests history will be mostly based on standard output generated by "yade --checks", a meaningfull checkTest should include some "print" command telling if something went wrong. If the script itself fails for some reason and can't generate an output, the log will contain "scriptName failure". 5. If the script defines differences on obtained and awaited data, it should print some useful information about the problem and increase the value of global variable resultStatus. After this occurs, the automatic test will stop the execution with error message. 6. An example check test can be found in checkTestTriax.py. It shows results comparison, output, and how to define the path to data files using "checksPath". 7. Users are encouraged to add their own scripts into the scripts/test/checks/ folder. Discussion of some specific checktests design in users question is welcome. 8. A check test should never need more than a few seconds to run. If your typical script needs more, try and reduce the number of element or the number of steps. 9. Failures are reported via a global variable "resultStatus", which should be ONLY INCREMENTED in a checkTests, never assigned to (resultStatus+=1 is ok, resultStatus=1 is bad), else the script would erase the history of the checkTests coming before it. trunk-2017.01a/scripts/checks-and-tests/checks/checkCapillaryModels.py000066400000000000000000000054171304022710500257140ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 # 3 pairs of spheres with different diameters, # different capillary bridge models and different # bridge volume are pulled out and the capillary forces # are messed after 250 iterations and compared to a # verified values (TODO: values check one more time). # Links to papers: # Comparison of different capillary bridge models for application in the discrete element method # (A. Gladkyy, R. Schwarze) # http://arxiv.org/pdf/1403.7926.pdf # Capillary forces between surfaces with nanoscale roughness (Yakov I. Rabinovich ...) # http://diyhpl.us/~bryan/papers2/Capillary%20forces%20between%20surfaces%20with%20nanoscale%20roughness.pdf from yade import utils, plot o = Omega() fr = 0.5;rho=2000 tc = 0.001; en = 0.7; et = 0.7; o.dt = 0.001*tc tolerance = 0.0001 r0 = 19.0e-6 r1 = 35.0e-6 r2 = 32.5e-6 r3 = 27.5e-6 Gamma1 = 27.0e-3 Gamma2 = 24.0e-3 Gamma3 = 28.0e-3 Theta = 10.0 VB1 = 2.0e-19 VB2 = 12.0e-19 VB3 = 36.0e-19 CapillarType1 = "Willett_numeric" CapillarType2 = "Willett_analytic" CapillarType3 = "Rabinovich" mat1 = O.materials.append(ViscElCapMat(frictionAngle=fr,density=rho,Vb=VB1,gamma=Gamma1,theta=Theta,Capillar=True,CapillarType=CapillarType1,tc=tc,en=en,et=et)) mat2 = O.materials.append(ViscElCapMat(frictionAngle=fr,density=rho,Vb=VB2,gamma=Gamma2,theta=Theta,Capillar=True,CapillarType=CapillarType2,tc=tc,en=en,et=et)) mat3 = O.materials.append(ViscElCapMat(frictionAngle=fr,density=rho,Vb=VB3,gamma=Gamma3,theta=Theta,Capillar=True,CapillarType=CapillarType3,tc=tc,en=en,et=et)) id1 = O.bodies.append(sphere(center=[0,0,0],radius=r0,material=mat1,fixed=True)) id2 = O.bodies.append(sphere(center=[0,0,(r0+r1)*0.99999],radius=r1,material=mat1,fixed=True)) id3 = O.bodies.append(sphere(center=[3.0*r1,0,0],radius=r0,material=mat2,fixed=True)) id4 = O.bodies.append(sphere(center=[3.0*r1,0,(r0+r2)*0.99999],radius=r2,material=mat2,fixed=True)) id5 = O.bodies.append(sphere(center=[6.0*r1,0,0],radius=r0,material=mat3,fixed=True)) id6 = O.bodies.append(sphere(center=[6.0*r1,0,(r0+r3)*0.99999],radius=r3,material=mat3,fixed=True)) o.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()],verletDist=(r0+r1)*5.0), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_ViscElCapMat_ViscElCapMat_ViscElCapPhys()], [Law2_ScGeom_ViscElCapPhys_Basic()], ), NewtonIntegrator(damping=0,gravity=[0,0,0]), ] O.bodies[id2].state.vel=[0,0,0.001] O.bodies[id4].state.vel=[0,0,0.001] O.bodies[id6].state.vel=[0,0,0.001] O.run(250,True) f1 = -O.forces.f(id2)[2] f2 = -O.forces.f(id4)[2] f3 = -O.forces.f(id6)[2] O.wait() if ((abs(2.07328148666e-07-f1)/f1)>tolerance): resultStatus += 1 if ((abs(6.78192074e-07-f2)/f2)>tolerance): resultStatus += 1 if ((abs(1.58617796928e-06-f3)/f3)>tolerance): resultStatus += 1 trunk-2017.01a/scripts/checks-and-tests/checks/checkClumpHopper.py000066400000000000000000000053111304022710500250570ustar00rootroot00000000000000# -*- coding: utf-8 # This script is used in --check to keep the functionality of adding/removal # of particles and clumps functional import itertools from numpy import * kinEnergyMax = 100000 # Parameters tc=0.001# collision time en=.3 # normal restitution coefficient es=.3 # tangential restitution coefficient frictionAngle=radians(35)# density=2700 # facets material facetMat=O.materials.append(ViscElMat(frictionAngle=frictionAngle,tc=tc,en=en,et=es)) # default spheres material dfltSpheresMat=O.materials.append(ViscElMat(density=density,frictionAngle=frictionAngle,tc=tc,en=en,et=es)) O.dt=.05*tc # time step Rs=0.05 # particle radius # Create geometry x0=0.; y0=0.; z0=0.; ab=.7; at=2.; h=1.; hl=h; al=at*3 zb=z0; x0b=x0-ab/2.; y0b=y0-ab/2.; x1b=x0+ab/2.; y1b=y0+ab/2. zt=z0+h; x0t=x0-at/2.; y0t=y0-at/2.; x1t=x0+at/2.; y1t=y0+at/2. zl=z0-hl;x0l=x0-al/2.; y0l=y0-al/2.; x1l=x0+al/2.; y1l=y0+al/2. vibrationPlate = O.bodies.append(geom.facetBunker((x0,y0,z0), dBunker=ab*4.0,dOutput=ab*1.7,hBunker=ab*3,hOutput=ab,hPipe=ab/3.0, wallMask=4,segmentsNumber=10,material=facetMat)) # Create engines O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), DomainLimiter(lo=(-4,-4,-1),hi=(4,4,4),iterPeriod=5000,label='domLim'), NewtonIntegrator(damping=0, gravity=[0,0,-9.81]), PyRunner(iterPeriod=6500,command='addBodies()',nDo=7,label='addb'), PyRunner(iterPeriod=10000,command='state()',label='state'), ] numSphereGen = 0 def addBodies(): global numSphereGen # Create clumps... clumpColor=(0.0, 0.5, 0.5) for k,l in itertools.product(arange(0,10),arange(0,10)): clpId,sphId=O.bodies.appendClumped([sphere(Vector3(x0t+Rs*(k*4+2),y0t+Rs*(l*4+2),i*Rs*2+zt+ab*3),Rs,color=clumpColor,material=dfltSpheresMat) for i in xrange(4)]) numSphereGen += len(sphId) # ... and spheres spheresColor=(0.4, 0.4, 0.4) for k,l in itertools.product(arange(0,9),arange(0,9)): sphAloneId=O.bodies.append( [sphere( Vector3(x0t+Rs*(k*4+4),y0t+Rs*(l*4+4),i*Rs*2.3+zt+ab*3),Rs,color=spheresColor,material=dfltSpheresMat) for i in xrange(4) ] ) numSphereGen += len(sphAloneId) def state(): global numSphereGen global resultStatus print "Iter %d: Total number of generated spheres %d, removed particles %d, current particles %d, kinEnergy %g"%(O.iter, numSphereGen, domLim.nDeleted, numSphereGen-domLim.nDeleted, utils.kineticEnergy()) if (utils.kineticEnergy() > kinEnergyMax): print "Kinetic energy is over a threshold value! Error!" resultStatus += 1 O.pause() addBodies() O.run(10, True) O.bodies.erase(64, True) O.run(50002, True) trunk-2017.01a/scripts/checks-and-tests/checks/checkGravity.py000066400000000000000000000057341304022710500242570ustar00rootroot00000000000000# -*- coding: utf-8 # 3 Spheres have an initial velociries: 0, +5, -5 # Their positions and velocities are checking during free fall # Checks the correctness of NewtonIntegrator and GravityEngine ## Omega o=Omega() ## PhysicalParameters Density=2400 frictionAngle=radians(35) sphereRadius=0.05 tc = 0.001 en = 0.3 et = 0.3 sphereMat=O.materials.append(ViscElMat(density=Density,frictionAngle=frictionAngle,tc=tc,en=en,et=et)) v_down = -5.0 v_up = 5.0 g = -9.81 tolerance = 1e-3 id_0=o.bodies.append(utils.sphere((0.0,0,0),0.2,material=sphereMat)) #The body has no initial vertical Velocity id_down=o.bodies.append(utils.sphere((1.0,0,0),0.2,material=sphereMat)) #The body has an initial vertical Velocity -5 id_up=o.bodies.append(utils.sphere((2.0,0,0),0.2,material=sphereMat)) #The body has an initial vertical Velocity +5 O.bodies[id_down].state.vel[1] = v_down O.bodies[id_up].state.vel[1] = v_up ## Engines o.engines=[ ForceResetter(), InsertionSortCollider([ Bo1_Sphere_Aabb(), Bo1_Facet_Aabb(), ]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0,gravity=[0,g,0]), PyRunner(command='checkPos()',iterPeriod=10000), ] def checkPos(): if ((O.bodies[id_0].state.pos[1] - getCurrentPos(0))/O.bodies[id_0].state.pos[1] > tolerance): warningMessagePos (0, O.bodies[id_0].state.pos[1], getCurrentPos(0)) if ((O.bodies[id_down].state.pos[1] - getCurrentPos(v_down))/O.bodies[id_down].state.pos[1] > tolerance): warningMessagePos (v_down, O.bodies[id_down].state.pos[1], getCurrentPos(0)) if ((O.bodies[id_up].state.pos[1] - getCurrentPos(v_up))/O.bodies[id_up].state.pos[1] > tolerance): warningMessagePos (v_up, O.bodies[id_up].state.pos[1], getCurrentPos(0)) if ((O.bodies[id_0].state.vel[1] - getCurrentVel(0))/O.bodies[id_0].state.vel[1] > tolerance): warningMessageVel (0, O.bodies[id_0].state.vel[1], getCurrentPos(0)) if ((O.bodies[id_down].state.vel[1] - getCurrentVel(v_down))/O.bodies[id_down].state.vel[1] > tolerance): warningMessageVel (v_down, O.bodies[id_down].state.vel[1], getCurrentPos(0)) if ((O.bodies[id_up].state.vel[1] - getCurrentVel(v_up))/O.bodies[id_up].state.vel[1] > tolerance): warningMessageVel (v_up, O.bodies[id_up].state.vel[1], getCurrentPos(0)) def getCurrentPos(inVel=0): t = O.time+O.dt return inVel*t + g*t*t/2 def getCurrentVel(inVel=0): t = O.time+O.dt return inVel + g*t def warningMessagePos(inVel, y_pos, y_pos_need): print "The body with the initial velocity %.3f, has an y-position %.3f, but it should be %.3f" % (inVel, y_pos, y_pos_need) global resultStatus resultStatus+=1 def warningMessageVel(inVel, y_vel, y_pos_vel): print "The body with the initial velocity %.3f, has an y-velocity %.3f, but it should be %.3f" % (inVel, y_vel, y_pos_vel) global resultStatus resultStatus+=1 O.dt=0.02*tc O.saveTmp('init'); O.run(1000000) O.wait() trunk-2017.01a/scripts/checks-and-tests/checks/checkLiquidMigration.py000066400000000000000000000064071304022710500257310ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 # The model checks liquid migration model if it is enabled during compilation from yade import utils, plot if ('LIQMIGRATION' in features): o = Omega() fr = 0.5;rho=2000 tc = 0.001; en = 0.7; et = 0.7; o.dt = 1.0 r1 = 1.0 r2 = 1.0 Gamma = 20.6*1e-3 Theta = 0 VB = 74.2*1e-12 tolerance = 1e-6 CapillarType = "Lambert" mat1 = O.materials.append(ViscElCapMat(frictionAngle=fr,density=rho,Vb=VB,gamma=Gamma,theta=Theta,Capillar=True,CapillarType=CapillarType,tc=tc,en=en,et=et)) d = 1.1 id0 = O.bodies.append(sphere(center=[0,0,0],radius=r1,material=mat1,fixed=True, color=[1,0,0])) id1 = O.bodies.append(sphere(center=[0,0,(r1+r2)*d],radius=r2,material=mat1,fixed=True, color=[0,1,0])) id2 = O.bodies.append(sphere(center=[0,0,-(r1+r2)*d],radius=r2,material=mat1,fixed=True, color=[0,1,0])) O.bodies[id0].state.Vf = 0.3e-1 O.bodies[id0].state.Vmin = 0.1e-1 O.bodies[id1].state.Vf = 0.4e-1 O.bodies[id1].state.Vmin = 0.1e-1 O.bodies[id2].state.Vf = 0.5e-1 O.bodies[id2].state.Vmin = 0.1e-1 vel = -0.15 O.bodies[id1].state.vel=[0,0,vel] O.bodies[id2].state.vel=[0,0,-vel] o.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()],verletDist=(r1+r2)*5.0), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_ViscElCapMat_ViscElCapMat_ViscElCapPhys()], [Law2_ScGeom_ViscElCapPhys_Basic()], ), LiqControl(particleconserve=True,label='liqcontrol'), NewtonIntegrator(damping=0,gravity=[0,0,0]), PyRunner(command='showData()',iterPeriod=1,dead=True), ] def showData(): print "Step %d"%O.iter print "idB=%d, Vf=%s, Vmin=%s;"%(id0, O.bodies[id0].state.Vf, O.bodies[id0].state.Vmin) print "idB=%d, Vf=%s, Vmin=%s;"%(id1, O.bodies[id1].state.Vf, O.bodies[id1].state.Vmin) print "idB=%d, Vf=%s, Vmin=%s;"%(id2, O.bodies[id2].state.Vf, O.bodies[id2].state.Vmin) try: print "Interaction[%d, %d].Vb=%s"%(id0, id1, O.interactions[id0,id1].phys.Vb) except: pass try: print "Interaction[%d, %d].Vb=%s"%(id0, id2, O.interactions[id0,id2].phys.Vb) except: pass print def switchVel(): O.bodies[id1].state.vel=-O.bodies[id1].state.vel O.bodies[id2].state.vel=-O.bodies[id2].state.vel resultStatus = 0 O.run(3, True) if ((abs((O.interactions[id0,id1].phys.Vb - 0.03)/0.03) > tolerance) or (abs((O.interactions[id0,id1].phys.Vb - 0.03)/0.03) > tolerance)): resultStatus += 1 switchVel() O.run(5, True) if ((abs((O.bodies[id0].state.Vf - 0.03)/0.03) > tolerance) or (abs((O.bodies[id1].state.Vf - 0.04)/0.04) > tolerance) or (abs((O.bodies[id2].state.Vf - 0.05)/0.05) > tolerance)): resultStatus += 1 liqcontrol.particleconserve=False switchVel() O.run(5, True) switchVel() O.run(5, True) if ((abs((O.bodies[id0].state.Vf - 0.0465)/0.0465) > tolerance) or (abs((O.bodies[id1].state.Vf - 0.0325)/0.0325) > tolerance) or (abs((O.bodies[id2].state.Vf - 0.041)/0.041) > tolerance)): resultStatus += 1 else: print "This checkLiquidMigration.py cannot be executed because LIQMIGRATION is disabled" trunk-2017.01a/scripts/checks-and-tests/checks/checkList.py000066400000000000000000000015331304022710500235360ustar00rootroot00000000000000# encoding: utf-8 # 2011 © Bruno Chareyre import yade,math,os,sys scriptsToRun=os.listdir(checksPath) resultStatus = 0 nFailed=0 skipScripts = ['checkList.py'] for script in scriptsToRun: if (script[len(script)-3:]==".py" and script not in skipScripts): try: print "###################################" print "running: ",script execfile(checksPath+"/"+script) if (resultStatus>nFailed): print "Status: FAILURE!!!" nFailed=resultStatus else: print "Status: success" print "___________________________________" except: print script," failure" O.reset() elif (script in skipScripts): print "###################################" print "Skipping %s, because it is in SkipScripts"%script if (resultStatus>0): print resultStatus, " tests are failed" sys.exit(1) else: sys.exit(0) trunk-2017.01a/scripts/checks-and-tests/checks/checkPolyhedraCrush.py000066400000000000000000000044651304022710500255660ustar00rootroot00000000000000from yade import plot, polyhedra_utils, ymport, export frictionIn = 0.0 densityIn = 3000.0 youngIn = 1E10 poissonIn = 0.3 sizeB = 0.020 odt = 0.00001 vel=0.01 tolerance = 0.05 startPos = sizeB def printWarning (f_awaited, f_real, n_awaited, n_real): print ("The awaited force is %.4f, but obtained force is %.4f; number of bodies: %d vs %d! Iteration %d"%(f_awaited, f_real, n_awaited, n_real, O.iter)) def printSuccess (): print ("Checkpoint: force values and number of bodies are OK! Iteration %d"%(O.iter)) def checkForcesBodies(fR, bodNum): if (abs(f[2] - fR)/f[2] > tolerance or len(O.bodies) <> bodNum): printWarning (fR, f[2], 4, len(O.bodies)) resultStatus += 1 else: printSuccess() mat1 = PolyhedraMat(density=densityIn, young=youngIn,poisson=poissonIn, frictionAngle=frictionIn,IsSplitable=True,strength=1) O.bodies.append(utils.wall(0,axis=2,sense=1, material = mat1)) vertices = [[0,0,0],[sizeB,0,0],[sizeB,sizeB,0],[sizeB,sizeB,sizeB],[0,sizeB,0],[0,sizeB,sizeB],[0,0,sizeB],[sizeB,0,sizeB]] t = polyhedra_utils.polyhedra(mat1,v=vertices) t.state.pos = (0,0,sizeB/2) O.bodies.append(t) topmesh=O.bodies.append(geom.facetBox((0.,0.,startPos),(sizeB,sizeB,0.), material=mat1)) O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Polyhedra_Aabb(), Bo1_Wall_Aabb(), Bo1_Facet_Aabb()], verletDist=.05*sizeB), InteractionLoop( [Ig2_Facet_Polyhedra_PolyhedraGeom(), Ig2_Wall_Polyhedra_PolyhedraGeom(), Ig2_Polyhedra_Polyhedra_PolyhedraGeom()], [Ip2_PolyhedraMat_PolyhedraMat_PolyhedraPhys()], [Law2_PolyhedraGeom_PolyhedraPhys_Volumetric()] ), NewtonIntegrator(damping=0.8,gravity=(0,0,-9.81)), PolyhedraSplitter(iterPeriod=1,label='Splitter'), TranslationEngine(translationAxis=[0,0,-1],velocity=vel,ids=topmesh, label='Tr'), PyRunner(command='addPlotData()',iterPeriod=10), ] O.dt=odt f=Vector3.Zero def addPlotData(): global f f=Vector3.Zero for i in topmesh: if (O.forces.f(i)): f+=O.forces.f(i) #from yade import qt #qt.Controller() #V = qt.View() O.run(250, True); checkForcesBodies(25.44893, 4) O.run(50, True); checkForcesBodies(28.791353, 4) O.run(10, True); checkForcesBodies(30.731547, 4) O.run(20, True); checkForcesBodies(33.483438, 7) trunk-2017.01a/scripts/checks-and-tests/checks/checkSaveLoadClumps.py000066400000000000000000000036531304022710500255120ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 # Script generates clumps and saves them # Then it tries to load the saved simulation # See https://bugs.launchpad.net/bugs/1560171 # Thanks to Bettina Suhr for providing the # minimal test script. from yade import pack import tempfile, shutil import time #define material for all bodies: id_Mat=O.materials.append(FrictMat(young=1e6,poisson=0.3,density=1000,frictionAngle=1)) partType='clumps' #define engines: O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(),Ig2_Facet_Sphere_ScGeom()], [Ip2_FrictMat_FrictMat_FrictPhys()], [Law2_ScGeom_FrictPhys_CundallStrack()] ), NewtonIntegrator(damping=0.7,gravity=[0,0,-9.81]) ] #create a box: O.bodies.append(geom.facetBox(center=(0.0,0.0,0.25),extents = (0.125,0.125,0.25), wallMask=31)) #add particles eiter spheres or clumps if partType=='spheres': sp=pack.SpherePack() sp.makeCloud( (-0.125,-0.125,0), ( 0.125,0.125,0.5), rMean=37.6e-3/2.,rRelFuzz=0.0,num=100) sp.toSimulation() O.bodies.updateClumpProperties(discretization=10)# correct mass, volume, inertia!! elif partType=='clumps': sp=pack.SpherePack() c1=pack.SpherePack([ ((0.,0.,0.),37.6e-3/2.), ((37.6e-3/2.,0.,0.),25e-3/2.) ])# overlap between both spheres sp.makeClumpCloud( (-0.125,-0.125,0), ( 0.125,0.125,0.5), [c1],num=80) sp.toSimulation() O.bodies.updateClumpProperties(discretization=10)# correct mass, volume, inertia!! else: print "ERROR! choose either spheres or clumps for partType!" O.dt=1e-6 #write some restart files tmp_dir = tempfile.mkdtemp() O.save(tmp_dir + '/restartMinWorkEx_'+partType+'_Initial') O.run(100000,True) O.save(tmp_dir + '/restartMinWorkEx_'+partType+str(O.iter)) time.sleep(1) O.reset() time.sleep(1) O.load(tmp_dir + '/restartMinWorkEx_'+partType +'100000') O.run(1000, True) trunk-2017.01a/scripts/checks-and-tests/checks/checkTestDummy.py000066400000000000000000000007331304022710500245570ustar00rootroot00000000000000# encoding: utf-8 # 2011 © Bruno Chareyre # A dummy test, just to give an example, and detect possible path problems from yade import pack,utils,export,plot import math,os,sys print 'checkTest mechanism' #Typical structure of a checkTest: #do something and get a result... if 0: #put a condition on the result here, is it the expected result? else: print "Dummy failed (we know it will not happen here, you get the idea)." resultStatus+=1 trunk-2017.01a/scripts/checks-and-tests/checks/checkTestNormalInelasticity.py000066400000000000000000000064241304022710500273010ustar00rootroot00000000000000# -*- coding: utf-8 -*- # Check test version of normalInelasticityTest #Def of the material which will be used O.materials.append(NormalInelasticMat(density=2600,young=4.0e9,poisson=.04,frictionAngle=.6,coeff_dech=3.0,label='Materiau1')) #Def of the bodies of the simulations : 2 spheres, with names which will be useful after O.bodies.append(utils.sphere([0,0,0], 1, fixed=True, wire=False, color=None, highlight=False)) #'Materiau1', as the latest material defined, will be used O.bodies.append(utils.sphere([0,2,0], 1, fixed=True, wire=False, color=None, highlight=False)) lowerSphere=O.bodies[0] upperSphere=O.bodies[1] #Def of the engines taking part to the simulation loop O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()],verletDist=0),# use of verletDist>0 without NewtonIntegrator let crash ?? InteractionLoop( [Ig2_Sphere_Sphere_ScGeom6D()], [Ip2_2xNormalInelasticMat_NormalInelasticityPhys(betaR=0.24)], [Law2_ScGeom6D_NormalInelasticityPhys_NormalInelasticity()] ), PyRunner(iterPeriod=1,command='letMove()') ] #Def of the python commands which will impose required displacements to the moving sphere def letMove():#Load for the first 10 iterations, unload for the 7 following iterations, then reload if mode=='normal': vImposed=[0,-1,0] if O.iter < 25 and O.iter>14: vImposed=[0,1,0] if mode=='tangential': vImposed=[1,0,0] upperSphere.state.vel=vImposed upperSphere.state.pos=upperSphere.state.pos+upperSphere.state.vel*O.dt # ------ Test of the law in the normal direction, using python commands to let move ------ # mode='normal' O.dt=1e-5 O.run(40,True) # ------ Test of the law in the tangential direction, still with python function ------ # mode='tangential' O.engines=O.engines+[PyRunner(iterPeriod=1,command='testInterac()')] def testInterac(): i=O.interactions[1,0] if (not(i.isReal)): print "!!! L'interaction n est plus reelle !!!! It", O.iter O.run(1000,True) ## ------ Test of the law for the moment, using blockedDOF_s and NewtonIntegrator ------ # ##To use blockedDOF_s, the body has to be dynamic.... upperSphere.dynamic=True upperSphere.state.blockedDOFs='xyzXYZ' upperSphere.state.angVel=Vector3(0,0,1) upperSphere.state.vel=Vector3(0,0,0) O.engines=O.engines[:3]+[NewtonIntegrator()] O.run(4000,True) # Reference value of force acting on upperSphere, (r2851) fRef=Vector3(-312380.72434640542,461541.17554873932,0) # Reference value of torque acting on upperSphere, (r2851) tRef=Vector3(0,0,-774632.12686359778) #Actual values: f=O.forces.f(1) t=O.forces.t(1) dF=fRef-f dT=tRef-t tolerance=0.01 if ( (dF.norm()/fRef.norm())>tolerance or (dT.norm()/tRef.norm())>tolerance): print "Regression concerning normalInelasticity-test. We compare loads acting on one sphere, moving with respect to another. At the end of the script (after some relative movements) we have a relative difference, compared to reference values, of" print "- force (the norm) equal to ", dF.norm()/fRef.norm() print "- torque (the norm) equal to ", dT.norm()/tRef.norm() print "Whereas tolerance is ", tolerance print " " print "Indeed here, we have f=",f print "And t=",t print "Because O.forces.f(1) = ", O.forces.f(1) print "Is interaction real ?" ,O.interactions[1,0].isReal resultStatus +=1 trunk-2017.01a/scripts/checks-and-tests/checks/checkTestTriax.py000066400000000000000000000034441304022710500245550ustar00rootroot00000000000000# encoding: utf-8 # 2011 © Bruno Chareyre # Check the result of a triaxial test on a dense 100 spheres packing with position defined, # comparing stresses at the "peak" state. The initial positions have been generated by # internal compaction without friction, so that it is initially at equilibrium without shear forces. # Positions and reference results are in data folder. from yade import pack,utils,export,plot import math,os,sys,shutil,tempfile tolerance=0.01 interactive=False errors=0 tt=TriaxialTest(internalCompaction=True,numberOfGrains=100,compactionFrictionDeg=0,sphereFrictionDeg=30,importFilename=checksPath+'/data/checkTestTriax.spheres') tt.generate("checkTest.yade") O.load("checkTest.yade") O.run(2020,True) if interactive: print O.engines[4].stress(0)[0],O.engines[4].stress(1)[0], O.engines[4].stress(2)[1], O.engines[4].stress(3)[1], O.engines[4].stress(4)[2], O.engines[4].stress(5)[2] os.system('gnuplot -e "plot \'./WallStresses\' using 1:3; replot'+checksPath+'\'/data/WallStressesCheckTest\' using 1:3; replot '+checksPath+'\'/data/WallStresses\' using 1:4; replot '+checksPath+'\'/data/WallStressesCheckTest\' using 1:4; pause -1"') if abs((O.engines[4].stress(3)[1]+107157.2)/107157.2)>tolerance : print "Triaxial checkTest: difference on peak stress" errors+=1 if abs((O.engines[4].stress(1)[0]+50058.7)/50058.7)>tolerance : print "Triaxial checkTest: difference on confining stress" errors+=1 if (errors): resultStatus +=1 #Test is failed if (errors): resultStatus +=1 #Test is failed dirpath = tempfile.mkdtemp() for fileName in ['./checkTest.yade', './_Unloaded_380_3.spheres', './_Unloaded_380_3.xml', './WallStresses', ]: if (os.path.exists(fileName)): shutil.move(fileName,dirpath) print "File %s moved into %s/ directory"%(fileName,dirpath) trunk-2017.01a/scripts/checks-and-tests/checks/checkViscElEng.py000066400000000000000000000026171304022710500244460ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 # 2 spheres. One is fixed, another one failing from up. # Calculate en (coefficient of restitution) and compare with precalculated value # Coefficient of restitution is the ratio of speeds after and before an impact # This check-simulation checks the correctness of ViscoElasticEngine from yade import utils, plot o = Omega() fr = 0.5;rho=2000 tc = 0.001; en = 0.7; et = 0.7; o.dt = 0.0002*tc r1 = 0.003 r2 = 0.002 mat1 = O.materials.append(ViscElMat(frictionAngle=fr,density=rho,tc=tc,en=en,et=et)) id1 = O.bodies.append(sphere(center=[0,0,0],radius=r1,material=mat1,fixed=True)) id2 = O.bodies.append(sphere(center=[0,0,(r1+r2*2.0)],radius=r2,material=mat1,fixed=False)) o.engines = [ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb()],verletDist=(r1+r2)*5.0), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0,gravity=[0,0,-9.81]), PyRunner(command='addPlotData()',iterPeriod=100), ] v0 = 0 en = 0 tolerance = 0.0001 def addPlotData(): global v0, en v = O.bodies[id2].state.vel[2] if v0<=0 and v>0: en=-v/v0 print ("Precalculated en value %.12f" % 0.736356797441) print ("Obtained en value %.12f" % en) O.pause() v0=v O.run(1000000) O.wait() if ((abs(0.736356797441-en)/en)>tolerance): resultStatus += 1 trunk-2017.01a/scripts/checks-and-tests/checks/checkViscElPM.py000066400000000000000000000066651304022710500242600ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 ################################################################################ # CONSTITUTIVE LAW TESTING: Law2_ScGeom_ViscElPhys_Basic() # # Two spheres with velocities (v,0,0) and (-v,0,0) collide. # This script checks if: # - the numerical displacement equals the analytical displacement at a certain # time before the spheres separate, for instance in t = 0.05 s # This also implies the consistency of the results in terms of velocity # (and acceleration). # - the normal stiffness and normal damping coefficients have been calculated # correctly in function of the normal coefficient (en) of restitution and the # impact time (tc); this is a consequence of the previous condition. # # Notice that: # - this script only checks the displacement before the separation because the # analytical solution (given below) supposes that the damping term is still # present, when the spheres separate. This is however not true in the # numerical model (see source code, prevent appearing of attraction forces # due to a viscous component). # - this script does not check the tangential (or shear) behaviour of # the constitutive law. # from yade import plot,ymport import math ################################################################################ # MATERIAL rho = 2000 # [kg/m^3] density mu = 0.75 # [-] friction coefficient tc = 0.2 # [s] contact time en = 0.3 # [-] normal restitution coefficient et = 0.2 # [-] tangential restitution coefficient frictionAngle = math.atan(mu) mat = O.materials.append(ViscElMat(tc=tc,en=en,et=et, frictionAngle=frictionAngle,density=rho)) ################################################################################ # GEOMETRY r = 0.1 # [m] sphere radius b1 = O.bodies.append(utils.sphere(center=(2*r,0,0),radius=r,material=mat)) b2 = O.bodies.append(utils.sphere(center=(0,0,0),radius=r,material=mat)) ################################################################################ # SIMULATION O.dt = 1e-5 # [s] fixed time step v = 2 # [m/s] velocity along x-axis O.bodies[b1].state.vel[0] = -v O.bodies[b2].state.vel[0] = v O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb(),Bo1_Wall_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom(), Ig2_Wall_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()] ), NewtonIntegrator(damping=0) ] ################################################################################ # RUN O.run(5001,True) ################################################################################ # COMPARE ANALYTICAL AND NUMERICAL SOLUTIONS m = 4./3. * math.pi * r**3 * rho # [kg] mass of the sphere # Normal stiffness and damping coefficients according to [Pournin2001] meff = m/2 kn = 2.0 * meff/tc**2 * (math.pi**2 + math.log(en)**2) cn = -4.0 * meff/tc * math.log(en) # Analytical solution of a linear spring damper system omega0 = math.sqrt(kn/m) zeta = cn / (2 * math.sqrt(kn * m)) omegad = omega0 * math.sqrt(1 - zeta**2) xAnalytical = v/omegad * math.exp(-zeta*omega0*O.time) * math.sin(omegad*O.time) # Comparison (if ok, resultStatus is not incremented) tolerance = 0.0001 xNumerical = O.bodies[b2].state.pos[0] if ((abs(xNumerical-xAnalytical)/xAnalytical)>tolerance): resultStatus += 1 trunk-2017.01a/scripts/checks-and-tests/checks/checkViscElPM2.py000066400000000000000000000056071304022710500243350ustar00rootroot00000000000000#!/usr/bin/env python # encoding: utf-8 ################################################################################ # CONSTITUTIVE LAW TESTING: Law2_ScGeom_ViscElPhys_Basic() # # Two spheres of different diameter and young modulus, with velocities # (v,0,0) and (-v,0,0) collide. # The script checks if the restitution coefficient applied is the one obtained # Law2_ScGeom_ViscElPhys_Basic() compute the stiffness and damping coefficient # differently depending on the input. This test is then different from # checkViscElPM.py and checkViscElEng.py # from yade import plot,ymport import math ################################################################################ # MATERIAL diameter1 = 1e-2 #[m] diameter of the first particle diameter2 = 1e-3 #[m] diameter of the second particle rho1 = 1500 # [kg/m^3] density of the first particle rho2 = 2500 # [kg/m^3] density of the second particle youngMod = 1e5 # [kg/m/s^2] young modulus of the particles poissonRatio = 0.5 # [-] poisson's ratio of the particles mu = 0.4 # [-] friction coefficient of both particle en = 0.5 # [-] normal restitution coefficient of both particle et = 1. # [-] tangential restitution coefficient of both particle, no damping frictionAngle = math.atan(mu) O.materials.append(ViscElMat(en=en,et=1.,young = youngMod,poisson = poissonRatio,frictionAngle=frictionAngle,density=rho1, label='Mat1')) O.materials.append(ViscElMat(en=en,et=1.,young = youngMod,poisson = poissonRatio,frictionAngle=frictionAngle,density=rho2, label='Mat2')) ################################################################################ v = 1e-1 # GEOMETRY O.bodies.append(sphere((0,0,0),diameter1/2.0, material = 'Mat1')) O.bodies[0].state.vel[2] = v O.bodies.append(sphere((0,0,(diameter1+diameter2)/2.+ 0.01*diameter1),diameter2/2.0, material = 'Mat2')) O.bodies[-1].state.vel[2] = -v ################################################################################ # SIMULATION O.dt = 1e-6 # [s] fixed time step O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb(),Bo1_Wall_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom(), Ig2_Wall_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()] ), NewtonIntegrator(damping=0.), PyRunner(command = 'check()',iterPeriod = int(0.05/O.dt)-1) ] ################################################################################ def check(): global resultStatus # Compare imposed restitution coefficient and obtained one enMeasured = (O.bodies[1].state.vel[2]-O.bodies[0].state.vel[2])/(2*v) tolerance = 1e-2 if (abs(enMeasured -en)/en)>tolerance: resultStatus+=1 ################################################################################ # RUN O.run(int(0.05/O.dt)) O.wait() ################################################################################ trunk-2017.01a/scripts/checks-and-tests/checks/checkWeight.py000066400000000000000000000024261304022710500240540ustar00rootroot00000000000000# -*- coding: utf-8 # Several spheres falling down into the box. # Their weight is measured and compares with real mass particles from yade import utils,pack,export,geom tc=0.001 en=.003 es=.003 frictionAngle=radians(35) density=2300 defMat=O.materials.append(ViscElMat(density=density,frictionAngle=frictionAngle,tc=tc,en=en,et=es)) O.dt=.1*tc # time step rad=0.2 # particle radius tolerance = 0.0001 SpheresID=[] SpheresID+=O.bodies.append(pack.regularHexa(pack.inSphere((Vector3(0.0,0.0,0.0)),0.5),radius=rad,gap=rad*0.5,material=defMat)) floorId=[] floorId+=O.bodies.append(geom.facetBox((0,0,0),(0.6,0.6,0.6),material=defMat)) #Floor #Calculate the weight of spheres sphMass = utils.getSpheresVolume()*density*9.81 # Create engines O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(),Bo1_Facet_Aabb()]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(), Ig2_Facet_Sphere_ScGeom()], [Ip2_ViscElMat_ViscElMat_ViscElPhys()], [Law2_ScGeom_ViscElPhys_Basic()], ), NewtonIntegrator(damping=0.0,gravity=[0.0,0.0,-9.81]) ] O.run(30000) O.wait() curForce = utils.sumForces(ids=floorId,direction=Vector3(0,0,1))*(-1) print ("Precalculated weight %f" % sphMass) print ("Obtained weight %f" % curForce) if (((sphMass-curForce)/curForce)>tolerance): resultStatus += 1 trunk-2017.01a/scripts/checks-and-tests/checks/checkWirePM.py000066400000000000000000000114061304022710500237660ustar00rootroot00000000000000# -*- coding: utf-8 -*- # 2011 © Klaus Thoeni # Check test version for WirePM tensile test tolerance=0.01 errors=0 #### define parameters for the net # wire diameter d = 2.7/1000. # particle radius radius = d*4. # define piecewise lineare stress-strain curve strainStressValues=[(0.0019230769,2.5e8),(0.0192,3.2195e8),(0.05,3.8292e8),(0.15,5.1219e8),(0.25,5.5854e8),(0.3,5.6585e8),(0.35,5.6585e8)] # elastic material properties particleVolume = 4./3.*pow(radius,3)*pi particleMass = 3.9/1000. density = particleMass/particleVolume young = strainStressValues[0][1] / strainStressValues[0][0] poisson = 0.3 #### material definition netMat = O.materials.append( WireMat( young=young,poisson=poisson,frictionAngle=radians(30),density=density,isDoubleTwist=True,diameter=d,strainStressValues=strainStressValues,lambdaEps=0.4,lambdak=0.66) ) wireMat = O.materials.append( WireMat( young=young,poisson=poisson,frictionAngle=radians(30),density=density,isDoubleTwist=False,diameter=3.4/1000,strainStressValues=strainStressValues ) ) #### get net packing kw = {'color':[1,1,0],'wire':True,'highlight':False,'fixed':False,'material':netMat} [netpack,lx,ly] = hexaNet( radius=radius, cornerCoord=[0,0,0], xLength=1.0, yLength=0.55, mos=0.08, a=0.04, b=0.04, startAtCorner=False, isSymmetric=True, **kw ) O.bodies.append(netpack) if abs((lx-0.96)/0.96)>tolerance: print "WirePM checkTest: difference on net dimension lx" errors+=1 if abs((ly-0.52)/0.52)>tolerance: print "WirePM checkTest: difference on net dimension ly" errors+=1 #### get bodies for single wire at the boundary in y-direction and change properties bb = uniaxialTestFeatures(axis=0) negIds,posIds=bb['negIds'],bb['posIds'] for id in negIds: O.bodies[id].material = O.materials[wireMat] O.bodies[id].shape.color = [0,0,1] for id in posIds: O.bodies[id].material = O.materials[wireMat] O.bodies[id].shape.color = [0,0,1] #### define engines to create link interactionRadius=2.8 O.engines=[ ForceResetter(), InsertionSortCollider([Bo1_Sphere_Aabb(aabbEnlargeFactor=interactionRadius,label='aabb')]), InteractionLoop( [Ig2_Sphere_Sphere_ScGeom(interactionDetectionFactor=interactionRadius,label='Ig2ssGeom')], [Ip2_WireMat_WireMat_WirePhys(linkThresholdIteration=1,label='interactionPhys')], [Law2_ScGeom_WirePhys_WirePM(linkThresholdIteration=1,label='interactionLaw')] ), NewtonIntegrator(damping=0.), ] #### define additional vertical interactions at the boundary createInteraction(negIds[0],negIds[2]) createInteraction(negIds[3],negIds[4]) createInteraction(negIds[5],negIds[6]) createInteraction(negIds[7],negIds[1]) createInteraction(posIds[0],posIds[2]) createInteraction(posIds[3],posIds[4]) createInteraction(posIds[5],posIds[6]) createInteraction(posIds[7],posIds[1]) #### time step definition for first time step to create links O.step() #### initialize values for UniaxialStrainer bb = uniaxialTestFeatures(axis=1) negIds,posIds,axis,crossSectionArea=bb['negIds'],bb['posIds'],bb['axis'],bb['area'] strainRateTension = 0.1 setSpeeds = True ##### delete horizontal interactions for corner particles bb = uniaxialTestFeatures(axis=1) negIds,posIds,axis,crossSectionArea=bb['negIds'],bb['posIds'],bb['axis'],bb['area'] ##### delete some interactions O.interactions.erase(0,4) O.interactions.erase(0,5) O.interactions.erase(1,154) O.interactions.erase(1,155) O.interactions.erase(2,26) O.interactions.erase(2,27) O.interactions.erase(3,176) O.interactions.erase(3,177) #### time step definition for deleting some links which have been created by the Ig2 functor O.step() #### initializes now the interaction detection factor aabb.aabbEnlargeFactor=-1. Ig2ssGeom.interactionDetectionFactor=-1. #### define engines for simulation with UniaxialStrainer O.engines = O.engines[:3] + [ UniaxialStrainer(strainRate=strainRateTension,axis=axis,asymmetry=1,posIds=posIds,negIds=negIds,crossSectionArea=crossSectionArea,blockDisplacements=True,blockRotations=False,setSpeeds=setSpeeds,label='strainer'), NewtonIntegrator(damping=0.5), ] #### time step definition for simulation ## critical time step proposed by Bertrand kn = 16115042 # stiffness of single wire from code O.dt = 0.2*sqrt(particleMass/(2.*kn)) O.run(30000,True) Fn = 0. for i in posIds: try: inter=O.interactions.withBody(i)[0] F = abs(inter.phys.normalForce[1]) except: F = 0 Fn += F un = O.bodies[O.bodies[posIds[0]].id].state.pos[1] - O.bodies[O.bodies[posIds[0]].id].state.refPos[1] if abs((un-0.0034)/0.034)>tolerance : print "WirePM checkTest: difference on peak displacement" print "Reference value:",0.034 print "Calculated value:",un errors+=1 if abs((Fn-6458.9)/6458.9)>tolerance : print "WirePM checkTest: difference on peak Force" print "Reference value:",6458.9 print "Calculated value:",Fn errors+=1 if (errors): resultStatus +=1 #Test is failed trunk-2017.01a/scripts/checks-and-tests/checks/data/000077500000000000000000000000001304022710500221625ustar00rootroot00000000000000trunk-2017.01a/scripts/checks-and-tests/checks/data/100spheres000066400000000000000000000075641304022710500240130ustar00rootroot000000000000000.0632457 0.137506 0.588536 0.063226 -1 0.842337 0.909075 0.228734 0.0629123 -1 0.513101 0.410777 0.29259 0.0625985 -1 0.713178 0.140678 0.552867 0.0622848 -1 0.572038 0.771198 0.580526 0.061971 -1 0.510268 0.830189 0.934033 0.0616573 -1 0.698458 0.909364 0.321995 0.0613435 -1 0.435077 0.850735 0.634324 0.0610297 -1 0.88327 0.425009 0.331716 0.060716 -1 0.513094 0.408062 0.754777 0.0604022 -1 0.666411 0.538952 0.581302 0.0600885 -1 0.142211 0.596396 0.440358 0.0597747 -1 0.740399 0.122601 0.228504 0.059461 -1 0.256304 0.747201 0.133182 0.0591472 -1 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trunk-2017.01a/scripts/checks-and-tests/collider-perf/000077500000000000000000000000001304022710500225405ustar00rootroot00000000000000trunk-2017.01a/scripts/checks-and-tests/collider-perf/README000066400000000000000000000023031304022710500234160ustar00rootroot00000000000000This example tests performance of InsertionSortCollider (with and without stride) and SpatialQuickSortCollider and was basis for http://yade.wikia.com/wiki/Colliders_performace, which features now-removed PersistentSAPCollider as well. To run the test, say: yade-trunk-multi perf.table perf.py It will take time to finish. To collet results and get graphs from the generated log files, say python mkGraph.py *.log To see other results, log files are named like perf.64k.q.log (64k spheres with SpatialQuickSortCollider), perf.32k.i.log (32k spheres, InsertionSortCollider), perf.40k.is.log (InsertionSortCollider with stride) etc. 1. File with nSpheres spheres (loose packing) is generated first, it if doesn't exist yet. This can take a few minutes, but is done only the first time for the particular sphere number. 2. First iteration on the scene (TriaxialTest and the selected collider) with timings is done and timing.stats() printed (appears in the log file). 3. Another 100 iterations are measured with timing.stats(), after which the test exits. (Note: InsertionSortCollider with stride is currently commented out in the table, as striding is not effective until later during the simulation.) trunk-2017.01a/scripts/checks-and-tests/collider-perf/mkGraph.py000066400000000000000000000026111304022710500245030ustar00rootroot00000000000000#encoding: utf-8 dta={'QS':{},'IS':{},'ISS':{}} import sys for f in sys.argv[1:]: print f,'', N=f.split('.')[1]; assert(N[-1]=='k'); N=1000*int(N[:-1]) if '.q.' in f: collider='QS' elif '.i.' in f: collider='IS' elif '.is.' in f: collider='ISS' else: raise RuntimeError("Unknown collider type for file "+f) for l in open(f): if 'Collider' in l: t=l.split()[2]; assert(t[-2:]=='us'); t=float(t[:-2])/1e6 if not dta[collider].has_key(N): dta[collider][N]=[t] else: dta[collider][N]+=[t*0.01] # the second time is per 100 iterations print ISS_N=dta['ISS'].keys(); ISS_N.sort() QS_N=dta['QS'].keys(); QS_N.sort() IS_N=dta['IS'].keys(); IS_N.sort() ISSinit=[dta['ISS'][N][0] for N in ISS_N]; ISSstep=[dta['ISS'][N][1] for N in ISS_N] QSinit=[dta['QS'][N][0] for N in QS_N]; QSstep=[dta['QS'][N][1] for N in QS_N] ISinit=[dta['IS'][N][0] for N in IS_N]; ISstep=[dta['IS'][N][1] for N in IS_N] from pylab import * plot(IS_N,ISinit,'y',ISS_N,ISSinit) gca().set_yscale('log') xlabel("Number of spheres") ylabel(u"Log time for the 1st collider step [s]") title("Colliders performance (QS=QuickSoft, IS=InsertionSort, IS/s=IS+stride)") legend(('IS init','IS/s init',),'upper left') ax2=twinx() plot(IS_N,ISstep,'k-',ISS_N,ISSstep,'r-',QS_N,QSstep,'g-',QS_N,QSinit,'b-') ylabel(u"Linear time per 1 step [s]") legend(('IS step','IS/s step','QS step','QS init'),'right') grid() savefig('colliders.svg') show() trunk-2017.01a/scripts/checks-and-tests/collider-perf/perf.py000066400000000000000000000015641304022710500240540ustar00rootroot00000000000000 utils.readParamsFromTable(nSpheres=8000,collider='InsertionSortCollider',noTableOk=True) # name of file containing sphere packing with given number of spheres spheresFile="packing-%dk.spheres"%(nSpheres/1000) fast='@stride' in collider import os if not os.path.exists(spheresFile): print "Generating packing" p=TriaxialTest(numberOfGrains=nSpheres,radiusMean=1e-3,lowerCorner=[0,0,0],upperCorner=[1,1,1],noFiles=True) p.load() utils.spheresToFile(spheresFile) O.reset() print "Packing %s done"%spheresFile else: print "Packing found (%s), using it."%spheresFile from yade import timing O.timingEnabled=True TriaxialTest(importFilename=spheresFile,fast=fast,noFiles=True).load() O.dt=utils.PWaveTimeStep() isc=O.engines[2] isc.sweepLength=1e-1 if not fast: utils.replaceCollider(eval(collider)) O.step() timing.stats() timing.reset() O.run(200,True) timing.stats() quit() trunk-2017.01a/scripts/checks-and-tests/collider-perf/perf.table000066400000000000000000000060611304022710500245100ustar00rootroot00000000000000!OMP_NUM_THREADS description nSpheres collider 4 128k.q 128000 'SpatialQuickSortCollider' 4 96k.q 96000 'SpatialQuickSortCollider' 4 64k.q 64000 'SpatialQuickSortCollider' 4 56k.q 56000 'SpatialQuickSortCollider' 4 48k.q 48000 'SpatialQuickSortCollider' 4 40k.q 40000 'SpatialQuickSortCollider' 4 36k.q 36000 'SpatialQuickSortCollider' 4 32k.q 32000 'SpatialQuickSortCollider' 4 28k.q 28000 'SpatialQuickSortCollider' 4 24k.q 24000 'SpatialQuickSortCollider' 4 20k.q 20000 'SpatialQuickSortCollider' 4 18k.q 18000 'SpatialQuickSortCollider' 4 16k.q 16000 'SpatialQuickSortCollider' 4 14k.q 14000 'SpatialQuickSortCollider' 4 12k.q 12000 'SpatialQuickSortCollider' 4 10k.q 10000 'SpatialQuickSortCollider' 4 9k.q 9000 'SpatialQuickSortCollider' 4 8k.q 8000 'SpatialQuickSortCollider' 4 7k.q 7000 'SpatialQuickSortCollider' 4 6k.q 6000 'SpatialQuickSortCollider' 4 5k.q 5000 'SpatialQuickSortCollider' 4 4k.q 4000 'SpatialQuickSortCollider' 4 3k.q 3000 'SpatialQuickSortCollider' 4 2k.q 2000 'SpatialQuickSortCollider' 4 1k.q 1000 'SpatialQuickSortCollider' 4 128k.i 128000 'InsertionSortCollider' 4 96k.i 96000 'InsertionSortCollider' 4 64k.i 64000 'InsertionSortCollider' 4 56k.i 56000 'InsertionSortCollider' 4 48k.i 48000 'InsertionSortCollider' 4 40k.i 40000 'InsertionSortCollider' 4 36k.i 36000 'InsertionSortCollider' 4 32k.i 32000 'InsertionSortCollider' 4 28k.i 28000 'InsertionSortCollider' 4 24k.i 24000 'InsertionSortCollider' 4 20k.i 20000 'InsertionSortCollider' 4 18k.i 18000 'InsertionSortCollider' 4 16k.i 16000 'InsertionSortCollider' 4 14k.i 14000 'InsertionSortCollider' 4 12k.i 12000 'InsertionSortCollider' 4 10k.i 10000 'InsertionSortCollider' 4 9k.i 9000 'InsertionSortCollider' 4 8k.i 8000 'InsertionSortCollider' 4 7k.i 7000 'InsertionSortCollider' 4 6k.i 6000 'InsertionSortCollider' 4 5k.i 5000 'InsertionSortCollider' 4 4k.i 4000 'InsertionSortCollider' 4 3k.i 3000 'InsertionSortCollider' 4 2k.i 2000 'InsertionSortCollider' 4 1k.i 1000 'InsertionSortCollider' #4 128k.is 128000 'InsertionSortCollider' #4 96k.is 96000 'InsertionSortCollider' #4 64k.is 64000 'InsertionSortCollider' #4 56k.is 56000 'InsertionSortCollider' #4 48k.is 48000 'InsertionSortCollider@stride' #4 40k.is 40000 'InsertionSortCollider@stride' #4 36k.is 36000 'InsertionSortCollider@stride' #4 32k.is 32000 'InsertionSortCollider@stride' #4 28k.is 28000 'InsertionSortCollider@stride' #4 24k.is 24000 'InsertionSortCollider@stride' #4 20k.is 20000 'InsertionSortCollider@stride' #4 18k.is 18000 'InsertionSortCollider@stride' #4 16k.is 16000 'InsertionSortCollider@stride' #4 14k.is 14000 'InsertionSortCollider@stride' #4 12k.is 12000 'InsertionSortCollider@stride' #4 10k.is 10000 'InsertionSortCollider@stride' #4 9k.is 9000 'InsertionSortCollider@stride' #4 8k.is 8000 'InsertionSortCollider@stride' #4 7k.is 7000 'InsertionSortCollider@stride' #4 6k.is 6000 'InsertionSortCollider@stride' #4 5k.is 5000 'InsertionSortCollider@stride' #4 4k.is 4000 'InsertionSortCollider@stride' #4 3k.is 3000 'InsertionSortCollider@stride' #4 2k.is 2000 'InsertionSortCollider@stride' #4 1k.is 1000 'InsertionSortCollider@stride' trunk-2017.01a/scripts/checks-and-tests/compare-identical.py000066400000000000000000000035011304022710500237420ustar00rootroot00000000000000""" This files tests simulation correctness by loading a simulation two times, and periodically comparing the results, showing diffs in the simulation XML, if any. It stops after the differece is first spotted. On openMP-enabled installs, it should be run with OMP_NUM_THREADS=1, otherwise there will be noise differences coming from non-deterministic order of interactions in the container (although they are the same). You can use OMP_NUM_THREADS=2 to see what happens if the simulations get different. """ # this is to provide some default simulation to test on # comment it out and provide your own simulation XML in init TriaxialTest().generate('/tmp/TriaxialTest.xml') # # what is the initial file to load initFile='/tmp/TriaxialTest.xml' # that is the prefix for HTML diffs, if any outPrefix='/tmp/scene_' # at which step to stop stopIter=2000 # how may steps to run between comparisons nSteps=100 # quiet annoying messages if O.numThreads>1: print "WARNING: You should run single-threaded with OMP_NUM_THREADS=1; interaction order will be probably different otherwise!" for scene in 0,1: O.load(initFile); O.interactions.serializeSorted=True; O.switchScene(); from hashlib import md5; import difflib,sys print "Identical at steps ", for i in xrange(0,stopIter/nSteps): sys.stdout.flush() for scene in 'A','B': O.run(nSteps,True); O.saveTmp(scene); O.switchScene() A,B=O.tmpToString('A'),O.tmpToString('B') # fast compare first using hash digest Ahash,Bhash=md5(A),md5(B) if Ahash.digest()==Bhash.digest(): print O.iter,; continue print "\nComputing differences..." diff=difflib.HtmlDiff(tabsize=3,wrapcolumn=80) outName=outPrefix+'%05d_diff.html'%O.iter out=open(outName,'w') out.write(diff.make_file(A.split('\n'),B.split('\n'),context=True,numlines=2)) print 'file://%s'%outName break # stop at the first different value trunk-2017.01a/scripts/checks-and-tests/dispatcher-torture.py000066400000000000000000000037461304022710500242250ustar00rootroot00000000000000""" Script that shows dispatch matrices when all available functors are loaded. Later ones will overwrite earlier ones, this is not what you will get in reality. Pipe the output to file and open it in browser: $ yade-trunk dispatcher-torture.py > /tmp/aa.html $ firefox /tmp/aa.html """ import collections Dispatch=collections.namedtuple('Dispatch',['basename','types']) dispatches=[ Dispatch('Law',('IGeom','IPhys')), Dispatch('IGeom',('Shape','Shape')), Dispatch('IPhys',('Material','Material')), Dispatch('Bound',('Shape',)), Dispatch('GlBound',('Bound',)), Dispatch('GlIGeom',('IGeom',)), Dispatch('GlIPhys',('IPhys',)), Dispatch('GlShape',('Shape',)), #Dispatch('GlState',('State',)) # broken for now ] sys.path.append('.') import HTML outStr='' for D in dispatches: functors=yade.system.childClasses(D.basename+'Functor') # create dispatcher with all available functors dispatcher=eval(D.basename+'Dispatcher([%s])'%(','.join(['%s()'%f for f in functors]))) if len(D.types)==1: allDim0=list(yade.system.childClasses(D.types[0])) table=HTML.Table(header_row=allDim0) row=[] for d0 in allDim0: dd0=eval(d0+'()') try: f=dispatcher.dispFunctor(dd0) row.append(f.name if f else '-') except RuntimeError as strerror: row.append('ambiguous (%s)'%(strerror)) table.rows.append(row) elif len(D.types)==2: # lists of types the dispatcher accepts allDim0=list(yade.system.childClasses(D.types[0])) allDim1=list(yade.system.childClasses(D.types[1])) table=HTML.Table(header_row=['']+allDim1) for d0 in allDim0: row=[''+d0+''] for d1 in allDim1: dd0,dd1=eval(d0+'()'),eval(d1+'()') try: f=dispatcher.dispFunctor(dd0,dd1) row.append(f.__class__.__name__ if f else '-') except RuntimeError: # ambiguous row.append('ambiguous') table.rows.append(row) else: raise ValueError("Dispatcher must be 1D or 2D, not %dD"%len(D.types)) outStr+='\n